Psyllid ID: psy3760

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300------
Protein Sequence
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHccccHHHHHHHHcccccHHHHHHHHHHHHcccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEcHHcHHHHHHHHHHHHHHHccccEEEEEEccHHHHHHHHHcccccEEEEcccccccccEEEEEEEEEEEEEEEcccccccccccccHHHHccccEEEEcccccHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHcccHHHHHHHHHcccccccEEEEEccccccccEEEEEEEccccccHHHHHHHHHHHHHHcHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHccEEEEEcccEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEcHHHHHHccHHHHHHHHHHccEEEEEEEEccHHHHHHHHHcccccEEEEcccccccccEEEEEEEEEcEEEEEcccccccccccccHHHHHccEEEEEccccccHHHHHHHHHHHccccEEEEEEccHHHHHHHHHHcccEEEEEHHHcccccccccEEEEcEccEccEEEEEEEEccccccHHHHHHHHHHcccccHHHHHHHHcc
Coil and Loop (DISEMBL)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRhgkrirgltkpgqAILRSIEIIMQEIEGLKKIGkefsaydtgnltiaTTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEilspsdklisipcyqweyviivpldhpllllnsislkeisnyplitydlsfsgrikldrefslqkltpyiVLETINSDIIKTYVELRMGIGIIAsiafdsnrdkNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
Flexible Loop (DISEMBL)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFirhgkrirgltkpgqaiLRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRefslqkltpyiVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSIsashlfgttisrviiKQGTYLRSYVYSFIkllspklnrkfinkilnn
Low Complexity Region (SEG)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAiieleeelsidifiRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
Disordered region (IsUnstruct)
*****FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI***
Disordered Region (DISOPRED)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF*NKI***
Disordered Region (DISEMBL)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
Disordered Region (DISPRO)
*NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN
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	306	2.2.26 [Sep-21-2011]
P06614	324	HTH-type transcriptional	yes	N/A	0.983	0.929	0.428	3e-74
P45600	324	HTH-type transcriptional	yes	N/A	0.983	0.929	0.425	3e-74
P0A9F3	324	HTH-type transcriptional	N/A	N/A	0.983	0.929	0.421	3e-73
P0A9F4	324	HTH-type transcriptional	yes	N/A	0.983	0.929	0.421	3e-73
P0A9F5	324	HTH-type transcriptional	N/A	N/A	0.983	0.929	0.421	3e-73
Q47083	316	HTH-type transcriptional	N/A	N/A	0.986	0.955	0.423	2e-70
P45105	323	HTH-type transcriptional	yes	N/A	0.983	0.931	0.417	6e-70
Q08598	316	HTH-type transcriptional	no	N/A	0.967	0.936	0.435	4e-65
Q55459	304	HTH-type transcriptional	N/A	N/A	0.774	0.779	0.300	2e-21
P37499	292	Uncharacterized HTH-type	yes	N/A	0.826	0.866	0.262	3e-20

>sp|P06614|CYSB_SALTY HTH-type transcriptional regulator CysB OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=cysB PE=1 SV=1

 Score =  278 bits (712), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 129/301 (42%), Positives = 191/301 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYIATTHTQARYALPGVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI E +    AD AI TE L   D L+ +PCY W   I+V  DHPL  
Sbjct: 121 RVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPDHPLAA 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
            +S++++ ++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 TSSVTIEALAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  I A  +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPLADPDLVRIDAHDIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 N 301
           +
Sbjct: 301 D 301

This protein is a positive regulator of gene expression for the cysteine regulon, a system of 10 or more loci involved in the biosynthesis of L-cysteine from inorganic sulfate. The inducer for cysB is N-acetylserine. CysB inhibits its own transcription.
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (taxid: 99287)

>sp|P45600|CYSB_KLEPN HTH-type transcriptional regulator CysB OS=Klebsiella pneumoniae GN=cysB PE=1 SV=2

 Score =  278 bits (712), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 128/301 (42%), Positives = 192/301 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L +ATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI E +    AD AI TE L   D L+ +PCY W   I+V  +HPL  
Sbjct: 121 RVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLAT 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S+S++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A+ +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 N 301
           +
Sbjct: 301 D 301

This protein is a positive regulator of gene expression for the cysteine regulon. The inducer for cysB is N-acetylserine. Thiosulfate and sulfide act as anti-inducers.

Klebsiella pneumoniae (taxid: 573)

>sp|P0A9F3|CYSB_ECOLI HTH-type transcriptional regulator CysB OS=Escherichia coli (strain K12) GN=cysB PE=3 SV=1

 Score =  275 bits (703), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 127/301 (42%), Positives = 191/301 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFSRSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYIATTHTQARYALPNVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI + +    AD AI TE L   + L+ +PCY W   I+V  DHPL  
Sbjct: 121 RVSLHMHQGSPTQIADAVSKGNADFAIATEALHLYEDLVMLPCYHWNRAIVVTPDHPLAG 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +I+++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KKAITIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A  +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVADPDLVRVDAHDIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 N 301
           +
Sbjct: 301 D 301

This protein is a positive regulator of gene expression for the cysteine regulon, a system of 10 or more loci involved in the biosynthesis of L-cysteine from inorganic sulfate. The inducer for cysB is N-acetylserine. CysB inhibits its own transcription.

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0A9F4|CYSB_ECOL6 HTH-type transcriptional regulator CysB OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=cysB PE=3 SV=1

 Score =  275 bits (703), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 127/301 (42%), Positives = 191/301 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFSRSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYIATTHTQARYALPNVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI + +    AD AI TE L   + L+ +PCY W   I+V  DHPL  
Sbjct: 121 RVSLHMHQGSPTQIADAVSKGNADFAIATEALHLYEDLVMLPCYHWNRAIVVTPDHPLAG 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +I+++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KKAITIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A  +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVADPDLVRVDAHDIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 N 301
           +
Sbjct: 301 D 301

This protein is a positive regulator of gene expression for the cysteine regulon. The inducer for cysB is N-acetylserine.

Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (taxid: 199310)

>sp|P0A9F5|CYSB_ECO57 HTH-type transcriptional regulator CysB OS=Escherichia coli O157:H7 GN=cysB PE=3 SV=1

 Score =  275 bits (703), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 127/301 (42%), Positives = 191/301 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFSRSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYIATTHTQARYALPNVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI + +    AD AI TE L   + L+ +PCY W   I+V  DHPL  
Sbjct: 121 RVSLHMHQGSPTQIADAVSKGNADFAIATEALHLYEDLVMLPCYHWNRAIVVTPDHPLAG 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +I+++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KKAITIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A  +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVADPDLVRVDAHDIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 N 301
           +
Sbjct: 301 D 301

This protein is a positive regulator of gene expression for the cysteine regulon. The inducer for cysB is N-acetylserine.

Escherichia coli O157:H7 (taxid: 83334)

>sp|Q47083|CBL_ECOLI HTH-type transcriptional regulator cbl OS=Escherichia coli (strain K12) GN=cbl PE=1 SV=2

 Score =  266 bits (679), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 128/302 (42%), Positives = 202/302 (66%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MN  Q + +REA RQ++NLTE A  L+TSQ GVS+ I ELE+EL I+IF+R GKR+ G+T
Sbjct: 1   MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFVRRGKRLLGMT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L   E I+ E   ++++   F+   +G LTIATTHTQARY+LP++IK F   FP
Sbjct: 61  EPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V+L L+QG P++I  +++N +ADI I +E LS   +L++ P ++W + ++VP DHPL  
Sbjct: 121 EVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
           ++ ++L+ I+ +PLITY    +GR ++D  F+ + L   IVL   +SD+IKTYV L +GI
Sbjct: 181 ISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G++A  +     ++NL  +   HLF      + +K+G   R+YV+ F++L +  L+ + I
Sbjct: 241 GLVAEQSSGEQEEENLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDI 300

Query: 301 NK 302
            +
Sbjct: 301 KR 302

May be an accessory regulatory protein within the cys regulon.

Escherichia coli (strain K12) (taxid: 83333)

>sp|P45105|CYSB_HAEIN HTH-type transcriptional regulator CysB OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=cysB PE=3 SV=1

 Score =  264 bits (675), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 126/302 (41%), Positives = 194/302 (64%), Gaps = 1/302 (0%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M +HQ R++ E V QN N+TEAA ALYTSQPG+SK +  LE+EL ++IF RHGK I+ +T
Sbjct: 1   MKMHQLRYIVEIVNQNLNVTEAANALYTSQPGISKQVRLLEDELGLEIFERHGKHIKSIT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             G+ I+     ++ + +G++ +  E++  + G L IATT+TQARY LP +I+ F+ ++P
Sbjct: 61  PAGKKIISIARELLVKAQGIRAVADEYTRPNHGVLRIATTNTQARYMLPSVIERFSKKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
            V L + QG+P QI + + + + D+AI TE     D L+ IPCY W   +IV  +HPL  
Sbjct: 121 DVSLHIHQGSPTQIHDALMSGEVDLAITTEAPYLFDDLVQIPCYWWNRAVIVSPEHPLAK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
           +  ++++E+  YPL+TY   F+G   LD  F+   + P IV    ++D+IKTYV L +G+
Sbjct: 181 VKELTIEELGKYPLVTYTFGFTGVSDLDYAFNSAGILPNIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GI+AS+A  +  D +L  I ASHLF  +++ +  K  T+LR+Y+Y F++  SP L R  +
Sbjct: 241 GIMASMAHTA-LDTDLVLIDASHLFRPSMTNIAFKHSTFLRNYMYDFMEYFSPHLTRSVV 299

Query: 301 NK 302
            K
Sbjct: 300 EK 301

This protein is a positive regulator of gene expression for the cysteine regulon. The inducer for cysB is N-acetylserine.

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (taxid: 71421)

>sp|Q08598|CBL_ENTAE HTH-type transcriptional regulator cbl OS=Enterobacter aerogenes GN=cbl PE=4 SV=1

 Score =  248 bits (633), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 129/296 (43%), Positives = 192/296 (64%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MN  Q + +REA RQ++NLTE A  LYTSQ GVS+ I ELEEEL I+IFIR GKR+ G+T
Sbjct: 1   MNFQQLKIIREAARQDYNLTEVANMLYTSQSGVSRHIRELEEELGIEIFIRRGKRLLGMT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L   E I+ E   ++++   F+   +G LTIATTHTQARY+LP +IK F   F 
Sbjct: 61  EPGKALLSIAERILNEASNVRRLADLFTNDASGVLTIATTHTQARYSLPPVIKAFRELFS 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
            V++ L+QG P++I  ++ N  ADI I +E LS    L + P ++W + ++VP DHPL  
Sbjct: 121 DVRVELVQGTPQEIEALLHNGGADIGIASERLSNDPTLAAFPWFRWHHSLLVPKDHPLTQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
           ++ ++L+ I+ +PLITY    +GR ++D  F+ + L P IVL   +SD+IKTYVEL +G+
Sbjct: 181 VSPLTLEAIARWPLITYRQGITGRSRIDEAFNRKGLMPDIVLSAQDSDVIKTYVELGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296
           G++A  + D+        +   HLF      + +K+G   R+YV+ FI+L +  L+
Sbjct: 241 GLVAEQSGDAREADTFTRLDTRHLFDANTVWLGLKRGQLQRNYVWRFIELCNAGLS 296

May be an accessory regulatory protein within the cys regulon.

Enterobacter aerogenes (taxid: 548)

>sp|Q55459|CMPR_SYNY3 HTH-type transcriptional activator CmpR OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=cmpR PE=1 SV=1

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 137/243 (56%), Gaps = 6/243 (2%)

Query: 3   LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
           LHQF  V  A+ +  + T+AA+ L+ +QP VS+ + +L + + + ++ + G++I  LT+ 
Sbjct: 6   LHQFE-VFAAIARTGSFTKAAEELFLTQPTVSQQMKQLTKAIGVPLYEQIGRKIY-LTEA 63

Query: 63  GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKV 122
           GQA+L + + I   ++ L+++  +      GNL +AT  T  +Y +P+++ EF  Q+P +
Sbjct: 64  GQAVLDASKNITSCLDQLQEVIADLQGLKKGNLRLATI-TTGKYFVPRLLGEFRQQYPGI 122

Query: 123 KLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY-QWEYVIIVPLDHPLLLL 181
            +SL  GN +QI E + N+  D+  + +   PS+  I+I  + +   V+I    HPL+  
Sbjct: 123 SISLQIGNRQQILERLANNLDDLYFLGK--PPSNLDINIRHFLENPLVVIASRQHPLVKE 180

Query: 182 NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIG 241
             ISL+ + N PLI  +     R+ ++  FS  +L   + +E  +++ IK  V   +GI 
Sbjct: 181 KKISLERLVNEPLIMRESGSGTRMAVEEFFSENRLKMNVEMEISSNEAIKQAVYGGLGIS 240

Query: 242 IIA 244
           I++
Sbjct: 241 ILS 243

Activates transcription of the cmpABCD operon under carbon dioxide-limited conditions. Specifically binds to the cmpR-cmpA intergenic region.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|P37499|YYBE_BACSU Uncharacterized HTH-type transcriptional regulator YybE OS=Bacillus subtilis (strain 168) GN=yybE PE=4 SV=2

 Score = 99.4 bits (246), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 125/259 (48%), Gaps = 6/259 (2%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M   Q  + +   R   ++T+AAK+L  +QP +S++I  LE  L + +F R G+ I  L 
Sbjct: 1   MEWEQLEYFQTLARMQ-HVTKAAKSLSITQPALSRSIARLENHLGVPLFDRQGRSI-SLN 58

Query: 61  KPGQAILRSIEIIMQE-IEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           + G   LR ++ +M+E  EG ++I +     D G +++   HT     +P +I  F  ++
Sbjct: 59  QYGHIFLRRVQAMMKEYTEGKEEI-QALLKPDQGVVSLGFLHTLGTTLVPDLIGSFQQEY 117

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P +   L Q +   + E +++   D+ ++  I  P + +  I  +  E  + VP DHPL 
Sbjct: 118 PNISFQLKQNHSYWLLERLKSGDLDLCLLASI-KPENPIQWIKLWSEELFVFVPNDHPLA 176

Query: 180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
              SI+L EI+    I     ++ R+ +D  F    + P I+ E   +     +V   +G
Sbjct: 177 SRESITLNEIAGERFILLKKGYALRMTVDELFEKANIQPNIMFEGEEATTAAGFVAAGLG 236

Query: 240 IGIIASI-AFDSNRDKNLR 257
           I I+  +   D ++   +R
Sbjct: 237 ISILPDLKGLDQSKITKIR 255

Bacillus subtilis (strain 168) (taxid: 224308)

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	306
399017224	313	transcriptional regulator [Herbaspirillu	1.0	0.977	0.709	1e-134
300312397	313	cys regulon transcription regulator prot	1.0	0.977	0.709	1e-134
415948476	313	HTH-type transcriptional regulator [Herb	1.0	0.977	0.705	1e-133
398832713	313	transcriptional regulator [Herbaspirillu	1.0	0.977	0.699	1e-132
340788687	313	regulatory protein CysB [Collimonas fung	1.0	0.977	0.679	1e-131
152980807	313	transcriptional regulator CysB-like prot	1.0	0.977	0.683	1e-129
134095567	313	transcriptional regulator CysB-like prot	1.0	0.977	0.689	1e-128
329903700	313	Regulatory protein CysB [Oxalobacteracea	1.0	0.977	0.663	1e-126
395761411	313	transcriptional regulator CysB-like prot	1.0	0.977	0.656	1e-125
427403367	312	hypothetical protein HMPREF9710_03960 [M	1.0	0.980	0.637	1e-121

>gi|399017224|ref|ZP_10719422.1| transcriptional regulator [Herbaspirillum sp. CF444] gi|398104128|gb|EJL94282.1| transcriptional regulator [Herbaspirillum sp. CF444]

 Score =  484 bits (1247), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 217/306 (70%), Positives = 269/306 (87%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQN+NLTEAAKALYTSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNYNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+LRS+E+IMQE++GLK+IGKEF+A+D+G+ TIATTHTQARY+LPK+++ FT ++P
Sbjct: 61  EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYSLPKVVQAFTQKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQITEM+RNDQADIAI TE L+  + L+S+PCYQWE+V++VP +HPLL 
Sbjct: 121 KVRLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPEHPLLK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             ++SL+EI+ YPLITYD +FSGR K+D  FSL+ L P IVLE I++D+IKTYVEL MG+
Sbjct: 181 SKNLSLEEIAGYPLITYDAAFSGRSKIDHAFSLRDLKPDIVLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD +RD+ LRSI A HLFGT +SRV +KQG YLRSYVY+FI+LL+P LNRK I
Sbjct: 241 GIIAGMAFDGDRDRGLRSIPAGHLFGTNVSRVALKQGAYLRSYVYTFIELLAPTLNRKLI 300

Query: 301 NKILNN 306
            +++  
Sbjct: 301 AQVMEG 306

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|300312397|ref|YP_003776489.1| cys regulon transcription regulator protein [Herbaspirillum seropedicae SmR1] gi|409406827|ref|ZP_11255289.1| cys regulon transcription regulator protein [Herbaspirillum sp. GW103] gi|300075182|gb|ADJ64581.1| cys regulon transcription regulator protein [Herbaspirillum seropedicae SmR1] gi|386435376|gb|EIJ48201.1| cys regulon transcription regulator protein [Herbaspirillum sp. GW103]

 Score =  483 bits (1243), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 217/306 (70%), Positives = 267/306 (87%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+LRS+E+IMQE++GLK+IGKEF+A+D+G+ TIATTHTQARYALPK+++ FT ++P
Sbjct: 61  EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV LSLLQGNPKQITEM+RNDQADIAI TE L+  + L+S+PCYQWE+V++VP DHPLL 
Sbjct: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S++L+EI+  PLITYD +FSGR K+D  FSL++L P +VLE I++D+IKTYVEL MG+
Sbjct: 181 SKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA IAFD+ RD+ LR+I A HLFGT +SRV +KQG YLR YVY+FI+LL+P LNRK I
Sbjct: 241 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300

Query: 301 NKILNN 306
            +++  
Sbjct: 301 AQVMEG 306

Source: Herbaspirillum seropedicae SmR1

Species: Herbaspirillum seropedicae

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|415948476|ref|ZP_11556747.1| HTH-type transcriptional regulator [Herbaspirillum frisingense GSF30] gi|407757891|gb|EKF67797.1| HTH-type transcriptional regulator [Herbaspirillum frisingense GSF30]

 Score =  481 bits (1238), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 216/306 (70%), Positives = 267/306 (87%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+LRS+E+IMQE++GLK+IGKEF+A+D+G+ TIATTHTQARYALPK+++ FT ++P
Sbjct: 61  EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV LSLLQGNPKQITEM+RNDQADIAI TE L+  + L+S+PCYQWE+V++VP +HPLL 
Sbjct: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPEHPLLQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S++L+EI+  PLITYD +FSGR K+D  FSL++L P +VLE I++D+IKTYVEL MG+
Sbjct: 181 SRSLTLEEIATNPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA IAFD+ RD+ LR+I A HLFGT +SRV +KQG YLR YVY+FI+LL+P LNRK I
Sbjct: 241 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300

Query: 301 NKILNN 306
            +++  
Sbjct: 301 AQVMEG 306

Source: Herbaspirillum frisingense GSF30

Species: Herbaspirillum frisingense

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|398832713|ref|ZP_10590869.1| transcriptional regulator [Herbaspirillum sp. YR522] gi|398222870|gb|EJN09229.1| transcriptional regulator [Herbaspirillum sp. YR522]

 Score =  478 bits (1230), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 214/306 (69%), Positives = 266/306 (86%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+LRS+E+IMQE++GLK+IGKEF+A+D+G+ TIATTHTQARYALPK+++ FT ++P
Sbjct: 61  EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV LSLLQGNP+QITEM+RNDQADIAI TE L+  D L+S+PCYQWE+V++VP DHPLL 
Sbjct: 121 KVHLSLLQGNPRQITEMVRNDQADIAIATEALTAIDGLVSLPCYQWEHVVVVPPDHPLLQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +++L+EI++ PLITYD +F+GR K+D  F L+ L P IVLE I++D+IKTYVEL MG+
Sbjct: 181 SKNLTLEEIASNPLITYDAAFTGRSKIDHAFGLRNLKPDIVLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA IAFD+ RD+ LR++ A HLFGT +SRV +KQG YLR YVY+FI+LL+P LNRK I
Sbjct: 241 GIIAGIAFDAERDRGLRALPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300

Query: 301 NKILNN 306
            +++  
Sbjct: 301 AQVMEG 306

Source: Herbaspirillum sp. YR522

Species: Herbaspirillum sp. YR522

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|340788687|ref|YP_004754152.1| regulatory protein CysB [Collimonas fungivorans Ter331] gi|340553954|gb|AEK63329.1| Regulatory protein CysB [Collimonas fungivorans Ter331]

 Score =  472 bits (1215), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 208/306 (67%), Positives = 265/306 (86%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQN+NLTEAAKALYTSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNYNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+LRS+E+IMQEI+GLK+IG E++A+D+G+ TIATTHTQARYALPK+++ FT +FP
Sbjct: 61  EPGRAVLRSVELIMQEIDGLKRIGNEYAAHDSGSFTIATTHTQARYALPKVVQAFTQKFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQ+ +M+RNDQAD+A+ TE +  +D L+++PCYQWE+V++VP DHPLL 
Sbjct: 121 KVRLSLLQGNPKQVADMVRNDQADLALATEAIVNADGLVTLPCYQWEHVVVVPPDHPLLQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +I+L+EI+ +PLITYD +F+GR K+D  FSL+ L P ++LE I++D+IKTYVEL MG+
Sbjct: 181 SKAITLEEIAAFPLITYDSAFTGRTKIDHAFSLRNLKPDVLLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD+ RD  LRSI   HLFGT ISR  +KQG YLRSYVY+FI+LL+P +NRK I
Sbjct: 241 GIIAGMAFDAERDTGLRSIPVGHLFGTNISRAAVKQGAYLRSYVYTFIELLAPTMNRKLI 300

Query: 301 NKILNN 306
            +++N 
Sbjct: 301 EQVMNG 306

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|152980807|ref|YP_001354140.1| transcriptional regulator CysB-like protein [Janthinobacterium sp. Marseille] gi|151280884|gb|ABR89294.1| cys regulon transcriptionnal regulator protein [Janthinobacterium sp. Marseille]

 Score =  466 bits (1198), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 209/306 (68%), Positives = 266/306 (86%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQ RFVREAVRQNFNLTEAAKAL+TSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQLRFVREAVRQNFNLTEAAKALFTSQPGVSKAIIELEEELGVDIFSRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L+S+E+IMQEI+GLK+IG EF+A+D+G+ TIATTHTQARY+LPK+++ FT +FP
Sbjct: 61  EPGRAVLKSVELIMQEIDGLKRIGNEFAAHDSGSFTIATTHTQARYSLPKVVQAFTQKFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQ+ +M+  DQAD+AI TE ++  + LIS+PCYQWE+ ++VP+DHPLL 
Sbjct: 121 KVRLSLLQGNPKQVADMVLMDQADLAIATESIASIEGLISLPCYQWEHQVVVPVDHPLLK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             SI+L+E++ YPLITYD +F+GR K+D  F+L+ L P I+LE I++D+IKTYVEL MGI
Sbjct: 181 SKSITLEELTAYPLITYDSAFAGRNKIDHAFALRNLKPDILLEAIDADVIKTYVELGMGI 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD+ RDKNLR+I A HLFGT +SRV +KQG YLRSYV++FI+LL+P LNRK +
Sbjct: 241 GIIAGMAFDAERDKNLRAIPAGHLFGTNVSRVALKQGAYLRSYVFTFIELLTPTLNRKLV 300

Query: 301 NKILNN 306
            ++LN 
Sbjct: 301 EQVLNG 306

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|134095567|ref|YP_001100642.1| transcriptional regulator CysB-like protein [Herminiimonas arsenicoxydans] gi|133739470|emb|CAL62521.1| HTH-type transcriptional regulator cysB (Cys regulon transcriptional activator) [Herminiimonas arsenicoxydans]

 Score =  463 bits (1191), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 211/306 (68%), Positives = 264/306 (86%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQ RFVREAVRQNFNLTEAAKAL+TSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQLRFVREAVRQNFNLTEAAKALFTSQPGVSKAIIELEEELGVDIFSRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L+S+E IM EIEGLK+IG EF+A+D+G+ TIATTHTQARY+LPK+++ FT +FP
Sbjct: 61  EPGRAVLKSVEAIMLEIEGLKRIGNEFAAHDSGSFTIATTHTQARYSLPKVVQAFTQKFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQI EM+  DQAD+AI TE ++  D LIS+PCYQWE+ I++PLDHPLL 
Sbjct: 121 KVRLSLLQGNPKQIAEMVLMDQADLAIATEAIANMDGLISLPCYQWEHQIVLPLDHPLLK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             SI+L+E++ YP+ITYD +F+GR K+D  F+L+ L P I+LE I++D+IKTYVEL MGI
Sbjct: 181 SKSITLEELAAYPIITYDSAFAGRNKIDHAFNLRNLKPDILLEAIDADVIKTYVELGMGI 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD+ RDKNLR+I A HLFGT +SRV +KQG YLRSYV++FI+LL+P LNRK +
Sbjct: 241 GIIAGMAFDTERDKNLRAIPAGHLFGTNVSRVALKQGAYLRSYVFTFIELLTPTLNRKLV 300

Query: 301 NKILNN 306
            ++L+ 
Sbjct: 301 EQVLSG 306

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|329903700|ref|ZP_08273585.1| Regulatory protein CysB [Oxalobacteraceae bacterium IMCC9480] gi|327548248|gb|EGF32946.1| Regulatory protein CysB [Oxalobacteraceae bacterium IMCC9480]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 203/306 (66%), Positives = 263/306 (85%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQFRFVREAVRQN+NLTEAAKAL+TSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQFRFVREAVRQNYNLTEAAKALFTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L+++E+IMQEI+ LK IGKEF+A+D+G+ TIATTHTQARYALPK+++ FT +FP
Sbjct: 61  EPGRAVLKAVEVIMQEIDSLKSIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQRFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQ+ +++ +  ADIA+ TE ++    L+SIPCYQWE+V++VP +HPLL 
Sbjct: 121 KVRLSLLQGNPKQVADLVLSGHADIALATESITTVAGLVSIPCYQWEHVVVVPPEHPLLK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S++L EI+ YPLITYD +F+GR K+D  F L+ L P ++LE I++D+IKTYVEL +G+
Sbjct: 181 SKSLTLDEIAAYPLITYDSAFTGRAKIDHAFQLRNLKPDVLLEAIDADVIKTYVELGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +A+D++RDKNLR ISA HLFGT +SRV +KQG YLRSYVY+FI+LL+P LNRK I
Sbjct: 241 GIIAGMAYDADRDKNLRMISAGHLFGTNVSRVALKQGAYLRSYVYTFIELLTPTLNRKLI 300

Query: 301 NKILNN 306
            ++++ 
Sbjct: 301 EQVMSG 306

Source: Oxalobacteraceae bacterium IMCC9480

Species: Oxalobacteraceae bacterium IMCC9480

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|395761411|ref|ZP_10442080.1| transcriptional regulator CysB-like protein [Janthinobacterium lividum PAMC 25724]

 Score =  452 bits (1164), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 201/306 (65%), Positives = 259/306 (84%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQ RFVREAVRQN+NLT+AAKAL+TSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQLRFVREAVRQNYNLTDAAKALFTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+ +L S+E+IMQEI+ +K+IGKEF+A D+G+ TIATTHTQARY LPK+++ F ++FP
Sbjct: 61  EPGRLVLESVELIMQEIDSMKRIGKEFAAQDSGSFTIATTHTQARYTLPKVVQAFMLKFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNP+QI EM++ DQAD+AI TE ++  D LI++PCYQWE+V++VPLDHPLL 
Sbjct: 121 KVRLSLLQGNPRQIAEMVQRDQADLAIATESIAAIDGLITLPCYQWEHVVVVPLDHPLLK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S++L+EI+ +PLITYD +F+GR K+D  F L+ L P ++LE I++D+IKTYVEL MGI
Sbjct: 181 SKSVTLEEIAAFPLITYDSAFAGRNKIDHAFVLRGLKPDVLLEAIDADVIKTYVELGMGI 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD+ RDK LR+I   HLFG  +SRV +KQG YLRSY+Y+FI+LL+P LNRK I
Sbjct: 241 GIIAGMAFDAERDKGLRAIPVGHLFGMNVSRVAVKQGAYLRSYIYTFIELLTPTLNRKLI 300

Query: 301 NKILNN 306
            + ++ 
Sbjct: 301 EQAMSG 306

Source: Janthinobacterium lividum PAMC 25724

Species: Janthinobacterium lividum

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|427403367|ref|ZP_18894364.1| hypothetical protein HMPREF9710_03960 [Massilia timonae CCUG 45783] gi|425717838|gb|EKU80793.1| hypothetical protein HMPREF9710_03960 [Massilia timonae CCUG 45783]

 Score =  441 bits (1133), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 195/306 (63%), Positives = 255/306 (83%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQ RFVREAVRQN+NLT+AAKAL+TSQPGVSKAIIELEEEL +DIF RHGKRIRGLT
Sbjct: 1   MNLHQLRFVREAVRQNYNLTDAAKALFTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+ +L+S+E+IMQEI+ LK+IGKE++A+D+G+ TIATTHTQARY LPK+++ F  ++P
Sbjct: 61  EPGRLVLQSVELIMQEIDSLKRIGKEYAAHDSGSFTIATTHTQARYMLPKVVQGFMQKYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LSLLQGNPKQI +M++NDQAD+AI TE ++  + LI++P YQWE+V++ P DHPL  
Sbjct: 121 KVRLSLLQGNPKQIADMVKNDQADLAIATESITAVEGLITLPAYQWEHVVVAPPDHPLFK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +ISL+EI++YP+ITYD +F+GR K+D  F L+ L P ++LE I++D+IKTYVEL MG+
Sbjct: 181 SRAISLEEIASYPVITYDAAFAGRSKIDHAFGLRNLKPDVLLEAIDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GIIA +AFD  RD+NLR++   HLFG   SRV IKQG YLRSY+Y+FI+LL+P LNRK +
Sbjct: 241 GIIAGMAFDPERDRNLRALPVGHLFGMNTSRVAIKQGAYLRSYIYTFIELLTPTLNRKMV 300

Query: 301 NKILNN 306
              +  
Sbjct: 301 ESAMRG 306

Source: Massilia timonae CCUG 45783

Species: Massilia timonae

Genus: Massilia

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

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	306
TIGR_CMR|SO_2649	324	SO_2649 "cys regulon transcrip	0.986	0.932	0.397	6.9e-63
UNIPROTKB|P0A9F3	324	cysB "CysB" [Escherichia coli	0.983	0.929	0.398	4.3e-61
UNIPROTKB|Q9KQU1	324	VC_1907 "Cys regulon transcrip	0.996	0.941	0.383	9e-61
TIGR_CMR|VC_1907	324	VC_1907 "cys regulon transcrip	0.996	0.941	0.383	9e-61
TIGR_CMR|CPS_1200	324	CPS_1200 "cys regulon transcri	0.993	0.938	0.384	1.9e-58
UNIPROTKB|Q47083	316	cbl [Escherichia coli K-12 (ta	0.986	0.955	0.394	3.2e-58
TIGR_CMR|BA_2439	300	BA_2439 "transcriptional regul	0.937	0.956	0.284	2.6e-24
TIGR_CMR|GSU_2817	296	GSU_2817 "transcriptional regu	0.941	0.972	0.245	1.6e-17
TIGR_CMR|GSU_0266	307	GSU_0266 "transcriptional regu	0.816	0.814	0.245	9.7e-17
UNIPROTKB|P27111	299	cynR "CynR DNA-binding transcr	0.790	0.809	0.261	1.2e-16

TIGR_CMR|SO_2649 SO_2649 "cys regulon transcriptional activator" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 120/302 (39%), Positives = 184/302 (60%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M L Q R++ E V+ N N++  A+ LYTSQPG+SK               R GK +  +T
Sbjct:     1 MKLQQLRYIAEVVKHNLNVSATAENLYTSQPGISKQVRMLEDELGIQIFGRSGKHLTHVT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               GQ ++     I+ ++E +KK+ +E++  D G L IATT TQARYALP II++F  ++P
Sbjct:    61 PAGQQVINIANDILGKVESIKKVSEEYTKPDQGELNIATTDTQARYALPNIIRQFIDRYP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             KV L + QG P QI+E      AD AI TE +     LI +PCY W   ++VP DHPL  
Sbjct:   121 KVNLHMHQGTPSQISEQAARGDADFAIATEAMHLYSDLIMLPCYHWNRSVVVPKDHPLAT 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
                IS+++++ +PL+TY   F    ++++ F+   L P +V    ++D++KTYV L +G+
Sbjct:   181 RTQISIEDLARFPLVTYVFGFDRASEIEKAFNRANLEPRVVFSATSADVLKTYVRLGLGV 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G+IAS+A D N DK+L +I A HLF  + +++  ++G++LRSY+Y FI+  +P L R  +
Sbjct:   241 GVIASMAIDPNIDKDLVAIDAGHLFAHSTTKIGFRKGSFLRSYMYDFIQHFAPHLTRDVV 300

Query:   301 NK 302
              K
Sbjct:   301 EK 302

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0019344 "cysteine biosynthetic process" evidence=ISS

UNIPROTKB|P0A9F3 cysB "CysB" [Escherichia coli K-12 (taxid:83333)]

 Score = 625 (225.1 bits), Expect = 4.3e-61, P = 4.3e-61
 Identities = 120/301 (39%), Positives = 182/301 (60%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M L Q R++ E V  N N++  A+ LYTSQPG+SK               R GK +  +T
Sbjct:     1 MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFSRSGKHLTQVT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               GQ I+R    ++ +++ +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct:    61 PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYIATTHTQARYALPNVIKGFIERYP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             +V L + QG+P QI + +    AD AI TE L   + L+ +PCY W   I+V  DHPL  
Sbjct:   121 RVSLHMHQGSPTQIADAVSKGNADFAIATEALHLYEDLVMLPCYHWNRAIVVTPDHPLAG 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
               +I+++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct:   181 KKAITIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G+IAS+A D   D +L  + A  +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct:   241 GVIASMAVDPVADPDLVRVDAHDIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query:   301 N 301
             +
Sbjct:   301 D 301

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IGI

GO:0008652 "cellular amino acid biosynthetic process" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;IDA

GO:0019344 "cysteine biosynthetic process" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q9KQU1 VC_1907 "Cys regulon transcriptional activator" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 622 (224.0 bits), Expect = 9.0e-61, P = 9.0e-61
 Identities = 117/305 (38%), Positives = 186/305 (60%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M L Q +++ E V  N N++  A+ LYTSQPG+SK               R GK +  +T
Sbjct:     1 MKLQQLKYIVEVVNHNLNVSATAENLYTSQPGISKQVRLLEDELGIQIFERSGKHLTQVT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               G+ I+R    I+  +E +K +  E +  + G L I+TTHTQARYALP++IK FT ++P
Sbjct:    61 PAGEHIVRIATEILSRVESIKAVAAEHTHPEMGTLNISTTHTQARYALPEVIKGFTKRYP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             +V L + QG P Q++E I    A+ AI TE L      I +PCY W   I+VP DHPL  
Sbjct:   121 RVSLHMHQGTPTQMSEAIAKGTANFAIATEALHLYQDAIMLPCYHWNRSIVVPKDHPLTK 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
                +++++++ YPL+TY   F+GR +LD  F+   +TP +V    ++D+IKTYV + +G+
Sbjct:   181 KEQVTIEDLAAYPLVTYVFGFTGRSELDSAFNRVGMTPKVVFTATDADVIKTYVRMGIGV 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G+IAS+A D  +D +L +I ASH+F  + + +  ++GT+LRSY++ F++  +P L R  +
Sbjct:   241 GVIASMAVDKKQDTDLVAIDASHIFSASTTSIGFRRGTFLRSYMFDFMERFAPHLTRPVV 300

Query:   301 NKILN 305
              + ++
Sbjct:   301 EQAIS 305

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

TIGR_CMR|VC_1907 VC_1907 "cys regulon transcriptional activator" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 622 (224.0 bits), Expect = 9.0e-61, P = 9.0e-61
 Identities = 117/305 (38%), Positives = 186/305 (60%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M L Q +++ E V  N N++  A+ LYTSQPG+SK               R GK +  +T
Sbjct:     1 MKLQQLKYIVEVVNHNLNVSATAENLYTSQPGISKQVRLLEDELGIQIFERSGKHLTQVT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               G+ I+R    I+  +E +K +  E +  + G L I+TTHTQARYALP++IK FT ++P
Sbjct:    61 PAGEHIVRIATEILSRVESIKAVAAEHTHPEMGTLNISTTHTQARYALPEVIKGFTKRYP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             +V L + QG P Q++E I    A+ AI TE L      I +PCY W   I+VP DHPL  
Sbjct:   121 RVSLHMHQGTPTQMSEAIAKGTANFAIATEALHLYQDAIMLPCYHWNRSIVVPKDHPLTK 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
                +++++++ YPL+TY   F+GR +LD  F+   +TP +V    ++D+IKTYV + +G+
Sbjct:   181 KEQVTIEDLAAYPLVTYVFGFTGRSELDSAFNRVGMTPKVVFTATDADVIKTYVRMGIGV 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G+IAS+A D  +D +L +I ASH+F  + + +  ++GT+LRSY++ F++  +P L R  +
Sbjct:   241 GVIASMAVDKKQDTDLVAIDASHIFSASTTSIGFRRGTFLRSYMFDFMERFAPHLTRPVV 300

Query:   301 NKILN 305
              + ++
Sbjct:   301 EQAIS 305

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

TIGR_CMR|CPS_1200 CPS_1200 "cys regulon transcription activator" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 600 (216.3 bits), Expect = 1.9e-58, P = 1.9e-58
 Identities = 117/304 (38%), Positives = 180/304 (59%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M L Q R++ E +  N N++  A +L+TSQPG+SK               R GK +  +T
Sbjct:     1 MKLQQLRYIVEVLNNNLNVSATADSLFTSQPGISKQVRMLEDELGIQIFGRSGKHLTHVT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             + GQ ++     I+ ++EG+K + +E +  D G L IATTHTQARYALP +I+ F  ++ 
Sbjct:    61 EAGQDVIDIATQILSKVEGIKAVAREHTQPDEGKLRIATTHTQARYALPDVIQGFIKRYS 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             KV L + QG P QI++     +AD AI TE L   + L+ +PCY W   IIV  DHPL  
Sbjct:   121 KVSLHMSQGTPAQISDAAAKGEADFAIATESLHLYNDLVMLPCYHWNRSIIVRPDHPLAK 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
               +I++ +I+ Y L+TY   F+GR +LD  F      P I     ++D+IKTYV L +G+
Sbjct:   181 KQNITIVDIAKYSLVTYVFGFTGRSELDAAFDAAGAKPKIAFTATDADVIKTYVRLGVGV 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G+IAS+A D   D +L  I ASHLF  + +++  ++G++LR+Y+Y FI+  +P L +  +
Sbjct:   241 GVIASMAIDERIDSDLVVIDASHLFNASTTKIGFRRGSFLRAYMYDFIERFAPHLTKDIV 300

Query:   301 NKIL 304
              + +
Sbjct:   301 TRAM 304

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0019344 "cysteine biosynthetic process" evidence=ISS

UNIPROTKB|Q47083 cbl [Escherichia coli K-12 (taxid:83333)]

 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 119/302 (39%), Positives = 190/302 (62%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             MN  Q + +REA RQ++NLTE A  L+TSQ GVS+               R GKR+ G+T
Sbjct:     1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFVRRGKRLLGMT 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             +PG+A+L   E I+ E   ++++   F+   +G LTIATTHTQARY+LP++IK F   FP
Sbjct:    61 EPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             +V+L L+QG P++I  +++N +ADI I +E LS   +L++ P ++W + ++VP DHPL  
Sbjct:   121 EVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQ 180

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             ++ ++L+ I+ +PLITY    +GR ++D  F+ + L   IVL   +SD+IKTYV L +GI
Sbjct:   181 ISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240

Query:   241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
             G++A  +     ++NL  +   HLF      + +K+G   R+YV+ F++L +  L+ + I
Sbjct:   241 GLVAEQSSGEQEEENLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDI 300

Query:   301 NK 302
              +
Sbjct:   301 KR 302

GO:0045883 "positive regulation of sulfur utilization" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

TIGR_CMR|BA_2439 BA_2439 "transcriptional regulator, LysR family" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 83/292 (28%), Positives = 134/292 (45%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             + L Q  +   AV +  + T+AA+ L  SQP +S+               R GK+I  LT
Sbjct:     4 IELRQLEYFL-AVSKELHFTKAAEKLNISQPSLSQQIRSLEHEVGMPLFDRIGKKI-SLT 61

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             + G+ +L   + I  EIE  +   ++ +    G+LTI +  T   Y LP  I  F   +P
Sbjct:    62 EAGRILLLHSKTIFHEIEQARSAIQDLNGLQQGSLTIGSLLTVVNYLLPPAILNFNNLYP 121

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK-LISIPCYQWEYVIIVPLDHPLL 179
              ++LS+L      I E +  ++ DI I    L   DK +IS P Y+ E +I+VP  H L 
Sbjct:   122 NIELSVLGLRTGDIREKLLQNELDIGIT--FLPVQDKEIISAPLYESELIIVVPTGHQLA 179

Query:   180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
               N +S+ E+ NYPLI    +F     +          P  +LE    + +   V   MG
Sbjct:   180 KHNHVSIAELQNYPLILLPKNFFLTELITSHCQKFNFKPKPILEISTMESLIQMVSKGMG 239

Query:   240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291
             I ++     D  ++KN+++I   +   T    +I ++  Y+ +    FIK L
Sbjct:   240 ITVLPKPYIDFLQNKNIQAIKIENPTPTIEIGLIYRKDKYMCAATREFIKQL 291

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

TIGR_CMR|GSU_2817 GSU_2817 "transcriptional regulator, LysR family" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 72/293 (24%), Positives = 135/293 (46%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             ++L Q   + E V Q  ++T+A+  L+ +Q  VS A              R GKR+  L 
Sbjct:     3 ISLRQLE-IFEKVAQCEHVTQASTQLFLTQSAVSMAIAELERVAGAPLFERRGKRLL-LN 60

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               G+ IL   E +++    +++  ++ +    G L +  + T   Y LP++I EF+  +P
Sbjct:    61 DRGRKILPEAEEVVRRTRAIEQFLEDSAGEPRGVLNVGASTTIGNYILPELIAEFSGNYP 120

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
               K+ L  GN  QI   +   + D+ ++ E +  S  L S P  + E V++V   HP   
Sbjct:   121 DAKVLLTIGNAHQIEHALEKGELDLGLI-EGIPHSGVLDSTPWKKDELVVVVGKGHPWAC 179

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
               + S++ + N P I  +     R   +   + + ++  I LE  +++ IK  +E  +G+
Sbjct:   180 DGAASVEMLGNAPWIMRETGSGTREVFEGAMAGKGISFSISLELGHTEAIKKAIEAGLGV 239

Query:   241 GIIASIAFDSNRDKN-LRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS 292
             G ++ IA +   +   L  I+       T+S +  +Q  Y    + +F  LL+
Sbjct:   240 GCLSRIAVNRELEHGWLVEIACPLDLKRTLS-LQTRQSGYKTRLLCAFWSLLN 291

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

TIGR_CMR|GSU_0266 GSU_0266 "transcriptional regulator, LysR family" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 211 (79.3 bits), Expect = 9.7e-17, P = 9.7e-17
 Identities = 62/253 (24%), Positives = 116/253 (45%)

Query:     1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
             M++ Q +F    VR   + T+AA+ L  +QP VS A              R  +++  LT
Sbjct:     1 MDIRQLQFFVAIVRFG-SFTKAAERLRVAQPAVSMAMKRLEEELDLVLFNRQERKV-SLT 58

Query:    61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
               G+  LR  E I++E+   +   +E      G + +      + Y  P+II++F+ ++P
Sbjct:    59 AEGEIFLRHAEKILEEVASTETEMEELRGLAKGEVRVGIPPMMSAYFFPQIIRDFSNRYP 118

Query:   121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
             ++ LS+      +I +MI + + D+ ++     P D L      + E ++ VP +H L  
Sbjct:   119 ELHLSVSGEGASKIQKMILDGELDMGVIAGASFP-DTLELRRFLREEVIVCVPKNHHLAE 177

Query:   181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +  + L+E + +PLI Y   +  R  +        L P I  ET    ++K+ +   MGI
Sbjct:   178 MERLPLQEFARHPLIFYKEGYYLRELVFDVMRGAGLNPAIRFETNLYTLVKSLIRKGMGI 237

Query:   241 GIIASIAFDSNRD 253
              +   +  + + D
Sbjct:   238 SVFLRMVVEEDDD 250

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

UNIPROTKB|P27111 cynR "CynR DNA-binding transcriptional repressor" [Escherichia coli K-12 (taxid:83333)]

 Score = 210 (79.0 bits), Expect = 1.2e-16, P = 1.2e-16
 Identities = 66/252 (26%), Positives = 118/252 (46%)

Query:    12 AVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLTKPGQAILRSIE 71
             AV ++ + T AA AL+ SQP +S+               R G+ IR LT  G+   +   
Sbjct:    11 AVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIR-LTDAGEVWRQYAS 69

Query:    72 IIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP 131
               +QE+   K+   + +    G+L IA T T   Y +  ++ +F  ++P + L L + + 
Sbjct:    70 RALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQ 129

Query:   132 KQITEMIRNDQADIAIV-TEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEIS 190
             ++I +M+  D+ D+ I    + SP  +L +IP       ++V   HPL +   ++L  + 
Sbjct:   130 EKIEDMLCRDELDVGIAFAPVHSP--ELEAIPLLTESLALVVAQHHPLAVHEQVALSRLH 187

Query:   191 NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL--RMGIGIIASIAF 248
             +  L+     F+ R ++D       L P +V+E  NS  I   +EL  R  +  +   A 
Sbjct:   188 DEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA-NS--ISAVLELIRRTSLSTLLPAAI 244

Query:   249 DSNRDKNLRSIS 260
              +  D  L++IS
Sbjct:   245 ATQHD-GLKAIS 255

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P45600	CYSB_KLEPN	No assigned EC number	0.4252	0.9836	0.9290	yes	N/A
P52595	CBBR_RHORU	No assigned EC number	0.2318	0.8758	0.8993	yes	N/A
P06614	CYSB_SALTY	No assigned EC number	0.4285	0.9836	0.9290	yes	N/A
A0T0G2	RBCR_PHATC	No assigned EC number	0.2614	0.8725	0.8697	yes	N/A
P37499	YYBE_BACSU	No assigned EC number	0.2625	0.8267	0.8664	yes	N/A
P45105	CYSB_HAEIN	No assigned EC number	0.4172	0.9836	0.9318	yes	N/A
P0A9F4	CYSB_ECOL6	No assigned EC number	0.4219	0.9836	0.9290	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	306
PRK12684	313	PRK12684, PRK12684, transcriptional regulator CysB	0.0
PRK12682	309	PRK12682, PRK12682, transcriptional regulator CysB	1e-155
PRK12683	309	PRK12683, PRK12683, transcriptional regulator CysB	1e-148
PRK12681	324	PRK12681, cysB, transcriptional regulator CysB; Re	1e-116
cd08413	198	cd08413, PBP2_CysB_like, The C-terminal substrate	1e-103
PRK12679	316	PRK12679, cbl, transcriptional regulator Cbl; Revi	1e-102
cd08444	198	cd08444, PBP2_Cbl, The C-terminal substrate bindin	8e-75
cd08443	198	cd08443, PBP2_CysB, The C-terminal substrate domai	6e-71
PRK12680	327	PRK12680, PRK12680, transcriptional regulator CysB	7e-54
COG0583	297	COG0583, LysR, Transcriptional regulator [Transcri	8e-44
cd05466	197	cd05466, PBP2_LTTR_substrate, The substrate bindin	2e-40
pfam03466	207	pfam03466, LysR_substrate, LysR substrate binding	1e-34
cd08420	201	cd08420, PBP2_CysL_like, C-terminal substrate bind	3e-24
cd08434	195	cd08434, PBP2_GltC_like, The substrate binding dom	2e-23
TIGR03339	279	TIGR03339, phn_lysR, aminoethylphosphonate catabol	1e-22
cd08415	196	cd08415, PBP2_LysR_opines_like, The C-terminal sub	6e-21
PRK11242	296	PRK11242, PRK11242, DNA-binding transcriptional re	1e-19
cd08440	197	cd08440, PBP2_LTTR_like_4, TThe C-terminal substra	4e-19
cd08419	197	cd08419, PBP2_CbbR_RubisCO_like, The C-terminal su	5e-18
CHL00180	305	CHL00180, rbcR, LysR transcriptional regulator; Pr	8e-18
PRK09791	302	PRK09791, PRK09791, putative DNA-binding transcrip	1e-17
TIGR02424	300	TIGR02424, TF_pcaQ, pca operon transcription facto	1e-16
cd08414	197	cd08414, PBP2_LTTR_aromatics_like, The C-terminal	9e-16
PRK11013	309	PRK11013, PRK11013, DNA-binding transcriptional re	5e-15
PRK09906	296	PRK09906, PRK09906, DNA-binding transcriptional re	5e-15
cd08412	198	cd08412, PBP2_PAO1_like, The C-terminal substrate-	1e-13
PRK09986	294	PRK09986, PRK09986, DNA-binding transcriptional ac	2e-13
PRK10837	290	PRK10837, PRK10837, putative DNA-binding transcrip	9e-13
cd08438	197	cd08438, PBP2_CidR, The C-terminal substrate bindi	3e-12
cd08426	199	cd08426, PBP2_LTTR_like_5, The C-terminal substrat	4e-12
pfam00126	60	pfam00126, HTH_1, Bacterial regulatory helix-turn-	9e-12
cd08456	196	cd08456, PBP2_LysR, The C-terminal substrate bindi	6e-11
PRK11151	305	PRK11151, PRK11151, DNA-binding transcriptional re	6e-11
cd08433	198	cd08433, PBP2_Nac, The C-teminal substrate binding	4e-10
cd08457	196	cd08457, PBP2_OccR, The C-terminal substrate-domai	7e-10
cd08435	201	cd08435, PBP2_GbpR, The C-terminal substrate bindi	1e-09
cd08411	200	cd08411, PBP2_OxyR, The C-terminal substrate-bindi	2e-09
PRK10086	311	PRK10086, PRK10086, DNA-binding transcriptional re	4e-09
cd08436	194	cd08436, PBP2_LTTR_like_3, The C-terminal substrat	4e-09
PRK11716	269	PRK11716, PRK11716, DNA-binding transcriptional re	5e-09
cd08451	199	cd08451, PBP2_BudR, The C-terminal substrate bindi	5e-09
PRK15421	317	PRK15421, PRK15421, DNA-binding transcriptional re	9e-09
TIGR03418	291	TIGR03418, chol_sulf_TF, putative choline sulfate-	2e-08
cd08421	198	cd08421, PBP2_LTTR_like_1, The C-terminal substrat	4e-08
cd08427	195	cd08427, PBP2_LTTR_like_2, The C-terminal substrat	1e-07
TIGR02036	302	TIGR02036, dsdC, D-serine deaminase transcriptiona	2e-07
cd08417	200	cd08417, PBP2_Nitroaromatics_like, The C-terminal	3e-07
PRK10341	312	PRK10341, PRK10341, DNA-binding transcriptional ac	3e-07
PRK11233	305	PRK11233, PRK11233, nitrogen assimilation transcri	8e-07
PRK11139	297	PRK11139, PRK11139, DNA-binding transcriptional ac	9e-07
cd08418	201	cd08418, PBP2_TdcA, The C-terminal substrate bindi	1e-06
cd08437	198	cd08437, PBP2_MleR, The substrate binding domain o	1e-06
cd08442	193	cd08442, PBP2_YofA_SoxR_like, The C-terminal subst	2e-06
cd08425	197	cd08425, PBP2_CynR, The C-terminal substrate-bindi	1e-05
cd08423	200	cd08423, PBP2_LTTR_like_6, The C-terminal substrat	1e-05
cd08448	197	cd08448, PBP2_LTTR_aromatics_like_2, The C-termina	1e-05
cd08449	197	cd08449, PBP2_XapR, The C-terminal substrate bindi	1e-05
cd08441	198	cd08441, PBP2_MetR, The C-terminal substrate bindi	4e-05
PRK10632	309	PRK10632, PRK10632, transcriptional regulator; Pro	4e-05
cd08452	197	cd08452, PBP2_AlsR, The C-terminal substrate bindi	5e-05
cd08416	199	cd08416, PBP2_MdcR, The C-terminal substrate-bindi	9e-05
cd08461	198	cd08461, PBP2_DntR_like_3, The C-terminal substrat	1e-04
PRK09508	314	PRK09508, leuO, leucine transcriptional activator;	2e-04
cd08430	199	cd08430, PBP2_IlvY, The C-terminal substrate bindi	3e-04
PRK03601	275	PRK03601, PRK03601, transcriptional regulator HdfR	5e-04
PRK15092	310	PRK15092, PRK15092, DNA-binding transcriptional re	6e-04
PRK10082	303	PRK10082, PRK10082, cell density-dependent motilit	7e-04
cd08447	198	cd08447, PBP2_LTTR_aromatics_like_1, The C-termina	0.002
cd08459	201	cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal	0.003

>gnl|CDD|237173 PRK12684, PRK12684, transcriptional regulator CysB-like protein; Reviewed

 Score =  504 bits (1301), Expect = 0.0
 Identities = 190/306 (62%), Positives = 252/306 (82%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNLHQ RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE+EL ++IF RHGKR+RGLT
Sbjct: 1   MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+ IL S+E I+QE+E LK++GKEF+A D GNLTIATTHTQARYALP  IKEF  ++P
Sbjct: 61  EPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV+LS+LQG+P QI EM+ + QAD+AI TE ++   +L+S+PCYQW + ++VP DHPLL 
Sbjct: 121 KVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVSLPCYQWNHCVVVPPDHPLLE 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
              ++L++++ YPLITYD +F+GR K+++ F+L+ L P IVLE I++D+IKTYVEL +G+
Sbjct: 181 RKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GI+A +AFD  RD+NLR+I A HLFG++ +R+ +++G YLR YVY+FI+L +P LNRK +
Sbjct: 241 GIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPTLNRKLV 300

Query: 301 NKILNN 306
            + L  
Sbjct: 301 EQALKG 306

Length = 313

>gnl|CDD|183679 PRK12682, PRK12682, transcriptional regulator CysB-like protein; Reviewed

 Score =  434 bits (1119), Expect = e-155
 Identities = 169/304 (55%), Positives = 230/304 (75%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MNL Q RFVREAVR+N NLTEAAKAL+TSQPGVSKAIIELEEEL I+IFIRHGKR++GLT
Sbjct: 1   MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L  IE I++E+  +K+IG +FS  D+G LTIATTHTQARY LP+++  F  ++P
Sbjct: 61  EPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV LSL QG+P +I  M+ + +ADI I TE L+    L ++PCY W++ +IVP DHPL  
Sbjct: 121 KVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLATLPCYDWQHAVIVPPDHPLAQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
              I+L++++ YPLITY   F+GR ++DR F+   L P IVLE I+SD+IKTYV L +G+
Sbjct: 181 EERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GI+A +A+  +RD +L ++ A HLFG   + V +K+G YLR+YVY FI+L +P L+R+ I
Sbjct: 241 GIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFIELCAPHLSRELI 300

Query: 301 NKIL 304
            + +
Sbjct: 301 KRAV 304

Length = 309

>gnl|CDD|237172 PRK12683, PRK12683, transcriptional regulator CysB-like protein; Reviewed

 Score =  417 bits (1073), Expect = e-148
 Identities = 152/304 (50%), Positives = 218/304 (71%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MN  Q R +REAVRQNFNLTE A ALYTSQ GVSK I +LE+EL ++IFIR GKR+ GLT
Sbjct: 1   MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+ +L+ +E ++ + E L+++ ++F+  D+G+LT+ATTHTQARYALPK++++F   FP
Sbjct: 61  EPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           KV L+L QG+P++I EM+ N +ADI I TE L     L+S P Y W +V++VP  HPL  
Sbjct: 121 KVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVSFPYYSWHHVVVVPKGHPLTG 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             +++L+ I+ YP+ITYD  F+GR ++D+ F+   L P IVL  +++D+IKTYVEL MG+
Sbjct: 181 RENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           GI+A++A+D  RD  L ++   HLF    +RV +++G YLR Y Y FI+L +P L+   I
Sbjct: 241 GIVAAMAYDPQRDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHLSEAEI 300

Query: 301 NKIL 304
              L
Sbjct: 301 AAAL 304

Length = 309

>gnl|CDD|183678 PRK12681, cysB, transcriptional regulator CysB; Reviewed

 Score =  338 bits (869), Expect = e-116
 Identities = 136/302 (45%), Positives = 194/302 (64%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             G+ I+R    I+ ++E +K +  E +  D G+L IATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI E      AD AI TE L   D LI +PCY W   ++VP DHPL  
Sbjct: 121 RVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLYDDLIMLPCYHWNRSVVVPPDHPLAK 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
              ++++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L +I ASHLF  + +++  ++GT+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVADPDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAPHLTRDVV 300

Query: 301 NK 302
            K
Sbjct: 301 EK 302

Length = 324

>gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold

 Score =  299 bits (768), Expect = e-103
 Identities = 103/197 (52%), Positives = 140/197 (71%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           LTIATTHTQARY LP +I  F  ++PKVKLSL QG P QI EM+   +ADIAI TE L  
Sbjct: 2   LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDD 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L+++PCY+W + +IVP  HPL  L  ++L++++ YPLITYD  F+GR  +DR F+  
Sbjct: 62  HPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARA 121

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
            L P IVL  +++D+IKTYV L +G+GIIA +A+D  RD +L ++ A HLFG   +R+ +
Sbjct: 122 GLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRDADLVALDAGHLFGPNTTRIAL 181

Query: 275 KQGTYLRSYVYSFIKLL 291
           ++GTYLRSY Y FI+L 
Sbjct: 182 RRGTYLRSYAYDFIELF 198

CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 198

>gnl|CDD|183676 PRK12679, cbl, transcriptional regulator Cbl; Reviewed

 Score =  302 bits (775), Expect = e-102
 Identities = 128/295 (43%), Positives = 196/295 (66%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           MN  Q + +REA RQ++NLTE A  L+TSQ GVS+ I ELE+EL I+IFIR GKR+ G+T
Sbjct: 1   MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
           +PG+A+L   E I+ E   ++++   F+   +G LTIATTHTQARY+LP++IK F   FP
Sbjct: 61  EPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V+L L+QG P++I  +++N +ADI I +E LS   +L++ P ++W + ++VP DHPL  
Sbjct: 121 EVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQ 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
           +  ++L+ I+ +PLITY    +GR ++D  F+ + L   IVL   +SD+IKTYV L +GI
Sbjct: 181 ITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295
           G++A  +     + NL  +   HLF      + +K+G   R+YV+ F++L +  L
Sbjct: 241 GLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGL 295

Length = 316

>gnl|CDD|176135 cd08444, PBP2_Cbl, The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold

 Score =  227 bits (581), Expect = 8e-75
 Identities = 97/196 (49%), Positives = 136/196 (69%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           LTIATTHTQARYALP +++ F  QFP V L L QG+P++I  M+ N QADI I TE L  
Sbjct: 2   LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALEN 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
             +L+S P Y W + IIVP+ HPL  +  ++++ I+ +P+ITY   F+GR ++DR FS  
Sbjct: 62  HPELVSFPYYDWHHHIIVPVGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRA 121

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
           +LTP IVL  +++D+IKTYV L MGIGI+A +AF+  RD NL  +  SHLFG   + + +
Sbjct: 122 ELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNLIKLDTSHLFGKNTTWIAL 181

Query: 275 KQGTYLRSYVYSFIKL 290
           ++G  LR++ Y FI+L
Sbjct: 182 RRGGDLRNFAYRFIEL 197

Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|176134 cd08443, PBP2_CysB, The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold

 Score =  217 bits (555), Expect = 6e-71
 Identities = 91/196 (46%), Positives = 131/196 (66%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L +ATTHTQARY LP +IK F  ++P+V L + QG+P QI EM+     D AI TE L  
Sbjct: 2   LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHD 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
            D LI++PCY W   ++V  DHPL    SIS++E++ YP++TY   F+GR +LD  F+  
Sbjct: 62  YDDLITLPCYHWNRCVVVKRDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRA 121

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVII 274
            LTP IVL   ++D+IKTYV L +G+G+IAS+A+D   D +L    A  LF  +++++  
Sbjct: 122 GLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDARDLFPWSVTKIAF 181

Query: 275 KQGTYLRSYVYSFIKL 290
           ++GT+LRSY+Y FI+ 
Sbjct: 182 RRGTFLRSYMYDFIQR 197

CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|183677 PRK12680, PRK12680, transcriptional regulator CysB-like protein; Reviewed

 Score =  178 bits (452), Expect = 7e-54
 Identities = 87/306 (28%), Positives = 163/306 (53%), Gaps = 2/306 (0%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++        N+T AA  ++ +QPG+SK + +LE+EL   +F+R G+ +  +T
Sbjct: 1   MTLTQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             G  ++     ++ E   ++           G LT+ TTHTQAR+ LP  + +    +P
Sbjct: 61  PAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPL-L 179
           +V + L Q       +++    ADIAIV+         I++P Y+W  +++VP  H L  
Sbjct: 121 QVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLYRWRRLVVVPRGHALDT 180

Query: 180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
              +  +  ++ +PLI+Y+ S      L R F+   L P I L  +++D+IKTYV   +G
Sbjct: 181 PRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLG 240

Query: 240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF 299
           +G++A +A ++N D++LR+  A       I+  ++ +   LR Y    + +L+P+++++ 
Sbjct: 241 VGLLAEMAVNAN-DEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALELVHVLAPQIDKRD 299

Query: 300 INKILN 305
           + ++L+
Sbjct: 300 LRRVLD 305

Length = 327

>gnl|CDD|223656 COG0583, LysR, Transcriptional regulator [Transcription]

 Score =  151 bits (382), Expect = 8e-44
 Identities = 81/299 (27%), Positives = 137/299 (45%), Gaps = 8/299 (2%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M+L Q R    AV +  + T AA+ L  SQ  VS+ I  LEEEL + +F R  +R+R LT
Sbjct: 1   MDLRQLR-AFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVR-LT 58

Query: 61  KPGQAILRSIEIIMQEIEGLK-KIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           + G+ +L     I+ E+E    +  +       G L IA   T A   LP ++  F  ++
Sbjct: 59  EAGERLLERARRILAELEEALAEAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARY 118

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P+++L L   +  ++ E +   + D+AI      P D L++ P +  E V++VP  HPL 
Sbjct: 119 PEIELELGTSD--RLLEDLVEGELDLAIRAGPPPPPDGLVARPLFSEELVLVVPASHPLA 176

Query: 180 LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239
             +   L ++   PLI  +     R  LD+  +L    P I LE  +++ +   V   +G
Sbjct: 177 ARH--GLPDLPGEPLILLEHGCILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAGLG 234

Query: 240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297
           I ++       +   + +R +            ++ ++   L   V +FI  L   L R
Sbjct: 235 IALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALAR 293

Length = 297

>gnl|CDD|176102 cd05466, PBP2_LTTR_substrate, The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily

 Score =  139 bits (352), Expect = 2e-40
 Identities = 60/200 (30%), Positives = 103/200 (51%), Gaps = 7/200 (3%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L I  + + A Y LP ++  F  ++P V+LSL++G   ++ E +   + D+AIV   +  
Sbjct: 2   LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L S P ++   V++VP DHPL    S++L ++++ PLI ++     R  LDR F+  
Sbjct: 62  PG-LESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEA 120

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISR--- 271
             TP I LE  + + IK  V   +GI ++   A +   D  L  +    L    +SR   
Sbjct: 121 GFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVL---PLEDPPLSRTIG 177

Query: 272 VIIKQGTYLRSYVYSFIKLL 291
           ++ ++G YL     +F++LL
Sbjct: 178 LVWRKGRYLSPAARAFLELL 197

This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 197

>gnl|CDD|217576 pfam03466, LysR_substrate, LysR substrate binding domain

 Score =  124 bits (314), Expect = 1e-34
 Identities = 52/204 (25%), Positives = 94/204 (46%), Gaps = 8/204 (3%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
            G L I    T A Y LP ++  F  ++P V+L L++G+ +++ +++   + D+AI    
Sbjct: 3   RGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELVEGDSEELLDLLAEGELDLAIRRGP 62

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
                 L + P ++   V++ P DHPL     +SL+++++ PLI  +     R  LDR  
Sbjct: 63  PDDPG-LEARPLFEEPLVLVAPPDHPLARGEPVSLEDLADEPLILLEPGSGLRDLLDRAL 121

Query: 212 SLQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSISASHLFGTTIS 270
               L P + LE  + + +   V   +GI ++  S       D  L  +    L    + 
Sbjct: 122 RAAGLRPRVALEVNSLEALLAAVAAGLGIALLPRSAVARELADGRLVVL---PLPDPPLP 178

Query: 271 R---VIIKQGTYLRSYVYSFIKLL 291
           R   ++ ++G  L   V +FI  L
Sbjct: 179 RPIYLVYRKGRRLSPAVRAFIDFL 202

The structure of this domain is known and is similar to the periplasmic binding proteins. Length = 207

>gnl|CDD|176112 cd08420, PBP2_CysL_like, C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold

 Score = 96.8 bits (242), Expect = 3e-24
 Identities = 58/205 (28%), Positives = 104/205 (50%), Gaps = 11/205 (5%)

Query: 94  NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS 153
            L I  + T   Y LP+++  F  ++P+V++SL  GN ++I E + + + D+ +V E   
Sbjct: 1   TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLV-EGPV 59

Query: 154 PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS 212
               LI  P  + E V++VP DHPL     ++ +E++  P I  +   SG R   +R  +
Sbjct: 60  DHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWILRE-PGSGTREVFERALA 118

Query: 213 ---LQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTI 269
              L  L   IV+E  +++ IK  VE  +GI I++ +A    ++  L  + A  + G  +
Sbjct: 119 EAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAV--RKELELGRLVALPVEGLRL 176

Query: 270 SR---VIIKQGTYLRSYVYSFIKLL 291
           +R   +I  +  YL     +F++ L
Sbjct: 177 TRPFSLIYHKDKYLSPAAEAFLEFL 201

CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201

>gnl|CDD|176125 cd08434, PBP2_GltC_like, The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold

 Score = 94.9 bits (237), Expect = 2e-23
 Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 1/147 (0%)

Query: 97  IATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSD 156
           +   H+     +P +I+ F  ++P V   L QG+  ++ + ++N + D+A+ + +     
Sbjct: 4   LGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPV-PDEP 62

Query: 157 KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL 216
            +  IP +  E V++VP DHPL   +S+ L E+++ P +     F  R  +D   +    
Sbjct: 63  DIEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGF 122

Query: 217 TPYIVLETINSDIIKTYVELRMGIGII 243
           TP I  E      I   V   +G+ I+
Sbjct: 123 TPKIAFEGEEDSTIAGLVAAGLGVAIL 149

GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 195

>gnl|CDD|132382 TIGR03339, phn_lysR, aminoethylphosphonate catabolism associated LysR family transcriptional regulator

 Score = 94.4 bits (235), Expect = 1e-22
 Identities = 60/240 (25%), Positives = 123/240 (51%), Gaps = 7/240 (2%)

Query: 20  TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79
           T AA+ L  SQP V+  + +LEE   +++F R+G+R+  LT  G  +L  +E + Q+   
Sbjct: 15  TRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLE-LTDAGHRLLPIVERLFQQEAE 73

Query: 80  LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR 139
            + + +E  A   G+L IA T   A Y +  ++  F  ++P +++S+  GN +++ + ++
Sbjct: 74  AEFLLRESGALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQ 130

Query: 140 NDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL 199
           + + D+A+ +E++    +L  +       V +V   HPL    S++L+E++  PL+  + 
Sbjct: 131 SYRVDVAVSSEVVD-DPRLDRVVLGNDPLVAVVHRQHPLAERESVTLEELAGQPLLMREP 189

Query: 200 SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSI 259
               R   +   +   + P   LE  + + I+  V   +G+ ++++      RD  LR +
Sbjct: 190 GSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVG--RDPRLRVL 247

This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). Length = 279

>gnl|CDD|176107 cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold

 Score = 88.0 bits (219), Expect = 6e-21
 Identities = 40/149 (26%), Positives = 67/149 (44%), Gaps = 1/149 (0%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L IA     A   LP+ I  F  + P V++SL   +   + E + + QAD+ + +  L  
Sbjct: 2   LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDH 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L S P      V ++P  HPL   + ++  +++  PLI+       R ++D  F   
Sbjct: 62  PG-LESEPLASGRAVCVLPPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERA 120

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII 243
            + P IV+ET  S      V   +G+ I+
Sbjct: 121 GVEPRIVIETQLSHTACALVAAGLGVAIV 149

This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196

>gnl|CDD|183051 PRK11242, PRK11242, DNA-binding transcriptional regulator CynR; Provisional

 Score = 86.5 bits (215), Expect = 1e-19
 Identities = 63/218 (28%), Positives = 120/218 (55%), Gaps = 6/218 (2%)

Query: 12  AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
           AV ++ N T AA+AL+ SQP +S+ I +LEE L + +F R G+ +R LT  G+  LR   
Sbjct: 11  AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVR-LTDAGEVYLRYAR 69

Query: 72  IIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP 131
             +Q++E  ++   + +    G+L +A T T   Y +  +I  F  ++P + L++ + + 
Sbjct: 70  RALQDLEAGRRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQ 129

Query: 132 KQITEMIRNDQADIAIV-TEILSPSDKLISIPCYQWEYVIIVPLDHPLL-LLNSISLKEI 189
           ++I  ++ +D+ D+ I    + SP  ++ + P +     ++V   HPL     +++L E+
Sbjct: 130 ERIEALLADDELDVGIAFAPVHSP--EIEAQPLFTETLALVVGRHHPLAARRKALTLDEL 187

Query: 190 SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS 227
           ++ PL+     F+ R ++DR F    +TP + +E  NS
Sbjct: 188 ADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEA-NS 224

Length = 296

>gnl|CDD|176131 cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 83.0 bits (206), Expect = 4e-19
 Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 15/172 (8%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           + +A   + A   LP ++  F  + P +++ L   + +Q+ E +R+ + D  I +E    
Sbjct: 2   VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSE-PEA 60

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L   P  +  +V++ P DHPL    S++  E++ YPLI        R  +DR  +  
Sbjct: 61  DPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAA 120

Query: 215 KLTPYIVLETINSDIIKTY-------VELRMGIGIIASIAFDSNRDKNLRSI 259
            LT     E        ++       V   +G+ ++ ++A        L + 
Sbjct: 121 GLTLRPAYEV-------SHMSTALGMVAAGLGVAVLPALALPLADHPGLVAR 165

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176111 cd08419, PBP2_CbbR_RubisCO_like, The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold

 Score = 80.2 bits (199), Expect = 5e-18
 Identities = 43/151 (28%), Positives = 81/151 (53%), Gaps = 6/151 (3%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L +A   T A+Y  P+++  F  + P V++SL  GN +Q+ E + +++ D+AI+     P
Sbjct: 2   LRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP--P 58

Query: 155 SD-KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS 212
            D  L++ P      V+I P DHPL     I L+ ++  P +  +   SG R+ ++R F+
Sbjct: 59  EDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREPFLLRE-PGSGTRLAMERFFA 117

Query: 213 LQKLTPYIVLETINSDIIKTYVELRMGIGII 243
              +T  + +E  +++ IK  V   +G+ ++
Sbjct: 118 EHGVTLRVRMELGSNEAIKQAVMAGLGLSVL 148

CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|177082 CHL00180, rbcR, LysR transcriptional regulator; Provisional

 Score = 81.6 bits (202), Expect = 8e-18
 Identities = 66/250 (26%), Positives = 117/250 (46%), Gaps = 7/250 (2%)

Query: 3   LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
           L Q R ++ A+    +  +AA++LY SQP VS  I  LE++L+I +F R   +   LT+ 
Sbjct: 7   LDQLRILK-AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKAS-LTEA 64

Query: 63  GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKV 122
           G+ +LR    I+   E   +  ++      G L I  + T   Y +P++I  F  ++P++
Sbjct: 65  GELLLRYGNRILALCEETCRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQI 124

Query: 123 KLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPCYQWEYVIIVPLDHPLLL 180
            + L   + ++I   + N Q DIAIV   +       L   P  + E  +I+P  HP   
Sbjct: 125 NVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILEITPYVEDELALIIPKSHPFAK 184

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLD---REFSLQKLTPYIVLETINSDIIKTYVELR 237
           L  I  +++     IT D + + R  +D    +  +      I +E  + + IK  V+  
Sbjct: 185 LKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSG 244

Query: 238 MGIGIIASIA 247
           +G   ++  A
Sbjct: 245 LGAAFVSVSA 254

Length = 305

>gnl|CDD|182077 PRK09791, PRK09791, putative DNA-binding transcriptional regulator; Provisional

 Score = 81.0 bits (200), Expect = 1e-17
 Identities = 53/194 (27%), Positives = 96/194 (49%), Gaps = 11/194 (5%)

Query: 3   LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
           +HQ R   E  RQ  ++  A++ L  SQP ++K+I ELEE L+  +F R  K +  LT  
Sbjct: 7   IHQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVT-LTDA 64

Query: 63  GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKV 122
           G++  +   +I++E+   ++  ++      G + I    + AR  +P +I  F  Q P+V
Sbjct: 65  GESFYQHASLILEELRAAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQV 124

Query: 123 KLSLLQGNPKQITEMI---RNDQADIAIVTEILSPSDKLISIP-CYQWEYVIIVPLDHPL 178
           K+ +++G   Q+  MI   R  + D  I T    P D   +     + ++ +     HP 
Sbjct: 125 KVRIMEG---QLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVFCRPGHP- 180

Query: 179 LLLNSISLKEISNY 192
             + + SLK++ +Y
Sbjct: 181 -AIGARSLKQLLDY 193

Length = 302

>gnl|CDD|233862 TIGR02424, TF_pcaQ, pca operon transcription factor PcaQ

 Score = 78.2 bits (193), Expect = 1e-16
 Identities = 66/252 (26%), Positives = 120/252 (47%), Gaps = 19/252 (7%)

Query: 8   FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
           FV E  RQ  ++  AA+AL+ +QP VSK + ELEE L   +F R  + IR LT+ G+  L
Sbjct: 11  FV-EVARQG-SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIR-LTRYGELFL 67

Query: 68  R----SIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVK 123
           R    S+  + Q +  L ++G      +   + I    T A   +P+++K F  + P+++
Sbjct: 68  RHAGASLAALRQGVASLSQLG----EGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLR 123

Query: 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISI---PCYQWEYVIIVPLDHPLLL 180
           + ++ G    + + +R    D+ +    L   + +  +     Y    V +V   HPLL 
Sbjct: 124 VRIMTGPNAYLLDQLRVGALDLVVGR--LGAPETMQGLSFEHLYNEPVVFVVRAGHPLLA 181

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRMG 239
             S+ +  +++YP++      + R   +R F    + P    +ET++    + YV+    
Sbjct: 182 APSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQESDA 241

Query: 240 IGIIAS--IAFD 249
           I II+   +A D
Sbjct: 242 IWIISRGVVALD 253

Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria [Energy metabolism, Other, Regulatory functions, DNA interactions]. Length = 300

>gnl|CDD|176106 cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold

 Score = 73.7 bits (182), Expect = 9e-16
 Identities = 37/156 (23%), Positives = 70/156 (44%), Gaps = 4/156 (2%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L I    +     LP++++ F  ++P V+L L +    +  E +R  + D+  V     P
Sbjct: 2   LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDP 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRI--KLDREFS 212
              L S P  +   V+ +P DHPL    S+SL ++++ P + +       +  ++     
Sbjct: 62  PG-LASRPLLREPLVVALPADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCR 120

Query: 213 LQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIA 247
               TP IV E  +   +   V   +G+ ++ AS+A
Sbjct: 121 RAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVA 156

This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 197

>gnl|CDD|236819 PRK11013, PRK11013, DNA-binding transcriptional regulator LysR; Provisional

 Score = 73.9 bits (182), Expect = 5e-15
 Identities = 60/236 (25%), Positives = 112/236 (47%), Gaps = 10/236 (4%)

Query: 12  AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
           AV    +LTEAA+ L+TSQP VS+ +   E+ + + +F    +R+RG   P    LR  E
Sbjct: 14  AVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLF----ERVRGRLHPTVQGLRLFE 69

Query: 72  IIMQEIEGLKKIGKEFSA---YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL- 127
            + +   GL +I     +   +  G L+IA     ++  LP + + F  ++P V L+++ 
Sbjct: 70  EVQRSYYGLDRIVSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVP 129

Query: 128 QGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLK 187
           Q +P  + E +   + D+ + TE L              + V ++P  HPL     ++  
Sbjct: 130 QESP-LLEEWLSAQRHDLGL-TETLHTPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPD 187

Query: 188 EISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
           + +    I+   + S R  LD+ F+   +   +V+ET ++  +   V   +G+ I+
Sbjct: 188 DFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGVSIV 243

Length = 309

>gnl|CDD|182137 PRK09906, PRK09906, DNA-binding transcriptional regulator HcaR; Provisional

 Score = 73.7 bits (181), Expect = 5e-15
 Identities = 65/246 (26%), Positives = 115/246 (46%), Gaps = 8/246 (3%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           M L   R FV  AV +  N T+AA+ L+T+QP +S+ I +LE  + + + +R  KR   L
Sbjct: 1   MELRHLRYFV--AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRD-KRKVAL 57

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  G+  L+    I+++ E  K   ++    D   LTI    +     LPK++  F ++ 
Sbjct: 58  TAAGEVFLQDARAILEQAEKAKLRARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRH 116

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P   + L+     Q  E +R  + D+  +   +  SD++  +       V+++P+DHPL 
Sbjct: 117 PDTLIELVSLITTQQEEKLRRGELDVGFMRHPVY-SDEIDYLELLDEPLVVVLPVDHPLA 175

Query: 180 LLNSISLKEISNYPLITYDLSFSGRIK--LDREFSLQKLTPYIVLETINSDIIKTYVELR 237
               I+  ++     I+ D ++SG +   +   F+     P IV    N  +    V + 
Sbjct: 176 HEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG 235

Query: 238 MGIGII 243
           +G  II
Sbjct: 236 LGCTII 241

Length = 296

>gnl|CDD|176104 cd08412, PBP2_PAO1_like, The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily

 Score = 68.3 bits (168), Expect = 1e-13
 Identities = 41/148 (27%), Positives = 77/148 (52%), Gaps = 2/148 (1%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L I    T A Y LP +++ F   +P V++ +++GN +++ E +R+ + D+A+  ++  P
Sbjct: 2   LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
            D +   P  +    + +P DHPL   + +SL +++  PLI  DL  S    L   F+  
Sbjct: 62  ED-IAFEPLARLPPYVWLPADHPLAGKDEVSLADLAAEPLILLDLPHSREYFLSL-FAAA 119

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGI 242
            LTP I   T + + +++ V   +G  +
Sbjct: 120 GLTPRIAYRTSSFEAVRSLVANGLGYSL 147

This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 198

>gnl|CDD|182183 PRK09986, PRK09986, DNA-binding transcriptional activator XapR; Provisional

 Score = 69.0 bits (169), Expect = 2e-13
 Identities = 58/239 (24%), Positives = 102/239 (42%), Gaps = 11/239 (4%)

Query: 12  AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIE 71
           AV +  +   AA  L  SQP +S  I ELE++L   +FIRH + +  LT  G+ ++    
Sbjct: 17  AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSV-VLTHAGKILMEESR 75

Query: 72  IIMQEIEG----LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL 127
            ++   E     +++IG+     + G + I    T     L   ++ F  + P V+  L 
Sbjct: 76  RLLDNAEQSLARVEQIGR----GEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLR 131

Query: 128 QGNPKQITEMIRNDQADIAIVTE-ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISL 186
           + +P      +   + D  I     L P+    S   ++  + + VP +HPL   +S+ L
Sbjct: 132 ELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLHESAFAVAVPEEHPLASRSSVPL 191

Query: 187 KEISNYPLITYDLSFSGRIK-LDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIA 244
           K + N   IT     S   K L R       +P I+ +      +   V + +GI ++ 
Sbjct: 192 KALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGITLLP 250

Length = 294

>gnl|CDD|182768 PRK10837, PRK10837, putative DNA-binding transcriptional regulator; Provisional

 Score = 67.0 bits (164), Expect = 9e-13
 Identities = 68/230 (29%), Positives = 107/230 (46%), Gaps = 23/230 (10%)

Query: 20  TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI------RGLTKPGQAILRSIEII 73
           T+A+  L  SQ  VS A+ +LE +L + +F R GKR+      R L     A+L      
Sbjct: 21  TQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ---- 76

Query: 74  MQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQ 133
             EIE L +        D G L I  + T   Y LP +I  +   +P++ L L  GN + 
Sbjct: 77  AVEIEQLFR-------EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQD 129

Query: 134 ITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP 193
           +   + + + DI ++ E    S +LIS P  + E V+    D P L    ++L++++  P
Sbjct: 130 VINAVLDFRVDIGLI-EGPCHSPELISEPWLEDELVVFAAPDSP-LARGPVTLEQLAAAP 187

Query: 194 LITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRMGIGI 242
            I  +     R  +D    L  L  + + +E  NS+ IK  V  R G+GI
Sbjct: 188 WILRERGSGTREIVDY-LLLSHLPRFELAMELGNSEAIKHAV--RHGLGI 234

Length = 290

>gnl|CDD|176129 cd08438, PBP2_CidR, The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold

 Score = 64.1 bits (157), Expect = 3e-12
 Identities = 28/137 (20%), Positives = 62/137 (45%), Gaps = 3/137 (2%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-SDKLISIPCYQW 166
              ++  F  ++P ++L L++   K++ + + N + D+ I    L    ++  S P    
Sbjct: 15  FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITV--LPVDEEEFDSQPLCNE 72

Query: 167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN 226
             V ++P  HPL    ++SL ++++ P I ++  F+   ++         TP I   +  
Sbjct: 73  PLVAVLPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQ 132

Query: 227 SDIIKTYVELRMGIGII 243
            D I   V   +G+ ++
Sbjct: 133 WDFIAELVAAGLGVALL 149

This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176117 cd08426, PBP2_LTTR_like_5, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 63.9 bits (156), Expect = 4e-12
 Identities = 36/145 (24%), Positives = 61/145 (42%), Gaps = 1/145 (0%)

Query: 96  TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
            +AT    A   LP +I  F  ++P V  ++   +   + E + + +ADI +        
Sbjct: 3   RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEP 62

Query: 156 DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK 215
             +            +VP  HPL    S++L +++ YPL     SFS R  LD  F+   
Sbjct: 63  G-IRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAG 121

Query: 216 LTPYIVLETINSDIIKTYVELRMGI 240
           +    VL + + + +K  V    GI
Sbjct: 122 VQLEPVLISNSIETLKQLVAAGGGI 146

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199

>gnl|CDD|215735 pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein, lysR family

 Score = 58.9 bits (144), Expect = 9e-12
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 3  LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
          L Q R       +  + T AA+ L  SQP VS+ I  LEEEL + +F R  + +R LT  
Sbjct: 1  LRQLRVFVAVAEEG-SFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLR-LTPA 58

Query: 63 GQ 64
          G+
Sbjct: 59 GE 60

Length = 60

>gnl|CDD|176145 cd08456, PBP2_LysR, The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold

 Score = 60.5 bits (147), Expect = 6e-11
 Identities = 34/166 (20%), Positives = 70/166 (42%), Gaps = 9/166 (5%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L IA     ++  LP+ IK F  + P V +S+   +   + + +   Q D+ +V+ +  P
Sbjct: 2   LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEP 61

Query: 155 ----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
                ++L+ I       V ++P  H L +   ++  ++   P I+   +   R ++D  
Sbjct: 62  PGIERERLLRIDG-----VCVLPPGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDAL 116

Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNL 256
           F    +   IV+ET  +  I   V   +G+ ++  +         L
Sbjct: 117 FEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAGL 162

LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196

>gnl|CDD|182999 PRK11151, PRK11151, DNA-binding transcriptional regulator OxyR; Provisional

 Score = 61.6 bits (150), Expect = 6e-11
 Identities = 45/183 (24%), Positives = 88/183 (48%), Gaps = 14/183 (7%)

Query: 22  AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI----RGLTKPGQA--ILRSIEIIMQ 75
           AA + + SQP +S  I +LE+EL + +  R  +++     GL    QA  +LR +++ ++
Sbjct: 21  AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKV-LK 79

Query: 76  EIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQIT 135
           E+   +  G+      +G L I    T   Y LP II      FPK+++ L +    Q+ 
Sbjct: 80  EMASQQ--GETM----SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLL 133

Query: 136 EMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLI 195
             + + + D AI+  +   S+  I +P +    ++ V  DHP    + + + +++   L+
Sbjct: 134 AQLDSGKLDCAILALV-KESEAFIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLL 192

Query: 196 TYD 198
             +
Sbjct: 193 MLE 195

Length = 305

>gnl|CDD|176124 cd08433, PBP2_Nac, The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold

 Score = 58.0 bits (141), Expect = 4e-10
 Identities = 30/147 (20%), Positives = 65/147 (44%), Gaps = 3/147 (2%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           +++    + A      +++    ++P ++L +++G    + E + N + D+A++     P
Sbjct: 2   VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYG-PPP 60

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L + P  + +  ++ P D PL     + L E++  PLI        R  +D   +  
Sbjct: 61  IPGLSTEPLLEEDLFLVGPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARA 120

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIG 241
            LT  +V+E  +   +K  V    G+G
Sbjct: 121 GLTLNVVVEIDSVATLKALV--AAGLG 145

The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|176146 cd08457, PBP2_OccR, The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold

 Score = 57.5 bits (139), Expect = 7e-10
 Identities = 37/153 (24%), Positives = 69/153 (45%), Gaps = 9/153 (5%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L IA     A   LP+ +  F    P + LSL+  +  Q+ E + + +AD+ I    L  
Sbjct: 2   LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEE 61

Query: 155 SDKLI----SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
               +    S+P      V+ VP+ HPL  L+ +S ++++   +IT +  +  R++++  
Sbjct: 62  RQGFLIETRSLPA-----VVAVPMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVA 116

Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
                +    ++E   S    + V   +GI II
Sbjct: 117 LGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149

This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196

>gnl|CDD|176126 cd08435, PBP2_GbpR, The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold

 Score = 56.5 bits (137), Expect = 1e-09
 Identities = 30/134 (22%), Positives = 60/134 (44%), Gaps = 4/134 (2%)

Query: 94  NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI--VTEI 151
            + +      A   LP  I     + P++ + +++G   ++ E +R  + D+AI  + + 
Sbjct: 1   TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADD 60

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
             P D L S        V++    HPL     ++L ++++YP +        R +L++ F
Sbjct: 61  EQPPD-LASEELADEPLVVVARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLF 119

Query: 212 SLQKL-TPYIVLET 224
           +   L  P  V+ET
Sbjct: 120 AAAGLPLPRNVVET 133

Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201

>gnl|CDD|176103 cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily

 Score = 56.0 bits (136), Expect = 2e-09
 Identities = 25/104 (24%), Positives = 53/104 (50%), Gaps = 1/104 (0%)

Query: 93  GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL 152
           G L +    T A Y LP+++      +PK++L L +   +++ E +R+ + D A++  + 
Sbjct: 1   GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLA-LP 59

Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
                L   P +   +++ VP DHPL    S++ ++++   L+ 
Sbjct: 60  VDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAGERLLL 103

OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 200

>gnl|CDD|182231 PRK10086, PRK10086, DNA-binding transcriptional regulator DsdC; Provisional

 Score = 56.2 bits (136), Expect = 4e-09
 Identities = 44/133 (33%), Positives = 71/133 (53%), Gaps = 15/133 (11%)

Query: 2   NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61
            LH F     A  Q+F L  AA  L  +   VS  I +LEEEL I +F+R  +++  LT+
Sbjct: 18  KLHTFEVA--ARHQSFAL--AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVE-LTE 72

Query: 62  PGQ----AILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTI 117
            G+    A+  S++ + QEI  +K   +E S    G LT+ +  + A+  L   + +FT 
Sbjct: 73  EGKRVFWALKSSLDTLNQEILDIK--NQELS----GTLTVYSRPSIAQCWLVPRLADFTR 126

Query: 118 QFPKVKLSLLQGN 130
           ++P + L++L GN
Sbjct: 127 RYPSISLTILTGN 139

Length = 311

>gnl|CDD|176127 cd08436, PBP2_LTTR_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 54.9 bits (133), Expect = 4e-09
 Identities = 38/166 (22%), Positives = 73/166 (43%), Gaps = 4/166 (2%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L I T  + A   LP+++  F  + P V + L Q     +   +R  + D+A V      
Sbjct: 2   LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERR 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L S    +   V +V  DHPL     ++L ++++ P + +      R ++DR F+  
Sbjct: 62  PPGLASRELAREPLVAVVAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAA 121

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSI 259
            +   +  E  + D++   V   +G+ ++ AS+A    R   L ++
Sbjct: 122 GVRRRVAFEVSDVDLLLDLVARGLGVALLPASVA---ARLPGLAAL 164

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 194

>gnl|CDD|236961 PRK11716, PRK11716, DNA-binding transcriptional regulator IlvY; Provisional

 Score = 55.6 bits (135), Expect = 5e-09
 Identities = 55/222 (24%), Positives = 94/222 (42%), Gaps = 25/222 (11%)

Query: 34  SKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG 93
           S+ I  LEEEL   +F+R  + +  LT+ G+ +    +  + + + L+    +     +G
Sbjct: 9   SRQIQRLEEELGQPLFVRDNRSVT-LTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSG 67

Query: 94  NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI--VTEI 151
            L++  + T A   LP I+  F  + P V++ L  G+     E +++ +AD+AI    E 
Sbjct: 68  ELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPET 127

Query: 152 LSPSD----KLISIPCYQWEYVIIVPLDHP----LLLLNSISLKEISNYPLITYDLSFSG 203
           L P+      +  IP      V+I P         L         I   P I   L   G
Sbjct: 128 L-PASVAFSPIDEIP-----LVLIAPALPCPVRQQLSQEKPDWSRI---PFI---LPEHG 175

Query: 204 --RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
             R ++D  F   K+ P I       + I + V L  G+G++
Sbjct: 176 PARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLL 217

Length = 269

>gnl|CDD|176142 cd08451, PBP2_BudR, The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold

 Score = 54.9 bits (133), Expect = 5e-09
 Identities = 25/90 (27%), Positives = 47/90 (52%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
           +P +I+ F   +P V+L+L + N  ++ E +R  + D A V   ++ SD L+     +  
Sbjct: 16  VPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEP 75

Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLITY 197
            ++ +P  HPL    SI L  +++ P I +
Sbjct: 76  MLVALPAGHPLARERSIPLAALADEPFILF 105

This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199

>gnl|CDD|185319 PRK15421, PRK15421, DNA-binding transcriptional regulator MetR; Provisional

 Score = 55.4 bits (133), Expect = 9e-09
 Identities = 54/232 (23%), Positives = 110/232 (47%), Gaps = 10/232 (4%)

Query: 11  EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI 70
           +A+R   +L  AA  L+ +Q  +S    +LE+ L   +F+R  + +R  T  G+ +L+  
Sbjct: 11  QALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLR-FTPQGEILLQLA 69

Query: 71  EIIMQEIEGLKKIGKEFSAYDTGNLTIATT-HTQARYALPKIIKEFTIQFPKVKLSLLQG 129
             ++ +I    +   E        L IA   H+  ++  P  ++ F   +P+V++    G
Sbjct: 70  NQVLPQISQALQACNE---PQQTRLRIAIECHSCIQWLTPA-LENFHKNWPQVEMDFKSG 125

Query: 130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI 189
                   ++  + D+ + ++IL P   L   P + +E  +++  DHPL     I+ +++
Sbjct: 126 VTFDPQPALQQGELDLVMTSDIL-PRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDL 184

Query: 190 SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI-NSDIIKTYVELRMGI 240
           ++  L+ Y +    R+ + R F LQ       L+++ N+ ++   V  RMGI
Sbjct: 185 ASETLLIYPVQ-RSRLDVWRHF-LQPAGVSPSLKSVDNTLLLIQMVAARMGI 234

Length = 317

>gnl|CDD|188320 TIGR03418, chol_sulf_TF, putative choline sulfate-utilization transcription factor

 Score = 54.0 bits (130), Expect = 2e-08
 Identities = 42/143 (29%), Positives = 64/143 (44%), Gaps = 9/143 (6%)

Query: 7   RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI 66
           R    A R   + T AA+ L ++QP VS+ I  LEEEL + +F R   R   LT+ GQ +
Sbjct: 7   RVFESAARLA-SFTAAARELGSTQPAVSQQIKRLEEELGVPLFER-KHRGVELTEDGQRL 64

Query: 67  LRSIEIIMQEIEGLKKIGKEFSAYDT-GNLTIATTHTQARYALPKIIKEFTIQFPKVKLS 125
               E + + ++ +        A      LT+AT    A Y L   +  F    P V +S
Sbjct: 65  F---EAVRRGLDTIDAATAALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVS 121

Query: 126 LLQGNPKQITEMIRNDQADIAIV 148
           ++        +  R D  D+AI+
Sbjct: 122 IVTSQDSH--DGQR-DDIDVAIL 141

Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate. Length = 291

>gnl|CDD|176113 cd08421, PBP2_LTTR_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 52.1 bits (126), Expect = 4e-08
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
           LP+ +  F    P V++ L +     I   +   +AD+ IV   +  +  L + P     
Sbjct: 15  LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAG-LETRPYRTDR 73

Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLI 195
            V++VP DHPL    S++  +  ++  +
Sbjct: 74  LVVVVPRDHPLAGRASVAFADTLDHDFV 101

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|176118 cd08427, PBP2_LTTR_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 50.7 bits (122), Expect = 1e-07
 Identities = 43/185 (23%), Positives = 74/185 (40%), Gaps = 18/185 (9%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L +    T     LP+ +     + P +++ ++ G   ++   +   + D AIV E   P
Sbjct: 2   LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFP 61

Query: 155 SDK-LISIPCYQWEYVIIVPLDH----PLLLLNSISLKEISNYPLITYDLS-FSGRIKLD 208
             K L+  P  +   V+I P +     P  LL        +  P I YD S + GR+ +D
Sbjct: 62  LPKDLVWTPLVREPLVLIAPAELAGDDPRELL--------ATQPFIRYDRSAWGGRL-VD 112

Query: 209 REFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTT 268
           R    Q +    V+E  + + I   V   +G+ I+  IA        +R +    L    
Sbjct: 113 RFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPRVRVLP---LGDPA 169

Query: 269 ISRVI 273
            SR +
Sbjct: 170 FSRRV 174

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 195

>gnl|CDD|131091 TIGR02036, dsdC, D-serine deaminase transcriptional activator

 Score = 51.1 bits (122), Expect = 2e-07
 Identities = 43/132 (32%), Positives = 72/132 (54%), Gaps = 15/132 (11%)

Query: 3   LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62
           +H F     A  Q+F+L  AA+ L  +   +S  I +LEEEL I +F+R  +++  LT  
Sbjct: 13  MHTFEVA--ARHQSFSL--AAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVE-LTHE 67

Query: 63  GQ----AILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQ 118
           G+    A+  S++ + QEI  +K   +E S    G LT+ +  + A+  L   I +FT +
Sbjct: 68  GKRIYWALKSSLDTLNQEILDIKN--QELS----GTLTLYSRPSFAQCWLVPRIGDFTRR 121

Query: 119 FPKVKLSLLQGN 130
           +P + L++L GN
Sbjct: 122 YPSISLTVLTGN 133

This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea [Regulatory functions, DNA interactions]. Length = 302

>gnl|CDD|176109 cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold

 Score = 49.5 bits (119), Expect = 3e-07
 Identities = 28/131 (21%), Positives = 53/131 (40%), Gaps = 6/131 (4%)

Query: 96  TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
            IA +       LP ++     + P V+L  +  +   + E + + + D+AI      P 
Sbjct: 3   RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP 62

Query: 156 DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK--LDREFSL 213
             L S P ++  +V +   DHP L    ++L++    P +    S  GR    +D   + 
Sbjct: 63  G-LRSQPLFEDRFVCVARKDHP-LAGGPLTLEDYLAAPHVLV--SPRGRGHGLVDDALAE 118

Query: 214 QKLTPYIVLET 224
             L+  + L  
Sbjct: 119 LGLSRRVALTV 129

This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 200

>gnl|CDD|182391 PRK10341, PRK10341, DNA-binding transcriptional activator TdcA; Provisional

 Score = 50.6 bits (121), Expect = 3e-07
 Identities = 41/154 (26%), Positives = 74/154 (48%), Gaps = 8/154 (5%)

Query: 22  AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL- 80
           AAK L  +QP VSK I ++E+   +++ +R    +  LT  GQ +L   E I +E++ + 
Sbjct: 27  AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVT-LTPAGQVLLSRSESITREMKNMV 85

Query: 81  KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN 140
            +I    S     +++           +  +I +F   FPK ++S+ +         IR+
Sbjct: 86  NEINGMSSE-AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRD 144

Query: 141 DQADIAIVTEILSPSDKLISI---PCYQWEYVII 171
            + D AI T  LS   KL  +   P ++ E+V++
Sbjct: 145 GRLDFAIGT--LSNEMKLQDLHVEPLFESEFVLV 176

Length = 312

>gnl|CDD|183045 PRK11233, PRK11233, nitrogen assimilation transcriptional regulator; Provisional

 Score = 49.3 bits (118), Expect = 8e-07
 Identities = 61/237 (25%), Positives = 111/237 (46%), Gaps = 28/237 (11%)

Query: 19  LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG-------QAILRSIE 71
           LT+AA+ L+ +QP +S+ +  LE EL+  + IR  KR    T+ G       +AILR  E
Sbjct: 18  LTQAAEVLHIAQPALSQQVATLEGELNQQLLIR-TKRGVTPTEAGKILYTHARAILRQCE 76

Query: 72  IIMQEIEGLKKIGKEFSAYDTGNLTI--ATTHTQARYALPKIIKEFTIQFPKVKLSLLQG 129
              Q    +  +G+  S    G ++I  A     +   +P +++    +FP + L L + 
Sbjct: 77  ---QAQLAVHNVGQALS----GQVSIGLAPGTAASSLTMP-LLQAVRAEFPGIVLYLHEN 128

Query: 130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI 189
           +   + E + N Q D+A++ E  SP   L S P  + +  ++   D P     S+ L  +
Sbjct: 129 SGATLNEKLMNGQLDMAVIYE-HSPVAGLSSQPLLKEDLFLVGTQDCP---GQSVDLAAV 184

Query: 190 SNYPLI---TYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
           +   L     Y      R+++D  FSL++LT  ++ E  +   +   +   MG+ ++
Sbjct: 185 AQMNLFLPRDYSAV---RLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVTVL 238

Length = 305

>gnl|CDD|182990 PRK11139, PRK11139, DNA-binding transcriptional activator GcvA; Provisional

 Score = 49.1 bits (118), Expect = 9e-07
 Identities = 34/142 (23%), Positives = 66/142 (46%), Gaps = 16/142 (11%)

Query: 11  EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI 70
           EA  ++ + T AA+ L+ +Q  VS  I  LE+ L + +F R  + +  LT+ GQ     I
Sbjct: 15  EAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLL-LTEEGQRYFLDI 73

Query: 71  EIIMQEI----EGLKKIGKEFSAYDTGNLTIATTHT-QARYALPKIIKEFTIQFPKVKLS 125
             I  ++      L+           G LT++   +   ++ +P++   F    P + + 
Sbjct: 74  REIFDQLAEATRKLRARS------AKGALTVSLLPSFAIQWLVPRLSS-FNEAHPDIDVR 126

Query: 126 LLQGNPKQITEMIRNDQADIAI 147
           L   +  ++ + +R+D  D+AI
Sbjct: 127 LKAVD--RLEDFLRDD-VDVAI 145

Length = 297

>gnl|CDD|176110 cd08418, PBP2_TdcA, The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 29/98 (29%), Positives = 51/98 (52%), Gaps = 3/98 (3%)

Query: 96  TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
           +I  +   A   +P +I  F  QFP V++S+ +G    +   +R+ + D AI T      
Sbjct: 3   SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMY 62

Query: 156 DK-LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY 192
            K LIS P ++ ++V++   DHP  L  + SL+E+ + 
Sbjct: 63  LKELISEPLFESDFVVVARKDHP--LQGARSLEELLDA 98

TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201

>gnl|CDD|176128 cd08437, PBP2_MleR, The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 41/175 (23%), Positives = 67/175 (38%), Gaps = 7/175 (4%)

Query: 106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPC 163
           Y  PK+ K+       +++   +G   ++ E +     DIA +   L+P  +  L S   
Sbjct: 13  YYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIA-LLGSLTPLENSALHSKII 71

Query: 164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLE 223
               ++IIV  DHPL     ++  ++     I  +  F      D         P IV  
Sbjct: 72  KTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYR 131

Query: 224 TINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISAS--HLFGTTISRVIIKQ 276
           T +  I+K+ V   +GIG +  IA     D +L +I           IS    K 
Sbjct: 132 TNDIHILKSMVRENVGIGFLTDIAV--KPDDHLVAIPLLDNEQPTFYISLAHRKD 184

MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold

 Score = 47.2 bits (113), Expect = 2e-06
 Identities = 34/149 (22%), Positives = 66/149 (44%), Gaps = 5/149 (3%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP 154
           L + +  T A   LP ++  +  ++PKV LSL  G    + + +   + D A V   +  
Sbjct: 2   LRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEH 61

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ 214
              L   P +Q E V++ P  HP         ++++   L+ +    S R +L+   + +
Sbjct: 62  PR-LEQEPVFQEELVLVSPKGHP----PVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEE 116

Query: 215 KLTPYIVLETINSDIIKTYVELRMGIGII 243
            ++P  ++E  +   I   V   MGI ++
Sbjct: 117 GVSPGKIMEFGSYHAILGCVAAGMGIALL 145

YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 193

>gnl|CDD|176116 cd08425, PBP2_CynR, The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 39/146 (26%), Positives = 71/146 (48%), Gaps = 7/146 (4%)

Query: 93  GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIV-TEI 151
           G+L +A T T   Y +  +I  F  ++P + LSL +   ++I   + +D+ D+ I    +
Sbjct: 1   GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPV 60

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDRE 210
            SP   + + P +     ++V   HPL     +++L +++  PL      F+ R  +DR 
Sbjct: 61  RSP--DIDAQPLFDERLALVVGATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRY 118

Query: 211 FSLQKLTPYIVLETINSDIIKTYVEL 236
           F  Q + P I +E  NS  I   +E+
Sbjct: 119 FQKQGIKPRIAIEA-NS--ISAVLEV 141

CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176115 cd08423, PBP2_LTTR_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE---- 150
           L +    T A   LP  +     + P +++ L +  P +  + +R  + D+A+V +    
Sbjct: 2   LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVT 61

Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPL 178
                  L  +P       +++P DHPL
Sbjct: 62  PPPDDPGLTRVPLLDDPLDLVLPADHPL 89

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 200

>gnl|CDD|176139 cd08448, PBP2_LTTR_aromatics_like_2, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 30/145 (20%), Positives = 63/145 (43%), Gaps = 17/145 (11%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
           LP+I++ F  ++P ++++L + +  +  E +   + D+  V     P+  L +   ++  
Sbjct: 15  LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAG-LSARLLHREP 73

Query: 168 YVIIVPLDHPLLLLNSISLKEISNYPLIT---------YDLSFSGRIKLDREFSLQKLTP 218
           +V  +P  HPL     I L+E++  P +          YD   +  + +D  F      P
Sbjct: 74  FVCCLPAGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIA--LCMDAGFH-----P 126

Query: 219 YIVLETINSDIIKTYVELRMGIGII 243
            I  E  +   +   V   MG+ ++
Sbjct: 127 KIRHEVRHWLTVVALVAAGMGVALV 151

This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176140 cd08449, PBP2_XapR, The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 34/157 (21%), Positives = 64/157 (40%), Gaps = 5/157 (3%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAIVTEILS 153
           L I    +     L   ++ F  Q+P V +   + +P  Q   ++   + D+  V    +
Sbjct: 2   LNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSK-RIDLGFVRFADT 60

Query: 154 PSD-KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFS 212
            +D  L S   ++   V+ +P +HPL    S++L ++ + P +   L+ S          
Sbjct: 61  LNDPPLASELLWREPMVVALPEEHPLAGRKSLTLADLRDEPFVFLRLANSRFADFLINCC 120

Query: 213 LQK-LTPYIVLETINSDIIKTYVELRMGIGII-ASIA 247
           LQ   TP I  E +    +   V    G+ ++  S A
Sbjct: 121 LQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYA 157

In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176132 cd08441, PBP2_MetR, The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold

 Score = 43.3 bits (103), Expect = 4e-05
 Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 7/93 (7%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQG---NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY 164
           L  ++ +F  ++P V+L L  G   +P      +   + D+ I ++ L P   +   P +
Sbjct: 15  LMPVLDQFRERWPDVELDLSSGFHFDPLP---ALLRGELDLVITSDPL-PLPGIAYEPLF 70

Query: 165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
            +E V++V  DHPL     I+ +++++  LITY
Sbjct: 71  DYEVVLVVAPDHPLAAKEFITPEDLADETLITY 103

MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional

 Score = 44.0 bits (104), Expect = 4e-05
 Identities = 28/112 (25%), Positives = 57/112 (50%), Gaps = 1/112 (0%)

Query: 20  TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79
           T AA+ L  S   +S+ + +LE+EL + +  R  + I GLT+ G+   +    ++ E++ 
Sbjct: 20  TAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSI-GLTEAGRIYYQGCRRMLHEVQD 78

Query: 80  LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP 131
           + +    F+    G L I  + T A+  L  +  +   ++P + ++L+ G P
Sbjct: 79  VHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIP 130

Length = 309

>gnl|CDD|176143 cd08452, PBP2_AlsR, The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold

 Score = 42.9 bits (101), Expect = 5e-05
 Identities = 26/95 (27%), Positives = 52/95 (54%), Gaps = 11/95 (11%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILSPS----DKLISIP 162
           LP I++E+  +FP VK+ L +  +P Q+ E+++  + DI  +   +  +    + + S P
Sbjct: 15  LPPIVREYRKKFPSVKVELRELSSPDQVEELLKG-RIDIGFLHPPIQHTALHIETVQSSP 73

Query: 163 CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
           C     V+ +P  HPL     I+++++ + P+IT 
Sbjct: 74  C-----VLALPKQHPLASKEEITIEDLRDEPIITV 103

AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197

>gnl|CDD|176108 cd08416, PBP2_MdcR, The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold

 Score = 42.3 bits (100), Expect = 9e-05
 Identities = 27/124 (21%), Positives = 59/124 (47%), Gaps = 5/124 (4%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT--EILSPSDKLISIPCYQ 165
           +P+II    ++ P++ + L  G+ K + + +++ + D  +V   E L+  D    +P ++
Sbjct: 15  VPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPD-FEVVPLFE 73

Query: 166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI 225
            +  + VP   PL   + I L+++ +   +T    F+     D  F +    P +V+   
Sbjct: 74  DDIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRV- 132

Query: 226 NSDI 229
            +DI
Sbjct: 133 -NDI 135

This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 199

>gnl|CDD|176150 cd08461, PBP2_DntR_like_3, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 32/148 (21%), Positives = 58/148 (39%), Gaps = 15/148 (10%)

Query: 95  LTIATTHTQARYALPKIIKEFTIQF----PKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
           L IA T     YA   I+           P V++++       +   +   + D+A+ T 
Sbjct: 2   LVIAATD----YAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTP 57

Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP--LITYDL-SFSGRIKL 207
             +P D L S P ++  YV +    HPLL    +SL +       +++     F+G    
Sbjct: 58  EYAP-DGLRSRPLFEERYVCVTRRGHPLLQGP-LSLDQFCALDHIVVSPSGGGFAGST-- 113

Query: 208 DREFSLQKLTPYIVLETINSDIIKTYVE 235
           D   +   LT  +VL   +  ++   + 
Sbjct: 114 DEALAALGLTRNVVLSVPSFLVVPEILA 141

This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|181918 PRK09508, leuO, leucine transcriptional activator; Reviewed

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query: 9  VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR 57
          V +AV Q  N+T AA  L  SQP VS A+  L+   + ++F+R+G+ I+
Sbjct: 29 VFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQ 77

Length = 314

>gnl|CDD|176121 cd08430, PBP2_IlvY, The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold

 Score = 40.6 bits (96), Expect = 3e-04
 Identities = 39/138 (28%), Positives = 63/138 (45%), Gaps = 4/138 (2%)

Query: 108 LPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE 167
           LP I++ F  Q P+V++ L  G+P    + + N +ADIAI         +L  +P     
Sbjct: 15  LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSP 74

Query: 168 YVIIVPLDHPLLLLNSISLKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI 225
            V I P      +   +S  EI  S  P I  +   + R +LD+ F  + + P I  +  
Sbjct: 75  LVFIAPNIAC-AVTQQLSQGEIDWSRLPFILPERGLA-RERLDQWFRRRGIKPNIYAQVA 132

Query: 226 NSDIIKTYVELRMGIGII 243
             + I + V L  G+GI+
Sbjct: 133 GHEAIVSMVALGCGVGIV 150

In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 199

>gnl|CDD|235137 PRK03601, PRK03601, transcriptional regulator HdfR; Provisional

 Score = 40.8 bits (96), Expect = 5e-04
 Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIM 74
          AA++LY +Q  VS  I +LE +L +++F RH   IR LT  G+ +L   E +M
Sbjct: 21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIR-LTAAGERLLPYAETLM 72

Length = 275

>gnl|CDD|237907 PRK15092, PRK15092, DNA-binding transcriptional repressor LrhA; Provisional

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 37/142 (26%), Positives = 70/142 (49%), Gaps = 29/142 (20%)

Query: 22  AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG-------QAILR-----S 69
           AA A+  +Q  VS+ +  LE+ +  ++F RHG R + LT+ G       + ILR      
Sbjct: 31  AAAAVCRTQSAVSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYARKILRFNDEAC 89

Query: 70  IEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSL-LQ 128
             ++   ++G+  IG   ++ DT + TI          LP ++   +  +PK+ L + ++
Sbjct: 90  SSLMYSNLQGVLTIG---ASDDTAD-TI----------LPFLLNRVSSVYPKLALDVRVK 135

Query: 129 GNPKQITEMIRNDQADIAIVTE 150
            N   + EM+ + + D+A+ T 
Sbjct: 136 RNA-FMMEMLESQEVDLAVTTH 156

Length = 310

>gnl|CDD|182228 PRK10082, PRK10082, cell density-dependent motility repressor; Provisional

 Score = 40.4 bits (94), Expect = 7e-04
 Identities = 30/127 (23%), Positives = 60/127 (47%), Gaps = 4/127 (3%)

Query: 18  NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
           N ++AA +   SQP  S+ I  LE+ + +++F R    ++ L++ G+     I  ++Q++
Sbjct: 27  NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQ-LSEQGKIFHSQIRHLLQQL 85

Query: 78  EGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEM 137
           E      +  S Y    + IA  H+ +   LP II +    F     ++   +  +  + 
Sbjct: 86  ESNLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAI---DVDEAVDK 142

Query: 138 IRNDQAD 144
           +R  Q+D
Sbjct: 143 LREGQSD 149

Length = 303

>gnl|CDD|176138 cd08447, PBP2_LTTR_aromatics_like_1, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 27/112 (24%), Positives = 42/112 (37%), Gaps = 17/112 (15%)

Query: 94  NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ--------ADI 145
           +L I  T   A   LP+++       P V L L         EM+  DQ         D+
Sbjct: 1   SLRIGFTAASAYSFLPRLLAAARAALPDVDLVL--------REMVTTDQIEALESGRIDL 52

Query: 146 AIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
            ++         L + P  +   V  VP  HPL     ++L+++   P I Y
Sbjct: 53  GLLRPPF-ARPGLETRPLVREPLVAAVPAGHPLAGAERLTLEDLDGQPFIMY 103

This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 198

>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold

 Score = 37.6 bits (88), Expect = 0.003
 Identities = 23/132 (17%), Positives = 53/132 (40%), Gaps = 4/132 (3%)

Query: 94  NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEIL 152
              IA +     Y LP+++       P V++  ++    ++ E + + + D+AI     L
Sbjct: 1   TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDL 60

Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFS 212
                      ++  YV +V  DHP  + ++++L++      +    S +G   +++   
Sbjct: 61  GAG--FFQQRLFRERYVCLVRKDHP-RIGSTLTLEQFLAARHVVVSASGTGHGLVEQALR 117

Query: 213 LQKLTPYIVLET 224
              +   I L  
Sbjct: 118 EAGIRRRIALRV 129

This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	306
PRK12681	324	cysB transcriptional regulator CysB; Reviewed	100.0
PRK12682	309	transcriptional regulator CysB-like protein; Revie	100.0
PRK12683	309	transcriptional regulator CysB-like protein; Revie	100.0
PRK12684	313	transcriptional regulator CysB-like protein; Revie	100.0
PRK11151	305	DNA-binding transcriptional regulator OxyR; Provis	100.0
PRK12679	316	cbl transcriptional regulator Cbl; Reviewed	100.0
PRK11242	296	DNA-binding transcriptional regulator CynR; Provis	100.0
PRK12680	327	transcriptional regulator CysB-like protein; Revie	100.0
PRK10341	312	DNA-binding transcriptional activator TdcA; Provis	100.0
CHL00180	305	rbcR LysR transcriptional regulator; Provisional	100.0
TIGR02424	300	TF_pcaQ pca operon transcription factor PcaQ. Memb	100.0
PRK11013	309	DNA-binding transcriptional regulator LysR; Provis	100.0
PRK09791	302	putative DNA-binding transcriptional regulator; Pr	100.0
PRK11233	305	nitrogen assimilation transcriptional regulator; P	100.0
PRK09906	296	DNA-binding transcriptional regulator HcaR; Provis	100.0
PRK10837	290	putative DNA-binding transcriptional regulator; Pr	100.0
PRK15421	317	DNA-binding transcriptional regulator MetR; Provis	100.0
PRK09986	294	DNA-binding transcriptional activator XapR; Provis	100.0
TIGR03339	279	phn_lysR aminoethylphosphonate catabolism associat	100.0
PRK09508	314	leuO leucine transcriptional activator; Reviewed	100.0
PRK11074	300	putative DNA-binding transcriptional regulator; Pr	100.0
PRK15243	297	transcriptional regulator SpvR; Provisional	100.0
PRK10094	308	DNA-binding transcriptional activator AllS; Provis	100.0
PRK11062	296	nhaR transcriptional activator NhaR; Provisional	100.0
PRK09801	310	transcriptional activator TtdR; Provisional	100.0
PRK11139	297	DNA-binding transcriptional activator GcvA; Provis	100.0
PRK11482	317	putative DNA-binding transcriptional regulator; Pr	100.0
PRK10632	309	transcriptional regulator; Provisional	100.0
PRK13348	294	chromosome replication initiation inhibitor protei	100.0
TIGR03298	292	argP transcriptional regulator, ArgP family. ArgP	100.0
PRK03601	275	transcriptional regulator HdfR; Provisional	100.0
PRK03635	294	chromosome replication initiation inhibitor protei	100.0
PRK10216	319	DNA-binding transcriptional regulator YidZ; Provis	100.0
PRK14997	301	LysR family transcriptional regulator; Provisional	100.0
TIGR03418	291	chol_sulf_TF putative choline sulfate-utilization	100.0
PRK10086	311	DNA-binding transcriptional regulator DsdC; Provis	100.0
PRK10082	303	cell density-dependent motility repressor; Provisi	100.0
PRK15092	310	DNA-binding transcriptional repressor LrhA; Provis	100.0
TIGR02036	302	dsdC D-serine deaminase transcriptional activator.	100.0
COG0583	297	LysR Transcriptional regulator [Transcription]	100.0
PRK11716	269	DNA-binding transcriptional regulator IlvY; Provis	100.0
PF03466	209	LysR_substrate: LysR substrate binding domain; Int	100.0
cd08444	198	PBP2_Cbl The C-terminal substrate binding domain o	99.97
cd08413	198	PBP2_CysB_like The C-terminal substrate domain of	99.97
cd08421	198	PBP2_LTTR_like_1 The C-terminal substrate binding	99.97
cd08411	200	PBP2_OxyR The C-terminal substrate-binding domain	99.97
cd08459	201	PBP2_DntR_NahR_LinR_like The C-terminal substrate	99.97
cd08433	198	PBP2_Nac The C-teminal substrate binding domain of	99.97
cd08437	198	PBP2_MleR The substrate binding domain of LysR-typ	99.97
cd08435	201	PBP2_GbpR The C-terminal substrate binding domain	99.97
cd08438	197	PBP2_CidR The C-terminal substrate binding domain	99.97
cd08443	198	PBP2_CysB The C-terminal substrate domain of LysR-	99.97
cd08417	200	PBP2_Nitroaromatics_like The C-terminal substrate	99.97
cd08440	197	PBP2_LTTR_like_4 TThe C-terminal substrate binding	99.97
cd08426	199	PBP2_LTTR_like_5 The C-terminal substrate binding	99.97
cd08412	198	PBP2_PAO1_like The C-terminal substrate-binding do	99.97
cd08425	197	PBP2_CynR The C-terminal substrate-binding domain	99.97
cd08434	195	PBP2_GltC_like The substrate binding domain of Lys	99.97
cd08436	194	PBP2_LTTR_like_3 The C-terminal substrate binding	99.97
cd08415	196	PBP2_LysR_opines_like The C-terminal substrate-dom	99.97
cd08464	200	PBP2_DntR_like_2 The C-terminal substrate binding	99.97
cd08463	203	PBP2_DntR_like_4 The C-terminal substrate binding	99.97
cd08420	201	PBP2_CysL_like C-terminal substrate binding domain	99.96
cd08418	201	PBP2_TdcA The C-terminal substrate binding domain	99.96
cd08458	196	PBP2_NocR The C-terminal substrate-domain of LysR-	99.96
cd08456	196	PBP2_LysR The C-terminal substrate binding domain	99.96
cd08423	200	PBP2_LTTR_like_6 The C-terminal substrate binding	99.96
cd08460	200	PBP2_DntR_like_1 The C-terminal substrate binding	99.96
cd08419	197	PBP2_CbbR_RubisCO_like The C-terminal substrate bi	99.96
cd08462	200	PBP2_NodD The C-terminal substsrate binding domain	99.96
cd08466	200	PBP2_LeuO The C-terminal substrate binding domain	99.96
cd08467	200	PBP2_SyrM The C-terminal substrate binding of LysR	99.96
cd08414	197	PBP2_LTTR_aromatics_like The C-terminal substrate	99.96
cd08441	198	PBP2_MetR The C-terminal substrate binding domain	99.96
cd08453	200	PBP2_IlvR The C-terminal substrate binding domain	99.96
cd08442	193	PBP2_YofA_SoxR_like The C-terminal substrate bindi	99.96
cd08449	197	PBP2_XapR The C-terminal substrate binding domain	99.96
cd08486	198	PBP2_CbnR The C-terminal substrate binding domain	99.96
cd08461	198	PBP2_DntR_like_3 The C-terminal substrate binding	99.96
cd08468	202	PBP2_Pa0477 The C-terminal substrate biniding doma	99.96
cd08446	198	PBP2_Chlorocatechol The C-terminal substrate bindi	99.96
cd08450	196	PBP2_HcaR The C-terminal substrate binding domain	99.96
cd08457	196	PBP2_OccR The C-terminal substrate-domain of LysR-	99.96
cd08427	195	PBP2_LTTR_like_2 The C-terminal substrate binding	99.96
cd08445	203	PBP2_BenM_CatM_CatR The C-terminal substrate bindi	99.96
cd08430	199	PBP2_IlvY The C-terminal substrate binding of LysR	99.96
cd08485	198	PBP2_ClcR The C-terminal substrate binding domain	99.96
cd08416	199	PBP2_MdcR The C-terminal substrate-binding domian	99.96
cd08448	197	PBP2_LTTR_aromatics_like_2 The C-terminal substrat	99.96
cd08469	221	PBP2_PnbR The C-terminal substrate binding domain	99.96
cd08429	204	PBP2_NhaR The C-terminal substrate binding domain	99.96
cd08451	199	PBP2_BudR The C-terminal substrate binding domain	99.95
cd05466	197	PBP2_LTTR_substrate The substrate binding domain o	99.95
cd08465	200	PBP2_ToxR The C-terminal substrate binding domain	99.95
cd08452	197	PBP2_AlsR The C-terminal substrate binding domain	99.95
cd08447	198	PBP2_LTTR_aromatics_like_1 The C-terminal substrat	99.95
cd08431	195	PBP2_HupR The C-terminal substrate binding domain	99.94
cd08432	194	PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal subst	99.93
cd08475	199	PBP2_CrgA_like_6 The C-terminal substrate binding	99.93
cd08471	201	PBP2_CrgA_like_2 The C-terminal substrate binding	99.93
cd08478	199	PBP2_CrgA The C-terminal substrate binding domain	99.93
cd08422	197	PBP2_CrgA_like The C-terminal substrate binding do	99.93
cd08481	194	PBP2_GcdR_like The C-terminal substrate binding do	99.92
cd08474	202	PBP2_CrgA_like_5 The C-terminal substrate binding	99.92
cd08472	202	PBP2_CrgA_like_3 The C-terminal substrate binding	99.92
cd08477	197	PBP2_CrgA_like_8 The C-terminal substrate binding	99.92
cd08479	198	PBP2_CrgA_like_9 The C-terminal substrate binding	99.91
cd08439	185	PBP2_LrhA_like The C-terminal substrate domain of	99.91
cd08428	195	PBP2_IciA_ArgP The C-terminal substrate binding do	99.91
cd08470	197	PBP2_CrgA_like_1 The C-terminal substrate binding	99.91
cd08473	202	PBP2_CrgA_like_4 The C-terminal substrate binding	99.91
cd08476	197	PBP2_CrgA_like_7 The C-terminal substrate binding	99.91
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	99.9
cd08483	190	PBP2_HvrB The C-terminal substrate-binding domain	99.9
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	99.9
TIGR02136	287	ptsS_2 phosphate binding protein. Members of this	99.9
cd08480	198	PBP2_CrgA_like_10 The C-terminal substrate binding	99.89
cd08482	195	PBP2_TrpI The C-terminal substrate binding domain	99.89
cd08488	191	PBP2_AmpR The C-terminal substrate domain of LysR-	99.89
cd08487	189	PBP2_BlaA The C-terminal substrate-binding domain	99.89
cd08484	189	PBP2_LTTR_beta_lactamase The C-terminal substrate-	99.88
PRK14498	633	putative molybdopterin biosynthesis protein MoeA/L	99.83
PRK10676	263	DNA-binding transcriptional regulator ModE; Provis	99.81
PF12727	193	PBP_like: PBP superfamily domain; InterPro: IPR024	99.44
PRK11553	314	alkanesulfonate transporter substrate-binding subu	99.33
PRK00489	287	hisG ATP phosphoribosyltransferase; Reviewed	99.2
COG2005	130	ModE N-terminal domain of molybdenum-binding prote	99.19
cd00134	218	PBPb Bacterial periplasmic transport systems use m	99.02
TIGR02122	320	TRAP_TAXI TRAP transporter solute receptor, TAXI f	99.01
TIGR01728	288	SsuA_fam ABC transporter, substrate-binding protei	98.9
PRK09729	68	hypothetical protein; Provisional	98.87
smart00062	219	PBPb Bacterial periplasmic substrate-binding prote	98.82
PF13531	230	SBP_bac_11: Bacterial extracellular solute-binding	98.79
PF12849	281	PBP_like_2: PBP superfamily domain; InterPro: IPR0	98.61
COG2998	280	TupB ABC-type tungstate transport system, permease	98.61
COG0725	258	ModA ABC-type molybdate transport system, periplas	98.49
PRK11050	152	manganese transport regulator MntR; Provisional	98.48
TIGR01256	216	modA molybdenum ABC transporter, periplasmic molyb	98.48
COG1910	223	Periplasmic molybdate-binding protein/domain [Inor	98.47
PF00497	225	SBP_bac_3: Bacterial extracellular solute-binding	98.42
PRK10677	257	modA molybdate transporter periplasmic protein; Pr	98.41
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	98.4
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	98.39
TIGR00975	314	3a0107s03 phosphate ABC transporter, phosphate-bin	98.37
PRK11917	259	bifunctional adhesin/ABC transporter aspartate/glu	98.29
PRK03902	142	manganese transport transcriptional regulator; Pro	98.26
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	98.22
TIGR03730	273	tungstate_WtpA tungstate ABC transporter binding p	98.2
PRK04168	334	molybdate ABC transporter periplasmic substrate-bi	98.03
PRK11260	266	cystine transporter subunit; Provisional	97.92
PF13556	59	HTH_30: PucR C-terminal helix-turn-helix domain; P	97.85
PRK09495	247	glnH glutamine ABC transporter periplasmic protein	97.82
TIGR00363	258	lipoprotein, YaeC family. This family of putative	97.8
PRK13777	185	transcriptional regulator Hpr; Provisional	97.8
TIGR01096	250	3A0103s03R lysine-arginine-ornithine-binding perip	97.78
COG0226	318	PstS ABC-type phosphate transport system, periplas	97.77
TIGR02995	275	ectoine_ehuB ectoine/hydroxyectoine ABC transporte	97.76
PRK14165	217	winged helix-turn-helix domain-containing protein/	97.76
TIGR03871	232	ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associa	97.74
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.72
PRK10797	302	glutamate and aspartate transporter subunit; Provi	97.7
TIGR01098	254	3A0109s03R phosphate/phosphite/phosphonate ABC tra	97.7
PRK03573	144	transcriptional regulator SlyA; Provisional	97.68
PRK10859	482	membrane-bound lytic transglycosylase F; Provision	97.65
PF13379	252	NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_	97.6
PRK10918	346	phosphate ABC transporter periplasmic substrate-bi	97.58
PRK11063	271	metQ DL-methionine transporter substrate-binding s	97.58
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	97.57
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	97.55
COG1846	126	MarR Transcriptional regulators [Transcription]	97.54
PRK09861	272	cytoplasmic membrane lipoprotein-28; Provisional	97.53
PRK10870	176	transcriptional repressor MprA; Provisional	97.48
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	97.47
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	97.4
TIGR02285	268	conserved hypothetical protein. Members of this fa	97.37
PRK15010	260	ABC transporter lysine/arginine/ornithine binding	97.36
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	97.33
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.32
TIGR01729	300	taurine_ABC_bnd taurine ABC transporter, periplasm	97.3
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	97.3
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	97.3
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	97.29
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.28
PF12974	243	Phosphonate-bd: ABC transporter, phosphonate, peri	97.27
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	97.24
TIGR03414	290	ABC_choline_bnd choline ABC transporter, periplasm	97.22
COG1654	79	BirA Biotin operon repressor [Transcription]	97.17
TIGR01276	309	thiB thiamine ABC transporter, periplasmic binding	97.08
PRK15437	259	histidine ABC transporter substrate-binding protei	97.07
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	97.05
PRK15007	243	putative ABC transporter arginine-biding protein;	97.04
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	97.03
COG4742	260	Predicted transcriptional regulator [Transcription	97.03
TIGR03261	334	phnS2 putative 2-aminoethylphosphonate ABC transpo	97.01
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.98
PF03180	237	Lipoprotein_9: NLPA lipoprotein; InterPro: IPR0048	96.97
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	96.92
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	96.91
PF09084	216	NMT1: NMT1/THI5 like; InterPro: IPR015168 This ent	96.89
PHA00738	108	putative HTH transcription regulator	96.88
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	96.85
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	96.85
TIGR03870	246	ABC_MoxJ methanol oxidation system protein MoxJ. T	96.8
PF04069	257	OpuAC: Substrate binding domain of ABC-type glycin	96.79
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.74
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.71
PRK11480	320	tauA taurine transporter substrate binding subunit	96.71
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	96.69
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.64
TIGR00971	315	3a0106s03 sulfate/thiosulfate-binding protein. Thi	96.63
COG2358	321	Imp TRAP-type uncharacterized transport system, pe	96.55
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	96.54
PRK11119	331	proX glycine betaine transporter periplasmic subun	96.54
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	96.54
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.47
PRK10852	338	thiosulfate transporter subunit; Provisional	96.46
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	96.39
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	96.38
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	96.36
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	96.32
COG4623	473	Predicted soluble lytic transglycosylase fused to	96.25
COG1339	214	Transcriptional regulator of a riboflavin/FAD bios	96.25
PF13518	52	HTH_28: Helix-turn-helix domain	96.24
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	96.24
PRK11205	330	tbpA thiamine transporter substrate binding subuni	96.22
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	96.21
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	96.18
TIGR03431	288	PhnD phosphonate ABC transporter, periplasmic phos	96.18
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.18
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.12
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.09
PRK09959	1197	hybrid sensory histidine kinase in two-component r	96.07
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	95.97
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	95.93
PRK01905	77	DNA-binding protein Fis; Provisional	95.9
COG0715	335	TauA ABC-type nitrate/sulfonate/bicarbonate transp	95.87
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.83
PRK09959	1197	hybrid sensory histidine kinase in two-component r	95.79
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	95.79
COG1342	99	Predicted DNA-binding proteins [General function p	95.77
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	95.68
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	95.66
PRK04217	110	hypothetical protein; Provisional	95.64
PF09114	96	MotA_activ: Transcription factor MotA, activation	95.5
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	95.48
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	95.44
PRK13509	251	transcriptional repressor UlaR; Provisional	95.37
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	95.35
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	95.35
COG1733	120	Predicted transcriptional regulators [Transcriptio	95.34
COG1609	333	PurR Transcriptional regulators [Transcription]	95.33
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.31
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.26
COG3888	321	Predicted transcriptional regulator [Transcription	95.26
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	95.24
PHA02591	83	hypothetical protein; Provisional	95.2
PRK00430	95	fis global DNA-binding transcriptional dual regula	95.15
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	95.12
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.1
COG2522	119	Predicted transcriptional regulator [General funct	95.07
PRK11169	164	leucine-responsive transcriptional regulator; Prov	94.97
PF02621	251	VitK2_biosynth: Menaquinone biosynthesis; InterPro	94.96
TIGR03427	328	ABC_peri_uca ABC transporter periplasmic binding p	94.96
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	94.91
COG2508	421	Regulator of polyketide synthase expression [Signa	94.86
COG0834	275	HisJ ABC-type amino acid transport/signal transduc	94.86
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.84
PRK09413	121	IS2 repressor TnpA; Reviewed	94.81
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	94.79
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	94.79
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.71
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	94.62
TIGR01254	304	sfuA ABC transporter periplasmic binding protein,	94.49
PRK00118	104	putative DNA-binding protein; Validated	94.38
COG1732	300	OpuBC Periplasmic glycine betaine/choline-binding	94.25
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	94.23
PRK01686	215	hisG ATP phosphoribosyltransferase catalytic subun	94.17
PRK15201	198	fimbriae regulatory protein FimW; Provisional	94.16
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	94.13
PF13730	55	HTH_36: Helix-turn-helix domain	94.09
COG4190	144	Predicted transcriptional regulator [Transcription	94.08
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	94.07
smart00351	125	PAX Paired Box domain.	94.06
PRK05638	442	threonine synthase; Validated	94.05
TIGR03227	367	PhnS 2-aminoethylphosphonate ABC transporter, peri	94.03
PF01379	215	Porphobil_deam: Porphobilinogen deaminase, dipyrom	94.01
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	93.96
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	93.96
PF01634	163	HisG: ATP phosphoribosyltransferase; InterPro: IPR	93.8
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.78
COG0040	290	HisG ATP phosphoribosyltransferase [Amino acid tra	93.77
PRK11477	385	carbohydrate diacid transcriptional activator CdaR	93.6
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	93.58
cd00131	128	PAX Paired Box domain	93.52
PRK14987	331	gluconate operon transcriptional regulator; Provis	93.5
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	93.48
PF13551	112	HTH_29: Winged helix-turn helix	93.44
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.41
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	93.26
PRK03975	141	tfx putative transcriptional regulator; Provisiona	93.23
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	93.23
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	93.22
PRK10423	327	transcriptional repressor RbsR; Provisional	93.19
COG3221	299	PhnD ABC-type phosphate/phosphonate transport syst	93.17
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	93.06
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	93.05
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	92.97
COG4189	308	Predicted transcriptional regulator [Transcription	92.91
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	92.88
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	92.83
PHA00542	82	putative Cro-like protein	92.78
COG0181	307	HemC Porphobilinogen deaminase [Coenzyme metabolis	92.62
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	92.61
PRK10752	329	sulfate transporter subunit; Provisional	92.6
PF05043	87	Mga: Mga helix-turn-helix domain; InterPro: IPR007	92.57
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	92.57
PRK15320	251	transcriptional activator SprB; Provisional	92.34
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	92.26
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	92.25
COG1497	260	Predicted transcriptional regulator [Transcription	92.16
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	92.14
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	92.05
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	91.92
PF14424	133	Toxin-deaminase: The BURPS668_1122 family of deami	91.82
PRK10840	216	transcriptional regulator RcsB; Provisional	91.63
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	91.57
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	91.55
COG4197	96	Uncharacterized protein conserved in bacteria, pro	91.5
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	91.37
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	91.33
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	91.3
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	91.19
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	91.19
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	91.15
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	91.11
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	91.1
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	91.07
TIGR00070	182	hisG ATP phosphoribosyltransferase. Members of thi	91.02
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	90.98
PRK11569	274	transcriptional repressor IclR; Provisional	90.76
PLN02245	403	ATP phosphoribosyl transferase	90.71
COG1464	268	NlpA ABC-type metal ion transport system, periplas	90.67
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	90.64
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	90.59
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	90.57
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	90.49
COG3355	126	Predicted transcriptional regulator [Transcription	90.48
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	90.09
COG1414	246	IclR Transcriptional regulator [Transcription]	90.08
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	89.97
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	89.92
PRK06474	178	hypothetical protein; Provisional	89.87
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	89.85
PRK09483	217	response regulator; Provisional	89.7
PRK01066	231	porphobilinogen deaminase; Provisional	89.66
PRK09775	442	putative DNA-binding transcriptional regulator; Pr	89.59
PRK13870	234	transcriptional regulator TraR; Provisional	89.53
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	89.49
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	89.45
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	89.42
PRK00072	295	hemC porphobilinogen deaminase; Reviewed	89.35
TIGR01764	49	excise DNA binding domain, excisionase family. An	89.29
COG2512	258	Predicted membrane-associated trancriptional regul	89.26
PRK09954	362	putative kinase; Provisional	89.2
PF12728	51	HTH_17: Helix-turn-helix domain	89.18
cd00494	292	HMBS Hydroxymethylbilane synthase (HMBS), also kno	89.12
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	89.01
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	88.92
PRK15046	349	2-aminoethylphosphonate ABC transporter substrate-	88.88
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	88.61
COG1568	354	Predicted methyltransferases [General function pre	88.44
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	88.41
PRK00215	205	LexA repressor; Validated	88.37
COG1910	223	Periplasmic molybdate-binding protein/domain [Inor	88.14
PF03401	274	TctC: Tripartite tricarboxylate transporter family	88.05
PRK09526	342	lacI lac repressor; Reviewed	88.01
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	87.96
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	87.55
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	87.39
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	87.36
PF12727	193	PBP_like: PBP superfamily domain; InterPro: IPR024	87.1
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	87.09
PRK10651	216	transcriptional regulator NarL; Provisional	87.01
PF13309	64	HTH_22: HTH domain	86.93
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	86.88
COG1458	221	Predicted DNA-binding protein containing PIN domai	86.82
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	86.53
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	86.45
COG1725	125	Predicted transcriptional regulators [Transcriptio	86.35
PHA02943	165	hypothetical protein; Provisional	86.33
PRK13583	228	hisG ATP phosphoribosyltransferase catalytic subun	86.29
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	86.21
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	86.16
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	85.96
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	85.81
PRK09492	315	treR trehalose repressor; Provisional	85.66
PRK12423	202	LexA repressor; Provisional	85.51
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	85.1
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	85.05
PRK15369	211	two component system sensor kinase SsrB; Provision	84.98
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	84.75
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.74
PF01316	70	Arg_repressor: Arginine repressor, DNA binding dom	84.68
PRK09333	150	30S ribosomal protein S19e; Provisional	84.65
COG3388	101	Predicted transcriptional regulator [Transcription	84.53
PRK10403	215	transcriptional regulator NarP; Provisional	84.47
smart00094	332	TR_FER Transferrin.	84.44
PF14502	48	HTH_41: Helix-turn-helix domain	84.35
COG2197	211	CitB Response regulator containing a CheY-like rec	84.19
COG1510	177	Predicted transcriptional regulators [Transcriptio	84.14
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	83.8
PRK13182	175	racA polar chromosome segregation protein; Reviewe	83.65
COG4588	252	AcfC Accessory colonization factor AcfC, contains	83.57
COG3415	138	Transposase and inactivated derivatives [DNA repli	83.51
COG2345	218	Predicted transcriptional regulator [Transcription	83.51
PF13343	242	SBP_bac_6: Bacterial extracellular solute-binding	83.43
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	83.21
PF11972	54	HTH_13: HTH DNA binding domain; InterPro: IPR02106	83.1
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	83.08
PRK09416	135	lstR lineage-specific thermal regulator protein; P	82.34
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	82.15
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	82.09
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	81.68
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	81.46
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	81.28
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	81.26
COG3432	95	Predicted transcriptional regulator [Transcription	81.22
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	81.18
PRK09863	584	putative frv operon regulatory protein; Provisiona	81.15
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	80.97
PF01090	139	Ribosomal_S19e: Ribosomal protein S19e; InterPro:	80.62
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	80.61

>PRK12681 cysB transcriptional regulator CysB; Reviewed

Probab=100.00  E-value=1.7e-58  Score=381.34  Aligned_cols=302  Identities=45%  Similarity=0.789  Sum_probs=277.9

Q ss_pred             CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      |++++|+||++|+++ | ||++||++||+||||||++|++||++||++||+|+++++.+||++|+.|+++++++++.+++
T Consensus         1 M~~~~L~~f~avae~g~-S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~~a~~il~~~~~   79 (324)
T PRK12681          1 MKLQQLRYIVEVVNHNL-NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVES   79 (324)
T ss_pred             CCHHHHHHHHHHHHccC-CHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999 7 99999999999999999999999999999999999999723999999999999999999999


Q ss_pred             HHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760          80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI  159 (306)
Q Consensus        80 ~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~  159 (306)
                      +...+.+......|+|+||++++++..++++++..|.+.||++++++....++++.+.|.+|++|++|+..+....+++.
T Consensus        80 ~~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~~~~L~~g~iDl~i~~~~~~~~~~l~  159 (324)
T PRK12681         80 IKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLYDDLI  159 (324)
T ss_pred             HHHHHHHhhCCCCCeEEEEechhHHHHhhHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCCCEEEecCcccCCCCeE
Confidence            99999888777889999999999999999999999999999999999999999999999999999999865423356789


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      +.+++.++++++++++||++....++++||.++||+.+..+...+..++.++...|+.|++.+++++..++..++.+|.|
T Consensus       160 ~~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G  239 (324)
T PRK12681        160 MLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLG  239 (324)
T ss_pred             EEEeccceeEEEeCCCChhhcCCCcCHHHHhCCCeEeccCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCCC
Confidence            99999999999999999999888899999999999999887777778888898899999999999999999999999999


Q ss_pred             eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ++++|.+.......++++.+++++......++++|+++...++.++.|++++++.+.+..++.+
T Consensus       240 i~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~~~~~~~~~~~~~~  303 (324)
T PRK12681        240 VGVIASMAVDPVADPDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAPHLTRDVVEKA  303 (324)
T ss_pred             EEEeehhhcccccCCceEEeecCCCCCceEEEEEEECCchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999998776554578999998775667799999999999999999999999999888877653

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=100.00  E-value=1.5e-58  Score=380.84  Aligned_cols=303  Identities=56%  Similarity=0.963  Sum_probs=279.1

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|+||++++++|+||++||++||+||||||++|++||++||++||+|++++++.||++|+.|++++++++++++++
T Consensus         1 m~l~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~~~~~~l~~~~~~   80 (309)
T PRK12682          1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGNI   80 (309)
T ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEECCCCcCccCHhHHHHHHHHHHHHHHHHHH
Confidence            89999999999999844999999999999999999999999999999999999996259999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+........|.|+||++++++..++++++..|.+.||++++++...+.+++.+.|.+|++|++|+..+....+++.+
T Consensus        81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~l~~  160 (309)
T PRK12682         81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLAT  160 (309)
T ss_pred             HHHHHHhcCCCCCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccCCCcceE
Confidence            99998888888899999999999999999999999999999999999999999999999999999998644334678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++.+..++++||.++|++.+..+...+..++.++...|+.+++.+++++..++++++..|.|+
T Consensus       161 ~~l~~~~~~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~Gi  240 (309)
T PRK12682        161 LPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV  240 (309)
T ss_pred             EEeeeeeEEEEecCCCccccCCCcCHHHHhcCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhCCce
Confidence            99999999999999999998778999999999999998876677788899999999999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      +++|.+.+.....++++.+|+.+......+|++|+++...++.++.|++++++.+..+.+.++
T Consensus       241 ~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~  303 (309)
T PRK12682        241 GIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFIELCAPHLSRELIKRA  303 (309)
T ss_pred             EEehhhhhhhccCCcEEEeeCCCCCcceeEEEeeecCCcCCHHHHHHHHHHHHHcCcHHHHHH
Confidence            999998776545788999999875556789999999999999999999999999999888775

>PRK12683 transcriptional regulator CysB-like protein; Reviewed

Probab=100.00  E-value=3.2e-58  Score=377.98  Aligned_cols=304  Identities=50%  Similarity=0.891  Sum_probs=279.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++++|+||++||++||+||||+|++|++||++||++||+|++++++.||++|+.|++++++++..++++
T Consensus         1 m~~~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~il~~~~~~   80 (309)
T PRK12683          1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL   80 (309)
T ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEeeCCCCcCCcCHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999833999999999999999999999999999999999999996149999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.|+||+++++...++++++..|.+.||++++++....++++.+.|.+|++|++|+..+....+++..
T Consensus        81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l~~  160 (309)
T PRK12683         81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVS  160 (309)
T ss_pred             HHHHHHhcCCCCceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCceE
Confidence            99999888888899999999999999999999999999999999999999999999999999999998644334678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .+++.++++++++++||++.+..++++||.++|+|.++.+...+..++.++...++.++..+++++..++..++..|.|+
T Consensus       161 ~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi  240 (309)
T PRK12683        161 FPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV  240 (309)
T ss_pred             EEcccCeEEEEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCCCe
Confidence            99999999999999999998888999999999999998888888889999999999999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +++|.+.+.....++++.+++++.....+++++|++++..++.++.|++++++...+..+--++
T Consensus       241 ~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~~  304 (309)
T PRK12683        241 GIVAAMAYDPQRDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHLSEAEIAAAL  304 (309)
T ss_pred             EEeehhhccccCCCceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhhhhHHHHHHHH
Confidence            9999988765445679999987755567999999999999999999999999988777665443

>PRK12684 transcriptional regulator CysB-like protein; Reviewed

Probab=100.00  E-value=5.8e-58  Score=377.38  Aligned_cols=304  Identities=63%  Similarity=1.069  Sum_probs=280.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|++|.+++++|+||++||++||+||||+|++|++||++||++||+|++++++.||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~il~~~~~~   80 (313)
T PRK12684          1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENL   80 (313)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHHHHHHHHHHH
Confidence            89999999999999955999999999999999999999999999999999999995259999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+........|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+.......+++.+
T Consensus        81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~~~~l~~  160 (313)
T PRK12684         81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVS  160 (313)
T ss_pred             HHHHHHHhccCCCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCCCCCceE
Confidence            99998888888899999999999999999999999999999999999999999999999999999998644334578999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||+..+.+++++||.++|+|.++.+...+..++.++...++.|++.+++++...+.++|.+|.|+
T Consensus       161 ~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv  240 (313)
T PRK12684        161 LPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGV  240 (313)
T ss_pred             EEeccceEEEEeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCCce
Confidence            99999999999999999998888999999999999998877777888999999999999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +++|.........++++.+++.++.....++++|+++...+|.++.|++++++.+.+...+.++
T Consensus       241 ~~lp~~~~~~~~~~~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~  304 (313)
T PRK12684        241 GIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPTLNRKLVEQAL  304 (313)
T ss_pred             EEeehhhccccccCCeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHHHHHhCHHHHHHHh
Confidence            9999987665445689999998755667899999999999999999999999999888777654

>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional

Probab=100.00  E-value=5.7e-58  Score=377.06  Aligned_cols=296  Identities=18%  Similarity=0.308  Sum_probs=273.9

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ .||++|+.|++++++++++++++
T Consensus         1 m~l~~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (305)
T PRK11151          1 MNIRDLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKV-LFTQAGLLLVDQARTVLREVKVL   78 (305)
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchheeeCCCce-eECccHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ............|.++||++++++..++++++..|.+.||++++++...+.+++.+.|.+|++|++|+... ...+++.+
T Consensus        79 ~~~~~~~~~~~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~  157 (305)
T PRK11151         79 KEMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALV-KESEAFIE  157 (305)
T ss_pred             HHHHHHhcccCCceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecC-CCCCCeEE
Confidence            98887777778899999999999999999999999999999999999999999999999999999998654 45578999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .+++.++++++++++||++.++.++++||.++|+|.+..+...+..+..++...+..+++.+++++...+.+++..|.|+
T Consensus       158 ~~l~~~~~~~~~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  237 (305)
T PRK11151        158 VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGI  237 (305)
T ss_pred             EEeccCcEEEEecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcCCCE
Confidence            99999999999999999998888999999999999998876676677788888898899999999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      +++|.+.+... ..++++.+|++...+..++|++|+++...+|.++.|++++++.+...+
T Consensus       238 ~ilp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (305)
T PRK11151        238 TLLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHF  297 (305)
T ss_pred             EEeeHHhhhhhcccCCEEEEECcCCccceEEEEEEcCCCcchHHHHHHHHHHHHHhcccH
Confidence            99999888554 457799999977666789999999999999999999999998887544

>PRK12679 cbl transcriptional regulator Cbl; Reviewed

Probab=100.00  E-value=1.8e-57  Score=374.92  Aligned_cols=299  Identities=43%  Similarity=0.756  Sum_probs=275.7

Q ss_pred             CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC-ccccCHhHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR-IRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~-~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      |++++|+||++++++ | ||++||++||+||||+|++|++||++||++||+|++++ + +||++|+.|+++++++++.++
T Consensus         1 m~~~~l~~f~~v~~~~~-s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~~~~~-~lT~~G~~l~~~a~~il~~~~   78 (316)
T PRK12679          1 MNFQQLKIIREAARQDY-NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLL-GMTEPGKALLVIAERILNEAS   78 (316)
T ss_pred             CChHHHHHHHHHHHcCC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECCCccc-ccCHhHHHHHHHHHHHHHHHH
Confidence            899999999999999 7 99999999999999999999999999999999999888 5 699999999999999999999


Q ss_pred             HHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760          79 GLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL  158 (306)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~  158 (306)
                      ++............|.++||++++++..++++++..|.+.||++.+++...+++++.+.|.+|++|++|+..+...++++
T Consensus        79 ~~~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l  158 (316)
T PRK12679         79 NVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL  158 (316)
T ss_pred             HHHHHHHHhccccCceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc
Confidence            99888877777778999999999999999999999999999999999999999999999999999999986543346789


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ...++++++++++++++||++.+.+++++||.++|||.+..+...+..++.++...|..|++.+++++...+++++..|.
T Consensus       159 ~~~~l~~~~~~~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  238 (316)
T PRK12679        159 VAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGL  238 (316)
T ss_pred             eEEEccCCcEEEEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcCC
Confidence            99999999999999999999888889999999999999988877777889999999999999999999999999999999


Q ss_pred             ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760         239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN  301 (306)
Q Consensus       239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  301 (306)
                      |++++|...+.....+.++.+++..+....++|++|+++...+|.+++|++++++.+.-..+.
T Consensus       239 Gi~~lp~~~~~~~~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~  301 (316)
T PRK12679        239 GIGLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIK  301 (316)
T ss_pred             cEEEecccccccccCCcEEEEECcccCCCceEEEEEeCCchhhHHHHHHHHHHhcccCHHHHH
Confidence            999999988765467889999887655667999999999999999999999999988766663

>PRK11242 DNA-binding transcriptional regulator CynR; Provisional

Probab=100.00  E-value=1.6e-57  Score=373.42  Aligned_cols=292  Identities=23%  Similarity=0.394  Sum_probs=271.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|++|.+|+++| ||++||++||+||||+|++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~f~~v~~~g-s~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~~~~il~~~~~~   78 (296)
T PRK11242          1 MLLRHIRYFLAVAEHG-NFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTV-RLTDAGEVYLRYARRALQDLEAG   78 (296)
T ss_pred             CChHHHHHHHHHHHhC-CHHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEcCCce-eechhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++.+
T Consensus        79 ~~~~~~~~~~~~~~i~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~  157 (296)
T PRK11242         79 RRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAP-VHSPEIEA  157 (296)
T ss_pred             HHHHHHhcCCCeeEEEEEeccchhhhhhHHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecC-CCCcceeE
Confidence            99888776667789999999999999999999999999999999999999999999999999999998655 56678999


Q ss_pred             eccccceEEEEecCCCCCCCCCC-cChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNS-ISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~-i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      .++++++++++++++||+++... ++++||.++||+.+..+...+..++.++...++.++..+.+++..++.+++..|.|
T Consensus       158 ~~l~~~~~~~~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  237 (296)
T PRK11242        158 QPLFTETLALVVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRL  237 (296)
T ss_pred             EEeeeccEEEEEcCCCcccccCCCcCHHHHhCCCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhCCe
Confidence            99999999999999999987654 99999999999999887667778889999999999999999999999999999999


Q ss_pred             eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      ++++|.+++..  .++++.+|+.+.....+++++|+++...++.+++|++++++.+.+
T Consensus       238 i~~~p~~~~~~--~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  293 (296)
T PRK11242        238 ATLLPAAIARE--HDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAE  293 (296)
T ss_pred             EEEeehhhccc--CCCeEEEECCCCCccceEEEEEeCCCCCCHHHHHHHHHHHHhhhh
Confidence            99999988765  577899898875566799999999999999999999999887654

>PRK12680 transcriptional regulator CysB-like protein; Reviewed

Probab=100.00  E-value=2.2e-57  Score=374.92  Aligned_cols=302  Identities=28%  Similarity=0.549  Sum_probs=274.8

Q ss_pred             CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccc-cCHhHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRG-LTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~-lT~~G~~l~~~a~~il~~~~   78 (306)
                      ||+++|++|++|+++ | ||++||++||+||||||++|++||++||++||+|+++++ + ||++|+.|+++++.+++.++
T Consensus         1 m~l~~L~~F~~vae~~g-S~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v-~~LT~~G~~l~~~a~~il~~~~   78 (327)
T PRK12680          1 MTLTQLRYLVAIADAEL-NITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSL-ESVTPAGVEVIERARAVLSEAN   78 (327)
T ss_pred             CCHHHHHHHHHHHHccC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEECCCcC-CccCccHHHHHHHHHHHHHHHH
Confidence            899999999999997 9 999999999999999999999999999999999999998 7 99999999999999999999


Q ss_pred             HHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760          79 GLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL  158 (306)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~  158 (306)
                      ++...++.......|.|+||++++++..++++++..|.+.||++++++...+++++.+.|.+|++|++|...+.......
T Consensus        79 ~~~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~  158 (327)
T PRK12680         79 NIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAG  158 (327)
T ss_pred             HHHHHHHHhccCCceEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcc
Confidence            99998887777788999999999999999999999999999999999999999999999999999999986543333445


Q ss_pred             eeeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      ...++++++++++++++||++.+ .+++++||.++|+|.+..+...+..+++++...|..+++.+++++..++.++|.+|
T Consensus       159 ~~~~l~~~~~~l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G  238 (327)
T PRK12680        159 IAVPLYRWRRLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG  238 (327)
T ss_pred             eEEEeeccceEEEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC
Confidence            58999999999999999999864 57999999999999999888778889999999999999999999999999999999


Q ss_pred             cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         238 MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       238 ~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      .|++++|..++.. ..+.++.+|++.+.....+|++|++++..++.++.|++++...++....+++++
T Consensus       239 ~Gia~lp~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (327)
T PRK12680        239 LGVGLLAEMAVNA-NDEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALELVHVLAPQIDKRDLRRVLD  305 (327)
T ss_pred             CCEEEeechhccC-CCCCeEEEECCCCCCCceEEEEEeCCchhHHHHHHHHHHhcCCCCHHHHHHHhc
Confidence            9999999988875 356799999876545567889999999999999999999988887766655543

>PRK10341 DNA-binding transcriptional activator TdcA; Provisional

Probab=100.00  E-value=1.5e-57  Score=375.17  Aligned_cols=298  Identities=16%  Similarity=0.193  Sum_probs=274.5

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|++|++++++| ||++||++||+||||+|++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         7 ~~~~~L~~F~av~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   84 (312)
T PRK10341          7 PKTQHLVVFQEVIRSG-SIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGV-TLTPAGQVLLSRSESITREMKNM   84 (312)
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-eEChhHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~  159 (306)
                      .+.+........|.|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|...+. ...+++.
T Consensus        85 ~~~~~~~~~~~~~~l~ig~~~~~~~~~l~~~l~~~~~~~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~  164 (312)
T PRK10341         85 VNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLH  164 (312)
T ss_pred             HHHHHHHcCCCceEEEEEechHHhHhhHHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCee
Confidence            999998877788999999999999999999999999999999999999999999999999999999986432 2357899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      ..++++++++++++++||+.  ..++++||.++||+....+...+..+.+++...++.+++.+++++..++.+++.+|.|
T Consensus       165 ~~~l~~~~~~lv~~~~~pl~--~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  242 (312)
T PRK10341        165 VEPLFESEFVLVASKSRTCT--GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADF  242 (312)
T ss_pred             EEEEecccEEEEEcCCCchh--ccCCHHHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhCCc
Confidence            99999999999999999985  3689999999999998877777777788888889999999999999999999999999


Q ss_pred             eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      ++++|..+......++++.+++++......++++|+++...+|+++.|++++++.+..+++++
T Consensus       243 i~~~p~~~~~~~~~~~l~~i~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  305 (312)
T PRK10341        243 LTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRR  305 (312)
T ss_pred             EEEeeHHhcCccccCcEEEEecCCCCCCCcEEEEEecCCCCCHHHHHHHHHHHHHhhhcchhh
Confidence            999999887654456799999987555678999999999999999999999999998888765

>CHL00180 rbcR LysR transcriptional regulator; Provisional

Probab=100.00  E-value=3.4e-57  Score=372.12  Aligned_cols=294  Identities=24%  Similarity=0.358  Sum_probs=271.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++|+| ||++||++||+|||++|++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         5 ~~l~~L~~f~~v~e~g-s~s~AA~~L~isqpavS~~i~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~ll~~~~~~   82 (305)
T CHL00180          5 FTLDQLRILKAIATEG-SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKA-SLTEAGELLLRYGNRILALCEET   82 (305)
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhcCCChHHHHHHHHHHHHhCCEEEEecCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCc
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKL  158 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~  158 (306)
                      .+.+++......|.++||+.++++..++++++..|.+.||++++++....+..+.+.|.+|++|++|+......  .+++
T Consensus        83 ~~~~~~~~~~~~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~  162 (305)
T CHL00180         83 CRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKIL  162 (305)
T ss_pred             HHHHHHhhcccCceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEcCccCcccccce
Confidence            99999888888999999999999999999999999999999999999988999999999999999998643222  2568


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHHHH
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTYVE  235 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~  235 (306)
                      ...+++.++++++++++||++.+..++++||.++|+|.+..+...+..+.+++...+..+   ++.+.+++..++.+++.
T Consensus       163 ~~~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  242 (305)
T CHL00180        163 EITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQ  242 (305)
T ss_pred             eEEEeccCcEEEEECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCcccceEEEEeCCHHHHHHHHH
Confidence            999999999999999999999988999999999999999988777778889999888765   57899999999999999


Q ss_pred             hccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         236 LRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       236 ~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      +|.|++++|.+.+... ..+.++.+|+++....+.+|++|++++..++.++.|++++++.++
T Consensus       243 ~g~g~~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~  304 (305)
T CHL00180        243 SGLGAAFVSVSAIEKELELGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEILTLFN  304 (305)
T ss_pred             cCCcEEEeEhHHHHHHhhcCcEEEEEcCCCCceEEEEEEEeCCCccCHHHHHHHHHHHHHhc
Confidence            9999999999877655 677899999887656789999999999999999999999997654

>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ

Probab=100.00  E-value=2.1e-57  Score=373.19  Aligned_cols=294  Identities=21%  Similarity=0.270  Sum_probs=272.5

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|++|++|+++| ||++||++||+|||+||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         3 m~l~~l~~f~~v~~~g-S~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   80 (300)
T TIGR02424         3 IKFRHLQCFVEVARQG-SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGI-RLTRYGELFLRHAGASLAALRQG   80 (300)
T ss_pred             ccHHHHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-cccHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~  159 (306)
                      ...++.......|.++||+++++...++++++..|.++||++++++...+..++.+.+.+|++|++|+.... ...+++.
T Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~  160 (300)
T TIGR02424        81 VASLSQLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLS  160 (300)
T ss_pred             HHHHHHhcCCCCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccccccee
Confidence            999988878889999999999999999999999999999999999999999999999999999999975332 2347899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ..++++++++++++++||++.+..++++||.++|++.+..+...+..++.++...+..+ ++.+++++...+..++..|.
T Consensus       161 ~~~l~~~~~~~~~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  240 (300)
T TIGR02424       161 FEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQESD  240 (300)
T ss_pred             eeeecCCceEEEEcCCCccccCCCCCHHHHhCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhCC
Confidence            99999999999999999999988899999999999999887777788899999999875 56789999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      |++++|.+.+... ..++++.++++......+++++|+++...+|.+++|++++++.++
T Consensus       241 gi~~lp~~~~~~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  299 (300)
T TIGR02424       241 AIWIISRGVVALDLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDALRSAAA  299 (300)
T ss_pred             ceEeCcHHHHhhhhcCCcEEEccCCCCCCCCceEEEEeCCCCCCHHHHHHHHHHHHHhc
Confidence            9999999888765 678899999887666679999999999999999999999988764

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

>PRK11013 DNA-binding transcriptional regulator LysR; Provisional

Probab=100.00  E-value=1.1e-56  Score=369.53  Aligned_cols=296  Identities=18%  Similarity=0.266  Sum_probs=273.1

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++.+
T Consensus         4 ~~l~~L~~f~av~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R~~~~v-~LT~~G~~l~~~a~~~l~~~~~~   81 (309)
T PRK11013          4 VSLRHIEIFHAVMTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRL-HPTVQGLRLFEEVQRSYYGLDRI   81 (309)
T ss_pred             ccHHHHHHHHHHHHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeeecCCCc-ccCHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999998 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.++||++++++..++++++..|.+.||++++++...+..++.+.|.+|++|++|.... ...+++..
T Consensus        82 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~  160 (309)
T PRK11013         82 VSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL-HTPAGTER  160 (309)
T ss_pred             HHHHHHHHcCCCCcEEEEEcHHHHHhhHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCCCEEEEcCC-CCCCCcee
Confidence            99888888778899999999999999999999999999999999999999999999999999999998644 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++..++++++||.++|+|.++.+...+..++.++...|+.+++..++++...+..++.+|.|+
T Consensus       161 ~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv  240 (309)
T PRK11013        161 TELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGV  240 (309)
T ss_pred             eeecceeEEEEEcCCCccccCCccCHHHHCCCcEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCeE
Confidence            99999999999999999998888999999999999999887778888999999999999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      +++|...+......++..+|++.. ....++++|++++..++.++.|++++++.+.+...
T Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~f~~~i~~~~~~~~~  299 (309)
T PRK11013        241 SIVNPLTALDYAGSGLVVRRFSIS-VPFTVSLIRPLHRPASALVDAFSEHLQQQAPALVT  299 (309)
T ss_pred             EEeChhhhccccCCCEEEEeCCCC-CceeEEEEecCCCCCCHHHHHHHHHHHHHHHHhhh
Confidence            999987766553455888888764 44699999999999999999999999998765543

>PRK09791 putative DNA-binding transcriptional regulator; Provisional

Probab=100.00  E-value=1.1e-56  Score=368.85  Aligned_cols=293  Identities=21%  Similarity=0.272  Sum_probs=270.8

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||+++|++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         5 ~~l~~L~~f~~v~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   82 (302)
T PRK09791          5 VKIHQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGV-TLTDAGESFYQHASLILEELRAA   82 (302)
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-eECccHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcc-ccCCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE-ILSPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~-~~~~~~~~~  159 (306)
                      ...++.......|.|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+.. .....+++.
T Consensus        83 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~p~i~~~~~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~~~~~  162 (302)
T PRK09791         83 QEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFT  162 (302)
T ss_pred             HHHHHHhhcccceEEEEEechHHHHhhhHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHCCCccEEEEecCCccccccee
Confidence            9999988888899999999999999999999999999999999999999999999999999999999843 222356799


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      +.++++++++++++++||+...  .+++||.++|++.+..+...+..+.+++...+..+++.+++++..++.+++..|.|
T Consensus       163 ~~~l~~~~~~l~~~~~~~~~~~--~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  240 (302)
T PRK09791        163 FEKLLEKQFAVFCRPGHPAIGA--RSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSDF  240 (302)
T ss_pred             EEEeccceEEEEEcCCCCcCCC--CCHHHHhcCCeecCCCCCcHHHHHHHHHHhcCCCCCcceEEccHHHHHHHHHcCCe
Confidence            9999999999999999998753  47999999999998877677788889999999999999999999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      ++++|..++... ..++++.++++...+...+|++|+++...++.++.|++++++.++.
T Consensus       241 i~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  299 (302)
T PRK09791        241 LSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFRRECGY  299 (302)
T ss_pred             EEEeeHhhhcccccCCceEEEecCCCCCCcceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            999999888665 6788999999876667899999999999999999999999987654

>PRK11233 nitrogen assimilation transcriptional regulator; Provisional

Probab=100.00  E-value=5.2e-56  Score=364.85  Aligned_cols=296  Identities=20%  Similarity=0.268  Sum_probs=268.8

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~F~~v~~~~-S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R~~r~v-~lT~~G~~l~~~a~~~l~~~~~~   78 (305)
T PRK11233          1 MNFRRLKYFVKIVDIG-SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGV-TPTEAGKILYTHARAILRQCEQA   78 (305)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEeCCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~  159 (306)
                      ...+........|.++||+++++. ..++++++..|.+.||++.+.+......++.+.|.+|++|++|+..+ ...+++.
T Consensus        79 ~~~~~~~~~~~~g~l~I~~~~~~~~~~~~~~~l~~~~~~~p~i~l~~~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~~~  157 (305)
T PRK11233         79 QLAVHNVGQALSGQVSIGLAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEH-SPVAGLS  157 (305)
T ss_pred             HHHHHhhccccCceEEEEcccchhhHHHHHHHHHHHHHHCCCcEEEEEECCcHHHHHHHHCCCCCEEEEcCC-cCCCCcE
Confidence            999888877788999999987654 57889999999999999999999988889999999999999998654 5567899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      ..++++++++++++++||   +..++++||.++|++....+...+..++.++...|..|++..++++..++..++.+|.|
T Consensus       158 ~~~l~~~~~~lv~~~~~~---~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~g  234 (305)
T PRK11233        158 SQPLLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMG  234 (305)
T ss_pred             EEEEeeeeEEEEEcCccC---CCCcCHHHHhCCCeecCCCCccHHHHHHHHHHHcCCCCceEEEEcCHHHHHHHHHcCCe
Confidence            999999999999999987   46799999999999988766666777888999999999988999999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      ++++|.+.+... ..+.++.+++..+.....++++|++++..++.++.|++++++.+.+...++
T Consensus       235 i~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~  298 (305)
T PRK11233        235 VTVLPESAARSLCGAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQAVKEILLSLVSSPVMEK  298 (305)
T ss_pred             eEecchhHhhcccccCceeEEeecCCccceEEEEEecCCCCCCHHHHHHHHHHHHHHHHHhhhh
Confidence            999999887654 455677777766556689999999999999999999999999988777654

>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional

Probab=100.00  E-value=7e-56  Score=363.42  Aligned_cols=291  Identities=21%  Similarity=0.328  Sum_probs=265.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+|||||||+|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~f~~v~~~g-s~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (296)
T PRK09906          1 MELRHLRYFVAVAEEL-NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKV-ALTAAGEVFLQDARAILEQAEKA   78 (296)
T ss_pred             CcHHHHHHHHHHHhhC-CHHHHHHHhCCCCcHHHHHHHHHHHHhCCeeeeeCCCcc-eEcHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+...... .+.++||+++++...++++++..|.+.||++.+++...+++++.+.|.+|++|++|+..+ ...+++.+
T Consensus        79 ~~~~~~~~~~-~~~l~Ig~~~~~~~~~l~~~~~~~~~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~  156 (296)
T PRK09906         79 KLRARKIVQE-DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHP-VYSDEIDY  156 (296)
T ss_pred             HHHHHhhhcc-CCcEEEEEecchhhhHHHHHHHHHHHHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCC-CCCCCceE
Confidence            9988876554 455999999999999999999999999999999999999999999999999999999765 46678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      .+++.++++++++++||++.+..++++||.++|++.+..+.  ..+..+..++...++.++..+++++..++++++.+|.
T Consensus       157 ~~l~~~~~~~v~~~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  236 (296)
T PRK09906        157 LELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL  236 (296)
T ss_pred             EEEecccEEEEecCCCccccCCCcCHHHHcCCCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCC
Confidence            99999999999999999998888999999999999987653  3467778899999999999999999999999999999


Q ss_pred             ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      |++++|.+.+.. ...+++.+++++......+|++|+++. .++.++.|++++++.++.
T Consensus       237 g~~~~p~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~  293 (296)
T PRK09906        237 GCTIIPGYMNNF-NTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERLAS  293 (296)
T ss_pred             cEEEeeHHHhhc-CCCCEEEeeCCCCcceeEEEEEECCCC-CCHHHHHHHHHHHhhhhc
Confidence            999999987654 345678888877555678999998875 699999999999988754

>PRK10837 putative DNA-binding transcriptional regulator; Provisional

Probab=100.00  E-value=3.8e-56  Score=364.18  Aligned_cols=285  Identities=22%  Similarity=0.319  Sum_probs=262.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|.+|+|+| ||++||++||+||||||++|++||+++|++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         3 m~l~~L~~f~~v~e~~-s~t~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   80 (290)
T PRK10837          3 ITLRQLEVFAEVLKSG-STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRL-VVNEHGRLLYPRALALLEQAVEI   80 (290)
T ss_pred             CcHHHHHHHHHHHHcC-CHHHHHHHhCCCccHHHHHHHHHHHHhCCccEeecCCeE-EECHhHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 89999999999999999999988


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+...    +..|.++||++++++..++++++..|.+.||++.+++...++.++.+.+.+|++|++|...+ ...+++..
T Consensus        81 ~~~~~----~~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~~~~  155 (290)
T PRK10837         81 EQLFR----EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGP-CHSPELIS  155 (290)
T ss_pred             HHHHH----hhCCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEecCC-CCCCceeE
Confidence            75443    35689999999999999999999999999999999999999999999999999999998644 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++ ...++++||.++||+.++.+...+..+..++...+..+++.+++++...+..++.+|.|+
T Consensus       156 ~~l~~~~~~lv~~~~hpl~-~~~i~~~~L~~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  234 (290)
T PRK10837        156 EPWLEDELVVFAAPDSPLA-RGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGI  234 (290)
T ss_pred             EEeecceEEEEEcCCChhh-cCCCCHHHHhcCCeEEecCCCcHHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCCcE
Confidence            9999999999999999998 467999999999999998877777788888888888899999999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      +++|.+.+... ..+.++.++++.+....++|++|+++...++.+++|++++++
T Consensus       235 ~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~  288 (290)
T PRK10837        235 SCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQE  288 (290)
T ss_pred             EEeeHHHHHHHHhCCcEEEEEcCCccceEEEEEEEeCCCCCCHHHHHHHHHHHh
Confidence            99999987665 677899999877666789999999999999999999999865

>PRK15421 DNA-binding transcriptional regulator MetR; Provisional

Probab=100.00  E-value=1.3e-55  Score=363.42  Aligned_cols=290  Identities=17%  Similarity=0.267  Sum_probs=260.7

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         2 m~l~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~~r~v-~lT~~G~~l~~~a~~il~~~~~~   79 (317)
T PRK15421          2 IEVKHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPL-RFTPQGEILLQLANQVLPQISQA   79 (317)
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEecCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999998


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ....+   ....|.|+||++.++...++++++..|.+.||++.+++....+.++.+.|.+|++|++|+..+ ...+++.+
T Consensus        80 ~~~~~---~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~-~~~~~~~~  155 (317)
T PRK15421         80 LQACN---EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDI-LPRSGLHY  155 (317)
T ss_pred             HHHhc---ccCceeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCc-ccCCCceE
Confidence            76543   345689999999988889999999999999999999999998889999999999999998654 55678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++.+..++++||.++|++....+...+..+..++...|+.+++. .+++...+.+++.+|.|+
T Consensus       156 ~~l~~~~~~lv~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~v~~g~Gi  234 (317)
T PRK15421        156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGI  234 (317)
T ss_pred             EEeccceEEEEEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCcee-ecCCHHHHHHHHHhCCcE
Confidence            9999999999999999999888999999999999998776555667778888889888765 789999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      +++|.+++... ..+.++.+++++ .....++++|+++...++.++.|++++++.+...
T Consensus       235 ~i~p~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~fi~~l~~~~~~~  292 (317)
T PRK15421        235 AALPHWVVESFERQGLVVTKTLGE-GLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDH  292 (317)
T ss_pred             EEecchhcchhhcCCcEEEeecCC-cceeEEEEEEEcCCCCChHHHHHHHHHHHhhhhh
Confidence            99999988765 556666666655 3456899999999999999999999999877654

>PRK09986 DNA-binding transcriptional activator XapR; Provisional

Probab=100.00  E-value=1.5e-55  Score=361.38  Aligned_cols=286  Identities=20%  Similarity=0.255  Sum_probs=260.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++|+|||||||++|++||++||++||+|+++++ +||++|+.|++++++++++++++
T Consensus         7 ~~l~~l~~f~~v~~~g-s~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   84 (294)
T PRK09986          7 IDLKLLRYFLAVAEEL-HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSV-VLTHAGKILMEESRRLLDNAEQS   84 (294)
T ss_pred             hhHHHHHHHHHHHHhc-CHHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc-cCCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI-LSPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~  159 (306)
                      ...++.......|.++||+++++...++++++..|.++||++++++...+++++.+.|.+|++|++|+... .....++.
T Consensus        85 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~  164 (294)
T PRK09986         85 LARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT  164 (294)
T ss_pred             HHHHHHHhccCcceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCCCeE
Confidence            99988877777899999999999999999999999999999999999998889999999999999998543 24567899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      +.++++++++++++++||+..+..++++||.++|+|.+..+... ...+.+++...++.+++.+++++..++..+|.+|.
T Consensus       165 ~~~l~~~~~~~v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  244 (294)
T PRK09986        165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGI  244 (294)
T ss_pred             EEEeecccEEEEEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcCC
Confidence            99999999999999999999888899999999999998775443 34778888889999999999999999999999999


Q ss_pred             ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      |++++|.+.+.. ..+++..+|++.. ...+++++|+++. .++.++.|++++
T Consensus       245 gi~~l~~~~~~~-~~~~l~~~~~~~~-~~~~~~l~~~~~~-~~~~~~~f~~~~  294 (294)
T PRK09986        245 GITLLPDSYAQI-PWPGVVFRPLKER-IPADLYAVYHPDQ-VTPALNKLLAAL  294 (294)
T ss_pred             eEEEccHHHhhc-CCCCeEEEECCCC-CceeEEEEEeCCC-CChHHHHHHhhC
Confidence            999999987653 3457888898764 4579999999886 699999999874

>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator

Probab=100.00  E-value=1.3e-54  Score=353.49  Aligned_cols=279  Identities=23%  Similarity=0.353  Sum_probs=257.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG   84 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~   84 (306)
                      +|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++...+
T Consensus         1 ~l~~f~~v~~~g-s~~~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~~~~~   78 (279)
T TIGR03339         1 QLKAFHAVARCG-SFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRL-ELTDAGHRLLPIVERLFQQEAEAEFLL   78 (279)
T ss_pred             CchhhHHHHhcC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCccEEEcCCeE-EEChhHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999 999999999999999999999999999999999999999 899999999999999999999999999


Q ss_pred             HhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccc
Q psy3760          85 KEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY  164 (306)
Q Consensus        85 ~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~  164 (306)
                      ........|.++||++.   ..++++++..|.+.||++++++...++.++.+.|.+|++|++|+... ...+++...+++
T Consensus        79 ~~~~~~~~~~l~ig~~~---~~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~  154 (279)
T TIGR03339        79 RESGALREGSLRIAATA---PYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEV-VDDPRLDRVVLG  154 (279)
T ss_pred             HHhccCcceEEEEeCch---HHHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecc-cCCCceEEEEcC
Confidence            98877778999999984   45899999999999999999999999999999999999999998644 556789999999


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeee
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIA  244 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p  244 (306)
                      ++++++|++++||++...+++++||.++|++.+..+...+..++.++...++.++..+++++..++.+++.+|.|++++|
T Consensus       155 ~~~~~lv~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp  234 (279)
T TIGR03339       155 NDPLVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVS  234 (279)
T ss_pred             CceEEEEECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcCCCEEEcc
Confidence            99999999999999988889999999999999988777778889999999999999999999999999999999999999


Q ss_pred             cceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         245 SIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       245 ~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+....  .++++.+++++......++++|+++...+|.++.|++.+
T Consensus       235 ~~~~~~--~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  279 (279)
T TIGR03339       235 AAEVGR--DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA  279 (279)
T ss_pred             hhhhcc--CCceEEEECCCCcccceEEEEEECCCCCCHHHHHHHhhC
Confidence            976543  577999998775556799999999999999999999753

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

>PRK09508 leuO leucine transcriptional activator; Reviewed

Probab=100.00  E-value=3.4e-55  Score=361.49  Aligned_cols=291  Identities=14%  Similarity=0.133  Sum_probs=258.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++..
T Consensus        22 ~~l~~L~~f~avae~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~l~~~~~~   99 (314)
T PRK09508         22 VDLNLLTVFDAVMQEQ-NITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGI-QPTARARQLFGPVRQALQLVQNE   99 (314)
T ss_pred             cChHHHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHhhCCCcEEEcCCCC-cCcHHHHHHHHHHHHHHHHHHHh
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999998875


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ............+.++||+..++...++++++..|.++||++.+++...+..++.+.|.+|++|++|+..+ ...+++..
T Consensus       100 ~~~~~~~~~~~~~~i~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~l~~  178 (314)
T PRK09508        100 LPGSGFEPESSERVFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEE-FDRPEFTS  178 (314)
T ss_pred             cCCCCCCccccccEEEEEechhHHHHHHHHHHHHHHHhCCCcEEEEEeCcchhHHHHHhcCCccEEEecCC-CCccccce
Confidence            43222112234678999999888788999999999999999999999998889999999999999999754 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||+. +..++++||.+++++..... .....++.++...|..+++.+++++...+.+++.+|.|+
T Consensus       179 ~~l~~~~~~lv~~~~hpl~-~~~~~~~~L~~~~~~~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~gi  256 (314)
T PRK09508        179 VPLFKDELVLVASKNHPRI-KGPITEEQLYNEQHAVVSLD-RFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQTHLV  256 (314)
T ss_pred             eeeecCceEEEEcCCCCcc-CCCCCHHHHhhCCCEEecCC-CCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhCChH
Confidence            9999999999999999987 45799999999998766532 234456778888899999999999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      +++|.+.+... ..++++.++++.....+.++++|+++...+|+.++|.+.+++.++
T Consensus       257 ~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~l~~~i~~~~~  313 (314)
T PRK09508        257 AIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEELLVSICK  313 (314)
T ss_pred             HHHHHHHHHHhhhccCceEeCCCCCCCCceEEEEeccccCCChHHHHHHHHHHHHhc
Confidence            99999888665 577899999987666789999999999999999999999998765

>PRK11074 putative DNA-binding transcriptional regulator; Provisional

Probab=100.00  E-value=8.7e-55  Score=356.98  Aligned_cols=287  Identities=16%  Similarity=0.208  Sum_probs=255.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|.+|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         2 ~~~~~L~~f~~v~e~~-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~l~~~~~~   79 (300)
T PRK11074          2 WSEYSLEVVDAVARTG-SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDV-ELTPAGEWFVKEARSVIKKMQET   79 (300)
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEEeCCCCc-eECccHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~  159 (306)
                      .+.+++......|.++||++++++..++++++..|.+.||++++++......++.+.|.+|++|++|+..+. ...+++.
T Consensus        80 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~  159 (300)
T PRK11074         80 RRQCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFA  159 (300)
T ss_pred             HHHHHHHhcCCCceEEEEEcCccchhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHCCCCCEEEecCccCCcccccc
Confidence            999998888889999999999999999999999999999999999999988999999999999999986432 2346799


Q ss_pred             eeccccceEEEEecCCCCCCCCC-CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLN-SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~-~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      +.++++++++++++++||++.+. .++++||.++|++....+.........++    ..++..+.+++...++++|.+|.
T Consensus       160 ~~~l~~~~~~~v~~~~hpl~~~~~~~~~~dl~~~p~i~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g~  235 (300)
T PRK11074        160 FRDMGMLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWL----LDNQRRLVVPDWESAINCLSAGL  235 (300)
T ss_pred             eeecccceEEEEEcCCCcccccCCCCCHHHHhhCCEEEecCCCcccccCccce----ecCCceEEECCHHHHHHHHHcCC
Confidence            99999999999999999998764 69999999999999876543211112222    12345788999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      |++++|.+.+... ..+.++.+++++....++++++|+++. .+|.+++|++++++.
T Consensus       236 gi~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~~~  291 (300)
T PRK11074        236 CVGMVPTHFAKPLINSGKLVELTLENPFPDSPCCLTWQQND-MSPALAWLLDYLGDS  291 (300)
T ss_pred             eEEeCCHHHhHHHHhCCceEEEecCCCCCCceEEEEEecCC-CChHHHHHHHHHhhc
Confidence            9999999988765 677899999987667789999999875 699999999999663

>PRK15243 transcriptional regulator SpvR; Provisional

Probab=100.00  E-value=2.9e-54  Score=348.33  Aligned_cols=280  Identities=15%  Similarity=0.152  Sum_probs=246.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI   83 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~   83 (306)
                      ++|+||++|+++| ||++||++||+||||+|++|++||++||++||+|+++++ +||++|+.||++|+++++.++++...
T Consensus         7 rqL~~F~aVae~g-Sfs~AA~~L~isQpavS~~Ik~LE~eLG~~LF~R~~r~~-~LT~aG~~ll~~a~~il~~~~~~~~~   84 (297)
T PRK15243          7 KKLKIFITLMETG-SFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTL-IPTEFAQTIYRKVKSHYIFLHALEQE   84 (297)
T ss_pred             HHHHHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHHHHHHHhCCccEEeCCCCe-eECHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999 999999999999999999999999999999999999999 79999999999999999999999998


Q ss_pred             HHhhccCCCCcEEEEecccchhhhhHHHHHHH-----HHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760          84 GKEFSAYDTGNLTIATTHTQARYALPKIIKEF-----TIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL  158 (306)
Q Consensus        84 ~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~-----~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~  158 (306)
                      +....  ..|.|+||+..     ++|+++..|     ...||++++.+...++..+.+.+.+|. |++++.......+++
T Consensus        85 ~~~~~--~~G~L~Ig~~~-----~lP~~~~~~~~~~~~~~~P~v~i~~~~~~~~~~~~~l~~~~-~i~i~~~~~~~~~~l  156 (297)
T PRK15243         85 IGPTG--KTKQLEIIFDE-----IYPESLKNLIISALTISGQKTNIMGRAVNSQIIEELCQTNN-CIVISARNYFHRESL  156 (297)
T ss_pred             HHhcC--CCceEEEEEec-----cchHHHHHHHHHHHHhhCCceEEEEecCCHHHHHHHHcCCC-cEEEecCCCCCCCCe
Confidence            87643  36999999653     666677665     447999999999888777777776665 688864332356889


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHh-CCCceeEEEEecCHHHHHHH--H
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSL-QKLTPYIVLETINSDIIKTY--V  234 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--v  234 (306)
                      .+.++++++++++++++||++.++  ++.||.++|||....+.+. +..++++|.. .|+ |++.+++++.++++++  |
T Consensus       157 ~~~~l~~e~lvlv~~~~hpla~~~--~l~~l~~~p~il~~~~~~~~r~~~~~~~~~~~gi-~~~~~e~~s~e~i~~lv~v  233 (297)
T PRK15243        157 VCRTSVEGGVMLFIPKKFFLCGKP--DINRLAGTPVLFHEGAKNFNLDTIYHFFEQTLGI-TNPAFSFDNVDLFSSLYRL  233 (297)
T ss_pred             eEEEeccCCEEEEEcCCCccccCC--CHHHHhcCCeEEecCCCccHHHHHHHHHHHhcCC-ChhheecccHHHHHHHHHH
Confidence            999999999999999999998765  8999999999999999886 7799999996 999 7899999999999999  4


Q ss_pred             HhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         235 ELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       235 ~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .+|.|++++|...+.....+.++.+|+++..  ...+++|+++++.+|+++.|++.+++.+++.
T Consensus       234 ~~glGia~lp~~~~~~~~~~~L~~~~i~~~~--~~~~lv~~k~~~ls~~~~~f~~~~~~~~~~~  295 (297)
T PRK15243        234 QQGLAMLLIPVRVCRALGLSTDHALHIKGVA--LCTSLYYPTKKRETPDYRKAIKLIQQELKQS  295 (297)
T ss_pred             hcCCeeecccHHHHHHHhhCceEEeccCcCc--eeEEEEecCCCCCChhHHHHHHHHHHHHhhc
Confidence            9999999999888775588899999998733  3459999999999999999999998777654

>PRK10094 DNA-binding transcriptional activator AllS; Provisional

Probab=100.00  E-value=2.8e-53  Score=348.54  Aligned_cols=288  Identities=13%  Similarity=0.153  Sum_probs=252.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         2 ~~~~~L~~f~~v~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   79 (308)
T PRK10094          2 FDPETLRTFIAVAETG-SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSV-TLTAAGEHLLSQARDWLSWLESM   79 (308)
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccc-hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc-cCCCCCc
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQ-ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI-LSPSDKL  158 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~-~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~  158 (306)
                      .+.+.....+..|.++||+.+.. ...++++++..|+++||++++++....+.++.+.|.+|++|++|+... ....+++
T Consensus        80 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~l~l~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l  159 (308)
T PRK10094         80 PSELQQVNDGVERQVNIVINNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTF  159 (308)
T ss_pred             HHHHHHhcCCCCccEEEEecccccCHHHHHHHHHHHHHhCCCcEEEEEeehhhhHHHHHhCCCccEEEecccCccccCCe
Confidence            99998887788999999998763 467899999999999999999999999999999999999999997432 2346789


Q ss_pred             eeeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      ...++++++++++++++||++++ ..++++||.++|+|.+..+...  ......  ....+...+.+++..+++.+|..|
T Consensus       160 ~~~~l~~~~~~~v~~~~hpl~~~~~~~~~~~L~~~~~i~~~~~~~~--~~~~~~--~~~~~~~~~~~~~~~~~~~~v~~g  235 (308)
T PRK10094        160 SLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSART--LTKRVA--WRLPGQKEIIVPDMETKIAAHLAG  235 (308)
T ss_pred             eEEEecceeEEEEECCCCCCcCCCCCCCHHHHHhCCeeEeeccccc--cchhhc--cccCCCcEEEECCHHHHHHHHHcC
Confidence            99999999999999999999874 4799999999999998765421  111111  112234567899999999999999


Q ss_pred             cceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         238 MGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       238 ~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .|++++|...+... ..+.++.++++......+++++|+++.. +|+++.|++.+++..
T Consensus       236 ~gi~~lp~~~~~~~~~~~~l~~~~l~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~  293 (308)
T PRK10094        236 VGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFGS-GKAVEDIVTLFTQRR  293 (308)
T ss_pred             CcEEeCChHhhhHHhhcCceEEEeCCCCCCCcceEEEEecCCC-CcHHHHHHHHHhCCC
Confidence            99999999888765 6678999998876667899999999874 999999999998654

>PRK11062 nhaR transcriptional activator NhaR; Provisional

Probab=100.00  E-value=1.4e-53  Score=349.06  Aligned_cols=282  Identities=14%  Similarity=0.138  Sum_probs=256.1

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         4 m~l~~L~~F~~v~e~g-s~s~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   81 (296)
T PRK11062          4 INYNHLYYFWMVCKEG-SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGL-EPTELGELVFRYADKMFTLSQEM   81 (296)
T ss_pred             cCHHHHHHHHHHHhcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCccceeecCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .+..+ ......|.|+||++++++..++++++..|...||++++++....+.++...|.+|++|++|+..+..  ..+++
T Consensus        82 ~~~~~-~~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l  160 (296)
T PRK11062         82 LDIVN-YRKESNLLFDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL  160 (296)
T ss_pred             HHHhc-ccccCceEEEEEecchhhHhhHHHHHHHHHhcCCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch
Confidence            98764 4566788999999999999999999999999999999999988888999999999999999853322  34679


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ...++++++++++++++||+.    .++++|.++|++.+..+...+..+..++...+..+++.+++++..++.+++.+|.
T Consensus       161 ~~~~l~~~~~~~~~~~~~~~~----~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  236 (296)
T PRK11062        161 FSKKLGECGVSFFCTNPLPEK----PFPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYHD  236 (296)
T ss_pred             hhhhhhccCcceEecCCCccc----cChHHHhcCCeeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcCC
Confidence            999999999999999999853    3689999999999887766677788999999999999999999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      |++++|.+.+... ..++++.++... ....++|++|+++...+|.++.|++.
T Consensus       237 Gi~~lp~~~~~~~~~~~~l~~l~~~~-~~~~~~~lv~~~~~~~~~~~~~f~~~  288 (296)
T PRK11062        237 AIFVAPSLYAQDFYADHSVVEIGRVD-NVKEEYHVIFAERMIQHPAVQRICNT  288 (296)
T ss_pred             ceEECCHHHHHHHHHcCCeEEcCCcc-ccceEEEEEEecCCCCcHHHHHHHhh
Confidence            9999999998766 678899887643 45679999999999999999999986

>PRK09801 transcriptional activator TtdR; Provisional

Probab=100.00  E-value=6.4e-54  Score=352.42  Aligned_cols=291  Identities=14%  Similarity=0.117  Sum_probs=247.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         6 ~~~~~L~~F~~v~~~g-s~t~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~l   83 (310)
T PRK09801          6 PLAKDLQVLVEIVHSG-SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGV-ALTESGQRCYEHALEILTQYQRL   83 (310)
T ss_pred             HHHHHHHHHHHHHHcC-CHHHHHHHhCcCHHHHHHHHHHHHHHhCCEeeeecCCCC-cccHhHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+.+++......|.|+||++++++..++++++..|.++||++++++...+.  ..+ +..|++|++|...+ ..++.+..
T Consensus        84 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~--~~~-~l~~~~Dl~i~~~~-~~~~~~~~  159 (310)
T PRK09801         84 VDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDR--QID-LVQDNIDLDIRIND-EIPDYYIA  159 (310)
T ss_pred             HHHHHhccCCCceEEEEeCcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCC--ccC-cccCCceEEEEeCC-CCCCCeEE
Confidence            999999888788999999999999999999999999999999999986442  344 44688999998544 44567888


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHH--HHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE--FSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ..+.+++++++++++|+......++++||.++|++....+...+..+...  ....+..+++.+++++..++.++|.+|.
T Consensus       160 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~v~~g~  239 (310)
T PRK09801        160 HLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGK  239 (310)
T ss_pred             EEeeccceEEEECHHHHHhcCCCCCHHHHhhCCEEEecCCCCCCCceEEecCCCEEEEecCCcEEECCHHHHHHHHHcCC
Confidence            88999999999999996443467999999999999877654443222211  1122445666889999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      |++++|.+.+... ..+.++.+ +++....++++++|++++..+++++.|++++++.++++
T Consensus       240 Gia~lp~~~~~~~~~~~~l~~~-~~~~~~~~~~~lv~~~~~~~~~~~~~~i~~l~~~~~~~  299 (310)
T PRK09801        240 GIMLRSEWDVLPFLESGKLVQV-LPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQR  299 (310)
T ss_pred             CEEecchhhHHHHHhCCCeEEe-CCCCCCCCcEEEEEcCCCcCCHHHHHHHHHHHHHHHHh
Confidence            9999999887654 56778865 44434567999999999999999999999998876543

>PRK11139 DNA-binding transcriptional activator GcvA; Provisional

Probab=100.00  E-value=6.7e-53  Score=345.67  Aligned_cols=285  Identities=16%  Similarity=0.119  Sum_probs=249.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      +++++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.||++++++++.++++
T Consensus         6 ~~l~~l~~f~~v~~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~r~l-~lT~~G~~l~~~~~~~l~~~~~~   83 (297)
T PRK11139          6 PPLNALRAFEAAARHL-SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSL-LLTEEGQRYFLDIREIFDQLAEA   83 (297)
T ss_pred             CchHHHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCchheEecCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+..  ....|.++||++++++..++++++..|.+.||++++++...+.   .+.+.+|++|++|+..+ ...+++..
T Consensus        84 ~~~~~~--~~~~g~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~i~l~~~~~---~~~l~~g~~Dl~i~~~~-~~~~~l~~  157 (297)
T PRK11139         84 TRKLRA--RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDR---LEDFLRDDVDVAIRYGR-GNWPGLRV  157 (297)
T ss_pred             HHHHhc--CCCCceEEEecChHHHHHHHHHHHHHHHHHCCCceEEEEeCCC---hhhhccCCCCEEEEeCC-CCCCCceE
Confidence            987764  3457899999999999999999999999999999999986433   57888999999999654 55678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC---ceeEEEEecCHHHHHHHHHhc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL---TPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      .++++++++++++++||++.+.+++++||.++|+|.....    ..+..++...+.   .++..+++++.+.+.+++.+|
T Consensus       158 ~~l~~~~~~~~~~~~~~~~~~~~i~~~dL~~~p~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  233 (297)
T PRK11139        158 EKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSR----EDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG  233 (297)
T ss_pred             EEeccceeEEEeCHHHhcccCCCCCHHHhhcCceEeecCc----ccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC
Confidence            9999999999999999988888899999999999987653    244567766665   456678899999999999999


Q ss_pred             cceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         238 MGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       238 ~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .|++++|.+.+... ..+.++ .++++.. ..+.++++|++++..+++++.|++++.+.++++
T Consensus       234 ~gi~~lp~~~~~~~~~~~~l~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~  295 (297)
T PRK11139        234 QGVALGNRVLAQPEIEAGRLV-CPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQE  295 (297)
T ss_pred             CCeEecchhhhHHHHHCCcee-cccccCcCCCccEEEEeccccccChhHHHHHHHHHHHhhcc
Confidence            99999999887665 445554 5555532 357899999999999999999999999887654

>PRK11482 putative DNA-binding transcriptional regulator; Provisional

Probab=100.00  E-value=3.5e-52  Score=342.97  Aligned_cols=287  Identities=17%  Similarity=0.162  Sum_probs=244.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|++++++++++++++
T Consensus        29 m~l~~L~~f~av~e~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v-~lT~~G~~l~~~~~~~l~~l~~~  106 (317)
T PRK11482         29 IDLNLLTIFEAVYVHK-GIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGV-TPTAYATHLHEYISQGLESILGA  106 (317)
T ss_pred             cchhHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCcceEecCCCc-cCCHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999887


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+....  ....|.|+||++++++..++++++..|.+.||++.++..  .+.++.+.|.+|++|++|...+ ...+++.+
T Consensus       107 ~~~~~~--~~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~--~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~  181 (317)
T PRK11482        107 LDITGS--YDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI--PISDAENQLSQFQTDLIIDTHS-CSNRTIQH  181 (317)
T ss_pred             hCCCcC--CCCCceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe--cchhHHHHHHCCCcCEEEeccC-CCCCceEE
Confidence            654332  234689999999999999999999999999999988754  4457899999999999998655 56688999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++.. .++++||.++|++...........+.+++......+++.+.+++..++..++.+|.|+
T Consensus       182 ~~l~~~~~~lv~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gv  260 (317)
T PRK11482        182 HVLFTDNVVLVCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASSDML  260 (317)
T ss_pred             EEEecCcEEEEEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcCCee
Confidence            999999999999999999864 6899999998754433222211233455555555677889999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      +++|...+... ..+.+..+++.+.. ..++++++|++++..+|.+++|++++++++
T Consensus       261 ~ilp~~~~~~~~~~~~l~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~  317 (317)
T PRK11482        261 GIMPSRFYNLFSRCWPLEKLPFPSLNEEQIDFSLHYNKLSLRDPVLENVIDVIRNAF  317 (317)
T ss_pred             EEeHHHHHHHHHhhCCceEecCCCCCCCCeEEEEEecccccCCcHHHHHHHHHHHhC
Confidence            99999887654 45678888886532 457999999999999999999999998753

>PRK10632 transcriptional regulator; Provisional

Probab=100.00  E-value=3.8e-53  Score=348.34  Aligned_cols=286  Identities=17%  Similarity=0.229  Sum_probs=246.4

Q ss_pred             Cc-hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           1 MN-LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         1 m~-~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      |+ +++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.+++
T Consensus         1 ~~~l~~L~~F~~v~e~g-S~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~i-~lT~~G~~l~~~a~~il~~~~~   78 (309)
T PRK10632          1 MERLKRMSVFAKVVEFG-SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSI-GLTEAGRIYYQGCRRMLHEVQD   78 (309)
T ss_pred             CcchHHHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeecccCCCc-eechhHHHHHHHHHHHHHHHHH
Confidence            66 99999999999999 999999999999999999999999999999999999999 8999999999999999999999


Q ss_pred             HHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760          80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI  159 (306)
Q Consensus        80 ~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~  159 (306)
                      +.+.++.......|.++||++++++..++++++..|.+.||++.+++...+..   ..+.+|++|++|+..+ ...+++.
T Consensus        79 ~~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~l~~~~~~---~~l~~~~~Dl~i~~~~-~~~~~l~  154 (309)
T PRK10632         79 VHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPA---PDLIADGLDVVIRVGA-LQDSSLF  154 (309)
T ss_pred             HHHHHHhccCCCceEEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEecCcc---cCcccCCeeEEEEecC-CCCCCeE
Confidence            99999988777789999999999999999999999999999999999886542   4678899999998654 5567899


Q ss_pred             eeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHH
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYV  234 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v  234 (306)
                      ..+++++++++|++++| ++.. .+++++||.++|++.+.......   ...+...+    ..++..+++++...++++|
T Consensus       155 ~~~l~~~~~~~v~~~~~-l~~~~~~~~~~~L~~~~~i~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V  230 (309)
T PRK10632        155 SRRLGAMPMVVCAAKSY-LAQYGTPEKPADLSSHSWLEYSVRPDNE---FELIAPEGISTRLIPQGRFVTNDPQTLVRWL  230 (309)
T ss_pred             EEEEeccceEEEECHHH-HHhCCCCCCHHHHhhCCeEEecCCCCCc---ceEecCCCeEEEEecCCeEEECCHHHHHHHH
Confidence            99999999998887654 6543 47899999999999986532111   12233333    2456688999999999999


Q ss_pred             Hhccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         235 ELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       235 ~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      .+|.|++++|...+... ..+.++.++.+.....+.+|++|+++...++.++.|++++++.++
T Consensus       231 ~~g~Gv~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~  293 (309)
T PRK10632        231 TAGAGIAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV  293 (309)
T ss_pred             HcCCcEEEcCHHHHHHHHhcCCeEEeCCCccCCCCcEEEEecCCCCCcHHHHHHHHHHHHHHH
Confidence            99999999999877655 567787776655455789999999999999999999999988874

>PRK13348 chromosome replication initiation inhibitor protein; Provisional

Probab=100.00  E-value=8.2e-52  Score=338.89  Aligned_cols=288  Identities=12%  Similarity=0.114  Sum_probs=246.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|+||.+|+++| ||++||++||+||||||++|++||++||++||+|+ +++ +||++|+.|++++++++...+++
T Consensus         2 m~l~~L~~f~~v~~~g-s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R~-r~i-~lT~~G~~l~~~a~~~~~~~~~~   78 (294)
T PRK13348          2 LDYKQLEALAAVVETG-SFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPC-RPTPAGQRLLRHLRQVALLEADL   78 (294)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeecC-CCC-ccChhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 99999999999999999999999999999999997 688 89999999999999998888888


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...... .....|+++||++++....++++.+..|... |++++++...++.++.+.|.+|++|++|...+ ...+++.+
T Consensus        79 ~~~~~~-~~~~~g~l~I~~~~~~~~~~~~~~l~~~~~~-~~i~i~~~~~~~~~~~~~L~~~~~d~~i~~~~-~~~~~~~~  155 (294)
T PRK13348         79 LSTLPA-ERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQP-KPMRGCLA  155 (294)
T ss_pred             HHHHHh-hcCCceEEEEEecchhHHHHHHHHHHHHHhC-CCeEEEEEEcchHHHHHHHhcCCeEEEEecCC-cccCCccc
Confidence            776654 4567799999998766777888999999876 89999999999999999999999999998543 44578999


Q ss_pred             eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      .++++++++++++++|+... ...++++||.++|+|.++.+....+.+...+...+..+.+..++++...+.++|.+|.|
T Consensus       156 ~~l~~~~~~~v~~~~~~~~~~~~~v~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  235 (294)
T PRK13348        156 EPLGTMRYRCVASPAFAARYFAQGLTRHSALKAPAVAFNRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHAHLAAIRHGLG  235 (294)
T ss_pred             ccccccceEEEEccchhhhhccCCCCHHHHcCCCEEEecCCchHHHHHHHHHHhccccccceEEeCcHHHHHHHHHcCCe
Confidence            99999999999999997543 46799999999999998876655444444443334445667789999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      ++++|.+++... ..+.++.++.   ...++++++|++++..+|.+++|++++++...+
T Consensus       236 i~~lp~~~~~~~~~~~~l~~l~~---~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~~  291 (294)
T PRK13348        236 YGMVPELLIGPLLAAGRLVDLAP---GHPVDVALYWHHWEVESPTMEALSQRVVEAARR  291 (294)
T ss_pred             eEeCCHHHHHHHHhcCeeeecCC---CCCCCceeEEeeccccChHHHHHHHHHHHHHHH
Confidence            999999988755 5556665542   246789999999999999999999999987654

>TIGR03298 argP transcriptional regulator, ArgP family

Probab=100.00  E-value=1.1e-51  Score=337.90  Aligned_cols=287  Identities=16%  Similarity=0.177  Sum_probs=250.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++++| ||++||++||+||||||++|++||++||++||+|+ +++ +||++|+.|++++++++...+.+
T Consensus         1 m~l~~l~~f~~v~~~~-s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~-r~~-~lT~~G~~l~~~~~~il~~~~~~   77 (292)
T TIGR03298         1 LDYRQLAALAAVVEEG-SFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPC-RATEAGQRLLRHARQVRLLEAEL   77 (292)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCchheecC-CCC-cCCHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 99999999999999999999999999999999996 798 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+........|.|+||+++.....++++++..|.+++ ++.+++...++.++.+.|.+|++|++|...+ ...+++.+
T Consensus        78 ~~~~~~~~~~~~g~l~i~~~~~~~~~~l~~~l~~~~~~~-~i~i~l~~~~~~~~~~~l~~g~~d~~i~~~~-~~~~~l~~  155 (292)
T TIGR03298        78 LAELPGLAPGAPVTLSIAVNADSLATWFLPALAPVLAQE-GVLLDLVVEDQDHTAELLRSGEVLGAVTTQA-KPVQGCRV  155 (292)
T ss_pred             HHHHHhhhccCCceEEEecccchhhhhhHHHHHHHHhCC-CceEEEEeCcchhHHHHHhCCCceEEEecCC-CCCCCceE
Confidence            988888777778999999987777788999999999986 8999999999889999999999999998654 55678999


Q ss_pred             eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      .++++++++++++++|+... ...++++||.++|+|.+..+...+. .+...+...+ .+ +.+++++.+.+.++|..|.
T Consensus       156 ~~l~~~~~~~v~~~~~~~~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~v~~g~  233 (292)
T TIGR03298       156 VPLGAMRYLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQDRFLRRLFGLPV-SP-PRHYVPSSEGFVEAARAGL  233 (292)
T ss_pred             EecCCceEEEEECchhhhhccCCCCCHHHhcCCCEEEeCCCCccHHHHHHHHhcCCC-CC-CeEecCCHHHHHHHHHhCC
Confidence            99999999999999987542 3579999999999999987765543 4444554433 34 3589999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      |++++|...+... ..+.++.++.+   ...+++++|++++..+|.+++|++++++..++
T Consensus       234 Gi~~~p~~~~~~~~~~~~l~~~~~~---~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  290 (292)
T TIGR03298       234 GWGMVPELQAEPHLAAGRLVDLAPG---RALDVPLYWHHWRLESRVLERLTDALVAAARR  290 (292)
T ss_pred             CeEeCcHHHHHHHHhcCCeEEecCC---CCCCceEEEeccCCCChHHHHHHHHHHHHHhh
Confidence            9999999888765 55666666532   35688999999999999999999999887654

ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).

>PRK03601 transcriptional regulator HdfR; Provisional

Probab=100.00  E-value=1.2e-51  Score=333.94  Aligned_cols=269  Identities=17%  Similarity=0.191  Sum_probs=238.5

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|.+|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         1 m~~~~l~~f~~v~~~g-s~s~AA~~L~isqpavS~~I~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (275)
T PRK03601          1 MDTELLKTFLEVSRTR-HFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNI-RLTAAGERLLPYAETLMNTWQAA   78 (275)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCceEEECCCce-EECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+.+...  ...|.++||++.++...++++++..|.+.||++++++....+.++.+.|.+|++|++|+... ...+++.+
T Consensus        79 ~~~~~~~--~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~  155 (275)
T PRK03601         79 KKEVAHT--SQHNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTEA-PKMDEFSS  155 (275)
T ss_pred             HHHHhhc--ccCceEEEeccHHHHHHHHHHHHHHHHHhCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCC-CccCCccE
Confidence            9888753  34689999999999999999999999999999999999999999999999999999998644 55678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||+.          .++|++....+...+......+ ..+  +.+.+++++...+.+++.+|.|+
T Consensus       156 ~~l~~~~~~~v~~~~~~~~----------~~~~~i~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~v~~g~gv  222 (275)
T PRK03601        156 QLLGHFTLALYTSAPSKKK----------SELNYIRLEWGADFQQHEAGLI-GAD--EVPILTTSSAELARQLLATLNGC  222 (275)
T ss_pred             EEecceeEEEEecCchhhc----------ccCCeEEccCCccHhHHHHHhc-ccC--CcceEEeCcHHHHHHHHHhCCCE
Confidence            9999999999999999853          3678998887766654433333 333  34578999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      +++|...+..  .++++.++... ....++|++|+++...+|.++.|.+.
T Consensus       223 ~~~p~~~~~~--~~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~  269 (275)
T PRK03601        223 AFLPVHWAKE--KGGLHTVPDST-TLSRPLYAIWLQNSDKQALIRDLLKT  269 (275)
T ss_pred             EEEcHHHHhh--cCCeEEcCCCc-cceeeeEEEeecCCccchHHHHHHhh
Confidence            9999988764  46788887643 45789999999999999999999875

>PRK03635 chromosome replication initiation inhibitor protein; Validated

Probab=100.00  E-value=1.5e-51  Score=336.93  Aligned_cols=287  Identities=15%  Similarity=0.161  Sum_probs=248.9

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++|+| ||++||++||+||||+|++|++||++||++||+|+ +|+ +||++|+.|+++++++++..+.+
T Consensus         2 m~~~~L~~f~~v~e~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~-~~~-~lT~~G~~l~~~a~~~~~~~~~~   78 (294)
T PRK03635          2 LDYKQLEALAAVVREG-SFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPC-RPTEAGQRLLRHARQVRLLEAEL   78 (294)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeecC-CCC-ccCHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 99999999999999999999999999999999997 798 79999999999999999999888


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.... ..|.|+||+++++...++++.+..|.++ |++++++......++.+.+.+|++|++|+..+ ...+++.+
T Consensus        79 ~~~~~~~~~-~~g~l~I~~~~~~~~~~l~~~l~~f~~~-~~i~i~l~~~~~~~~~~~l~~~~~d~~i~~~~-~~~~~l~~  155 (294)
T PRK03635         79 LGELPALDG-TPLTLSIAVNADSLATWFLPALAPVLAR-SGVLLDLVVEDQDHTAELLRRGEVVGAVTTEP-QPVQGCRV  155 (294)
T ss_pred             HHHHhcccc-cceEEEEeecchhHHHHHHHHHHHHHhC-CCcEEEEEecCcHHHHHHHhCCCceEEEeccC-CCCCCcee
Confidence            887777666 7899999999877888999999999986 79999999998889999999999999998644 45578999


Q ss_pred             eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHH-HHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKL-DREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      .++++++++++++++||... ..+++++||.++|||.+..+...+..+ .+++... ..+++.+++++..+++++|..|.
T Consensus       156 ~~l~~~~~~lv~~~~~~~~~~~~~~~~~~l~~~~~I~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~  234 (294)
T PRK03635        156 DPLGAMRYLAVASPAFAARYFPDGVTAEALAKAPAVVFNRKDDLQDRFLRQAFGLP-PGSVPCHYVPSSEAFVRAALAGL  234 (294)
T ss_pred             eecccceEEEEEcchHHHhhccCCCCHHHHhhCCeEeecCCCchHHHHHHHhhccC-cccCceeecCCHHHHHHHHHhCC
Confidence            99999999999999998543 256899999999999998776655433 3455443 23567899999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      |++++|.+.+... ..+.++.++  . .....++++|+++...++.+++|++++++..++
T Consensus       235 gi~~lp~~~~~~~~~~~~l~~l~--~-~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~~  291 (294)
T PRK03635        235 GWGMIPELQIEPELASGELVDLT--P-GRPLDVPLYWQHWRLESRLLDRLTDALLAAAAQ  291 (294)
T ss_pred             CeEeCcHHHHhhhhccCceeecC--C-CCCCCceeeeeeeccCCHHHHHHHHHHHHHHHh
Confidence            9999999988765 455555443  2 235688999999999999999999999987654

>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional

Probab=100.00  E-value=1.5e-51  Score=340.47  Aligned_cols=290  Identities=13%  Similarity=0.089  Sum_probs=251.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ .||++|+.+++.++.+++..+++
T Consensus         8 mdl~~L~~f~av~e~g-s~t~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~~~~~~~~   85 (319)
T PRK10216          8 LDLNLLLCLQLLMQER-SVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGL-SPTPLMVSMEQNLAEWMQMGNQL   85 (319)
T ss_pred             cCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEEecCCCc-ccCHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999988888


Q ss_pred             HHHHHhhccCCCC-cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-----
Q psy3760          81 KKIGKEFSAYDTG-NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-----  154 (306)
Q Consensus        81 ~~~~~~~~~~~~~-~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-----  154 (306)
                      .+....  ....+ .++||++++++..++++++..|.+.||++++++...+. ...+.|.+|++|++|+..+...     
T Consensus        86 ~~~~~~--~~~~~~~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~  162 (319)
T PRK10216         86 LDKPHH--QTPRGLKFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDY-DSLDAITRGEVDIGFTGRESHPRSREL  162 (319)
T ss_pred             hccccC--CCccCCEEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCc-chHHHHhcCCccEEEecCCCCcccccc
Confidence            753221  23456 79999999999999999999999999999999998755 4789999999999998543211     


Q ss_pred             ----CCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHH
Q psy3760         155 ----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDII  230 (306)
Q Consensus       155 ----~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (306)
                          +..+...+++.++++++++++||+.. .+++++||.++|||.+..+......++.++...|..|++.+++++..++
T Consensus       163 ~~~~~~~~~~~~l~~~~~~~v~~~~hp~~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (319)
T PRK10216        163 LSLLPLAIDFEVLFSDLPCVWLRKDHPALH-EEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQS  241 (319)
T ss_pred             ccccccccceeeeeecceEEEEeCCCCccC-CCCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHH
Confidence                23578899999999999999999765 4799999999999999776555667889999999999999999999999


Q ss_pred             HHHHHhc--cceeeeecceecc-c-ccCCceeeecCCCC-----ccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         231 KTYVELR--MGIGIIASIAFDS-N-RDKNLRSISASHLF-----GTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       231 ~~~v~~g--~gi~~~p~~~~~~-~-~~~~l~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      ..++..|  .|++++|.+.... . ..++++.+|++.+.     ..++++++|++++..+|.+++|++.+++.+.
T Consensus       242 ~~~v~~~~~~gi~ilp~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~  316 (319)
T PRK10216        242 LFMAAQPDHLLLATAPRYCQYYNQLHQLPLVALPLPFDESQQKKLEVPFTLLWHKRNSHNPKIVWLRETIKNLYA  316 (319)
T ss_pred             HHHHHcCCcceEeccHHHHHHHHhhcCCceEecCCCCCcccccccceeEEEEeCCccCCCHHHHHHHHHHHHHHH
Confidence            9999985  5899999975431 1 33468888776432     3568999999999999999999999988764

>PRK14997 LysR family transcriptional regulator; Provisional

Probab=100.00  E-value=1.8e-52  Score=343.88  Aligned_cols=289  Identities=14%  Similarity=0.192  Sum_probs=243.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|++++++++..++++
T Consensus         2 ~~l~~L~~f~~va~~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   79 (301)
T PRK14997          2 TDLNDFAWFVHVVEEG-GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQF-NVTEVGQTFYEHCKAMLVEAQAA   79 (301)
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeeccCcc-eEcHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~  159 (306)
                      ...+++......|.|+||++++++..++++++..|.++||++++++...+..  . .+.+|++|++|+..+. ...+++.
T Consensus        80 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~--~-~~~~~~~Dl~i~~~~~~~~~~~~~  156 (301)
T PRK14997         80 QDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRR--V-DVVGEGVDVAIRVRPRPFEDSDLV  156 (301)
T ss_pred             HHHHHhccCCCceeEEEECcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCCc--c-ccccccccEEEEecCCcCCCCCce
Confidence            9999888777889999999999999999999999999999999999876543  3 3557889999986432 2457799


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHH
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~  235 (306)
                      ..++++++++++++++|+...+.+++++||.++|++....+.... .+ ..+...+    ..+.+.+.+++..++.++|.
T Consensus       157 ~~~l~~~~~~l~~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  234 (301)
T PRK14997        157 MRVLADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIH-RW-ELYGPQGARAEVHFTPRMITTDMLALREAAM  234 (301)
T ss_pred             EEEccccceEEEECHHHHHhCCCCCCHHHHhcCCceeecCCCCCC-ce-eEecCCCceEEEeCCCcEEECCHHHHHHHHH
Confidence            999999999999999997554567899999999999986654321 11 1111112    12344568899999999999


Q ss_pred             hccceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         236 LRMGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       236 ~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      +|.|++++|.+.+... ..+.++.+ +++.. ....+|++|+++...+|.++.|++++++.+.+
T Consensus       235 ~G~Gi~~~p~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~  297 (301)
T PRK14997        235 AGVGLVQLPVLMVKEQLAAGELVAV-LEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYAR  297 (301)
T ss_pred             hCCCEEECcHHHHHHHHHcCCeEEe-CCCccCCCCcEEEEECCCCccCHHHHHHHHHHHHHHHH
Confidence            9999999999988765 56677754 44322 23468999999999999999999999887644

>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor

Probab=100.00  E-value=6.8e-53  Score=344.89  Aligned_cols=284  Identities=20%  Similarity=0.167  Sum_probs=245.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      .|+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         1 ~~l~~L~~f~~v~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   78 (291)
T TIGR03418         1 LSLQALRVFESAARLA-SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGI-ELTEDGQRLFEAVRAGLDTIDLA   78 (291)
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCce-eEcHhHHHHHHHHHHHHHHHHHH
Confidence            3799999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+.++..  ...|.++||++++++..++++++..|.+.||++.+++...+.  .. .+.+|++|++|...+ ...+++..
T Consensus        79 ~~~~~~~--~~~g~l~ig~~~~~~~~~l~~~l~~~~~~~p~i~i~~~~~~~--~~-~~~~~~~D~~i~~~~-~~~~~~~~  152 (291)
T TIGR03418        79 TAQLRAR--REHETLTLATDFAFATYWLMPRLHRFKRAMPDVDVSLVTSQD--SL-DPQRDDIDVAILFGD-GRWPGGEA  152 (291)
T ss_pred             HHHHhcC--CCCceEEEeccHHHHHHHHhhhhHHHHHhCCCceEEEEecCC--cc-cccCCCCcEEEEeCC-CCCCCchH
Confidence            9988753  357899999999999999999999999999999999987543  23 457899999998654 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCce---eEEEEecCHHHHHHHHHh
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTP---YIVLETINSDIIKTYVEL  236 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~~  236 (306)
                      .++++++++++++++||++....++++||.++|+|.+..+..... .++.++...+..+   ...+++++...+..++..
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  232 (291)
T TIGR03418       153 HRLFSEEVTPVCSPALLAARATPLSAADLLRLPLLHLEPTQPARWFDWAGWFDAHGLERPPAPGGLTFNNYTLVIQAAIG  232 (291)
T ss_pred             hHhhcchhhhcCCHHHHhhcCCCCChhHHhhCCEEeeccccCCCCccHHHHHHHcCCCcccCCCCeeeccHHHHHHHHHh
Confidence            999999999999999998877789999999999999876544332 3678888888754   347889999999999999


Q ss_pred             ccceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         237 RMGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       237 g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      |.|++++|...+... ..+.++ .++++.. ....+|++|++++..+|+++.|++++++
T Consensus       233 g~gi~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~  290 (291)
T TIGR03418       233 GQGVALGWAPLVDELLEAGQLV-RLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDWLLD  290 (291)
T ss_pred             CCceEEechHhhHHHHhCCccc-ccCCcccCCCCcEEEEeCchhhcChHHHHHHHHHhc
Confidence            999999999776554 444444 5555433 3579999999999999999999999865

Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.

>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional

Probab=100.00  E-value=7.6e-52  Score=340.93  Aligned_cols=286  Identities=18%  Similarity=0.187  Sum_probs=242.5

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|+||++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ +||++|+.|+++|+++++.++++
T Consensus        14 ~~l~~L~~f~~va~~g-s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~-~LT~~G~~l~~~a~~~l~~~~~~   91 (311)
T PRK10086         14 WQLSKLHTFEVAARHQ-SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKV-ELTEEGKRVFWALKSSLDTLNQE   91 (311)
T ss_pred             CcHHHHHHHHHHHHcC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCeeEEEcCCCc-ccCHhHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999 999999999999999999999999999999999999999 89999999999999999999988


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+..  ....|.++||++.+++..++++++..|.+.||++.+++...+...   .+.+|++|++|+..+ ...+++.+
T Consensus        92 ~~~~~~--~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~i~~~~~~~~~---~l~~~~~Di~i~~~~-~~~~~l~~  165 (311)
T PRK10086         92 ILDIKN--QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENV---NFQRAGIDLAIYFDD-APSAQLTH  165 (311)
T ss_pred             HHHHHh--cCCCceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEeCCccc---CCccCCccEEEEeCC-CCCCCceE
Confidence            776653  345789999999999999999999999999999999998876542   688999999998654 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecC----CCCcHHHHHHHHHhCCCc---eeEEEEecCHHHHHHH
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL----SFSGRIKLDREFSLQKLT---PYIVLETINSDIIKTY  233 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~----~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~  233 (306)
                      .++++++++++++++|+.......++.||.++|++....    +... ..+..++...++.   ++..+.+++...+..+
T Consensus       166 ~~l~~~~~~lv~~~~~~~~~~l~~~~~~l~~~~li~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (311)
T PRK10086        166 HFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGT-DEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIA  244 (311)
T ss_pred             EEeecccEEEecCHHHHhhcCCCCCHHHHHhchhhcccccccccccc-cchHHHHHhcCCCcccCCCCceeccHHHHHHH
Confidence            999999999999998653222234689999999987541    1122 3455666777765   4668899999999999


Q ss_pred             HHhccceeeeecceeccc-ccCCceeeecCCC--CccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         234 VELRMGIGIIASIAFDSN-RDKNLRSISASHL--FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       234 v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      +.+|.|++++|...+... ..+.++ +++++.  .....+|++|+++ ..+|.++.|++++++.++.
T Consensus       245 v~~G~Gi~~lp~~~~~~~~~~g~l~-~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~fi~~l~~~~~~  309 (311)
T PRK10086        245 AMNHIGVAMGRKRLVQKRLASGELV-APFGDMEVKCHQHYYVTTLPG-RQWPKIEAFIDWLKEQVKT  309 (311)
T ss_pred             HHhCCceEeecHHhHHHHHhCCcee-cccCCCccCCCCcEEEEeCCc-cCCHHHHHHHHHHHHHhhc
Confidence            999999999999887765 555565 577653  2467899999999 8999999999999887653

>PRK10082 cell density-dependent motility repressor; Provisional

Probab=100.00  E-value=1.5e-50  Score=332.40  Aligned_cols=285  Identities=17%  Similarity=0.196  Sum_probs=244.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++.++++++++
T Consensus        11 m~~~~l~~F~av~e~g-S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~e~~   88 (303)
T PRK10082         11 IETKWLYDFLTLEKCR-NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPL-QLSEQGKIFHSQIRHLLQQLESN   88 (303)
T ss_pred             cchHHHHHHHHHHhcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEecCCCC-ccCHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~  159 (306)
                      .+.+.+......|.|+||+..+++..++++++..|..   .+.+.+....+.++.+.+.+|++|++|+..+.. ..+++.
T Consensus        89 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~---~~~~~~~~~~~~~~~~~l~~g~~Dlai~~~~~~~~~~~~~  165 (303)
T PRK10082         89 LAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPP---LFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFD  165 (303)
T ss_pred             HHHHHhhccccCceEEEEecchhHHHHhHHHHHhhhh---hceEEEecCCHHHHHHHHHCCCCCEEEEecCccccccCee
Confidence            9988887777789999999999999999999998874   456777777888999999999999999864422 246799


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC-CceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK-LTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      +.+++.++++++++++||.  .+.... ++.++|++.+..+...+..+..+++..+ +.++..+.+++...+..++.+|.
T Consensus       166 ~~~l~~~~~~~v~~~~~~~--~~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  242 (303)
T PRK10082        166 HIRLFESQLFPVCASDEHG--EALFNL-AQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGC  242 (303)
T ss_pred             EEEecceeEEEEecCCccC--Cccccc-ccCCCceEEeCCCccHHHHHHHHHhhhcccceeeEEEechHHHHHHHHHcCC
Confidence            9999999999999998863  222233 3588999998877666666777777765 67777788888889999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      |++++|.+.+... ..++++.++++.......++ +|++++..++++++|++++++.
T Consensus       243 Gi~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~f~~~~~~~  298 (303)
T PRK10082        243 GIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAY-AYRMNTRMNPVAERFWRELREL  298 (303)
T ss_pred             CEEEcChHHHHHHHHcCCEEEecCCccceeEEEE-EEecccccCHHHHHHHHHHhhc
Confidence            9999999887655 56789988876533334454 6999988999999999999874

>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional

Probab=100.00  E-value=4.7e-50  Score=328.84  Aligned_cols=277  Identities=17%  Similarity=0.178  Sum_probs=243.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      |++++|++|++|+++| ||++||++|++||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus        11 m~l~~L~~F~~v~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~~~~-~LT~~G~~l~~~a~~il~~~~~~   88 (310)
T PRK15092         11 LDLDLLRTFVAVADLN-TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNK-LLTEHGIQLLGYARKILRFNDEA   88 (310)
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEECCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999998


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+.  .....|.|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+   .+++..
T Consensus        89 ~~~~~--~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~g~~Di~i~~~~---~~~~~~  163 (310)
T PRK15092         89 CSSLM--YSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHR---PSSFPA  163 (310)
T ss_pred             HHHhc--CCCceeEEEEeCChHHHHHHHHHHHHHHHHHCCCcEEEEEECCcHHHHHHHhCCCeeEEEEecC---CCCCCc
Confidence            87764  3457889999999999999999999999999999999999998889999999999999998643   234566


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++..++++++++++||+....        ..|++....+...+..+..++...+..+++.+++++..++.++|.+|.|+
T Consensus       164 ~~l~~~~~~~~~~~~~~l~~~~--------~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi  235 (310)
T PRK15092        164 LNLRTSPTLWYCAAEYVLQKGE--------PIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGV  235 (310)
T ss_pred             eEeeecCcEEEecCCCCCCCCC--------ceeEEecCCCChHHHHHHHHHHHcCCCeeEEEEcCCHHHHHHHHHcCceE
Confidence            6788889999999999876432        34889888777777788889998898999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCC--CCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         241 GIIASIAFDSNRDKNLRSISASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      +++|...+.    ++++.+++..  +.....++++|+++...++.++.|++++++...
T Consensus       236 ~~lp~~~~~----~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~  289 (310)
T PRK15092        236 TARPVEMMS----PDLRVLGESEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMESYHN  289 (310)
T ss_pred             EEcchhhcC----ccceecccccCCCCCCCeEEEEEECCCcCCHHHHHHHHHHHHHhc
Confidence            999987653    3566665532  223457899999999999999999999988753

>TIGR02036 dsdC D-serine deaminase transcriptional activator

Probab=100.00  E-value=1.1e-50  Score=332.67  Aligned_cols=284  Identities=18%  Similarity=0.185  Sum_probs=236.7

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus         8 ~~l~~L~~F~~va~~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   85 (302)
T TIGR02036         8 FQLSKMHTFEVAARHQ-SFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKV-ELTHEGKRIYWALKSSLDTLNQE   85 (302)
T ss_pred             cCHHHHHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCceEEECCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999998


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+.  .....|.|+||++.+++..++++++..|.++||++.+++...+..   ..+.++++|++|+..+ ...+++.+
T Consensus        86 ~~~~~--~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~---~~l~~~~~Dl~i~~~~-~~~~~l~~  159 (302)
T TIGR02036        86 ILDIK--NQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNEN---INFQGAGIDVAIYFDD-APPAKLTC  159 (302)
T ss_pred             HHHHH--hCCCCCeEEEEechHHHHHHHHHHHHHHHHHCCCceEEEEeCCcc---cccccCCccEEEEcCC-CCCCCcee
Confidence            87665  244578999999999999999999999999999999999876642   2467789999998654 45678999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec----CCCCcHHHHHHHHHhC---CCceeEEEEecCHHHHHHH
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD----LSFSGRIKLDREFSLQ---KLTPYIVLETINSDIIKTY  233 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~  233 (306)
                      .++++++++++++++|+.....+.+++||.++|||...    .+.... .+..|....   +..++..+.+++...+..+
T Consensus       160 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (302)
T TIGR02036       160 HFIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTD-EWHSWANHYAVNNLPTSSGIGFDRSDLAVIA  238 (302)
T ss_pred             EEeecCcEEEEECHHHHhhccCCCCHHHHhCCCceeeccccccCCCCC-chHHHHHHcCCCccCcCCCceecChHHHHHH
Confidence            99999999999999986333345799999999999764    222222 233344432   2334556788999999999


Q ss_pred             HHhccceeeeecceeccc-ccCCceeeecCCC--CccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         234 VELRMGIGIIASIAFDSN-RDKNLRSISASHL--FGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       234 v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      +.+|.|++++|.+++... ..+.++. ++++.  ....++|++|+++. .+|.++.|++++++.+
T Consensus       239 v~~g~Gi~~lp~~~~~~~~~~g~l~~-~l~~~~~~~~~~~~lv~~~~~-~~~~~~~fi~~l~~~~  301 (302)
T TIGR02036       239 AMNNAGVAMGRKSLVQKRLASGELVA-PFGDMTVKCHQRYYVATLPNR-QNPKIELFIIWLREQV  301 (302)
T ss_pred             HHhCCcEEEechHhHHHHHHCCCEEc-ccCCcCCCCCCcEEEEeCCCc-CChHHHHHHHHHHHhh
Confidence            999999999999887655 6777775 45442  24568999999986 4899999999997653

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

>COG0583 LysR Transcriptional regulator [Transcription]

Probab=100.00  E-value=1.3e-47  Score=315.11  Aligned_cols=290  Identities=27%  Similarity=0.394  Sum_probs=253.8

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++|++||||+|++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus         1 ~~l~~L~~F~~v~~~~-s~t~AA~~L~isqsavS~~I~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (297)
T COG0583           1 MDLRQLRAFVAVAEEG-SFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRV-RLTEAGERLLERARRILAELEEA   78 (297)
T ss_pred             CcHHHHHHHHHHHHcC-cHHHHHHHhCCCChHHHHHHHHHHHHhCchheeecCCce-eeCHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999998 79999999999999999999999


Q ss_pred             HHHHHhhccCCC-CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-Cc
Q psy3760          81 KKIGKEFSAYDT-GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-KL  158 (306)
Q Consensus        81 ~~~~~~~~~~~~-~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-~~  158 (306)
                      ............ +.++||+++++...++++++..|.+.||++.+.+...+  .+.+.+.+|++|++|...+. ..+ ++
T Consensus        79 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~l~~~~~~~P~~~~~~~~~~--~~~~~l~~~~~D~~i~~~~~-~~~~~~  155 (297)
T COG0583          79 LAEAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARYPEIELELGTSD--RLLEDLVEGELDLAIRAGPP-PPPDGL  155 (297)
T ss_pred             HHHHHHHhccCCCceEEEEecchhhhhhhHHHHHHHHHhCCCeEEEeCchH--HHHHHHHcCCCCEEEecCCC-CCCCce
Confidence            987776554444 59999999999988999999999999996666665543  47889999999999997653 333 89


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ...+++.++++++++++||+..+..  ++++...+++........+......+...+..+...+.+++..++++++.+|.
T Consensus       156 ~~~~l~~~~~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  233 (297)
T COG0583         156 VARPLFSEELVLVVPASHPLAARHG--LPDLPGEPLILLEHGCILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAGL  233 (297)
T ss_pred             EEEEcccceEEEEecCCCCCccccc--HHHHhcCCEEecCCCccHHHHHHHHHHHcCCCccceeeecCHHHHHHHHHcCC
Confidence            9999999999999999999988765  89999999999998888888888888888777778889999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      |++++|..++... ....+..++...+.....+|++|+++...++.+++|++++++.+..
T Consensus       234 gi~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  293 (297)
T COG0583         234 GIALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALAR  293 (297)
T ss_pred             CcEECcHHHhhccCCcCceEEeeccCCCCceeEEEEEeCCccCCHHHHHHHHHHHHhhhc
Confidence            9999999988776 3245667777663444459999998656799999999999987654

>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional

Probab=100.00  E-value=2.9e-47  Score=308.67  Aligned_cols=266  Identities=20%  Similarity=0.299  Sum_probs=238.7

Q ss_pred             hCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcEEEEecccchh
Q psy3760          26 LYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQAR  105 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~  105 (306)
                      ||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++.+.++.......|.++||+++.++.
T Consensus         1 L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~   79 (269)
T PRK11716          1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSV-TLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAY   79 (269)
T ss_pred             CCcChHHHHHHHHHHHHHhCCeeEEecCCce-eECHhHHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEEEecchHHH
Confidence            7999999999999999999999999999999 899999999999999999999999999887778899999999999999


Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecCCCCCCC-CCCc
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL-LNSI  184 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~l~~-~~~i  184 (306)
                      .++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+....+++...+++.++++++++++||+.. ....
T Consensus        80 ~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~  159 (269)
T PRK11716         80 SHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPCPVRQQLSQ  159 (269)
T ss_pred             HHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceEEEEcccceEEEEEcCCcchhhhcccc
Confidence            999999999999999999999999999999999999999999865433356689999999999999999997543 3456


Q ss_pred             ChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCC
Q psy3760         185 SLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASH  263 (306)
Q Consensus       185 ~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~  263 (306)
                      +..++.++|++....+ ..+..+..+++..++.+++.+++++...+++++.+|.|++++|.+++... ..+.++.++++.
T Consensus       160 ~~~~l~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~  238 (269)
T PRK11716        160 EKPDWSRIPFILPEHG-PARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLLPEVVLENSPVRNRVQILERVP  238 (269)
T ss_pred             chhhHhhCCeeecCCC-chHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcCCCeEeccHHHhhcCcccCCeeeccCCC
Confidence            8889999999987554 34567788999999999999999999999999999999999999988665 556788888876


Q ss_pred             CCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         264 LFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       264 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .....+++++|++++..+|.+++|+++++.
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  268 (269)
T PRK11716        239 PITPFELGVCVQKKRLEEPLIDAFWQLLEN  268 (269)
T ss_pred             CCCcceEEEEEccccCcCHHHHHHHHHHhc
Confidence            556679999999999999999999999875

>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []

Probab=100.00  E-value=6e-33  Score=216.19  Aligned_cols=207  Identities=24%  Similarity=0.352  Sum_probs=194.3

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~  168 (306)
                      ++.+|+|+||+++++...++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.+++++++
T Consensus         2 ~~~~~~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~   80 (209)
T PF03466_consen    2 QGERGTLRIGASPSFASSLLPPLLAEFRERHPNIRIEIREGDSDELIEALRSGELDLAITFGP-PPPPGLESEPLGEEPL   80 (209)
T ss_dssp             CTSEEEEEEEEEHHHHHHTHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSS-SSSTTEEEEEEEEEEE
T ss_pred             CccceEEEEEEEhHHHHHHHHHHHHHHHHHCCCcEEEEEeccchhhhHHHhcccccEEEEEee-ccccccccccccceee
Confidence            356789999999999999999999999999999999999999999999999999999999765 5889999999999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++++||++.+++++++||.++|++.+..+...+..+.+++...++.++..+++++..++..++.+|.|++++|.+++
T Consensus        81 ~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  160 (209)
T PF03466_consen   81 VLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASGDGIAILPDSLA  160 (209)
T ss_dssp             EEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTTSEBEEEEHHHH
T ss_pred             eeeeeccccccccccchhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccccceeecCcccc
Confidence            99999999999999999999999999999988889999999999999999999999999999999999999999999998


Q ss_pred             ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      ... ..++++.+++++.....+++++|++++..+|.+++|++++++.++
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  209 (209)
T PF03466_consen  161 QDELESGELVFLPLPDPPLPRPIYLVWRKDRPLSPAIQWFIDLLREHFA  209 (209)
T ss_dssp             HHHHHCTTEEEEEESSSTEEEEEEEEEETTGTTHHHHHHHHHHHHHHH-
T ss_pred             cccccCCCEEEEECCCCCCceEEEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            665 789999999998555689999999999999999999999998763

This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....

>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=1.7e-29  Score=195.20  Aligned_cols=198  Identities=49%  Similarity=0.866  Sum_probs=177.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++++++..++++++..|+++||++++++....++++.+.|.+|++|++|+.......+++...++++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~~~~   80 (198)
T cd08444           1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELVSFPYYDWHHHIIVP   80 (198)
T ss_pred             CeEEeecchhhhhhhhHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCcEEeeccccceeEEec
Confidence            48999999999999999999999999999999999999999999999999999986442345789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+.+++++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+.+.....
T Consensus        81 ~~hpl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~~  160 (198)
T cd08444          81 VGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRD  160 (198)
T ss_pred             CCCccccCCCcCHHHHhCCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcCCcEEeccHHHHhhhhc
Confidence            99999887889999999999999887766777788899999999999999999999999999999999999988765444


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.+++.+......+|++|++++..++.++.|++++
T Consensus       161 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~  198 (198)
T cd08444         161 TNLIKLDTSHLFGKNTTWIALRRGGDLRNFAYRFIELC  198 (198)
T ss_pred             CceEEeecCCCccceeEEEEEcCCCccCHHHHHHHhhC
Confidence            67888888665556799999999999999999999864

Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati

>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold

Probab=99.97  E-value=1.9e-29  Score=194.97  Aligned_cols=198  Identities=52%  Similarity=0.955  Sum_probs=178.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|........+++.+.++++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~   80 (198)
T cd08413           1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVTLPCYRWNHCVIVP   80 (198)
T ss_pred             CeEEeecchhhhhhccHHHHHHHHhCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcEEEEeeeeeEEEEec
Confidence            48999999999999999999999999999999999998899999999999999986443346789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.++.++++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+.+.....
T Consensus        81 ~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~~  160 (198)
T cd08413          81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRD  160 (198)
T ss_pred             CCCcccccCCCCHHHHhcCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhCCCEEEccccccCcccc
Confidence            99999988889999999999999887766677788899999999999999999999999999999999999987765456


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.+++.+......++++|+++...++.++.|++++
T Consensus       161 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~  198 (198)
T cd08413         161 ADLVALDAGHLFGPNTTRIALRRGTYLRSYAYDFIELF  198 (198)
T ss_pred             CcEEEeecCCcCcceeEEEEEeehhhhhHHHHHHHhhC
Confidence            78999999875566789999999999999999999863

CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi

>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=4.2e-29  Score=192.77  Aligned_cols=197  Identities=17%  Similarity=0.215  Sum_probs=178.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (198)
T cd08421           1 HVRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGN-VDAAGLETRPYRTDRLVVVVP   79 (198)
T ss_pred             CEEEEeccchhhhhhHHHHHHHHHHCCCceEEEEecCcHHHHHHHhcCCceEEEEecC-CCCCCcEEEEeecCcEEEEeC
Confidence            4899999999999999999999999999999999988889999999999999999654 556789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++.+..++++||.++|++.+..+...+..+.++++..+..+++.+++++...+..++.+|.|++++|...+... .
T Consensus        80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~  159 (198)
T cd08421          80 RDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYAR  159 (198)
T ss_pred             CCCCccccCCCCHHHhcCCceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcCCCeEEccchhhhhhcc
Confidence            999998888899999999999999877777777888888899999999999999999999999999999999888754 6


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .++++.+++.+.....+++++|++++..++.++.|++++
T Consensus       160 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (198)
T cd08421         160 ALGLRVVPLDDAWARRRLLLCVRSFDALPPAARALVDHL  198 (198)
T ss_pred             cCCeEEEeccCCcccceEEEEEeCCCcCCHHHHHHHhhC
Confidence            788999988765456789999999999999999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi

>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily

Probab=99.97  E-value=4.8e-29  Score=192.81  Aligned_cols=198  Identities=18%  Similarity=0.287  Sum_probs=179.3

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++....++++++++++
T Consensus         1 g~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~   79 (200)
T cd08411           1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALP-VDEPGLEEEPLFDEPFLLAV   79 (200)
T ss_pred             CeEEEEecHHHHhhhhHHHHHHHHHHCCCcEEEEEeCcHHHHHHHHHcCCccEEEEecc-CCCCCceEEEeeccceEEEe
Confidence            57999999999999999999999999999999999998999999999999999998654 44578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc-c
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS-N  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~  251 (306)
                      +++||++.+..++++||.++|++.+..+...++.+..++...+..++..+++++...+.+++..|.|++++|...+.. .
T Consensus        80 ~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  159 (200)
T cd08411          80 PKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPSEE  159 (200)
T ss_pred             cCCCCccccCccCHHHHcCCceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCCEEEeCHHHhcccc
Confidence            999999888889999999999999887766777888899999998999999999999999999999999999998876 3


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.+..+++++.....+++++|+++...++.++.|++++
T Consensus       160 ~~~~~l~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  200 (200)
T cd08411         160 LRGDRLVVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI  200 (200)
T ss_pred             cCCCceEEEECCCCCcceEEEEEEcCCccCCHHHHHHHhhC
Confidence             5667888888765556799999999999999999999874

OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre

>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold

Probab=99.97  E-value=1.6e-29  Score=195.69  Aligned_cols=200  Identities=14%  Similarity=0.127  Sum_probs=179.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++.+++..++++++..|.+.||++.+++....+.++.+.|.+|++|++|...+ ..++++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~~   79 (201)
T cd08459           1 TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLP-DLGAGFFQQRLFRERYVCLVR   79 (201)
T ss_pred             CeEEEeChHHHHHHHHHHHHHHHHHCCCCeEEEEecCccCHHHHhhCCCceEEEEcCC-CCcccceEEEeecCceEEEEc
Confidence            4899999999999999999999999999999999998889999999999999998654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++.+. ++++||.++|++.+..+...+..+.+++...++.++..+++++..++.+++.+|.|++++|.+.+... .
T Consensus        80 ~~~~l~~~~-i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  158 (201)
T cd08459          80 KDHPRIGST-LTLEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFAR  158 (201)
T ss_pred             CCCccccCC-cCHHHHhhCCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcCCEEEecHHHHHHHHhh
Confidence            999988665 99999999999998876556667888999999999999999999999999999999999999887655 5


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .++++.++++......+++++|+++...+|.+++|++.+++.|
T Consensus       159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (201)
T cd08459         159 AGGLRIVPLPFPLPPFEVKLYWHRRFHRDPGNRWLRQLVAELF  201 (201)
T ss_pred             cCCeeEecCCCCCCCceEEEEEccccCCChHHHHHHHHHHhhC
Confidence            6789999887755678999999999999999999999998764

This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o

>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=5.5e-29  Score=192.14  Aligned_cols=197  Identities=18%  Similarity=0.243  Sum_probs=179.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (198)
T cd08433           1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGP-PPIPGLSTEPLLEEDLFLVGP   79 (198)
T ss_pred             CeEEEechhhhhhcchHHHHHHHHHCCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCC-CCCCCeeEEEeccccEEEEec
Confidence            4899999999999999999999999999999999988889999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++.+..++++||.++|++....+...+..+.++++..+..++..+++++...+.+++..|.|++++|...+... .
T Consensus        80 ~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~  159 (198)
T cd08433          80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA  159 (198)
T ss_pred             CCCccccCCCCCHHHhCCCceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcCCcEEEcchhhhhhhhh
Confidence            999998777899999999999998877667778889999999999999999999999999999999999999888765 6


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .++++.++++......+++++|+++...+|.++.|++++
T Consensus       160 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  198 (198)
T cd08433         160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL  198 (198)
T ss_pred             cCceEEEECCCCCcceEEEEEEcCCCCCCHHHHHHHHhC
Confidence            788999998765567899999999999999999999864

The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.

>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold

Probab=99.97  E-value=7.8e-29  Score=191.35  Aligned_cols=196  Identities=21%  Similarity=0.302  Sum_probs=176.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~v~  172 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+.... ...+++...+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~~~~l~~~~~~~~~   80 (198)
T cd08437           1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSALHSKIIKTQHFMIIV   80 (198)
T ss_pred             CeEEeeChHHHHHHhHHHHHHHHHhCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccceEEEeecceEEEEe
Confidence            48999999999999999999999999999999999999999999999999999986431 24578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      +++||++.+..++++||.++|++....+...+..++.++...|..+++.+++++..++.+++.+|.|++++|...+..  
T Consensus        81 ~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~--  158 (198)
T cd08437          81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKP--  158 (198)
T ss_pred             cCCCcccccCcccHHHHcCCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcCCcEEEEEhhhccC--
Confidence            999999988889999999999999887766677788889999999999999999999999999999999999987743  


Q ss_pred             cCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .++++.+++++ ....++++++|+++...++.++.|++++
T Consensus       159 ~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (198)
T cd08437         159 DDHLVAIPLLDNEQPTFYISLAHRKDQLLTPAQKKLLDLL  198 (198)
T ss_pred             CCCeEEEEccCCcccCeEEEEEEcCccCCCHHHHHHHhhC
Confidence            67788888876 4557899999999999999999998864

MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom

>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold

Probab=99.97  E-value=6.9e-29  Score=191.86  Aligned_cols=198  Identities=17%  Similarity=0.256  Sum_probs=177.8

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~  172 (306)
                      +|+||++++++..++++++..|.++||++++++...++.++.+.+.+|++|++|+..+.. ..+++...+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~~~   80 (201)
T cd08435           1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA   80 (201)
T ss_pred             CeEEEechHHHHHHHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcEEEEcccCcEEEEE
Confidence            489999999999999999999999999999999999899999999999999999864422 2578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-eeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-PYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++||++.+..++++||.++|++.+..+...+..+.++++..+.. +++.+++++..++.+++.+|.|++++|.+++...
T Consensus        81 ~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  160 (201)
T cd08435          81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE  160 (201)
T ss_pred             eCCCcCcccCCcCHHHHhcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcCCeEEEeEHHHhhhh
Confidence            999999988889999999999999988777777888999999986 6788999999999999999999999999988765


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..++++.+++++......++++|++++..++.+++|++++
T Consensus       161 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  201 (201)
T cd08435         161 LRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL  201 (201)
T ss_pred             hccCceEEecccCCCCcccEEEEEcCCCCCCHHHHHHHHhC
Confidence             6778998888765567799999999998999999999874

Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma

>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=6.9e-29  Score=191.23  Aligned_cols=197  Identities=18%  Similarity=0.307  Sum_probs=178.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++.+++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (197)
T cd08438           1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFDSQPLCNEPLVAVLP   79 (197)
T ss_pred             CeEEEecchhhhhhcHHHHHHHHHHCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEecc-cccCCceeEEeccccEEEEec
Confidence            4899999999999999999999999999999999999999999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+..++++||.++|++.+..+...+..+.+++...+..++..+++++...+++++.+|.|++++|.+.+.....
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~  159 (197)
T cd08438          80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN  159 (197)
T ss_pred             CCCChhhccccCHHHHcCCCeEEECCCccHHHHHHHHHHHcCCCCCEEEeeCCHHHHHHHHHcCCceEEechhhHhhhcc
Confidence            99999988889999999999999987776677788889999999999999999999999999999999999988764456


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.+++.+......++++|+++...++.++.|++++
T Consensus       160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  197 (197)
T cd08438         160 AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL  197 (197)
T ss_pred             CCeEEEEcCCCCceEEEEEEEeCCCcCCHHHHHHHhhC
Confidence            67999998765566799999999988899999998864

This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate

>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold

Probab=99.97  E-value=8.6e-29  Score=191.27  Aligned_cols=197  Identities=46%  Similarity=0.840  Sum_probs=178.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++++++..++++++..|.+.||++++++...++.++.+.+.+|++|++|........+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~~   80 (198)
T cd08443           1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITLPCYHWNRCVVVK   80 (198)
T ss_pred             CEEEeeccceeeeECcHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCceEeeeeeceEEEEEc
Confidence            48999999999999999999999999999999999999999999999999999986442345789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+.+++++||.++|++.++.+...+..++.++...++.++..+++++..++.+++.+|.|++++|.+.......
T Consensus        81 ~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~~p~~~~~~~~~  160 (198)
T cd08443          81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDD  160 (198)
T ss_pred             CCCccccCCCCCHHHHhcCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcCCcEEEeecccccccCC
Confidence            99999988889999999999999987766677788899999999999999999999999999999999999987755456


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      ++++.+++.+......++++|+++...++.+++|++.
T Consensus       161 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (198)
T cd08443         161 PDLVIRDARDLFPWSVTKIAFRRGTFLRSYMYDFIQR  197 (198)
T ss_pred             CCEEEEEcccccCceeeeeEEEcCCcCCHHHHHHHhh
Confidence            6899999987666778999999999999999999874

CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci

>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold

Probab=99.97  E-value=4.3e-29  Score=193.02  Aligned_cols=198  Identities=15%  Similarity=0.145  Sum_probs=179.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~~~~~i~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (200)
T cd08417           1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFP-ELPPGLRSQPLFEDRFVCVAR   79 (200)
T ss_pred             CeEEeccHHHHHHHHHHHHHHHHhhCCCeEEEeccCCHHHHHHHHHcCCCCEEEeecc-cCCCccchhhhhcCceEEEec
Confidence            4899999999999999999999999999999999999999999999999999999755 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++. ..++++||.++|++.+..+...++.+..++...++.+++.+++++..++++++..|.|++++|...+... .
T Consensus        80 ~~~~~~~-~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  158 (200)
T cd08417          80 KDHPLAG-GPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAE  158 (200)
T ss_pred             CCCcccc-cccCHHHHhCCCeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcCCeeeeccHHHHHhhcc
Confidence            9999987 7799999999999998877667788899999999999999999999999999999999999999887665 4


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .++++.++++...+...++++|++++..++.+++|++.+++
T Consensus       159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (200)
T cd08417         159 RLGLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAE  199 (200)
T ss_pred             cCCcEEecCCCCCCcceeEEEeccccccChHHHHHHHHHhh
Confidence            67888888876555689999999999899999999998875

This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate

>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=1.5e-28  Score=189.20  Aligned_cols=197  Identities=22%  Similarity=0.342  Sum_probs=177.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||+++++...++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (197)
T cd08440           1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCP   79 (197)
T ss_pred             CeEEEeccchhhhHHHHHHHHHHHhCCCcEEEEEeCChHHHHHHHHcCCccEEEEeCC-CCCCCeeEEEeecccEEEEec
Confidence            4899999999999999999999999999999999988889999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.++.++++||.++|++.+..+...+..+.+++...++.++..+.+++..++.+++.+|.|++++|.+.+.....
T Consensus        80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  159 (197)
T cd08440          80 KDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADH  159 (197)
T ss_pred             CCCCcccCCccCHHHHccCCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCeEEEcchhHHHHhhc
Confidence            99999887789999999999999887766777788899999999999999999999999999999999999987653356


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.++++.......++++|+++...++.+++|++++
T Consensus       160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  197 (197)
T cd08440         160 PGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL  197 (197)
T ss_pred             CceEEEEcCCCccceEEEEEEcCCCcCCHHHHHHHHhC
Confidence            77898988765567799999999998999999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct

>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=1.9e-28  Score=189.27  Aligned_cols=197  Identities=23%  Similarity=0.308  Sum_probs=177.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++...++.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (199)
T cd08426           1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSP-PPEPGIRVHSRQPAPIGAVVP   79 (199)
T ss_pred             CeEEEecHHHHHHHHHHHHHHHHHhCCCeEEEEEeCCcHHHHHHHHCCCccEEEecCC-CCCCCeEEEeeccCcEEEEec
Confidence            4899999999999999999999999999999999998899999999999999998644 455789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++..+.++++||.++|++.+..+...+..+..++...+..+++.+++++...+.+++.+|.|++++|.+.+... .
T Consensus        80 ~~hpl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  159 (199)
T cd08426          80 PGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIR  159 (199)
T ss_pred             CCCCcccCCccCHHHHhCCCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcCCCEEEEchHhhhHhhh
Confidence            999998888899999999999998877667777888999999999999999999999999999999999999887655 6


Q ss_pred             cCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .++++.+++++.. ...+++++|+++...++.++.|++++
T Consensus       160 ~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  199 (199)
T cd08426         160 RGQLVAVPLADPHMNHRQLELQTRAGRQLPAAASAFLQLL  199 (199)
T ss_pred             cCcEEEEEcCCcccCceEEEEEEcCCCCCCHHHHHHHHhC
Confidence            7789999888643 34689999999999999999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi

>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily

Probab=99.97  E-value=2.9e-28  Score=187.98  Aligned_cols=196  Identities=22%  Similarity=0.375  Sum_probs=175.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (198)
T cd08412           1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDL-DLPEDIAFEPLARLPPYVWLP   79 (198)
T ss_pred             CEEEecccccchhhhHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCC-CCCcccceeeeeccceEEEec
Confidence            4899999999999999999999999999999999999999999999999999999654 456889999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc-c-
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS-N-  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~-  251 (306)
                      ++||++.++.++++||.++|++....+. .+..+.+++...++.+++.+++++..++.+++.+|.|++++|.+.+.. . 
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  158 (198)
T cd08412          80 ADHPLAGKDEVSLADLAAEPLILLDLPH-SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSY  158 (198)
T ss_pred             CCCCCCCCCcCCHHHHcCCcEEecCchh-HHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcCCCEEEeeccccccccc
Confidence            9999988778999999999999986643 455677889999999999999999999999999999999999988875 3 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ..+.++.+|++.......++++|++++..+|.+++|++++
T Consensus       159 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (198)
T cd08412         159 DGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA  198 (198)
T ss_pred             CCCceEEeecCCccccEEEEEEEecCCCCCHHHHHHHhhC
Confidence            5678999998765566799999999999999999999864

This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll

>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=2.4e-28  Score=188.43  Aligned_cols=195  Identities=21%  Similarity=0.338  Sum_probs=175.7

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.++||+++++...++++++..|.++||++++++......++.+.|.+|++|++|+..+ ...+++...+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~   79 (197)
T cd08425           1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAP-VRSPDIDAQPLFDERLALVV   79 (197)
T ss_pred             CeEEEEechhhhhhhhHHHHHHHHHHCCCcEEEEEECcHHHHHHHHHcCCccEEEEecC-CCCCCcEEEEeccccEEEEe
Confidence            57999999999999999999999999999999999988889999999999999998654 55678999999999999999


Q ss_pred             cCCCCCCCCC-CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLN-SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~-~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++||++... .++++||.++|++.+......+..+..++...+..+++.+++++..++.+++.+|.|++++|...+.. 
T Consensus        80 ~~~~pl~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-  158 (197)
T cd08425          80 GATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIARE-  158 (197)
T ss_pred             cCCCchhHhcccCCHHHHhcCCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcCCcEEeechhhhcc-
Confidence            9999998765 49999999999999887766777788999999999999999999999999999999999999988754 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                       .++++.+++........++++|++++..++.++.|+++
T Consensus       159 -~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (197)
T cd08425         159 -QPGLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAAL  196 (197)
T ss_pred             -cCCeEEEECCCCCcCceEEEEEcCCcccCHHHHHHHhh
Confidence             46788888876555678999999999899999999875

CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding

>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold

Probab=99.97  E-value=3.2e-28  Score=187.12  Aligned_cols=195  Identities=21%  Similarity=0.387  Sum_probs=175.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~v~~   79 (195)
T cd08434           1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPV-PDEPDIEWIPLFTEELVLVVP   79 (195)
T ss_pred             CeEEEecchhhhhhhHHHHHHHHHhCCCeEEEEecCcHHHHHHHHHcCCccEEEEccC-CCCCCeeEEEeecceEEEEec
Confidence            4899999999999999999999999999999999999999999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+.+++++||.++|++....+...+..+.+++...+..++..+++++..++.+++.+|.|++++|.+.+.  ..
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~--~~  157 (195)
T cd08434          80 KDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLL--NP  157 (195)
T ss_pred             CCCccccCCccCHHHhcCCceEEecCCccHHHHHHHHHHHcCCccceEEEEccHHHHHHHHHcCCceEEecchhhh--CC
Confidence            9999988888999999999999987766666677888888898888889999999999999999999999998872  35


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.++++.......++++|+++...++.+++|++++
T Consensus       158 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  195 (195)
T cd08434         158 PGVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV  195 (195)
T ss_pred             CceEEEECCCCCccEEEEEEEcCCcccCHHHHHHHHhC
Confidence            67888998865566789999999999999999999874

GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,

>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=3.7e-28  Score=186.73  Aligned_cols=194  Identities=20%  Similarity=0.294  Sum_probs=175.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+....+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~~~~   80 (194)
T cd08436           1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVA   80 (194)
T ss_pred             CEEEEeehHHHHHHHHHHHHHHHHHCCCcEEEEecCCHHHHHHHHHcCCccEEEEecCCCCCCCcEEEEeecceEEEEec
Confidence            48999999999999999999999999999999999988899999999999999986553256889999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+..++++||.++|++.+..+...+..+..++...+..++..+++++...+.+++.+|.|++++|.+.+.  ..
T Consensus        81 ~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~--~~  158 (194)
T cd08436          81 PDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAA--RL  158 (194)
T ss_pred             CCCcccCCCccCHHHHhCCCeEEecCcccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcCCceEEecchhhc--CC
Confidence            9999988878999999999999988776667788889998998888999999999999999999999999998874  36


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.++++ .....+++++|+++.. ++.++.|++++
T Consensus       159 ~~l~~~~~~-~~~~~~~~l~~~~~~~-~~~~~~~~~~~  194 (194)
T cd08436         159 PGLAALPLE-PAPRRRLYLAWSAPPP-SPAARAFLELL  194 (194)
T ss_pred             CCeEEEecC-CcceEEEEEEEeCCCC-CHHHHHHHhhC
Confidence            789988887 4667899999999999 99999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi

>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold

Probab=99.97  E-value=2.9e-28  Score=187.63  Aligned_cols=196  Identities=23%  Similarity=0.279  Sum_probs=176.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (196)
T cd08415           1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP-LDHPGLESEPLASGRAVCVLP   79 (196)
T ss_pred             CeEEEecccccccccHHHHHHHHHHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCC-CCCCcceeeeecccceEEEEc
Confidence            4899999999999999999999999999999999999999999999999999999654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++..+.++++||.++|++....+...+..+.+++...+..++..+++++...+.+++.+|.|++++|.+++.....
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  159 (196)
T cd08415          80 PGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAG  159 (196)
T ss_pred             CCCChHhcCccCHHHhcCCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcCCCeEEechhhhhcccC
Confidence            99999888889999999999999987766677888899999999999999999999999999999999999988765445


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ++++.+|+.. ....+++++|+++...+|.+++|+++|
T Consensus       160 ~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  196 (196)
T cd08415         160 AGLVVRPFRP-AIPFEFALVRPAGRPLSRLAQAFIDLL  196 (196)
T ss_pred             CCeEEeecCC-CcceEEEEEEecCccCCHHHHHHHHhC
Confidence            5788888876 346789999999998999999999864

This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa

>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold

Probab=99.97  E-value=9e-29  Score=191.21  Aligned_cols=198  Identities=13%  Similarity=0.077  Sum_probs=178.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (200)
T cd08464           1 TFRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFG-ELPAWLKREVLYTEGYACLFD   79 (200)
T ss_pred             CEEEEechHHHHHHHHHHHHHHHHHCCCcEEEEecCCcccHHHHHhcCcccEEEecCC-CCcccceeeeecccceEEEEe
Confidence            4899999999999999999999999999999999998889999999999999999654 456889999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||+.. .+++++||.++|++....+...+..+.+++...|+.++..+++++..++..++.+|.|++++|.+.+... .
T Consensus        80 ~~~~~~~-~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  158 (200)
T cd08464          80 PQQLSLS-APLTLEDYVARPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAWAA  158 (200)
T ss_pred             CCCcccc-CCCCHHHHhcCCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCCCceeecHHHHHHHhhh
Confidence            9998764 6799999999999998776666667889999999999999999999999999999999999999988765 5


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .++++.++++.......++++|+++...++.+++|++.+++
T Consensus       159 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~  199 (200)
T cd08464         159 ALGLRASPPPLDLPEFPISLLWHARTDNDPALVWLREQIVQ  199 (200)
T ss_pred             cCCceeecCCCCCCCceEEEEEcccccCCchHHHHHHHHhh
Confidence            67899888876555679999999999999999999998875

This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra

>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold

Probab=99.97  E-value=2e-28  Score=189.95  Aligned_cols=199  Identities=15%  Similarity=0.115  Sum_probs=178.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      .++||+++++...++++++..|.++||++.+++... .++++.+.|.+|++|++|...+ ...+++...+++++++++++
T Consensus         1 ~~~Ig~~~~~~~~~~~~~l~~~~~~~P~~~v~~~~~~~~~~l~~~L~~g~lDl~i~~~~-~~~~~l~~~~l~~~~~~lv~   79 (203)
T cd08463           1 TFRIAAPDYLNALFLPELVARFRREAPGARLEIHPLGPDFDYERALASGELDLVIGNWP-EPPEHLHLSPLFSDEIVCLM   79 (203)
T ss_pred             CEEEEechhhHHHHhHHHHHHHHHHCCCCEEEEEeCCcchhHHHHHhcCCeeEEEeccc-cCCCCcEEeEeecCceEEEE
Confidence            489999999999999999999999999999999985 4578999999999999998544 45577999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCC-CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSF-SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++||++.+..++++||.++|++.+..+. ..+..+.++++..++.+++.+++++..++.+++.+|+|++++|...+...
T Consensus        80 ~~~h~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~v~~~~~i~~~p~~~~~~~  159 (203)
T cd08463          80 RADHPLARRGLMTLDDYLEAPHLAPTPYSVGQRGVIDSHLARLGLKRNIVVTVPYFGLAPYMLAQSDLVFTTGRHFAEHY  159 (203)
T ss_pred             eCCCCcccCCCCCHHHHhhCCcEEEEcCCCCCCchHHHHHHHcCCCceEEEEeChHHHHHHHHhCCCeeEecHHHHHHHh
Confidence            99999988888999999999999986543 45677888999999999999999999999999999999999999887665


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                       ..++++.++++......+++++|++++..+|++++|++.+++
T Consensus       160 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~  202 (203)
T cd08463         160 AKLLPLAVVDAPIEFPRMRYYQLWHERSHRSPEHRWLRRLVAS  202 (203)
T ss_pred             hhhcCceEeCCCCCCCCeeEEEeecccccCChHHHHHHHHHhh
Confidence             567899999887666789999999999999999999999875

This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra

>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.3e-28  Score=187.25  Aligned_cols=197  Identities=27%  Similarity=0.414  Sum_probs=176.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||+++++...++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (201)
T cd08420           1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGP-VDHPDLIVEPFAEDELVLVVP   79 (201)
T ss_pred             CeEEeeccchhhhhhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEecCC-CCCcceEEEeecCccEEEEec
Confidence            4899999999999999999999999999999999999999999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC---CceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK---LTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      ++||++.+..++++||.++|++.+..+...+..+..++...+   ..+++.+++++..++.+++.+|.|++++|.+.+..
T Consensus        80 ~~~~~~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  159 (201)
T cd08420          80 PDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRK  159 (201)
T ss_pred             CCCCccccCccCHHHHhcCCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcCCCEEEeeHHHHHh
Confidence            999999888899999999999999887777777888888554   45678899999999999999999999999988765


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . ..++++.+++++......++++|+++...++.+++|++++
T Consensus       160 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  201 (201)
T cd08420         160 ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL  201 (201)
T ss_pred             hhcCCceEEEECCCCcceEEEEEEEecCCcCCHHHHHHHHhC
Confidence            5 6788999999865667799999999998999999999864

CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology

>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=3.5e-28  Score=188.01  Aligned_cols=199  Identities=20%  Similarity=0.237  Sum_probs=177.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~  172 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+.. ..+++.+.+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~   80 (201)
T cd08418           1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVA   80 (201)
T ss_pred             CEEEEechHHHHhhhHHHHHHHHHHCCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcceeEEeecCCceEEEe
Confidence            489999999999999999999999999999999999999999999999999999864422 2468999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      +++||+..  ..+++||.++|++....+...+..+.+++...+..+++.+++++...+.+++.+|.|++++|..++... 
T Consensus        81 ~~~~~~~~--~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  158 (201)
T cd08418          81 RKDHPLQG--ARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPL  158 (201)
T ss_pred             CCCCcccc--CCCHHHHcCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhCCEEEEeEHHHhhhhh
Confidence            99999875  359999999999998776666777888999999999999999999999999999999999999888765 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..++++.++++.......++++|+++...+|.+++|++.++++
T Consensus       159 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  201 (201)
T cd08418         159 DSFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY  201 (201)
T ss_pred             hcCCEEEecCCCCCCCCceEEEEecCCCCCHHHHHHHHHHHhC
Confidence            5788999988775566799999999988999999999998763

TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding

>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.7e-28  Score=186.78  Aligned_cols=196  Identities=16%  Similarity=0.150  Sum_probs=175.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|+++||++++++...+..++.+.+.+|++|++|...+ ...+++...++++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (196)
T cd08458           1 SLRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILA-GDYPGLTTEPVPSFRAVCLLP   79 (196)
T ss_pred             CeEEEEcchhhhhhhHHHHHHHHHHCCCcEEEEeccChHHHHHHHHcCCCCEEEEecc-CCCCCceEEEeccCceEEEec
Confidence            4899999999999999999999999999999999999989999999999999999654 455789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.++.++++||.++|++....+...+..+..+++..+..+++.+++++..++++++.+|.|++++|...+.....
T Consensus        80 ~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~l~~~~~~~~~~  159 (196)
T cd08458          80 PGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTADYYSA  159 (196)
T ss_pred             CCCccccCCccCHHHhCCCccEEecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCcEEEECchhhhhccC
Confidence            99999988889999999999999887777778888999999998899999999999999999999999999987755444


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +++..+++.. .....++++|+++...++.++.|++.+
T Consensus       160 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~f~~~~  196 (196)
T cd08458         160 NPVIQRSFDP-VVPYHFAIVLPTDSPPPRLVSEFRAAL  196 (196)
T ss_pred             CCeEEeeCCC-CceEEEEEEeeCCCCCCHHHHHHHhhC
Confidence            6788888864 345789999999988899999999864

This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an

>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.4e-28  Score=186.73  Aligned_cols=196  Identities=18%  Similarity=0.238  Sum_probs=175.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (196)
T cd08456           1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTL-HEPPGIERERLLRIDGVCVLP   79 (196)
T ss_pred             CeEEEecHHHHHhhHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecC-CCCCCeeEEEeeccCeEEEec
Confidence            4899999999999999999999999999999999999889999999999999998644 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+..++++||.++|++.+..+...+..++.++...++.+++.+++++..++++++..|.|++++|...+.....
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  159 (196)
T cd08456          80 PGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAA  159 (196)
T ss_pred             CCCchhccCccCHHHcCCCcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcCCeEEEeChhhhccccc
Confidence            99999888889999999999999887766677788899999999999999999999999999999999999987766534


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +++..++++. .....++++|+++...++.++.|++++
T Consensus       160 ~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  196 (196)
T cd08456         160 AGLVVRRFSP-AVPFEVSLIRPKHRPSSALVAAFSACL  196 (196)
T ss_pred             CCEEEeeCCC-CCcceEEEEecCCCCCCHHHHHHHhhC
Confidence            5688888875 346789999999988999999999864

LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational

>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2.5e-28  Score=188.61  Aligned_cols=196  Identities=19%  Similarity=0.271  Sum_probs=176.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc----CCCCCceeeccccceEE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL----SPSDKLISIPCYQWEYV  169 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~----~~~~~~~~~~l~~~~~~  169 (306)
                      +++||++++++..++++++..|.+.||++++++...++.++.+.+.+|++|++|+....    ...+++...++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~~~l~~~~~~   80 (200)
T cd08423           1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLD   80 (200)
T ss_pred             CEEEEehhHHHHHhhhHHHHHHHHhCCCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcEEEEeccCcEE
Confidence            48999999999999999999999999999999999988899999999999999986431    34678999999999999


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++++++||++.++.++++||.++|++....+...+..+.+++...+..++..+++++..++.+++.+|.|++++|.+.+.
T Consensus        81 ~~~~~~~p~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  160 (200)
T cd08423          81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALG  160 (200)
T ss_pred             EEecCCCCccccCCCCHHHhcCCceEEecCCchHHHHHHHHHHHcCCCCCeeeeeccHHHHHHHHHcCCCHhhhhhHHHH
Confidence            99999999998888999999999999988777677777888999999999999999999999999999999999998876


Q ss_pred             ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         250 SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       250 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . ..+++..++++.. ....++++|++++..++.++.|++++
T Consensus       161 ~-~~~~l~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~~  200 (200)
T cd08423         161 A-RPPGVVVRPLRPP-PTRRIYAAVRAGAARRPAVAAALEAL  200 (200)
T ss_pred             h-hcCCeEEEeCCCC-CceEEEEEEcCCcccChHHHHHHhhC
Confidence            5 5677888888765 66799999999998999999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi

>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold

Probab=99.96  E-value=1.1e-28  Score=190.88  Aligned_cols=198  Identities=12%  Similarity=0.055  Sum_probs=177.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+ ++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus         1 ~~~i~~~~~~~~~~l~~~l~~~~~~~P~v~v~l~~~~~-~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   78 (200)
T cd08460           1 TFTIRANDGFVAAFGPALLAAVAAEAPGVRLRFVPESD-KDVDALREGRIDLEIGVLG-PTGPEIRVQTLFRDRFVGVVR   78 (200)
T ss_pred             CEEEEechhHHHHHHHHHHHHHHHHCCCCEEEEecCch-hHHHHHHCCCccEEEecCC-CCCcchheeeeeccceEEEEe
Confidence            48999999999999999999999999999999998877 8899999999999998644 345679999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++.+ .++++||.++|++.+..+...+..+..++...+..+++.+++++..++.+++.+|.|++++|..++... .
T Consensus        79 ~~hpl~~~-~~~l~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  157 (200)
T cd08460          79 AGHPLARG-PITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGSDLIALVPERVTAAARA  157 (200)
T ss_pred             CCCCCCCC-CCCHHHHhcCCCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence            99999875 589999999999999877777778899999999999999999999999999999999999999887654 4


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .++++.++++.+....+++++|+++...++++++|.+.+++.
T Consensus       158 ~~~l~~~~~~~~~~~~~i~l~~~~~~~~~~~~~~l~~~~~~~  199 (200)
T cd08460         158 GLGLRTFPLPLELPAVTVSQAWHPRFDADPAHRWLRECVREV  199 (200)
T ss_pred             cCCceEECCCCCCCCeeeEEeEcCccccChHHHHHHHHHHHh
Confidence            577888888865567899999999999999999999988765

This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra

>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.1e-28  Score=186.94  Aligned_cols=196  Identities=22%  Similarity=0.366  Sum_probs=175.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++ +....++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~-~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~   78 (197)
T cd08419           1 RLRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP-PEDLDLVAEPFLDNPLVVIAP   78 (197)
T ss_pred             CEEEEEe-chhHhHhhHHHHHHHHHCCCceEEEEECCHHHHHHHHhcCCccEEEecCC-CCCCCeEEEEeccCCEEEEec
Confidence            4899999 77888999999999999999999999999999999999999999998644 445689999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++....++++||.++|++....+...+..+..++...+..+++.+++++..++.+++.+|.|++++|.+.+... .
T Consensus        79 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  158 (197)
T cd08419          79 PDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELA  158 (197)
T ss_pred             CCCCCcCCCCcCHHHHhCCCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhCCceEeecHHHHHHHHh
Confidence            999998877899999999999998877666777888999999999999999999999999999999999999887655 6


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+.++.++++.......++++|+++...++.+++|++++
T Consensus       159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  197 (197)
T cd08419         159 TGRLAVLDVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL  197 (197)
T ss_pred             hCCeEEEEcCCcceEEEEEEEEcCCCcCCHHHHHHHhhC
Confidence            778999888765556789999999988999999998864

CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t

>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2.1e-28  Score=189.42  Aligned_cols=197  Identities=17%  Similarity=0.148  Sum_probs=174.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.+.||++.+++..... ++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~i~~~~~~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   78 (200)
T cd08462           1 HFRIIASDYVITVLLPPVIERVAREAPGVRFELLPPDD-QPHELLERGEVDLLIAPER-FMSDGHPSEPLFEEEFVCVVW   78 (200)
T ss_pred             CEEEEecHHhHHHHHHHHHHHHHHHCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCC-CCCCCceeeeeeccceEEEEc
Confidence            48999999999999999999999999999999998766 9999999999999999654 455789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHH-HHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKL-DREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      ++||++. ..++++||.++|++.+..+...+..+ +.++...++.+++.+++++..++.+++.+|.|++++|.+.+... 
T Consensus        79 ~~hpl~~-~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~giailp~~~~~~~~  157 (200)
T cd08462          79 ADNPLVG-GELTAEQYFSAGHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGTNRIATLHRRLAEQFA  157 (200)
T ss_pred             CCCCccC-CCCCHHHHhhCCCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcCchhhhhHHHHHHhhh
Confidence            9999985 67999999999999987765544444 34568889999999999999999999999999999999888665 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ..+.++.++++......+++++|++++..++.+++|++.+++
T Consensus       158 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~  199 (200)
T cd08462         158 RRLPLRILPLPFPLPPMREALQWHRYRNNDPGLIWLRELIIE  199 (200)
T ss_pred             hcCCceEeCCCcCCCCeeEEEEEcccccCChHHHHHHHHHhc
Confidence            667799999886566789999999999999999999998875

The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T

>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=1.8e-28  Score=189.56  Aligned_cols=197  Identities=16%  Similarity=0.123  Sum_probs=175.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus         1 ~~~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~   79 (200)
T cd08466           1 TFNIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVP-FRDPSFKSELLFEDELVCVAR   79 (200)
T ss_pred             CEEEEechHHHHHHHHHHHHHHHHHCCCCEEEEecCchHhHHHHHHcCCccEEEeccc-CCCCCceeeeecccceEEEEe
Confidence            4899999999999999999999999999999999999989999999999999998654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC-ceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      ++||++. ..++++||.+++++.++.. .....+..++...+. .+++.+++++..++.+++.+|.|++++|..++... 
T Consensus        80 ~~~~~~~-~~~~~~~L~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~  157 (200)
T cd08466          80 KDHPRIQ-GSLSLEQYLAEKHVVLSLR-RGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYA  157 (200)
T ss_pred             CCCCCCC-CCcCHHHHhhCCcEEecCC-CCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCCCeehhhHHHHHHHhh
Confidence            9999875 4689999999999998743 344567888888888 78889999999999999999999999999888765 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ..++++.++++......+++++|++++..+|.+++|++.+++
T Consensus       158 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (200)
T cd08466         158 EQLNLQILPLPFKTKPIPLYMVWHKSRERDPAHQWLREQIKQ  199 (200)
T ss_pred             hcCCeeEecCCCCCCCccEEEEEcCCCCCChHHHHHHHHHhh
Confidence            567899888876555679999999999999999999998875

LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo

>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=3.9e-28  Score=187.89  Aligned_cols=197  Identities=14%  Similarity=0.088  Sum_probs=175.2

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecC
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPL  174 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~  174 (306)
                      ++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...+++++++++++++
T Consensus         2 ~~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~~   80 (200)
T cd08467           2 FTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFA-VPPDGLVVRRLYDDGFACLVRH   80 (200)
T ss_pred             eEEEechhhHHHHHHHHHHHHHhhCCCCEEEEecCCcccHHHHhhCCCcCEEEecCC-CCCccceeEEeeeccEEEEEcC
Confidence            799999999999999999999999999999999998889999999999999998643 3456799999999999999999


Q ss_pred             CCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-cc
Q psy3760         175 DHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RD  253 (306)
Q Consensus       175 ~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~  253 (306)
                      +||++.+ .++++||.++|++.+..+...+..+..+++..|+.+++.+++++..++.+++.+|.|++++|...+... ..
T Consensus        81 ~h~l~~~-~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~~  159 (200)
T cd08467          81 GHPALAQ-EWTLDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAM  159 (200)
T ss_pred             CCccccC-CCCHHHHhCCCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcCCeEEeeHHHHHHHHhhc
Confidence            9999865 589999999999999877666677888999999999999999999999999999999999999887654 44


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      +.++.++++.....++++++|+++...++..++|.+.|++
T Consensus       160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~i~~  199 (200)
T cd08467         160 LPLRVVPPPVDLGTFPVMLIWHERYQHDPAHRWLRKLIAA  199 (200)
T ss_pred             CCeeEecCCCCCCCeeEEEEecccccCChHHHHHHHHHhh
Confidence            6788787765445679999999999999999999998875

Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are

>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold

Probab=99.96  E-value=8.7e-28  Score=185.07  Aligned_cols=194  Identities=18%  Similarity=0.263  Sum_probs=174.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|+++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (197)
T cd08414           1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPP-PDPPGLASRPLLREPLVVALP   79 (197)
T ss_pred             CEEEEeeHHHHHHHHHHHHHHHHHHCCCcEEEEecCChHHHHHHHHcCCccEEEEcCC-CCCCCeeEEEEeeccEEEEec
Confidence            4899999999999999999999999999999999998899999999999999999654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++||+.....++++||.++|++.+..+.  ..+..+..++...+..++..+++++..++.+++.+|.|++++|...+.. 
T Consensus        80 ~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-  158 (197)
T cd08414          80 ADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARL-  158 (197)
T ss_pred             CCCccccCCccCHHHhccCCEEEecCCcchhHHHHHHHHHHHcCCCcccceecccHHHHHHHHHcCCcEEEccChhhhc-
Confidence            9999988888999999999999987763  4667888999999998888899999999999999999999999988765 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      ..+++..+++++.....+++++|+++.. ++.++.|+++
T Consensus       159 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~f~~~  196 (197)
T cd08414         159 QRPGVVYRPLADPPPRSELALAWRRDNA-SPALRAFLEL  196 (197)
T ss_pred             cCCCeEEEECCCCCcceEEEEEEecCCC-CHHHHHHHhh
Confidence            4567888888775567899999999988 9999999875

This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca

>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold

Probab=99.96  E-value=7e-28  Score=186.02  Aligned_cols=196  Identities=17%  Similarity=0.195  Sum_probs=175.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++.+++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (198)
T cd08441           1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDP-LPLPGIAYEPLFDYEVVLVVA   79 (198)
T ss_pred             CEEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCC-cCCCCcEEEEccCCcEEEEEc
Confidence            4899999999999999999999999999999999998889999999999999998654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++....++++||.++|++.+..+...+..+..++...++.++..+++++..++.+++.+|.|++++|...+... .
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  159 (198)
T cd08441          80 PDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLD  159 (198)
T ss_pred             CCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhCCcEEEeeHHHHHHHHh
Confidence            999998777899999999999998776666677888999999988888999999999999999999999999887665 6


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      .+.++.+++.++.....++++|+++...++.++.|++.
T Consensus       160 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~  197 (198)
T cd08441         160 QGLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLEL  197 (198)
T ss_pred             cCceEEEeccCCceEEEEEEEEEcCCcCChHHHHHHhh
Confidence            67899898865455679999999998889999999874

MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha

>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold

Probab=99.96  E-value=8.8e-28  Score=185.75  Aligned_cols=195  Identities=17%  Similarity=0.217  Sum_probs=172.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeeccccceEEEE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQWEYVII  171 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~~~~~~v  171 (306)
                      .|+||+.++++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+..  .++++...++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~l~~~~~~~v   80 (200)
T cd08453           1 RLSLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPALAYRPLLSEPLVLA   80 (200)
T ss_pred             CEEEEEechHHhHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcceeEEEeeeCceEEE
Confidence            489999999999999999999999999999999999888999999999999999864422  257899999999999999


Q ss_pred             ecCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         172 VPLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++++||++.++.++++||.++|++.++.+.  ..++.+..++...+..++..+++++..++++++.+|.|++++|.++..
T Consensus        81 ~~~~hp~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  160 (200)
T cd08453          81 VPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRN  160 (200)
T ss_pred             EECCCccccCCCCCHHHhccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcCCcEEEeEhHHhh
Confidence            999999998888999999999999987654  356778899999999999999999999999999999999999997753


Q ss_pred             ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         250 SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       250 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                       ...++++.+++++......++++|+++.. ++.+++|+++
T Consensus       161 -~~~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~  199 (200)
T cd08453         161 -LARPGVVYRELADPAPVLETGLVWRRDDA-SPVLARFLDL  199 (200)
T ss_pred             -cCCCceEEEECCCCCcceeEEEEEccccc-ChHHHHHHhh
Confidence             34577999998875556799999998875 9999999875

The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport

>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=1.1e-27  Score=183.91  Aligned_cols=192  Identities=21%  Similarity=0.351  Sum_probs=173.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (193)
T cd08442           1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGP-VEHPRLEQEPVFQEELVLVSP   79 (193)
T ss_pred             CeEEeccccchhhhhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCC-CCCCCcEEEEeecCcEEEEec
Confidence            4899999999999999999999999999999999999989999999999999998644 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||++.    +++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+++... .
T Consensus        80 ~~~~~~~----~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  155 (193)
T cd08442          80 KGHPPVS----RAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQG  155 (193)
T ss_pred             CCCcccc----cHHHhCCCceEEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhCCcEEEcCHHHHhhhhh
Confidence            9999763    6999999999999877777778889999999999999999999999999999999999999988765 5


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+.++.++++.......++++|++++. ++.+++|++++
T Consensus       156 ~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~  193 (193)
T cd08442         156 RGSVSIHPLPEPFADVTTWLVWRKDSF-TAALQAFLDLL  193 (193)
T ss_pred             cCceEEEecCCCCCceEEEEEEeCCCC-CHHHHHHHHhC
Confidence            678888888765556789999999998 99999999864

YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides

>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=1.2e-27  Score=184.32  Aligned_cols=195  Identities=17%  Similarity=0.210  Sum_probs=172.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~  172 (306)
                      +++||++++++..++++++..|.++||++++++....+.+..+.|.+|++|++|+..... ..+++...+++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~   80 (197)
T cd08449           1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASELLWREPMVVAL   80 (197)
T ss_pred             CeEEEEechHhhhhHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHhCCCccEEEecccccCCCCCceEEEEEEeeEEEEe
Confidence            489999999999999999999999999999999999899999999999999999854422 2678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecC-CCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDL-SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++||++.+..++++||.++|++.+.. +...+..+.+++...+..++..+++++..++.+++.+|.|++++|..++.. 
T Consensus        81 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-  159 (197)
T cd08449          81 PEEHPLAGRKSLTLADLRDEPFVFLRLANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYARL-  159 (197)
T ss_pred             cCCCCCCCCCCCCHHHHCCCCEEEecCCCchHHHHHHHHHHhCCCCCceeccCCchHhHHHHhhcCCcEEEchhhhhcc-
Confidence            999999888789999999999999876 344566778888889998888999999999999999999999999987754 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ..++++.+++++. ...+++++|+++.. ++.++.|++++
T Consensus       160 ~~~~l~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~  197 (197)
T cd08449         160 PWPGVRFIPLKQA-ISADLYAVYHPDSA-TPVIQAFLALL  197 (197)
T ss_pred             CcCCeEEEECCCC-CcceEEEEECCCCC-CHHHHHHHhhC
Confidence            3457888888875 67899999999887 99999998864

In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their

>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2e-27  Score=183.65  Aligned_cols=195  Identities=12%  Similarity=0.065  Sum_probs=172.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++.+++..++++++.+|.++||++.+++....+.++.+.|.+|++|++++... ...+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~-~~~~~~~~~~l~~~~~~lv~   79 (198)
T cd08486           1 GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFF-PRHPGIEIVNIAQEDLYLAV   79 (198)
T ss_pred             CeEEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCC-CCCCceEEEEEeeccEEEEe
Confidence            57999999999999999999999999999999999999999999999999999998643 55678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++||++.+..++++||.++|++.++.+.  ..+..+..++...|+.++..+++++..++.+++.+|.|++++|.+....
T Consensus        80 ~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~  159 (198)
T cd08486          80 HRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAI  159 (198)
T ss_pred             cCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCceEEEcchhhccc
Confidence            99999998889999999999999987654  3677888999999999999999999999999999999999999977643


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                       ..+++..+++.+.....+++++|++++. ++.+++|+++
T Consensus       160 -~~~~l~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  197 (198)
T cd08486         160 -RWPDIAFARIVGTRVKVPISCIFRKEKQ-PPILARFVEH  197 (198)
T ss_pred             -CCCCeEEEECcCCCCCceEEEEEcCCCC-ChHHHHHHhh
Confidence             2346888888764556799999988874 6788888875

This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha

>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.6e-28  Score=186.96  Aligned_cols=196  Identities=17%  Similarity=0.176  Sum_probs=175.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....++++.+.+.+|++|++|.... ...+++.+.++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~~~l~~~~~~lv~~   79 (198)
T cd08461           1 TLVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPE-YAPDGLRSRPLFEERYVCVTR   79 (198)
T ss_pred             CEEEEechHHHHHHhHHHHHHHHHHCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCc-cCCccceeeeeecCcEEEEEc
Confidence            4899999999999999999999999999999999988888999999999999998643 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecC-CCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDL-SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      ++||+.. ..+++++|.++|++.... +...+..+.+++...++.++..+++++..++++++.+|.|++++|...+... 
T Consensus        80 ~~~p~~~-~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~-  157 (198)
T cd08461          80 RGHPLLQ-GPLSLDQFCALDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAATDMVAFVPSRLVPNL-  157 (198)
T ss_pred             CCChhhc-CCCCHHHHhhCCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcCCeEEEchHHHHHhh-
Confidence            9999887 678999999999998765 4556677889999999988889999999999999999999999999887653 


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                       ++++.++++.......++++|++++..++.+++|++.+++
T Consensus       158 -~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (198)
T cd08461         158 -EGLQEVELPLEPPGFDVVMAWHERTHRDPAHRWLRELLAA  197 (198)
T ss_pred             -cCceeecCCCCCCCccEEEecChhhcCCHHHHHHHHHHhh
Confidence             6788888876556679999999998899999999998876

This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra

>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=1.4e-27  Score=185.11  Aligned_cols=198  Identities=16%  Similarity=0.091  Sum_probs=177.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeeccccceEEEE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQWEYVII  171 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~~~~~~v  171 (306)
                      +++||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+..  ..+++...++++++++++
T Consensus         1 ~~~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~~l~~~~~~~~   80 (202)
T cd08468           1 RFRFAVTDYTALAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEERDWWEDTYVVI   80 (202)
T ss_pred             CEEEEechHHHHHHhHHHHHHHHhhCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEEEEEEecCcEEEE
Confidence            489999999999999999999999999999999999999999999999999999864422  157899999999999999


Q ss_pred             ecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         172 VPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++++||++.  .++++||.++|++....+...+..+.++++..+..+++.+++++..++..++.+|.|++++|.+++...
T Consensus        81 ~~~~hpl~~--~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~p~~~~~~~  158 (202)
T cd08468          81 ASRDHPRLS--RLTLDAFLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASSDLLMTLPRQAARAL  158 (202)
T ss_pred             EeCCCCCcC--CCCHHHHhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcCCeeeecHHHHHHHh
Confidence            999999976  799999999999999876666677888999999999999999999999999999999999999887665


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                       ..++++.++++...+..+++++|++++..+++.++|++.+++
T Consensus       159 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  201 (202)
T cd08468         159 AEALPLELFDLPFDMPPYRLKLYSHRQHENSAANQWLIEQLDG  201 (202)
T ss_pred             hhcCCcEEecCCCCCCceeEEeeEeccccCCHHHHHHHHHHhh
Confidence             556788888886666789999999999999999999998875

LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec

>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2.5e-27  Score=182.88  Aligned_cols=195  Identities=17%  Similarity=0.182  Sum_probs=170.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+... ...+++...+++++++++++
T Consensus         1 g~l~ig~~~~~~~~~l~~~i~~~~~~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~   79 (198)
T cd08446           1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFY-PVEPDIAVENVAQERLYLAV   79 (198)
T ss_pred             CeEEEEechHHHHHHHHHHHHHHHHHCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecC-CCCCCceeEEeeeccEEEEE
Confidence            57999999999999999999999999999999999988888999999999999998644 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++||++.+..++++||.++|++.+..+.  ..++.+..++...+..+++.+++++..++.+++.+|.|++++|.+.+..
T Consensus        80 ~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  159 (198)
T cd08446          80 PKSHPLAARPAVSLADLRNEPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAAL  159 (198)
T ss_pred             eCCCCcccCCccCHHHHcCCCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcCCcEEEchhhhhcc
Confidence            99999987778999999999999976552  2455667788888988888899999999999999999999999988754


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                       ..+++..+|++.......++++|+++. .+++++.|+++
T Consensus       160 -~~~~l~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~  197 (198)
T cd08446         160 -RWPGVVFRPLADAEAKVPLSCIYRKDD-RSPILRAFLDV  197 (198)
T ss_pred             -CCCCeEEEECCCCCcceeEEEEEcCCC-CCHHHHHHHhh
Confidence             245688888876555678999999888 79999999875

This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf

>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold

Probab=99.96  E-value=3.5e-27  Score=181.71  Aligned_cols=194  Identities=15%  Similarity=0.124  Sum_probs=170.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (196)
T cd08450           1 VLTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPE-IQSDGIDYQLLLKEPLIVVLP   79 (196)
T ss_pred             CEEEEEehhhhhhhHHHHHHHHHhhCCCcEEEEEecChHHHHHHHhcCCccEEEEeCC-CCCCCcEEEEEEccceEEEec
Confidence            3899999999999999999999999999999999998889999999999999998654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCC-cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFS-GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      ++||++.+..++++||.++|++....+.. .++.+..++...|+.++..+++++..++..++.+|.|++++|...... .
T Consensus        80 ~~~pl~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~  158 (196)
T cd08450          80 ADHRLAGREKIPPQDLAGENFISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNL-L  158 (196)
T ss_pred             CCCCcccCceECHHHhCCCCeEeecCCCchHHHHHHHHHHHCCCCcEeeeeechHHHHHHHHhcCCcEEEeehhhhhc-c
Confidence            99999988889999999999999876644 466788899999999999999999999999999999999999986543 3


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      .+++..++++.......++++|+++. .++.++.|+++
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  195 (196)
T cd08450         159 PPSVVARPLSGETPTIDLVMGYNKAN-TSPLLKRFLSR  195 (196)
T ss_pred             cCCeEEEEccCCCCceEEEEEEcCCC-CCHHHHHHHhc
Confidence            45688888876555679999998876 68999998864

HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an

>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=3.3e-27  Score=182.01  Aligned_cols=196  Identities=20%  Similarity=0.220  Sum_probs=173.3

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++.+++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (196)
T cd08457           1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGP-LEERQGFLIETRSLPAVVAVP   79 (196)
T ss_pred             CEEEEeehhHhccccHHHHHHHHHHCCCeEEEEEecCcHHHHHHHHcCCccEEEeccC-CCCCCcEEEEeccCCeEEEee
Confidence            4899999999999999999999999999999999988889999999999999999654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||++.+..++++||.++|+|.+..+...+..+.+++...++.+++.+++++..++.+++.+|.|++++|...+.....
T Consensus        80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~~~  159 (196)
T cd08457          80 MGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPL  159 (196)
T ss_pred             CCCccccCCccCHHHhCCCceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcCCeEEEEChHHhhcccC
Confidence            99999988889999999999999887766677788899999999999999999999999999999999998766544334


Q ss_pred             CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +++..++++. .....+|++|+++...++.++.|++++
T Consensus       160 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~  196 (196)
T cd08457         160 DGIVIRPFDT-FIDAGFLVVRAANGPPSTMVDRFIDEF  196 (196)
T ss_pred             CCeEEEecCC-CCceeEEEEecCCCCCCHHHHHHHhhC
Confidence            5677888865 345789999999988999999999864

This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h

>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2.9e-27  Score=181.90  Aligned_cols=194  Identities=19%  Similarity=0.244  Sum_probs=171.4

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-CCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-SDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-~~~~~~~~l~~~~~~~v~  172 (306)
                      .++||++++++..++++++..|.+.||++++++....++++.+.+.+|++|++|+...... .+++.+.+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~   80 (195)
T cd08427           1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLVWTPLVREPLVLIA   80 (195)
T ss_pred             CEEEEeeHHHHHHHhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccccCceEEEcccCcEEEEE
Confidence            4899999999999999999999999999999999998999999999999999999644333 578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      +++||++.    ..++|.++|++.+..+...+..+.+++...++.++..+++++...+.+++.+|.|++++|.+.+....
T Consensus        81 ~~~~p~~~----~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~  156 (195)
T cd08427          81 PAELAGDD----PRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPA  156 (195)
T ss_pred             CCCCCcch----HHHHhcCCCeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhCCcEEEccHHHHhhhc
Confidence            99999753    35779999999987766667778889999999999999999999999999999999999998876335


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+++..++++......+++++|+++...+|.++.|+++|
T Consensus       157 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  195 (195)
T cd08427         157 GPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL  195 (195)
T ss_pred             cCceEEEECCCCCceEEEEEEEeCCccCCHHHHHHHhhC
Confidence            678999998765567899999999988999999999864

LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi

>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold

Probab=99.96  E-value=4.9e-27  Score=182.09  Aligned_cols=198  Identities=18%  Similarity=0.224  Sum_probs=172.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         2 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   80 (203)
T cd08445           2 TFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLR-IEDPAIRRIVLREEPLVVALP   80 (203)
T ss_pred             eEEEEEehHHHHhHHHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCC-CCCCCceeEEEEeccEEEEee
Confidence            6999999999999999999999999999999999998999999999999999998543 455789999999999999999


Q ss_pred             CCCCCCCCC-CcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         174 LDHPLLLLN-SISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       174 ~~~~l~~~~-~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      ++||++.+. +++++||.++|++.+..+.  ..++.+..++...++.+++.+++++..++.+++.+|.|++++|..... 
T Consensus        81 ~~hpl~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~-  159 (203)
T cd08445          81 AGHPLAQEKAPLTLAQLADEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASVQR-  159 (203)
T ss_pred             CCCCCccCCCCcCHHHhcCCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcCCCeEEehHHhhc-
Confidence            999998766 7999999999999976542  234566778888898888899999999999999999999999998754 


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ...++++.+++++......++++|+++. .+|.+++|++.+++.
T Consensus       160 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~  202 (203)
T cd08445         160 LRRDDVVYRPLLDPDATSPIIMSVRAGD-ESPYIALILQLIREL  202 (203)
T ss_pred             cCCCCeEEEECCCCCCceEEEEEEcCCC-CChHHHHHHHHHHhh
Confidence            2466788889887555678899888775 489999999998763

This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes

>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2e-27  Score=183.49  Aligned_cols=196  Identities=21%  Similarity=0.306  Sum_probs=172.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++.+++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+....+++.+.++++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~~~l~~~~~~~~~~   80 (199)
T cd08430           1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAP   80 (199)
T ss_pred             CeEEEeccccceeeccHHHHHHHHHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCcccEEEeeccceEEEEEe
Confidence            48999999999999999999999999999999999989899999999999999986443334679999999999999999


Q ss_pred             CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      ++||++.+ ..++++||.++|++....+. .+..+..++...+..+++.+++++..++.+++.+|.|++++|..++... 
T Consensus        81 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~lp~~~~~~~~  159 (199)
T cd08430          81 NIACAVTQQLSQGEIDWSRLPFILPERGL-ARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALGCGVGIVPELVLDNSP  159 (199)
T ss_pred             CCchhhhhhccccccccccCCeEEccCCh-HHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhCCeEEEccHHHhhhhh
Confidence            99998765 36789999999999877654 4667888999999989989999999999999999999999999888765 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      ..++++.++++.......++++|+++...++.++.|++.
T Consensus       160 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  198 (199)
T cd08430         160 LKDKVRILEVQPELEPFEVGLCCLKKRLNEPLIKAFWQV  198 (199)
T ss_pred             ccCcceEEEcCCCCCceEEEEEEccCcccChHHHHHHhh
Confidence            556799999875445679999999998889999999864

In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i

>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold

Probab=99.96  E-value=6.6e-27  Score=180.72  Aligned_cols=196  Identities=14%  Similarity=0.121  Sum_probs=171.3

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++.+++..++++++..|.+.||++++++....++++.+.|.+|++|++|+... ...+++...++.++++++++
T Consensus         1 g~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~~~   79 (198)
T cd08485           1 GELRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFY-PYQEGVVVRNVTNERLFLGA   79 (198)
T ss_pred             CeEEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEecCC-CCCCCeEEEEeeccceEEEe
Confidence            57999999999999999999999999999999999998999999999999999998643 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++||++....++++||.++|++.++.+.  ..++.+.+++...++.++..+++++..++.+++.+|.|++++|..++..
T Consensus        80 ~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  159 (198)
T cd08485          80 QKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAGVGVTIVPETVAMI  159 (198)
T ss_pred             CCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcCCceEECcchhhcc
Confidence            99999876778999999999999986543  3466777889989999999999999999999999999999999987653


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . .+++..+++.+.....+++++|+++. .++.++.|++++
T Consensus       160 ~-~~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~f~~~~  198 (198)
T cd08485         160 S-WPDFGFTELVGSKATVPVSCIYRHDH-IAPILKTFLNLL  198 (198)
T ss_pred             c-cCCeEEEeCCCCCCceeEEEEecccc-cChHHHHHHhhC
Confidence            2 34678888876556789999998865 699999999864

In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th

>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold

Probab=99.96  E-value=7.2e-27  Score=180.37  Aligned_cols=197  Identities=14%  Similarity=0.252  Sum_probs=171.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~v~  172 (306)
                      .++||+++++...++++++..|.++||++++++....+.++.+.+.+|++|++|...+. ...+++...+++++++++++
T Consensus         1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~~~~l~~~~~~~v~   80 (199)
T cd08416           1 RLRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEVVPLFEDDIFLAV   80 (199)
T ss_pred             CEEEEechHHHHhhhHHHHHHHHHhCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeEEEEeecceEEEEE
Confidence            48999999999999999999999999999999999888889999999999999986542 24578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      +++||++.+..++++||.+++++.+..+...+..+.+++...++.++..+++++...+.+++.+|.|++++|.+.+... 
T Consensus        81 ~~~hp~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  159 (199)
T cd08416          81 PATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVY-  159 (199)
T ss_pred             CCCCcccccCccCHHHhcCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcCCcEEEechhhhhhc-
Confidence            9999998877899999999999998776656667788888899988899999999999999999999999999887543 


Q ss_pred             cCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+.+..+++... ....+++++|++++..+|.++.|++++
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  199 (199)
T cd08416         160 EDKVQLIPLAEPYQIRQTIGLVFLRSRERDPNLLALAAEC  199 (199)
T ss_pred             cCCeEEEECCcccCCceeEEEEEcCCCcCCHHHHHHHhhC
Confidence            345666666542 235689999999999999999999864

This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom

>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold

Probab=99.96  E-value=7.3e-27  Score=179.90  Aligned_cols=195  Identities=16%  Similarity=0.201  Sum_probs=170.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|.... ...+++...++++++++++++
T Consensus         1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (197)
T cd08448           1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSR-RLPAGLSARLLHREPFVCCLP   79 (197)
T ss_pred             CeEEEEchhHHHHHHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCcceEEEeCC-CCCcCceEEEEecCcEEEEee
Confidence            4899999999999999999999999999999999998999999999999999998644 556889999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++||++.++.++++||.++|++.+..+.  ..++.+..++...+..++..+++++..++++++.+|.|++++|...+...
T Consensus        80 ~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  159 (197)
T cd08448          80 AGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLARAG  159 (197)
T ss_pred             CCCCCcCCCCcCHHHhCCCcEEeeCcccChHHHHHHHHHHHHcCCceeeeeccccHHHHHHHHHcCCceEecchhhhhhc
Confidence            9999998888999999999999976543  24566778888888888888999999999999999999999999887653


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+++.+++++......++++|+++.. ++.++.|++++
T Consensus       160 -~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  197 (197)
T cd08448         160 -LAGVRFLPLKGATQRSELYAAWKASAP-NPALQAFLAAL  197 (197)
T ss_pred             -cCceEEEECCCCCccEEEEEEEcCCCC-CHHHHHHHHhC
Confidence             345777777764456789999998877 99999998864

This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve

>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=2.1e-27  Score=186.72  Aligned_cols=198  Identities=13%  Similarity=0.157  Sum_probs=175.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||+.++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~~~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~l~~~~l~~~~~~~v~~   79 (221)
T cd08469           1 SFVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFE-QIPPRFRRRTLFDEDEVWVMR   79 (221)
T ss_pred             CEEEEEChHHHHHHHHHHHHHHHHHCCCcEEEEeeCChhhHHHHHHCCCccEEEecCC-CCCccceeeeeeccceEEEEe
Confidence            4899999999999999999999999999999999998889999999999999998654 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCC---------------------cHHHHHHHHHhCCCceeEEEEecCHHHHHH
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFS---------------------GRIKLDREFSLQKLTPYIVLETINSDIIKT  232 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (306)
                      ++||+.. ..++++||.++|++....+..                     .++.+..+++..+..+++.+++++..++..
T Consensus        80 ~~~pl~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (221)
T cd08469          80 KDHPAAR-GALTIETLARYPHIVVSLGGEEEGAVSGFISERGLARQTEMFDRRALEEAFRESGLVPRVAVTVPHALAVPP  158 (221)
T ss_pred             CCCcCCC-CCCCHHHHHhCCeEEEecCCCccchHHHHHHHcCCCcccccccchhhhhhhhhccccceEEEEcCcHHHHHH
Confidence            9999876 679999999999999865432                     134466778888999999999999999999


Q ss_pred             HHHhccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         233 YVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       233 ~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ++.+|.|++++|.+.+... ..++++.++++.......++++|+++...++.+++|++.+++
T Consensus       159 ~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~lv~~~~~~~~~~~~~l~~~~~~  220 (221)
T cd08469         159 LLADSDMLALLPRSLARAFAERGGLVMKEPPYPPPPVQIRAVWHERHDNDPAVAWLREMIRD  220 (221)
T ss_pred             HHhCCchhhhHHHHHHHHHhhcCCcEEeCCCCCCCCceEEEEecccccCChHHHHHHHHHhh
Confidence            9999999999999888665 567899999876556789999999999999999999998875

PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet

>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold

Probab=99.96  E-value=3.5e-27  Score=183.11  Aligned_cols=198  Identities=14%  Similarity=0.076  Sum_probs=172.5

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCceeeccccceEEEEe
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~~~~l~~~~~~~v~  172 (306)
                      |+||+.++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|...+...  ..++...+++++++++++
T Consensus         2 l~ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~   81 (204)
T cd08429           2 FRVGVADAVPKSIAYRLLEPAMDLHEPIRLVCREGKLEQLLADLALHRLDMVLADRPMPSSLDVKGYSHRLGECGVSFFA   81 (204)
T ss_pred             eeEEcchhhhHHHHHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHHcCCccEEEecCCCccccchheeeccccccceEEEe
Confidence            799999999999999999999999999999999999999999999999999998644222  136778999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      ++.|+... .+++++||.++|+|.+..+...+..+.++++..|..++..+++++..++.+++.+|.|++++|...+... 
T Consensus        82 ~~~~~~~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~G~Gv~~lp~~~~~~~~  160 (204)
T cd08429          82 APPLAKRL-EKPFPASLDEAPLLLPGEDSALRRKLLQWFERQGLRPQIVGEFDDSALMKAFGQAGAGIFAAPTVIADEVA  160 (204)
T ss_pred             cCCccccc-ccCCHhHhccCCeeecCCCCcHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHcCCCeEeccHHHHHHHH
Confidence            98876432 4579999999999998887778888999999999999999999999999999999999999999887653 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..+.++.++... ...+.+|++|+++...++.++.|++.+++.
T Consensus       161 ~~~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~  202 (204)
T cd08429         161 RQYGVVEIGRTD-EVVEEFYAISVERRITHPAVVAISEAARSA  202 (204)
T ss_pred             hcCCeEeeccCc-cceeeEEEEeecccCCCHHHHHHHHhhccc
Confidence            456677765433 356789999999999999999999999875

NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine

>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold

Probab=99.95  E-value=1.2e-26  Score=179.00  Aligned_cols=196  Identities=21%  Similarity=0.255  Sum_probs=169.1

Q ss_pred             cEEEEecccchh-hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          94 NLTIATTHTQAR-YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        94 ~l~I~~~~~~~~-~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      +|+||++.+++. .++++++..|.+.||++.+++....+.++.+.+.+|++|++|+.......+++...+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~   80 (199)
T cd08451           1 RLRVGFTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEPMLVAL   80 (199)
T ss_pred             CeeEEeeeeeeeecccHHHHHHHHHHCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCceeEEEeecccEEEEe
Confidence            489999998764 6999999999999999999999999989999999999999998644333678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++||++.++.++++||.++|++....+.  ..+..+.+++...+..+++.+++++..++.+++.+|.|++++|..++..
T Consensus        81 ~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  160 (199)
T cd08451          81 PAGHPLARERSIPLAALADEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQL  160 (199)
T ss_pred             cCCCCCcccCccCHHHhcCCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcCCCEEEechHHHhh
Confidence            99999988778999999999999976543  3456778888888988889999999999999999999999999988754


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . .+++..+++.+..+..+++++|+++.. ++.++.|++.+
T Consensus       161 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  199 (199)
T cd08451         161 Q-APGVVYRPLAGAPLTAPLALAYRRGER-SPAVRNFIALV  199 (199)
T ss_pred             c-cCCeEEEEccCCCCCceEEEEEcCCCC-CHHHHHHHhhC
Confidence            2 346777888765566899999998876 99999998753

This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra

>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily

Probab=99.95  E-value=1.7e-26  Score=177.21  Aligned_cols=196  Identities=29%  Similarity=0.471  Sum_probs=177.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||+++++...++++++..|.+++|++++++....+.++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus         1 ~l~I~~~~~~~~~~l~~~i~~~~~~~p~i~i~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~   79 (197)
T cd05466           1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP-VDDPGLESEPLFEEPLVLVVP   79 (197)
T ss_pred             CeEEEechhhHHHHhHHHHHHHHHHCCCCEEEEEECChHHHHHHHHcCCceEEEEcCC-CCCCcceEeeeeccceEEEec
Confidence            4899999999999999999999999999999999998889999999999999999755 466789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||+..+..++++||.++|++.+..+......+..++...+..++..+.+++...+..++.+|.|++++|.+.+. . .
T Consensus        80 ~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~-~~~  158 (197)
T cd05466          80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELA  158 (197)
T ss_pred             CCCCcccCcEecHHHHcCCCEEEecCCchHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHhCCCEEEehHHHHh-hhh
Confidence            9999988777999999999999998876666677778888898888899999999999999999999999999877 4 6


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .++++.++++......+++++|+++...++.+++|++++
T Consensus       159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  197 (197)
T cd05466         159 DGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL  197 (197)
T ss_pred             cCCeEEEEecCCcceEEEEEEEcCCCccCHHHHHHHhhC
Confidence            788999988865677899999999988899999999874

This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin

>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold

Probab=99.95  E-value=6.6e-27  Score=181.00  Aligned_cols=198  Identities=12%  Similarity=0.117  Sum_probs=173.4

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|+||+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~   79 (200)
T cd08465           1 VFRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFP-ELPEELHAETLFEERFVCLAD   79 (200)
T ss_pred             CEEEEechhhHHHhhhHHHHHHHHHCCCcEEEEecCChHhHHHHHHCCCccEEEeccc-cCCcCeeEEEeeeccEEEEEe
Confidence            4899999999999999999999999999999999999999999999999999998654 345789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh-ccceeeeecceecccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL-RMGIGIIASIAFDSNR  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-g~gi~~~p~~~~~~~~  252 (306)
                      ++||. .+..+++++|.++|++.+..+...+..++.+++..++.+++.+++++..++.+++.+ |.|+++.|........
T Consensus        80 ~~h~~-~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  158 (200)
T cd08465          80 RATLP-ASGGLSLDAWLARPHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAGTDLILTVARRALDALRL  158 (200)
T ss_pred             CCCCc-cCCCcCHHHHhhCCcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHcCChhhHhHHHHHHHhcc
Confidence            99965 456799999999999999877666778899999999999999999999999999998 5566777654443225


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .++++.++++...+..+++++|++++..+++.++|++.+++
T Consensus       159 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~i~~  199 (200)
T cd08465         159 DERLAVFAPPFPIPPFAFQQIWHQRREGDPAHRWLRERIQE  199 (200)
T ss_pred             cCCceEeCCCCCCCCceEEeeecccccCChHHHHHHHHHhh
Confidence            67899998887666789999999999999999999998875

In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After

>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold

Probab=99.95  E-value=2.1e-26  Score=177.73  Aligned_cols=193  Identities=18%  Similarity=0.217  Sum_probs=170.0

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecC
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPL  174 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~  174 (306)
                      |+||++++++..++++++..|+++||++++++....+.++.+.|.+|++|++|...+ ...+++...+++++++++++++
T Consensus         2 l~ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~~   80 (197)
T cd08452           2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPP-IQHTALHIETVQSSPCVLALPK   80 (197)
T ss_pred             EEEEEeHHHHHhHHHHHHHHHHHHCCCcEEEEEecChHHHHHHHHCCCccEEEeeCC-CCCCCeeEEEeeeccEEEEEeC
Confidence            799999999999999999999999999999999999999999999999999999644 5567899999999999999999


Q ss_pred             CCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760         175 DHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR  252 (306)
Q Consensus       175 ~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~  252 (306)
                      +||++.+.+++++||.++|++....+.  ..++.+..++...+..+++.+++++.+++.+++.+|.|++++|...... .
T Consensus        81 ~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~-~  159 (197)
T cd08452          81 QHPLASKEEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKL-F  159 (197)
T ss_pred             CCccccCCCCCHHHhcCCCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcCCCEEEchHHHhhc-C
Confidence            999988778999999999999987653  2456777888989998999999999999999999999999999987533 3


Q ss_pred             cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      .++++.+++.+......++++|+++.. +|.++.|++.
T Consensus       160 ~~~~~~~~l~~~~~~~~~~l~~~~~~~-~~~~~~f~~~  196 (197)
T cd08452         160 NLEVAYRKIDQINLNAEWSIAYRKDNH-NPLLKHFIHI  196 (197)
T ss_pred             CCCeEEEECCCCCcceeEEEEECCCCC-ChHHHHHHhc
Confidence            567888898775566799999988874 8989988763

AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip

>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold

Probab=99.95  E-value=2.9e-26  Score=176.83  Aligned_cols=195  Identities=16%  Similarity=0.185  Sum_probs=168.8

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++....+++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   79 (198)
T cd08447           1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPP-FARPGLETRPLVREPLVAAVP   79 (198)
T ss_pred             CEEEEEehHHHHHHHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCceEEEecCC-CCCCCeeEEEeecCceEEEec
Confidence            4899999999999999999999999999999999999999999999999999999654 455789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCC--cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFS--GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++||++.+..++++||.++|++.+.....  .++.+..++...+..++..+++++..++.+++.+|.|++++|..++...
T Consensus        80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  159 (198)
T cd08447          80 AGHPLAGAERLTLEDLDGQPFIMYSPTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLR  159 (198)
T ss_pred             CCCchhhcCcccHHHhCCCeEEEeCCCCCchHHHHHHHHHHHcCCCCCceeecCCHHHHHHHHHcCCCeEEhhHHHhhcC
Confidence            99999887789999999999999865433  3567788898899888888999999999999999999999999877543


Q ss_pred             ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 ~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ...+..+++... ....+++++|+++. .++.+++|++++
T Consensus       160 -~~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  198 (198)
T cd08447         160 -FEGVVFRPLDLPRDVPVELHLAWRRDN-DNPALRALLDLI  198 (198)
T ss_pred             -cCCeEEEECCCCCCCceEEEEEEcCCC-CCHHHHHHHhhC
Confidence             334566676553 35679999999875 589999998764

This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve

>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold

Probab=99.94  E-value=1.3e-25  Score=172.86  Aligned_cols=192  Identities=16%  Similarity=0.123  Sum_probs=160.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||++++++..++++++..|.+.||++++++....++++.+.|.+|++|++|+.......+++...+++.++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~   80 (195)
T cd08431           1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA   80 (195)
T ss_pred             CEEEEEccccChHHHHHHHHHHHHHCCCCceEEEEeccchHHHHHhCCCCCEEEEecCCCCCCceEEEecccceEEEEEc
Confidence            48999999999999999999999999999999999888899999999999999985433345689999999999999999


Q ss_pred             CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC-CceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQK-LTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++||++.. ..+++++|.++|++.+..+......     ...+ ..++..+++++..++++++.+|.|++++|.+.+...
T Consensus        81 ~~hpl~~~~~~~~~~~L~~~~~i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~  155 (195)
T cd08431          81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPP-----RSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPE  155 (195)
T ss_pred             CCChhhhccCCCCHHHHhhCcEEEEcCCCccccc-----ccceeccCCCceEEcCHHHHHHHHHhCCceEecCHHHHHhh
Confidence            99999865 4799999999999998765432111     1112 245677889999999999999999999999887655


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++.+++.+.....+++++|+++. .++.+++|++.+
T Consensus       156 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~  195 (195)
T cd08431         156 LASGELVEKALEDPRPPQELFLAWRKDQ-RGKALAWFVQRL  195 (195)
T ss_pred             hhCCceEeeccCCCCCCceEEEEEecCC-CCHHHHHHHHhC
Confidence             567788888877566789999999886 688999988753

HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p

>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold

Probab=99.93  E-value=1.3e-25  Score=172.52  Aligned_cols=192  Identities=14%  Similarity=0.025  Sum_probs=161.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||+.+++...++++++..|.+.||++++++....   ..+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~---~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   76 (194)
T cd08432           1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSD---RLVDFAREGIDLAIRYGD-GDWPGLEAERLMDEELVPVCS   76 (194)
T ss_pred             CEEEEccHHHHHHHHHHHhHHHHHHCCCeEEEEEecC---CccccccccccEEEEecC-CCCCCcceEEccCCcEEEecC
Confidence            4899999999999999999999999999999998765   457799999999998654 446789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R  252 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~  252 (306)
                      ++||.. ++.++++||.++|++....+...+..+.+.+...+..+++.+++++..++.+++.+|.|++++|...+... .
T Consensus        77 ~~~~~~-~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~  155 (194)
T cd08432          77 PALLAG-LPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA  155 (194)
T ss_pred             HHHHHh-cCCCCHHHhhcCceEEecCcccccHHHHhcCCeeccccCCeEEECCHHHHHHHHHhCCCeEEeeHHHhhhhhc
Confidence            999854 45689999999999998766555666666677778888999999999999999999999999999887654 4


Q ss_pred             cCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         253 DKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       253 ~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+.+. .+++. .....+++++|++++..+|.+++|++++
T Consensus       156 ~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (194)
T cd08432         156 AGRLV-RPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL  194 (194)
T ss_pred             CCceE-eccccccCCCCCEEEEeccccccchHHHHHHhhC
Confidence            55554 33333 3456799999999999999999998753

This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris

>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.93  E-value=1.7e-25  Score=172.66  Aligned_cols=196  Identities=15%  Similarity=0.140  Sum_probs=160.2

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+++||++++++..++++++..|.++||++++++..  ..+..+.+.++ +|++|........+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~--~~~~~~~l~~~-~D~~i~~~~~~~~~~l~~~~l~~~~~~~v~   77 (199)
T cd08475           1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSF--SDRFVDLIEEG-IDLAVRIGELADSTGLVARRLGTQRMVLCA   77 (199)
T ss_pred             CeEEEechHHHHHhhHHHHHHHHHHHCCCeEEEEEe--ccchhhHhhcC-ccEEEEeCCCCCCCCeEEEEcccceEEEEE
Confidence            579999999999999999999999999999999974  34567777655 999997544334467999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCC-CCcH-HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLS-FSGR-IKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++|+...+..++++||.++|++..... .... ..+...+...+..+++.+++++..++++++..|.|++++|.+++..
T Consensus        78 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  157 (199)
T cd08475          78 SPAYLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVAD  157 (199)
T ss_pred             CHHHHHhcCCCCCHHHHhhCCCEEecCCCCCCCeEEecCCCCeeeEeccCcEEECCHHHHHHHHHhCCCEEeeeHHHHHh
Confidence            9999876566799999999999998764 2221 2223334455677888999999999999999999999999988876


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . ..+.++.++...+....+++++|+++...++.+++|++++
T Consensus       158 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  199 (199)
T cd08475         158 HLQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL  199 (199)
T ss_pred             HhhcCcEEEecCCCcCCCccEEEEeCCcccCCHHHHHHHhhC
Confidence            5 5667777765544556799999999999999999999874

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.93  E-value=2.1e-25  Score=172.42  Aligned_cols=198  Identities=13%  Similarity=0.133  Sum_probs=158.5

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+|+||+.++++..++++++..|.+.||++++++....  ++.+ +.+|++|++|+..+ ...+++...+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~--~~~~-~~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~   76 (201)
T cd08471           1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLD--RVVN-LLEEGVDVAVRIGH-LPDSSLVATRVGSVRRVVCA   76 (201)
T ss_pred             CeEEEEccHHHHHHHHHHHHHHHHHHCCCcEEEEEEcC--ccch-hhcccccEEEEecC-CCCCCeEEEEccccceEEEE
Confidence            57999999999999999999999999999999998642  3443 56789999998644 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++|+...+..++++||.++|++....+..... .+...+...++.+++.+++++..++.+++.+|.|++++|.+++...
T Consensus        77 ~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~  156 (201)
T cd08471          77 SPAYLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE  156 (201)
T ss_pred             CHHHHHhcCCCCCHHHHhcCCeEEEecCCCCCceeEecCCcEEEEecCCcEEECCHHHHHHHHHcCCcEEEechhHHHHH
Confidence            999865555579999999999999876543211 1222333345667888999999999999999999999999876544


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                       ..+.++.+..+.......++++|++++..++.++.|++++++.
T Consensus       157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~  200 (201)
T cd08471         157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPR  200 (201)
T ss_pred             hhcCceEEecccccCCCCcEEEEecCcccCCHHHHHHHHHHHhh
Confidence             5566776644433446799999999988999999999998764

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain

Probab=99.93  E-value=7.7e-26  Score=174.72  Aligned_cols=196  Identities=15%  Similarity=0.156  Sum_probs=155.8

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEE
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVII  171 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v  171 (306)
                      .|.|+||++++++..++++++..|.++||++++++..  ++.+. .+.+|++|++|+..+ ...+++...++++++++++
T Consensus         2 ~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~--~~~~~-~l~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v   77 (199)
T cd08478           2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVS--NEGII-DLIERKTDVAIRIGE-LTDSTLHARPLGKSRLRIL   77 (199)
T ss_pred             CceEEEeCHHHHHHHHHHHHHHHHHHHCCCeEEEEEe--ccccc-cchhccccEEEEecC-CCCCCceEEEcccccEEEE
Confidence            4789999999999999999999999999999999973  33444 478899999998644 4567899999999999999


Q ss_pred             ecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         172 VPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++++|+......++++||.++|+|.+..+...+......+...+..+++.+++++...++.++..|.|++++|.+++...
T Consensus        78 ~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~  157 (199)
T cd08478          78 ASPDYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKD  157 (199)
T ss_pred             ECHHHHHhcCCCCCHHHHHhChhhhccCCCCCCCceeeCCCCcEEeccceEEECCHHHHHHHHHhCCCEEeccHHHHHHH
Confidence            99999433334699999999999987665443322222233334566778899999999999999999999999887654


Q ss_pred             -ccCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++.+.... ....++++++|++++..++.++.|++++
T Consensus       158 ~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  199 (199)
T cd08478         158 IAEGRLIPLFAEQTSDVRQPINAVYYRNTALSLRIRCFIDFL  199 (199)
T ss_pred             HhCCCeEEeccccccCCCccEEEEECccccCChhhhhhhhhC
Confidence             456677664432 2346799999999999999999999864

This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh

>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain

Probab=99.93  E-value=3e-25  Score=170.79  Aligned_cols=195  Identities=15%  Similarity=0.187  Sum_probs=157.2

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+|+||++++++..++++++..|.++||++++++....  .+. .+.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~--~~~-~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~   76 (197)
T cd08422           1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSD--RLV-DLVEEGFDLAIRIGE-LPDSSLVARRLGPVRRVLVA   76 (197)
T ss_pred             CeEEEEecHHHHHHHHHHHHHHHHHhCCceEEEEecCc--ccc-chhhcCccEEEEeCC-CCCcchhhhhhhccCcEEEE
Confidence            57999999999999999999999999999999998643  334 466788999998654 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++|+...+..++++||.++|++.+..+... ...+...+...+..+++.+++++..++++++.+|.|++++|.+.+...
T Consensus        77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  156 (197)
T cd08422          77 SPAYLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED  156 (197)
T ss_pred             CHHHHHhcCCCCCHHHHhcCCcEeecCccCcccceeecccCcccccccccEEEccHHHHHHHHHcCCcEEEecHHHHhhh
Confidence            9999654445689999999999998775221 112223333346778889999999999999999999999999887655


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++.++.+.......++++|++++..++.++.|++++
T Consensus       157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  197 (197)
T cd08422         157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL  197 (197)
T ss_pred             ccCCeEEEecCcccCCCceEEEEEcccccCCHHHHHHHhhC
Confidence             5556666554434556899999999999999999998864

This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own

>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold

Probab=99.92  E-value=9.1e-25  Score=167.86  Aligned_cols=190  Identities=13%  Similarity=0.041  Sum_probs=157.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++.+++..++++++.+|.++||++++++......   +.+.+|++|++++..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~---~~l~~~~~Dl~l~~~~-~~~~~~~~~~l~~~~~~~v~~   76 (194)
T cd08481           1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEP---FDFSQGSFDAAIHFGD-PVWPGAESEYLMDEEVVPVCS   76 (194)
T ss_pred             CEEEEecHHHHHHHHHhhhhHHHHHCCCceEEEEecccc---cCcccCCCCEEEEcCC-CCCCCccceecccCeeeecCC
Confidence            489999999999999999999999999999999976543   3688999999998644 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      ++|| +.++.++++||.++|++......   ..+.+++...|..+   ...+++++...+.+++.+|.|++++|...+..
T Consensus        77 ~~~~-~~~~~~~~~dl~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~  152 (194)
T cd08481          77 PALL-AGRALAAPADLAHLPLLQQTTRP---EAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEE  152 (194)
T ss_pred             HHHH-hcCCCCcHHHHhhCceEecCCCC---cCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhCCCeEEecHHHHHH
Confidence            9997 55567899999999999865332   24577788887753   34578899999999999999999999988765


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . ..+.++..+.+......+++++|+++...++.+++|++++
T Consensus       153 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i  194 (194)
T cd08481         153 ELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL  194 (194)
T ss_pred             HHHCCCEEeecCccccCCCeEEEEeCcccccCHHHHHHHhhC
Confidence            5 5566765544333346799999999999999999999864

GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas

>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.92  E-value=3.4e-25  Score=171.43  Aligned_cols=195  Identities=15%  Similarity=0.144  Sum_probs=155.4

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecccc-ceEEE
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ-WEYVI  170 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~-~~~~~  170 (306)
                      .|.|+||++++++..++++++..|.++||++++++...+.   ...+.+|++|++|+... ...+++...+++. +++++
T Consensus         2 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~---~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~   77 (202)
T cd08474           2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDG---LVDIVAEGFDAGIRLGE-SVEKDMVAVPLGPPLRMAV   77 (202)
T ss_pred             CcEEEEeCcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCC---cccccccCccEEEEcCC-CCCCCeEEEEeccccceEE
Confidence            5789999999999999999999999999999999987542   45688999999998644 4467799999999 69999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCC-CC--cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLS-FS--GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA  247 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~  247 (306)
                      +++++|+...+..++++||.++|++.+... ..  ....+...+...++.+++.+++++..++.++|.+|.|++++|.+.
T Consensus        78 v~~~~~~~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~  157 (202)
T cd08474          78 VASPAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDL  157 (202)
T ss_pred             EeCHHHHHhcCCCCCHHHHhhCCeeeeeCCCCCcCcceEEecCCCeEEEecCCcEEECCHHHHHHHHHcCCCEEEeeHHH
Confidence            999998544445799999999999987643 21  222223333444556778899999999999999999999999988


Q ss_pred             eccc-ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         248 FDSN-RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       248 ~~~~-~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +... ..+.++.+ +.+. ....+++++|++++..+|.++.|++++
T Consensus       158 ~~~~~~~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i  202 (202)
T cd08474         158 VAEHLASGRLVRV-LEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL  202 (202)
T ss_pred             HHHHHHCCCcEEe-CCcccCCCCCEEEEEeCCCCCCHHHHHHHhhC
Confidence            7654 55666654 3332 456799999999988999999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.92  E-value=9.7e-25  Score=168.84  Aligned_cols=196  Identities=13%  Similarity=0.107  Sum_probs=157.8

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++++++..++++++..|.++||++++++...  +++.+.+ .+++|++|+..+ ...+++...+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~--~~~~~~l-~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~   76 (202)
T cd08472           1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVS--DRPVDLI-REGVDCVIRVGE-LADSSLVARRLGELRMVTCA   76 (202)
T ss_pred             CeEEEeccHHHHHHHHHHHHHHHHHHCCCcEEEEEEC--CCcchhh-cccccEEEEcCC-CCCccEEEEEccceeEEEEE
Confidence            5799999999999999999999999999999999753  3455544 567999998544 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++|+...+..++++||.++|++.+..+.. ...+...+...+    +.+++.+++++...+++++..|.|++++|..++
T Consensus        77 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~lp~~~~  155 (202)
T cd08472          77 SPAYLARHGTPRHPEDLERHRAVGYFSART-GRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMV  155 (202)
T ss_pred             CHHHHHhCCCCCCHHHHhcCceEEEeccCC-CCccceEEecCCCceEEeccCeEEECCHHHHHHHHHcCCeEEECcHHHH
Confidence            999965545578999999999998765432 222333444445    567788999999999999999999999999887


Q ss_pred             ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ... ..+.++.++.........++++|+++...+|.++.|++++++
T Consensus       156 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  201 (202)
T cd08472         156 RPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE  201 (202)
T ss_pred             HHHHhcCccEEeeccccCCCCcEEEEecCcccCChhHHHHHHHHhh
Confidence            654 566777665443345679999999988889999999999875

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.92  E-value=1.2e-24  Score=167.66  Aligned_cols=195  Identities=13%  Similarity=0.168  Sum_probs=154.8

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++++++..++++++..|.++||++++++...  ..+.+.+ +|++|++|...+ ...+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~--~~~~~~~-~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~   76 (197)
T cd08477           1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLS--DRLVDLV-EEGFDAAFRIGE-LADSSLVARPLAPYRMVLCA   76 (197)
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHHHHCCCcEEEEEec--CCcchhh-hcCccEEEECCC-CCCCCeeEEEeeeeEEEEEE
Confidence            5799999999999999999999999999999999863  3455544 577999998644 45688999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++|+...+..++++||.++|++.+..+..... .........++.+++.+++++..+++.++.+|.|++++|.+.+...
T Consensus        77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~~p~~~~~~~  156 (197)
T cd08477          77 SPDYLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAED  156 (197)
T ss_pred             CHHHHhhCCCCCCHHHHhhCcceeecCCCCCccEEEecCCCceEEecCCcEEEcCHHHHHHHHHcCCceEechHHHHHHH
Confidence            999954444579999999999998876422111 1111122235677888999999999999999999999999887654


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++.+..........++++|++++..++.++.|++++
T Consensus       157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  197 (197)
T cd08477         157 LASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL  197 (197)
T ss_pred             HHcCCcEEeCCcccCCCCcEEEEecCCccccHHHHHHHhhC
Confidence             5677776654433456799999999988899999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.91  E-value=1.2e-24  Score=167.86  Aligned_cols=195  Identities=11%  Similarity=0.064  Sum_probs=154.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++++++..++++++..|.++||++++++...+   ..+.+.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~~~~---~~~~l~~g~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~~~   76 (198)
T cd08479           1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTD---RPVDLVEEGFDLDIRVGD-LPDSSLIARKLAPNRRILCA   76 (198)
T ss_pred             CcEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEecC---ccccccccCccEEEEcCC-CCCccceeeeccCCceEEEE
Confidence            57999999999999999999999999999999998643   346899999999998543 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHH--HHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK--LDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++|+......++++||.++|++.+.........  +...+...+..++..+++++..+++.++.+|.|++++|...+..
T Consensus        77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~~p~~~~~~  156 (198)
T cd08479          77 SPAYLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAP  156 (198)
T ss_pred             CHHHHHhCCCCCCHHHHhhCcCeEecccCCCccceEEecCCCeEEEeeCCeEEECCHHHHHHHHHcCCcEEeccHHHHHH
Confidence            9998654445799999999999987654322111  22223344566788899999999999999999999999977654


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      . ..+.++.+.........+++++|++++..++.++.|++++
T Consensus       157 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  198 (198)
T cd08479         157 YLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL  198 (198)
T ss_pred             HHhCCceEEecCcccCCCCCEEEEccccccccHHHHHHHhhC
Confidence            4 4566665533222345799999999988999999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold

Probab=99.91  E-value=1.1e-22  Score=155.19  Aligned_cols=182  Identities=15%  Similarity=0.165  Sum_probs=154.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +++||+++++...++++++..|.++||++++++....+.++.+.|.+|++|++|+..+   .+++...+++.++++++++
T Consensus         1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~~l~~~~~~~v~~   77 (185)
T cd08439           1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHP---PPGASATILRRSPTVWYCA   77 (185)
T ss_pred             CeEEEcchhHhHHHHHHHHHHHHHHCCCeEEEEEECChHHHHHHHHCCCCcEEEEecc---CCCCCceEEEEecCEEEEC
Confidence            4899999999999999999999999999999999998889999999999999998532   3568889999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD  253 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~  253 (306)
                      ++||+..+.+        .|++....+...+..+..++...++.+++.+++++...+.+++.+|.|++++|...+..   
T Consensus        78 ~~~~~~~~~~--------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~---  146 (185)
T cd08439          78 AGYILAPGEP--------LPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPP---  146 (185)
T ss_pred             CCCccCcCCC--------ccEEEcCCCCcHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHcCceeeecccCCCCc---
Confidence            9999775432        37888877666777888899999999999999999999999999999999999987643   


Q ss_pred             CCceeeecCC--C-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         254 KNLRSISASH--L-FGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       254 ~~l~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ++..+|+..  + .....++++|+++. .++.++.|+++|
T Consensus       147 -~l~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~f~~~~  185 (185)
T cd08439         147 -DLRILGESEGLPPLPDTGYTLCLDPNR-PSELAQAFFEAL  185 (185)
T ss_pred             -cceEeccccCCCCCCcceEEEEecCCC-ccHHHHHHHhhC
Confidence             577777753  1 23568999998655 588999998864

This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari

>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold

Probab=99.91  E-value=4.2e-23  Score=158.89  Aligned_cols=191  Identities=11%  Similarity=0.132  Sum_probs=155.3

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      +|+||++.+....++++.+.+|.+++ ++++++...++.++.+.+.+|++|+++...+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~-~v~l~l~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~   78 (195)
T cd08428           1 TLPVAVNADSLATWFLPALAPVLKRE-RILLDLIVDDEDRTHDLLRDGEVVGCISTQA-QPMQGCRSDYLGSMDYLLVAS   78 (195)
T ss_pred             CEEEEechhHHHHHhHHHHHHHHhCc-CeEEEEEeCCchhHHHHHHcCcceEEEEecC-CCCCCceeEEeeeeeEEEEEC
Confidence            48999997766677888999999995 9999999998889999999999999997544 455789999999999999999


Q ss_pred             CCCCCCC-CCCcChhhhcCCCeEeecCCCCcH-HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLL-LNSISLKEISNYPLITYDLSFSGR-IKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++|+... ...++++||.++|+|.+..+...+ ..+...+...+ .+++.+++++...+.+++.+|.|++++|...+...
T Consensus        79 ~~~~~~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~G~Gi~~lp~~~~~~~  157 (195)
T cd08428          79 PDFAARYFPNGLTREALLKAPAVAFNRKDDLHQSFLQQHFGLPP-GSYPCHYVPSSEAFVDLAAQGLAYGMIPELQIEPE  157 (195)
T ss_pred             CcchhhcCCCCCCHHHHhcCcEEEEcCCCchhHHHHHHHhccCC-CCceEEEECCHHHHHHHHHhCCeeEeccHHHHHHH
Confidence            9998543 357999999999999988766553 23344443333 44567889999999999999999999999887654


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                       ..+.++.++  . ....+++++|++++..+++++.|++.
T Consensus       158 ~~~~~l~~l~--~-~~~~~~~l~~~~~~~~s~~~~~~~~~  194 (195)
T cd08428         158 LASGELIDLA--P-GHLLRVTLYWHRWNLESGLMKRLSRA  194 (195)
T ss_pred             hcCCCEEEcc--C-cccccceEEEecccccCHHHHHhhhc
Confidence             455565443  2 34579999999999999999999875

The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-

>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain

Probab=99.91  E-value=1.6e-24  Score=167.00  Aligned_cols=195  Identities=10%  Similarity=0.054  Sum_probs=154.4

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++++++..++++++..|.++||++++++...  ..+.+ +.++++|+||+..+ ...+++...+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~--~~~~~-~~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~   76 (197)
T cd08470           1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELT--NRVVD-LVSEGFDLAIRLGR-LTDSSLMARRLASRRHYVCA   76 (197)
T ss_pred             CeEEEEcCHHHHHHHHHHHHHHHHHHCCCeEEEEEec--CCccc-hhccCccEEEEcCC-CCccchhhhhccCCceEEEE
Confidence            5799999999999999999999999999999999853  24455 55678999998544 45577999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-  251 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-  251 (306)
                      +++|+...+..++++||.++|++...... .  .+.......+..+++.+++++..++++++.+|.|++++|.+.+... 
T Consensus        77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~  153 (197)
T cd08470          77 SPAYLERHGTPHSLADLDRHNCLLGTSDH-W--RFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHL  153 (197)
T ss_pred             CHHHHHHcCCCCCHHHHhhCCceeccCcC-c--eEcCCCcEEEecCCCcEEECCHHHHHHHHHcCCcEEEechHHhHHHH
Confidence            99986544456899999999999854321 1  1111122235567778999999999999999999999999877654 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..+.++.++..+......++++|++++..++.++.|++++++.
T Consensus       154 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  196 (197)
T cd08470         154 AAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA  196 (197)
T ss_pred             HcCCcEEccccccCCCCcEEEEeCCchhccHHHHHHHHHHHhc
Confidence            5566776654434456799999999988899999999998764

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene

>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.91  E-value=2.3e-24  Score=166.73  Aligned_cols=197  Identities=14%  Similarity=0.096  Sum_probs=153.9

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEE
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~  170 (306)
                      .|+++||++++++..++++++..|.++||++++++.....  .. .+.+|++|++|+.... ...+++.+.+++++++++
T Consensus         2 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~--~~-~~~~~~~D~~i~~~~~~~~~~~~~~~~l~~~~~~~   78 (202)
T cd08473           2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNR--RV-DLIEEGIDVALRVRFPPLEDSSLVMRVLGQSRQRL   78 (202)
T ss_pred             CceEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEEcCC--cc-cccccCccEEEEeCCCCCCCcceeEEeccCcceEE
Confidence            4789999999999999999999999999999999987543  23 3558899999974332 335789999999999999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCc--HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSG--RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++|+...+..++++||.++|++.+..+...  +..+...+...+..+++.+++++...+++++.+|.|++++|.+.+
T Consensus        79 v~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  158 (202)
T cd08473          79 VASPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC  158 (202)
T ss_pred             EECHHHHHhCCCCCChHHHhhCCeEEEEccCCCCceEeecCCCcEEEecCCCcEEECCHHHHHHHHHhCCCeeeccHHHH
Confidence            999998543334479999999999998765322  111222233345556778899999999999999999999999887


Q ss_pred             ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ... ..+.++.+..........++++|++++..+++++.|++++
T Consensus       159 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  202 (202)
T cd08473         159 REALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL  202 (202)
T ss_pred             HHHHHcCcEEEeccCCcCCCccEEEEecCCCCCCHHHhhHHhhC
Confidence            654 5666765543333345689999999999999999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.91  E-value=4.8e-24  Score=164.15  Aligned_cols=193  Identities=14%  Similarity=0.179  Sum_probs=149.1

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+|+||++ . ...++++++..|.++||++++++..  +.++.+.+.+ ++|++|+..+ ...+++...++.++++++++
T Consensus         1 g~l~ig~~-~-~~~~l~~~l~~~~~~~P~v~i~~~~--~~~~~~~l~~-~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~   74 (197)
T cd08476           1 GRLRVSLP-L-VGGLLLPVLAAFMQRYPEIELDLDF--SDRLVDVIDE-GFDAVIRTGE-LPDSRLMSRRLGSFRMVLVA   74 (197)
T ss_pred             CeEEEEec-c-hHHHHHHHHHHHHHHCCCeEEEEEe--cCCccccccc-CeeEEEEeCC-CCCCCeeEEEeecccEEEEE
Confidence            57999998 4 5678889999999999999999964  3455665655 4999998644 45678999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCC-cHHHH--HHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFS-GRIKL--DREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      +++|+...+..++++||.++|++.+..... ....+  ...+...+..++..+++++...+.+++.+|.|++++|...+.
T Consensus        75 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~ilp~~~~~  154 (197)
T cd08476          75 SPDYLARHGTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVR  154 (197)
T ss_pred             CHHHHHhCCCCCCHHHHhcCceEEeeccCCCCCcceEEecCCceEEEecCCceEECCHHHHHHHHHhCCeEEEcCHHHHH
Confidence            999964444578999999999998754322 11111  112233356678889999999999999999999999998776


Q ss_pred             cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .. ..+.++.++..+.....+++++|++++..++.++.|++++
T Consensus       155 ~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  197 (197)
T cd08476         155 EALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM  197 (197)
T ss_pred             HHhhcCCeEEccccccCCCCCEEEEecccccCCHHHHHHHhhC
Confidence            54 5566776654443456789999999998999999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=99.90  E-value=1.6e-23  Score=139.18  Aligned_cols=83  Identities=16%  Similarity=0.167  Sum_probs=77.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      |+.+++++|.+|+++| ||++||+.||+|||++|++|++||+.||.+||+|+     ++|+ +||++|+.|++.++++.+
T Consensus         2 ~~~~~l~~~~av~~~g-Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~-~lT~~G~~l~~~~~~~~~   79 (99)
T TIGR00637         2 ADPRRVALLKAIARMG-SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGA-VLTEYGQRLIQLYDLLER   79 (99)
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCe-eECHHHHHHHHHHHHHHH
Confidence            6889999999999999 99999999999999999999999999999999998     4588 799999999999999999


Q ss_pred             HHHHHHHHHH
Q psy3760          76 EIEGLKKIGK   85 (306)
Q Consensus        76 ~~~~~~~~~~   85 (306)
                      .++.+.+...
T Consensus        80 ~~~~~~~~~~   89 (99)
T TIGR00637        80 ILEKAFSVLE   89 (99)
T ss_pred             HHHHHHHHhh
Confidence            9988886443

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

>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold

Probab=99.90  E-value=2.3e-23  Score=159.60  Aligned_cols=187  Identities=18%  Similarity=0.170  Sum_probs=153.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++++++..++++++..|.++||++++++....   ....+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~---~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   76 (190)
T cd08483           1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSA---DLVDLRPDGIDVAIRYGN-GDWPGLESEPLTAAPFVVVAA   76 (190)
T ss_pred             CeEEEeCcHHHHhhHHhhHHHHHHHCCCceEEEEecC---CcCCCCCCCcCEEEEecC-CCCCCcEEEeecccceEeeeC
Confidence            3899999999999999999999999999999997532   356799999999999643 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee--EEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY--IVLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++| ++.+..++++||.++|++.....    ..+..++...|..++  ..+++++...+.+++.+|.|++++|...+...
T Consensus        77 ~~~-~~~~~~~~~~~L~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~  151 (190)
T cd08483          77 PGL-LGDRKVDSLADLAGLPWLQERGT----NEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPD  151 (190)
T ss_pred             HHH-HhhCCCCCHHHHhcCceeccCCc----hHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcCCcEEeecHHhhHHH
Confidence            997 56666799999999999985422    345678888888765  46889999999999999999999999887654


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++.++... .....++++|+++. .++.++.|++++
T Consensus       152 ~~~~~l~~~~~~~-~~~~~~~l~~~~~~-~~~~~~~f~~~l  190 (190)
T cd08483         152 IAAGRLTVLFEEE-EEGLGYHIVTRPGV-LRPAAKAFVRWL  190 (190)
T ss_pred             HHCCCcccccccc-CCCCcEEEEecCCC-CCHHHHHHhhhC
Confidence             456676665442 34578999998875 689999998864

The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=99.90  E-value=7.2e-24  Score=128.53  Aligned_cols=60  Identities=37%  Similarity=0.588  Sum_probs=56.4

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ   64 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~   64 (306)
                      |++|++|++++++| |+++||+.||+|||++|++|++||++||++||+|+++++ .||++|+
T Consensus         1 l~~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~-~lT~~G~   60 (60)
T PF00126_consen    1 LRQLRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVPLFERSGRGL-RLTEAGE   60 (60)
T ss_dssp             HHHHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSSE-EE-HHHH
T ss_pred             ChHHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEECCCCe-eEChhhC
Confidence            68999999999999 999999999999999999999999999999999999998 7999996

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>TIGR02136 ptsS_2 phosphate binding protein

Probab=99.90  E-value=1.7e-22  Score=163.84  Aligned_cols=211  Identities=15%  Similarity=0.164  Sum_probs=164.0

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCceee
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLISI  161 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~~  161 (306)
                      .+..|+||+++++.. ++++++..|.++||++++++....+.++++.|.+|++|++++..+...         ..++...
T Consensus        34 ~~~~lrig~s~s~~~-~lp~~l~~f~~~~P~i~v~i~~~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~  112 (287)
T TIGR02136        34 GSSTITIDGSTTVAP-LAEAAAEEFQKIHPGVSVTVQGAGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEH  112 (287)
T ss_pred             ccceEEEeccchHHH-HHHHHHHHHHhhCCCceEEEccCCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEE
Confidence            456899999999764 899999999999999999999999999999999999999998643221         1248899


Q ss_pred             ccccceEEEEecCCC-CCCCC-----------CCcCh----hhhcCCCeEeec--CCCCcHHHHHHHH-HhCCCceeEEE
Q psy3760         162 PCYQWEYVIIVPLDH-PLLLL-----------NSISL----KEISNYPLITYD--LSFSGRIKLDREF-SLQKLTPYIVL  222 (306)
Q Consensus       162 ~l~~~~~~~v~~~~~-~l~~~-----------~~i~~----~dl~~~~~i~~~--~~~~~~~~~~~~~-~~~~~~~~~~~  222 (306)
                      +++.++++++++++| |++..           ...++    +||.++|++...  .+...+..+.+++ ...+..++.. 
T Consensus       113 ~l~~~~l~lvv~~~h~pl~~~~~~~L~~l~~~~~~s~~~l~~dL~~~pli~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-  191 (287)
T TIGR02136       113 KVAVDGLAVVVNKKNVPVDDLTVEQLKKIYSGEITNWKEVGGDLPNKPIVVVGRNAGSGTRDTFEEEVMGKAKIKPGKN-  191 (287)
T ss_pred             EEEEeeEEEEECCCCCccccCCHHHHHHHhcCCcCcHhhcCCCCCCCceEEEecCCCCChHHHHHHHhccccccCccce-
Confidence            999999999999998 98753           23466    455689998854  4445777777765 4556666554 


Q ss_pred             EecCHHHHHHHHHhcc-ceeeeecceeccc-ccCCceeee-----cCC--CCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         223 ETINSDIIKTYVELRM-GIGIIASIAFDSN-RDKNLRSIS-----ASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~~~~l~~~~-----~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ++++.++++++|..|. |++++|...+... ....+..++     +..  ....++++++|++++..++.++.|++++++
T Consensus       192 ~~~s~~~i~~~V~~g~~gia~lp~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~~~~l~L~~~~~~~~~~~~~~f~~~l~~  271 (287)
T TIGR02136       192 EQESNGAVVSIVSSNPGAIGYLGLGYVDDSVKTLKVNGVEPSKENIANGSYPLSRPLFMYVNGKPKKPELVAEFIDFVLS  271 (287)
T ss_pred             ecCCcHHHHHHHhcCCCceEEeehHHhhCCcceEEECCccCCHHHHhCCCccceeeEEEEEcCCCCCcHHHHHHHHHHhC
Confidence            9999999999999997 8999999887653 211111111     111  135779999999999999999999999988


Q ss_pred             Hh-hHHHHHhh
Q psy3760         294 KL-NRKFINKI  303 (306)
Q Consensus       294 ~~-~~~~~~~~  303 (306)
                      .- .+...++.
T Consensus       272 ~~~~~~~~~~~  282 (287)
T TIGR02136       272 DDGGERIVEEL  282 (287)
T ss_pred             chHhhHHHHHc
Confidence            77 56655554

Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.

>cd08480 PBP2_CrgA_like_10 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold

Probab=99.89  E-value=2.1e-23  Score=161.04  Aligned_cols=191  Identities=12%  Similarity=0.157  Sum_probs=149.7

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |.|+||++.+++..++++++..|.++||++++++...  .+..+ +.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus         1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~--~~~~~-~~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~   76 (198)
T cd08480           1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLT--DEVVD-LLAERTDVAIRVGP-LPDSSLVARKLGESRRVIVA   76 (198)
T ss_pred             CeEEEEccHHHHhHhhHHHHHHHHHHCCCeEEEEEec--CCccc-cccccccEEEEeCC-CCCCCeEEEEcccceEEEEE
Confidence            5799999999999999999999999999999999742  34444 55899999998644 45578999999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHH-HHhCCCc----eeEEEEecCHHHHHHHHHhccceeeeecce
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE-FSLQKLT----PYIVLETINSDIIKTYVELRMGIGIIASIA  247 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~-~~~~~~~----~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~  247 (306)
                      +++|+......++++||.++|+|.......    +..+ +...+..    ++..+++++..++++++..|.|++++|...
T Consensus        77 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~  152 (198)
T cd08480          77 SPSYLARHGTPLTPQDLARHNCLGFNFRRA----LPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFH  152 (198)
T ss_pred             CHHHHHhcCCCCCHHHHHhCcceeecccCc----ccCeeEcCCCcEEEEEecCcEEECCHHHHHHHHHcCCeEEeccHHH
Confidence            999964444678999999999997643221    2233 3434432    344678999999999999999999999977


Q ss_pred             eccc-ccCCceeeecC-CCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         248 FDSN-RDKNLRSISAS-HLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       248 ~~~~-~~~~l~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +... ..+.++.+... .+.....++++|+++...++.++.|++++
T Consensus       153 ~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  198 (198)
T cd08480         153 VADDIAAGRLVPVLEEYNPGDREPIHAVYVGGGRLPARVRAFLDFL  198 (198)
T ss_pred             HHHHHhcCCeEEeCCCCCCCCCccEEEEEcCcccCChhhhhhhhcC
Confidence            6543 55667755322 22345789999999999999999999864

This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene

>cd08482 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold

Probab=99.89  E-value=2.6e-22  Score=154.51  Aligned_cols=190  Identities=12%  Similarity=0.017  Sum_probs=151.5

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++.+++..++++++..|.++||++++++...+.  ..+ +..+++|++|+..+....+++...++.+++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~i~~f~~~~P~v~i~~~~~~~--~~~-~~~~~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~~   77 (195)
T cd08482           1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDG--PVD-SLRDGIDAAIRFNDAPWPAGMQVIELFPERVGPVCS   77 (195)
T ss_pred             CeEEEecHHHHHHHHHhhHHHHHHHCCCceEEEEecCC--ccc-cccCCcCEEEEcCCCCCCCCceEEEeecCcEEeeeC
Confidence            38999999999999999999999999999999987542  333 455789999986543335789999999999999999


Q ss_pred             CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc---eeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT---PYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++||++.+ ..++++||.++|++.....   ...+..++...|..   ++..+++++...+.+++..|.|++++|...+.
T Consensus        78 ~~~~~~~~~~~~~l~~L~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Gv~~lp~~~~~  154 (195)
T cd08482          78 PSLAPTVPLRQAPAAALLGAPLLHTRSR---PQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVR  154 (195)
T ss_pred             HHHHhhCCCCCCCHHHHhcCceeccCCC---HHHHHHHHHHcCCCcCCcccCceeCchHHHHHHHHcCCceEeccHHhhH
Confidence            99998765 4689999999999986432   13456677777764   35678999999999999999999999998876


Q ss_pred             cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .. ..+.++. +++. ......+++|++++..++.++.|++++
T Consensus       155 ~~~~~~~l~~-~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~  195 (195)
T cd08482         155 DDLASGRLVA-PWGF-IETGSHYVLLRPARLRDSRAGALADWL  195 (195)
T ss_pred             HHHhCCCeec-cCCc-CcCCCceEEEeccccCChHHHHHhhhC
Confidence            54 5666664 4543 334567778877776789999999864

TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cy

>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold

Probab=99.89  E-value=2.5e-22  Score=154.10  Aligned_cols=186  Identities=12%  Similarity=0.018  Sum_probs=150.8

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++.+++..++++++.+|.++||++++++...+..   ..+.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~~---~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~   76 (191)
T cd08488           1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNR---VDIAAEGLDYAIRFGS-GAWHGIDATRLFEAPLSPLCT   76 (191)
T ss_pred             CEEEEecHHHHHHHHHhHHHHHHHHCCCcEEEEEecCCc---cccCCCCccEEEEecC-CCCCCcEEEEccCCcEEEEeC
Confidence            389999999999999999999999999999999876543   2566889999998644 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce----eEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP----YIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      +++  +. ..++++||.++|++.....    ..+.+++...+..+    ...+++++...+.+++.+|.|++++|.+++.
T Consensus        77 ~~l--~~-~~~~~~dL~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~  149 (191)
T cd08488          77 PEL--AR-QLREPADLARHTLLRSYRA----DEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFS  149 (191)
T ss_pred             HHH--hc-ccCCHHHHhhCcEEecCCc----cHHHHHHHHcCCCCccccccccccCchHHHHHHHHhCCCeEEechHhhH
Confidence            873  33 4689999999999974322    24567788777654    3456789999999999999999999998775


Q ss_pred             cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .. ..+.++ +++........++++|++++..++.++.|++++
T Consensus       150 ~~~~~~~l~-~~l~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~  191 (191)
T cd08488         150 RQLASGALV-QPFATTLSTGSYWLTRLQSRPETPAMSAFSAWL  191 (191)
T ss_pred             HHHHCCCee-ccccccccCCcEEEEeccccCCCHHHHHHHhhC
Confidence            44 444454 677654456689999999999999999999874

AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl

>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold

Probab=99.89  E-value=3.9e-22  Score=152.68  Aligned_cols=186  Identities=13%  Similarity=0.057  Sum_probs=149.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||+.++++..++++.+..|.++||++++++....  .+.+ +.+|++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~--~~~~-~~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~   76 (189)
T cd08487           1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNN--NVVD-LATEGLDFAIRFGE-GLWPATHNERLLDAPLSVLCS   76 (189)
T ss_pred             CeEEEecHHHHHHHHhHHHHHHHHHCCCceEEeeecC--Cccc-cccCCcCEEEEecC-CCCCCceeeeeccCceeeeeC
Confidence            4899999999999999999999999999999998653  3444 66678999998644 445789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      ++|+   ...++++||.++|++....    .+.+.+++...|..++..  .++++..++..++.+|.|++++|...+...
T Consensus        77 ~~~~---~~~~~~~~l~~~~~i~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~  149 (189)
T cd08487          77 PEIA---KRLSHPADLINETLLRSYR----TDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSRE  149 (189)
T ss_pred             HHHh---ccCCCHHHHhcCceeecCC----chHHHHHHHHcCCCCccccCCccccHHHHHHHHHhCCCeEeehHHHHHHH
Confidence            9984   2468999999999996422    123556788888776542  578999999999999999999999877554


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.++ .+++.......++++|++++..+|.+++|++++
T Consensus       150 ~~~~~l~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~  189 (189)
T cd08487         150 IENGQLV-QPFKIEVETGSYWLTWLKSKPMTPAMELFRQWI  189 (189)
T ss_pred             HhCCCEE-cccCcccCCCcEEEEecccccCCHHHHHHHhhC
Confidence             444444 466654456789999999999999999999874

This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is

>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold

Probab=99.88  E-value=5.3e-22  Score=151.99  Aligned_cols=186  Identities=14%  Similarity=0.027  Sum_probs=149.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP  173 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~  173 (306)
                      .|+||++++++..++++++..|.++||++++++...+.  ..+ +.++++|++|+..+ ...+++...++++++++++++
T Consensus         1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~--~~~-~~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~~   76 (189)
T cd08484           1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNN--RVD-IAAEGLDFAIRFGE-GAWPGTDATRLFEAPLSPLCT   76 (189)
T ss_pred             CEEEEecHHHHHHHHHhhhHHHHHHCCCceEEEecccC--ccc-cccCCccEEEEecC-CCCCCceEEEccCCceEEeeC
Confidence            38999999999999999999999999999999987543  334 44556999999644 456789999999999999999


Q ss_pred             CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760         174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLETINSDIIKTYVELRMGIGIIASIAFDSN  251 (306)
Q Consensus       174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~  251 (306)
                      +++  + ...++++||.++|++.....    ..+.+++...+..+..  .+++++...+.+++.+|.|++++|...+...
T Consensus        77 ~~~--~-~~~~~~~~L~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~  149 (189)
T cd08484          77 PEL--A-RRLSEPADLANETLLRSYRA----DEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRE  149 (189)
T ss_pred             HHH--h-cccCChhHhhcCceEecCCC----chHHHHHHHcCCCCCcccCcccccHHHHHHHHHhCCCeEEecHHhHHHH
Confidence            885  2 24689999999999964321    2356678878877544  4788999999999999999999999877654


Q ss_pred             -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                       ..+.+. .+++.....++++++|+++...++.++.|++++
T Consensus       150 ~~~~~l~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l  189 (189)
T cd08484         150 LASGALV-QPFKITVSTGSYWLTRLKSKPETPAMSAFSQWL  189 (189)
T ss_pred             HHCCCEE-eecccccCCCCEEEEeccccccchhhHHHHhhC
Confidence             445554 466654456789999999999999999999864

This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol

>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional

Probab=99.83  E-value=9.5e-20  Score=163.05  Aligned_cols=186  Identities=17%  Similarity=0.172  Sum_probs=162.5

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--------------CCCC
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--------------PSDK  157 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--------------~~~~  157 (306)
                      .++|+||++.+++..++++++..     |++++++...++.++++.|.+|++|+|++.....              ..++
T Consensus       416 ~~~L~Ig~~~~~~~~~Lp~~l~~-----P~v~i~v~~~~s~~vl~~L~~GeiDlai~~~~~~~~~~~~~~~~~~~~~~~~  490 (633)
T PRK14498        416 PPTLVIIGSHDPGLDLLLDLLAR-----RGLRLRSLHVGSMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGED  490 (633)
T ss_pred             ccceEEEccCchHHHHHHHHhhc-----cCCceeEEecCCHHHHHHHHcCCceEEEEcccCcccccccHHHHHhhcCCCC
Confidence            58999999999999999998887     9999999999999999999999999999864321              1335


Q ss_pred             ceeeccccceEEEEecCCCCCCCCCCcChhhhcCC--CeEeecCCCCcHHHHHHHHHhCCCceeE----EEEecCHHHHH
Q psy3760         158 LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY--PLITYDLSFSGRIKLDREFSLQKLTPYI----VLETINSDIIK  231 (306)
Q Consensus       158 ~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~  231 (306)
                      +.+.++++++++++++++||++   .++++||.++  ||+....+...+..++++|.+.|+.++.    .+++++.+++.
T Consensus       491 l~~~~l~~d~lvlvvp~~hPl~---~isl~dL~~~~~plI~~~~gs~~r~~le~~l~~~Gi~~~~i~~~~~e~~s~~~i~  567 (633)
T PRK14498        491 AVLVKGYRREQGLVVRKGNPKG---IEGIEDLVRKDVRFVNRQRGSGTRILLDYHLKELAIDPERINGYDREEKTHMAVA  567 (633)
T ss_pred             EEEEEEEEEeEEEEECCCCCCC---CCCHHHhccCCcEEEecCCCchHHHHHHHHHHHcCCCHHHCCCcccccCCHHHHH
Confidence            8999999999999999999975   4899999999  9999999988999999999999999874    68999999999


Q ss_pred             HHHHhc---cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         232 TYVELR---MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       232 ~~v~~g---~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .+|.+|   .|+++++.  . .  ..++..++++.    ..++++|++++..++++++|++++++.
T Consensus       568 ~~V~~G~~d~Gi~i~~~--~-~--~~~l~~i~l~~----~~~~l~~~~~~~~s~a~~aFl~~l~~~  624 (633)
T PRK14498        568 AAVAQGRADAGLGIRAA--A-K--ALGLDFIPLAE----EEYDLLIPKERLEKPAVRAFLEALKSP  624 (633)
T ss_pred             HHHHcCCCcchHhHHHH--H-H--HcCCCCeeeee----EEEEEEEEhhHccCHHHHHHHHHHcCH
Confidence            999999   89999985  1 1  23577777763    268999999999999999999999764

>PRK10676 DNA-binding transcriptional regulator ModE; Provisional

Probab=99.81  E-value=2.4e-19  Score=141.80  Aligned_cols=98  Identities=14%  Similarity=0.164  Sum_probs=83.1

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +++++++|.+|+++| ||++||+.||+|||++|++|++||+++|.+||+|.     ++|+ +||++|+.|+    ++++.
T Consensus        18 ~~~~l~~l~~v~~~g-S~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~-~lT~~G~~l~----~~~~~   91 (263)
T PRK10676         18 DPRRISLLKQIALTG-SISQGAKLAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGA-VLTRYGERLI----QLYDL   91 (263)
T ss_pred             CHHHHHHHHHHHHHC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCc-EECHHHHHHH----HHHHH
Confidence            689999999999999 99999999999999999999999999999999998     8888 7999999999    57777


Q ss_pred             HHHHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHH
Q psy3760          77 IEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEF  115 (306)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~  115 (306)
                      ++++...+.+...          ........+++++..|
T Consensus        92 ~~~~~~~~~~~~~----------~~~~~~~~l~~~l~~~  120 (263)
T PRK10676         92 LAQIQQKAFDVLD----------DDALPLDSLLAAISRF  120 (263)
T ss_pred             HHHHHHHHHHHhh----------hcccchHHHHHHHHHh
Confidence            7776666555432          3334556677777777

>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []

Probab=99.44  E-value=1e-11  Score=94.09  Aligned_cols=171  Identities=16%  Similarity=0.169  Sum_probs=141.8

Q ss_pred             HHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC--------------CCceeeccccceEEEEecCCCCC
Q psy3760         113 KEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS--------------DKLISIPCYQWEYVIIVPLDHPL  178 (306)
Q Consensus       113 ~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~--------------~~~~~~~l~~~~~~~v~~~~~~l  178 (306)
                      ..|.+++|++.+.+...++...+..|.+|.+|++.++......              ..+....++.....+++++++|+
T Consensus         2 e~~~~~~~~~~v~~~~~gS~~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~~r~~Gl~v~~~np~   81 (193)
T PF12727_consen    2 EEFARREPGVRVAVQYTGSRAGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLARREQGLIVRPGNPK   81 (193)
T ss_pred             hHHHhhCCCCeEEEEecCCHHHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeEEeeeEEEeCCCCc
Confidence            4688899999999999999999999999999999986432211              24667888888999999999985


Q ss_pred             CCCCCcChhhh--cCCCeEeecCCCCcHHHHHHHHHhCCCcee----EEEEecCHHHHHHHHHhc-cceeeeecceeccc
Q psy3760         179 LLLNSISLKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPY----IVLETINSDIIKTYVELR-MGIGIIASIAFDSN  251 (306)
Q Consensus       179 ~~~~~i~~~dl--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~  251 (306)
                         ...+++||  .+..+|..+.+++.+..+++++...++.+.    ..-+..+...+..+|..| .-+++.....+.. 
T Consensus        82 ---~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~AD~G~g~~~~A~~-  157 (193)
T PF12727_consen   82 ---GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGKADAGIGIRAAAEE-  157 (193)
T ss_pred             ---cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCCCCEEeehHHHHHh-
Confidence               45689999  677899999999999999999999988752    235788999999999999 5677766666543 


Q ss_pred             ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                       -.+|.++|+..    ..+.++.+++....|.+++|+++++
T Consensus       158 -~~gL~Fvpl~~----E~~dlv~~~~~~~~~~vq~ll~~l~  193 (193)
T PF12727_consen  158 -FYGLDFVPLAE----ERYDLVIRREDLEDPAVQALLDFLQ  193 (193)
T ss_pred             -hcCCCcEEccc----cceEEEEEhhHcCCHHHHHHHHHhC
Confidence             35899999987    3788999999999999999999885

It is often associated with a helix-turn-helix domain.

>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional

Probab=99.33  E-value=7.7e-11  Score=97.53  Aligned_cols=201  Identities=12%  Similarity=0.059  Sum_probs=133.0

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC---CCCCceeec--
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS---PSDKLISIP--  162 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~--  162 (306)
                      ....++||||+.++....+++..+..|.+.+|++++++... +...+.+.|.+|++|+++......   ...++....  
T Consensus        23 ~~~~~~lrIg~~~~~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~g~~~~~v~  102 (314)
T PRK11553         23 ESSPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVG  102 (314)
T ss_pred             cCCCCeEEEEeCCCchHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEccCCHHHHHHHhCCCCEEEEE
Confidence            44678999999998888889999999999999999999987 456899999999999999742111   123343333  


Q ss_pred             ---cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhcc
Q psy3760         163 ---CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELRM  238 (306)
Q Consensus       163 ---l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g~  238 (306)
                         ......+++++++|++.     +++||.+.++.. ..+...+..+..+++..|+.+.. .....+...+..++.+|.
T Consensus       103 ~~~~~~~~~~lvv~~~s~i~-----s~~dL~Gk~I~~-~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~  176 (314)
T PRK11553        103 VEPPKPKAEVILVAENSPIK-----TVADLKGHKVAF-QKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGN  176 (314)
T ss_pred             EecCCCcceEEEEeCCCCCC-----CHHHhCCCEEee-cCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCC
Confidence               33345789999999864     899999999554 55666777888899999987633 234446666778888884


Q ss_pred             ceee-eecceeccc-ccCCceeeecCC-CCccceEEEEEeC-CccccHHHHHHHHHHhHHh
Q psy3760         239 GIGI-IASIAFDSN-RDKNLRSISASH-LFGTTISRVIIKQ-GTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       239 gi~~-~p~~~~~~~-~~~~l~~~~~~~-~~~~~~~~l~~~~-~~~~~~~~~~~~~~l~~~~  295 (306)
                      .=++ +.+...... ..+....+.... ......++++..+ ....+..+++|++.+.+..
T Consensus       177 vDa~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A~  237 (314)
T PRK11553        177 VDAWAIWDPYYSAALLQGGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEAD  237 (314)
T ss_pred             CCEEEEcCcHHHHHHhcCCcEEeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHHH
Confidence            3333 333332222 233444332222 1222233333322 1345678888888876653

>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed

Probab=99.20  E-value=1.8e-10  Score=93.46  Aligned_cols=166  Identities=15%  Similarity=0.188  Sum_probs=123.6

Q ss_pred             HHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccceEEEEecCCCCCCCCCCcChhh
Q psy3760         114 EFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKE  188 (306)
Q Consensus       114 ~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~d  188 (306)
                      .|...+|++.+++....+.++...|.+|++|++++......     ...+....+....++++++++|++.     +++|
T Consensus        36 ~~~~~~p~~~ie~~~~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~i~-----sl~D  110 (287)
T PRK00489         36 SLIATDEDNPIEVLFLRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDSDWQ-----GVED  110 (287)
T ss_pred             ceEeecCCCCEEEEEECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCCCCC-----ChHH
Confidence            47788999999999999999999999999999998522111     2233344577889999999999864     4899


Q ss_pred             hcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCCCCcc
Q psy3760         189 ISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGT  267 (306)
Q Consensus       189 l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~  267 (306)
                      |.+.....     .....+.+++.+.|+.++++...++.+.   ++..|.+.++++....... ..++++.+  + ....
T Consensus       111 L~Gk~ia~-----~~~~~~~~~l~~~gi~~~iv~~~gs~ea---a~~~G~aDaivd~~~~~~~l~~~~L~~v--~-~~~~  179 (287)
T PRK00489        111 LAGKRIAT-----SYPNLTRRYLAEKGIDAEVVELSGAVEV---APRLGLADAIVDVVSTGTTLRANGLKIV--E-VILR  179 (287)
T ss_pred             hCCCEEEE-----cCcHHHHHHHHHcCCceEEEECCCchhh---hhcCCcccEEEeeHHHHHHHHHCCCEEE--E-eeee
Confidence            98885544     2346778899999998887777777775   4556999999986544333 44567776  2 3345


Q ss_pred             ceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         268 TISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       268 ~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      ...++++++ ++.++..+.|++.+...++
T Consensus       180 ~~~~li~~k-~~~~~~~~~~i~~~l~~l~  207 (287)
T PRK00489        180 SEAVLIARK-GWLDPEKQEKIDQLLTRLQ  207 (287)
T ss_pred             eeEEEEEcc-cccChhHHHHHHHHHHHHH
Confidence            578999998 6678888888887776663

>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]

Probab=99.19  E-value=3.7e-10  Score=77.41  Aligned_cols=83  Identities=19%  Similarity=0.184  Sum_probs=72.6

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +...++.+.+|.++| |++.||+.++||.-..+..|+.+|+-+|.+|+++..     +|- .||+.|+++++....+-..
T Consensus        18 g~g~~~LL~~I~etG-SIs~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga-~LT~~g~~ll~~y~~l~~~   95 (130)
T COG2005          18 GPGRIELLKAIAETG-SISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGA-VLTDFGERLLEEYRLLEKE   95 (130)
T ss_pred             CchHHHHHHHHHHhC-CHHHHHHHcCCCHHHHHHHHHHHHHHhCCCeeeeccCCCCCCcc-hhHHHHHHHHHHHHHHHHH
Confidence            446788999999999 999999999999999999999999999999999762     334 7999999999999999888


Q ss_pred             HHHHHHHHHh
Q psy3760          77 IEGLKKIGKE   86 (306)
Q Consensus        77 ~~~~~~~~~~   86 (306)
                      +++.......
T Consensus        96 ~~~~~~~~~~  105 (130)
T COG2005          96 IEEALRKLED  105 (130)
T ss_pred             HHHHHHHHhh
Confidence            8887764443

>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions

Probab=99.02  E-value=1.9e-08  Score=78.15  Aligned_cols=185  Identities=14%  Similarity=0.128  Sum_probs=119.9

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCC-ceeeccccceEEEEecCCCCCCCCC
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDK-LISIPCYQWEYVIIVPLDHPLLLLN  182 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~-~~~~~l~~~~~~~v~~~~~~l~~~~  182 (306)
                      .+...++..+.++.+ +++++...+..+..+.|.+|++|+++.......  ... .-..++....++++++++++..   
T Consensus        23 G~~~~~~~~~~~~~g-~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   98 (218)
T cd00134          23 GFDVDLAKAIAKELG-VKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIK---   98 (218)
T ss_pred             eeeHHHHHHHHHHhC-CeEEEEeCCHHHHHHHHhcCCcCEEeecCcCCHHHHhhccCcccceeccEEEEEECCCCCC---
Confidence            455689999999886 999999999999999999999999998531111  111 2344788889999999998743   


Q ss_pred             CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecc-eeccc-cc--CCcee
Q psy3760         183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASI-AFDSN-RD--KNLRS  258 (306)
Q Consensus       183 ~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~-~~--~~l~~  258 (306)
                        +++||.+.++... .+......+.+.+.     ......+++...++.++..|.+-+++... ..... ..  ..+..
T Consensus        99 --~~~dl~g~~i~~~-~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~  170 (218)
T cd00134          99 --SVKDLKGKKVAVQ-KGSTAEKYLKKALP-----EAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKI  170 (218)
T ss_pred             --ChHHhCCCEEEEE-cCchHHHHHHHhCC-----cccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEE
Confidence              8999999988877 33333333333322     23455788899999999999766655543 32222 22  56777


Q ss_pred             eecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         259 ISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       259 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ++.........+.+..++.  .......|-+++.+.-+....+.+.
T Consensus       171 ~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~l~~~~~~g~~~~i~  214 (218)
T cd00134         171 VGPSIDLEPLGFGVAVGKD--NKELLDAVNKALKELRADGELKKIS  214 (218)
T ss_pred             eccccCCCccceEEEEcCC--CHHHHHHHHHHHHHHHhCccHHHHH
Confidence            6665333333444443333  2355666666665554444445444

PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.

>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family

Probab=99.01  E-value=1.9e-08  Score=83.59  Aligned_cols=167  Identities=16%  Similarity=0.133  Sum_probs=115.7

Q ss_pred             CCCCcEEEEecccchhh-hhHHHH-HHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc--------------
Q psy3760          90 YDTGNLTIATTHTQARY-ALPKII-KEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL--------------  152 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~-~l~~~l-~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~--------------  152 (306)
                      ...+.|+||+..+...+ .++..+ ..+.+.+|++++++.. .++.+.++.|.+|++|+++.....              
T Consensus        27 ~~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~  106 (320)
T TIGR02122        27 GEPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFE  106 (320)
T ss_pred             CCCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccC
Confidence            55679999998776664 444444 5567888999999998 566688999999999999985221              


Q ss_pred             CCCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEecCHHH
Q psy3760         153 SPSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LETINSDI  229 (306)
Q Consensus       153 ~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~  229 (306)
                      ....++. ...++.+.+++++++++++.     +++||.+.+++....+...+..+..+++..|+.+...  +...+...
T Consensus       107 ~~~~~~~~v~~~~~~~~~lvv~~d~~i~-----sl~dL~gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~  181 (320)
T TIGR02122       107 GPVEKLRALASLYPEYIQIVVRKDSGIK-----TVADLKGKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAE  181 (320)
T ss_pred             CCCccHHhHHHhccccEEEEEECCCCCC-----cHHHcCCCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHH
Confidence            0123333 34677888899999998753     8899999998887666666667788888889876432  34456677


Q ss_pred             HHHHHHhccceeee-----ecceeccc-ccCCceeeec
Q psy3760         230 IKTYVELRMGIGII-----ASIAFDSN-RDKNLRSISA  261 (306)
Q Consensus       230 ~~~~v~~g~gi~~~-----p~~~~~~~-~~~~l~~~~~  261 (306)
                      +...+.+|..=+++     |...+... ..++++.+++
T Consensus       182 ~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~l~~l~~  219 (320)
T TIGR02122       182 AADALKDGKIDAAFYTAGTPTAAITELATSLDIRIVPI  219 (320)
T ss_pred             HHHHHHCCCccEEEEecCCChHHHHHHHhcCCeEEEeC
Confidence            78888888332222     11122233 5567766665

This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.

>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family

Probab=98.90  E-value=1.2e-07  Score=77.49  Aligned_cols=195  Identities=11%  Similarity=0.031  Sum_probs=126.6

Q ss_pred             EEEEecc-cchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeecccc--
Q psy3760          95 LTIATTH-TQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQ--  165 (306)
Q Consensus        95 l~I~~~~-~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~--  165 (306)
                      ||||+.+ +....+++.....|.+..|++++++... +..+..+.|.+|++|+++......     ....+.......  
T Consensus         1 l~vg~~~~~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~   80 (288)
T TIGR01728         1 VRIGYQKNGHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDN   80 (288)
T ss_pred             CeEEecCCCchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCC
Confidence            6899988 6677788999999999999899999885 556889999999999998642111     112344333322  


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc-cceeee
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR-MGIGII  243 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g-~gi~~~  243 (306)
                      ....++++++++..     +++||.+.++.. ..+......+...+...|+.+.. .....+...+..++.+| ..++++
T Consensus        81 ~~~~~v~~~~~~i~-----s~~dL~Gk~i~~-~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda~~~  154 (288)
T TIGR01728        81 KATAIVVIKGSPIR-----TVADLKGKRIAV-PKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDAWAI  154 (288)
T ss_pred             CceEEEECCCCCCC-----CHHHcCCCEEEe-cCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCEEEe
Confidence            36778888776532     789999988554 44555566777888888987643 33435567788899998 666667


Q ss_pred             ecceeccc-ccCCceeee-cCCCCccc-eEEEEEeCC--ccccHHHHHHHHHHhHHh
Q psy3760         244 ASIAFDSN-RDKNLRSIS-ASHLFGTT-ISRVIIKQG--TYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       244 p~~~~~~~-~~~~l~~~~-~~~~~~~~-~~~l~~~~~--~~~~~~~~~~~~~l~~~~  295 (306)
                      +....... ..+..+.+. ..+..... ...++.+++  ...+..++.|++.+.+..
T Consensus       155 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a~  211 (288)
T TIGR01728       155 WEPWGSALVEEGGARVLANGEGIGLPGQPGFLVVRREFAEAHPEQVQRVLKVLVKAR  211 (288)
T ss_pred             ccchHhHHhhccCCEEEEcCCccCCCCcceEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence            76555444 334444332 22211111 233444443  224566788887775554

Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.

>PRK09729 hypothetical protein; Provisional

Probab=98.87  E-value=1e-08  Score=62.81  Aligned_cols=62  Identities=11%  Similarity=0.118  Sum_probs=56.1

Q ss_pred             HHHHhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         232 TYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       232 ~~v~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .||++|.|++++|+..... ..++++.+|++ +.+.+.++++|+++...+++++.|++++.+..
T Consensus         2 ~mV~~GLGIsIlP~l~l~~-~~~~v~~~~L~-~~~~R~IgLa~~~~~~~s~Aa~~f~~~l~~~~   63 (68)
T PRK09729          2 NFIRQGLGIALQPELTLKS-IAGELCSVPLE-PTFYRQISLLAKEKPVEGSPLFLLQTCTEQLV   63 (68)
T ss_pred             hHHHcCCcEEEchHHHhcc-CCCCEEEEECC-CCceEEEEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence            6899999999999999876 46899999996 57889999999999999999999999998764

>smart00062 PBPb Bacterial periplasmic substrate-binding proteins

Probab=98.82  E-value=4.9e-07  Score=70.12  Aligned_cols=184  Identities=12%  Similarity=0.117  Sum_probs=112.3

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CC-CceeeccccceEEEEecCCCCCCCCC
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SD-KLISIPCYQWEYVIIVPLDHPLLLLN  182 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~-~~~~~~l~~~~~~~v~~~~~~l~~~~  182 (306)
                      .+...++..+.++. ++.+++...+..++.+.+.+|++|+++.......  .. -....++.....+++++++++     
T Consensus        24 G~~~~~~~~~~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----   97 (219)
T smart00062       24 GFDVDLAKAIAKEL-GLKVEFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDSP-----   97 (219)
T ss_pred             cchHHHHHHHHHHh-CCeEEEEeccHHHHHHHHHCCcccEEeccccCCHHHHhheeeccceeeceeEEEEecCCC-----
Confidence            34555788888876 5999999988999999999999999998532111  11 224567777888999999886     


Q ss_pred             CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc-cc---CCce
Q psy3760         183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN-RD---KNLR  257 (306)
Q Consensus       183 ~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~~---~~l~  257 (306)
                      ..+++||.+.++.... +.....    ++...+... .....++...+..++.+|. ..++++....... ..   ..+.
T Consensus        98 ~~~~~dL~g~~i~~~~-g~~~~~----~~~~~~~~~-~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~  171 (219)
T smart00062       98 IKSLEDLKGKKVAVVA-GTTGEE----LLKKLYPEA-KIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELK  171 (219)
T ss_pred             CCChHHhCCCEEEEec-CccHHH----HHHHhCCCc-eEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCcee
Confidence            3588999888777665 333322    333222222 3445667788888888884 4455555543332 12   2344


Q ss_pred             eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         258 SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       258 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .++... .....++++.+++..  .....+-+.+...-+....+++.
T Consensus       172 ~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~i~  215 (219)
T smart00062      172 IVGDPL-DTPEGYAFAVRKGDP--ELLDKINKALKELKADGTLKKIY  215 (219)
T ss_pred             eccCCC-CCCcceEEEEECCCH--HHHHHHHHHHHHHHhCchHHHHH
Confidence            332222 222577888777742  33444444444433444455544

bacterial proteins, eukaryotic ones are in PBPe

>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A

Probab=98.79  E-value=1.8e-06  Score=68.23  Aligned_cols=200  Identities=15%  Similarity=0.112  Sum_probs=138.7

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC------CCCCc--eeecccc
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS------PSDKL--ISIPCYQ  165 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~------~~~~~--~~~~l~~  165 (306)
                      |+|.+...+ ...+.++...| +++|++++++...++.++.+.|..| +.|+.+......      .....  ...++..
T Consensus         1 L~V~~~~~~-~~~~~~l~~~f-~~~~g~~v~v~~~~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~   78 (230)
T PF13531_consen    1 LTVYAASGL-APALEELAEAF-EKQPGIKVEVSFGGSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR   78 (230)
T ss_dssp             EEEEEEGGG-HHHHHHHHHHH-HHHHCEEEEEEEECHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE
T ss_pred             CEEEEcccH-HHHHHHHHHHH-HhccCCeEEEEECChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc
Confidence            577777764 55788899999 5589999999999999999999987 899999863211      11222  5788999


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcCC--CeEeecCCC-CcHHHHHHHHHhCC---C----ceeEEEEecCHHHHHHHHH
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISNY--PLITYDLSF-SGRIKLDREFSLQK---L----TPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i~~~~~~-~~~~~~~~~~~~~~---~----~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+++++++++.|.   ...+|+||.+-  .+...++.. .....+...+...+   .    ..+.....++...+...+.
T Consensus        79 ~~~vl~~~~~~~~---~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~~~~l~~~~~~~~~~~~~~~~~v~  155 (230)
T PF13531_consen   79 SPLVLAVPKGNPK---GIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQELLDALQKNIVQYVPSTSQVLSAVA  155 (230)
T ss_dssp             EEEEEEEETTSTT---STTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHHHHHHHHTEEEEESSHHHHHHHHH
T ss_pred             CceEEEeccCccc---ccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHHHHHHHHhCcccccchHHHHHHHH
Confidence            9999999999864   34579999764  455555433 33445556666655   2    2466667888888888888


Q ss_pred             hc-cceeeeecceeccc-ccCCceeeecCCCCc--cceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         236 LR-MGIGIIASIAFDSN-RDKNLRSISASHLFG--TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       236 ~g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~--~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      .| .-+++++...+... ....+..+++++...  ...+.+...++....++.+.|+++|++.=.++.
T Consensus       156 ~g~~d~~~~~~s~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~L~s~~~q~~  223 (230)
T PF13531_consen  156 SGEADAGIVYESQAIFARQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFIDFLLSPEGQQI  223 (230)
T ss_dssp             TTSSSEEEEEHHHHHHCTSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHHHHTSHHHHHH
T ss_pred             cCCCcceeeHHHHHHHhhcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHHHHCCHHHHHH
Confidence            88 44555555554321 456777777776444  356667666777778999999999987543333

...

>PF12849 PBP_like_2: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []

Probab=98.61  E-value=6.1e-07  Score=73.13  Aligned_cols=202  Identities=17%  Similarity=0.174  Sum_probs=130.8

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------------C
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------------S  155 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------------~  155 (306)
                      ..+.|+++.+.++ ..++..+...|.+.+|++++.+...++...+..|.+|.+|++++..+...               .
T Consensus         8 ~~~~i~~~GS~~~-~~~~~~~~~~~~~~~~~~~v~v~~~gS~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~   86 (281)
T PF12849_consen    8 GSGTIRIAGSSTV-APIMEALAEAFERQYPGVKVTVESSGSGAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWG   86 (281)
T ss_dssp             EE-EEEEEEHSTT-HHHHHHHHHHHHHHSTTBEEEEEEE-HHHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHH
T ss_pred             ceeEEEEEecCHH-HHHHHHHHHHHHHHCCCcEEEEEeCCCHHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccc
Confidence            3467999999885 66888899999999999999999999999999999999999999733221               1


Q ss_pred             CCceeeccccceEEEEecCCCCCCC-----------CCCcChhhhc---CCC--eEeecCCCCcHHHHHHHHHhCCCcee
Q psy3760         156 DKLISIPCYQWEYVIIVPLDHPLLL-----------LNSISLKEIS---NYP--LITYDLSFSGRIKLDREFSLQKLTPY  219 (306)
Q Consensus       156 ~~~~~~~l~~~~~~~v~~~~~~l~~-----------~~~i~~~dl~---~~~--~i~~~~~~~~~~~~~~~~~~~~~~~~  219 (306)
                      .++...+++.+.+++++++++|+..           .+..+|.|+.   +.|  ++....+.+.+..+.+++........
T Consensus        87 ~~~~~~~va~d~i~iv~n~~np~~~Lt~~ql~~I~~G~It~W~~~~~~~~~~I~~~~r~~~Sgt~~~f~~~l~~~~~~~~  166 (281)
T PF12849_consen   87 GGLVQIPVARDAIVIVVNKDNPLNNLTREQLRDIFSGEITNWSDLGGGPDRPIKVVGRSDGSGTREFFTNYLLGGSPWTA  166 (281)
T ss_dssp             CTEEEEEEEEEEEEEEEETTTTTEEETHHHHHHHHCTS--BGGGTTTCHSSB-EEEEESSTSHHHHHHHHHHHHHHHHHT
T ss_pred             cccEEEEEEEeeEEEEEcCCCccccccHHHHHHHHhhhhhcccccccCCCCceEEEeCCCCCcHHHHHHHHHhccCCccc
Confidence            5678899999999999999998762           2233566652   334  44445555666677766655411111


Q ss_pred             EEEEecCHHHHHHHHHhccceeeeecceecc-----cc-----------------cCCcee----------eec------
Q psy3760         220 IVLETINSDIIKTYVELRMGIGIIASIAFDS-----NR-----------------DKNLRS----------ISA------  261 (306)
Q Consensus       220 ~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-----~~-----------------~~~l~~----------~~~------  261 (306)
                      ..+.......+...+..-.+++++.......     ..                 ...+..          .|.      
T Consensus       167 ~~~~~~~~~~v~~~~~~~~~ig~v~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~l~~~~~~~~v~p~~~~i~~  246 (281)
T PF12849_consen  167 KAIGANGSEGVAQAVSTPGAIGYVSLSYALSNRAASIADLPNAIGYFVLPTTANVQKALKALSINPGDGSVAPTQENIAS  246 (281)
T ss_dssp             TTEEESHHHHHHHHHHCTTEECCCCHHHHCSTCCEEEEEEEECCHHCCHHCHHHHCHCTECTHHT--TTTEEEEECHHST
T ss_pred             cceeccCCccceeeccCCCceEEEecccccccccccccccccccccccccchhHHHHHHhhccccccceeeeecccCCcC
Confidence            1122233455555555555556655431110     00                 111111          111      


Q ss_pred             CCCCccceEEEEEeCCccc-cHHHHHHHHHHhH
Q psy3760         262 SHLFGTTISRVIIKQGTYL-RSYVYSFIKLLSP  293 (306)
Q Consensus       262 ~~~~~~~~~~l~~~~~~~~-~~~~~~~~~~l~~  293 (306)
                      ...+..+.+|++++++... .+.++.|++|+.+
T Consensus       247 g~YPl~r~~y~~~~~~~~~~~~~~~~Fl~~~lS  279 (281)
T PF12849_consen  247 GSYPLSRPLYLYTNKDPLQPDPLVRAFLDFVLS  279 (281)
T ss_dssp             TSSSCEEEEEEEEESTTSSHHHHHHHHHHHHHS
T ss_pred             CCCCeEeEEEEEEECCCCCCcHHHHHHHHHHcC
Confidence            1234567889998887544 8999999999864

It is often associated with a helix-turn-helix domain.; PDB: 1QUL_A 1OIB_A 1A54_A 1IXH_A 1A40_A 1QUJ_A 1A55_A 1IXI_A 2ABH_A 1QUK_A ....

>COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism]

Probab=98.61  E-value=3.1e-05  Score=58.21  Aligned_cols=212  Identities=12%  Similarity=0.117  Sum_probs=148.4

Q ss_pred             ccCCCCcEEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC------CCCCcee
Q psy3760          88 SAYDTGNLTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS------PSDKLIS  160 (306)
Q Consensus        88 ~~~~~~~l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~------~~~~~~~  160 (306)
                      .......||++++.+.-.. +|..++..|. +++++.+++...++...++.=++|++|+.|++.+..      ..-++..
T Consensus        25 ~sa~~~~LrmATTTSt~dtGLLd~l~p~fE-~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHapk~E~~fv~~G~gv~r  103 (280)
T COG2998          25 SSADAAELRMATTTSTEDTGLLDVLLPKFE-KYTGYDVQVVAVGTGKALKMGERGDVDVVIVHAPKAEKEFVKDGFGVDR  103 (280)
T ss_pred             cCcccceEEEeeeccccccccHHHHHHhhh-hccCceEEEEEecchHHHhhhccCCcCEEEEeCcHHHHHHHHcCCCccC
Confidence            3556789999998876554 6666667776 789999999999999999999999999999974422      2346677


Q ss_pred             eccccceEEEEecCCCCCCCCCCcC----hhhh--cCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEe--cCHHHH
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSIS----LKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LET--INSDII  230 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~----~~dl--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~~  230 (306)
                      +++.-..|++|.|++.|.--+...+    ++.+  ...+||+..+.++....-...++..|+.|+..  +..  .-+...
T Consensus       104 ~~vmYNdFiiVgp~~dpA~~k~~kn~~e~fe~Ia~~ka~FvSRGD~SGT~~~E~~lWk~~g~~p~~~~wY~s~G~GMg~t  183 (280)
T COG2998         104 RPVMYNDFIIVGPADDPAGIKDAKNGKEAFEKIAEEKAKFVSRGDNSGTDSKELSLWKVTGIEPTVKGWYISAGQGMGDT  183 (280)
T ss_pred             cceeeeeEEEECCcccchhcccchhHHHHHHHHHHcCCeeEecCCCCCccHHHHHHHHHcCCCCCCCcceeecCcchHHH
Confidence            8888889999999998855444333    2333  45789999888887777778888889887553  222  334566


Q ss_pred             HHHHHhccceeeeecceeccc-ccCCceeeecCCCCccceEE--EEEeC--CccccHHHHHHHHHHhHHhhHHHH
Q psy3760         231 KTYVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISR--VIIKQ--GTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       231 ~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~--l~~~~--~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      +.+...-.++++..+...-.+ ..+.|+.+--.++...-.|.  .+-++  ....-.....|++|+.+.-.++.+
T Consensus       184 L~~A~Ek~aytLtDrgTylaYr~r~~L~iv~~gd~~L~N~Ysvi~vNP~r~~~vny~~A~kfi~w~~s~~gq~~I  258 (280)
T COG2998         184 LNMANEKKAYTLTDRGTYLAYRNRPTLVIVLEGDPSLFNPYSVIAVNPKRVKGVNYTAATKFIEWLMSEKGQNLI  258 (280)
T ss_pred             HHHhhhhceeEeeccceeeEecCccceEEEecCCccccCceeEEEEchhcCCCcCchHHHHHHHHHhhHHHHHHH
Confidence            777777788888887655555 66777776655533322333  33223  223456788999999776554444

>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]

Probab=98.49  E-value=0.00012  Score=58.32  Aligned_cols=204  Identities=16%  Similarity=0.131  Sum_probs=140.5

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC-----C---CCCcee
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS-----P---SDKLIS  160 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~-----~---~~~~~~  160 (306)
                      .....|+|....++.. -+..+..+|.+++ ++++.+..+++..+.+++.+| .+|+-++.....     .   ...-..
T Consensus        27 ~~~~~i~VfAAaSL~~-~l~~i~~~F~~~~-~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~~  104 (258)
T COG0725          27 QEAATITVFAAASLTD-ALEEIAKQFEKET-GVKVEVEFGGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSR  104 (258)
T ss_pred             ccCceEEEEEehhhHH-HHHHHHHHHHHHH-CCeEEEEecchHHHHHHHHcCCCcCEEEECCHHHHHHHHhcCCccCCce
Confidence            3456899999988755 5559999999999 999999999999999999997 799999863211     1   122246


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecC-CCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHH
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDL-SFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTY  233 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~  233 (306)
                      ..+....++++.+++.+....   .++++...+   +..-++ ..+....-.+.++..|+-.   .......+...+...
T Consensus       105 ~~fa~n~lvl~~~~~~~~~~~---~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~  181 (258)
T COG0725         105 IVFAGNRLVLAVPKGSKKKIE---SLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAY  181 (258)
T ss_pred             EEeeCCeEEEEEeCCCccCcc---cHHHHhcCcCcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHH
Confidence            778889999999988764332   277777643   333332 3334556677777777753   355677888899999


Q ss_pred             HHhc---cceeeeecceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760         234 VELR---MGIGIIASIAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN  301 (306)
Q Consensus       234 v~~g---~gi~~~p~~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  301 (306)
                      |..|   .|+.+.++.....   +.....+++.. .....+.+...++...++..++|++++.+.-.+...+
T Consensus       182 V~~G~ad~g~vy~sd~~~~~---~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s~~a~~il~  250 (258)
T COG0725         182 VETGEADAGFVYVSDALLSK---KVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSPEAQEILE  250 (258)
T ss_pred             HHcCCCCeEEEEEEhhhccC---CceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhCHHHHHHHH
Confidence            9999   4444444333222   23333344432 2235667777788877899999999998855544443

>PRK11050 manganese transport regulator MntR; Provisional

Probab=98.48  E-value=6.9e-07  Score=65.09  Aligned_cols=61  Identities=21%  Similarity=0.206  Sum_probs=52.7

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQEIEGLKK   82 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~~~~~~~   82 (306)
                      +.+..|+.+++|+|++|+.|++||+. |  ++.|. ++++ .||+.|+.++..+......++.+..
T Consensus        53 t~~eLA~~l~is~stVsr~l~~Le~~-G--lI~r~~~~~v-~LT~~G~~l~~~~~~~~~~le~~l~  114 (152)
T PRK11050         53 RQVDIAARLGVSQPTVAKMLKRLARD-G--LVEMRPYRGV-FLTPEGEKLAQESRERHQIVENFLL  114 (152)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEecCCce-EECchHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999997 5  55554 5677 8999999999999988888877553

>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein

Probab=98.48  E-value=6.8e-05  Score=58.55  Aligned_cols=186  Identities=16%  Similarity=0.093  Sum_probs=114.9

Q ss_pred             hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCC----ceeeccccceEEEEecCC
Q psy3760         105 RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDK----LISIPCYQWEYVIIVPLD  175 (306)
Q Consensus       105 ~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~----~~~~~l~~~~~~~v~~~~  175 (306)
                      ...+..++..|.+++| +++++...++.++...+..|. +|+.+......    ...+    +....+....++++++++
T Consensus         5 ~~~~~~~~~~f~~~~g-i~V~~~~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~l~~~~~   83 (216)
T TIGR01256         5 TDALKEIAKQFEKRTG-NKVVFSFGSSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAGNKLVLISPKN   83 (216)
T ss_pred             HHHHHHHHHHHHHhhC-CeEEEEeCChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEccEEEEEEECC
Confidence            3466778999999997 999999999999999999874 99999853211    0111    222336777888888776


Q ss_pred             CCCCCCCCcChhhhc----CCCeEeecCCC-CcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHHhc-cceeeeec
Q psy3760         176 HPLLLLNSISLKEIS----NYPLITYDLSF-SGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVELR-MGIGIIAS  245 (306)
Q Consensus       176 ~~l~~~~~i~~~dl~----~~~~i~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~  245 (306)
                      .     .+-+++||.    +..++..++.. ........+++..+    +.++.. ...+...+..++..| ..+++...
T Consensus        84 ~-----~~~s~~dL~~~~~~~~i~~~~P~~~~~g~~~~~~~~~~g~~~~l~~n~~-~~~~~~~~~~~~~~Ge~~~~~~~~  157 (216)
T TIGR01256        84 R-----VVDDLDILKKWVADKRVAIGDPKHAPYGAAAKEVLQKLGLWETLKKKLV-YGEDVRQALQFVETGNAPAGIVAL  157 (216)
T ss_pred             C-----CcCcHHHHhhcccCCeEEecCCCcCcChHHHHHHHHHCCChhhhhhhee-ecCcHHHHHHHHHcCCCCEEeeeh
Confidence            2     234688884    23445544332 23334455555554    345544 455777888888888 45555554


Q ss_pred             ceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         246 IAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       246 ~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      ..+.... +....++++.. .....+.+...++.......++|++++.+.=.+.
T Consensus       158 ~~~~~~~-~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s~e~q~  210 (216)
T TIGR01256       158 SDVIPSK-KVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKSPEAKE  210 (216)
T ss_pred             hhhcccC-CccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHHcCHHHHH
Confidence            4333221 22233444432 2233445555566666889999999997654333

The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.

>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]

Probab=98.47  E-value=6.4e-06  Score=61.61  Aligned_cols=153  Identities=20%  Similarity=0.173  Sum_probs=116.2

Q ss_pred             hhHHHHHHHcCCeeEEEEccccC-------------CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCC--CeE
Q psy3760         131 PKQITEMIRNDQADIAIVTEILS-------------PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY--PLI  195 (306)
Q Consensus       131 ~~~~~~~l~~~~~Di~i~~~~~~-------------~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i  195 (306)
                      +-.-+-.+..|++|++=..-.+.             -.+.......+.-++.+++++++|   +.--+++||...  .+|
T Consensus        27 S~gG~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~Re~Gl~v~~gnp---k~i~~~edl~~~d~~fV  103 (223)
T COG1910          27 SMGGLLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNP---KNISSLEDLLRKDLRFV  103 (223)
T ss_pred             cccchHhhhhcccceeeeeeccCCCCceehhhhhhcCCCceEEEeeeeeeeeeEEecCCC---CccccHHHHhhcCcEEE
Confidence            33446679999999997641111             012244556666788999999997   334589999877  899


Q ss_pred             eecCCCCcHHHHHHHHHhCCCceeE----EEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCCCccceE
Q psy3760         196 TYDLSFSGRIKLDREFSLQKLTPYI----VLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHLFGTTIS  270 (306)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~  270 (306)
                      ..+.+++.|..+++.+...+..|+.    ..++.+...+...|++| .-+++--.+.+   ...+|.++|+...    .|
T Consensus       104 NR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvGlr~~A---~~~gL~Fipl~~E----~Y  176 (223)
T COG1910         104 NRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVGLRHAA---EKYGLDFIPLGDE----EY  176 (223)
T ss_pred             ecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCCCCccccHHHHH---HHcCCceEEcccc----eE
Confidence            9999999999999999999887643    36778888999999998 33444333443   3568999999872    78


Q ss_pred             EEEEeCCccccHHHHHHHHHHhH
Q psy3760         271 RVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       271 ~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .++.+++....|.+++|++.|++
T Consensus       177 D~virke~~~~~~vr~fi~~L~s  199 (223)
T COG1910         177 DFVIRKERLDKPVVRAFIKALKS  199 (223)
T ss_pred             EEEEehhHccCHHHHHHHHHhcc
Confidence            89999999999999999999985

>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane

Probab=98.42  E-value=1.2e-05  Score=62.92  Aligned_cols=193  Identities=15%  Similarity=0.094  Sum_probs=117.5

Q ss_pred             hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCCce-eeccccceEEEEecCCCCCCC
Q psy3760         104 ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDKLI-SIPCYQWEYVIIVPLDHPLLL  180 (306)
Q Consensus       104 ~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~~~-~~~l~~~~~~~v~~~~~~l~~  180 (306)
                      ...+...++..+.++. ++.+++...+...+...|.+|++|+++....  ......+. +.+++....+++++++.+...
T Consensus        21 ~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~~   99 (225)
T PF00497_consen   21 PSGIDVDLLRAIAKRL-GIKIEFVPMPWSRLLEMLENGKADIIIGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDAPPI   99 (225)
T ss_dssp             EESHHHHHHHHHHHHH-TCEEEEEEEEGGGHHHHHHTTSSSEEESSEB-BHHHHTTEEEESESEEEEEEEEEETTSTCST
T ss_pred             EEEEhHHHHHHHHhhc-ccccceeecccccccccccccccccccccccccccccccccccccccchhheeeecccccccc
Confidence            3457788888888876 8889998878889999999999999984211  11122333 558999999999997642111


Q ss_pred             CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc-eeeeecceeccc-ccCCce-
Q psy3760         181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG-IGIIASIAFDSN-RDKNLR-  257 (306)
Q Consensus       181 ~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~~-~~~~l~-  257 (306)
                      ...-+++||.+.++..... ......+.+....   ..++ ..+++...++.++.+|.. ..+.+...+... ...... 
T Consensus       100 ~~~~~~~dl~~~~i~~~~g-~~~~~~l~~~~~~---~~~~-~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~  174 (225)
T PF00497_consen  100 KTIKSLDDLKGKRIGVVRG-SSYADYLKQQYPS---NINI-VEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLEN  174 (225)
T ss_dssp             SSHSSGGGGTTSEEEEETT-SHHHHHHHHHTHH---TSEE-EEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCE
T ss_pred             ccccchhhhcCcccccccc-hhHHHHhhhhccc---hhhh-cccccHHHHHHHHhcCCeeeeeccchhhhhhhhhccccc
Confidence            1222567897776666554 3333344443322   2233 368999999999999966 555555555443 222222 


Q ss_pred             eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         258 SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       258 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ............++++.+++.  +...+.|-+.|.+.-+...++++.
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~--~~l~~~~n~~i~~l~~~G~~~~i~  219 (225)
T PF00497_consen  175 IVVIPPPISPSPVYFAVRKKN--PELLEIFNKAIRELKQSGEIQKIL  219 (225)
T ss_dssp             EEEEEEEEEEEEEEEEEETTT--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             ccccccccccceeEEeecccc--cHHHHHHHHHHHHHHhCcHHHHHH
Confidence            222122233446666666542  455555655565555554555554

The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....

>PRK10677 modA molybdate transporter periplasmic protein; Provisional

Probab=98.41  E-value=0.00026  Score=56.71  Aligned_cols=199  Identities=15%  Similarity=0.128  Sum_probs=123.8

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCCc----ee
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDKL----IS  160 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~~----~~  160 (306)
                      .....|+|.+..++. ..+..+...|.+++ ++++.+...++..+.+++..|. +|+.+......    ...++    ..
T Consensus        24 ~~~~~l~v~~a~~~~-~~~~~l~~~Fe~~~-g~~v~~~~~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~  101 (257)
T PRK10677         24 ADEGKITVFAAASLT-NALQDIAAQYKKEK-GVDVVSSFASSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATR  101 (257)
T ss_pred             ccCCcEEEEEecChH-HHHHHHHHHHHhhh-CCeEEEEecccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcch
Confidence            344579999998764 68888999999886 9999999999999999999887 99999853111    01111    13


Q ss_pred             eccccceEEEEecCCCCCCCC---CCcChhhhcCC-CeEeecCC-CCcHHHHHHHHHhCCCc----eeEEEEecCHHHHH
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLL---NSISLKEISNY-PLITYDLS-FSGRIKLDREFSLQKLT----PYIVLETINSDIIK  231 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~---~~i~~~dl~~~-~~i~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~  231 (306)
                      ..+....++++++++.|....   .+-+|+||.+- .+...++. .+........++..|+-    .+ ....++...+.
T Consensus       102 ~~~a~n~lvl~~~~~~~~~~i~~~~~~~~~dLl~~~~iai~dP~~~p~G~~a~~~l~~~g~~~~l~~k-~~~~~~v~~~~  180 (257)
T PRK10677        102 YTLLGNSLVVVAPKASEQKDFTIDKKTDWKSLLNGGRLAVGDPDHVPAGIYAKEALQKLGAWDTLSPK-LARAEDVRGAL  180 (257)
T ss_pred             heeecCEEEEEEECCCccccccccCccCHHHhcCCCeEEEcCCCCChHHHHHHHHHHHcCCHHHHHhh-hcccccHHHHH
Confidence            468888999999998765431   23468888653 34444443 23444555666666541    12 22346677788


Q ss_pred             HHHHhc-cceeeeecceecccccCCceee-ecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         232 TYVELR-MGIGIIASIAFDSNRDKNLRSI-SASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       232 ~~v~~g-~gi~~~p~~~~~~~~~~~l~~~-~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .++..| .-+++...+.+..  ..++..+ .++. ......+.+...++.. ++..++|++++.+.
T Consensus       181 ~~v~~G~ad~gi~~~s~a~~--~~~~~~~~~~P~e~~~~i~~~~avlk~~~-~~~Ak~Fi~fl~S~  243 (257)
T PRK10677        181 ALVERNEAPLGIVYGSDAVA--SKKVKVVGTFPEDSHKPVEYPMAIVKGHN-NATVKAFYDYLKGP  243 (257)
T ss_pred             HHHHcCCCCEEEEEeeeeec--cCCCeEEEECCcccCCcceeeEEEEcCCC-CHHHHHHHHHHcCH
Confidence            899888 3334443333222  2223322 2222 2223344444445544 57899999999654

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=98.40  E-value=2.6e-06  Score=59.51  Aligned_cols=76  Identities=25%  Similarity=0.350  Sum_probs=62.4

Q ss_pred             CchhhHHHHHHHHHhcCC--HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFN--LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s--~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      |+..++.++..+.+.+ .  .+.-|+.++++++++|+.|++||+.   -|+.|..       ..+ .||+.|+.+++.+.
T Consensus        26 lt~~q~~iL~~l~~~~-~~t~~ela~~~~~~~~tvs~~l~~Le~~---GlI~r~~~~~D~R~~~v-~LT~~G~~~~~~~~  100 (118)
T TIGR02337        26 LTEQQWRILRILAEQG-SMEFTQLANQACILRPSLTGILARLERD---GLVTRLKASNDQRRVYI-SLTPKGQALYASLS  100 (118)
T ss_pred             CCHHHHHHHHHHHHcC-CcCHHHHHHHhCCCchhHHHHHHHHHHC---CCEEeccCCCCCCeeEE-EECHhHHHHHHHhh
Confidence            4567888888888766 5  7899999999999999999999997   5666632       244 89999999999999


Q ss_pred             HHHHHHHHHH
Q psy3760          72 IIMQEIEGLK   81 (306)
Q Consensus        72 ~il~~~~~~~   81 (306)
                      +.........
T Consensus       101 ~~~~~~~~~~  110 (118)
T TIGR02337       101 PQIEEIYAAI  110 (118)
T ss_pred             HHHHHHHHHH
Confidence            9888776643

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.

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

Probab=98.39  E-value=2.3e-06  Score=57.39  Aligned_cols=60  Identities=23%  Similarity=0.309  Sum_probs=51.2

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLKK   82 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~~   82 (306)
                      ++..|+.+++|+|++|+.++.||+.   -|+.|.+ +++ .||+.|..+++.+......++....
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~---glI~r~~~~~~-~lT~~g~~~~~~~~~~~~~~~~~l~   62 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKD---GLVEYEPYRGI-TLTEKGRRLARRLLRKHRLLERFLV   62 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHC---CCEEEcCCCce-EechhHHHHHHHHHHHHHHHHHHHH
Confidence            4688999999999999999999996   5888887 466 8999999999888887776666554

iron dependent repressor

>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein

Probab=98.37  E-value=4.4e-05  Score=62.97  Aligned_cols=152  Identities=12%  Similarity=-0.001  Sum_probs=98.9

Q ss_pred             EEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC------CCceeeccccceEE
Q psy3760          96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS------DKLISIPCYQWEYV  169 (306)
Q Consensus        96 ~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~------~~~~~~~l~~~~~~  169 (306)
                      +++.+.+ ...++..+...|.+.||++++.+...++...++.+.+|.+||+....+..+.      .++...++..+.++
T Consensus         2 ~~~GStt-~~pl~~~~~~~y~~~~~~v~v~v~~~GSg~Gi~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~pva~dai~   80 (314)
T TIGR00975         2 TGAGSTF-PYPLYTKWFPDYQKSNPGVTINYQGIGSGAGIAQFAAGTVDFGASDAPLSEADLASRGSGLLQFPTVIGAIV   80 (314)
T ss_pred             eeeccCc-HHHHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEeeEEeeeEE
Confidence            3444444 4668888899999999999999999999999999999999999997554322      25677888888999


Q ss_pred             EEecC-CCC-----CCC--------CCCcChhh-----------hcCCCe--EeecCCCCcHHHHHHHHHhC--------
Q psy3760         170 IIVPL-DHP-----LLL--------LNSISLKE-----------ISNYPL--ITYDLSFSGRIKLDREFSLQ--------  214 (306)
Q Consensus       170 ~v~~~-~~~-----l~~--------~~~i~~~d-----------l~~~~~--i~~~~~~~~~~~~~~~~~~~--------  214 (306)
                      +++++ +.+     |..        .+.-+|+|           +.+.|.  +....+.+.+..+.+++...        
T Consensus        81 vivn~~~~~~~~l~Lt~~~L~~If~G~It~W~d~~i~~~np~~~~p~~~I~vv~R~~~SGT~~~f~~~l~~~~~~~~~~~  160 (314)
T TIGR00975        81 VTYNLPGVSKGELKLDGPVLAKIFLGKIKTWNDPAIAALNPGVKLPGTAITVVHRSDGSGTTFNFTNYLSKVSPEWKEKV  160 (314)
T ss_pred             EEEeCCCCCccccccCHHHHHHHhCCCCcccCchhhhhcCCCCCCCCCceEEEeCCCCCchHHHHHHHHHhhChhhhhcc
Confidence            99985 322     110        22334665           122443  34455556777777665321        


Q ss_pred             --CC--ceeEEEEecCHHHHHHHHHhc-cceeeeeccee
Q psy3760         215 --KL--TPYIVLETINSDIIKTYVELR-MGIGIIASIAF  248 (306)
Q Consensus       215 --~~--~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~  248 (306)
                        +.  .........+...+.+.|... .+|+++....+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~v~~~V~~~p~aIGY~~~~~~  199 (314)
T TIGR00975       161 GAGTTVQWPAGVGGKGNDGVVAGVKQTPGAIGYVEWSYA  199 (314)
T ss_pred             CCCceecCCcccccCCCHHHHHHHhcCCCceEEeeHHHH
Confidence              10  001123444556667777654 89999876544

This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.

>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed

Probab=98.29  E-value=0.00025  Score=56.99  Aligned_cols=179  Identities=13%  Similarity=0.087  Sum_probs=111.2

Q ss_pred             CCCcEEEEecccchh------------hhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CC
Q psy3760          91 DTGNLTIATTHTQAR------------YALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SP  154 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~------------~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~  154 (306)
                      .+|.|+||+......            .+-..++..+.++-  .++.+++...........|.+|++|+++.....  ..
T Consensus        36 ~~g~l~vg~~~~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR  115 (259)
T PRK11917         36 SKGQLIVGVKNDVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPER  115 (259)
T ss_pred             hCCEEEEEECCCCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEEcChhhHHHHHHCCCccEEEecccCChhh
Confidence            367999999753221            35567788888863  346777777776677789999999999874221  22


Q ss_pred             CCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760         155 SDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTY  233 (306)
Q Consensus       155 ~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (306)
                      ...+. +.+++.....++++++.+     .-+++||.+.+.... .+......+.+.++..+... .....++.....++
T Consensus       116 ~~~~~fs~py~~~~~~lvv~~~~~-----~~s~~dL~g~~V~v~-~gs~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~  188 (259)
T PRK11917        116 KRIYNFSEPYYQDAIGLLVLKEKN-----YKSLADMKGANIGVA-QAATTKKAIGEAAKKIGIDV-KFSEFPDYPSIKAA  188 (259)
T ss_pred             hheeeeccCceeeceEEEEECCCC-----CCCHHHhCCCeEEEe-cCCcHHHHHHHhhHhcCCce-eEEecCCHHHHHHH
Confidence            23343 457888899999998864     247899998885554 44444455566666555432 23456788888899


Q ss_pred             HHhccceeeeec-ceecccccCCceeeecCCCCccceEEEEEeCCc
Q psy3760         234 VELRMGIGIIAS-IAFDSNRDKNLRSISASHLFGTTISRVIIKQGT  278 (306)
Q Consensus       234 v~~g~gi~~~p~-~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~  278 (306)
                      +.+|..=+++-. .....+.......+  .......+++++.+++.
T Consensus       189 l~~GrvDa~~~d~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~k~~  232 (259)
T PRK11917        189 LDAKRVDAFSVDKSILLGYVDDKSEIL--PDSFEPQSYGIVTKKDD  232 (259)
T ss_pred             HHcCCCcEEEecHHHHHHhhhcCCeec--CCcCCCCceEEEEeCCC
Confidence            999965444433 32223222222222  22222335667767663

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=98.26  E-value=8.8e-06  Score=58.80  Aligned_cols=74  Identities=16%  Similarity=0.218  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus         5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      -|+.+..+.+.+  .+++..|+.|++|+|++|+.|++|++. |.-... ..+++ +||+.|+.+......--..++.+.
T Consensus         9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~-Gli~~~-~~~~i-~LT~~G~~~a~~~~~~h~~~e~~l   84 (142)
T PRK03902          9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD-EYLIYE-KYRGL-VLTPKGKKIGKRLVYRHELLEQFL   84 (142)
T ss_pred             HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC-CCEEEe-cCceE-EECHHHHHHHHHHHHHHHHHHHHH
Confidence            355555555442  166778999999999999999999999 764333 35777 899999998777654444444444

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=98.22  E-value=1.8e-05  Score=53.55  Aligned_cols=76  Identities=21%  Similarity=0.274  Sum_probs=60.9

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      |+...+.+|..+.+.+ .+.+..|+.+++|++++++.|++|++.   .++.+..       ..+ .+|+.|..++..+..
T Consensus         8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~---g~v~~~~~~~~~r~~~~-~lT~~g~~~~~~~~~   83 (101)
T smart00347        8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK---GLIRRLPSPEDRRSVLV-SLTEEGRELIEELLE   83 (101)
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC---CCeEecCCCCCCCeEEE-EECHhHHHHHHHHHH
Confidence            4667888999998764 377888999999999999999999996   4444332       245 799999999999998


Q ss_pred             HHHHHHHH
Q psy3760          73 IMQEIEGL   80 (306)
Q Consensus        73 il~~~~~~   80 (306)
                      .+..+...
T Consensus        84 ~~~~~~~~   91 (101)
T smart00347       84 ARHETLAE   91 (101)
T ss_pred             HHHHHHHH
Confidence            88876653

>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA

Probab=98.20  E-value=0.00081  Score=54.08  Aligned_cols=194  Identities=13%  Similarity=0.039  Sum_probs=120.4

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH-c-CCeeEEEEccccC----CCCCc--eeecccc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR-N-DQADIAIVTEILS----PSDKL--ISIPCYQ  165 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~-~-~~~Di~i~~~~~~----~~~~~--~~~~l~~  165 (306)
                      +|+|.+..++ ...+..+...|.+++|++++++...++..+..++. + ..+|+.++.....    ...++  ....+..
T Consensus         2 ~L~V~aAasL-~~~~~ei~~~Fe~~~~gvkv~~~~~gSg~L~~Qi~e~Gap~DVfisAd~~~~~~L~~~g~~~~~~~~a~   80 (273)
T TIGR03730         2 KLKIFHAGSL-SVPFEEMEKEFEAKHPNVDVQREAAGSVAAVRKITELGKPADILASADYTLIPQMMIPNYADWYIMFAT   80 (273)
T ss_pred             eEEEEEccCc-HHHHHHHHHHHHhhCCCceEEEEeCcHHHHHHHHHHcCCCeeEEEeCCHHHHHHHHhCCCcCceeeEEc
Confidence            4788888886 45777899999999999999999999999999995 4 5899999863211    11222  3457889


Q ss_pred             ceEEEEecCCCCCCCC-CCcCh-hhhcC--CCeEeecCC-CCcH-------HHHHHHHHhCC------------------
Q psy3760         166 WEYVIIVPLDHPLLLL-NSISL-KEISN--YPLITYDLS-FSGR-------IKLDREFSLQK------------------  215 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~-~~i~~-~dl~~--~~~i~~~~~-~~~~-------~~~~~~~~~~~------------------  215 (306)
                      .+++++++++.++... ..-++ ++|.+  ..+...++. ....       ..-.+.+...|                  
T Consensus        81 n~LVL~~~~~~~~~~~~~~~~~~~~L~~~~~rIai~dP~~~P~G~~a~~~~~~A~~~l~~~gl~~~l~~~~~~~~~~~~~  160 (273)
T TIGR03730        81 NEIVLAYTDKSKYADEINSDNWYEILQRPDVRWGFSDPNDDPCGYRSLMVIQLAELYYNDPTIFDNLLLKNTNITVEENN  160 (273)
T ss_pred             ccEEEEEeCCCCcccccCcchHHHHhcCCCcEEEEcCCCCCCchHHHHHHHHHHHHHhcCCCHHHHHhhhcccccccccC
Confidence            9999999887654321 11244 44532  234444433 2222       12233322222                  


Q ss_pred             ------------CceeEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCC-------------------
Q psy3760         216 ------------LTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASH-------------------  263 (306)
Q Consensus       216 ------------~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~-------------------  263 (306)
                                  ..++..+...+...+...+.+| .-++++..+.+..   .++.++.+++                   
T Consensus       161 ~~~~~~~~~~~~~~~~k~~~~~~v~~~~~~v~sG~aD~g~vY~S~A~~---~~~~~~~lP~~~n~~~~~~~~~y~~v~~~  237 (273)
T TIGR03730       161 GTYLIHVPKEIDVNRSKIFIRPKEVELLSLLESGEIDYAFIYKSVAVQ---HGLKYIELPDEINLGDYSYADFYKKVSVE  237 (273)
T ss_pred             CcccccCcccccccccceeecCchHhHHHHHHCCCCcEEEEEeeeccc---CCCceEECChhccCCChhhhcccceEEEE
Confidence                        1124566777889999999998 4444444443322   2344444443                   


Q ss_pred             --------CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         264 --------LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       264 --------~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                              ....+.+.+...++....+..++|+++|
T Consensus       238 ~~~~~~~~~~~pi~y~~ai~~~~~~~~~a~~F~~fl  273 (273)
T TIGR03730       238 LGGGKKTITGKPIVYGITVPKNAPNREEAIEFLKFL  273 (273)
T ss_pred             ecCCCceEecCCEEEEEeccCCCCCHHHHHHHHhhC
Confidence                    1123455566667776678899999875

Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.

>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional

Probab=98.03  E-value=0.001  Score=55.31  Aligned_cols=203  Identities=16%  Similarity=0.093  Sum_probs=122.8

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH--cCCeeEEEEccccC----CCCCc--eeec
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR--NDQADIAIVTEILS----PSDKL--ISIP  162 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~--~~~~Di~i~~~~~~----~~~~~--~~~~  162 (306)
                      ....|+|.+..++ ...+..+...|.+++|++++++...++..+..++.  ...+|+.++.....    ...++  ....
T Consensus        30 ~~~~l~V~aA~sl-~~~l~~i~~~fe~~~~gv~v~~~~~gSg~L~~QI~e~Gap~DVfisAd~~~~~~l~~~g~~~~~~~  108 (334)
T PRK04168         30 PKGKLKIFHAGSL-SVPFEEYEKEFEAYHPNVDVQREAGGSVKCVRKITELGKKADIMASADYTLIPKMMMPDYADWYVR  108 (334)
T ss_pred             CCccEEEEeCCch-HHHHHHHHHHHHHhCCCeeEEEEeCcHHHHHHHHHhcCCCCCEEEECchhHHHHHhccCccceeEE
Confidence            4567999999885 45677899999999999999999999999999995  45899999863211    11222  3457


Q ss_pred             cccceEEEEecCCCCCCC-CCCcChhhhc-C--CCeEeecCC-CCcHHHHHHHH-------HhCCCc-------------
Q psy3760         163 CYQWEYVIIVPLDHPLLL-LNSISLKEIS-N--YPLITYDLS-FSGRIKLDREF-------SLQKLT-------------  217 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~-~~~i~~~dl~-~--~~~i~~~~~-~~~~~~~~~~~-------~~~~~~-------------  217 (306)
                      +...+++++.+++.+... ..+.+|.++. +  ..+...++. .+....-.+.|       ...|+-             
T Consensus       109 fa~n~lVl~~~~~~~~~~~~~~~~~~~lL~~~~~~Iai~~P~~~P~G~~a~~~l~~a~~~l~~~gl~~~l~~~~~~~~~~  188 (334)
T PRK04168        109 FATNEIVLAYTDKSKYADEINSDNWYEILQRPDVKFGFSDPNDDPCGYRSLMVLQLAELYYNDPTIYDKLIAKNTNIKVN  188 (334)
T ss_pred             EEcccEEEEEcCCChhhhhcccccHHHHhcCCCcEEEcCCCCCCCchHHHHHHHHHHHHHhCCchHHHHHHhhccccccc
Confidence            888999999988765432 1223466633 2  234444432 22222111111       111110             


Q ss_pred             ------e-------eEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCCC------------------
Q psy3760         218 ------P-------YIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHLF------------------  265 (306)
Q Consensus       218 ------~-------~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~~------------------  265 (306)
                            +       +..+...+...+...+..| .-++++..+.+..   .++.++.+++..                  
T Consensus       189 ~~~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~G~aDagivy~S~a~~---~~~~~i~lP~~~n~~~~~~~~~y~~~~~~~  265 (334)
T PRK04168        189 ENLIISPKEIEVNTDKVFVRPKEVELLSLLETGNMDYAFIYKSVAVQ---HNLKYIELPDEINLGNYKYADFYKKVSVTV  265 (334)
T ss_pred             cccccCcccccccccceeecccchhhHHHHhcCCccEEEEEeeehhh---CCCCeeECchhhcCCChhhhhhhhEEEEEe
Confidence                  0       0133445566888888888 4455555444332   245555555421                  


Q ss_pred             ---------ccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         266 ---------GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       266 ---------~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                               ....+.+...++.......++|++++.+.-.+
T Consensus       266 ~~~~~~~~~~pi~y~~ai~~~s~n~e~A~~Fi~fl~S~e~q  306 (334)
T PRK04168        266 TGTGKTITAKPIVYGITVPKNAPNREAAIEFLKYLLSEPGG  306 (334)
T ss_pred             cCCCccccCceeeeeeeeecCCCCHHHHHHHHHHHcCHHHH
Confidence                     12344455566666677899999999765333

>PRK11260 cystine transporter subunit; Provisional

Probab=97.92  E-value=0.0013  Score=53.17  Aligned_cols=175  Identities=13%  Similarity=0.038  Sum_probs=105.2

Q ss_pred             CCCcEEEEecccc-----------hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCC
Q psy3760          91 DTGNLTIATTHTQ-----------ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~  157 (306)
                      ..+.|+||+....           ...+...++..+.++. ++++++...+..++.+.+.+|++|+++....  ......
T Consensus        39 ~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~e~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~  117 (266)
T PRK11260         39 ERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL-GVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK  117 (266)
T ss_pred             cCCeEEEEeCCCcCCceEECCCCCEEEehHHHHHHHHHHH-CCeEEEEeCCHHHHHHHHhcCCCCEEEeccccCHHHHhc
Confidence            4578999985321           1345677777777764 7889999889999999999999999975211  112222


Q ss_pred             c-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      + -+.++....++++++++.+.   ..-+++||.+..+... .+...    ..+++..... .....+++...++.++.+
T Consensus       118 ~~fs~p~~~~~~~~~~~~~~~~---~~~~~~dL~g~~Igv~-~G~~~----~~~l~~~~~~-~~i~~~~~~~~~l~~L~~  188 (266)
T PRK11260        118 YDFSTPYTVSGIQALVKKGNEG---TIKTAADLKGKKVGVG-LGTNY----EQWLRQNVQG-VDVRTYDDDPTKYQDLRV  188 (266)
T ss_pred             cccCCceeecceEEEEEcCCcC---CCCCHHHcCCCEEEEe-cCCcH----HHHHHHhCCC-CceEecCCHHHHHHHHHc
Confidence            2 25567777788888876542   2346788877765553 33332    3344443222 234567788888999999


Q ss_pred             ccceee-eecceeccc--ccCC-ceeeecCCCCccceEEEEEeCC
Q psy3760         237 RMGIGI-IASIAFDSN--RDKN-LRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       237 g~gi~~-~p~~~~~~~--~~~~-l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                      |..=++ .+......+  ..+. +...  .......++++..+++
T Consensus       189 GrvD~~i~d~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~v~~~  231 (266)
T PRK11260        189 GRIDAILVDRLAALDLVKKTNDTLAVA--GEAFSRQESGVALRKG  231 (266)
T ss_pred             CCCCEEEechHHHHHHHHhCCCcceec--CCccccCceEEEEeCC
Confidence            944443 344333322  2222 2221  1222234677777765

>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B

Probab=97.85  E-value=3.3e-05  Score=46.23  Aligned_cols=43  Identities=23%  Similarity=0.362  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      ++++.+..++++|.++||+.|++-..|+.++|+++|+.+|..+
T Consensus         2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl   44 (59)
T PF13556_consen    2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKIEELLGLDL   44 (59)
T ss_dssp             --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T
T ss_pred             hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCC
Confidence            3455666666459999999999999999999999999999876

>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed

Probab=97.82  E-value=0.0031  Score=50.31  Aligned_cols=199  Identities=10%  Similarity=0.055  Sum_probs=116.2

Q ss_pred             CCCCcEEEEecccch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCC
Q psy3760          90 YDTGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDK  157 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~  157 (306)
                      ...+.|+||+.....          ..+...++..+.+.- ++.++++..+...+++.+.+|++|+++.....  .....
T Consensus        22 ~~~~~l~v~~~~~~~P~~~~~~g~~~G~~vdl~~~ia~~l-g~~~~~~~~~~~~~~~~l~~G~vDi~~~~~~~t~~R~~~  100 (247)
T PRK09495         22 AADKKLVVATDTAFVPFEFKQGDKYVGFDIDLWAAIAKEL-KLDYTLKPMDFSGIIPALQTKNVDLALAGITITDERKKA  100 (247)
T ss_pred             ccCCeEEEEeCCCCCCeeecCCCceEEEeHHHHHHHHHHh-CCceEEEeCCHHHHHHHHhCCCcCEEEecCccCHHHHhh
Confidence            346789999863211          134556777777764 68888888889999999999999998753211  11122


Q ss_pred             c-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      + -+.+++...+.++++++++    ..-+++||.+.+..... +...    ..++....... .....++...+..++.+
T Consensus       101 ~~fs~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~I~v~~-g~~~----~~~l~~~~~~~-~i~~~~~~~~~~~~L~~  170 (247)
T PRK09495        101 IDFSDGYYKSGLLVMVKANNN----DIKSVKDLDGKVVAVKS-GTGS----VDYAKANIKTK-DLRQFPNIDNAYLELGT  170 (247)
T ss_pred             ccccchheecceEEEEECCCC----CCCChHHhCCCEEEEec-CchH----HHHHHhcCCCC-ceEEcCCHHHHHHHHHc
Confidence            2 2457778888888887764    23488999988865544 3222    23333332222 23457788889999999


Q ss_pred             ccceeeeecc-eec----ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         237 RMGIGIIASI-AFD----SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       237 g~gi~~~p~~-~~~----~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      |..=+++... ...    ....+.+...+..  .....+++..+++.   .....|=+.+++.-.....+++.
T Consensus       171 grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~a~~~~~---~l~~~~n~al~~~~~~g~~~~i~  238 (247)
T PRK09495        171 GRADAVLHDTPNILYFIKTAGNGQFKAVGDS--LEAQQYGIAFPKGS---ELREKVNGALKTLKENGTYAEIY  238 (247)
T ss_pred             CceeEEEeChHHHHHHHHhCCCCceEEecCc--ccccceEEEEcCcH---HHHHHHHHHHHHHHHCCcHHHHH
Confidence            9655544332 221    1112334443322  22335667666654   34444444444443333344443

>TIGR00363 lipoprotein, YaeC family

Probab=97.80  E-value=0.01  Score=47.45  Aligned_cols=200  Identities=8%  Similarity=0.004  Sum_probs=112.4

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQW  166 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~  166 (306)
                      .+||||+........+......+.+. .++++++... +..+..+.|.+|++|+.+..+.+.     ...++....++..
T Consensus        18 ~~l~vG~~~~~~~~~~~~~~~~~~~~-~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~~   96 (258)
T TIGR00363        18 LHIKVGVISGAEQQVAEVAAKVAKEK-YGLDVELVEFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGNT   96 (258)
T ss_pred             CcEEEEeCCCChHHHHHHHHHHHHHh-cCCEEEEEEeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEeee
Confidence            46999998765555554444443332 3677777653 456788999999999997643321     1234444444432


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhc-CCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEEEecC
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEIS-NYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVLETIN  226 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~-~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~~~~~  226 (306)
                      ..   .+-+  +...+--+++||. +..... +.+..........|+..|+.                  | ++.+.--+
T Consensus        97 ~~---~p~~--~ys~~~~sl~dlk~G~~IAi-p~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~  170 (258)
T TIGR00363        97 FV---YPLA--GYSKKIKNVNELQDGAKVAV-PNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELE  170 (258)
T ss_pred             EE---eccc--ccCcCCCCHHHcCCCCEEEE-eCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcC
Confidence            21   2111  1223455899997 555554 44434444555689998883                  3 34454445


Q ss_pred             HHHHHHHHHhc-cceeeeec-ceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760         227 SDIIKTYVELR-MGIGIIAS-IAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN  301 (306)
Q Consensus       227 ~~~~~~~v~~g-~gi~~~p~-~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  301 (306)
                      ...+.+.+.+| ...+++.. +........  +-....-.+  ...-..++++.+...++.++.|++.+++.=-+..++
T Consensus       171 ~~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~--~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~  247 (258)
T TIGR00363       171 TSQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKD--SPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQ  247 (258)
T ss_pred             HHHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCC--CCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHH
Confidence            55566777775 34444444 443331111  112222111  122345667777778999999999987654444443

This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=97.80  E-value=0.0002  Score=53.74  Aligned_cols=78  Identities=18%  Similarity=0.139  Sum_probs=60.5

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ -|.+.-|+.+++++||+|+.|++||+. |.--..+     ....+ .||+.|+.+++.+.+..
T Consensus        43 Lt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~k-GlI~R~~~~~DrR~~~I-~LTekG~~l~~~l~~~~  120 (185)
T PRK13777         43 LNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEER-GYLTFSKKEDDKRNTYI-ELTEKGEELLLETMEEY  120 (185)
T ss_pred             CCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeeEE-EECHHHHHHHHHHHHHH
Confidence            3556788888888764 247888999999999999999999997 5544432     23344 79999999999998887


Q ss_pred             HHHHHH
Q psy3760          75 QEIEGL   80 (306)
Q Consensus        75 ~~~~~~   80 (306)
                      ...+..
T Consensus       121 ~~~e~~  126 (185)
T PRK13777        121 DPENNS  126 (185)
T ss_pred             HHHHHH
Confidence            776653

>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein

Probab=97.78  E-value=0.0035  Score=50.07  Aligned_cols=140  Identities=14%  Similarity=0.100  Sum_probs=92.9

Q ss_pred             CcEEEEecccc-----------hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC-c
Q psy3760          93 GNLTIATTHTQ-----------ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK-L  158 (306)
Q Consensus        93 ~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~-~  158 (306)
                      +.|++|+....           ...+...++..+.+.. +++++++..+..+.+..+.+|++|+++......  .... .
T Consensus        24 ~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~~~  102 (250)
T TIGR01096        24 GSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRM-KAKCKFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQID  102 (250)
T ss_pred             CeEEEEECCCCCCceEECCCCCEEeehHHHHHHHHHHh-CCeEEEEeCCHHHHHHHHhCCCcCEEEecCccCHHHhhccc
Confidence            68999986321           1246677887777664 588899888999999999999999997532111  1122 2


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      -+.+++.....++++++.+.    .-+++||.+.+..... +......+.+.+.. +.  + ...+.+...++.++.+|.
T Consensus       103 ~s~p~~~~~~~~~~~~~~~~----~~~~~dl~g~~i~~~~-g~~~~~~l~~~~~~-~~--~-~~~~~s~~~~~~~L~~g~  173 (250)
T TIGR01096       103 FSDPYYATGQGFVVKKGSDL----AKTLEDLDGKTVGVQS-GTTHEQYLKDYFKP-GV--D-IVEYDSYDNANMDLKAGR  173 (250)
T ss_pred             cccchhcCCeEEEEECCCCc----CCChHHcCCCEEEEec-CchHHHHHHHhccC-Cc--E-EEEcCCHHHHHHHHHcCC
Confidence            36778888899999887653    2378889877665543 33333333333321 21  2 345688999999999994


Q ss_pred             ceee
Q psy3760         239 GIGI  242 (306)
Q Consensus       239 gi~~  242 (306)
                      .=++
T Consensus       174 vD~~  177 (250)
T TIGR01096       174 IDAV  177 (250)
T ss_pred             CCEE
Confidence            4443

>COG0226 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]

Probab=97.77  E-value=0.0033  Score=52.09  Aligned_cols=204  Identities=15%  Similarity=0.113  Sum_probs=134.9

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHH-HHHcCCeeEEEEccccCC---------CCCcee
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE-MIRNDQADIAIVTEILSP---------SDKLIS  160 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~-~l~~~~~Di~i~~~~~~~---------~~~~~~  160 (306)
                      ..+.|+++.+.+ ...+...+...|.+.||++.+.+...++..-.. .+..+ +||+-+..+..+         ...+..
T Consensus        41 ~~~~l~~~GStt-v~p~~~~~a~~~~~~~~~~~v~~q~~GSg~G~~~~~~~~-vDig~ss~p~~~~e~~~~~~~~~~l~~  118 (318)
T COG0226          41 ASGSLTIAGSTT-VAPLMEAWAEEFQKAYPNVKVNVQAGGSGAGIKQALAGG-VDIGASSRPLKDSEKEADAKAGKKLVE  118 (318)
T ss_pred             ccceEEEeccCc-HHHHHHHHHHHHHHHCCCeeEEEecCCChHHHHHHhcCC-CccccCCCCCCcchHHHHHhcCCCceE
Confidence            467899988877 577899999999999999999999988888777 55555 999998654331         124778


Q ss_pred             eccccceEEEEecCCCC-CCC-----------CCCcChhhhcC----CC--eEeecCCCCcHHHHHHHHHh------CC-
Q psy3760         161 IPCYQWEYVIIVPLDHP-LLL-----------LNSISLKEISN----YP--LITYDLSFSGRIKLDREFSL------QK-  215 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~-l~~-----------~~~i~~~dl~~----~~--~i~~~~~~~~~~~~~~~~~~------~~-  215 (306)
                      .++..+-+++++.++.+ ...           .+..+|.|+..    .+  .+..+.+++.+..+..++..      .+ 
T Consensus       119 ~pva~d~i~vi~N~~~~~~~~Lt~~~l~~If~G~it~W~d~~~~~~n~~I~vv~R~~~SGT~~~F~~~l~~~~~~~~~g~  198 (318)
T COG0226         119 FPVAIDAIVVIVNLPNPDVLNLTKDQLADIFSGKITNWNDVGGQLLNPGITVVGRSDGSGTTETFTEYLLGWKKKVGAGK  198 (318)
T ss_pred             eeEEeeeEEEEEcCCCccccccCHHHHHHHhcCCCccccccCcccCCCCceEEecCCCCchHHHHHHHHHhhhhccccCc
Confidence            99999999999999988 222           23335564432    23  34444456677777777764      12 


Q ss_pred             -CceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc-cc-----CCc--e---eeec------CCC-CccceEEEEEe
Q psy3760         216 -LTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN-RD-----KNL--R---SISA------SHL-FGTTISRVIIK  275 (306)
Q Consensus       216 -~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~-----~~l--~---~~~~------~~~-~~~~~~~l~~~  275 (306)
                       ..-...........+...|.+. .+|+++-...+..- ..     ...  +   .-|.      ... +..+..|++++
T Consensus       199 ~~~~~~~~~~~~n~~v~~~v~~tp~aIGYv~~~y~~~n~~~~~~~~~~~~~~~~~v~p~~~~i~~~~y~Pi~~~~~~~v~  278 (318)
T COG0226         199 TVDWPAAVGGKGNEGVVAAVSQTPGAIGYVGYAYAVQNNLKLAALANKAGGVGPTVEPTAENIANGKYSPIVRPLFIYVN  278 (318)
T ss_pred             ccccCccccCCCcHHHHHHHhcCCCceEEEeehhhhcccchhhhhhcccCCcCccccCHHHHHhcCCccccceeeEEEEc
Confidence             1111244556667777878765 88888877665431 00     011  0   1111      112 44567788877


Q ss_pred             CCcc--ccHHHHHHHHHHhHHhh
Q psy3760         276 QGTY--LRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       276 ~~~~--~~~~~~~~~~~l~~~~~  296 (306)
                      ++..  ..+.+++|++++...=+
T Consensus       279 ~~~~~~~~~~~~~Fi~~~~~~~~  301 (318)
T COG0226         279 KNPKDTKAPAVKAFLDWALSPGG  301 (318)
T ss_pred             CCccccchHHHHHHHHHHhcccc
Confidence            6654  58999999988865433

>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein

Probab=97.76  E-value=0.003  Score=51.36  Aligned_cols=204  Identities=9%  Similarity=0.019  Sum_probs=118.2

Q ss_pred             CCCcEEEEecccch----------hhhhHHHHHHHHHhCCCcE-EEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCC
Q psy3760          91 DTGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVK-LSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~-i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~  157 (306)
                      .+|.|++|+....+          ..+...++..+.+.. ++. +.+...+..+++..+.+|++|+++....  ......
T Consensus        31 ~~~~l~v~~~~~pP~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~~~  109 (275)
T TIGR02995        31 EQGFARIAIANEPPFTYVGADGKVSGAAPDVARAIFKRL-GIADVNASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQ  109 (275)
T ss_pred             hCCcEEEEccCCCCceeECCCCceecchHHHHHHHHHHh-CCCceeeccCCHHHHHHHHHCCCcCEEeecccCCHHHHhc
Confidence            35789998864322          245567888887774 453 6777788889999999999999765211  112222


Q ss_pred             c-eeeccccceEEEEecCCCCCCCCCCcChhhhcC---CCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760         158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN---YPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTY  233 (306)
Q Consensus       158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~---~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (306)
                      + -+.+++...+.++++++++..   .-+++||.+   ..+.. ..+..    ..++++..+........+++...++.+
T Consensus       110 ~~fs~py~~~~~~~~~~~~~~~~---i~~~~dl~~~~g~~Igv-~~g~~----~~~~l~~~~~~~~~i~~~~~~~~~i~~  181 (275)
T TIGR02995       110 VAFTQPILCDAEALLVKKGNPKG---LKSYKDIAKNPDAKIAA-PGGGT----EEKLAREAGVKREQIIVVPDGQSGLKM  181 (275)
T ss_pred             cccccceeecceeEEEECCCCCC---CCCHHHhccCCCceEEE-eCCcH----HHHHHHHcCCChhhEEEeCCHHHHHHH
Confidence            2 356788888999999987532   236778864   34443 33322    245565555443345577899999999


Q ss_pred             HHhccceeeeecce-eccc-c---cCCceee-ecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         234 VELRMGIGIIASIA-FDSN-R---DKNLRSI-SASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       234 v~~g~gi~~~p~~~-~~~~-~---~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      +..|..=+++-... .... .   .+.+..+ ++...+....+++..+++  .......|=+.|++..+....+++.+
T Consensus       182 L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~n~~l~~~~~sG~~~~i~~  257 (275)
T TIGR02995       182 VQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPE--DKELRDAFNVELAKLKESGEFAKIIA  257 (275)
T ss_pred             HHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCC--CHHHHHHHHHHHHHHHhChHHHHHHH
Confidence            99996655544322 2211 1   2233332 222211112224444443  34555555555665555555555543

Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.

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

Probab=97.76  E-value=0.00014  Score=55.75  Aligned_cols=101  Identities=19%  Similarity=0.202  Sum_probs=63.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec----CCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH----GKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~----~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~   93 (306)
                      |.+.-|+.|++|++|+|+.|++||+.   -|+.|.    +..+ .+|+.|+.+++   +....+..+...  .......|
T Consensus        23 S~~eLA~~L~iS~~Tvsr~Lk~LEe~---GlI~R~~~~r~~~v-~LTekG~~ll~---~~~~d~~~if~~--~~ei~l~G   93 (217)
T PRK14165         23 SSSEFANHTGTSSKTAARILKQLEDE---GYITRTIVPRGQLI-TITEKGLDVLY---NEYADYSRIFSI--KDNLELEG   93 (217)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEEEcCCceEE-EECHHHHHHHH---HHHHHHHHHhcc--cccceehh
Confidence            47799999999999999999999986   566665    4455 89999999884   444444444422  11123345


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHh-----CCCc-EEEEE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQ-----FPKV-KLSLL  127 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~-----~p~~-~i~~~  127 (306)
                      .+.=|...+--..-++....+|.+.     ||+. ++.+.
T Consensus        94 ~v~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypGTLNv~l~  133 (217)
T PRK14165         94 NVVKGLGEGKYYINIKGYKIQFEEKLGFIPYPGTLNVKLD  133 (217)
T ss_pred             hhhhccCCccEEEeCHHHHHHHHHHhCCcCCCCcEEEEec
Confidence            5555555542222344566666655     5543 55553

>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein

Probab=97.74  E-value=0.01  Score=46.71  Aligned_cols=185  Identities=12%  Similarity=0.090  Sum_probs=102.9

Q ss_pred             hhhhHHHHHHHHHhCCCcEEEEEeC--ChhHHHHHHHcCCeeEEEEccccCCCCCce-eeccccceEEEEecCCCCCCCC
Q psy3760         105 RYALPKIIKEFTIQFPKVKLSLLQG--NPKQITEMIRNDQADIAIVTEILSPSDKLI-SIPCYQWEYVIIVPLDHPLLLL  181 (306)
Q Consensus       105 ~~~l~~~l~~~~~~~p~~~i~~~~~--~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~  181 (306)
                      ..+-..++..+.++ -++++++...  ........+.+|++|+++.. + .....+. +.+++...++++++++++.   
T Consensus        19 ~G~~~el~~~i~~~-~g~~i~~~~~~~~~~~~~~~l~~g~~Di~~~~-~-~r~~~~~fs~py~~~~~~lv~~~~~~~---   92 (232)
T TIGR03871        19 EGFENKIAQLLADD-LGLPLEYTWFPQRRGFVRNTLNAGRCDVVIGV-P-AGYEMVLTTRPYYRSTYVFVTRKDSLL---   92 (232)
T ss_pred             CchHHHHHHHHHHH-cCCceEEEecCcchhhHHHHHhcCCccEEEec-c-CccccccccCCcEeeeEEEEEeCCCcc---
Confidence            34677788888776 4677776643  34445678999999998774 2 2223333 4578888999999988642   


Q ss_pred             CCcChhh--hcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE---EE-----ecCHHHHHHHHHhccc-eeeeecceecc
Q psy3760         182 NSISLKE--ISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV---LE-----TINSDIIKTYVELRMG-IGIIASIAFDS  250 (306)
Q Consensus       182 ~~i~~~d--l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-----~~~~~~~~~~v~~g~g-i~~~p~~~~~~  250 (306)
                      ..-+++|  +.+.++.... +...    .+.+...+...+..   ..     ..+...+++++.+|.. .++.....+..
T Consensus        93 ~~~~~~d~~l~g~~V~v~~-g~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~  167 (232)
T TIGR03871        93 DVKSLDDPRLKKLRIGVFA-GTPP----AHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGY  167 (232)
T ss_pred             cccchhhhhhcCCeEEEEc-CChH----HHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEeccHHHHH
Confidence            2236666  7777765544 3222    33344444332211   11     2367889999999966 44444433322


Q ss_pred             c---ccCCceeeecCC----CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         251 N---RDKNLRSISASH----LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       251 ~---~~~~l~~~~~~~----~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .   ..+.+...+...    ......+++..+++.  +...+.|-+++.+. .+ ..+++.
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~n~~l~~~-~~-~~~~i~  224 (232)
T TIGR03871       168 FAKQAGPPLVVVPLLPEDGGIPFDYRIAMGVRKGD--KAWKDELNAVLDRR-QA-EIDAIL  224 (232)
T ss_pred             HHHhCCCCceeeccccCCCCCCccceEEEEEecCC--HHHHHHHHHHHHHH-HH-HHHHHH
Confidence            1   122343333221    112234455556543  45566666666553 22 345444

This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.72  E-value=0.00032  Score=50.83  Aligned_cols=70  Identities=19%  Similarity=0.198  Sum_probs=55.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+.   -|+.|.       ...+ .||+.|+.+++.+..
T Consensus        38 lt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~---GlI~R~~~~~DrR~~~l-~LT~~G~~~~~~~~~  113 (144)
T PRK11512         38 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLV-KLTTSGAAICEQCHQ  113 (144)
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEeccCcccCCeeEe-EEChhHHHHHHHHHH
Confidence            3556778888887655 247899999999999999999999984   455543       3444 899999999998876


Q ss_pred             HH
Q psy3760          73 IM   74 (306)
Q Consensus        73 il   74 (306)
                      ..
T Consensus       114 ~~  115 (144)
T PRK11512        114 LV  115 (144)
T ss_pred             HH
Confidence            64

>PRK10797 glutamate and aspartate transporter subunit; Provisional

Probab=97.70  E-value=0.0089  Score=49.25  Aligned_cols=147  Identities=6%  Similarity=0.070  Sum_probs=94.6

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHH----HHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcc--cc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEF----TIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTE--IL  152 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~----~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~--~~  152 (306)
                      +|.|++|+.....           ..+-..++..+    .+..  +++++++........+..|.+|++|+++...  ..
T Consensus        39 ~g~L~Vg~~~~~pP~~f~~~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~~~~~~i~~L~~G~~Di~~~~~~~t~  118 (302)
T PRK10797         39 NGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNL  118 (302)
T ss_pred             CCeEEEEEcCCCCCcceECCCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEcChHhHHHHHHCCCccEEecCCccCc
Confidence            5789998864321           12334444433    3333  3789999998888889999999999987532  11


Q ss_pred             CCCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHH
Q psy3760         153 SPSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIK  231 (306)
Q Consensus       153 ~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (306)
                      .....+. +.|++.....++++++.+     .-+++||.+...... .+......+..+... +...-....+++....+
T Consensus       119 eR~~~~~fS~Py~~~~~~lv~r~~~~-----i~sl~dL~Gk~V~v~-~gs~~~~~l~~~~~~-~~~~~~i~~~~~~~~~l  191 (302)
T PRK10797        119 ERQKQAAFSDTIFVVGTRLLTKKGGD-----IKDFADLKGKAVVVT-SGTTSEVLLNKLNEE-QKMNMRIISAKDHGDSF  191 (302)
T ss_pred             chhhcceecccEeeccEEEEEECCCC-----CCChHHcCCCEEEEe-CCCcHHHHHHHHhhh-cCCceEEEEeCCHHHHH
Confidence            2333444 457778888999988753     347899988875554 443433444443332 21123456778999999


Q ss_pred             HHHHhccceeeeec
Q psy3760         232 TYVELRMGIGIIAS  245 (306)
Q Consensus       232 ~~v~~g~gi~~~p~  245 (306)
                      .++.+|..=+++-+
T Consensus       192 ~~L~~GrvDa~i~d  205 (302)
T PRK10797        192 RTLESGRAVAFMMD  205 (302)
T ss_pred             HHHHcCCceEEEcc
Confidence            99999977776554

>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein

Probab=97.70  E-value=0.011  Score=47.35  Aligned_cols=180  Identities=17%  Similarity=0.127  Sum_probs=103.6

Q ss_pred             CCCcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC----CCCC-ce-
Q psy3760          91 DTGNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS----PSDK-LI-  159 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~----~~~~-~~-  159 (306)
                      ..+.|+||+.+......+    ..+...+.++. ++++++.. .+..+.++.+.+|++|+++......    ...+ .. 
T Consensus        30 ~~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~-g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~  108 (254)
T TIGR01098        30 VPKELNFGILPGENASNLTRRWEPLADYLEKKL-GIKVQLFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVF  108 (254)
T ss_pred             CCCceEEEECCCCCHHHHHHHHHHHHHHHHHHh-CCcEEEEeCCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceE
Confidence            457899999876554332    34555555553 78888876 4667899999999999999642110    1111 11 


Q ss_pred             eeccc-c-----ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHH-hCCCce----eEEEEecCH
Q psy3760         160 SIPCY-Q-----WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS-LQKLTP----YIVLETINS  227 (306)
Q Consensus       160 ~~~l~-~-----~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~-~~~~~~----~~~~~~~~~  227 (306)
                      ..+.. .     ....++++++++.     -+++||.+.......++... ......++. ..+..+    ..+....+.
T Consensus       109 ~~~~~~~~~~~~~~~~lvv~~d~~i-----~~~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~  183 (254)
T TIGR01098       109 ALTAVSTDGSPGYYSVIIVKADSPI-----KSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSH  183 (254)
T ss_pred             EeeccccCCCCceEEEEEEECCCCC-----CChHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCch
Confidence            11111 1     2357888888753     37899988877766543322 222233343 344332    233455667


Q ss_pred             HHHHHHHHhccc-eeeeecceeccc-cc-----CCceeeecCCCCccceEEEEEeCCc
Q psy3760         228 DIIKTYVELRMG-IGIIASIAFDSN-RD-----KNLRSISASHLFGTTISRVIIKQGT  278 (306)
Q Consensus       228 ~~~~~~v~~g~g-i~~~p~~~~~~~-~~-----~~l~~~~~~~~~~~~~~~l~~~~~~  278 (306)
                      ..+.+++..|.. .++.+......+ ..     .++..+......+  ...++.+++.
T Consensus       184 ~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~  239 (254)
T TIGR01098       184 DASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIP--NDPIAVRKDL  239 (254)
T ss_pred             HHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEEecCCCC--CCCEEEECCC
Confidence            788899999854 555665444332 11     2455555433222  3456666663

A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=97.68  E-value=0.00037  Score=50.54  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=59.4

Q ss_pred             CchhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.+  .+.+.-|+.+++++||+|+.|++||+.   -|+.|.       ...+ .||+.|+.++..+.
T Consensus        29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~---GlV~r~~~~~DrR~~~l-~LT~~G~~~~~~~~  104 (144)
T PRK03573         29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK---GLISRQTCASDRRAKRI-KLTEKAEPLISEVE  104 (144)
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC---CCEeeecCCCCcCeeee-EEChHHHHHHHHHH
Confidence            3566788888888642  267899999999999999999999984   445543       2344 79999999999999


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      +....+.+
T Consensus       105 ~~~~~~~~  112 (144)
T PRK03573        105 AVINKTRA  112 (144)
T ss_pred             HHHHHHHH
Confidence            88877665

>PRK10859 membrane-bound lytic transglycosylase F; Provisional

Probab=97.65  E-value=0.0035  Score=55.24  Aligned_cols=177  Identities=15%  Similarity=0.061  Sum_probs=105.0

Q ss_pred             CCcEEEEecccch---------hhhhHHHHHHHHHhCCCcEEEEE-eCChhHHHHHHHcCCeeEEEEccccC--CCCCce
Q psy3760          92 TGNLTIATTHTQA---------RYALPKIIKEFTIQFPKVKLSLL-QGNPKQITEMIRNDQADIAIVTEILS--PSDKLI  159 (306)
Q Consensus        92 ~~~l~I~~~~~~~---------~~~l~~~l~~~~~~~p~~~i~~~-~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~  159 (306)
                      .|.|+||+.....         ..+-..++..+.+. -+++++++ ..+.++++..|.+|++|+++......  ....+.
T Consensus        42 ~g~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~-LGv~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt~T~eR~~~~~  120 (482)
T PRK10859         42 RGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADY-LGVKLEIKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFR  120 (482)
T ss_pred             CCEEEEEEecCCCeeEecCCCcccHHHHHHHHHHHH-hCCcEEEEecCCHHHHHHHHhCCCCCEEeccCcCChhhhccCc
Confidence            5789999864321         23556788888776 37888887 45788999999999999876432111  122222


Q ss_pred             -eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc
Q psy3760         160 -SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR  237 (306)
Q Consensus       160 -~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g  237 (306)
                       +.++.....+++++++.+    ..-+++||.+..+..... ......+........ ..+. .....+.+.++.++.+|
T Consensus       121 FS~Py~~~~~~lv~r~~~~----~i~~l~dL~Gk~I~V~~g-S~~~~~L~~l~~~~p-~i~~~~~~~~s~~e~l~aL~~G  194 (482)
T PRK10859        121 FGPPYYSVSQQLVYRKGQP----RPRSLGDLKGGTLTVAAG-SSHVETLQELKKKYP-ELSWEESDDKDSEELLEQVAEG  194 (482)
T ss_pred             ccCCceeeeEEEEEeCCCC----CCCCHHHhCCCeEEEECC-CcHHHHHHHHHHhCC-CceEEecCCCCHHHHHHHHHCC
Confidence             456777888889888763    234789999888766543 333334443333221 1111 22346889999999999


Q ss_pred             cceeeeec-ceeccc--ccCCceeeecCCCCccceEEEEEeCC
Q psy3760         238 MGIGIIAS-IAFDSN--RDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       238 ~gi~~~p~-~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                      ..=+++-+ ..+...  ..+++......  ....+++++.+++
T Consensus       195 ~iDa~v~d~~~~~~~~~~~p~l~v~~~l--~~~~~~~~av~k~  235 (482)
T PRK10859        195 KIDYTIADSVEISLNQRYHPELAVAFDL--TDEQPVAWALPPS  235 (482)
T ss_pred             CCCEEEECcHHHHHHHHhCCCceeeeec--CCCceeEEEEeCC
Confidence            55444433 222111  23445432211  1234566777763

>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A

Probab=97.60  E-value=0.006  Score=48.86  Aligned_cols=202  Identities=12%  Similarity=0.055  Sum_probs=111.1

Q ss_pred             CCCcEEEEecccchhhhhHHHH-HHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC-----C-----CCCc
Q psy3760          91 DTGNLTIATTHTQARYALPKII-KEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-----P-----SDKL  158 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l-~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-----~-----~~~~  158 (306)
                      ...+||||+.+.....-+.-.. ..+.+++ +++++++. .+..++.+.+.+|++|++.+ ....     .     ...+
T Consensus         4 ~~~~l~ig~~~~~~~~p~~~a~~~g~f~~~-G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~   81 (252)
T PF13379_consen    4 EPTTLRIGYLPGPDYAPLYVAQEKGLFEKE-GLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDI   81 (252)
T ss_dssp             SESEEEEEETSSGGGHHHHHHHHTTHHHHT-TSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----E
T ss_pred             CCcEEEEEeecchHHHHHHHHHHcChHHHc-CCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccce
Confidence            3568999998875433221111 2244444 55566655 35668999999999999999 2210     1     1122


Q ss_pred             e-eeccccceEEEEecCCCCCCCCCCcChhhh-------cCCCeEeecCCCCcHHHHHHHHHhCCCce--eEEEEecCHH
Q psy3760         159 I-SIPCYQWEYVIIVPLDHPLLLLNSISLKEI-------SNYPLITYDLSFSGRIKLDREFSLQKLTP--YIVLETINSD  228 (306)
Q Consensus       159 ~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl-------~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~  228 (306)
                      . ...+..+...++++++.... ...-+++||       .+..+.....++...-.+..++++.|+.+  .+.+..-+..
T Consensus        82 ~~~~~~~~~g~~lvv~~~~~~~-~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~~  160 (252)
T PF13379_consen   82 VVLAGLSQNGNALVVRNDLKDA-SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPPP  160 (252)
T ss_dssp             EEEEECSBSSEEEEECGGGTTC-STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--GH
T ss_pred             EEeeccCCCceEEEEcCccccC-CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCHH
Confidence            2 22344556677777653111 234578999       66677776666555556778999999987  3344444448


Q ss_pred             HHHHHHHhc-cceeeeecceeccc-ccCC-ceeeecCCCCccceEE-EEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         229 IIKTYVELR-MGIGIIASIAFDSN-RDKN-LRSISASHLFGTTISR-VIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       229 ~~~~~v~~g-~gi~~~p~~~~~~~-~~~~-l~~~~~~~~~~~~~~~-l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                      .+..++++| .-.++++....... ..+. -..+...+.....+.+ ++.+++-  ..+..+++|++.+.+..
T Consensus       161 ~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~~p~~~~~~~~~~~~~~p~~v~~~~~a~~~A~  233 (252)
T PF13379_consen  161 EMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGNHPCCVIVARRDFLEENPEAVKAFLEALQEAQ  233 (252)
T ss_dssp             HHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT-B-EEEEEEHHHHHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCCCCeEEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence            888888888 33333445444333 2332 3333333322222333 3444432  23567888888876654

>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional

Probab=97.58  E-value=0.017  Score=48.31  Aligned_cols=151  Identities=14%  Similarity=0.043  Sum_probs=101.0

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC----CCceeeccccceE
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS----DKLISIPCYQWEY  168 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~----~~~~~~~l~~~~~  168 (306)
                      ..|+++.+.+ ...++..+...|.+. +++++++...++..-+..+.+|.+||+-+..+..+.    .++...++.-+.+
T Consensus        27 ~~i~~~GSt~-~~pl~~~~a~~y~~~-~~v~v~~~~~GSG~Gi~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~daI  104 (346)
T PRK10918         27 ASLTGAGATF-PAPVYAKWADTYQKE-TGNKVNYQGIGSSGGVKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGV  104 (346)
T ss_pred             ceEEEEccCh-HHHHHHHHHHHHHhh-cCCEEEEecCccHHHHHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEEEEE
Confidence            4688777766 566888888999764 789999999999999999999999999996543322    2466788888899


Q ss_pred             EEEec-CCCCCC---C----------CCCcChhh-----------hcCCCeEee--cCCCCcHHHHHHHHHhCCC-----
Q psy3760         169 VIIVP-LDHPLL---L----------LNSISLKE-----------ISNYPLITY--DLSFSGRIKLDREFSLQKL-----  216 (306)
Q Consensus       169 ~~v~~-~~~~l~---~----------~~~i~~~d-----------l~~~~~i~~--~~~~~~~~~~~~~~~~~~~-----  216 (306)
                      +++++ ++.+..   .          .+..+|.|           +.+.|...+  ..+++.+..+.+.+....-     
T Consensus       105 aivvN~~~~~~~~Ltl~~~~L~~If~G~It~W~d~~I~~~NP~~~lpd~~I~vv~R~d~SGTt~~Ft~~l~~~~~~w~~~  184 (346)
T PRK10918        105 VLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWNDEAIAKLNPGVKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKSK  184 (346)
T ss_pred             EEEEeCCCCCccceeeCHHHHHHHhcCCCCCCCchhhhccCCCCCCCCCCeEEEECCCCCchHHHHHHHHHhcChhhhhc
Confidence            99998 555521   1          23335777           445555544  4456677777777643210     


Q ss_pred             --------ceeEEEEecCHHHHHHHHHhc-cceeeeecc
Q psy3760         217 --------TPYIVLETINSDIIKTYVELR-MGIGIIASI  246 (306)
Q Consensus       217 --------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~  246 (306)
                              -|. .........+...|.+. .+|+++...
T Consensus       185 ~~~g~~~~~p~-~~~~~gn~~v~~~V~~~p~aIGYv~~~  222 (346)
T PRK10918        185 VGAGSTVNWPT-GLGGKGNDGIAAFVQRLPGAIGYVEYA  222 (346)
T ss_pred             cCcCccccCcc-ccccCCCHHHHHHHhcCCCceEeeeHH
Confidence                    011 12333444666777665 788888653

>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional

Probab=97.58  E-value=0.027  Score=45.45  Aligned_cols=201  Identities=7%  Similarity=0.047  Sum_probs=112.7

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQW  166 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~  166 (306)
                      ..|+||+..+... .+..++....+..-++++++... +.....+.|.+|++|+.+..+...-     ..+.....++. 
T Consensus        31 ~~I~IG~~~~~~~-~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~~~-  108 (271)
T PRK11063         31 NHIKVGVIVGAEQ-QVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVGN-  108 (271)
T ss_pred             CcEEEEeCCCChH-HHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEEeE-
Confidence            4699999876444 34556666655555788888874 4478899999999999775432111     12333333322 


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhc-CCCeEeecCCCCcHHHHHHHHHhCCC------------------ce-eEEEEecC
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEIS-NYPLITYDLSFSGRIKLDREFSLQKL------------------TP-YIVLETIN  226 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~-~~~~i~~~~~~~~~~~~~~~~~~~~~------------------~~-~~~~~~~~  226 (306)
                        ..++|.+  +...+--+++||. +.....+... ........+|+..|+                  .| ++.+.--+
T Consensus       109 --~~vvp~~--~ys~~i~si~DL~~Gk~IAip~d~-~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~  183 (271)
T PRK11063        109 --TFVYPIA--GYSKKIKSLDELQDGSQVAVPNDP-TNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELE  183 (271)
T ss_pred             --EEEEEee--ccccCCCCHHHhcCCCEEEecCCC-ccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECc
Confidence              2223322  1122345899998 5555454433 333344447888777                  22 34444445


Q ss_pred             HHHHHHHHHhc-cceeeeecceeccc--cc-CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         227 SDIIKTYVELR-MGIGIIASIAFDSN--RD-KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       227 ~~~~~~~v~~g-~gi~~~p~~~~~~~--~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      ...+.+...+| .-.++++...+...  .. .+-....-.+ . .+-..++.++....++.++.+++.+++-=-+..+++
T Consensus       184 ~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~-~-~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~  261 (271)
T PRK11063        184 APQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKD-S-PYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANK  261 (271)
T ss_pred             HHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCCC-C-CeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHH
Confidence            55666666764 33444554443332  11 1222222222 2 233456667777789999999998876544444443

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=97.57  E-value=0.00064  Score=46.58  Aligned_cols=72  Identities=14%  Similarity=0.255  Sum_probs=54.2

Q ss_pred             chhhHHHHHHHH----Hh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCc-cccCHhHHHHHHHH
Q psy3760           2 NLHQFRFVREAV----RQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRI-RGLTKPGQAILRSI   70 (306)
Q Consensus         2 ~~~~l~~f~~v~----~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~-~~lT~~G~~l~~~a   70 (306)
                      +..++.++..+.    .. +-+.+.-|+.+++++|++|+.|++||+.   -++.|.     +|.+ +.||+.|+.+++.+
T Consensus        24 s~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k---g~I~r~~~~~D~R~~~i~lT~~G~~~~~~~  100 (109)
T TIGR01889        24 SLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK---GYLSKERSEDDERKVIISINKEQRSKIESL  100 (109)
T ss_pred             CHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC---CCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence            456777787777    22 1379999999999999999999999984   455543     1221 37999999999888


Q ss_pred             HHHHHH
Q psy3760          71 EIIMQE   76 (306)
Q Consensus        71 ~~il~~   76 (306)
                      ..-++.
T Consensus       101 ~~~~~~  106 (109)
T TIGR01889       101 ISEIEQ  106 (109)
T ss_pred             HHHHHH
Confidence            776654

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.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=97.55  E-value=0.00064  Score=49.40  Aligned_cols=62  Identities=19%  Similarity=0.199  Sum_probs=49.1

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI   83 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~   83 (306)
                      .+.-|+.|+|++||+|..+++|++ .|.--+++ .+|+ +||+.|+.+.....+.-..++.+...
T Consensus        27 ~~diA~~L~Vsp~sVt~ml~rL~~-~GlV~~~~-y~gi-~LT~~G~~~a~~~~r~hrlle~fL~~   88 (154)
T COG1321          27 TKDIAERLKVSPPSVTEMLKRLER-LGLVEYEP-YGGV-TLTEKGREKAKELLRKHRLLERFLVD   88 (154)
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHH-CCCeEEec-CCCe-EEChhhHHHHHHHHHHHHHHHHHHHH
Confidence            466799999999999999999986 35444443 4666 89999999888888777777777654

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=97.54  E-value=0.00032  Score=49.38  Aligned_cols=73  Identities=19%  Similarity=0.280  Sum_probs=59.2

Q ss_pred             CchhhHHHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.+ ..  +.-|+.+++++|++|+.|++||+.   -|+.|..       ..+ .+|+.|+.++..+.
T Consensus        20 lt~~q~~~L~~l~~~~-~~~~~~la~~l~i~~~~vt~~l~~Le~~---glv~r~~~~~DrR~~~l-~lT~~G~~~~~~~~   94 (126)
T COG1846          20 LTPPQYQVLLALYEAG-GITVKELAERLGLDRSTVTRLLKRLEDK---GLIERLRDPEDRRAVLV-RLTEKGRELLEQLL   94 (126)
T ss_pred             CCHHHHHHHHHHHHhC-CCcHHHHHHHHCCCHHHHHHHHHHHHHC---CCeeecCCccccceeeE-EECccHHHHHHHhc
Confidence            3567889999999999 77  899999999999999999999985   3555442       233 89999999999999


Q ss_pred             HHHHHHH
Q psy3760          72 IIMQEIE   78 (306)
Q Consensus        72 ~il~~~~   78 (306)
                      .......
T Consensus        95 ~~~~~~~  101 (126)
T COG1846          95 PAAQELL  101 (126)
T ss_pred             cHHHHHH
Confidence            8444433

>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional

Probab=97.53  E-value=0.014  Score=47.01  Aligned_cols=205  Identities=6%  Similarity=0.004  Sum_probs=114.1

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChh-HHHHHHHcCCeeEEEEccccC-----CCCCceeeccccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQW  166 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~-~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~  166 (306)
                      ..|+||+..+... -+..+...+.+..+++++++...+.. ...+.|.+|++|+.+..+.+.     ...+.....+.  
T Consensus        32 ~tLkVG~~~~~~~-~~~e~a~~~~k~~~G~~Velv~fsd~~~~n~AL~~G~ID~n~~qh~~yl~~~~~~~g~~lv~~~--  108 (272)
T PRK09861         32 KHIKVGVINGAEQ-DVAEVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVG--  108 (272)
T ss_pred             CcEEEEEcCCchH-HHHHHHHHHHHHcCCCeEEEEecCchhhHHHHHHcCCcceehhhhHHHHHHHHHhcCCCeEEEe--
Confidence            4799999887655 45556777766656899999865433 445899999999998643211     11222222222  


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC---------Cc----------eeEEEEecCH
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK---------LT----------PYIVLETINS  227 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~---------~~----------~~~~~~~~~~  227 (306)
                       ..+++|-+  +...+--+++||.+-.-|..+.+.....+....++..|         ..          .+..+.--..
T Consensus       109 -~~~~~P~~--~Ys~~iksl~DL~~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~  185 (272)
T PRK09861        109 -NTFVFPMA--GYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEG  185 (272)
T ss_pred             -EEEEEeee--ccccCCCCHHHcCCCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCH
Confidence             23333322  22334458999995555555543343344455555544         22          1344444555


Q ss_pred             HHHHHHHHhc--cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         228 DIIKTYVELR--MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       228 ~~~~~~v~~g--~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ..+...+..|  +++.+-..+....-..+.-..+-.+.....+-..++++.+...++.+++|++.+++.--+..+++.
T Consensus       186 ~q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~  263 (272)
T PRK09861        186 AQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETI  263 (272)
T ss_pred             HHhHhhccCcccCEEEEchhHHHHcCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence            5666767774  444444444433211110011211211112344566787888899999999998776555555443

>PRK10870 transcriptional repressor MprA; Provisional

Probab=97.48  E-value=0.00076  Score=50.57  Aligned_cols=73  Identities=22%  Similarity=0.201  Sum_probs=56.7

Q ss_pred             chhhHHHHHHHHHh--cCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ--NFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         2 ~~~~l~~f~~v~~~--~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a   70 (306)
                      +..++.++..+.+.  + ++  +.-|+.+++++|++|+.|++||+.   -|+.|.       ...+ .||+.|+.+++.+
T Consensus        54 t~~q~~iL~~L~~~~~~-~it~~eLa~~l~l~~~tvsr~v~rLe~k---GlV~R~~~~~DrR~~~v-~LT~~G~~~~~~i  128 (176)
T PRK10870         54 NETLFMALITLESQENH-SIQPSELSCALGSSRTNATRIADELEKR---GWIERRESDNDRRCLHL-QLTEKGHEFLREV  128 (176)
T ss_pred             CHHHHHHHHHHhcCCCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCCCCCCCeeEE-EECHHHHHHHHHH
Confidence            44567788888753  4 44  788999999999999999999984   455653       1233 8999999999999


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      .+.......
T Consensus       129 ~~~~~~~~~  137 (176)
T PRK10870        129 LPPQHNCLH  137 (176)
T ss_pred             HHHHHHHHH
Confidence            887776654

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

Probab=97.47  E-value=0.00032  Score=38.62  Aligned_cols=32  Identities=19%  Similarity=0.155  Sum_probs=24.8

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      +-.++.+++++.++||+.||||++|+.+.|++
T Consensus        10 i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk   41 (42)
T PF02954_consen   10 IRQALERCGGNVSKAARLLGISRRTLYRKLKK   41 (42)
T ss_dssp             HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            33455566669999999999999999999986

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

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

Probab=97.40  E-value=0.0017  Score=41.54  Aligned_cols=65  Identities=23%  Similarity=0.311  Sum_probs=44.7

Q ss_pred             HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee---E-EecCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760          12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI---F-IRHGKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus        12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L---f-~R~~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      ..+.- +|+.=.+.|++|.+++|++++.||+.==++-   | .|.++..+++|+.|+..++.-...++++
T Consensus        11 ~~~~~-~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L~~~   79 (80)
T PF13601_consen   11 ANEEA-TFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAALREI   79 (80)
T ss_dssp             HHSEE-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHHHHH
T ss_pred             hcCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHHHHh
Confidence            34566 8999999999999999999999998632222   1 1223334589999999988877776653

>TIGR02285 conserved hypothetical protein

Probab=97.37  E-value=0.029  Score=45.34  Aligned_cols=212  Identities=11%  Similarity=0.032  Sum_probs=118.5

Q ss_pred             CCcEEEEecccch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCCce
Q psy3760          92 TGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDKLI  159 (306)
Q Consensus        92 ~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~~~  159 (306)
                      ..+|+++..+..+          ..+...++..+.+..+++++++...+...++..+ +|+.|.++.....  .....+.
T Consensus        17 ~~~l~~~~~~~pPf~~~~~~~~~~G~~~~i~~~i~~~~~~~~~~~~~~pw~r~l~~l-~~~~d~~~~~~~~t~eR~~~~~   95 (268)
T TIGR02285        17 KEAITWIVNDFPPFFIFSGPSKGRGVFDVILQEIRRALPQYEHRFVRVSFARSLKEL-QGKGGVCTVNLLRTPEREKFLI   95 (268)
T ss_pred             cceeEEEecccCCeeEeCCCCCCCChHHHHHHHHHHHcCCCceeEEECCHHHHHHHH-hcCCCeEEeeccCCcchhhcee
Confidence            3577877754222          1234556677888777889999999999999999 6666666532221  2223333


Q ss_pred             -eeccc-cceEEEEecCCCCCCCC----CCcChhhh---cCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHH
Q psy3760         160 -SIPCY-QWEYVIIVPLDHPLLLL----NSISLKEI---SNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDI  229 (306)
Q Consensus       160 -~~~l~-~~~~~~v~~~~~~l~~~----~~i~~~dl---~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  229 (306)
                       +.|+. ....+++++++.+..-.    .++++.++   .+.. +....+......+++.+...+..+.. ....++...
T Consensus        96 Fs~P~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~~l~g~~-vgv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  174 (268)
T TIGR02285        96 FSDPTLRALPVGLVLRKELTAGVRDEQDGDVDLKKLLASKKKR-LGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGN  174 (268)
T ss_pred             ecCCccccCCceEEEccchhhhccccCCCCccHHHHhcCCCeE-EEEecceeccHHHHHHHHhCCcccceeeeccchHHH
Confidence             34555 35788888887642211    13455544   4433 44444444444566777666544332 344567777


Q ss_pred             HHHHHHhccceeeeec-ceeccc-c-----cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         230 IKTYVELRMGIGIIAS-IAFDSN-R-----DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       230 ~~~~v~~g~gi~~~p~-~~~~~~-~-----~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      +.+++..|..=+++-+ ..+..+ .     ...+...++........+++..+++.........|=+.|++..+....++
T Consensus       175 ~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~  254 (268)
T TIGR02285       175 LFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYK  254 (268)
T ss_pred             HHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHH
Confidence            8999999955554433 322222 1     12355555443222335677777653223455555555555555555666


Q ss_pred             hhc
Q psy3760         303 ILN  305 (306)
Q Consensus       303 ~~~  305 (306)
                      +.+
T Consensus       255 i~~  257 (268)
T TIGR02285       255 YFD  257 (268)
T ss_pred             HHH
Confidence            543

Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.

>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional

Probab=97.36  E-value=0.012  Score=47.42  Aligned_cols=203  Identities=11%  Similarity=0.062  Sum_probs=115.3

Q ss_pred             CCCcEEEEecc-cch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          91 DTGNLTIATTH-TQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~-~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ....|+||+.. ..+          ..+...++..+.+. -++++++...+..++++.+..|++|+++......  ....
T Consensus        24 ~~~~l~v~~~~~~pPf~~~~~~g~~~G~~vdl~~~ia~~-lg~~~~~~~~~~~~~~~~l~~g~~Di~~~~~~~t~eR~~~  102 (260)
T PRK15010         24 LPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKR-MQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQE  102 (260)
T ss_pred             cCCeEEEEecCCcCCceeECCCCCEEeeeHHHHHHHHHH-hCCceEEEeCCHHHHHHHHHCCCCCEEEecCcCCHHHHhh
Confidence            34678999863 111          13556778787776 4788888888888999999999999987532211  2222


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. +.++.....+++++++.+..    .+++||.+.+.-. ..+..........+...+.  + ....++...++.++.+
T Consensus       103 ~~fs~p~~~~~~~~~~~~~~~~~----~~~~dl~g~~Igv-~~gs~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~l~~  174 (260)
T PRK15010        103 IAFSDKLYAADSRLIAAKGSPIQ----PTLDSLKGKHVGV-LQGSTQEAYANETWRSKGV--D-VVAYANQDLVYSDLAA  174 (260)
T ss_pred             cccccceEeccEEEEEECCCCCC----CChhHcCCCEEEE-ecCchHHHHHHHhcccCCc--e-EEecCCHHHHHHHHHc
Confidence            32 56777888999999887532    2678998877444 4443322222222222232  2 3346788888999999


Q ss_pred             ccceeeeec-ceecc-c-c---cCCceeeecCCC---CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         237 RMGIGIIAS-IAFDS-N-R---DKNLRSISASHL---FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       237 g~gi~~~p~-~~~~~-~-~---~~~l~~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      |..=+++-+ ..... + .   ...+...+....   .....+++..+++  .......|=+.|++.-+....+++.
T Consensus       175 griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~--~~~L~~~ln~~l~~l~~~G~~~~i~  249 (260)
T PRK15010        175 GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKD--DAELTAAFNKALGELRQDGTYDKMA  249 (260)
T ss_pred             CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCC--CHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            955444433 22211 1 1   123333322111   1112344555543  2445555555555554444555554

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=97.33  E-value=0.00064  Score=42.23  Aligned_cols=56  Identities=29%  Similarity=0.402  Sum_probs=42.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      ||.+-++.+   .+...|.+.-|+.+++|.+++++.|+.||+ .|.++..+ ++|. .+.+.
T Consensus         1 ~~~~il~~L---~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~-~g~~i~~~-~~g~-~l~~~   56 (69)
T TIGR00122         1 MPLRLLALL---ADNPFSGEKLGEALGMSRTAVNKHIQTLRE-WGVDVLTV-GKGY-RLPPP   56 (69)
T ss_pred             ChHHHHHHH---HcCCcCHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEec-CCce-EecCc
Confidence            555555553   333338899999999999999999999986 59998877 6776 56443

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.

>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=97.32  E-value=0.00076  Score=38.44  Aligned_cols=43  Identities=21%  Similarity=0.223  Sum_probs=34.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ -|.+..|+.+|+|.+++++.|++|++.
T Consensus         1 l~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    1 LDETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             --HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            6778888888888866 367788999999999999999999874

...

>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein

Probab=97.30  E-value=0.02  Score=47.23  Aligned_cols=192  Identities=9%  Similarity=0.024  Sum_probs=103.7

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEccccC---CCCCceeecc-----cc
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEILS---PSDKLISIPC-----YQ  165 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~l-----~~  165 (306)
                      ++||+........+...-..|.+++ ++++++.... ...+.+.|.+|++|+++......   ...+.....+     ..
T Consensus         1 ~~~~~~~~~~p~~va~~~G~~~k~~-Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~   79 (300)
T TIGR01729         1 VTVGYQTIVEPFKVAQADGAAAKEA-GATIDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIG   79 (300)
T ss_pred             CEEEecCCCCHHHHHHHcCchHHhc-CCeeEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCC
Confidence            5788877654445555444555443 7778877764 45788999999999998632111   1122221111     11


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHhc-cceeee
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVELR-MGIGII  243 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g-~gi~~~  243 (306)
                      ....++++++.+     .-+++||.+.++... .+......+..++...|+.+..+ +..-....+..++.+| .-.+++
T Consensus        80 ~~~~lv~~~~s~-----I~s~~DLkGK~Igv~-~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~vDa~~~  153 (300)
T TIGR01729        80 KSEALVAREGSG-----IEKPEDLKGKNVAVP-FVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGDIDAAYV  153 (300)
T ss_pred             ccceEEecCCCC-----CCChhHcCCCEEEeC-CCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCCcCEEEE
Confidence            234566665543     237899999886654 33344556677888888876432 3323455677778887 223334


Q ss_pred             ecceeccc-ccCCceeeecCCC---CccceEEEEEeCCc--cccHHHHHHHHHHhHH
Q psy3760         244 ASIAFDSN-RDKNLRSISASHL---FGTTISRVIIKQGT--YLRSYVYSFIKLLSPK  294 (306)
Q Consensus       244 p~~~~~~~-~~~~l~~~~~~~~---~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~  294 (306)
                      +....... ..+.+..-.....   .+. ...++.+++-  ..+..+++|++.+.+.
T Consensus       154 ~~p~~~~~~~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~p~~~~~~~~a~~~a  209 (300)
T TIGR01729       154 WPPALSELLKSGKVISDSEQVGAWGAPT-FDGWVVRKDFAEKNPEFVAAFTKVLADA  209 (300)
T ss_pred             ecHHHHHHHhcCcEEecchhccccCCCc-eeEEEECHHHHHHCHHHHHHHHHHHHHH
Confidence            44333333 3332221110100   111 1234444331  2467788888777654

This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=97.30  E-value=0.00058  Score=52.59  Aligned_cols=58  Identities=26%  Similarity=0.354  Sum_probs=45.7

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCccccCHhH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRIRGLTKPG   63 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~~~lT~~G   63 (306)
                      +.++++++..+.+.| .+.+..|+.+++|+||+++.|++||+. |  +..|.   ++.+ .+|+.|
T Consensus       142 s~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~-G--lI~r~~~r~~~~-~lT~~G  203 (203)
T TIGR01884       142 SREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKK-G--LVEQKGRKGKRY-SLTKLG  203 (203)
T ss_pred             CHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-C--CEEEEcCCccEE-EeCCCC
Confidence            456778888888744 278999999999999999999999976 4  44444   3555 799876

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.

>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=97.30  E-value=0.00041  Score=39.34  Aligned_cols=40  Identities=25%  Similarity=0.309  Sum_probs=32.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..++++..+.+...++..-|+.+++|||++|++++.|++.
T Consensus         3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~   42 (47)
T PF01022_consen    3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREA   42 (47)
T ss_dssp             HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence            4566666666655588999999999999999999999873

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 ....

>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=97.29  E-value=0.00069  Score=41.06  Aligned_cols=43  Identities=28%  Similarity=0.321  Sum_probs=37.4

Q ss_pred             CchhhHHHHHHHHHhcC---CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNF---NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~---s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |+..++.++..+.+.+.   +.+.-|+.+++++|++|+.|++||+.
T Consensus         3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~   48 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK   48 (62)
T ss_dssp             STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            56778899999999884   68999999999999999999999974

...

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

Probab=97.28  E-value=0.00057  Score=42.32  Aligned_cols=60  Identities=25%  Similarity=0.257  Sum_probs=40.1

Q ss_pred             chhhHHHHHHHH---HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CC-CccccCHhH
Q psy3760           2 NLHQFRFVREAV---RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GK-RIRGLTKPG   63 (306)
Q Consensus         2 ~~~~l~~f~~v~---~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~-~~~~lT~~G   63 (306)
                      +..++.++..+.   +.- +.+.-|+.++++++++|+.|++|++. |.---.++   ++ ..++||++|
T Consensus         2 t~~q~~vL~~l~~~~~~~-t~~~l~~~~~~~~~~vs~~i~~L~~~-glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    2 TRPQWQVLRALAHSDGPM-TQSDLAERLGISKSTVSRIIKKLEEK-GLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             -HHHHHHHHHHT--TS-B-EHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEESSCTTSEEEEE-HHH
T ss_pred             CHHHHHHHHHHHccCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCcCCeeEEEeCCCC
Confidence            456777888887   444 88999999999999999999999986 33322222   23 223899998

>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A

Probab=97.27  E-value=0.0087  Score=47.63  Aligned_cols=177  Identities=17%  Similarity=0.155  Sum_probs=101.2

Q ss_pred             HHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC----CCCCceee--ccc-----cceEEEEecCCC
Q psy3760         109 PKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS----PSDKLISI--PCY-----QWEYVIIVPLDH  176 (306)
Q Consensus       109 ~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~----~~~~~~~~--~l~-----~~~~~~v~~~~~  176 (306)
                      .++...+.+.. ++.+++... +..+..+.+.+|++|+++......    ...++...  ...     ....+++++++.
T Consensus        17 ~~l~~~L~~~~-g~~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds   95 (243)
T PF12974_consen   17 APLADYLSKQL-GVPVELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADS   95 (243)
T ss_dssp             HHHHHHHHHHH-TSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTS
T ss_pred             HHHHHHHHHHh-CCCEEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCC
Confidence            34555555544 788888886 468899999999999999851100    01122211  111     346788888887


Q ss_pred             CCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHH-HhCCCce----eEEEEecCHHHHHHHHHhc-cceeeeecceec
Q psy3760         177 PLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREF-SLQKLTP----YIVLETINSDIIKTYVELR-MGIGIIASIAFD  249 (306)
Q Consensus       177 ~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~-~~~~~~~----~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~  249 (306)
                      +.     -+++||.+..+....+.+.. .-.-...+ ++.|+.+    ..+ .+.+...++.++.+| .-++.++.....
T Consensus        96 ~i-----~~l~dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~-~~~~~~~~~~~l~~G~~Da~~~~~~~~~  169 (243)
T PF12974_consen   96 PI-----TSLADLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQV-FVGSHDAVLEALLNGKADAAAIPSDAFE  169 (243)
T ss_dssp             S-------SHHHHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEE-EEE-HHHHHHHHHTTSSSEEEEEHHHHH
T ss_pred             CC-----CChhhcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEE-EeCCHHHHHHHHHcCCccEEEEechhHH
Confidence            52     37999999999988776543 23344556 6788874    445 777999999999998 556667776665


Q ss_pred             cc-c-----cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         250 SN-R-----DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       250 ~~-~-----~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .. .     ..+++.+--..+.+  ...++.+++- .....+++.+.+.+.-
T Consensus       170 ~~~~~~~~~~~~~rvl~~s~~~p--~~~~~~~~~~-~~~~~~~l~~al~~~~  218 (243)
T PF12974_consen  170 RLEAEGPDIPSQLRVLWTSPPYP--NWPLVASPDL-PPELRQRLRDALLSLS  218 (243)
T ss_dssp             HHHHH-HHHHTTEEEEEEEEEEE----EEEEETTS--HHHHHHHHHHHHHTT
T ss_pred             HHHHccCcccccEEEEEEeCCCC--CcEEEEeCCC-CHHHHHHHHHHHHcCC
Confidence            54 2     23566665443222  2234445553 2344556666665543

>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=97.24  E-value=0.0014  Score=39.54  Aligned_cols=49  Identities=29%  Similarity=0.302  Sum_probs=36.1

Q ss_pred             hhHHHHHHH-HHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC
Q psy3760           4 HQFRFVREA-VRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG   53 (306)
Q Consensus         4 ~~l~~f~~v-~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~   53 (306)
                      ..++++..+ ...+.|++..|+.++++++++|++|+.||+ .|.-=-.|.|
T Consensus        11 ~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~-aGli~~~~~g   60 (61)
T PF12840_consen   11 TRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE-AGLIEVEREG   60 (61)
T ss_dssp             HHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH-TTSEEEEEET
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEeccC
Confidence            345666666 444459999999999999999999999998 5654444443

...

>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein

Probab=97.22  E-value=0.075  Score=43.48  Aligned_cols=197  Identities=10%  Similarity=0.033  Sum_probs=120.4

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCceee-
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLISI-  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~~-  161 (306)
                      ...|+||....-...++..++..+.+.. +..+++...++..+.+.|.+|++|+....-.+..         ..++... 
T Consensus         7 ~~~I~ig~~~w~~~~~~~~i~~~iLE~~-Gy~Ve~~~~~~~~~~~al~~GdiD~~~e~W~p~~~~~~~~~~~~~~l~~lg   85 (290)
T TIGR03414         7 CKTVRFADVGWTDITATTALASVLLEGL-GYQPKVTLLSVPVTYAGLKDGDLDVFLGNWMPAMEPDIKPYLESGSVEVLG   85 (290)
T ss_pred             CCeEEEeeCCcchHHHHHHHHHHHHHHc-CCcceeEEccHHHHHHHHHcCCceEeccccCCcCHHHHHhhccCCeEEEec
Confidence            4569999999988889999998888865 7777888888888999999999999886522111         1123321 


Q ss_pred             c-cccceEEEEecCCCCCCCCCCcChhhhcCC------CeEeecCCCCcHHHHHHHHH--hCCCceeEEEEecCHHHH--
Q psy3760         162 P-CYQWEYVIIVPLDHPLLLLNSISLKEISNY------PLITYDLSFSGRIKLDREFS--LQKLTPYIVLETINSDII--  230 (306)
Q Consensus       162 ~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~------~~i~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~--  230 (306)
                      + .....+.+++|+.-.  ...--+++||.++      .++..+++......+.+..+  ..|+. .......+...+  
T Consensus        86 ~~~~~~~~g~~Vp~y~a--e~~i~sisDL~~~a~~f~g~~~g~~~g~~~~~~~~~~~~~~~ygL~-~~~~~~~s~~a~~a  162 (290)
T TIGR03414        86 PNLEGAKYTLAVPTYVA--DAGLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQKMIDKNAFGLG-GFKLVESSEAGMLA  162 (290)
T ss_pred             ccCCCceEEEEEChhhh--hcCCCCHHHHhhHHHhcCCEEEcccCChhHHHHHHHHHhhccCCCC-CceEeecCHHHHHH
Confidence            2 234467888887643  2234478888653      23444544443334444555  44554 122222333343  


Q ss_pred             --HHHHHhccc---eeeeecceecccccCCceeeecCCCC-----ccceEEEEEeCCcc-ccHHHHHHHHHHhHHh
Q psy3760         231 --KTYVELRMG---IGIIASIAFDSNRDKNLRSISASHLF-----GTTISRVIIKQGTY-LRSYVYSFIKLLSPKL  295 (306)
Q Consensus       231 --~~~v~~g~g---i~~~p~~~~~~~~~~~l~~~~~~~~~-----~~~~~~l~~~~~~~-~~~~~~~~~~~l~~~~  295 (306)
                        .+.+++|..   .+.-|+++...   .+++.+..+...     +..+++.+.+++-. ..|.+.+|++-+.-..
T Consensus       163 ~~~~A~~~~e~~v~~~w~P~w~~~~---~dl~~LeD~~~~~g~~~~~~~i~~v~~~~~~~~~P~~~~~L~~~~~~~  235 (290)
T TIGR03414       163 QVARAVKRKEWVVFLGWEPHPMNTN---FKMTYLTGGDDYFGPNYGGATVYTNTRKGYAAECPNVGKLLTNLTFTL  235 (290)
T ss_pred             HHHHHHHCCCCEEEEEecCchhhhc---cceeECCCCccccCCCCCCCeEEEEeccchHHHChHHHHHHHhCCcCH
Confidence              577788844   45567777654   356666553311     12355666666543 3588888887765444

Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=97.17  E-value=0.00087  Score=42.26  Aligned_cols=43  Identities=30%  Similarity=0.213  Sum_probs=38.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |-.+-|++||+|..||+++|++|+ +.|++.+.+.++|. +|...
T Consensus        21 SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kGY-~L~~~   63 (79)
T COG1654          21 SGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKGY-LLPQL   63 (79)
T ss_pred             cHHHHHHHHCccHHHHHHHHHHHH-HhCCceEecCCCce-eccCc
Confidence            668899999999999999999999 88999999998887 56543

>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein

Probab=97.08  E-value=0.1  Score=43.23  Aligned_cols=199  Identities=14%  Similarity=0.024  Sum_probs=109.0

Q ss_pred             CcEEEEecccchhhhh--HHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHc----CCeeEEEEccccC----CCCC----
Q psy3760          93 GNLTIATTHTQARYAL--PKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRN----DQADIAIVTEILS----PSDK----  157 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l--~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~----~~~Di~i~~~~~~----~~~~----  157 (306)
                      +.|+|.+-.++...+.  +.++..|.+ .+++++++... ++.++...|..    ..+|+++......    ...+    
T Consensus         2 ~~l~vy~~~~~~~~~~~~~~~~~~Fe~-~~gi~V~~~~~~s~~~l~~kl~~e~~~~~~DVv~~~~~~~~~~~~~~gll~p   80 (309)
T TIGR01276         2 PVLTVYTYDSFAADWGPGPVVKKAFEA-DCNCELKLVALEDGVSLLNRLRLEGKNSKADVVLGLDNNLLDAASKTGLFAK   80 (309)
T ss_pred             CeEEEEEccccccCCCCchHHHHHHHH-HHCCEEEEEecCcHHHHHHHHHHcCCCCCCCEEEecCcHHHHHHHHCCCccc
Confidence            5688887666555444  357788875 46999999986 57778988875    4799998631110    0000    


Q ss_pred             ----------------ceeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCC-CcHH-HHHHHHHhCC
Q psy3760         158 ----------------LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSF-SGRI-KLDREFSLQK  215 (306)
Q Consensus       158 ----------------~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~-~~~~-~~~~~~~~~~  215 (306)
                                      -.+.++....++++.+++..  ...+-+|+||.+-    .+.+.++.. .... .+.......|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~i~yn~~~~--~~~P~sw~DL~~~~~~g~i~~~~p~~s~~g~~~~~~~~~~~g  158 (309)
T TIGR01276        81 SGVAADAVNVPGGWNNDTFVPFDYGYFAFVYDKNKL--KNPPQSLKELVESDQNWRVIYQDPRTSTPGLGLLLWMQKVYG  158 (309)
T ss_pred             CCCChhhccCCccccCCeEEEEeeEEEEEEECcccc--CCCCCCHHHHhccccCCeEEeeCCCCCcHHHHHHHHHHHHcC
Confidence                            12456666678888888764  2345689999772    222323221 2111 1111111111


Q ss_pred             ---------CceeEEEEecCHHHHHHHHHhcc-ceeeeecc--eeccc--ccCCceeeecCCCCccceEEEEEeCCcccc
Q psy3760         216 ---------LTPYIVLETINSDIIKTYVELRM-GIGIIASI--AFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLR  281 (306)
Q Consensus       216 ---------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~--~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~  281 (306)
                               +..+......+......++.+|. .+++....  .....  ....+..+.+++........+...++.+..
T Consensus       159 ~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~  238 (309)
T TIGR01276       159 DDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQP  238 (309)
T ss_pred             ccHHHHHHHHHHcCceeCCChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCH
Confidence                     11122223334445667888884 44544432  11111  112233333333333334455557787788


Q ss_pred             HHHHHHHHHHhHH
Q psy3760         282 SYVYSFIKLLSPK  294 (306)
Q Consensus       282 ~~~~~~~~~l~~~  294 (306)
                      ..+++|++++.+.
T Consensus       239 e~A~~Fidflls~  251 (309)
T TIGR01276       239 ELAQKFLQFLVSP  251 (309)
T ss_pred             HHHHHHHHHHcCH
Confidence            9999999998654

This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.

>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional

Probab=97.07  E-value=0.074  Score=42.74  Aligned_cols=205  Identities=8%  Similarity=0.036  Sum_probs=115.2

Q ss_pred             CCCCcEEEEecccchh-----------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCC
Q psy3760          90 YDTGNLTIATTHTQAR-----------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSD  156 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~-----------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~  156 (306)
                      ...+.|++|+.+....           .+...++..+.++. ++++++...+...++..+++|++|+++......  ...
T Consensus        23 a~~~~l~v~~~~~~~P~~~~~~~g~~~G~~vdi~~~ia~~l-g~~i~~~~~pw~~~~~~l~~g~~D~~~~~~~~t~eR~~  101 (259)
T PRK15437         23 AIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRI-NTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQ  101 (259)
T ss_pred             ccCCeEEEEeCCCCCCcceeCCCCCEEeeeHHHHHHHHHHc-CCceEEEeCCHHHHHHHHHCCCCCEEEecCCCCHHHhh
Confidence            3457899998642111           24677888877764 678888888899999999999999887532211  122


Q ss_pred             Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+ -+.+++.....++++++++..    .+++||.+.+..... +..........+...+   ......++...++.++.
T Consensus       102 ~~~fs~p~~~~~~~~~~~~~~~~~----~~~~dl~g~~Igv~~-g~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~L~  173 (259)
T PRK15437        102 EIAFTDKLYAADSRLVVAKNSDIQ----PTVESLKGKRVGVLQ-GTTQETFGNEHWAPKG---IEIVSYQGQDNIYSDLT  173 (259)
T ss_pred             hccccchhhcCceEEEEECCCCCC----CChHHhCCCEEEEec-CcHHHHHHHhhccccC---ceEEecCCHHHHHHHHH
Confidence            22 256778888999999887643    267899888754443 3322222222111111   12346678888899999


Q ss_pred             hcccee-eeecceecc--ccc---CCceee--ecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         236 LRMGIG-IIASIAFDS--NRD---KNLRSI--SASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       236 ~g~gi~-~~p~~~~~~--~~~---~~l~~~--~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      +|..=+ +........  ...   ..+...  .+.. .....++++..+++  .......|=+.+.+.-+....+++.+
T Consensus       174 ~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~--~~~l~~~~n~~l~~~~~~G~~~~i~~  250 (259)
T PRK15437        174 AGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKE--DNELREALNKAFAEMRADGTYEKLAK  250 (259)
T ss_pred             cCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCC--CHHHHHHHHHHHHHHHHCCcHHHHHH
Confidence            985544 333322211  111   122221  1221 11122344555543  34455555555555545555666543

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=97.05  E-value=0.015  Score=40.10  Aligned_cols=64  Identities=20%  Similarity=0.200  Sum_probs=46.6

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHhHHHHHH
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKPGQAILR   68 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~G~~l~~   68 (306)
                      ..++++..+.+.| .+...-|+.+++||||+|++|+.|++ .|.---+|.|+... ++.+....+..
T Consensus        17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~-AGLV~~~r~Gr~~~Y~l~~~~~~~~~   82 (117)
T PRK10141         17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE-SGLLLDRKQGKWVHYRLSPHIPAWAA   82 (117)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCceEEEEEcCEEEEEECchHHHHHH
Confidence            4567777776532 27899999999999999999999985 56666677766532 67776544333

>PRK15007 putative ABC transporter arginine-biding protein; Provisional

Probab=97.04  E-value=0.089  Score=41.75  Aligned_cols=199  Identities=6%  Similarity=-0.018  Sum_probs=110.7

Q ss_pred             CCCCcEEEEecccc-h----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCC
Q psy3760          90 YDTGNLTIATTHTQ-A----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSD  156 (306)
Q Consensus        90 ~~~~~l~I~~~~~~-~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~  156 (306)
                      ...+.|++|+.... +          ..+...++..+.+. -++.+++...+..++.+.+.+|++|+++....  .....
T Consensus        18 ~~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~   96 (243)
T PRK15007         18 TAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKE-IDATCTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREK   96 (243)
T ss_pred             ccCCcEEEEeCCCCCCceeeCCCCCEEeeeHHHHHHHHHH-hCCcEEEEeCCHHHHhHHHhCCCcCEEEEcCccCHHHhc
Confidence            34578999986321 1          23556777777775 47888888888889999999999998875311  11122


Q ss_pred             Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+ -+.+++....+++.+.++      .-+++||.+..+.... +..    ..+++.......+ ....++......++.
T Consensus        97 ~~~fs~p~~~~~~~~v~~~~~------~~~~~dL~g~~Igv~~-g~~----~~~~l~~~~~~~~-~~~~~~~~~~~~~L~  164 (243)
T PRK15007         97 QVLFTTPYYDNSALFVGQQGK------YTSVDQLKGKKVGVQN-GTT----HQKFIMDKHPEIT-TVPYDSYQNAKLDLQ  164 (243)
T ss_pred             ccceecCccccceEEEEeCCC------CCCHHHhCCCeEEEec-CcH----HHHHHHHhCCCCe-EEEcCCHHHHHHHHH
Confidence            23 245666666777766553      2468999888775543 322    2234443322222 345678888888999


Q ss_pred             hccc-eeeeecceeccc--ccCCceeee--cCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         236 LRMG-IGIIASIAFDSN--RDKNLRSIS--ASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~--~~~~l~~~~--~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      +|.. ..+.+......+  ..+++..+.  +.. ......+.+..+++.  .+....|=+.|.+..+....+++
T Consensus       165 ~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~ln~~l~~l~~~g~~~~i  236 (243)
T PRK15007        165 NGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGN--TELQQKLNTALEKVKKDGTYETI  236 (243)
T ss_pred             cCCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCCC--HHHHHHHHHHHHHHHhCCcHHHH
Confidence            9954 444444333222  234444332  111 111234556666542  33444444444443333334443

>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth

Probab=97.03  E-value=0.00056  Score=39.61  Aligned_cols=28  Identities=36%  Similarity=0.484  Sum_probs=21.4

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIR   51 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R   51 (306)
                      =.+||+.||++|+||||+|+.     |-.+|..
T Consensus        15 Q~kaA~~lGV~Q~AIsKAlr~-----gR~I~v~   42 (59)
T PF09048_consen   15 QAKAARALGVTQSAISKALRA-----GRNIFVT   42 (59)
T ss_dssp             HHHHHHHHTS-HHHHHHHHHC-----T-EEEEE
T ss_pred             hHHHHHHcCCcHHHHHHHHHc-----CCcEEEE
Confidence            489999999999999999974     5555553

Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=97.03  E-value=0.0084  Score=47.19  Aligned_cols=80  Identities=16%  Similarity=0.256  Sum_probs=67.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG   84 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~   84 (306)
                      .-..++.+.+..+|+..--..|++|.+++..||++|++   .-|+.++++.. +||+-|+.+...++++++.++-+.+..
T Consensus        15 Rk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~---~~LV~~~~~~Y-~LS~~G~iiv~km~~ll~tl~v~e~n~   90 (260)
T COG4742          15 RKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKD---KGLVVQEGDRY-SLSSLGKIIVEKMEPLLDTLEVFEENY   90 (260)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCcHHHHHHHHHHhh---CCCEEecCCEE-EecchHHHHHHHHHHHHHHHHHHHhhh
Confidence            34566777775559999999999999999999999987   56899998887 899999999999999999999888754


Q ss_pred             Hhhc
Q psy3760          85 KEFS   88 (306)
Q Consensus        85 ~~~~   88 (306)
                      .--.
T Consensus        91 dyW~   94 (260)
T COG4742          91 DYWS   94 (260)
T ss_pred             hHHh
Confidence            4433

>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein

Probab=97.01  E-value=0.12  Score=43.36  Aligned_cols=203  Identities=13%  Similarity=0.098  Sum_probs=110.2

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH----cCCeeEEEEccccC----CCCC----
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR----NDQADIAIVTEILS----PSDK----  157 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~----~~~~Di~i~~~~~~----~~~~----  157 (306)
                      ...++|+|....  .......++..|.++||++++++...++.++...+.    +..+|+.+......    ...+    
T Consensus        19 ~~~~~l~vy~~~--~~~~~~~l~~~Fe~~~pgi~V~~~~~~s~~~~~kl~ae~~~~~~Dvv~~~~~~~~~~~~~~gll~~   96 (334)
T TIGR03261        19 KANTELTVYTAI--EDELIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSLALLDKEGMLKP   96 (334)
T ss_pred             ccCCeEEEEEec--cHHHHHHHHHHHHHHCCCceEEEEECChHHHHHHHHHHhhCCCCCEEEecCchHHHhhhhcccccc
Confidence            345789988663  356788999999999999999998888878877763    34689986521100    0011    


Q ss_pred             ------------c-------eeeccccceEEEEecCCCCCCC--CCCcChhhhcCC----CeEeecCCC-Cc-HHHHHHH
Q psy3760         158 ------------L-------ISIPCYQWEYVIIVPLDHPLLL--LNSISLKEISNY----PLITYDLSF-SG-RIKLDRE  210 (306)
Q Consensus       158 ------------~-------~~~~l~~~~~~~v~~~~~~l~~--~~~i~~~dl~~~----~~i~~~~~~-~~-~~~~~~~  210 (306)
                                  +       ......-...+++.+++..-..  ..+-+++||.+.    .+.+.++.. +. ...+..+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yN~~~~~~~g~~~P~sw~dL~~p~~~g~i~~~dp~~s~~~~~~~~~~  176 (334)
T TIGR03261        97 YKPKGLDALNPKFRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVMPNPASSGTGFLDVSAW  176 (334)
T ss_pred             CCCcChhhcCHhhhCCCCCCceEeeeeeEEEEEEehHHHHhcCCCCCCChHHhcCHHhcCCEecCCCccchHHHHHHHHH
Confidence                        0       0111212244555555431111  235689999763    233333322 21 1111222


Q ss_pred             HHhCC----------CceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc-c-cCCceeeecCCCCccceEEEEEeCC
Q psy3760         211 FSLQK----------LTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN-R-DKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       211 ~~~~~----------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                      +...|          +.++......+.....+++.+|. .+++...+.+... . ...+..+-..+........+...++
T Consensus       177 ~~~~G~~~~~~~l~~l~~n~~~~~~s~~~~~~~v~~Ge~~i~~~~~~~~~~~~~~g~~v~~~~P~eG~~~~~~~~ai~k~  256 (334)
T TIGR03261       177 LQMMGEDKGWDYMDKLHKNIAVYTHSGSKPCKLAGMGEFPIGISMAYRALKEKKKGAPIDVVFPKEGLGWDIEATAIIKG  256 (334)
T ss_pred             HHHhChHHHHHHHHHHHhccCccCCCChHHHHHHhCCCceEEEEecHHHHHHHhCCCCeEEEecCCCCeeeeeeeEEEcC
Confidence            22222          12344344455566778888884 4444444332222 2 2334443333322222335555677


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .+....+++|++++.+.
T Consensus       257 a~~~e~A~~fidfllS~  273 (334)
T TIGR03261       257 SKNNDAAKKLVDWSISD  273 (334)
T ss_pred             CCCHHHHHHHHHHHcCH
Confidence            77889999999999654

This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.

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

Probab=96.98  E-value=0.0045  Score=39.10  Aligned_cols=68  Identities=26%  Similarity=0.341  Sum_probs=48.4

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~i   73 (306)
                      ....++..+.+.+.+.+..|+.++++++++++.++.|++. |.---.+.+ .+..++|+ |..++..++.+
T Consensus         8 ~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~-g~i~~~~~~~~~~~~~~~-g~~~~~~~~~~   76 (78)
T cd00090           8 TRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD-AERLLALLESL   76 (78)
T ss_pred             HHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHC-CCeEEEEeccEEEEEeCC-chHHHHHHHHh
Confidence            3455666666663489999999999999999999999774 433222222 22237999 99888887654

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.

>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence

Probab=96.97  E-value=0.13  Score=40.62  Aligned_cols=197  Identities=12%  Similarity=0.121  Sum_probs=117.3

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-------CCCCc-eeecccc
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-------PSDKL-ISIPCYQ  165 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-------~~~~~-~~~~l~~  165 (306)
                      ||||+.+.....++-.+-..+.+.  +++++++.. +..+.-..|.+|++|+-+..+...       ....+ ...+.+-
T Consensus         1 ikIG~~~~~~~~i~~~v~~~~~~~--Gi~vevv~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~~   78 (237)
T PF03180_consen    1 IKIGVTPGPDAEILEAVKEKLKKK--GIDVEVVEFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTYI   78 (237)
T ss_dssp             EEEEEETTCHHHHHHHHHHHHHHT--TEEEEEEEESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEEE
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHhc--CCeEEEEEecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEecceeE
Confidence            689999876676777444444444  588888774 667889999999999999863321       11122 2333444


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEEEecC
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVLETIN  226 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~~~~~  226 (306)
                      .++.++. +.       --+++|+.+---|..+.+.....+-...|+..|+-                  | +..+.--+
T Consensus        79 ~p~glYS-~k-------~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aGLI~Lk~~~~~~~t~~DI~~Npk~l~~~evd  150 (237)
T PF03180_consen   79 EPMGLYS-KK-------YKSLDDLPDGATVAIPNDPSNQARALKLLQEAGLITLKDGVGLTATVDDITENPKNLKFKEVD  150 (237)
T ss_dssp             ---EEEE-SS-------SSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTTSEEE-TT-GCC-SGGGEEEETTSEEEEEE-
T ss_pred             EeEEEee-cc-------cCchhhcCCCCEEEEeCCccchhHHHHHHHhCCeEEEcCCCCCccChhhhhhcccCceEEEec
Confidence            4555553 23       34888888777777777666666667788888762                  1 22233223


Q ss_pred             HHHHHHHHHhccceeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         227 SDIIKTYVELRMGIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       227 ~~~~~~~v~~g~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      ...+.+.+..-++..+-+.++...-  ....+...+... ...+-..++++.+...+|.++.+++.+++.=-+..+++
T Consensus       151 ~~~l~~~l~dvD~avi~~~~a~~agl~~~~~~~~~e~~~-~~~y~n~lv~r~~~~d~~~ik~l~ea~~s~~v~~~i~~  227 (237)
T PF03180_consen  151 AAQLPRALDDVDAAVINGNYALDAGLDPKKDLLFEEPDA-DKPYANVLVVREDDKDDPWIKKLVEAYQSPEVKKFIEE  227 (237)
T ss_dssp             GGGHHHHTTTSSEEEE-HHHHHHTT--CCCHSSEE-SSS-SCGGEEEEEEEGGGTTCHHHHHHHHHHTSHHHHHHHHH
T ss_pred             HhhHHhhcccCCEEEecHhHHHHcCcCcccceeeeeccc-CcceeEEEEEECCccCCHHHHHHHHHHCCHHHHHHHHH
Confidence            4455555555455554455554332  222233333222 34567788889988899999999999886544444443

Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.

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

Probab=96.92  E-value=0.0055  Score=38.89  Aligned_cols=64  Identities=19%  Similarity=0.253  Sum_probs=46.3

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +..+.+.+.+++.-+...|++.+++.+-|..|++.   -|..+.++.. .+|+.|..+++..+.+.+-
T Consensus        12 L~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~---gLI~~~~~~Y-~lTekG~~~l~~l~~~~~~   75 (77)
T PF14947_consen   12 LKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEK---GLIKKKDGKY-RLTEKGKEFLEELEELIEL   75 (77)
T ss_dssp             HHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHT---TSEEEETTEE-EE-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC---cCeeCCCCEE-EECccHHHHHHHHHHHHHH
Confidence            33342344499999999999999999999999974   3457766776 8999999999988877654

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

Probab=96.91  E-value=0.0039  Score=34.17  Aligned_cols=24  Identities=33%  Similarity=0.339  Sum_probs=21.4

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      |+.+-|+.+|+|.+++.++|++||
T Consensus        19 s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen   19 SYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHhC
Confidence            899999999999999999999997

...

>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins

Probab=96.89  E-value=0.056  Score=42.02  Aligned_cols=183  Identities=11%  Similarity=0.028  Sum_probs=105.1

Q ss_pred             hhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC---CCCCceee----ccccceEEEEecCCC
Q psy3760         105 RYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS---PSDKLISI----PCYQWEYVIIVPLDH  176 (306)
Q Consensus       105 ~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~----~l~~~~~~~v~~~~~  176 (306)
                      ..++..-..-|.+.  ++++++... +..+..+.|.+|++|+++......   ...+....    ...+....++++++.
T Consensus         6 p~~vA~~~G~f~~~--gl~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s   83 (216)
T PF09084_consen    6 PLYVAQEKGYFKEE--GLDVEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDS   83 (216)
T ss_dssp             HHHHHHHTTHHHHT--TEEEEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTT
T ss_pred             HHHHHHHcCCCccC--eEEEEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccC
Confidence            33444444445555  777777765 557899999999999999862211   11222222    222445677777776


Q ss_pred             CCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHhc--ccee-eeecceeccc-
Q psy3760         177 PLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVELR--MGIG-IIASIAFDSN-  251 (306)
Q Consensus       177 ~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g--~gi~-~~p~~~~~~~-  251 (306)
                      .     .-+++||.+.++.... +......+..+++..|+.++.+ +...+......++.+|  +++. ..|.+..... 
T Consensus        84 ~-----i~~~~DLkGK~i~v~~-~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~vDa~~~~~~~~~~~~~~  157 (216)
T PF09084_consen   84 G-----IKSPADLKGKKIGVSR-GSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQVDAAILWYPPWEPYEIA  157 (216)
T ss_dssp             S------SSGGGGTTSEEEEST-TSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTSSSEEEEEEECTCHHHHH
T ss_pred             C-----CCCHHHhCCCEEEEec-CcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCCCCEEEEccCChHHHHHH
Confidence            4     3489999998887766 6566678889999999976433 3333355555577777  4333 4444222221 


Q ss_pred             -ccCCceeeecCCCCc-cc-eEEEEEeCC--ccccHHHHHHHHHHhHHh
Q psy3760         252 -RDKNLRSISASHLFG-TT-ISRVIIKQG--TYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       252 -~~~~l~~~~~~~~~~-~~-~~~l~~~~~--~~~~~~~~~~~~~l~~~~  295 (306)
                       ....+.......... .. ...++.+++  ...+..++.|++.+.+..
T Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pe~~~~f~~a~~~a~  206 (216)
T PF09084_consen  158 SKGKKLRVLELSDYGPPNYPVSVLVARDEFLEKNPEAVKAFLKAYAKAI  206 (216)
T ss_dssp             HCCSCEEEEEGGGCCGGCS-SEEEEEEHHHHHHSHHHHHHHHHHHHHHH
T ss_pred             HcCCceeeeeccccCcccccceEEEEchHHHHHCHHHHHHHHHHHHHHH
Confidence             334455566554221 22 222333332  223567888887776653

These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....

>PHA00738 putative HTH transcription regulator

Probab=96.88  E-value=0.0028  Score=42.09  Aligned_cols=58  Identities=10%  Similarity=0.118  Sum_probs=39.8

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHh
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKP   62 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~   62 (306)
                      ..++++..+.+.+ .+...-|+.+++|||+||++|+.|++ .|.---.|.|+.+. ++.+.
T Consensus        13 tRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre-AGLV~srK~Gr~vyY~Ln~~   72 (108)
T PHA00738         13 LRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNE-QGYIELYKEGRTLYAKIREN   72 (108)
T ss_pred             HHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH-CCceEEEEECCEEEEEECCC
Confidence            3456666666631 27889999999999999999999986 34444444444432 44444

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=96.85  E-value=0.0042  Score=36.76  Aligned_cols=45  Identities=16%  Similarity=0.121  Sum_probs=36.9

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++.+++..+.+.. |....|+.+++|.+++.+.++++.+.||++
T Consensus         5 ~~~e~~i~~~~~~g~-s~~eia~~l~is~~tv~~~~~~~~~kl~~~   49 (58)
T smart00421        5 TPREREVLRLLAEGL-TNKEIAERLGISEKTVKTHLSNIMRKLGVR   49 (58)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            345566666655555 999999999999999999999999999864

lux regulon (activates the bioluminescence operon

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

Probab=96.85  E-value=0.0058  Score=35.29  Aligned_cols=43  Identities=26%  Similarity=0.247  Sum_probs=35.0

Q ss_pred             chhhHHHHHHHHHhc-------CCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           2 NLHQFRFVREAVRQN-------FNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-------~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +-+|.+++....+.|       -|+..-|+.||||.||+|.+|++-|+.+
T Consensus         2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            346777777777765       2678999999999999999999998764

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

>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ

Probab=96.80  E-value=0.19  Score=40.09  Aligned_cols=130  Identities=12%  Similarity=0.093  Sum_probs=74.9

Q ss_pred             hhHHHHHHHHHhCCCcEEEEEeCChhHHH---HHHHcCCeeEEEEccccCCCCCc-eeeccccceEEEEecCCCCCCCCC
Q psy3760         107 ALPKIIKEFTIQFPKVKLSLLQGNPKQIT---EMIRNDQADIAIVTEILSPSDKL-ISIPCYQWEYVIIVPLDHPLLLLN  182 (306)
Q Consensus       107 ~l~~~l~~~~~~~p~~~i~~~~~~~~~~~---~~l~~~~~Di~i~~~~~~~~~~~-~~~~l~~~~~~~v~~~~~~l~~~~  182 (306)
                      +-..++..+.++. ++++++.....+.+.   ..|.+|++|+++.. . ..+.++ -+.|......+++++++....   
T Consensus        21 fdvdl~~~ia~~l-g~~~~~~~~~~~~~~~~~~~L~~g~~Dii~~~-~-~t~~r~~fS~PY~~~~~~~v~~k~~~~~---   94 (246)
T TIGR03870        21 FENKIAAALAAAM-GRKVVFVWLAKPAIYLVRDGLDKKLCDVVLGL-D-TGDPRVLTTKPYYRSSYVFLTRKDRNLD---   94 (246)
T ss_pred             chHHHHHHHHHHh-CCCeEEEEeccchhhHHHHHHhcCCccEEEeC-C-CChHHHhcccCcEEeeeEEEEeCCCCCC---
Confidence            4456777777774 788888877755544   69999999998853 2 222333 367888888999999886321   


Q ss_pred             CcCh--hhhcCC-CeEeecCCCCcHHHHHHHHHh-CC---------Cc-eeEEEEecCHHHHHHHHHhccceeee
Q psy3760         183 SISL--KEISNY-PLITYDLSFSGRIKLDREFSL-QK---------LT-PYIVLETINSDIIKTYVELRMGIGII  243 (306)
Q Consensus       183 ~i~~--~dl~~~-~~i~~~~~~~~~~~~~~~~~~-~~---------~~-~~~~~~~~~~~~~~~~v~~g~gi~~~  243 (306)
                      .-++  .+|.+. +.... .+......+.+.... ..         .. +...+...+...+.+++.+|..=+.+
T Consensus        95 ~~~~~d~~L~g~~~vgv~-~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i  168 (246)
T TIGR03870        95 IKSWNDPRLKKVSKIGVI-FGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAV  168 (246)
T ss_pred             CCCccchhhccCceEEEe-cCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEE
Confidence            1233  357776 54444 343332222221100 00         00 11112222457788999999654443

This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in

>PF04069 OpuAC: Substrate binding domain of ABC-type glycine betaine transport system; InterPro: IPR007210 This domain is a part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation

Probab=96.79  E-value=0.018  Score=46.28  Aligned_cols=192  Identities=9%  Similarity=-0.016  Sum_probs=123.8

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcCCeeEEE-EccccCCC----------CCce--
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAI-VTEILSPS----------DKLI--  159 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~~~Di~i-~~~~~~~~----------~~~~--  159 (306)
                      +|+||........++..++..+.+.. +..+++...+. ..+.+.|.+|++|+.. ...+ ...          ..+.  
T Consensus         2 ~I~ig~~~w~~~~~~a~i~~~~Le~~-G~~v~~~~~~~~~~~~~al~~G~iD~~~~~w~~-~~~~~~~~~~~~~~~~~~l   79 (257)
T PF04069_consen    2 PIVIGSKNWTESQILAEIYAQLLEAA-GYVVEVVNLGSTPVIFAALASGDIDIYPEEWTP-TTYEAYKKALEEKLGVVWL   79 (257)
T ss_dssp             EEEEEEESSHHHHHHHHHHHHHHHHT-TEEEEEEEESSHHHHHHHHHTTSSSEEEEEEET-TTHHHHHHHHHHHHEEEEE
T ss_pred             eEEEecCCCcHHHHHHHHHHHHHHHC-CCeEEEecCCchHHHHHHHHCCCCeEEhhhcCc-hhHHHHHHhhhhcCccccC
Confidence            68999999999999999999999998 88999998887 8899999999999999 4322 211          1222  


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCC----------eEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH-
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----------LITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD-  228 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  228 (306)
                      ....+.....+++++.-... ..--+++||.++.          ++..+++..........++..|+. +......+.. 
T Consensus        80 ~~~~~~~~~g~~Vp~~~ae~-~~i~si~dL~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ygl~-~~~~~~~s~~~  157 (257)
T PF04069_consen   80 GPLGAGNTYGWAVPKYVAEK-PGIKSISDLAKPAEDLEFGGKGEFYGRPDGWGCTTFNEQLLKAYGLD-NFELFPGSEAA  157 (257)
T ss_dssp             EEEEEEEEEEEEEEHHHHHH-HT-SBGGGGGTCGGGCEEEETTEEECSSTTHHHHHHHHHHHHHCTCT-TSEEESSEHHH
T ss_pred             CccccCCEEEEEEecccccc-cCcccHHHHhhcccccccCCCCceeeCCCCcchhhHHHHHHHhcCCC-cceecccccch
Confidence            22344567788888764211 1234778886543          455555554556667888888984 3333223333 


Q ss_pred             ---HHHHHHHhccce---eeeecceecccccCCceeeecCCC-Ccc-ceEEEEEeCCcc-ccHHHHHHHHHHh
Q psy3760         229 ---IIKTYVELRMGI---GIIASIAFDSNRDKNLRSISASHL-FGT-TISRVIIKQGTY-LRSYVYSFIKLLS  292 (306)
Q Consensus       229 ---~~~~~v~~g~gi---~~~p~~~~~~~~~~~l~~~~~~~~-~~~-~~~~l~~~~~~~-~~~~~~~~~~~l~  292 (306)
                         .+.+.+.+|..+   +.-|+++...   .+++.+.-+.. .+. ..+..+++++-. ..|.+..+++.+.
T Consensus       158 ~~~~~~~A~~~~~~~v~~~w~p~~~~~~---~~l~~L~D~~~~~~~~~~~~~~~r~~~~~~~P~~~~~l~~~~  227 (257)
T PF04069_consen  158 MDAALYAAYKRGEPIVFYAWSPDWMIAK---YDLVVLEDPKGFFPPAYNVVPVVRKGFAEDHPEAAEFLNRFS  227 (257)
T ss_dssp             HHHHHHHHHHTTSSSEEEEETSSTHHHH---STEEE-BTTTCTSSSSEEEEEEEEHHHHHHSHHHHHHHHCTT
T ss_pred             hHHHHHHHHHcCCCEEEEEecCChhhcc---CCeEEeecCCCCCCCCCEEEEEecHHHHhhChHHHHHHHhcC
Confidence               556666777443   3445555443   46777775542 222 566666665432 3566777777765

This domain is often fused to the permease component of the transporter complex. It is often found in integral membrane proteins or proteins predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis []. OpuBC is closely related and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine []. L-carnitine is important for osmoregulation in Listeria monocytogenes. This domain is found also in proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).; GO: 0005215 transporter activity, 0005488 binding, 0006810 transport; PDB: 3R6U_A 3TMG_C 3MAM_A 1SW5_C 1SW4_B 1SW1_A 1SW2_A 3O66_A 1R9Q_A 1R9L_A ....

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.74  E-value=0.02  Score=37.67  Aligned_cols=63  Identities=17%  Similarity=0.145  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHHHHH
Q psy3760           5 QFRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         5 ~l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~~a~   71 (306)
                      .+.++..+.+.  +.|++..|+.++++++++++.|+.|++. |  ++.+.  +++. .+++....+-..+.
T Consensus         7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~-g--~l~~~~~~~~y-~l~~~~~~~~~~~~   73 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-G--YVEQDGQNGRY-RLGPKVLELGQSYL   73 (91)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-C--CeeecCCCCce-eecHHHHHHHHHHH
Confidence            34455555543  2489999999999999999999999874 3  34443  4445 68776655554443

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

Probab=96.71  E-value=0.0026  Score=35.38  Aligned_cols=34  Identities=24%  Similarity=0.268  Sum_probs=22.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      -.....+.+.|.|+.+-|+.||+|++||++-|++
T Consensus        10 R~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen   10 RNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             --HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            3344455677889999999999999999999875

>PRK11480 tauA taurine transporter substrate binding subunit; Provisional

Probab=96.71  E-value=0.12  Score=42.97  Aligned_cols=192  Identities=9%  Similarity=0.004  Sum_probs=104.3

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceee---
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISI---  161 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~---  161 (306)
                      ....||||+..+....++...-..|.++ -++++++... +...+.+.+.+|++|+++......     ....+...   
T Consensus        21 ~~~~v~~~y~~~~~~~~vA~~~g~f~~~-~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~   99 (320)
T PRK11480         21 QAVNVTVAYQTSAEPAKVAQADNTFAKE-SGATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPIEVFLLA   99 (320)
T ss_pred             CCCeEEEEecCCCcHHHHHHHcCchHHH-cCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCeEEEEee
Confidence            4668999998765545555444445343 3667777554 456788999999999997632110     11112211   


Q ss_pred             ccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc--c
Q psy3760         162 PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR--M  238 (306)
Q Consensus       162 ~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g--~  238 (306)
                      ........+++++       ..-+++||.+.++.... +......+..+++..|+.+.. .+.--....+..++.+|  +
T Consensus       100 ~~~~~~~~lv~~~-------~I~s~~DLkGK~Iav~~-~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~VD  171 (320)
T PRK11480        100 SKLGNSEALVVKK-------TISKPEDLIGKRIAVPF-ISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGDID  171 (320)
T ss_pred             ccCCcceEEEecC-------CCCChHHcCCCEEecCC-CCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCCcC
Confidence            1111223444432       13478999998877643 334445678889999998743 33333456677778887  4


Q ss_pred             ceeeeecceeccc-ccCCceeeecCC-----CCccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASH-----LFGTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~-----~~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                      ++.+ ........ ..+.  .+.-..     ..+.. ..++.+.+.  ..+..++.|++.+.+..
T Consensus       172 Aa~~-~~p~~~~~~~~g~--~l~~~~~~~~~~~~~~-~~lv~~~~~i~~~p~~v~~f~~A~~~a~  232 (320)
T PRK11480        172 GAYV-WAPAVNALEKDGK--VLTDSEQVGQWGAPTL-DVWVVRKDFAEKHPEVVKAFAKSAIDAQ  232 (320)
T ss_pred             EEEE-cchHHHHHHhCCe--EEecchhhcccCCCce-EEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence            4333 33322222 2222  221111     01111 233444321  24678888888776553

>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=96.69  E-value=0.0053  Score=36.68  Aligned_cols=43  Identities=28%  Similarity=0.323  Sum_probs=35.8

Q ss_pred             CchhhHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++..++.++..+.+.+. +.+.=|+.+++++|++|+.+++||+.
T Consensus         1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~   44 (59)
T PF01047_consen    1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKK   44 (59)
T ss_dssp             STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence            46778888888888872 47788999999999999999999974

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 ....

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.64  E-value=0.0071  Score=36.75  Aligned_cols=55  Identities=27%  Similarity=0.195  Sum_probs=40.2

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-CccccCH-hHHHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-RIRGLTK-PGQAILRS   69 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-~~~~lT~-~G~~l~~~   69 (306)
                      .+.. +++..|+.+++|.+++++.|++|++. |.---.+.++ ....+|+ .|..++..
T Consensus         8 ~~~~-~~~~i~~~l~is~~~v~~~l~~L~~~-g~i~~~~~~~~~~~~~~~~~~~~~~~~   64 (66)
T smart00418        8 EGEL-CVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKRVYYSLTDEKVADLLEE   64 (66)
T ss_pred             cCCc-cHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeeecCCEEEEEEchHHHHHHHHh
Confidence            5566 99999999999999999999999975 4444333332 2236888 77766654

>TIGR00971 3a0106s03 sulfate/thiosulfate-binding protein

Probab=96.63  E-value=0.075  Score=44.06  Aligned_cols=196  Identities=13%  Similarity=0.071  Sum_probs=103.4

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHh---CCCcE--EEEEeCChhHHHHHHHcC-CeeEEEEccccC----CCCCce----
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQ---FPKVK--LSLLQGNPKQITEMIRND-QADIAIVTEILS----PSDKLI----  159 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~---~p~~~--i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~~~----  159 (306)
                      +|..+.- +.....+..+...|.++   .++++  +++..+++..+..++.+| .+|+.+......    ...++.    
T Consensus        12 ~~~~~~~-~~~~~~~~~i~~~fe~~~~~~~g~~v~v~~~~g~Sg~l~~Qi~~Ga~~Dvf~sa~~~~~~~l~~~g~i~~~~   90 (315)
T TIGR00971        12 QLLNVSY-DPTRELYEQYNKAFEAHWKQDTGDNVVIRQSHGGSGKQATSVINGIEADVVTLALAYDVDAIAERGRIDKDW   90 (315)
T ss_pred             EEEeecc-cccHHHHHHHHHHHHHHHHhcCCCceEEEEecCCcHHHHHHHHcCCCcCEEecCCHHHHHHHHHCCCCCcch
Confidence            3443333 34577888899999885   57877  556889999999999996 789999853210    111221    


Q ss_pred             eeccccc------eEEEEecCCCCCCCCCCcChhhhcC--CCeEeecCCCC-c--HHHHHH---HHHhCC----------
Q psy3760         160 SIPCYQW------EYVIIVPLDHPLLLLNSISLKEISN--YPLITYDLSFS-G--RIKLDR---EFSLQK----------  215 (306)
Q Consensus       160 ~~~l~~~------~~~~v~~~~~~l~~~~~i~~~dl~~--~~~i~~~~~~~-~--~~~~~~---~~~~~~----------  215 (306)
                      ...+...      .+++++++++|..   .-+|+||.+  ..++..++... .  ...+..   +....+          
T Consensus        91 ~~~~~~n~~~~~~~lvl~v~k~~~~~---i~sw~dL~~~~~kiai~dp~~sg~~~~~~L~~~g~~~~~~~g~~~~a~~~l  167 (315)
T TIGR00971        91 IKRLPDNSAPYTSTIVFLVRKGNPKQ---IHDWNDLIKPGVSVITPNPKSSGGARWNYLAAWGYALHHNNGDQAKAQQFV  167 (315)
T ss_pred             hhhCccCCCccceeEEEEEeCCCCCC---CCCHHHHhCCCcEEEeCChhhHHHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            1122223      7999999998732   348999853  33343333221 1  111110   111101          


Q ss_pred             --CceeEEEE-ecCHHHHHHHHHhc-cceeeeecceeccc-c---cCCceeeecCCCCccceEEEEEeC----CccccHH
Q psy3760         216 --LTPYIVLE-TINSDIIKTYVELR-MGIGIIASIAFDSN-R---DKNLRSISASHLFGTTISRVIIKQ----GTYLRSY  283 (306)
Q Consensus       216 --~~~~~~~~-~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~---~~~l~~~~~~~~~~~~~~~l~~~~----~~~~~~~  283 (306)
                        ...++... .++...+..++.+| .-++++....+... .   ...+..+-..+..+ ..+.+.+-+    .......
T Consensus       168 ~~l~~nv~~~~~~~~~~~~~~v~~Ge~dagivy~sda~~~~~~~~~~~i~iviP~e~~~-i~~~iavv~~~~~~~~~~e~  246 (315)
T TIGR00971       168 TALLKNVEVLDSGARGATNTFVERGIGDVLIAWENEALLARKELGKDKFEIVTPSESIL-AEPTVSVVDKVVEKKGTKKV  246 (315)
T ss_pred             HHHHhhccccCCCchHHHHHHHHcCceeEEEEEcHHHHHHHHhcCCCCeEEEECCCCcc-ccccEEEEEcccCCCCCHHH
Confidence              22344333 33355677778777 33344443332211 1   12454442222222 222233322    1233678


Q ss_pred             HHHHHHHHhHH
Q psy3760         284 VYSFIKLLSPK  294 (306)
Q Consensus       284 ~~~~~~~l~~~  294 (306)
                      .++|++++.+.
T Consensus       247 A~~FidfLlS~  257 (315)
T TIGR00971       247 AEAYLKYLYSP  257 (315)
T ss_pred             HHHHHHHhcCH
Confidence            99999999654

This model describes binding proteins functionally associated with the sulfate ABC transporter. In the model bacterium E. coli, two different members work with the same transporter; mutation analysis says each enables the uptake of both sulfate and thiosulfate. In many species, a single binding protein is found, and may be referred to in general terms as a sulfate ABC transporter sulfate-binding protein.

>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]

Probab=96.55  E-value=0.028  Score=45.95  Aligned_cols=168  Identities=10%  Similarity=0.059  Sum_probs=109.2

Q ss_pred             CCCcEEEEecccchhh-hhHHHHHHHHHh-CCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--------------
Q psy3760          91 DTGNLTIATTHTQARY-ALPKIIKEFTIQ-FPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS--------------  153 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~-~l~~~l~~~~~~-~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~--------------  153 (306)
                      ....++||+....+.+ -+..-+.+..+. .+++.+++.. ..+-+-++.+.+|++|++++.....              
T Consensus        24 ~~~~itigTG~~~G~YY~ig~~ia~~~~~~~~~i~~~v~~tggSv~Nl~~i~~Ge~d~alvq~d~a~~ay~G~g~f~~~~  103 (321)
T COG2358          24 EPKFITIGTGSTGGVYYPIGGGLAQLLNKDEKGIECSVVPTGGSVENLKLLASGEADLALVQSDVAYEAYNGTGSFEGKG  103 (321)
T ss_pred             CceEEEEeecCCCceeeehHHHHHHHHhccCCCeEEEEeeccchHHHHHhHhcCccchhhhhHHHHHHHHhCcccccccc
Confidence            4557999997765544 334445555454 7888888877 4677789999999999999752110              


Q ss_pred             CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH--HH
Q psy3760         154 PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD--II  230 (306)
Q Consensus       154 ~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~  230 (306)
                      ..++++ .-.++.+.+.++++++.-     --++.||.+.++-.-+++++.+-..+..+...|+.+...-..-.+.  ..
T Consensus       104 ~~~~lr~v~~lype~~~vv~r~d~~-----Ikti~DL~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~  178 (321)
T COG2358         104 KDENLRAVAALYPEPFHVVTRKDAG-----IKTIADLKGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAES  178 (321)
T ss_pred             cccchhhheecccceEEEEEecCCC-----cceehhcCCCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhh
Confidence            112333 456777788888887753     4589999999999999999998889999999999865431111222  22


Q ss_pred             HHHHHhc--cceee---eecceeccc-ccCCceeeecCC
Q psy3760         231 KTYVELR--MGIGI---IASIAFDSN-RDKNLRSISASH  263 (306)
Q Consensus       231 ~~~v~~g--~gi~~---~p~~~~~~~-~~~~l~~~~~~~  263 (306)
                      .+++.+|  ++..+   .|...+... ..-+++.+|+++
T Consensus       179 ~~~l~~g~iDA~~~~~G~p~~ai~el~~~~~i~lv~i~~  217 (321)
T COG2358         179 ADALKNGTIDAAFYVAGVPNPAISELATTCDIVLVPISG  217 (321)
T ss_pred             HHHhhCCcccEEEEecCCCCccHHHHHhhCCeEEEeCCH
Confidence            5556666  33222   334444333 334666666654

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=96.54  E-value=0.0061  Score=36.28  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=38.7

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+.++++..+++-. |..+.|+.+++|..||..+++.+-+.||++
T Consensus         5 T~~E~~vl~~l~~G~-~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~   49 (58)
T PF00196_consen    5 TERELEVLRLLAQGM-SNKEIAEELGISEKTVKSHRRRIMKKLGVK   49 (58)
T ss_dssp             -HHHHHHHHHHHTTS--HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred             CHHHHHHHHHHHhcC-CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence            446788999999888 999999999999999999999999999864

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional

Probab=96.54  E-value=0.09  Score=43.83  Aligned_cols=202  Identities=6%  Similarity=-0.029  Sum_probs=123.3

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEE-EEEeCChhHHHHHHHcCCeeEEEEccccCCC-------C--Cc
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKL-SLLQGNPKQITEMIRNDQADIAIVTEILSPS-------D--KL  158 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i-~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~-------~--~~  158 (306)
                      .+...+|+||....-.......++..+.+.. +.++ ++...+...+.+.|.+|++|+....-.+...       .  .+
T Consensus        25 ~~~~~~V~~~~~~W~~~~~~t~v~~~iLe~~-GY~V~e~~~~~~~~~~~ala~GdiDv~~~~W~P~~~~~~~~~~~~~~v  103 (331)
T PRK11119         25 PGKGITVQPAQSTIAEETFQTLLVSRALEKL-GYDVNKPKEVDYNVFYTSIANGDATFTAVNWFPLHDDMYEAAGGDKKF  103 (331)
T ss_pred             CCCCeEEEEeecCccHHHHHHHHHHHHHHHc-CCceeeecccCcHHHHHHHHcCCCeEehhhcccccHHHHHHhhccCcE
Confidence            3456689999999888888888888888765 8888 7888888899999999999998854221110       1  11


Q ss_pred             -eeec-cccceEEEEecCCCCCCCCCCcChhhhcC--CC------------eEeecCCCCcHHHHHHHHHhCCCceeEEE
Q psy3760         159 -ISIP-CYQWEYVIIVPLDHPLLLLNSISLKEISN--YP------------LITYDLSFSGRIKLDREFSLQKLTPYIVL  222 (306)
Q Consensus       159 -~~~~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~~--~~------------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (306)
                       ..-. +......+++|+.-.... .--+++||.+  +.            ++..+++........+.++..|+.-+...
T Consensus       104 ~~~g~~~~~a~~G~~VP~yv~e~~-gI~Si~DL~~~~~a~~F~~e~~gkg~i~g~~~G~~~~~~~~~~l~~yGL~~~~~~  182 (331)
T PRK11119        104 YREGVYVGGAAQGYLIDKKTADKY-NITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEAVINHQLKAYGLEDTVTH  182 (331)
T ss_pred             EeccccCCCcceeeeecHHHHHHc-CCCCHHHhCCcHHHHhcCCCCCCCcceECCCCCccccHHHHHHHHhcCCCcceeE
Confidence             1111 122356666665321010 2347888873  12            55566776666666777888888632333


Q ss_pred             EecCHH----HHHHHHHhccceee---eecceeccc-ccCCceeeecCCC--------------------CccceEEEEE
Q psy3760         223 ETINSD----IIKTYVELRMGIGI---IASIAFDSN-RDKNLRSISASHL--------------------FGTTISRVII  274 (306)
Q Consensus       223 ~~~~~~----~~~~~v~~g~gi~~---~p~~~~~~~-~~~~l~~~~~~~~--------------------~~~~~~~l~~  274 (306)
                      ...+..    .+.+.++++..+.+   -|.++...+ ...+++.+..+..                    .+...++.+.
T Consensus       183 ~~~S~aam~a~l~~A~~~~epiv~~~W~Phw~~~~~~~~~dl~~L~~P~~~~~~~~~~~~~~~~Dpk~~g~p~~~v~~v~  262 (331)
T PRK11119        183 NQGNYAALMADTIARYKEGKPVLYYTWTPYWVSDVLKPGKDVVWLQVPFSSLPGDQKNADTKLPNGKNYGFPVNTMHIVA  262 (331)
T ss_pred             CCCCHHHHHHHHHHHHHcCCCEEEEEecchhHHhhccCCCCeEEeccCCCCcccccccccCCCCCccccCCCcccEEEEE
Confidence            333333    45566677766555   566665554 3336776632210                    1234566666


Q ss_pred             eCC-ccccHHHHHHHHHHh
Q psy3760         275 KQG-TYLRSYVYSFIKLLS  292 (306)
Q Consensus       275 ~~~-~~~~~~~~~~~~~l~  292 (306)
                      +++ ....|.+..|++-+.
T Consensus       263 r~~f~e~~Pea~~~L~~~~  281 (331)
T PRK11119        263 NKAFAEKNPAAAKLFEIMK  281 (331)
T ss_pred             chHHHHHChHHHHHHHhcC
Confidence            553 334678888876553

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=96.54  E-value=0.012  Score=51.83  Aligned_cols=77  Identities=18%  Similarity=0.119  Sum_probs=57.7

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC---CCccccCHhHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG---KRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~---~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      |+..+..++..+.+.+ .|.+.-|+.++++++++++.|+.||+. |  |..|..   +.+ .||+.|+.++....+-...
T Consensus         4 Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~k-G--lV~~~~~~~~~i-~LTeeG~~~~~~g~pE~rl   79 (489)
T PRK04172          4 LHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEK-G--LVKVEERVEEVY-VLTEEGKKYAEEGLPERRL   79 (489)
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhC-C--CEEEEeeeEEEE-EECHHHHHHHHhcCHHHHH
Confidence            3556778888887644 146778999999999999999999997 5  444433   345 8999999999877766555


Q ss_pred             HHHHH
Q psy3760          77 IEGLK   81 (306)
Q Consensus        77 ~~~~~   81 (306)
                      ++.+.
T Consensus        80 ~~~l~   84 (489)
T PRK04172         80 LNALK   84 (489)
T ss_pred             HHhhH
Confidence            55444

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.47  E-value=0.0059  Score=34.61  Aligned_cols=39  Identities=28%  Similarity=0.337  Sum_probs=30.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT   60 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT   60 (306)
                      |....|+.+++|++++++.|++|++   ..++.+.++.+ .+|
T Consensus        10 s~~~la~~l~~s~~tv~~~l~~L~~---~g~l~~~~~~~-~i~   48 (48)
T smart00419       10 TRQEIAELLGLTRETVSRTLKRLEK---EGLISREGGRI-VIL   48 (48)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEeCCEE-EEC
Confidence            6788999999999999999999998   44556665554 343

>PRK10852 thiosulfate transporter subunit; Provisional

Probab=96.46  E-value=0.26  Score=41.21  Aligned_cols=196  Identities=12%  Similarity=0.067  Sum_probs=103.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHH----hCCCcEEE--EEeCChhHHHHHHHcC-CeeEEEEccccC----CCCC-ce--
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTI----QFPKVKLS--LLQGNPKQITEMIRND-QADIAIVTEILS----PSDK-LI--  159 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~----~~p~~~i~--~~~~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~-~~--  159 (306)
                      .+.+++..  ....+..+...|.+    ++|++.++  ...+++.....++.+| .+|+.+......    ...+ +.  
T Consensus        28 ~~~~sy~~--~~e~~~~i~~~F~~~~~~~~~g~~v~i~~s~ggSg~~~~qi~~G~~ADV~~~A~~~~~d~l~~~g~li~~  105 (338)
T PRK10852         28 LLNSSYDV--SRELFAALNPPFEQQWAKDNPGDKLTIKQSHAGSSKQALAILQGLKADVVTYNQVTDVQILHDKGKLIPA  105 (338)
T ss_pred             EEeeeccC--CHHHHHHHHHHHHHHHHhhCCCCceEEEEcCCCcHHHHHHHhcCCCcCEEecCCHHHHHHHHHCCCCCCc
Confidence            34444443  46677788888876    67787774  5667777888888886 789998753111    0122 11  


Q ss_pred             -e-eccc------cceEEEEecCCCCCCCCCCcChhhhc--CCCeEeecCCCC-c--HHHHHHH---HHhCC--------
Q psy3760         160 -S-IPCY------QWEYVIIVPLDHPLLLLNSISLKEIS--NYPLITYDLSFS-G--RIKLDRE---FSLQK--------  215 (306)
Q Consensus       160 -~-~~l~------~~~~~~v~~~~~~l~~~~~i~~~dl~--~~~~i~~~~~~~-~--~~~~~~~---~~~~~--------  215 (306)
                       + ..+.      ...+++++++++|   +.+-+|+||.  +..+++.++... .  +..+..+   ....|        
T Consensus       106 ~~~~~~~~n~~p~~s~lV~vv~kgnp---k~i~sw~DL~~~~~kI~i~nP~tSg~g~~~~La~~~~~~~~~G~d~~~a~~  182 (338)
T PRK10852        106 DWQSRLPNNSSPFYSTMAFLVRKGNP---KNIHDWNDLVRSDVKLIFPNPKTSGNARYTYLAAWGAADKADGGDKAKTEQ  182 (338)
T ss_pred             chhhcccccCCcccceEEEEEECCCC---CCCCCHHHhcCCCcEEEECCCCcchHHHHHHHHHHHHHHHHcCCChHHHHH
Confidence             1 1222      2379999999998   3355899995  345666654322 2  1112211   11112        


Q ss_pred             ----CceeEE-EEecCHHHHHHHHHhcc-ceeeeecceecc----cccCCceeeecCCCC-ccceEEEEEeC--CccccH
Q psy3760         216 ----LTPYIV-LETINSDIIKTYVELRM-GIGIIASIAFDS----NRDKNLRSISASHLF-GTTISRVIIKQ--GTYLRS  282 (306)
Q Consensus       216 ----~~~~~~-~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~----~~~~~l~~~~~~~~~-~~~~~~l~~~~--~~~~~~  282 (306)
                          +..++. +..+........+..|. -+++....-+..    .....+..+...... ...++.++-..  +....+
T Consensus       183 ~l~~l~~Nv~v~~~~~~~a~~~~v~~Ge~Dvgi~yesda~~~~~~~~~~~~~iV~P~~~~~~~~pvAvv~k~~~~~~~~e  262 (338)
T PRK10852        183 FMTQFLKNVEVFDTGGRGATTTFAERGLGDVLISFESEVNNIRKQYEAQGYEVVVPKTNILAEFPVAWVDKNVQANGTEK  262 (338)
T ss_pred             HHHHHHhcCCEecCCCcHHHHHHHHcCCccEEEEechHHHHHHHhcCCCCeEEEeCCCCceeeeeEEEEEeccccCCCHH
Confidence                112333 33455777788888773 334443332211    112333333223222 22233333211  234478


Q ss_pred             HHHHHHHHHhHH
Q psy3760         283 YVYSFIKLLSPK  294 (306)
Q Consensus       283 ~~~~~~~~l~~~  294 (306)
                      ..++|+++|.+.
T Consensus       263 ~AkaFidfL~S~  274 (338)
T PRK10852        263 AAKAYLNYLYSP  274 (338)
T ss_pred             HHHHHHHHhcCH
Confidence            899999999654

>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=96.39  E-value=0.0055  Score=37.68  Aligned_cols=40  Identities=30%  Similarity=0.380  Sum_probs=32.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~   61 (306)
                      |....|+.+++|++++++.|+.|++.   .+..+.+ +++ .+||
T Consensus        27 s~~ela~~~g~s~~tv~r~l~~L~~~---g~i~~~~~~~~-~l~~   67 (67)
T cd00092          27 TRQEIADYLGLTRETVSRTLKELEEE---GLISRRGRGKY-RVNP   67 (67)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCCCeE-EeCC
Confidence            78899999999999999999999996   4555555 555 5664

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

Probab=96.38  E-value=0.014  Score=34.31  Aligned_cols=45  Identities=16%  Similarity=0.144  Sum_probs=37.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++.++|....+.. |....|+.+++|.+++.++++++.+.+|.+
T Consensus         2 ~~~e~~i~~~~~~~~-s~~eia~~l~~s~~tv~~~~~~~~~~l~~~   46 (57)
T cd06170           2 TPREREVLRLLAEGK-TNKEIADILGISEKTVKTHLRNIMRKLGVK   46 (57)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            445666776666655 999999999999999999999998888763

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>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=96.36  E-value=0.019  Score=33.66  Aligned_cols=38  Identities=32%  Similarity=0.267  Sum_probs=31.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |...-|+.|++|..||.+-|+.|++.+ .++-.+.++|.
T Consensus        17 t~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~~~~GY   54 (55)
T PF08279_consen   17 TAKELAEELGVSRRTIRRDIKELREWG-IPIESKRGKGY   54 (55)
T ss_dssp             EHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEETTTEE
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEeeCCCCc
Confidence            788999999999999999999997776 88877777664

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 ....

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=96.32  E-value=0.033  Score=35.61  Aligned_cols=62  Identities=19%  Similarity=0.206  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL   67 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~   67 (306)
                      ++....+++.|.++..||+..|||..|+.|.++...++=-.-|.+|+.+.--.|+.-.....
T Consensus        15 ~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~   76 (85)
T PF13011_consen   15 LRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVE   76 (85)
T ss_pred             HHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHH
Confidence            44555677777799999999999999999999999988556689999766535665544433

>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]

Probab=96.25  E-value=0.16  Score=42.19  Aligned_cols=190  Identities=15%  Similarity=0.198  Sum_probs=107.8

Q ss_pred             CCcEEEEecccchhh---------hhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcCCeeEEEEccccCCCCCceee
Q psy3760          92 TGNLTIATTHTQARY---------ALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAIVTEILSPSDKLISI  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~---------~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~  161 (306)
                      .|.|++++..+-.++         +=-.+..+|.+ |-++.+.+..... +++.+.|.+|+.|++-.. -.....++...
T Consensus        22 rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa~-yLgV~Lki~~~~n~dqLf~aL~ng~~DL~Aag-l~~~~~~l~~~   99 (473)
T COG4623          22 RGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFAD-YLGVKLKIIPADNIDQLFDALDNGNADLAAAG-LLYNSERLKNF   99 (473)
T ss_pred             cCeEEEEeecCccceeccCCCccchhHHHHHHHHH-HhCCeEEEEecCCHHHHHHHHhCCCcceeccc-ccCChhHhccc
Confidence            678999886543333         33566777766 5689999998755 899999999999998763 22332333322


Q ss_pred             ---cc-ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEe---cCHHHHHHHH
Q psy3760         162 ---PC-YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLET---INSDIIKTYV  234 (306)
Q Consensus       162 ---~l-~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~v  234 (306)
                         |. ...+..+|.+++..    .+-++++|.+..+.........  .-...+++... |.-...+   -....++.+|
T Consensus       100 ~~gP~y~svs~qlVyRkG~~----Rp~~l~~L~g~~i~v~~gs~~~--~~l~~lk~~ky-P~l~~k~d~~~~~~dLle~v  172 (473)
T COG4623         100 QPGPTYYSVSQQLVYRKGQY----RPRSLGQLKGRQITVAKGSAHV--EDLKLLKETKY-PELIWKVDDKLGVEDLLEMV  172 (473)
T ss_pred             CCCCceecccHHHHhhcCCC----CCCCHHHccCceeeccCCcHHH--HHHHHHHHhhc-chhhhhhcccccHHHHHHHH
Confidence               22 24456677777763    4678999988666555443211  11223333222 3323333   3567888889


Q ss_pred             Hhc-cceeeeecceeccc--ccCCce-eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         235 ELR-MGIGIIASIAFDSN--RDKNLR-SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       235 ~~g-~gi~~~p~~~~~~~--~~~~l~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..| .++++.....+...  -.++|. .+.+.+.   .++..+.+.+. .+.....+++++-+.
T Consensus       173 ~~Gkldytiads~~is~~q~i~P~laVafd~tde---~~v~Wy~~~~d-d~tL~a~ll~F~~~~  232 (473)
T COG4623         173 AEGKLDYTIADSVEISLFQRVHPELAVAFDLTDE---QPVAWYLPRDD-DSTLSAALLDFLNEA  232 (473)
T ss_pred             hcCCcceeeeccHHHHHHHHhCccceeeeecccc---cCceeeccCCc-hHHHHHHHHHHHHHh
Confidence            988 67777665444433  334444 3444442   23333334422 244444444444443

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

Probab=96.25  E-value=0.0097  Score=44.05  Aligned_cols=93  Identities=19%  Similarity=0.254  Sum_probs=55.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGN   94 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~   94 (306)
                      |.++.|+.|++|+++.+|.|++||++   .+..|.   .+.++.+|+.|..++...   ++.+..+......  -...|.
T Consensus        21 t~~ela~~l~~S~qta~R~l~~le~~---~~I~R~~~~~Gq~i~iTekG~~~L~~~---~~d~~r~~~~~~~--i~i~G~   92 (214)
T COG1339          21 TSSELAKRLGVSSQTAARKLKELEDE---GYITRTISKRGQLITITEKGIDLLYKE---YEDLSRIFDSGGN--IVIEGE   92 (214)
T ss_pred             cHHHHHHHhCcCcHHHHHHHHhhccC---CcEEEEecCCCcEEEehHhHHHHHHHH---HHHHHHHhcCCCc--eEEEEE
Confidence            67889999999999999999999974   455543   233348999999987643   2222222211110  122344


Q ss_pred             EEEEecccchhhhhHHHHHHHHHh
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQ  118 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~  118 (306)
                      +.=|..+.--..-++....+|++.
T Consensus        93 V~SGlGEG~yyvS~~~Y~~qf~ek  116 (214)
T COG1339          93 VVSGLGEGRYYVSLPGYRRQFREK  116 (214)
T ss_pred             EecccccceEEEecHHHHHHHHHH
Confidence            444544432111235666777665

>PF13518 HTH_28: Helix-turn-helix domain

Probab=96.24  E-value=0.013  Score=33.86  Aligned_cols=38  Identities=18%  Similarity=0.169  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS   45 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg   45 (306)
                      +++...+.+.. |...+|+.+|||.++|.+.+++.++ -|
T Consensus         3 ~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~-~G   40 (52)
T PF13518_consen    3 LQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYRE-GG   40 (52)
T ss_pred             HHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHh-cC
Confidence            44555666666 9999999999999999999999997 44

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=96.24  E-value=0.066  Score=42.90  Aligned_cols=40  Identities=25%  Similarity=0.287  Sum_probs=34.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      ++..-|+.+++|.+|+.|-|+.||++   .|+.|..+|. .+++
T Consensus        21 ~v~eLa~~l~VS~~TIRRDL~~Le~~---g~l~r~~Gga-~~~~   60 (256)
T PRK10434         21 SVEELAQYFDTTGTTIRKDLVILEHA---GTVIRTYGGV-VLNK   60 (256)
T ss_pred             EHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCE-EcCC
Confidence            78899999999999999999999986   6788888887 4543

>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional

Probab=96.22  E-value=0.6  Score=39.08  Aligned_cols=199  Identities=14%  Similarity=0.056  Sum_probs=108.6

Q ss_pred             CCCcEEEEecccchhhh--hHHHHHHHHHhCCCcEEEEEeCChh-HHHHHHH----cCCeeEEEEccccC----CCCCc-
Q psy3760          91 DTGNLTIATTHTQARYA--LPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIR----NDQADIAIVTEILS----PSDKL-  158 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~--l~~~l~~~~~~~p~~~i~~~~~~~~-~~~~~l~----~~~~Di~i~~~~~~----~~~~~-  158 (306)
                      ..++|+|.+..++...+  ...++..|.+++ ++++++...++. ++...+.    ++.+|+.+......    ...++ 
T Consensus        21 ~~~~L~vy~~~~~~~~~~~~~~i~~~Fe~~t-gikV~~~~~~s~~~~~~kl~~e~~~~~~DV~~~~~~~~~~~l~~~gll   99 (330)
T PRK11205         21 AKPVLTVYTYDSFAAEWGPGPAVKKAFEAEC-GCELKFVALEDGVSLLNRLRLEGKNSKADVVLGLDNNLLAAAKQTGLF   99 (330)
T ss_pred             CCCeEEEEEcccccccCCCchHHHHHHHHHH-CCEEEEEecCcHHHHHHHHHhcCCCCCCCEEEECCchHHHHHHHCCCc
Confidence            45789999976665543  357889998885 899999886664 7888777    36899998532100    00010 


Q ss_pred             -------------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCC-Cc-HHHHH-----
Q psy3760         159 -------------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSF-SG-RIKLD-----  208 (306)
Q Consensus       159 -------------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~-~~-~~~~~-----  208 (306)
                                         ...++....++++.+++..  ...+-+++||.+.    .....++.. .. ...+.     
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yn~~~~--~~~P~sw~DL~~~~~~g~i~~~dp~~s~~~~~~~~~~~~~  177 (330)
T PRK11205        100 APSGVDTSAVTVPGGWNDDTFVPYDYGYFAFVYDKEKL--KNPPKSLKELVESDQNWKVIYQDPRTSTPGLGLLLWMKKV  177 (330)
T ss_pred             ccccCChhhccCcccccCCceeeEeeeeEEEEEccccc--CCCCCCHHHHhChhhcCCEEecCCCCCcHHHHHHHHHHHh
Confidence                               0233444566677777653  2345689999752    233333221 11 11111     


Q ss_pred             ------HHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecce--eccccc--CCceeeecCCCCccceEEEEEeCC
Q psy3760         209 ------REFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIA--FDSNRD--KNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       209 ------~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~--~~~~~~--~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                            +.++.  +..+..-...+.....+++.+|. .+++.....  ......  ..+....+++......-++...++
T Consensus       178 ~g~~~~~~~~~--L~~~~~~~~~~~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~  255 (330)
T PRK11205        178 YGDDAPQAWQK--LAKKTVTVTKGWSEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVEVAARTAA  255 (330)
T ss_pred             cCchHHHHHHH--HHhCCeeeCCChHHHHHHHHcCCccEEEeCCCcHHHHHhhccCCceeEEEcCCCCeEEEEEEEEeCC
Confidence                  11111  11222222345567778888883 444443321  111111  133333333322222334555677


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .+....+++|++++.+.
T Consensus       256 a~n~e~A~~Fi~fllS~  272 (330)
T PRK11205        256 SKQPELAQKFLQFMVSP  272 (330)
T ss_pred             CCCHHHHHHHHHHHcCH
Confidence            77788999999998654

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

Probab=96.21  E-value=0.029  Score=36.87  Aligned_cols=68  Identities=24%  Similarity=0.264  Sum_probs=49.1

Q ss_pred             HHHHHHH-hcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----C--CccccCHhHHHHHHHHHHHHHHHH
Q psy3760           8 FVREAVR-QNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----K--RIRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         8 ~f~~v~~-~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~--~~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      ++.++.. .. .|+.=.+.+ ++|+..++++++.||+.   -|+.|..     .  .. +||+.|+.|.+....+.+=.+
T Consensus        10 IL~~l~~g~~-rf~el~~~l~~is~~~L~~~L~~L~~~---GLv~r~~~~~~p~~v~Y-~LT~~G~~l~~~l~~l~~W~~   84 (90)
T PF01638_consen   10 ILRALFQGPM-RFSELQRRLPGISPKVLSQRLKELEEA---GLVERRVYPEVPPRVEY-SLTEKGKELLPVLEALEEWGE   84 (90)
T ss_dssp             HHHHHTTSSE-EHHHHHHHSTTS-HHHHHHHHHHHHHT---TSEEEEEESSSSSEEEE-EE-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCC-cHHHHHHhcchhHHHHHHHHHHHHHHc---chhhcccccCCCCCCcc-CCCcCHHHHHHHHHHHHHHHH
Confidence            3444444 34 789999999 99999999999999984   4556541     1  24 899999999998888876655


Q ss_pred             HH
Q psy3760          79 GL   80 (306)
Q Consensus        79 ~~   80 (306)
                      +-
T Consensus        85 ~~   86 (90)
T PF01638_consen   85 EH   86 (90)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=96.18  E-value=0.017  Score=32.25  Aligned_cols=31  Identities=19%  Similarity=0.250  Sum_probs=21.7

Q ss_pred             HHHHHhc-CCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          10 REAVRQN-FNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        10 ~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      +..++.| .|+.+||+..||+++||+++++.-
T Consensus         9 i~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g~   40 (45)
T PF05225_consen    9 IEAVKNGKMSIRKAAKKYGVPRSTLRRRLRGK   40 (45)
T ss_dssp             HHHHHTTSS-HHHHHHHHT--HHHHHHHHHHT
T ss_pred             HHHHHhCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence            3334444 699999999999999999988753

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein

Probab=96.18  E-value=0.56  Score=38.37  Aligned_cols=150  Identities=15%  Similarity=0.069  Sum_probs=84.9

Q ss_pred             CcEEEEecccchhh----hhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccc-----cCCCCCce-ee
Q psy3760          93 GNLTIATTHTQARY----ALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEI-----LSPSDKLI-SI  161 (306)
Q Consensus        93 ~~l~I~~~~~~~~~----~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~-----~~~~~~~~-~~  161 (306)
                      ..|+||+.......    .+.++...+.++ .++++++.. .+....++.+.+|++|+++....     ........ ..
T Consensus        27 ~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~-~g~~v~~~~~~~~~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~  105 (288)
T TIGR03431        27 KELNFGIIPTENASDLKQRWEPLADYLSKK-LGVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAI  105 (288)
T ss_pred             CeEEEEEcCCCCHHHHHHHHHHHHHHHHHH-hCCcEEEEeCCCHHHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEE
Confidence            57999997654332    233455556555 478888654 56778899999999999996411     01111100 00


Q ss_pred             cc---ccc--eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHH--HHHHHhCCCcee----EEEEecCHHHH
Q psy3760         162 PC---YQW--EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKL--DREFSLQKLTPY----IVLETINSDII  230 (306)
Q Consensus       162 ~l---~~~--~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~--~~~~~~~~~~~~----~~~~~~~~~~~  230 (306)
                      ..   +..  ..+++++++.+     .-+++||.+.......++......+  ....+..|....    .+....+...+
T Consensus       106 ~~~~~~~~~y~~~lvv~~ds~-----i~sl~DL~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~  180 (288)
T TIGR03431       106 EVNADGSTGYYSVLIVKKDSP-----IKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAA  180 (288)
T ss_pred             eccCCCCCceEEEEEEeCCCC-----CCcHHHhCCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHH
Confidence            00   011  14667777754     3488999887766654443322222  223355565422    22233367788


Q ss_pred             HHHHHhccc-eeeeeccee
Q psy3760         231 KTYVELRMG-IGIIASIAF  248 (306)
Q Consensus       231 ~~~v~~g~g-i~~~p~~~~  248 (306)
                      ...+.+|.. .++++...+
T Consensus       181 ~~al~~G~vDa~~~~~~~~  199 (288)
T TIGR03431       181 ILAVANGTVDAATTNDENL  199 (288)
T ss_pred             HHHHHcCCCCeEeccHHHH
Confidence            888898855 445555443

Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.18  E-value=0.012  Score=35.08  Aligned_cols=36  Identities=31%  Similarity=0.324  Sum_probs=28.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR   55 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~   55 (306)
                      |...-|+.+++|++++++.++.|+++ |. +-...++|
T Consensus        22 s~~~la~~~~vs~~tv~~~l~~L~~~-g~-i~~~~~~g   57 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEAE-GL-VQRRPGSG   57 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEecCCe
Confidence            67788999999999999999999985 65 33333444

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.12  E-value=0.015  Score=39.68  Aligned_cols=43  Identities=26%  Similarity=0.306  Sum_probs=35.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ .|++.-|+.+|+|++++++++++|++.
T Consensus         1 ld~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~   44 (108)
T smart00344        1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE   44 (108)
T ss_pred             CCHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4556777777777643 289999999999999999999999995

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

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.09  E-value=0.018  Score=44.39  Aligned_cols=49  Identities=22%  Similarity=0.320  Sum_probs=37.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec------CCC--ccccCHhHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH------GKR--IRGLTKPGQAILRS   69 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~------~~~--~~~lT~~G~~l~~~   69 (306)
                      |...-|+.+++|++|++++|++||+. |  |+.|.      ++.  .+.||+.|...++.
T Consensus        17 t~~eLA~~lgis~~tV~~~L~~Le~~-G--lV~r~~~~~~~gRp~~~y~LT~~G~~~~~~   73 (203)
T TIGR02702        17 TAAALAEALAISPQAVRRHLKDLETE-G--LIEYEAVVQGMGRPQYHYQLSRQGREQFPQ   73 (203)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-C--CeEEeecccCCCCCceEEEECcchhhhccc
Confidence            67788999999999999999999996 4  44433      121  12799999998765

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.

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=96.07  E-value=0.27  Score=48.96  Aligned_cols=143  Identities=13%  Similarity=0.092  Sum_probs=90.7

Q ss_pred             CCcEEEEecccch------------hhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEc--cccCCCC
Q psy3760          92 TGNLTIATTHTQA------------RYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVT--EILSPSD  156 (306)
Q Consensus        92 ~~~l~I~~~~~~~------------~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~--~~~~~~~  156 (306)
                      .+.|++|+.....            ..+...++..+.+. -+++++++.. +++++++.|.+|++|+++..  .......
T Consensus        55 ~~~l~vgv~~~~~p~~~~~~~~g~~~G~~~D~l~~ia~~-lG~~~e~v~~~~~~~~l~~l~~g~iDl~~~~~~~~~~r~~  133 (1197)
T PRK09959         55 KKNLVIAVHKSQTATLLHTDSQQRVRGINADYLNLLKRA-LNIKLTLREYADHQKAMDALEEGEVDIVLSHLVASPPLND  133 (1197)
T ss_pred             CCeEEEEecCCCCCCceeecCCCccceecHHHHHHHHHh-cCCceEEEeCCCHHHHHHHHHcCCCcEecCcccccccccc
Confidence            4679999864321            22445566666554 5899999986 88999999999999997652  1112222


Q ss_pred             Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+ -+.|++....+++++++..     .-+++++.+....... +....    ..+++.. +--....+++...++.++.
T Consensus       134 ~~~fs~py~~~~~~~v~~~~~~-----~~~~~~l~~~~i~~~~-g~~~~----~~~~~~~-p~~~i~~~~s~~~al~av~  202 (1197)
T PRK09959        134 DIAATKPLIITFPALVTTLHDS-----MRPLTSSKPVNIARVA-NYPPD----EVIHQSF-PKATIISFTNLYQALASVS  202 (1197)
T ss_pred             chhcCCCccCCCceEEEeCCCC-----CCCcccccCeEEEEeC-CCCCH----HHHHHhC-CCCEEEeCCCHHHHHHHHH
Confidence            22 3557677777888877653     2345566555444433 33332    2333322 1123568899999999999


Q ss_pred             hccceeeeecc
Q psy3760         236 LRMGIGIIASI  246 (306)
Q Consensus       236 ~g~gi~~~p~~  246 (306)
                      .|..=+++...
T Consensus       203 ~G~~Da~i~~~  213 (1197)
T PRK09959        203 AGQNDYFIGSN  213 (1197)
T ss_pred             cCCCCEEEccH
Confidence            99877666553

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

Probab=95.97  E-value=0.032  Score=37.80  Aligned_cols=44  Identities=27%  Similarity=0.343  Sum_probs=36.0

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+++.........++|+...|+.||||.||+-.++.+|=+.+|.
T Consensus        36 ~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   36 PEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            34555555555444499999999999999999999999999998

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

Probab=95.93  E-value=0.011  Score=33.84  Aligned_cols=36  Identities=25%  Similarity=0.257  Sum_probs=23.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      +.++..+.+ |.|..++|+.+|+|++|+++.+++.++
T Consensus         8 ~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~   43 (50)
T PF13384_consen    8 AQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYRE   43 (50)
T ss_dssp             --HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred             HHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence            445555556 459999999999999999999998764

>PRK01905 DNA-binding protein Fis; Provisional

Probab=95.90  E-value=0.019  Score=36.44  Aligned_cols=30  Identities=17%  Similarity=0.020  Sum_probs=24.7

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ++.+++.+.++||+.||||++++.+.++++
T Consensus        45 aL~~~~gn~s~aAr~LGIsrstL~rklkk~   74 (77)
T PRK01905         45 VMEQAGGNQSLAAEYLGINRNTLRKKLQQH   74 (77)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            334444389999999999999999999985

>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]

Probab=95.87  E-value=0.23  Score=41.56  Aligned_cols=197  Identities=10%  Similarity=0.002  Sum_probs=106.5

Q ss_pred             CCcEEEEecccch--hhhhHHHHHHHHHhCCCc-EEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CC--Ccee
Q psy3760          92 TGNLTIATTHTQA--RYALPKIIKEFTIQFPKV-KLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SD--KLIS  160 (306)
Q Consensus        92 ~~~l~I~~~~~~~--~~~l~~~l~~~~~~~p~~-~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~--~~~~  160 (306)
                      .-.++++..+...  ..++...-..|.+.  ++ .+++... +.....+.|..|.+|++....+...     ..  .+..
T Consensus        30 ~~~~~~~~~~~~~~~~~~va~~kG~f~~~--Gl~~v~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~  107 (335)
T COG0715          30 KVTILLGWLPNPDHAPLYVAKEKGFFKKE--GLDDVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKV  107 (335)
T ss_pred             ceeeeecccCchhHHHHHHHHHhChHhHh--CCCceEEEEcCCChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEE
Confidence            4456666655311  22233333333443  34 4666554 5567889999999999964322111     11  1111


Q ss_pred             --ecccc-ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHh
Q psy3760         161 --IPCYQ-WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVEL  236 (306)
Q Consensus       161 --~~l~~-~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~  236 (306)
                        ..... ....+++.++.+     ..+++||.+.++.....+....-.+..++...|+.+..+ +..-....+...+..
T Consensus       108 va~~~~~~~~~~i~~~~~~~-----i~~~adlkGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~  182 (335)
T COG0715         108 VAALVQNGNGIALLVLKDSG-----IKSVADLKGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAA  182 (335)
T ss_pred             eeecccCCceeEEEeccCCC-----cccccCCCCceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhc
Confidence              11112 134555555543     235899999999888877545568889999999987443 333344456666655


Q ss_pred             c-cceeeeecceeccc-ccCCceeeecCCCCc--cceEEEEEeCCcc--ccHHHHHHHHHHhHHh
Q psy3760         237 R-MGIGIIASIAFDSN-RDKNLRSISASHLFG--TTISRVIIKQGTY--LRSYVYSFIKLLSPKL  295 (306)
Q Consensus       237 g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~--~~~~~l~~~~~~~--~~~~~~~~~~~l~~~~  295 (306)
                      | .......+...... ..+.-+.+.......  ....+++.++...  ....+++|++.+.+..
T Consensus       183 g~vda~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~a~~~a~  247 (335)
T COG0715         183 GQVDAFVVWEPWNAAAEGEGGGRVLLDGADLWGNHPELVLVVRKEFIEANPEAVKAFLKALAKAT  247 (335)
T ss_pred             CCcceEEecCCchhhhhccCCeEEEEcchhhhccCchhhhhhHHHHHHHCHHHHHHHHHHHHHHH
Confidence            5 33344444443333 444444444433222  2233344443222  4778899988886654

>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=95.83  E-value=0.011  Score=35.33  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=22.7

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.+.-|+.|++|+||+|..+++|++.
T Consensus        24 ~~~~iA~~L~vs~~tvt~ml~~L~~~   49 (60)
T PF01325_consen   24 RTKDIAERLGVSPPTVTEMLKRLAEK   49 (60)
T ss_dssp             BHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHCCChHHHHHHHHHHHHC
Confidence            56788999999999999999999874

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 ....

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=95.79  E-value=0.72  Score=46.00  Aligned_cols=193  Identities=8%  Similarity=0.005  Sum_probs=107.8

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEcccc-CCCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEIL-SPSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~-~~~~~~  158 (306)
                      .+.|++|+.+...           ..+...++..+.+.- ++++++.... ..+....|.+|++|+....... .....+
T Consensus       301 ~~~l~v~~~~~~pP~~~~d~~g~~~G~~~Dll~~i~~~~-g~~~~~v~~~~~~~~~~~l~~g~~D~i~~~~~t~~r~~~~  379 (1197)
T PRK09959        301 HPDLKVLENPYSPPYSMTDENGSVRGVMGDILNIITLQT-GLNFSPITVSHNIHAGTQLNPGGWDIIPGAIYSEDRENNV  379 (1197)
T ss_pred             CCceEEEcCCCCCCeeEECCCCcEeeehHHHHHHHHHHH-CCeEEEEecCCHHHHHHHHHCCCceEeecccCCccccccc
Confidence            4689999875322           245566777776654 6888877754 4456778999999987653221 122223


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhh-cCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEI-SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                       -+.|++..+++++++++...       ..++ .+.. |....+...    ..++...... .....+++...++.++.+
T Consensus       380 ~fs~py~~~~~~~v~~~~~~~-------~~~~~~g~~-vav~~g~~~----~~~~~~~~p~-~~~~~~~~~~~~l~av~~  446 (1197)
T PRK09959        380 LFAEAFITTPYVFVMQKAPDS-------EQTLKKGMK-VAIPYYYEL----HSQLKEMYPE-VEWIKVDNASAAFHKVKE  446 (1197)
T ss_pred             eeccccccCCEEEEEecCCCC-------ccccccCCE-EEEeCCcch----HHHHHHHCCC-cEEEEcCCHHHHHHHHHc
Confidence             36688888999888766421       1122 2333 333333322    2333333212 234678999999999999


Q ss_pred             ccceeeeeccee-ccc-c---cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         237 RMGIGIIASIAF-DSN-R---DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       237 g~gi~~~p~~~~-~~~-~---~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      |..=+++..... ..+ .   .+.+..+..+. .....+++..+++.   +.....++..-..+.+...++
T Consensus       447 G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~av~k~~---~~L~~~lnk~l~~i~~~~~~~  513 (1197)
T PRK09959        447 GELDALVATQLNSRYMIDHYYPNELYHFLIPG-VPNASLSFAFPRGE---PELKDIINKALNAIPPSEVLR  513 (1197)
T ss_pred             CCCCEEehhhHHHHHHHHhcccccceeeecCC-CCchheEEeeCCCC---HHHHHHHHHHHHhCCHHHHHH
Confidence            977666544322 222 1   13344444333 23346777777764   334444443333343334433

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=95.79  E-value=0.0075  Score=32.08  Aligned_cols=23  Identities=30%  Similarity=0.335  Sum_probs=20.0

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      +-. |+++||+.||+++++|++.|
T Consensus        15 ~F~-Si~eAa~~l~i~~~~I~~~l   37 (37)
T PF07453_consen   15 SFD-SIREAARYLGISHSTISKYL   37 (37)
T ss_pred             EEc-CHHHHHHHhCCCHHHHHHhC
Confidence            346 99999999999999999864

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

Probab=95.77  E-value=0.014  Score=37.63  Aligned_cols=50  Identities=10%  Similarity=0.121  Sum_probs=41.7

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI   50 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~   50 (306)
                      |+++-|+.+-.+--.+.+...||.+++||++|+++.+++-....-.-|++
T Consensus        34 lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLve   83 (99)
T COG1342          34 LTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVE   83 (99)
T ss_pred             ecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhc
Confidence            46677788777777777999999999999999999999988887666654

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=95.68  E-value=0.013  Score=32.71  Aligned_cols=36  Identities=19%  Similarity=0.226  Sum_probs=28.3

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      -++++....+.+.|.|+.+.|+.+|+|.+||-|-++
T Consensus         8 ~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    8 KEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            346777888889988999999999999999998764

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=95.66  E-value=0.028  Score=41.10  Aligned_cols=42  Identities=10%  Similarity=0.073  Sum_probs=33.7

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.| .|+++-|+++|+|++|+.++|++|++.
T Consensus         8 D~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~   50 (153)
T PRK11179          8 DNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA   50 (153)
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            445566666665552 399999999999999999999999985

>PRK04217 hypothetical protein; Provisional

Probab=95.64  E-value=0.04  Score=37.39  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=40.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR   51 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R   51 (306)
                      |+-++.+.+......|.|+...|+.+++|.+||.+.+++..+.|-..|...
T Consensus        43 Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~   93 (110)
T PRK04217         43 MTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEG   93 (110)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            344566777777756669999999999999999999998888885555433

>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase

Probab=95.50  E-value=0.14  Score=32.64  Aligned_cols=73  Identities=16%  Similarity=0.259  Sum_probs=55.8

Q ss_pred             hhhHHHHHHHHHhcC-CHHHHHHHh--CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           3 LHQFRFVREAVRQNF-NLTEAAKAL--YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~-s~~~aA~~l--~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      -+..-+|+.+++..| +.+..++.|  .++.+.+-+.|..|   +..-|.+++|-|++ .|..|..++..|-.+..+.+.
T Consensus        16 E~~~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvL---IKkglIEKSGDGlv-~T~~g~~Ii~~AA~l~a~en~   91 (96)
T PF09114_consen   16 ENAANILIQVAKKNFITASEVREALATEMNKASVNSNIGVL---IKKGLIEKSGDGLV-ITEEGMDIIIQAAELWAQENA   91 (96)
T ss_dssp             HHHHHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHH---HHTTSEEEETTEEE-E-HHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHH---HHcCcccccCCceE-EechHHHHHHHHHHHHHhcCC
Confidence            355678888998776 667788877  68888888878776   44679999999995 999999999999988876543

Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=95.48  E-value=0.02  Score=34.13  Aligned_cols=25  Identities=28%  Similarity=0.104  Sum_probs=21.3

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      ++.-.| |.++.|+.||||+++||+.
T Consensus         5 aI~~~G-~~~~lAkalGVs~~aVs~W   29 (60)
T PF14549_consen    5 AIKYFG-GQSKLAKALGVSPQAVSQW   29 (60)
T ss_dssp             HHHHHS-SHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHC-CHHHHHHHHCCCHHHHHHh
Confidence            455668 9999999999999999988

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=95.44  E-value=0.18  Score=40.63  Aligned_cols=62  Identities=13%  Similarity=0.013  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760           5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR   68 (306)
Q Consensus         5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~   68 (306)
                      -+.++-.+.+.+  .|++.-|+.++++.||++|.|+.|++ .|.--....++.. +||+.+..+..
T Consensus        13 al~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~-~g~v~~~~~~~~Y-~Lg~~~~~l~~   76 (263)
T PRK09834         13 GLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE-EGYVRRSASDDSF-RLTLKVRQLSE   76 (263)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCEEEecCCCcE-EEcHHHHHHHH
Confidence            345555555543  37999999999999999999999986 3544444446677 79987766543

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=95.37  E-value=0.35  Score=38.65  Aligned_cols=48  Identities=10%  Similarity=0.081  Sum_probs=36.2

Q ss_pred             HHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760           6 FRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus         6 l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      -+++-.+.+.| .+....|+.+++|++|+.|-|++||++   .++.|.++|.
T Consensus         8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~---g~i~r~~gga   56 (251)
T PRK13509          8 QILLELLAQLGFVTVEKVIERLGISPATARRDINKLDES---GKLKKVRNGA   56 (251)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEecCCc
Confidence            33444444433 267889999999999999999999974   5678887776

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=95.35  E-value=0.043  Score=45.64  Aligned_cols=44  Identities=32%  Similarity=0.372  Sum_probs=38.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      |.+.-|+.+++|+++++++|+.|+ +.|..+..+.++|. .+.+..
T Consensus        20 s~~~LA~~lgvsr~tV~~~l~~L~-~~G~~i~~~~~~Gy-~L~~~~   63 (319)
T PRK11886         20 SGEQLGEELGISRAAIWKHIQTLE-EWGLDIFSVKGKGY-RLAEPL   63 (319)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH-HCCCceEEecCCeE-EecCcc
Confidence            778889999999999999999999 69999999887787 565543

>TIGR01481 ccpA catabolite control protein A

Probab=95.35  E-value=0.48  Score=39.51  Aligned_cols=109  Identities=13%  Similarity=0.182  Sum_probs=59.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~   93 (306)
                      ++...|+..|+|.+||||.|.             ++.++   .+      +..+++++..+++-.    ..+.+..+.++
T Consensus         3 ti~dIA~~agvS~~TVSrvLn-------------~~~~v---s~------~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~   60 (329)
T TIGR01481         3 TIYDVAREAGVSMATVSRVVN-------------GNPNV---KP------ATRKKVLEVIKRLDYRPNAVARGLASKRTT   60 (329)
T ss_pred             cHHHHHHHhCCCHHHHHHHhC-------------CCCCC---CH------HHHHHHHHHHHHHCCCCCHHHHHHhhCCCC
Confidence            678899999999999999984             22232   22      222233333333321    11223333344


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      .|-+-++. +...++..++..+.+...  +..+.+....  .   .+.++.+.++++|-.|..
T Consensus        61 ~Igvv~~~-~~~~f~~~l~~~i~~~~~~~g~~~~i~~~~~~~~~~~~~~~~l~~~~vdGiIi~  122 (329)
T TIGR01481        61 TVGVIIPD-ISNIYYAELARGIEDIATMYKYNIILSNSDEDPEKEVQVLNTLLSKQVDGIIFM  122 (329)
T ss_pred             EEEEEeCC-CCchhHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEe
Confidence            55555543 344566666655544322  5566554332  1   134566778899998875

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=95.34  E-value=0.11  Score=36.07  Aligned_cols=62  Identities=21%  Similarity=0.192  Sum_probs=48.4

Q ss_pred             HhcCCHHHHHHHhC-CCchHHHHHHHHHHHHcCceeEEecCCC------ccccCHhHHHHHHHHHHHHHHHHH
Q psy3760          14 RQNFNLTEAAKALY-TSQPGVSKAIIELEEELSIDIFIRHGKR------IRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus        14 ~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~~Lf~R~~~~------~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      ... .|+.=-+.++ |||..+|+++++||+.   -|+.|.-..      -.+||+.|+.|.+-...+.+=.+.
T Consensus        35 g~~-RF~eL~r~i~~Is~k~Ls~~Lk~Le~~---Glv~R~~~~~~PprveY~LT~~G~~L~~vl~~l~~Wg~~  103 (120)
T COG1733          35 GPK-RFNELRRSIGGISPKMLSRRLKELEED---GLVERVVYPEEPPRVEYRLTEKGRDLLPVLLALADWGEK  103 (120)
T ss_pred             CCC-cHHHHHHHccccCHHHHHHHHHHHHHC---CCEEeeecCCCCceeEEEEhhhHHHHHHHHHHHHHHHHH
Confidence            444 7999999999 9999999999999984   466776332      128999999999988887554443

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=95.33  E-value=0.23  Score=41.66  Aligned_cols=137  Identities=12%  Similarity=0.099  Sum_probs=76.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH-HHHHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL-KKIGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~-~~~~~~~~~~~~~~l~   96 (306)
                      ++...|+..|+|.+|+||.|..              ++.  .+++=   -+++.+..+++.-. ....+.+..+.++.|-
T Consensus         2 TikDVA~~AGVS~sTVSrvln~--------------~~~--Vs~eT---r~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig   62 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLNG--------------SPY--VSEET---REKVLAAIKELGYRPNAVARSLRTGRTKTIG   62 (333)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC--------------CCC--CCHHH---HHHHHHHHHHHCCCCCHHHHHHHhCCCCEEE
Confidence            5778999999999999998842              222  22211   22222233332222 1223444444555666


Q ss_pred             EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCCh-----hHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760          97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGNP-----KQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV  169 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~~-----~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~  169 (306)
                      +-++ .+...++..++..+.+..-  +.++.+...+.     .+..+.+.+.++|-.|........+......-...+++
T Consensus        63 ~i~p-~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~~~~~~~~~~~l~~~~~P~V  141 (333)
T COG1609          63 LVVP-DITNPFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLGERPNDSLLELLAAAGIPVV  141 (333)
T ss_pred             EEeC-CCCCchHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCHHHHHHHHhcCCCEE
Confidence            6555 3344677777777666543  55555555443     23578899999999999652222222223333345666


Q ss_pred             EEecC
Q psy3760         170 IIVPL  174 (306)
Q Consensus       170 ~v~~~  174 (306)
                      ++-..
T Consensus       142 ~i~~~  146 (333)
T COG1609         142 VIDRS  146 (333)
T ss_pred             EEeCC
Confidence            66543

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=95.31  E-value=0.074  Score=30.62  Aligned_cols=43  Identities=14%  Similarity=0.102  Sum_probs=34.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +-++.+.|...+..|.|....|+.+|+|++++.+.+.+..+.+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l   54 (55)
T cd06171          12 PEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL   54 (55)
T ss_pred             CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            3455667777764445999999999999999999999887654

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

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

Probab=95.26  E-value=0.046  Score=33.27  Aligned_cols=40  Identities=28%  Similarity=0.258  Sum_probs=30.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT   60 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT   60 (306)
                      |...-|+.+++|.+++++.|++|++ -|. +....++|+ .+|
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~-~G~-i~~~~~~~~-~l~   66 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEA-EGL-VERRPGRGT-FVA   66 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH-CCC-EEecCCCeE-EeC
Confidence            4778899999999999999999998 455 444445565 454

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

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=95.26  E-value=0.11  Score=40.53  Aligned_cols=177  Identities=16%  Similarity=0.104  Sum_probs=106.0

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---C--CCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---G--KRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG   93 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~--~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~   93 (306)
                      =++-.+-+|.|.||+|-.++.||++   ..+.|.   |  +.++ |.                        +...--..+
T Consensus        23 Q~eIeel~GlSKStvSEaLs~LE~~---giv~RrkvsGKs~rVw-La------------------------ey~Py~d~~   74 (321)
T COG3888          23 QTEIEELMGLSKSTVSEALSELEKQ---GIVKRRKVSGKSKRVW-LA------------------------EYSPYPDSR   74 (321)
T ss_pred             HHHHHHHhCcchhHHHHHHHHHHhc---CeeeeeeecCcceEEe-ec------------------------ccCCCCCcc
Confidence            3567788999999999999999986   344443   1  2221 11                        122334567


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecccc---ceEE-
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ---WEYV-  169 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~---~~~~-  169 (306)
                      -+|||+-.+.....+.++...+.+.-=.+.+++... .-++...|-.|.+|+|...--        .+.++.   -... 
T Consensus        75 ~lRiGiLRatEYp~~i~aaKnl~e~ki~a~iR~Ydd-aisit~DLv~g~ld~~lSPii--------Tq~ifsi~~rni~I  145 (321)
T COG3888          75 FLRIGILRATEYPFFISAAKNLEERKISATIRFYDD-AISITRDLVEGKLDFGLSPII--------TQIIFSISYRNIRI  145 (321)
T ss_pred             cEEEeeeecccchhHhHHHHhhhhccceEEEEEecc-HHHHHHHHHhhhhhhcccHHH--------HHHHHHHHhcceEE
Confidence            899999988777788888888887754455555544 447888999999999997411        111111   1111 


Q ss_pred             --EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc--cceee
Q psy3760         170 --IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR--MGIGI  242 (306)
Q Consensus       170 --~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~~  242 (306)
                        -|++.+.-+..      ..  -...+.......+...+.++.+..++. . .-.+.+...++.-..+|  .+|++
T Consensus       146 ~g~vAsgGgGi~~------n~--cn~~~~tsesSsmm~~~ref~~~egi~-~-I~yfs~p~~mid~l~~g~~r~IaI  212 (321)
T COG3888         146 IGGVASGGGGIIG------NT--CNRIASTSESSSMMWLFREFKNIEGIP-S-ISYFSDPESMIDFLEKGIVRYIAI  212 (321)
T ss_pred             EeccccCCCceec------cc--cceeeeecccHHHHHHHHHHHhhcCCc-c-eeeecCHHHHHhHhhhcceeEEEE
Confidence              22222222111      11  112444444444444555555555554 3 44567788888888888  55555

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

Probab=95.24  E-value=0.026  Score=37.85  Aligned_cols=48  Identities=13%  Similarity=0.250  Sum_probs=41.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      |+++-++.+..+.-.|.|-..||+++|||++|+++.+.+-...+-.-|
T Consensus        42 L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL   89 (106)
T PF02001_consen   42 LTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESARKKIADAL   89 (106)
T ss_pred             eeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence            456788888888888889999999999999999999998887774444

>PHA02591 hypothetical protein; Provisional

Probab=95.20  E-value=0.034  Score=34.25  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=27.2

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .-..+++.|+|..+-|+.||+||++|++-++
T Consensus        51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            3456889999999999999999999998765

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

Probab=95.15  E-value=0.046  Score=36.18  Aligned_cols=26  Identities=23%  Similarity=0.100  Sum_probs=23.1

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ++++.++||+.||||++|+.+.+++.
T Consensus        67 ~~gn~s~AAr~LGIsRsTL~rKLkr~   92 (95)
T PRK00430         67 TRGNQTRAALMLGINRGTLRKKLKKY   92 (95)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            43389999999999999999999975

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=95.12  E-value=0.072  Score=34.96  Aligned_cols=43  Identities=21%  Similarity=0.210  Sum_probs=38.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhC-CCchHHHHHHHHHHHHcCc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALY-TSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~   46 (306)
                      +++-.+++....|.|++..|+.+| .+.|||++.++++|+.+..
T Consensus        32 R~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence            567777888887889999999999 9999999999999998853

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.10  E-value=0.052  Score=39.72  Aligned_cols=36  Identities=33%  Similarity=0.367  Sum_probs=28.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |+.+..=++ . |++.-|+.+|+|+++++++|++||+.
T Consensus        14 L~~L~~d~r-~-~~~eia~~lglS~~~v~~Ri~~L~~~   49 (154)
T COG1522          14 LRLLQEDAR-I-SNAELAERVGLSPSTVLRRIKRLEEE   49 (154)
T ss_pred             HHHHHHhCC-C-CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            333333333 4 79999999999999999999999985

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=95.07  E-value=0.03  Score=38.40  Aligned_cols=28  Identities=25%  Similarity=0.252  Sum_probs=24.4

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .+.+.|.|-.+.|+-||+||||||+=|+
T Consensus        17 ~L~eeG~Sq~~iA~LLGltqaAVS~Yls   44 (119)
T COG2522          17 ELIEEGLSQYRIAKLLGLTQAAVSQYLS   44 (119)
T ss_pred             HHHHcCCcHHHHHHHhCCCHHHHHHHHc
Confidence            4566688999999999999999998775

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=94.97  E-value=0.039  Score=40.93  Aligned_cols=42  Identities=14%  Similarity=0.122  Sum_probs=33.2

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |--+.+++..+.+.+ .|++.-|+++|+|++|+.++|++||+.
T Consensus        13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~   55 (164)
T PRK11169         13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ   55 (164)
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            334566666665543 388999999999999999999999985

>PF02621 VitK2_biosynth: Menaquinone biosynthesis; InterPro: IPR003773 This entry describes proteins of unknown function, which appear to be putative periplasmic binding proteins

Probab=94.96  E-value=0.74  Score=36.82  Aligned_cols=183  Identities=13%  Similarity=0.127  Sum_probs=89.7

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCCceeec------cccc
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDKLISIP------CYQW  166 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~~~~~~------l~~~  166 (306)
                      +|||..+.+....   +.-.+ ...+...++++.....++.+.+.+|++|++.++...  ...+++...+      .+..
T Consensus         1 lrig~i~y~N~~P---l~~~l-~~~~~~~~~~~~~~P~~Ln~~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i~s~g~v   76 (251)
T PF02621_consen    1 LRIGRIPYLNDLP---LFYGL-IKGEPFDFEIVRGVPSELNQMLLEGELDVALISSIEYARNADDYLILPDLSISSDGPV   76 (251)
T ss_dssp             EEEEEESSHHHHH---HHHHH-HCTSSCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHCTCTTTEEEESCECEEECCSS
T ss_pred             CEEEecCCCCccc---eeehh-hcCCCCceEEEECCHHHHHHHHHcCCCCEEEcCHHHHHHhhhhheecCCcEEEEcCCc
Confidence            5788887654433   33333 333467788999999999999999999999987221  1223333332      1111


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc-cceeeeec
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR-MGIGIIAS  245 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~  245 (306)
                      .=+++.+ +        .+++++.+.+. ..+..+.....+.+.+-.....|..+..  . .....++.+| ++.-++-+
T Consensus        77 ~Sv~l~s-~--------~p~~~l~~~~i-al~~~S~TS~~Llrill~~~~~p~~~~~--~-~~~~~~~~~~~da~LlIGD  143 (251)
T PF02621_consen   77 YSVLLFS-K--------VPIEELDGKKI-ALTGESTTSVALLRILLEEFYKPEYVPM--P-DDIPPAMLAGADAALLIGD  143 (251)
T ss_dssp             SSEEEEE-S--------S-CCC-TTSEE-EESTTTSHHHHHHHHHHCCTT--EEEEE----CGHHHHHHTTSSEEEEECH
T ss_pred             cceEEEE-C--------CChHHcCCCeE-EcCCCCHHHHHHHHHHHHhccccceeec--C-chhhHHhhcCCCEEEEEch
Confidence            1122222 2        23344444444 4444445545555555444444443333  3 4555555555 45445544


Q ss_pred             ceecccccCCceeeecC-------CCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         246 IAFDSNRDKNLRSISAS-------HLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       246 ~~~~~~~~~~l~~~~~~-------~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      ........+......+.       +.+...-.| +.+++... ..+..+.+.+++...
T Consensus       144 ~Al~~~~~~~~~v~DLg~~W~~~tGlPfvfa~~-~vrk~~~~-~~~~~~~~~l~~s~~  199 (251)
T PF02621_consen  144 EALTYKSQGLPYVYDLGEEWYELTGLPFVFAVW-VVRKDLPE-EEIKELVQALRKSKQ  199 (251)
T ss_dssp             HHHHGGGGTTEEEEEHHHHHHHHHSS-EEEEEE-EEETTSHH-HHHHHHHHHHHHHHH
T ss_pred             HHcCCccCCCcEEEEHHHHHHHHHCCCceeEEE-EEecccCH-HHHHHHHHHHHHHHH
Confidence            43322123344555543       222222222 23555432 566677777766654

; PDB: 3A3U_A 2CZL_A 1ZBM_A 2NXO_C 2I6E_E.

>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region

Probab=94.96  E-value=1.9  Score=36.10  Aligned_cols=189  Identities=6%  Similarity=-0.042  Sum_probs=99.9

Q ss_pred             CcEEEEecccchhhhhHHHH----HHHHHhC--CCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC----CCCCce--
Q psy3760          93 GNLTIATTHTQARYALPKII----KEFTIQF--PKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS----PSDKLI--  159 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l----~~~~~~~--p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~----~~~~~~--  159 (306)
                      ..+|||++.+.+  +.|-.+    .-|.+.+  -++++++... +..+.++.+.+|++|++.......    ...+..  
T Consensus         2 ~~~~i~~~~w~G--~~p~~lA~~~G~fe~~l~~~Gl~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~~   79 (328)
T TIGR03427         2 DKFKVCWSIYAG--WMPWGYAAQQGIVDKWADKYGITIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAAGGVDTT   79 (328)
T ss_pred             CceEEEecCCcc--HHHHHHHHHcCchhhhHHHcCCeEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCeE
Confidence            469999998654  333333    2222111  2567777764 456778889999999986542110    122222  


Q ss_pred             eeccc---cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHH
Q psy3760         160 SIPCY---QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVE  235 (306)
Q Consensus       160 ~~~l~---~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~  235 (306)
                      ..-+.   .....+++++        .-+++||.+.+..... +......+...++..|+.+. +.+.--+...+..+..
T Consensus        80 iv~v~~~~~g~~~ivv~~--------i~svaDLKGKkIav~~-gs~~~~ll~~aL~~aGL~~~DV~~v~~~~~d~~aAl~  150 (328)
T TIGR03427        80 ALIVGDFSNGNDGIVLKG--------GKSLADLKGQKVNLVE-LSVSHYLLARALESVGLSEKDVKVVNTSDADIVAAFI  150 (328)
T ss_pred             EEEEEccCCCceEEEECC--------CCCHHHcCCCEEeccC-CChHHHHHHHHHHHcCCCHHHeEEEeCChHHHHHHHh
Confidence            11111   1123344432        3589999999887644 44445677889999999863 3333334466677788


Q ss_pred             hc--cceeeeecceeccc-ccCCceeeecCCCCcc-ceEEEEEeCC--ccccHHHHHHHHHHhH
Q psy3760         236 LR--MGIGIIASIAFDSN-RDKNLRSISASHLFGT-TISRVIIKQG--TYLRSYVYSFIKLLSP  293 (306)
Q Consensus       236 ~g--~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~-~~~~l~~~~~--~~~~~~~~~~~~~l~~  293 (306)
                      +|  ++++ +++...... ..++.+.+.-....+. ...+++.+.+  ...+..++.|++...+
T Consensus       151 ~G~VDAa~-~~eP~~s~~~~~~g~~~l~~~~~~~~~~~~~lv~~~~~l~~~pe~v~~~~~a~~k  213 (328)
T TIGR03427       151 TKDVTAVV-TWNPQLSEIKAQPGANEVFDSSQIPGEILDLMVVNTQTLKANPNLGKALTGAWYE  213 (328)
T ss_pred             cCCCcEEE-EcCchHHHHHhCCCcEEecccccCCCcceEEEEECHHHHHHCHHHHHHHHHHHHH
Confidence            77  4443 444333222 3344444422221221 1223343332  1134567777665544

Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=94.91  E-value=0.029  Score=32.53  Aligned_cols=25  Identities=32%  Similarity=0.287  Sum_probs=22.6

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      +-. |+++||+.|++++++|++.++.
T Consensus        16 ~f~-S~~eAa~~lg~~~~~I~~~~~~   40 (53)
T smart00497       16 EFS-SIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             Eec-CHHHHHHHhCCCHHHHHHHHhC
Confidence            446 9999999999999999999886

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]

Probab=94.86  E-value=0.056  Score=46.90  Aligned_cols=44  Identities=23%  Similarity=0.360  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      .++++.+-.+++.++++||++|+|=+-|+-++|+++|+.+|..|
T Consensus       355 Ll~TL~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~dL  398 (421)
T COG2508         355 LLETLRAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGIDL  398 (421)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHhcccHHHHHHHHHHHHHHhCCCC
Confidence            45555555555559999999999999999999999999999988

>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]

Probab=94.86  E-value=1.7  Score=35.03  Aligned_cols=189  Identities=11%  Similarity=0.053  Sum_probs=109.4

Q ss_pred             hhHHHHHHHHHhCCCc-EEEEEeCChhHHHHHHHcCCeeEEEEccccCC----CCCceeeccccceEEEEecCCCCCCCC
Q psy3760         107 ALPKIIKEFTIQFPKV-KLSLLQGNPKQITEMIRNDQADIAIVTEILSP----SDKLISIPCYQWEYVIIVPLDHPLLLL  181 (306)
Q Consensus       107 ~l~~~l~~~~~~~p~~-~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~----~~~~~~~~l~~~~~~~v~~~~~~l~~~  181 (306)
                      +-..+...+.+..... .+.+.....+.++..+.+|++|+++......+    .-.+ +.|.+.....+++.++.+..  
T Consensus        61 ~dvdl~~~ia~~l~~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~er~~~~~f-s~py~~~~~~~~~~~~~~~~--  137 (275)
T COG0834          61 FDVDLAKAIAKRLGGDKKVEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKVDF-SDPYYYSGQVLLVKKDSDIG--  137 (275)
T ss_pred             eeHHHHHHHHHHhCCcceeEEeccchhhhhHHHhcCCcCEEEeccccCHHHhccccc-cccccccCeEEEEECCCCcC--
Confidence            3455666666665544 47777778889999999999999998622222    2234 78888889999998876532  


Q ss_pred             CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce-ecc--c--ccCCc
Q psy3760         182 NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA-FDS--N--RDKNL  256 (306)
Q Consensus       182 ~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~--~--~~~~l  256 (306)
                       .-+.+||.+..........   .....+..... ........++...+..++.+|..=+++-+.. ...  .  .....
T Consensus       138 -~~~~~DL~gk~v~v~~gt~---~~~~~~~~~~~-~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~  212 (275)
T COG0834         138 -IKSLEDLKGKKVGVQLGTT---DEAEEKAKKPG-PNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGL  212 (275)
T ss_pred             -cCCHHHhCCCEEEEEcCcc---hhHHHHHhhcc-CCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCC
Confidence             3478999996666655433   22333333332 2234567788889999999996666654432 222  1  12222


Q ss_pred             eeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         257 RSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       257 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .............+.+..+++. .......+-..+.+..+....+++.
T Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~in~~l~~l~~~G~~~~i~  259 (275)
T COG0834         213 YVLLVFPGLSVEYLGIALRKGD-DPELLEAVNKALKELKADGTLQKIS  259 (275)
T ss_pred             ceeeeccCCCcceeEEEeccCC-cHHHHHHHHHHHHHHHhCccHHHHH
Confidence            2222211111135555666662 2334444444444444444444443

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

Probab=94.84  E-value=0.035  Score=28.21  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=20.6

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          20 TEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        20 ~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..-|..+|.|.-++||.+++||++
T Consensus         6 ~diA~~lG~t~ETVSR~l~~l~~~   29 (32)
T PF00325_consen    6 QDIADYLGLTRETVSRILKKLERQ   29 (32)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHc
Confidence            466899999999999999999974

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 ....

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=94.81  E-value=0.55  Score=32.79  Aligned_cols=38  Identities=8%  Similarity=0.062  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++....+.+.|.|+..+|++++||.+++.+.+++.++.
T Consensus        19 ~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~   56 (121)
T PRK09413         19 IAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEG   56 (121)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence            34455556667799999999999999999999999764

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=94.79  E-value=0.35  Score=38.67  Aligned_cols=36  Identities=17%  Similarity=0.287  Sum_probs=31.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      +....|+.+++|..|+.|-|+.||++   -+..|..+|.
T Consensus        21 ~~~ela~~l~vS~~TiRRdL~~Le~~---g~l~r~~GGa   56 (252)
T PRK10906         21 STEELVEHFSVSPQTIRRDLNDLAEQ---NKILRHHGGA   56 (252)
T ss_pred             eHHHHHHHhCCCHHHHHHHHHHHHHC---CCEEEecCCE
Confidence            67899999999999999999999995   4568887886

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

Probab=94.79  E-value=0.087  Score=34.97  Aligned_cols=42  Identities=26%  Similarity=0.249  Sum_probs=33.7

Q ss_pred             chhhHHHHHHHHH---------hcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR---------QNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~---------~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +-++.++++.+++         ...|-+.-|+.+|+|++++||.|++||+.
T Consensus        24 ~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~   74 (95)
T TIGR01610        24 SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR   74 (95)
T ss_pred             CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4467788888774         12356778999999999999999999985

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

>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=94.71  E-value=0.07  Score=30.84  Aligned_cols=40  Identities=25%  Similarity=0.302  Sum_probs=31.4

Q ss_pred             hhHHHHHHHHHhcC--CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNF--NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~--s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +-+.++-.+++.+.  +++.-|+.++++.|++.|.++.|++.
T Consensus         4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~   45 (52)
T PF09339_consen    4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE   45 (52)
T ss_dssp             HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34566666666662  49999999999999999999999874

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=94.62  E-value=0.067  Score=30.77  Aligned_cols=37  Identities=22%  Similarity=0.272  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      .+...-|+.+++|++++++.|+.|++.   .++.+..+|+
T Consensus        15 ~s~~~l~~~l~~s~~tv~~~l~~L~~~---g~i~~~~~~~   51 (53)
T smart00420       15 VSVEELAELLGVSEMTIRRDLNKLEEQ---GLLTRVHGGA   51 (53)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEeecCc
Confidence            478888999999999999999999986   3455555553

>TIGR01254 sfuA ABC transporter periplasmic binding protein, thiB subfamily

Probab=94.49  E-value=2.3  Score=35.05  Aligned_cols=197  Identities=15%  Similarity=0.036  Sum_probs=105.0

Q ss_pred             CcEEEEecccch--hhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHc----CCeeEEEEcccc--------C---C
Q psy3760          93 GNLTIATTHTQA--RYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRN----DQADIAIVTEIL--------S---P  154 (306)
Q Consensus        93 ~~l~I~~~~~~~--~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~----~~~Di~i~~~~~--------~---~  154 (306)
                      ++|+|.+-.+..  ...+..+...|.+ ++++++++...+ ..++++.+..    +.+|+.+.....        .   +
T Consensus         2 ~~l~v~~~~~~~~~~~~~~~i~~~Fe~-~~gi~V~~~~~~~~~~~~~~l~~~~~~~~~Dv~~~~~~~~~~~~~~~gll~~   80 (304)
T TIGR01254         2 PVVTVYTYDSFAADWGLGPVVEKAFEA-DCNCKVKFVALEDAGELLNRLRLEGKNPKADVVLGLDNNLLEAASKTGLLAP   80 (304)
T ss_pred             CEEEEEEcccccCcccchHHHHHHHhh-hcCcEEEEEECCCHHHHHHHHHhcCCCCCCCEEEEeCHHHHHHHHHcCCccc
Confidence            578999866633  3477788888987 689999998875 4678788764    468999852110        0   0


Q ss_pred             -CCCc------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCC-Cc-HHHHH-------
Q psy3760         155 -SDKL------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSF-SG-RIKLD-------  208 (306)
Q Consensus       155 -~~~~------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~-~~-~~~~~-------  208 (306)
                       .+..            ...++.-..++++.+++..  ...+-+++||.+-.    ..+..+.. .. ...+.       
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~i~yn~~~~--~~~P~sw~dL~~~~~~g~i~~~~p~~~~~~~~~~~~~~~~~g  158 (304)
T TIGR01254        81 SGVALDKVNVPGGWNNATFLPFDYGYVAFVYDKNKL--QNPPQSLKELVEPEQDLLVIYQDPRTSSPGLGLLLWMQSVYG  158 (304)
T ss_pred             CCccccccccccccCCCeEEEEeeeeEEEEEchHHh--cCCCCCHHHHhCHHhcCcEEecCCCCChhHHHHHHHHHHhcC
Confidence             0000            1134444566777777643  22356899986532    22222211 11 11111       


Q ss_pred             -----HHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeec--ceeccc--ccCCceeeecCCCCccceEEEEEeCCc
Q psy3760         209 -----REFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIAS--IAFDSN--RDKNLRSISASHLFGTTISRVIIKQGT  278 (306)
Q Consensus       209 -----~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~--~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~  278 (306)
                           ++++...  .+......+......++.+|. .+++.-.  ......  ....+..+.+++........+...++.
T Consensus       159 ~~~~~~~~~~L~--~~~~~~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ai~k~a  236 (304)
T TIGR01254       159 EDDAPQAWKQLR--KKTVTVTKGWSEAYGTFLGGEYDLVLSYATSPAYHVLFEKKDNYAALNFSEGHYLQVEGAARLKGA  236 (304)
T ss_pred             hHHHHHHHHHHH--hCCeecCCCCHHHHHHHhcCCccEEEEeccchhhhhhhccCCceeEEecCCCCEEEEEEEEEECCC
Confidence                 2222111  111112233345567788884 3444322  111111  123455445444322223355556777


Q ss_pred             cccHHHHHHHHHHhHH
Q psy3760         279 YLRSYVYSFIKLLSPK  294 (306)
Q Consensus       279 ~~~~~~~~~~~~l~~~  294 (306)
                      .....+++|++++.+.
T Consensus       237 ~n~e~A~~fi~fllsp  252 (304)
T TIGR01254       237 KQPELADKFVQFLLSP  252 (304)
T ss_pred             CCHHHHHHHHHHHcCH
Confidence            7889999999998544

The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP).

>PRK00118 putative DNA-binding protein; Validated

Probab=94.38  E-value=0.15  Score=34.20  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=33.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS   45 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg   45 (306)
                      ++-++|......|.|++..|+.+|+|.+|+.+++.+....+.
T Consensus        21 kqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr   62 (104)
T PRK00118         21 KQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE   62 (104)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            445566665666679999999999999999999987776663

>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]

Probab=94.25  E-value=1.9  Score=34.98  Aligned_cols=210  Identities=11%  Similarity=0.126  Sum_probs=128.5

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe--CChhHHHHHHHcCCeeEEEEc--------cccCC----C
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ--GNPKQITEMIRNDQADIAIVT--------EILSP----S  155 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~--~~~~~~~~~l~~~~~Di~i~~--------~~~~~----~  155 (306)
                      ....+|+||.-..-...++..++..+.+.+ ++.+....  +++.-....|.+|++|+-.-+        ....+    +
T Consensus        30 ~~~~~I~VgsK~~tE~~IL~~m~~~lle~~-~~kv~~~~~lG~t~v~~~Al~~G~IDiYpEYTGt~~~~~lk~~~~~~~d  108 (300)
T COG1732          30 SAAKTIVVGSKIFTEQYILGNILKQLLEKN-GIKVEDKTGLGGTAVVRNALKSGDIDIYPEYTGTALFSFLKKDPPASKD  108 (300)
T ss_pred             ccCCCEEEecCCCcHHHHHHHHHHHHHHhc-CCceeeccCCCchHHHHHHHHcCCCCeEeeecchhhhhhcccCccccCC
Confidence            457799999999889999999999999998 88777766  355567899999999998643        11000    0


Q ss_pred             C---------------Cceeecc--ccceEEEEecCCCCCCCCCCcChhhhcCCCe-EeecCCCCc---HHHHHHHHHhC
Q psy3760         156 D---------------KLISIPC--YQWEYVIIVPLDHPLLLLNSISLKEISNYPL-ITYDLSFSG---RIKLDREFSLQ  214 (306)
Q Consensus       156 ~---------------~~~~~~l--~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~-i~~~~~~~~---~~~~~~~~~~~  214 (306)
                      +               .+.+..-  +...+.+.++++.... ..--++.||..+.= +....+..+   .+.+...-+..
T Consensus       109 p~~~y~~vK~~~~k~~~l~wl~p~~~nNTyA~av~~~~A~~-~~i~TiSDLak~~~~l~~g~~~eF~~R~DG~~~l~k~Y  187 (300)
T COG1732         109 PKKVYETVKKLDAKQFKLVWLKPAGFNNTYALAVRKDVAEK-YNLETISDLAKHSNQLKLGADSEFAERADGLPALQKAY  187 (300)
T ss_pred             HHHHHHHHHHHHHhcCCEEEecccCCCcceEEEecHHHHHH-hCCccHHHHHHhhhhceecCChhhhccccccHHHHHHh
Confidence            0               1221111  2345666666664211 22347888876532 222222222   13344455566


Q ss_pred             CCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCC-CCccceEEEEEeCC-ccccHHHHHHHHHH
Q psy3760         215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASH-LFGTTISRVIIKQG-TYLRSYVYSFIKLL  291 (306)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~-~~~~~~~~l~~~~~-~~~~~~~~~~~~~l  291 (306)
                      |+.++..+..-+.....+++.+|. +-...-+..+.. ...+|+++.-+- ..|.+....+.+.+ ....|.++..++-+
T Consensus       188 g~~~~~~~~~m~~gl~y~Al~~g~-~d~~~~YsTDg~I~~~~L~VLkDDK~~fP~Y~~apvvre~vlk~~Pel~~~l~~l  266 (300)
T COG1732         188 GFDFKPDLRTMDGGLTYQALKNGT-VDAADAYSTDGRIAAYGLKVLKDDKGFFPPYQAAPVVREEVLKKHPELKTILNKL  266 (300)
T ss_pred             CCccCCCceecCchHHHHHHHcCC-CCeEeeccccccccccCcEEEecCCcCCCCCcccceecHHHHhHCHHHHHHHHHH
Confidence            777665244445558899999985 222333333322 456788887664 34455555565554 33467888888888


Q ss_pred             hHHhhHHHHHh
Q psy3760         292 SPKLNRKFINK  302 (306)
Q Consensus       292 ~~~~~~~~~~~  302 (306)
                      ...+.....+.
T Consensus       267 ~~kid~~tMq~  277 (300)
T COG1732         267 SGKIDTETMQA  277 (300)
T ss_pred             hccCCHHHHHH
Confidence            77776666554

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=94.23  E-value=0.2  Score=28.59  Aligned_cols=37  Identities=19%  Similarity=0.160  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      -+++....-.+.|+...|+.+|+|.+++++..++-=+
T Consensus        10 r~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~   46 (50)
T PF04545_consen   10 REVIRLRYFEGLTLEEIAERLGISRSTVRRILKRALK   46 (50)
T ss_dssp             HHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            3444444444459999999999999999998876543

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed

Probab=94.17  E-value=1.7  Score=33.62  Aligned_cols=159  Identities=11%  Similarity=0.101  Sum_probs=91.0

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-----CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-----KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-----~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++.-.-..++...+..|.+|+||+..+.....     .+.-..++.-++++.+|++.+...     ..+.....-|.. 
T Consensus        47 i~~~~~r~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~-----~~~~~~~~rIAT-  120 (215)
T PRK01686         47 VRFLLVRATDVPTYVEHGAADLGIVGKDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAP-----AVKQGPRLRVAT-  120 (215)
T ss_pred             EEEEEECHHHHHHHHhCCCccEEEeeeeEeeecCCCeEEEecCCccCEEEEEEEECcccccc-----hhhccCCCEEEe-
Confidence            444444567899999999999999853222111     122344567789999998876321     112111122222 


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCC
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                         .+.+...++|...|+...++....+.+.+   ..-|.+=+++.-... ..++..+|+.+.   .....+..++.++.
T Consensus       121 ---kYp~it~~yf~~~gv~~~iv~l~GsvE~a---P~~GlAD~IvDivsTG~TLr~NgL~~ie---~Il~s~A~LI~n~~  191 (215)
T PRK01686        121 ---KYPNIARRYFAEKGEQVEIIKLYGSVELA---PLVGLADAIVDIVETGNTLRANGLVEVE---EIMDISARLIVNRA  191 (215)
T ss_pred             ---CCHHHHHHHHHHcCCeEEEEECcCceeec---cccCCccEEEEeecChHHHHHCcCEEee---EEEeeEEEEEEecc
Confidence               23467788999999876655444555442   222322222221111 112456777775   24456778888776


Q ss_pred             cc--ccHHHHHHHHHHhHHhhH
Q psy3760         278 TY--LRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       278 ~~--~~~~~~~~~~~l~~~~~~  297 (306)
                      ..  ..+.++.+++.+++.+..
T Consensus       192 s~~~k~~~i~~l~~~l~~~~~a  213 (215)
T PRK01686        192 SLKLKREEIRPLIEKLREAVES  213 (215)
T ss_pred             cchhhHHHHHHHHHHHHHHHhc
Confidence            43  346788888888776543

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=94.16  E-value=0.16  Score=37.42  Aligned_cols=45  Identities=13%  Similarity=0.166  Sum_probs=40.9

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      ++-+..++|.-+++-. |...-|+.|++|..||...++++=+.||+
T Consensus       134 LSpRErEVLrLLAqGk-TnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        134 FSVTERHLLKLIASGY-HLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            3557788999999877 99999999999999999999999999987

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=94.13  E-value=0.31  Score=34.61  Aligned_cols=77  Identities=17%  Similarity=0.164  Sum_probs=51.7

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc-----eeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI-----DIFIRHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~-----~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +-++.+++....+. .|..+.|+.||+|++++++..++.-+.|..     .|.....-.+.-.-+.|..++.-...++..
T Consensus         8 te~qr~VL~Lr~~G-lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~~a~~~~~~~~g~~~~~~~~~v~~~   86 (137)
T TIGR00721         8 TERQIKVLELREKG-LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFIKSPVRILCRRGDDLDEIPKRLFKK   86 (137)
T ss_pred             CHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHhcCCEEEEecCCCcHHHhHHHHHHH
Confidence            34566666665554 499999999999999999777776666653     233322323212557778888877777776


Q ss_pred             HHH
Q psy3760          77 IEG   79 (306)
Q Consensus        77 ~~~   79 (306)
                      .++
T Consensus        87 ~d~   89 (137)
T TIGR00721        87 ADE   89 (137)
T ss_pred             HhH
Confidence            554

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

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.09  E-value=0.08  Score=30.96  Aligned_cols=26  Identities=42%  Similarity=0.405  Sum_probs=24.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |...-|+.+|+|..||.+.|++||+.
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~   52 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEK   52 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            78999999999999999999999973

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=94.08  E-value=0.29  Score=33.87  Aligned_cols=56  Identities=14%  Similarity=0.245  Sum_probs=44.6

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      +.++.+-.+++++ .|++++|+..+--.+.+++-++.|+ .+|+--|+++++.. .|+-
T Consensus        65 ~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~-~~GlI~fe~~gq~k-~P~~  121 (144)
T COG4190          65 RNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA-DLGLIFFEEDGQRK-QPVV  121 (144)
T ss_pred             hHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH-hcCeEEEecCCccc-Ccee
Confidence            4556666665542 3999999999999999999999997 48999999987665 5653

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=94.07  E-value=0.17  Score=29.40  Aligned_cols=40  Identities=18%  Similarity=0.120  Sum_probs=28.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++=++|.-..-.|.|+.+.|+.+|+|.+++-+++.+--+.
T Consensus        14 ~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   14 RQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             HHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            3445566666677799999999999999999999875543

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>smart00351 PAX Paired Box domain

Probab=94.06  E-value=0.17  Score=35.55  Aligned_cols=35  Identities=20%  Similarity=0.193  Sum_probs=29.1

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++.+++.|.|..++|+.+++|.+++++.+++..++
T Consensus        26 iv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~   60 (125)
T smart00351       26 IVELAQNGVRPCDISRQLCVSHGCVSKILGRYYET   60 (125)
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            34444556699999999999999999999998764

>PRK05638 threonine synthase; Validated

Probab=94.05  E-value=0.13  Score=44.86  Aligned_cols=63  Identities=27%  Similarity=0.330  Sum_probs=45.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhC--CCchHHHHHHHHHHHHcCceeEE---ecCCC-ccccCHhHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALY--TSQPGVSKAIIELEEELSIDIFI---RHGKR-IRGLTKPGQAILRSI   70 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~--isq~~~s~~i~~LE~~lg~~Lf~---R~~~~-~~~lT~~G~~l~~~a   70 (306)
                      .+.++..+.+...+...-++.++  +|+++++++|++||+. |  |..   +.++. ..+||+.|+.++...
T Consensus       373 r~~IL~~L~~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~-G--LV~~~~~~g~~~~Y~Lt~~g~~~l~~~  441 (442)
T PRK05638        373 KLEILKILSEREMYGYEIWKALGKPLKYQAVYQHIKELEEL-G--LIEEAYRKGRRVYYKLTEKGRRLLENL  441 (442)
T ss_pred             HHHHHHHHhhCCccHHHHHHHHcccCCcchHHHHHHHHHHC-C--CEEEeecCCCcEEEEECcHHHHHHHhc
Confidence            34555555554447899999998  9999999999999976 2  332   22333 238999999988753

>TIGR03227 PhnS 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein

Probab=94.03  E-value=3.4  Score=35.20  Aligned_cols=200  Identities=10%  Similarity=0.058  Sum_probs=106.6

Q ss_pred             CCcEEEEecccchh---hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH----cCCeeEEEEccccC-----------
Q psy3760          92 TGNLTIATTHTQAR---YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR----NDQADIAIVTEILS-----------  153 (306)
Q Consensus        92 ~~~l~I~~~~~~~~---~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~----~~~~Di~i~~~~~~-----------  153 (306)
                      .+.|+|.+..++..   .++..++..|.++ +++++++...++.++...+.    ++.+|+++......           
T Consensus        35 ~~~L~Vy~~~g~~~~~~~~~~~i~~~Fe~~-~Gi~V~~~~~~s~~~~~rl~~e~~~~~~DVv~~~~~~~~~~~~~Gll~~  113 (367)
T TIGR03227        35 AAVVLVYSADGLEDGDNSLYQDQFDAFEKA-EGIKVNIVEAGGGEVVERAAKEKGNPKADVIVTAPPFIQQAAAEGLLAN  113 (367)
T ss_pred             CCeEEEEecCcccccchHHHHHHHHHHHHH-HCCEEEEEeCChHHHHHHHHhhccCCCCCEEEeCcHHHHHHHHCCCccC
Confidence            46799999877653   5788899999988 49999999988888777665    35799988631100           


Q ss_pred             -CCCCc------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCC-CCc-HHHHHHHHHhC
Q psy3760         154 -PSDKL------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLS-FSG-RIKLDREFSLQ  214 (306)
Q Consensus       154 -~~~~~------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~-~~~-~~~~~~~~~~~  214 (306)
                       +.+..            .+.++....++++..++..  ...+-+|+||.+-.    +...++. ... ...+.......
T Consensus       114 ~~~~~~~~~~~~~~~~~g~~~p~~~~~~~i~YN~d~~--~~~P~sw~DL~~p~~~Gki~~~~p~~s~~~~~~l~~~~~~~  191 (367)
T TIGR03227       114 FNSDAAKAIPAIAKAADGLWAPFVKNYFSFAINPKLL--KSAPASFADLLDADFKGKLAYSNPAQAADGMAVIILAFALF  191 (367)
T ss_pred             CCCcccccCchhhcCCCCeEEEEeeceeEEEEchhhc--CCCCCCHHHHhChhccCCEeecCCCcCccHHHHHHHHHHHc
Confidence             00110            1123333344666666642  23467899997632    2222221 111 11111111111


Q ss_pred             C-----------CceeEEEEecCHHHHHHHHHhccce-eeeecce-eccc-ccC-Cceee-ecCCC-----CccceEEEE
Q psy3760         215 K-----------LTPYIVLETINSDIIKTYVELRMGI-GIIASIA-FDSN-RDK-NLRSI-SASHL-----FGTTISRVI  273 (306)
Q Consensus       215 ~-----------~~~~~~~~~~~~~~~~~~v~~g~gi-~~~p~~~-~~~~-~~~-~l~~~-~~~~~-----~~~~~~~l~  273 (306)
                      |           +.++.....++......++.+|... +..+... .... ..+ .+..+ |-+..     .......+.
T Consensus       192 G~~d~a~~~l~~l~~n~~~~~~~~~~~~~~~~~Gev~i~~g~~~~~~~~~~~~g~~i~~~~P~~g~g~~~~~~~~~~~~~  271 (367)
T TIGR03227       192 GSEDAAFAYLAKLEANNKFHSAGTGKLNALLNKGEIAVANGDLQMDLADAEHGGLNIKIFFPAADAGEPPSAFAIPYAIG  271 (367)
T ss_pred             CCchHHHHHHHHHHhcCCccCCCchhHHHHHhcCceEEEccHHHHHHHHHHhcCCCeEEEeecCCCCCCCcccccceeEE
Confidence            1           1234433344555666777777533 2111111 1111 112 34433 22110     112233455


Q ss_pred             EeCCccccHHHHHHHHHHhHH
Q psy3760         274 IKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       274 ~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..++.+.....++|++++.+.
T Consensus       272 I~k~a~n~e~A~~Fidfllsp  292 (367)
T TIGR03227       272 LVKGAPNQDAGKKLIDFLLSA  292 (367)
T ss_pred             EecCCCCHHHHHHHHHHHcCH
Confidence            567777889999999998654

This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to pfam01547 for the "Bacterial extracellular solute-binding protein" domain.

>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []

Probab=94.01  E-value=2.2  Score=32.97  Aligned_cols=175  Identities=14%  Similarity=0.116  Sum_probs=86.0

Q ss_pred             cEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeCC--------------------hhHHHHHHHcCCeeEEEEcccc
Q psy3760          94 NLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQGN--------------------PKQITEMIRNDQADIAIVTEIL  152 (306)
Q Consensus        94 ~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~~--------------------~~~~~~~l~~~~~Di~i~~~~~  152 (306)
                      .|+||+-.+ ++..-...+...+.+.+|++++++....                    ..++.+.|.+|++|+++.+...
T Consensus         1 ~irIGtR~S~LAl~Qa~~V~~~L~~~~P~~~~ei~~i~T~GD~~~~~~L~~~ggkg~Ftkele~aLl~g~iDiAVHSlKD   80 (215)
T PF01379_consen    1 KIRIGTRGSKLALAQAEMVIDRLKKAFPDLEFEIVTIKTTGDRDLDRPLSKIGGKGLFTKELEEALLDGEIDIAVHSLKD   80 (215)
T ss_dssp             -EEEEEESSHHHHHHHHHHHHHHHHHSTTSEEEEEEE--CCHH--------TT--HCCCHHHHHHHHTTS-SEEEEEGGG
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHHhCCCceEEEEEccCCCCcccccchhhcCCccHHHHHHHHHHHcCCccEEEecccc
Confidence            478998665 4444556666888889999999886521                    4578899999999999987432


Q ss_pred             C---CCCCcee--eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760         153 S---PSDKLIS--IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS  227 (306)
Q Consensus       153 ~---~~~~~~~--~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (306)
                      -   .++++..  .+=..++.-+++.+++     ...++++|.....|..+   +.+.  ...+.......++.-.-.|+
T Consensus        81 lP~~l~~gl~iaav~~R~dprD~Lv~~~~-----~~~~l~~Lp~ga~IGTs---S~RR--~aql~~~~pdl~~~~iRGNv  150 (215)
T PF01379_consen   81 LPTELPEGLVIAAVLKREDPRDVLVSRGR-----DGKSLEDLPKGARIGTS---SLRR--RAQLKRLRPDLEVVPIRGNV  150 (215)
T ss_dssp             S-SS--TTEEEEEE-------EEEEE-GC-----TTSSCCCS-TT-EEE------HHH--HHHHHHH-TTSEEE---S-H
T ss_pred             CCCCCCCCceEeccCCCCCCccEEEEecC-----CCCChHHCccccccCCC---CHHH--HHHHHHhccCCeEEEecCCH
Confidence            2   2344432  2222233333333221     12356666555555443   2332  22222233345666667899


Q ss_pred             HHHHHHHHhccceee-eecceeccc-ccCCce-eeecCC---CCccceEEEEEeCCc
Q psy3760         228 DIIKTYVELRMGIGI-IASIAFDSN-RDKNLR-SISASH---LFGTTISRVIIKQGT  278 (306)
Q Consensus       228 ~~~~~~v~~g~gi~~-~p~~~~~~~-~~~~l~-~~~~~~---~~~~~~~~l~~~~~~  278 (306)
                      ++-+.-+..|..=++ +..--.... ....+. .++.+.   .+-+.-+.+-++++.
T Consensus       151 ~TRL~KL~~g~~daiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d  207 (215)
T PF01379_consen  151 DTRLRKLDEGEYDAIILAAAGLKRLGLEDRISEILDPEEMLPAPGQGALAVECRKDD  207 (215)
T ss_dssp             HHHHHHHHCTS-SEEEEEHHHHHHCT-GGGESEEE-TTTS-B-TTTT-EEEEEETT-
T ss_pred             HHHHHHhcccCCCEEEhhhChhhhccccceeeeecCchhcCCCCCCeEEEEEEecCc
Confidence            999999998843333 333222222 222222 244443   122567777777763

The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=93.96  E-value=0.08  Score=32.45  Aligned_cols=21  Identities=19%  Similarity=-0.015  Sum_probs=19.8

Q ss_pred             hcCCHHHHHHHhCCCchHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      -| |.++.|+.||||++|||+.
T Consensus        10 FG-s~~kvA~aLGIs~~AVsQW   30 (75)
T PRK09744         10 FG-SKTKLANAAGVRLASVAAW   30 (75)
T ss_pred             hC-cHHHHHHHHCCCHHHHHHH
Confidence            48 9999999999999999987

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=93.96  E-value=0.12  Score=30.79  Aligned_cols=50  Identities=26%  Similarity=0.230  Sum_probs=37.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR   55 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~   55 (306)
                      +-|.++.. -+.= ++...|+.+|+|..++-+-|.+|.+.|+..+.....+|
T Consensus         9 ~Ll~~L~~-~~~~-~~~ela~~l~~S~rti~~~i~~L~~~f~~~~~i~~~k~   58 (59)
T PF08280_consen    9 KLLELLLK-NKWI-TLKELAKKLNISERTIKNDINELNEFFPENISITIQKG   58 (59)
T ss_dssp             HHHHHHHH-HTSB-BHHHHHHHCTS-HHHHHHHHHHHHTT--TCCCCEEECT
T ss_pred             HHHHHHHc-CCCC-cHHHHHHHHCCCHHHHHHHHHHHHHHhhhhceeeeecC
Confidence            34555666 4454 89999999999999999999999999988877665444

; PDB: 2WTE_A 3SQN_A.

>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2

Probab=93.80  E-value=1.8  Score=31.86  Aligned_cols=149  Identities=16%  Similarity=0.213  Sum_probs=89.9

Q ss_pred             hhHHHHHHHcCCeeEEEEccccC--------CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCC
Q psy3760         131 PKQITEMIRNDQADIAIVTEILS--------PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFS  202 (306)
Q Consensus       131 ~~~~~~~l~~~~~Di~i~~~~~~--------~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~  202 (306)
                      ..++...+..|.+|+||+.....        +-..+.-..++.-++++.+|.+.+.     -+++++....-|..    .
T Consensus         3 ~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~v~~~~dL~fg~crl~vAvp~~~~~-----~~~~~l~~~~rIAT----k   73 (163)
T PF01634_consen    3 PQDIPTYVEDGIADLGITGKDVLLESGLGRADVEELLDLGFGKCRLVVAVPEDWPY-----KSVEDLKAGLRIAT----K   73 (163)
T ss_dssp             GGHHHHHHHTTSSSEEEEEHHHHHHHTHH-SSEEEEEEESCSEEEEEEEEETTSCG-----CCGGGGSSTEEEEE----S
T ss_pred             hHHHHHHHHCCCCcEEEeehheeccCCCCccceEEEeecccccEEEEEEEECCcCC-----CCHHHhccCCEEEE----C
Confidence            45778899999999999852111        1122345566778899999988762     35667764333332    3


Q ss_pred             cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCCcc--
Q psy3760         203 GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQGTY--  279 (306)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~--  279 (306)
                      +.+...++|.+.|+...++....+.+..   ...|.+=+++---.. ..++..+|+.+   +.....+..|+.++...  
T Consensus        74 yp~l~~~yf~~~g~~~~ii~l~GsvE~a---p~~glAD~IvDiv~TG~TLr~NgL~~i---~~i~~s~a~LI~n~~~~~~  147 (163)
T PF01634_consen   74 YPNLTRRYFAEKGINVEIIKLSGSVELA---PPLGLADAIVDIVETGTTLRANGLKEI---ETILESSARLIANKASLKE  147 (163)
T ss_dssp             -HHHHHHHHHHCT-EEEEEE-SS-TTHH---HHTTSSSEEEEEESSSHHHHHTTEEEE---EEEEEEEEEEEEEHHHHHH
T ss_pred             CHHHHHHHHHHcCCcEEEEEccCCcccc---CCCCCCCEEEEeccCcHHHHHCCCEEe---EEEEEEEEEEEEcCccchh
Confidence            4567789999999887777666666655   445533344332111 11245677777   33445678888877653  


Q ss_pred             ccHHHHHHHHHHhHH
Q psy3760         280 LRSYVYSFIKLLSPK  294 (306)
Q Consensus       280 ~~~~~~~~~~~l~~~  294 (306)
                      ..+.++.+++.|+..
T Consensus       148 k~~~i~~l~~~l~~v  162 (163)
T PF01634_consen  148 KEEKIDELVTRLRGV  162 (163)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhh
Confidence            344566666666553

4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.78  E-value=1.2  Score=35.28  Aligned_cols=36  Identities=19%  Similarity=0.291  Sum_probs=28.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      +....|+.|++|+.|+.|-|++||+.   .+..|..+|.
T Consensus        20 ~~~eLa~~l~VS~~TiRRdL~~L~~~---~~l~r~~Gga   55 (240)
T PRK10411         20 TTEALAEQLNVSKETIRRDLNELQTQ---GKILRNHGRA   55 (240)
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEecCeE
Confidence            66788999999999999999999994   2345665554

>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]

Probab=93.77  E-value=2.7  Score=34.01  Aligned_cols=162  Identities=14%  Similarity=0.164  Sum_probs=100.7

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC--------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeE
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD--------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLI  195 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~--------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i  195 (306)
                      +++.-....++..-+..|.+|+||+....-...        .+.-..++.-++++.+|++.+     ..+.+++.+-.-|
T Consensus        45 I~~~~vR~~DIP~yV~~G~~DlGItG~D~l~E~~~~~~~v~~l~dL~fG~crl~vAvp~~~~-----~~~~~~l~~~~rI  119 (290)
T COG0040          45 IELLLVRAQDIPTYVEDGVADLGITGEDVLRESGLDDASVEELLDLGFGGCRLVVAVPEESD-----YTSPEDLKGRLRI  119 (290)
T ss_pred             eEEEEEChHHhhHHHhcCceeeeeechhhhhhcccCccCceehccCCCCcEEEEEEecCCcC-----ccChhHhcCCceE
Confidence            455555567899999999999999953322222        233556778899999999875     2345555433233


Q ss_pred             eecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEE
Q psy3760         196 TYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVII  274 (306)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~  274 (306)
                      ..    .+.+...++|+..|....++.-..+.+.+   ...|.+=+++.-... ..++..+|+.+.   .....+-+++.
T Consensus       120 AT----kYp~l~~~yf~~~g~~~~Ii~l~GsvE~a---P~~GlADaIvDivsTG~TLkaNgL~~id---~i~~ssa~LI~  189 (290)
T COG0040         120 AT----KYPNLARKYFAEKGIDVEIIKLSGSVELA---PALGLADAIVDIVSTGTTLKANGLKEIE---VIYDSSARLIV  189 (290)
T ss_pred             EE----ccHHHHHHHHHHcCceEEEEEccCcEeec---cccCccceEEEeecCCHhHHHCCCEEEE---EEEeeEEEEEe
Confidence            32    24567788999999988777666665543   344544444433221 122456677762   23455777777


Q ss_pred             e-C--CccccHHHHHHHHHHhHHhhHHHH
Q psy3760         275 K-Q--GTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       275 ~-~--~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      + +  .+...+.++.++..++..++.+..
T Consensus       190 n~~~~~~~k~~~i~~l~~rl~gvi~a~~~  218 (290)
T COG0040         190 NAKASLKDKQELIDQLVTRLKGVIEARGS  218 (290)
T ss_pred             ccccccchhHHHHHHHHHHHHHHHhhcce
Confidence            7 2  223345688888888887766544

>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional

Probab=93.60  E-value=0.15  Score=43.73  Aligned_cols=42  Identities=19%  Similarity=0.280  Sum_probs=37.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      +++.+-.++++|+++||++|++-+-|+.++|+++|+.+|..+
T Consensus       325 ~TL~~y~~~~~ni~~tA~~L~iHrNTL~YRL~kI~eltG~d~  366 (385)
T PRK11477        325 RTLAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLDL  366 (385)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHhhHHHHHHHHHHHhCcCc
Confidence            466666676559999999999999999999999999999886

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

Probab=93.58  E-value=0.12  Score=30.04  Aligned_cols=39  Identities=18%  Similarity=-0.055  Sum_probs=31.4

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      ++.-+-..- ++..-|...|||+||+|+.++.+++.|...
T Consensus        12 ~L~~LR~~~-~~~~La~~FgIs~stvsri~~~~~~~L~~~   50 (53)
T PF13613_consen   12 TLMYLRLNL-TFQDLAYRFGISQSTVSRIFHEWIPLLYQV   50 (53)
T ss_pred             HHHHHHcCC-cHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence            344444444 999999999999999999999999887544

>cd00131 PAX Paired Box domain

Probab=93.52  E-value=0.79  Score=32.34  Aligned_cols=38  Identities=24%  Similarity=0.171  Sum_probs=31.6

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +.+++.|.|...+|+.+++|+++|++.+++.+++=.+.
T Consensus        27 v~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~   64 (128)
T cd00131          27 VELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIR   64 (128)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence            34455666999999999999999999999999865444

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=93.50  E-value=1.1  Score=37.44  Aligned_cols=112  Identities=13%  Similarity=0.122  Sum_probs=60.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      ++..-|+..|+|.+||||.|.             .+.++ .  +   ..-+++.++.+++.-.-+ ..+.+..+.+..|-
T Consensus         7 ti~dIA~~agVS~~TVSrvLn-------------~~~~v-s--~---~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig   67 (331)
T PRK14987          7 VLQDVADRVGVTKMTVSRFLR-------------NPEQV-S--V---ALRGKIAAALDELGYIPNRAPDILSNATSRAIG   67 (331)
T ss_pred             cHHHHHHHhCCCHHHhhhhhC-------------CCCCC-C--H---HHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEE
Confidence            788999999999999999984             22233 2  2   222233333333321111 11222333334444


Q ss_pred             EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      +-++. +...++..++..+.+..-  ++.+.+...+  .   .+.++.+.+..+|-+|..
T Consensus        68 vi~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiI~~  126 (331)
T PRK14987         68 VLLPS-LTNQVFAEVLRGIESVTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDGLILT  126 (331)
T ss_pred             EEeCC-CcchhHHHHHHHHHHHHHHCCCEEEEecCCCCHHHHHHHHHHHHhcCCCEEEEc
Confidence            44432 445566666665544432  5566554332  2   134566778889999985

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

Probab=93.48  E-value=1.1  Score=36.00  Aligned_cols=58  Identities=14%  Similarity=0.166  Sum_probs=42.4

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ   64 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~   64 (306)
                      ++-+++-.|.+.| -++...|+.+++|..||-|=|.+||++   -+..|.++|.+.+.....
T Consensus         6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~R~hGGa~~~~~~~~   64 (253)
T COG1349           6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ---GLLLRVHGGAVLPDSESE   64 (253)
T ss_pred             HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHC---CcEEEEeCCEecCCCccc
Confidence            4445555666655 146789999999999999999999986   467888888743344343

>PF13551 HTH_29: Winged helix-turn helix

Probab=93.44  E-value=0.24  Score=33.89  Aligned_cols=44  Identities=16%  Similarity=0.113  Sum_probs=33.5

Q ss_pred             HHHHHHHHhcCC-HHHHHHHhCCCchHHHHHHHHHHHHcC-ceeEEec
Q psy3760           7 RFVREAVRQNFN-LTEAAKALYTSQPGVSKAIIELEEELS-IDIFIRH   52 (306)
Q Consensus         7 ~~f~~v~~~~~s-~~~aA~~l~isq~~~s~~i~~LE~~lg-~~Lf~R~   52 (306)
                      .++..+.+-. + ..++|+.+|+|.+|+.+.+++.++ -| ..|..|.
T Consensus         3 ~~l~l~~~g~-~~~~~ia~~lg~s~~Tv~r~~~~~~~-~G~~~l~~~~   48 (112)
T PF13551_consen    3 QILLLLAEGV-STIAEIARRLGISRRTVYRWLKRYRE-GGIEGLLPRK   48 (112)
T ss_pred             HHHHHHHcCC-CcHHHHHHHHCcCHHHHHHHHHHHHc-ccHHHHHhcc
Confidence            4455555554 7 999999999999999999999984 44 3565643

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.41  E-value=0.36  Score=34.38  Aligned_cols=57  Identities=21%  Similarity=0.240  Sum_probs=37.4

Q ss_pred             hCCCchHHHHHHHHHHHH--cCceeEEec---CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEE--LSIDIFIRH---GKRIRGLTKPGQAILRSIEIIMQEIEGLKK   82 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~--lg~~Lf~R~---~~~~~~lT~~G~~l~~~a~~il~~~~~~~~   82 (306)
                      ..++++++...|++||+.  +-...-.-.   .+.+.++|+.|+..+.....-...+....+
T Consensus        53 ~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~~~l~  114 (138)
T TIGR02719        53 SSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQNMLD  114 (138)
T ss_pred             CCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999986  222211111   133348999999988776655555444433

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

>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=93.26  E-value=0.23  Score=29.32  Aligned_cols=43  Identities=14%  Similarity=0.135  Sum_probs=34.7

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      +.-...= |+...|+.+++|..|+.|-|..||+.=   +..|..+|.
T Consensus         9 l~~~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g---~i~r~~GG~   51 (57)
T PF08220_consen    9 LKEKGKV-SVKELAEEFGVSEMTIRRDLNKLEKQG---LIKRTHGGA   51 (57)
T ss_pred             HHHcCCE-EHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEEcCEE
Confidence            3334444 788999999999999999999999864   478887776

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=93.23  E-value=0.87  Score=32.57  Aligned_cols=77  Identities=19%  Similarity=0.183  Sum_probs=50.5

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH----HHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE----LEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~----LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +-++.++|.... .|.|..+.|+.||+|++++++..+.    |++...+-.|.+. +..+.-.=++|..++.-.+.++..
T Consensus         8 t~rqreVL~lr~-~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~~l~a~~~v~~~~G~d~~~ip~~v~~~   86 (141)
T PRK03975          8 TERQIEVLRLRE-RGLTQQEIADILGTSRANVSSIEKRARENIEKARETLAFAETLNAPVRVTIPAGTDLFDIPKRIYKE   86 (141)
T ss_pred             CHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEEecCCCcHHHhHHHHHHH
Confidence            446677776654 5559999999999999999877665    4433333333332 333212557788888877777766


Q ss_pred             HHH
Q psy3760          77 IEG   79 (306)
Q Consensus        77 ~~~   79 (306)
                      .++
T Consensus        87 ~d~   89 (141)
T PRK03975         87 ADE   89 (141)
T ss_pred             hhH
Confidence            444

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=93.23  E-value=0.17  Score=33.72  Aligned_cols=41  Identities=24%  Similarity=0.280  Sum_probs=30.4

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +|-++|-.-.....|++.-|+.+|||..||+..|++-++.|
T Consensus        21 kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L   61 (101)
T PF04297_consen   21 KQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKL   61 (101)
T ss_dssp             HHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            55566666666667999999999999999999999877655

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

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

Probab=93.22  E-value=0.13  Score=35.77  Aligned_cols=43  Identities=19%  Similarity=0.181  Sum_probs=35.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +|.+.|+.++.-.-.- ++.+-|+.+++|+++|++.+++|--..
T Consensus        57 id~~~L~~~v~~~pd~-tl~Ela~~l~Vs~~ti~~~Lkrlg~t~   99 (119)
T PF01710_consen   57 IDRDELKALVEENPDA-TLRELAERLGVSPSTIWRALKRLGITR   99 (119)
T ss_pred             ccHHHHHHHHHHCCCc-CHHHHHHHcCCCHHHHHHHHHHcCchh
Confidence            3566777777777777 889999999999999999999886544

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

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=93.19  E-value=0.8  Score=38.11  Aligned_cols=110  Identities=14%  Similarity=0.175  Sum_probs=55.5

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEEEE
Q psy3760          20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLTIA   98 (306)
Q Consensus        20 ~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~I~   98 (306)
                      ..-|+..|+|.+||||.|..             +.++   .+   ..-+++.+..+++.-.-+ ..+.+..+..+.|-+-
T Consensus         2 ~dIA~~agVS~~TVSrvLn~-------------~~~v---s~---~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi   62 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINK-------------DRFV---SE---AITAKVEAAIKELNYAPSALARSLKLNQTRTIGML   62 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhCC-------------CCCC---CH---HHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEE
Confidence            45799999999999999961             2232   22   222222222222221111 1122233334445444


Q ss_pred             ecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          99 TTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        99 ~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      ++. +...++..++..+.+..  -+..+.+....  .   .+.++.+.++++|-.|+.
T Consensus        63 ~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiI~~  119 (327)
T PRK10423         63 ITA-STNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL  119 (327)
T ss_pred             eCC-CCCCcHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence            443 23344555554443332  24565554332  2   234566778889988875

>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]

Probab=93.17  E-value=4.2  Score=33.48  Aligned_cols=194  Identities=15%  Similarity=0.091  Sum_probs=112.4

Q ss_pred             CcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--------CCCCce
Q psy3760          93 GNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS--------PSDKLI  159 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~--------~~~~~~  159 (306)
                      ..+++|+.++-...-+    .++...+.++ -++.++... .+...+++.+..|++|++.......        ....+.
T Consensus        35 ~~l~~gi~p~e~~~~~~~~~~pl~~~L~~~-lG~~V~~~~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~  113 (299)
T COG3221          35 KELRVGIVPTENPTNLIPAWAPLADYLEKE-LGIPVEFFVATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLA  113 (299)
T ss_pred             cceEEEEcCCCChHHHHHHHHHHHHHHHHH-hCCceEEEecccHHHHHHHHhCCCeeEEecCchhHHHHHhhccccccee
Confidence            4699999887555443    3444444443 466676666 4677899999999999998742100        011111


Q ss_pred             ee--ccc--cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCC-Cc----eeEEEEecCHHH
Q psy3760         160 SI--PCY--QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQK-LT----PYIVLETINSDI  229 (306)
Q Consensus       160 ~~--~l~--~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~-~~----~~~~~~~~~~~~  229 (306)
                      ..  .=+  ...=++++.++.|+     -+++|+.+..+...++.+.- .-.-..++...| ..    ...+....+++.
T Consensus       114 ~~~~~dg~~~Y~S~~i~~~ds~i-----~sl~dlkgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~  188 (299)
T COG3221         114 QTVQKDGSPGYYSVIIVRADSPI-----KSLEDLKGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDA  188 (299)
T ss_pred             eeeccCCCcceeEEEEEeCCCCc-----chHHHhcCCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHH
Confidence            11  001  11345666777663     46779999999998876543 223345566666 43    245556676889


Q ss_pred             HHHHHHhc-cceeeeecceeccc----cc---CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         230 IKTYVELR-MGIGIIASIAFDSN----RD---KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       230 ~~~~v~~g-~gi~~~p~~~~~~~----~~---~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .+..|.+| .-++.+........    ..   .+++.+-..++.+.  .-++|+++.. ....+++.+.+.+.-
T Consensus       189 a~~aV~nG~vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~--~pi~vr~~L~-~~~k~kl~~af~~l~  259 (299)
T COG3221         189 AVLAVANGQVDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPN--DPIAVRSDLP-ADLKEKLRDAFLDLA  259 (299)
T ss_pred             HHHHHHcCCceEEeccHHHHhhhhhcccccchhhceEEEecCCCCC--CCEEEeCCCC-HHHHHHHHHHHHhcC
Confidence            99999988 33333333222221    22   35666655554333  3456666643 555666666665553

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=93.06  E-value=0.44  Score=31.96  Aligned_cols=55  Identities=15%  Similarity=0.095  Sum_probs=41.5

Q ss_pred             HhCCCchHHHHHHHHHHHHcCceeEEe----c----CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760          25 ALYTSQPGVSKAIIELEEELSIDIFIR----H----GKRIRGLTKPGQAILRSIEIIMQEIEGLKK   82 (306)
Q Consensus        25 ~l~isq~~~s~~i~~LE~~lg~~Lf~R----~----~~~~~~lT~~G~~l~~~a~~il~~~~~~~~   82 (306)
                      .+.++++++...|++||++=   |..+    .    .+..+++|+.|+.++.......+.+.+...
T Consensus        34 ~~~i~~gtlY~~L~rLe~~G---lI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~~~~~~~i~   96 (100)
T TIGR03433        34 VLQVEEGSLYPALHRLERRG---WIAAEWGESENNRRAKFYRLTAAGRKQLAAETESWARLSAAIA   96 (100)
T ss_pred             ccccCCCcHHHHHHHHHHCC---CeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999862   4443    1    123348999999999999888777766554

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

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

Probab=93.05  E-value=0.29  Score=29.36  Aligned_cols=40  Identities=20%  Similarity=0.161  Sum_probs=34.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      .++.|+.+.-...|+..||+.||+++.++.+.+......+
T Consensus         2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wl   41 (65)
T PF05344_consen    2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWL   41 (65)
T ss_pred             cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4567777777777999999999999999999999988776

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=92.97  E-value=0.25  Score=25.77  Aligned_cols=33  Identities=18%  Similarity=0.189  Sum_probs=24.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      ....+....+.+.|....|+.+++|.+++++.+
T Consensus        10 ~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569          10 QIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            344455555555599999999999999998753

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=92.91  E-value=0.22  Score=38.20  Aligned_cols=27  Identities=37%  Similarity=0.370  Sum_probs=25.1

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .++++.|+.|+++||++|..|+.||+-
T Consensus        38 lNvneiAe~lgLpqst~s~~ik~Le~a   64 (308)
T COG4189          38 LNVNEIAEALGLPQSTMSANIKVLEKA   64 (308)
T ss_pred             CCHHHHHHHhCCchhhhhhhHHHHHhc
Confidence            479999999999999999999999973

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=92.88  E-value=0.43  Score=28.77  Aligned_cols=45  Identities=16%  Similarity=0.183  Sum_probs=39.5

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +.+..++...+++-. |..+-|..|++|..|+..+++.+...+|+.
T Consensus         6 t~rE~~v~~l~~~G~-s~~eia~~l~is~~tV~~h~~~i~~Kl~~~   50 (65)
T COG2771           6 TPREREILRLVAQGK-SNKEIARILGISEETVKTHLRNIYRKLGVK   50 (65)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            446677777888877 999999999999999999999999999874

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=92.83  E-value=0.62  Score=37.77  Aligned_cols=57  Identities=4%  Similarity=-0.106  Sum_probs=39.3

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760           5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus         5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      -+.++-.+.+.+  .+++.-|+.++++.||+.|-++.|++. |.--.+..++.. .|+..-
T Consensus        27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~-G~l~~~~~~~~Y-~lG~~l   85 (271)
T PRK10163         27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDSQLGWW-HIGLGV   85 (271)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcCCCCeE-EecHHH
Confidence            344455555432  379999999999999999999999874 554444344555 566543

>PHA00542 putative Cro-like protein

Probab=92.78  E-value=0.25  Score=31.71  Aligned_cols=32  Identities=22%  Similarity=0.279  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      .+....+.+.|.|..++|+.+|||+++||+..
T Consensus        21 ~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e   52 (82)
T PHA00542         21 DELVCALIRAGWSQEQIADATDVSQPTICRIY   52 (82)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34445556667799999999999999999865

>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]

Probab=92.62  E-value=4.8  Score=32.80  Aligned_cols=141  Identities=16%  Similarity=0.120  Sum_probs=81.8

Q ss_pred             CcEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeC--------------------ChhHHHHHHHcCCeeEEEEccc
Q psy3760          93 GNLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQG--------------------NPKQITEMIRNDQADIAIVTEI  151 (306)
Q Consensus        93 ~~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~--------------------~~~~~~~~l~~~~~Di~i~~~~  151 (306)
                      ..|+||+-.| ++..-...+...+++.||++.++++..                    ...++.+.|.+|++|+|+.+..
T Consensus         2 ~~irIgTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~i~d~pL~~iGgkGlFtkEle~all~g~~DiAVHSlK   81 (307)
T COG0181           2 MKLRIGTRGSKLALAQANEVIERLKAAYPDLEVEIVTIKTKGDRILDKPLSKIGGKGLFTKELEQALLEGEIDIAVHSLK   81 (307)
T ss_pred             CceEEecCCCHHHHHHHHHHHHHHHHhCCCceEEEEEEecccchhccchHHHcCCcEEEHHHHHHHHHcCCCCEEEeecc
Confidence            3688998665 444455566678888899888887432                    2456788899999999998743


Q ss_pred             cCCCCCceeeccccceEEEEecCCCCCCC---CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH
Q psy3760         152 LSPSDKLISIPCYQWEYVIIVPLDHPLLL---LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD  228 (306)
Q Consensus       152 ~~~~~~~~~~~l~~~~~~~v~~~~~~l~~---~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (306)
                      .-+ ..+    =..-.++.+..+.+|...   ....++++|..-..|..+   +.|.  ...++.......+..--.|++
T Consensus        82 DvP-~~~----p~gL~laai~~R~dprDalVs~~~~~l~~LP~Ga~VGTS---SlRR--~aql~~~rPdl~i~~lRGNVd  151 (307)
T COG0181          82 DVP-TEL----PEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTS---SLRR--QAQLKALRPDLKIEPLRGNVD  151 (307)
T ss_pred             cCC-ccC----CCCceEEEecCCCChhheEEECCCCchhhCCCCCccccc---hHHH--HHHHHHhCCCCeEEeccCcHH
Confidence            222 110    011233444444444221   122245666554455432   3333  223333443445555668888


Q ss_pred             HHHHHHHhccceeee
Q psy3760         229 IIKTYVELRMGIGII  243 (306)
Q Consensus       229 ~~~~~v~~g~gi~~~  243 (306)
                      +=++-+..|..=+++
T Consensus       152 TRL~KL~~g~yDAII  166 (307)
T COG0181         152 TRLRKLDEGEYDAII  166 (307)
T ss_pred             HHHHHhhcCCccHHH
Confidence            888888888555543

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

Probab=92.61  E-value=0.15  Score=28.55  Aligned_cols=21  Identities=19%  Similarity=0.265  Sum_probs=18.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++..-|+.+|+|.+|+|+.|.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln   21 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLN   21 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHh
Confidence            467889999999999999874

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PRK10752 sulfate transporter subunit; Provisional

Probab=92.60  E-value=3.6  Score=34.45  Aligned_cols=101  Identities=16%  Similarity=0.162  Sum_probs=63.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCC---CcEEEEEe--CChhHHHHHHHcC-CeeEEEEccccC----CCCCce----
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFP---KVKLSLLQ--GNPKQITEMIRND-QADIAIVTEILS----PSDKLI----  159 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p---~~~i~~~~--~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~~~----  159 (306)
                      .+.++++.+  ......+...|.+.|+   ++.+++..  .++.++..++.+| .+|+.+......    ...++.    
T Consensus        24 ~~~v~~~~~--~~~~~~~~~~f~~~~~~~tG~~V~v~~s~ggSg~l~~qI~~g~~aDV~~~a~~~~~~~l~~~gli~~~~  101 (329)
T PRK10752         24 LLNVSYDPT--RELYEQYNKAFSAHWKQQTGDNVVIRQSHGGSGKQATSVINGIEADVVTLALAYDVDAIAERGRIDKNW  101 (329)
T ss_pred             EEecccCch--HHHHHHHHHHHHHHHHhccCCceEEEeCCCChHHHHHHHHcCCCCCEEEeCCHHHHHHHHHCCCCCCcc
Confidence            455565554  4455667777776553   77777755  8999999999976 799998853111    111221    


Q ss_pred             eeccccc------eEEEEecCCCCCCCCCCcChhhhcC--CCeEeecC
Q psy3760         160 SIPCYQW------EYVIIVPLDHPLLLLNSISLKEISN--YPLITYDL  199 (306)
Q Consensus       160 ~~~l~~~------~~~~v~~~~~~l~~~~~i~~~dl~~--~~~i~~~~  199 (306)
                      ...+...      .+++++++++|.   .+-+++||.+  ..+++.++
T Consensus       102 ~~~l~~n~~~~~~~lviiv~~gnp~---~i~~w~DL~~~~~~I~i~dP  146 (329)
T PRK10752        102 IKRLPDNSAPYTSTIVFLVRKGNPK---QIHDWNDLIKPGVSVITPNP  146 (329)
T ss_pred             hhhhhccccccceeEEEEEECCCCC---CCCCHHHhcCCCcEEEECCC
Confidence            1223333      788999999883   3348999854  34444444

>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=92.57  E-value=0.17  Score=32.87  Aligned_cols=44  Identities=20%  Similarity=0.298  Sum_probs=32.1

Q ss_pred             HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc---CceeEEecCCCccccC
Q psy3760          12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL---SIDIFIRHGKRIRGLT   60 (306)
Q Consensus        12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l---g~~Lf~R~~~~~~~lT   60 (306)
                      --+.- |+..-|+.+++|.||+.+.|+++++.|   |.+|   .++|+ .++
T Consensus        27 ~~~~~-s~~~la~~~~iS~sti~~~i~~l~~~l~~~~l~i---~~~~~-~l~   73 (87)
T PF05043_consen   27 NNEYV-SIEDLAEELFISRSTIYRDIKKLNKYLKKYGLKI---SKKGY-RLE   73 (87)
T ss_dssp             H-SEE-EHHHHHHHHT--HHHHHHHHHHHHHHHHCCT-EE----SSEE-EEE
T ss_pred             cCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCeEE---eCCCe-EEE
Confidence            34455 999999999999999999999999877   8888   44555 455

The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=92.57  E-value=1.9  Score=34.96  Aligned_cols=36  Identities=14%  Similarity=0.127  Sum_probs=30.4

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      +...-|+.+++|..|+-|-|..||++ |  +..|..+|.
T Consensus        33 tv~eLa~~l~VS~~TIRRDL~~Le~~-G--~l~r~~GGa   68 (269)
T PRK09802         33 QVNDLSALYGVSTVTIRNDLAFLEKQ-G--IAVRAYGGA   68 (269)
T ss_pred             eHHHHHHHHCCCHHHHHHHHHHHHhC-C--CeEEEeCCE
Confidence            78889999999999999999999886 4  445776666

>PRK15320 transcriptional activator SprB; Provisional

Probab=92.34  E-value=0.42  Score=35.89  Aligned_cols=45  Identities=16%  Similarity=0.061  Sum_probs=40.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+.++++..+++-. |-.+-|++|++|.+|||+..++|-+.||.+
T Consensus       166 SdREIEVL~LLAkG~-SNKEIAekL~LS~KTVSTYKnRLLeKLgAk  210 (251)
T PRK15320        166 TQAKYALLILLSSGH-PAIELAKKFGLGTKTVSIYRKKVMYRLGMD  210 (251)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence            346788899999887 999999999999999999999999999864

>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins

Probab=92.26  E-value=0.21  Score=28.89  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=20.8

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      -++-|.+.|+|.|.+-.++++||.-
T Consensus         7 as~iAd~~GiTRSvIVNALRKleSa   31 (61)
T PF08222_consen    7 ASKIADRVGITRSVIVNALRKLESA   31 (61)
T ss_dssp             HHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCccHHHHHHHHHHHHhc
Confidence            4788999999999999999999973

CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=92.25  E-value=0.37  Score=37.04  Aligned_cols=41  Identities=15%  Similarity=0.144  Sum_probs=34.8

Q ss_pred             chhhHHHHHHHHHh-------cCCHHHHHHHhCCC-chHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ-------NFNLTEAAKALYTS-QPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~-------~~s~~~aA~~l~is-q~~~s~~i~~LE~~   43 (306)
                      +-.|.+++..+.+.       - |.+.-|+.++++ .+|++++|++||+.
T Consensus         5 t~~q~~iL~~l~~~~~~~~~~~-~~~ela~~~~~~s~~tv~~~l~~L~~~   53 (199)
T TIGR00498         5 TARQQEVLDLIRAHIESTGYPP-SIREIARAVGLRSPSAAEEHLKALERK   53 (199)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence            55677777777754       5 788999999998 99999999999986

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.

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=92.16  E-value=1.4  Score=34.26  Aligned_cols=60  Identities=27%  Similarity=0.242  Sum_probs=44.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL   67 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~   67 (306)
                      |+-.++.+.+=..+-..-|++|++|..++|.+|++|-++   -|.+..|++-.+.|..|..++
T Consensus        14 qIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~e---G~i~~~gR~~Y~iTkkG~e~l   73 (260)
T COG1497          14 QILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKE---GLIEKEGRGEYEITKKGAEWL   73 (260)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhc---cceeecCCeeEEEehhHHHHH
Confidence            444555555333367889999999999999999999875   466666664448999997754

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

Probab=92.14  E-value=0.72  Score=36.85  Aligned_cols=54  Identities=19%  Similarity=0.215  Sum_probs=38.3

Q ss_pred             HHHHHHHHH--hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760           6 FRFVREAVR--QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus         6 l~~f~~v~~--~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      |.++-.+.+  .+.|++.-|+.++++.||+.|-++.|++ .|.  ..|++++. +|++.-
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~-~G~--l~~~~~~Y-~lG~~~   67 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE-LGY--VTSDGRLF-WLTPRV   67 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCC--EEeCCCEE-EecHHH
Confidence            344444443  2348999999999999999999999975 453  45666666 676653

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.

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=92.05  E-value=1.6  Score=36.66  Aligned_cols=109  Identities=14%  Similarity=0.106  Sum_probs=57.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~   93 (306)
                      ++...|+..|+|.+||||.|.              +++.  .+++      .-+++++..+++-.    ..+.++.+..+
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn--------------~~~~--Vs~~------tr~rV~~~a~elgY~pn~~ar~l~~~~~~   60 (343)
T PRK10727          3 TIKDVARLAGVSVATVSRVIN--------------NSPK--ASEA------SRLAVHSAMESLSYHPNANARALAQQSTE   60 (343)
T ss_pred             CHHHHHHHhCCCHHHHHHHhC--------------CCCC--CCHH------HHHHHHHHHHHHCCCCCHHHHhhhhCCCC
Confidence            678899999999999999984              2232  2222      22233333333321    11222232333


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      .|-+-++ .+...++..++..+.+..-  +..+.+....  .   .+.++.+.+.++|-+|+.
T Consensus        61 ~Igvi~~-~~~~~f~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~  122 (343)
T PRK10727         61 TVGLVVG-DVSDPFFGAMVKAVEQVAYHTGNFLLIGNGYHNEQKERQAIEQLIRHRCAALVVH  122 (343)
T ss_pred             eEEEEeC-CCCcchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEe
Confidence            3333333 3344566666655544322  3444443322  1   135667778889988875

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=91.92  E-value=0.31  Score=40.80  Aligned_cols=50  Identities=16%  Similarity=0.058  Sum_probs=39.1

Q ss_pred             CHHHHHHH--hCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHH
Q psy3760          18 NLTEAAKA--LYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRS   69 (306)
Q Consensus        18 s~~~aA~~--l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~   69 (306)
                      +-..-|+.  +++|.+|+-+-++.||+. |.--=..++.|.| ||+.|-++|-.
T Consensus        27 ~s~~l~~~~~l~~S~aTIR~dm~~Le~~-G~l~~~h~sagrI-PT~kGYR~YVd   78 (339)
T PRK00082         27 GSKTLSKRYGLGVSSATIRNDMADLEEL-GLLEKPHTSSGRI-PTDKGYRYFVD   78 (339)
T ss_pred             CHHHHHHHhCCCCChHHHHHHHHHHHhC-CCcCCCcCCCCCC-cCHHHHHHHHH
Confidence            55667766  999999999999999887 6533334456665 99999999876

>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases

Probab=91.82  E-value=1.1  Score=31.79  Aligned_cols=36  Identities=19%  Similarity=0.463  Sum_probs=31.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG  129 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~  129 (306)
                      |+|.+.+.-..+..... ++.+|...||++.+.+...
T Consensus        97 G~i~l~te~~pC~SC~~-vi~qF~~~~pni~~~v~~~  132 (133)
T PF14424_consen   97 GTIDLFTELPPCESCSN-VIEQFKKDFPNIKVNVVYN  132 (133)
T ss_pred             ceEEEEecCCcChhHHH-HHHHHHHHCCCcEEEEecC
Confidence            89999998887777666 9999999999999998754

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=91.63  E-value=0.48  Score=36.83  Aligned_cols=45  Identities=20%  Similarity=0.107  Sum_probs=40.5

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |-.+-|++|++|..||..+++++=..||++
T Consensus       152 t~rE~evl~~~~~G~-s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~  196 (216)
T PRK10840        152 SPKESEVLRLFAEGF-LVTEIAKKLNRSIKTISSQKKSAMMKLGVE  196 (216)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            456778888888876 999999999999999999999999999975

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=91.57  E-value=0.29  Score=30.39  Aligned_cols=28  Identities=14%  Similarity=0.088  Sum_probs=24.6

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      .|.|+...|+.||+|.+|+..+++.++.
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~   58 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKGETK   58 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence            4459999999999999999999987654

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

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

Probab=91.55  E-value=0.57  Score=28.80  Aligned_cols=36  Identities=17%  Similarity=0.157  Sum_probs=28.7

Q ss_pred             HHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           8 FVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         8 ~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++..+.+.|   .+...-|+.||++.+++.|+|..||++
T Consensus        11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~   49 (68)
T smart00550       11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK   49 (68)
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            344444543   267889999999999999999999987

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

>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]

Probab=91.50  E-value=0.38  Score=30.99  Aligned_cols=33  Identities=18%  Similarity=0.136  Sum_probs=30.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      +..|++..-.| .=.++|..|++|+|.+++.++-
T Consensus         3 ls~~va~~vvg-~q~a~a~LLgvsp~~vnQw~~g   35 (96)
T COG4197           3 LSIFVACAVVG-GQKALARLLGVSPPSVNQWIKG   35 (96)
T ss_pred             hhHHHHHHHHc-cHHHHHHHHccCchHHHHHhhh
Confidence            67899999999 9999999999999999998864

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=91.37  E-value=0.41  Score=31.10  Aligned_cols=32  Identities=6%  Similarity=0.071  Sum_probs=25.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .+++..+.+-. |.++.|+.+|+|.+||++..+
T Consensus        41 ~~I~~ll~~G~-S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        41 LQVAKMLKQGK-TYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             HHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHH
Confidence            45555566655 999999999999999999443

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=91.33  E-value=1.8  Score=36.27  Aligned_cols=112  Identities=14%  Similarity=0.154  Sum_probs=58.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      ++..-|+..|+|.+||||.|..             +.+   ..++-+   +.+.++.+++.-.-+ ..+.+..+.+..|-
T Consensus         3 Ti~dIA~~agVS~~TVSrvLn~-------------~~~---vs~~tr---~~V~~~a~elgY~pn~~a~~l~~~~~~~i~   63 (341)
T PRK10703          3 TIKDVAKRAGVSTTTVSHVINK-------------TRF---VAEETR---NAVWAAIKELHYSPSAVARSLKVNHTKSIG   63 (341)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC-------------CCC---CCHHHH---HHHHHHHHHHCCCcCHHHHHHhhCCCCeEE
Confidence            6788899999999999999853             122   233322   222222222221111 11222333334444


Q ss_pred             EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      +-++. ....++..++..+.+...  +.++.+....  .   .+.++.+.++.+|-.|+.
T Consensus        64 vi~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~  122 (341)
T PRK10703         64 LLATS-SEAPYFAEIIEAVEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVM  122 (341)
T ss_pred             EEeCC-CCCchHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence            44433 234455555555544322  4555554322  2   245667888889988774

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=91.30  E-value=2.1  Score=35.99  Aligned_cols=109  Identities=10%  Similarity=0.166  Sum_probs=57.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHH----HHHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLK----KIGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~----~~~~~~~~~~~~   93 (306)
                      ++..-|+..|+|++||||.|..             +.++ .  +      +.-+++++..+++-    ...+.+..+...
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn~-------------~~~V-s--~------~tr~kV~~~a~elgY~pn~~a~~l~~~~~~   60 (346)
T PRK10401          3 TIRDVARQAGVSVATVSRVLNN-------------SALV-S--A------DTREAVMKAVSELGYRPNANAQALATQVSD   60 (346)
T ss_pred             CHHHHHHHhCCCHHHHHHHHCC-------------CCCC-C--H------HHHHHHHHHHHHHCCCCCHHHHHhhcCCCC
Confidence            6788999999999999999852             1233 1  1      11222333333221    112233333344


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      .|-+-++. +...++..++..+.+...  +..+.+....  .   .+.++.+.++.+|-+|..
T Consensus        61 ~Igvi~~~-~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~~~~~~~~~~i~~l~~~~vdGiIi~  122 (346)
T PRK10401         61 TIGVVVMD-VSDAFFGALVKAVDLVAQQHQKYVLIGNSYHEAEKERHAIEVLIRQRCNALIVH  122 (346)
T ss_pred             EEEEEeCC-CCCccHHHHHHHHHHHHHHCCCEEEEEcCCCChHHHHHHHHHHHhcCCCEEEEe
Confidence            55554443 344455555544433322  4455443322  1   135667778889988875

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=91.19  E-value=0.53  Score=37.15  Aligned_cols=44  Identities=11%  Similarity=0.068  Sum_probs=39.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-+ |....|+.|++|..|+..++++..+.||+
T Consensus       173 t~re~evl~~~a~G~-t~~eIa~~l~is~~Tv~~~l~~~~~kl~~  216 (232)
T TIGR03541       173 SEREREVLAWTALGR-RQADIAAILGISERTVENHLRSARRKLGV  216 (232)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            457788888888766 99999999999999999999999999985

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

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

Probab=91.19  E-value=0.53  Score=26.98  Aligned_cols=31  Identities=13%  Similarity=0.140  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      ++..+.+.. |++..|+.+|+|..+|.+.+++
T Consensus        20 i~~~~~~~~-s~~~vA~~~~vs~~TV~ri~~~   50 (52)
T PF13542_consen   20 ILKLLRESR-SFKDVARELGVSWSTVRRIFDR   50 (52)
T ss_pred             HHHHHhhcC-CHHHHHHHHCCCHHHHHHHHHh
Confidence            445566667 9999999999999999998765

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

Probab=91.15  E-value=1.9  Score=27.15  Aligned_cols=61  Identities=18%  Similarity=0.130  Sum_probs=43.7

Q ss_pred             chhhHHHHHHHHHh--------cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe---cCCCccccCHhHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ--------NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR---HGKRIRGLTKPGQAILR   68 (306)
Q Consensus         2 ~~~~l~~f~~v~~~--------~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R---~~~~~~~lT~~G~~l~~   68 (306)
                      +-++-++|.++++.        | |= .-|+.+++|..||-..++.||+ +|  |++.   ...|. .||..|-+++.
T Consensus         3 t~rq~~IL~alV~~Y~~~~~PVg-Sk-~ia~~l~~s~aTIRN~M~~Le~-lG--lve~~p~~s~Gr-iPT~~aYr~~~   74 (78)
T PF03444_consen    3 TERQREILKALVELYIETGEPVG-SK-TIAEELGRSPATIRNEMADLEE-LG--LVESQPHPSGGR-IPTDKAYRALN   74 (78)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCcC-HH-HHHHHHCCChHHHHHHHHHHHH-CC--CccCCCCCCCCC-CcCHHHHHHHc
Confidence            34566666666653        3 33 3456799999999999999986 55  6653   24666 49999998774

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

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=91.11  E-value=0.58  Score=37.16  Aligned_cols=45  Identities=11%  Similarity=0.084  Sum_probs=41.0

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-+ |-...|+.|++|..||..+|+++-+.||+.
T Consensus       181 T~rE~evl~~~a~G~-t~~eIa~~l~is~~TV~~h~~~~~~KL~~~  225 (240)
T PRK10188        181 SKREKEILKWTAEGK-TSAEIAMILSISENTVNFHQKNMQKKFNAP  225 (240)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            557788999999877 999999999999999999999999999953

>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=91.10  E-value=0.3  Score=30.02  Aligned_cols=39  Identities=23%  Similarity=0.249  Sum_probs=29.8

Q ss_pred             hHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         5 ~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..+++..+.+.| .+...-|+.++++++++++.|++|++.
T Consensus        10 E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~   49 (68)
T PF01978_consen   10 EAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEK   49 (68)
T ss_dssp             HHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            345555554322 377889999999999999999999974

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.

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=91.07  E-value=0.74  Score=26.66  Aligned_cols=36  Identities=11%  Similarity=0.232  Sum_probs=24.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      +++... ++.|.|....|+.+|++++||+..++.=++
T Consensus        13 ~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~k~~   48 (53)
T PF04218_consen   13 LEIIKR-LEEGESKRDIAREFGVSRSTVSTILKNKDK   48 (53)
T ss_dssp             HHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred             HHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHhHHH
Confidence            344444 445559999999999999999998886444

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>TIGR00070 hisG ATP phosphoribosyltransferase

Probab=91.02  E-value=2  Score=32.26  Aligned_cols=95  Identities=15%  Similarity=0.182  Sum_probs=60.8

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccCCCCC--c---eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK--L---ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~--~---~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++...-..++...+.+|.+|++|+..+.....+  +   .-..++.-+++++++++.+.     -+.+++.+....+- 
T Consensus        42 i~~~~~r~~Dip~yV~~G~aDlGI~G~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~-----~~~~~l~~~rIATk-  115 (182)
T TIGR00070        42 IEFLLLRPQDIPTYVEHGAADLGITGYDVLLESGADVYELLDLGFGKCRLVLAVPQESDI-----SSVEDLKGKRIATK-  115 (182)
T ss_pred             EEEEEEccchhHHHHhCCCccEEEecchhhhhCCCCEEEEeecCcCceEEEEEEECCCCC-----CChHHhCCCEEEEC-
Confidence            4444445668899999999999997533222222  2   12345678999999998752     25677765554442 


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHH
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSD  228 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (306)
                          +.+...++|.+.|+...++..-.+.+
T Consensus       116 ----yp~i~~~~f~~~Gi~v~ii~l~GsvE  141 (182)
T TIGR00070       116 ----YPNLARRYFEKKGIDVEIIKLNGSVE  141 (182)
T ss_pred             ----CHHHHHHHHHHcCCeEEEEECcceee
Confidence                23577889999998765544444443

Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.

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

Probab=90.98  E-value=1.2  Score=27.20  Aligned_cols=53  Identities=13%  Similarity=0.020  Sum_probs=34.8

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i   73 (306)
                      ++++.+|+.+|||.+++.    ..|++.|..-..|+.+|.-.-|..=-.-+...+.+
T Consensus         1 ~~i~e~A~~~gVs~~tlr----~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l   53 (68)
T cd04763           1 YTIGEVALLTGIKPHVLR----AWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRW   53 (68)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHH
Confidence            478999999999999876    45777776556676444313565544444444443

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

>PRK11569 transcriptional repressor IclR; Provisional

Probab=90.76  E-value=1.9  Score=35.07  Aligned_cols=55  Identities=7%  Similarity=0.081  Sum_probs=36.9

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760           6 FRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus         6 l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |.++-.+.+.  +.+++.-|+.+|++.||+.|.++.|++. |.--.+-.+++. +|.+.
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~-G~l~~~~~~~~Y-~lG~~   87 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-GFVRQVGELGHW-AIGAH   87 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcCCCCeE-ecCHH
Confidence            3444444442  2389999999999999999999999863 444333234555 56443

>PLN02245 ATP phosphoribosyl transferase

Probab=90.71  E-value=7.1  Score=33.35  Aligned_cols=171  Identities=15%  Similarity=0.099  Sum_probs=91.9

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-----Cce----eeccccceEEEEecCCCCCCCCCCcChhhhcCCCe
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-----KLI----SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL  194 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-----~~~----~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~  194 (306)
                      +++.-.-..++...+.+|.+|+||+..+.....     ...    -..++.-++++.+|++.-.  ...-+++||.+.+.
T Consensus       113 iev~flR~~DIp~yV~~G~~DlGItG~D~l~E~~~~~~~~v~~l~~LgFG~crlvvAvP~~~~~--~~~~s~~dL~g~~~  190 (403)
T PLN02245        113 LEVWFQRPKDIVRKLLSGDLDLGIVGYDMLREYGQGNEDLVIVHDALGFGDCHLSIAIPKYGIF--ENINSLKELAQMPQ  190 (403)
T ss_pred             eEEEEECHHHHHHHHhCCCccEEEeeeeeeeccCCCccceEEEeecCCCCceEEEEEEEccCCc--cccCCHHHhccccc
Confidence            444445567899999999999999853322221     111    2234678899999976200  11346788876331


Q ss_pred             Eee----cCCCCcHHHHHHHHHhCCCc-eeEEEEecCHHHHHHHHHhccceeeeecc-eecccccCCceeeecCCCCccc
Q psy3760         195 ITY----DLSFSGRIKLDREFSLQKLT-PYIVLETINSDIIKTYVELRMGIGIIASI-AFDSNRDKNLRSISASHLFGTT  268 (306)
Q Consensus       195 i~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~~~~~l~~~~~~~~~~~~  268 (306)
                      ...    .-...+-+...++|.+.|+. ..++....+.+.   +..-|.+=+++.-- .-..++..+|+.+.-.. ....
T Consensus       191 ~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE~---AP~lGlADaIvDIVsTGtTLraNgLk~i~~~~-Il~S  266 (403)
T PLN02245        191 WTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEA---APAMGIADAILDLVSSGTTLRENNLKEIEGGV-VLES  266 (403)
T ss_pred             ccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCceec---ccccCchhhhcchhccHHHHHHCCCEEccCce-EEEE
Confidence            111    00112446778899999985 455444444443   22233221222110 00112345677764212 3345


Q ss_pred             eEEEEEeCCcc-----ccHHHHHHHHHHhHHhhHHHH
Q psy3760         269 ISRVIIKQGTY-----LRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       269 ~~~l~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      +..|+.++...     ....++.+++.|+..+.++..
T Consensus       267 ~A~LIan~~sl~~~~~~~~~i~~ll~rl~~vl~A~~~  303 (403)
T PLN02245        267 QAVLVASRRALLERKGALEVVHEILERLEAHLRAEGQ  303 (403)
T ss_pred             EEEEEEecchhhcchhHHHHHHHHHHHHHHHHhhhcE
Confidence            77788776632     233677777777776654443

>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]

Probab=90.67  E-value=7.5  Score=31.10  Aligned_cols=204  Identities=9%  Similarity=0.008  Sum_probs=114.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQW  166 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~  166 (306)
                      ..|+||+++.--..++-.......+. -++.+.+++. +...--..|.+|++|+=...+.+.-     ..+.....++..
T Consensus        29 ~~I~vg~~~~p~a~ile~~~k~~~~k-~Gi~l~i~~FtDY~~PN~AL~~gdiDaN~FQH~pyL~~~~k~~~~~Lv~vg~~  107 (268)
T COG1464          29 KTIKVGATPGPHAEILEVVVKPALKK-KGLDLKIVEFTDYVQPNEALADGDIDANAFQHKPYLDQFNKEHGGKLVAVGNT  107 (268)
T ss_pred             CcEEEeecCCchHHHHHHHHHHHHHh-cCceEEEEEecCCcchhHHHhcCCccchhhhchHHHHHHHHHcCCCEEEEeeE
Confidence            58999999887777777666666554 3788888774 5556778999999999877543211     112222233322


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-eeEE------------------EEecCH
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-PYIV------------------LETINS  227 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~------------------~~~~~~  227 (306)
                      ++.-+   +  +..++--+++||.+---|..+.+.....+-...|++.|+- .+..                  +.-=+.
T Consensus       108 ~i~Pm---g--~YSkk~ksl~el~~GatIaiPNDpsN~gRAL~lL~~aGLIkLk~~~~~~aT~~DI~eNPK~lki~EldA  182 (268)
T COG1464         108 HIEPM---G--LYSKKYKSLAELKDGATIAIPNDPTNEGRALLLLQKAGLIKLKDGVNLLATPKDITENPKNLKIKELEA  182 (268)
T ss_pred             Eeccc---e--ecchhcCcHhhCCCCCEEECCCCCCchhHHHHHHHHCCcEEEcCCCcccCCHHHHhhCcccCeEEEcch
Confidence            21111   1  1123345788888777777776666666777788888762 1110                  110111


Q ss_pred             HHHHHHHHhccceeeeecceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         228 DIIKTYVELRMGIGIIASIAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       228 ~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ..+-+.+...++..+-+.+....--++  +....+... ...+--.++.++....++.++.|++.+++---+.++++.
T Consensus       183 aqlpRaLddvD~AvIN~nyA~~AgL~p~kdai~~e~~~-~spY~Niivvr~~d~d~~~ik~lv~a~qs~evk~~i~k~  259 (268)
T COG1464         183 AQLPRALDDVDAAVINTNYALQAGLNPKKDALFEEDKD-SSPYVNIIVVREEDKDDPAVKKLVEAYQSDEVKAFIEKK  259 (268)
T ss_pred             HhccccccccCEEEEcchHHHHcCCCccccceeccccc-CCcceEEEEEcccccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence            122222233333333333333332111  222333212 233455677788888999999999998776555555543

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=90.64  E-value=3.2  Score=34.52  Aligned_cols=111  Identities=19%  Similarity=0.207  Sum_probs=58.7

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDT   92 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~   92 (306)
                      ++...|+..|+|.+||||.|..           +.+ +++   .++      .-+++++..+++-.    ..+.+..+..
T Consensus         2 ti~dIA~~aGVS~~TVSrvLn~-----------~~~~~~V---s~~------tr~rV~~~a~elgY~pn~~a~~l~~~~~   61 (328)
T PRK11303          2 KLDEIARLAGVSRTTASYVING-----------KAKQYRV---SDK------TVEKVMAVVREHNYHPNAVAAGLRAGRT   61 (328)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC-----------CCCCCCc---CHH------HHHHHHHHHHHhCCCCCHHHHHhhcCCC
Confidence            5778899999999999999951           110 122   222      22233333333321    1222333334


Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      +.|-+-++. +...++..++..+.+..  -+..+.+....  .   .+.++.+.++.+|-+|..
T Consensus        62 ~~Igvv~~~-~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~  124 (328)
T PRK11303         62 RSIGLIIPD-LENTSYARIAKYLERQARQRGYQLLIACSDDQPDNEMRCAEHLLQRQVDALIVS  124 (328)
T ss_pred             ceEEEEeCC-CCCchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEc
Confidence            445544443 33445555555554432  24555554321  2   235667778899988774

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=90.59  E-value=0.73  Score=35.62  Aligned_cols=44  Identities=11%  Similarity=0.139  Sum_probs=40.1

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |-..-|++|++|..|+..+++++=+.||+
T Consensus       136 T~RE~eVL~ll~~G~-snkeIA~~L~iS~~TV~~h~~~I~~KLgv  179 (207)
T PRK11475        136 SPTEREILRFMSRGY-SMPQIAEQLERNIKTIRAHKFNVMSKLGV  179 (207)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            456788888999877 99999999999999999999999999996

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

Probab=90.57  E-value=0.7  Score=35.75  Aligned_cols=44  Identities=7%  Similarity=0.057  Sum_probs=40.3

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |-.+-|++|++|..|+..+++++=+.||+
T Consensus       139 T~RE~eVL~lla~G~-snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        139 SRTESSMLRMWMAGQ-GTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            456788999999877 99999999999999999999999999997

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=90.49  E-value=0.79  Score=35.26  Aligned_cols=44  Identities=14%  Similarity=-0.089  Sum_probs=40.0

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..++|..+++-. |-..-|++|++|..|+.++++++=+.||+
T Consensus       145 S~RE~eVL~Lia~G~-SnkEIA~~L~IS~~TVk~hvs~I~~KLgv  188 (217)
T PRK13719        145 TKYQNDVFILYSFGF-SHEYIAQLLNITVGSSKNKISEILKFFGI  188 (217)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            456788888899866 99999999999999999999999999997

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=90.48  E-value=0.84  Score=31.78  Aligned_cols=46  Identities=17%  Similarity=0.231  Sum_probs=34.8

Q ss_pred             hhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec
Q psy3760           4 HQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH   52 (306)
Q Consensus         4 ~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~   52 (306)
                      .+.++|.++.  +.+.+...-|+.||.|.||+.|++++|.+   .=|.+|.
T Consensus        28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~---~GlV~Re   75 (126)
T COG3355          28 LDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE---AGLVERE   75 (126)
T ss_pred             HHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH---cCCeeee
Confidence            3456666666  34457889999999999999999999975   3455554

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=90.09  E-value=3  Score=34.65  Aligned_cols=110  Identities=23%  Similarity=0.288  Sum_probs=58.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC--CccccCHhHHHHHHHHHHHHHHHHHHH---H-HHHhhccCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK--RIRGLTKPGQAILRSIEIIMQEIEGLK---K-IGKEFSAYD   91 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~--~~~~lT~~G~~l~~~a~~il~~~~~~~---~-~~~~~~~~~   91 (306)
                      ++..-|+..|+|.+||||.|.            ..++  ++   .+      +.-+++++..+++-   + ..+.+..+.
T Consensus         1 ti~dIA~~aGVS~~TVSrvLn------------~~~~~~~v---s~------~tr~rV~~~a~~lgY~pn~~a~~l~~~~   59 (327)
T TIGR02417         1 TLSDIAKLAGVSKTTASYVIN------------GKAKEYRI---SQ------ETVERVMAVVREQGYQPNIHAASLRAGR   59 (327)
T ss_pred             CHHHHHHHhCCCHHHHHHHHc------------CCCCCCcc---CH------HHHHHHHHHHHHhCCCCCHHHHHhhcCC
Confidence            467789999999999999995            1111  23   22      22233333333321   1 112233333


Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~  149 (306)
                      ...|-+-++. +...++..++..+.+..  -++.+.+...+  .   ...++.+.+..+|-+|..
T Consensus        60 ~~~Igvi~~~-~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~~~~~~~~l~~~~vdgiIi~  123 (327)
T TIGR02417        60 SRTIGLVIPD-LENYSYARIAKELEQQCREAGYQLLIACSDDNPDQEKVVIENLLARQVDALIVA  123 (327)
T ss_pred             CceEEEEeCC-CCCccHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence            3444444432 33445555555554332  35666665432  1   235667788889988875

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=90.08  E-value=3.6  Score=32.80  Aligned_cols=57  Identities=16%  Similarity=0.039  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHhcCC--HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHH
Q psy3760           5 QFRFVREAVRQNFN--LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQA   65 (306)
Q Consensus         5 ~l~~f~~v~~~~~s--~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~   65 (306)
                      -|.++-.+++...+  ++.-|+++|++.||+.|.+..|++.   -+..+++  +.. +|++.--.
T Consensus         6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~---G~v~~d~~~g~Y-~Lg~~~~~   66 (246)
T COG1414           6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL---GYVEQDPEDGRY-RLGPRLLE   66 (246)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC---CCEEEcCCCCcE-eehHHHHH
Confidence            34455555544435  9999999999999999999999873   4566665  345 67664433

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.97  E-value=0.47  Score=31.17  Aligned_cols=40  Identities=20%  Similarity=0.249  Sum_probs=30.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      |-.||-.=...-.|++.-|+..+||.+||.-.|++-|+.|
T Consensus        22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L   61 (105)
T COG2739          22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKIL   61 (105)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHHHHH
Confidence            3334433333335999999999999999999999998876

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

Probab=89.92  E-value=0.6  Score=29.29  Aligned_cols=36  Identities=17%  Similarity=0.132  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      +.+...+.+.|.|+...|+.+||++++|++.+++..
T Consensus        13 ~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen   13 LQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            344444434455999999999999999999999996

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

>PRK06474 hypothetical protein; Provisional

Probab=89.87  E-value=0.97  Score=33.99  Aligned_cols=41  Identities=12%  Similarity=0.184  Sum_probs=33.3

Q ss_pred             hhhHHHHHHHHHhc--CCHHHHHHHh-CCCchHHHHHHHHHHHH
Q psy3760           3 LHQFRFVREAVRQN--FNLTEAAKAL-YTSQPGVSKAIIELEEE   43 (306)
Q Consensus         3 ~~~l~~f~~v~~~~--~s~~~aA~~l-~isq~~~s~~i~~LE~~   43 (306)
                      -..++++..+.+.+  .|....++.+ +++++|++++|+.|++.
T Consensus        11 p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~   54 (178)
T PRK06474         11 PVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS   54 (178)
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence            34567777777755  3788889999 89999999999999874

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

Probab=89.85  E-value=0.38  Score=26.89  Aligned_cols=22  Identities=27%  Similarity=0.218  Sum_probs=20.3

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      |..++|+.+++|.+++.+.+++
T Consensus         2 s~~e~a~~lgvs~~tl~~~~~~   23 (49)
T cd04762           2 TTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHc
Confidence            7889999999999999998886

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

>PRK09483 response regulator; Provisional

Probab=89.70  E-value=0.87  Score=35.12  Aligned_cols=44  Identities=14%  Similarity=0.170  Sum_probs=38.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |..+-|+.|++|..||..+++++-..||+
T Consensus       150 t~rE~~vl~~~~~G~-~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v  193 (217)
T PRK09483        150 SERELQIMLMITKGQ-KVNEISEQLNLSPKTVNSYRYRMFSKLNI  193 (217)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            345667777777766 99999999999999999999999999996

>PRK01066 porphobilinogen deaminase; Provisional

Probab=89.66  E-value=8.4  Score=30.13  Aligned_cols=183  Identities=15%  Similarity=0.064  Sum_probs=94.3

Q ss_pred             CCcEEEEecccchhhh-hHHHHHHHHHhCCCcEEEEEe----CC----------------hhHHHHHHHcCCeeEEEEcc
Q psy3760          92 TGNLTIATTHTQARYA-LPKIIKEFTIQFPKVKLSLLQ----GN----------------PKQITEMIRNDQADIAIVTE  150 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~-l~~~l~~~~~~~p~~~i~~~~----~~----------------~~~~~~~l~~~~~Di~i~~~  150 (306)
                      ...|+||+-.+-...+ ...+...+.+.+|++.+++..    ++                ..++.+.|.+|++|+|+-+.
T Consensus        15 ~~~irIgTR~S~LAl~Qa~~v~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSl   94 (231)
T PRK01066         15 KRPLRIASRQSSLAVAQVHECLRLLRSFFPKLWFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHSA   94 (231)
T ss_pred             CceEEEEeCCCHHHHHHHHHHHHHHHHhCCCCcEEEEEEeccCcccccccHHHcCCceeeHHHHHHHHHcCCCCEEEecC
Confidence            3469999977644444 444456666778988888753    11                33778899999999999873


Q ss_pred             ccCC-CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecC
Q psy3760         151 ILSP-SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN  226 (306)
Q Consensus       151 ~~~~-~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (306)
                      ..-+ ++++.        +.++.++..|-.   .+...++++|..--.|...   +.+.. .+ +.......++.-.-.|
T Consensus        95 KDlPt~~gl~--------l~av~~RedprDvLv~~~~~~l~~Lp~ga~IGTS---S~RR~-aq-l~~~rPdl~v~~iRGN  161 (231)
T PRK01066         95 KDLPEPPKLT--------VVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSS---SLRRE-EL-LKLLFPSGIILDIRGT  161 (231)
T ss_pred             CcCCCCCCCE--------EEEEcCCCCCceEEEECCCCchhhCCCCCEEeCC---hHHHH-HH-HHHHCCCCEEEeCcCC
Confidence            3211 33333        222333333211   0111345555444444332   23322 22 2222233455555688


Q ss_pred             HHHHHHHHHhccceeeee-cceeccc-ccCCc-eeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760         227 SDIIKTYVELRMGIGIIA-SIAFDSN-RDKNL-RSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL  290 (306)
Q Consensus       227 ~~~~~~~v~~g~gi~~~p-~~~~~~~-~~~~l-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  290 (306)
                      +.+=+.-+..|..=+++- .--...+ ....+ ..++.+..+-+.-+.+.++++   +..+..+++.
T Consensus       162 V~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~A~gQGalaie~R~~---d~~~~~ll~~  225 (231)
T PRK01066        162 IEERLKLLEEKKYDAIVVAKAAVLRLGLRLPYTKELPPPYHPLQGRLAITASKH---IRSWKGLFLP  225 (231)
T ss_pred             HHHHHHHhcCCCCCchhhHHHHHHhcCCcccceeECCCCCCCCCCeEEEEEecC---CHHHHHHHHH
Confidence            888888887774333322 2111222 11112 234444434466777877765   3334444443

>PRK09775 putative DNA-binding transcriptional regulator; Provisional

Probab=89.59  E-value=0.44  Score=41.40  Aligned_cols=26  Identities=27%  Similarity=0.201  Sum_probs=24.0

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ... |.+.=|+.|++|||++||+|+.|
T Consensus        12 g~~-~~~eL~~~l~~sq~~~s~~L~~L   37 (442)
T PRK09775         12 GPL-SAAELAARLGVSQATLSRLLAAL   37 (442)
T ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHHh
Confidence            345 99999999999999999999999

>PRK13870 transcriptional regulator TraR; Provisional

Probab=89.53  E-value=0.93  Score=35.83  Aligned_cols=45  Identities=11%  Similarity=0.099  Sum_probs=41.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++.-+++-+ |-...|..|+||..||..+|++.-+.||+.
T Consensus       175 T~RE~E~L~W~A~GK-T~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        175 DPKEATYLRWIAVGK-TMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            457889999999988 999999999999999999999999999874

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

Probab=89.49  E-value=1.8  Score=26.32  Aligned_cols=53  Identities=15%  Similarity=0.260  Sum_probs=33.3

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      +|+..+|+.+|+|++|+-    ..|++.|.. +.|+.+|.-.-|+.--.-+..++.+.
T Consensus         1 ~~i~evA~~~gvs~~tlR----~~~~~g~l~-~~~~~~g~R~y~~~~l~~l~~i~~l~   53 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLR----YYEKEFNLY-IPRTENGRRYYTDEDIELLKKIKTLL   53 (67)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHhcCCC-CCCCCCCceeeCHHHHHHHHHHHHHH
Confidence            378899999999999876    456665554 55654443135555555444444443

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

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=89.45  E-value=5.7  Score=33.24  Aligned_cols=112  Identities=18%  Similarity=0.176  Sum_probs=57.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      ++..-|+..|+|++||||.|.             .++++  =-+..++..+.++++    .-..+ ..+.+..+....|-
T Consensus         8 Ti~dIA~~agVS~~TVSr~Ln-------------~~~~v--s~~tr~~V~~~a~el----gY~p~~~a~~l~~~~~~~Ig   68 (342)
T PRK10014          8 TIHDVALAAGVSVSTVSLVLS-------------GKGRI--STATGERVNQAIEEL----GFVRNRQASALRGGQSGVIG   68 (342)
T ss_pred             cHHHHHHHhCCCHHHHHHHHC-------------CCCCC--CHHHHHHHHHHHHHh----CCCcCHHHHhhccCCCCEEE
Confidence            788999999999999999974             11222  122223333333222    21111 11222333334454


Q ss_pred             EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeC--Ch---hHHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQG--NP---KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~--~~---~~~~~~l~~~~~Di~i~~  149 (306)
                      +-++. +...++..++..+.+..-  +..+.+...  +.   .+.++.+.+..+|-.|..
T Consensus        69 vv~~~-~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~  127 (342)
T PRK10014         69 LIVRD-LSAPFYAELTAGLTEALEAQGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIA  127 (342)
T ss_pred             EEeCC-CccchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEe
Confidence            44443 234455555444333221  345444332  22   245667778889998885

>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=89.42  E-value=0.6  Score=28.41  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=22.7

Q ss_pred             CHHHHHHHhCCC-chHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTS-QPGVSKAIIELEE   42 (306)
Q Consensus        18 s~~~aA~~l~is-q~~~s~~i~~LE~   42 (306)
                      |+..-|+.+|++ .+++.++|+.||+
T Consensus        27 t~rEIa~~~g~~S~~tv~~~L~~Le~   52 (65)
T PF01726_consen   27 TVREIAEALGLKSTSTVQRHLKALER   52 (65)
T ss_dssp             -HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhCCCChHHHHHHHHHHHH
Confidence            788999999997 9999999999995

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.

>PRK00072 hemC porphobilinogen deaminase; Reviewed

Probab=89.35  E-value=11  Score=30.92  Aligned_cols=183  Identities=14%  Similarity=0.127  Sum_probs=95.4

Q ss_pred             CcEEEEecccchh-hhhHHHHHHHHHhCCCcEEEEEeC----C----------------hhHHHHHHHcCCeeEEEEccc
Q psy3760          93 GNLTIATTHTQAR-YALPKIIKEFTIQFPKVKLSLLQG----N----------------PKQITEMIRNDQADIAIVTEI  151 (306)
Q Consensus        93 ~~l~I~~~~~~~~-~~l~~~l~~~~~~~p~~~i~~~~~----~----------------~~~~~~~l~~~~~Di~i~~~~  151 (306)
                      ..++||+-.+-.. .-...+...+.+.+|++++++...    +                ..++.+.|.+|++|+++.+..
T Consensus         3 ~~irIGtR~S~LAl~Qt~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlK   82 (295)
T PRK00072          3 RKIRIGTRGSKLALWQAEWVKDRLKAAHPGLEVELVPIKTKGDKILDVPLAKIGGKGLFVKELEEALLEGEIDIAVHSLK   82 (295)
T ss_pred             ccEEEEeCCCHHHHHHHHHHHHHHHHHCCCCeEEEEEeeccCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccC
Confidence            3589999766433 344555566777789888887541    2                236778999999999999743


Q ss_pred             cCC---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEec
Q psy3760         152 LSP---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI  225 (306)
Q Consensus       152 ~~~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (306)
                      .-+   ++++.        +..+.+++.|-.   .++.-++++|..-..|...   +.|.. . .+.......+++-.-.
T Consensus        83 DlP~~l~~gl~--------i~avl~R~dprDvlv~~~~~~l~~Lp~ga~IGTs---S~RR~-a-ql~~~~Pdl~~~~iRG  149 (295)
T PRK00072         83 DVPTELPEGLV--------LAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTS---SLRRQ-A-QLLALRPDLEIKPLRG  149 (295)
T ss_pred             cCCCCCCCCcE--------EEEEecCCCCceEEEECCCCChhHCCCCCEEecC---cHHHH-H-HHHHHCcCCEEEECcc
Confidence            222   23333        233333333311   1112366776554444432   33332 2 2222222234444458


Q ss_pred             CHHHHHHHHHhccceeee-ecceeccc-ccCCc-eeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         226 NSDIIKTYVELRMGIGII-ASIAFDSN-RDKNL-RSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       226 ~~~~~~~~v~~g~gi~~~-p~~~~~~~-~~~~l-~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      |+++=+.-+.+|..=+++ ..--.... ....+ ..++.+.   .+-+.-+.+.++++   +..+..+++.|
T Consensus       150 NV~TRL~KL~~g~~DaivLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~---d~~~~~~l~~i  218 (295)
T PRK00072        150 NVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEMLPAPGQGALGIECRAD---DEEILELLAPL  218 (295)
T ss_pred             CHHHHHHHhhCCCCCEeehHhhHHHHcCCccccceecChhhcCCcccccceeeeeecC---CHHHHHHHHHc
Confidence            999999999888443332 22222222 11112 2344333   12244566666654   45555665555

>TIGR01764 excise DNA binding domain, excisionase family

Probab=89.29  E-value=0.44  Score=26.71  Aligned_cols=22  Identities=36%  Similarity=0.303  Sum_probs=19.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      |+.+||+.||+|.+++.+.+++
T Consensus         3 t~~e~a~~lgis~~ti~~~~~~   24 (49)
T TIGR01764         3 TVEEAAEYLGVSKDTVYRLIHE   24 (49)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHc
Confidence            7899999999999999998864

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

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=89.26  E-value=0.91  Score=36.27  Aligned_cols=58  Identities=21%  Similarity=0.125  Sum_probs=44.3

Q ss_pred             hhhHHHHHHHHHhcCCHHHH--HHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760           3 LHQFRFVREAVRQNFNLTEA--AKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT   60 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~a--A~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT   60 (306)
                      -+..+++..+.+.|+-++++  .+++|.|.+|+||++++||+.==++++.+.+...++|.
T Consensus       195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~  254 (258)
T COG2512         195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELR  254 (258)
T ss_pred             HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEe
Confidence            45677888888988336555  58999999999999999998765677777666554443

>PRK09954 putative kinase; Provisional

Probab=89.20  E-value=0.8  Score=38.90  Aligned_cols=54  Identities=26%  Similarity=0.207  Sum_probs=39.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT   60 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT   60 (306)
                      ||-++.+++..+-+.+ .|.+.-|+.|++|++++.++|++|++ -|..    .+++. .+.
T Consensus         1 ~~~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~-~g~i----~~~~~-~l~   55 (362)
T PRK09954          1 MNNREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMR-KGRI----KGKGY-ILT   55 (362)
T ss_pred             CChHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCc----CCcEE-EEc
Confidence            5556666666666653 26777899999999999999999997 4543    34555 354

>PF12728 HTH_17: Helix-turn-helix domain

Probab=89.18  E-value=0.43  Score=27.26  Aligned_cols=22  Identities=32%  Similarity=0.261  Sum_probs=19.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      |..+||+.|++|.+++.+.+++
T Consensus         3 t~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    3 TVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHc
Confidence            7889999999999999988863

>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12

Probab=89.12  E-value=11  Score=30.79  Aligned_cols=181  Identities=16%  Similarity=0.179  Sum_probs=92.2

Q ss_pred             EEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEeC----C----------------hhHHHHHHHcCCeeEEEEccccC
Q psy3760          95 LTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQG----N----------------PKQITEMIRNDQADIAIVTEILS  153 (306)
Q Consensus        95 l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~~----~----------------~~~~~~~l~~~~~Di~i~~~~~~  153 (306)
                      |+||+-.|-... -...+...+.+.+|++++++...    +                ..++.+.|.+|++|+++.+...-
T Consensus         1 irIgtR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlKDl   80 (292)
T cd00494           1 IRIGTRKSKLALIQTNKVIEKLKELCPGIEVEIVIIKTTGDKILDKPLAKIGGKGLFTKELEEALLNGEIDLAVHSLKDV   80 (292)
T ss_pred             CEEEcCCCHHHHHHHHHHHHHHHHhCCCCeEEEEEEEecCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccccC
Confidence            467775553333 33334455666688887777441    1                22677899999999999874322


Q ss_pred             C---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760         154 P---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS  227 (306)
Q Consensus       154 ~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (306)
                      +   ++++.        +..+.++..|-.   .+...++++|..-..|...   +.|..  ..+.......+++-.-.|+
T Consensus        81 P~~lp~gl~--------i~av~~RedprDvlv~~~~~~l~~Lp~ga~IGTs---S~RR~--aql~~~rpdl~~~~iRGNV  147 (292)
T cd00494          81 PTELPEGLV--------LGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTS---SLRRQ--AQLKRKRPDLKFEPLRGNV  147 (292)
T ss_pred             CCCCCCCcE--------EEEEecCCCCceEEEECCCCChhHCCCCCEEecC---CHHHH--HHHHHHCCCCEEEEcCCCH
Confidence            2   23333        223333333211   1112366777655545432   33332  2233333334555566899


Q ss_pred             HHHHHHHHhccceeee-ecceeccc-ccCCc-eeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         228 DIIKTYVELRMGIGII-ASIAFDSN-RDKNL-RSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       228 ~~~~~~v~~g~gi~~~-p~~~~~~~-~~~~l-~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      .+=+.-+.+|..=+++ ..--.... ....+ ..++.+.   .+-+.-+.+-++++   +..+..+++.|
T Consensus       148 ~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~---d~~~~~ll~~i  214 (292)
T cd00494         148 DTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKG---DEELLALLKPL  214 (292)
T ss_pred             HHHHHHhcCCCCCEeehHhhHHHHcCCcccCccccCccccCCccccceEEEEEecC---CHHHHHHHHHC
Confidence            9999989888433332 22212222 11112 2333332   12245666666655   34455555555

HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=89.01  E-value=0.7  Score=30.29  Aligned_cols=33  Identities=24%  Similarity=0.264  Sum_probs=25.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      +.++-.+.+.+.|-.+.|+.+|||+++|||-=+
T Consensus        45 ~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn   77 (94)
T TIGR01321        45 IRIVNELLNGNMSQREIASKLGVSIATITRGSN   77 (94)
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence            445555655444999999999999999997543

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

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

Probab=88.92  E-value=0.44  Score=29.11  Aligned_cols=37  Identities=19%  Similarity=0.261  Sum_probs=27.9

Q ss_pred             CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHH
Q psy3760          27 YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI   66 (306)
Q Consensus        27 ~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l   66 (306)
                      .+|..||.++++.||+. |  +..|.+++...+|+.|..+
T Consensus        29 ~~se~avRrrLr~me~~-G--lt~~~g~~G~~iT~~G~~~   65 (66)
T PF08461_consen   29 ELSEEAVRRRLRAMERD-G--LTRKVGRQGRIITEKGLDE   65 (66)
T ss_pred             hhhHHHHHHHHHHHHHC-C--CccccCCcccccCHHHHhh
Confidence            56779999999999987 4  5555544333699999875

>PRK15046 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional

Probab=88.88  E-value=13  Score=31.36  Aligned_cols=98  Identities=11%  Similarity=0.142  Sum_probs=63.7

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc----CCeeEEEEccccC----------C-
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN----DQADIAIVTEILS----------P-  154 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~----~~~Di~i~~~~~~----------~-  154 (306)
                      ...+.|+|.+.... ..++..++..|.+++ +++|++...++.++...+..    +.+|+++......          + 
T Consensus        32 ~~~~~L~v~~~~~~-~~~~~~ii~~Fe~~~-gikV~~~~~~s~~~~~kl~~~~~~~~~DVv~~~~~~~~~~~~~Gll~~~  109 (349)
T PRK15046         32 WAADAVTVYSADGL-EDWYQDVFPAFTKAT-GIKVNYVEAGSGEVVNRAAKEKSNPQADVLVTLPPFIQQAAAEGLLQPY  109 (349)
T ss_pred             ccCCcEEEEeccch-HHHHHHHHHHHHhhh-CcEEEEEeCChHHHHHHHHhhhcCCCCCEEEeCcHHHHHHHhCCCcccc
Confidence            34467999987554 357889999998875 89999999888888877753    4799987531100          0 


Q ss_pred             -CCC---c---------eeeccccceEEEEecCCCCCCCCCCcChhhhcC
Q psy3760         155 -SDK---L---------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN  191 (306)
Q Consensus       155 -~~~---~---------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~  191 (306)
                       ..+   +         .+.++....++++..++..  ...+-+|+||.+
T Consensus       110 ~~~~~~~i~~~~~d~~g~~~~~~~~~~~l~Yn~~~~--~~~P~sw~dL~~  157 (349)
T PRK15046        110 SSVNAKAVPAIAKDADGTYAPFVNNYLSFIYNPKVL--KTAPATWADLLD  157 (349)
T ss_pred             CccchhcCchhhcCCCCCEEeeecceeEEEEchhhc--cCCCCCHHHHhC
Confidence             000   0         1233444455677777653  234678999976

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

Probab=88.61  E-value=0.41  Score=30.54  Aligned_cols=24  Identities=33%  Similarity=0.297  Sum_probs=17.0

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .|.|=..+|+.+|+|||.||+-.+
T Consensus        30 ~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   30 RGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             CT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCChhHHHHHHc
Confidence            334567899999999999998653

>COG1568 Predicted methyltransferases [General function prediction only]

Probab=88.44  E-value=1.7  Score=34.70  Aligned_cols=57  Identities=18%  Similarity=0.198  Sum_probs=50.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR   68 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~   68 (306)
                      .++.++..++ |+-+-+..-..+-|.++.-+..||++   .+..++.+++ ++|+.|+.|.+
T Consensus        26 ~vl~ail~~~-d~wkIvd~s~~plp~v~~i~~~l~~e---giv~~~~g~v-~~TekG~E~~e   82 (354)
T COG1568          26 NVLSAILATN-DFWKIVDYSDLPLPLVASILEILEDE---GIVKIEEGGV-ELTEKGEELAE   82 (354)
T ss_pred             HHHHHHHcCc-chHhhhhhccCCchHHHHHHHHHHhc---CcEEEecCcE-eehhhhHHHHH
Confidence            3677889999 99999999999999999999999985   5777788887 99999999865

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=88.41  E-value=13  Score=30.68  Aligned_cols=21  Identities=14%  Similarity=0.218  Sum_probs=19.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++..-|+..|+|++||||.|.
T Consensus         3 ti~dIA~~agVS~sTVSr~Ln   23 (311)
T TIGR02405         3 TIKDIARLAGVGKSTVSRVLN   23 (311)
T ss_pred             cHHHHHHHhCCCHHHHHHHhC
Confidence            678899999999999999993

This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis

>PRK00215 LexA repressor; Validated

Probab=88.37  E-value=1.2  Score=34.28  Aligned_cols=42  Identities=21%  Similarity=0.178  Sum_probs=32.4

Q ss_pred             chhhHHHHHHHHH----hcC--CHHHHHHHhCC-CchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR----QNF--NLTEAAKALYT-SQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~----~~~--s~~~aA~~l~i-sq~~~s~~i~~LE~~   43 (306)
                      +-+|.+++..+.+    .+.  |++.-|+.+++ |+||+++.|+.||+.
T Consensus         3 t~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~   51 (205)
T PRK00215          3 TKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK   51 (205)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence            4456666655543    232  68899999999 999999999999985

>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]

Probab=88.14  E-value=0.27  Score=37.52  Aligned_cols=48  Identities=15%  Similarity=0.147  Sum_probs=40.8

Q ss_pred             ChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecCCCC
Q psy3760         130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHP  177 (306)
Q Consensus       130 ~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~  177 (306)
                      ........+.+|++|++++.......-++.++||.++++-++++++..
T Consensus       138 th~avA~aVa~G~AD~GvGlr~~A~~~gL~Fipl~~E~YD~virke~~  185 (223)
T COG1910         138 THDAVASAVASGRADAGVGLRHAAEKYGLDFIPLGDEEYDFVIRKERL  185 (223)
T ss_pred             ccHHHHHHHHcCCCCccccHHHHHHHcCCceEEcccceEEEEEehhHc
Confidence            345678899999999999975555668899999999999999999873

>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []

Probab=88.05  E-value=8.7  Score=31.23  Aligned_cols=137  Identities=12%  Similarity=0.009  Sum_probs=69.3

Q ss_pred             ccccceEEEEecCCCCCCCCCCcChhhh----cCCC--eEeecCCC-CcHHHH-HHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760         162 PCYQWEYVIIVPLDHPLLLLNSISLKEI----SNYP--LITYDLSF-SGRIKL-DREFSLQKLTPYIVLETINSDIIKTY  233 (306)
Q Consensus       162 ~l~~~~~~~v~~~~~~l~~~~~i~~~dl----~~~~--~i~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (306)
                      .+..++.+++++++.|.     -+++||    ...|  +..-..+. ...+.. ..+.+..|+..+.+- .+.....+..
T Consensus        74 ~~~~~~~vl~v~~dsp~-----~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~~~~Vp-y~G~~~~~~a  147 (274)
T PF03401_consen   74 RIASDPNVLVVRADSPY-----KTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIKFTHVP-YDGGAEALTA  147 (274)
T ss_dssp             EEEEEEEEEEEETTSS------SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT---EEEE--SSHHHHHHH
T ss_pred             hhhccceEEEEeCCCcc-----ccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCceEEEE-eCCccHHHHH
Confidence            35567889999999874     366666    2323  33222222 223333 344566688766553 4455555555


Q ss_pred             HHhc-cceeeeecceeccc-ccCCceeeec--------------------CCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         234 VELR-MGIGIIASIAFDSN-RDKNLRSISA--------------------SHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       234 v~~g-~gi~~~p~~~~~~~-~~~~l~~~~~--------------------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +..| .-+++.....+..+ +.++++.+-.                    ++.....-..++.+++.+ ...+..+.+.+
T Consensus       148 llgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp-~~~~~~l~~a~  226 (274)
T PF03401_consen  148 LLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTP-DEIVDKLADAI  226 (274)
T ss_dssp             HHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS--HHHHHHHHHHH
T ss_pred             HhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCC-HHHHHHHHHHH
Confidence            5555 33333333222233 5555554311                    010111122355577775 77888888999


Q ss_pred             hHHhhHHHHHhhhc
Q psy3760         292 SPKLNRKFINKILN  305 (306)
Q Consensus       292 ~~~~~~~~~~~~~~  305 (306)
                      ++.++.....+.++
T Consensus       227 ~~~~~~pe~~~~~~  240 (274)
T PF03401_consen  227 KKALEDPEFQEFLE  240 (274)
T ss_dssp             HHHHT-HHHHHHHH
T ss_pred             HHHhCCHHHHHHHH
Confidence            98887777766543

Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.

>PRK09526 lacI lac repressor; Reviewed

Probab=88.01  E-value=15  Score=30.79  Aligned_cols=112  Identities=13%  Similarity=0.138  Sum_probs=57.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      ++..-|+..|+|++||||.|..             +.++   .+   .--+++.++.+++.-.-+ ..+.++.+..+.|-
T Consensus         7 ti~dIA~~aGVS~~TVSrvLn~-------------~~~v---s~---~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig   67 (342)
T PRK09526          7 TLYDVARYAGVSYQTVSRVLNQ-------------ASHV---SA---KTREKVEAAMAELNYVPNRVAQQLAGKQSLTIG   67 (342)
T ss_pred             cHHHHHHHhCCCHHHHHHHhcC-------------CCCC---CH---HHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEE
Confidence            7889999999999999999831             1222   11   112222222222221111 11223333344444


Q ss_pred             EEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h----hHHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P----KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~----~~~~~~l~~~~~Di~i~~  149 (306)
                      +-++. +...+...++..+.+..  -++.+.+...+  .    .+.++.+.+..+|-+|+.
T Consensus        68 vv~~~-~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~  127 (342)
T PRK09526         68 LATTS-LALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIIN  127 (342)
T ss_pred             EEeCC-CCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence            44443 22333344444443321  25666664322  1    245677888899988874

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=87.96  E-value=4.5  Score=32.50  Aligned_cols=45  Identities=13%  Similarity=0.155  Sum_probs=33.9

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQA   65 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~   65 (306)
                      .|++.-|+.++++.||+.|-++.|++. |.  ..|.  ++.. +|++.-..
T Consensus        29 l~l~eia~~lgl~kstv~Rll~tL~~~-G~--l~~~~~~~~Y-~lG~~~~~   75 (257)
T PRK15090         29 IGITELSQRVMMSKSTVYRFLQTMKTL-GY--VAQEGESEKY-SLTLKLFE   75 (257)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHC-CC--EEEcCCCCcE-EecHHHHH
Confidence            389999999999999999999999863 44  4443  4555 67765433

>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences

Probab=87.55  E-value=0.35  Score=29.56  Aligned_cols=32  Identities=22%  Similarity=0.113  Sum_probs=23.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHH-HHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVS-KAII   38 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s-~~i~   38 (306)
                      |+-+..+...+ +-..-|+.|+||++++| ...+
T Consensus         3 i~rl~~~~g~~-~~~~lA~~lgis~st~s~~~~~   35 (66)
T PF07022_consen    3 IERLKEALGVK-SDKELAERLGISKSTLSNNWKK   35 (66)
T ss_dssp             HHHHHHHHT-S-SCHHHHCCTT--HHHHH-HHHH
T ss_pred             HHHHHHHhCCC-CHHHHHHHhCcCHHHhhHHHHh
Confidence            56677788888 88999999999999999 5543

The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=87.39  E-value=1.6  Score=34.05  Aligned_cols=44  Identities=14%  Similarity=0.218  Sum_probs=39.6

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..++|..+++-. |...-|+.|++|..|+..+++++=..+|+
T Consensus       157 t~rE~~Vl~l~~~G~-s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        157 THREKEILNKLRIGA-SNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            456788999999855 99999999999999999999999888886

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=87.36  E-value=0.68  Score=34.24  Aligned_cols=42  Identities=33%  Similarity=0.345  Sum_probs=32.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |...-|+.+++|.||+++.|+.||+.   .++.|.+.|...+.|.
T Consensus        77 t~~~ia~~l~iS~~Tv~r~ik~L~e~---~iI~k~~~G~Y~iNP~  118 (165)
T PF05732_consen   77 TQKEIAEKLGISKPTVSRAIKELEEK---NIIKKIRNGAYMINPN  118 (165)
T ss_pred             eHHHHHHHhCCCHHHHHHHHHHHHhC---CcEEEccCCeEEECcH
Confidence            56778999999999999999999984   3455555554468876

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []

Probab=87.10  E-value=0.57  Score=35.76  Aligned_cols=50  Identities=12%  Similarity=0.141  Sum_probs=41.6

Q ss_pred             EeCChhHHHHHHHcCCeeEEEEccccCCC-CCceeeccccceEEEEecCCC
Q psy3760         127 LQGNPKQITEMIRNDQADIAIVTEILSPS-DKLISIPCYQWEYVIIVPLDH  176 (306)
Q Consensus       127 ~~~~~~~~~~~l~~~~~Di~i~~~~~~~~-~~~~~~~l~~~~~~~v~~~~~  176 (306)
                      ...+..++...+.+|.+|++++....... .++.+.|+..+++.++++++.
T Consensus       129 ~~~th~~vA~aVa~G~AD~G~g~~~~A~~~~gL~Fvpl~~E~~dlv~~~~~  179 (193)
T PF12727_consen  129 EANTHLAVAAAVASGKADAGIGIRAAAEEFYGLDFVPLAEERYDLVIRRED  179 (193)
T ss_pred             cccChHHHHHHHHcCCCCEEeehHHHHHhhcCCCcEEccccceEEEEEhhH
Confidence            34456688999999999999997553434 699999999999999999876

It is often associated with a helix-turn-helix domain.

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=87.09  E-value=1.2  Score=29.14  Aligned_cols=30  Identities=20%  Similarity=0.187  Sum_probs=26.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      ..+..+.+.. .+++.|+..|||++++++..
T Consensus        35 ~~l~~~r~~~-glSqLAe~~GIs~stLs~iE   64 (89)
T TIGR02684        35 HALGYIARAR-GMTQLARKTGLSRESLYKAL   64 (89)
T ss_pred             HHHHHHHHHC-ChHHHHHHHCCCHHHHHHHH
Confidence            4567888898 99999999999999999753

gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.

>PRK10651 transcriptional regulator NarL; Provisional

Probab=87.01  E-value=1.6  Score=33.37  Aligned_cols=43  Identities=7%  Similarity=0.060  Sum_probs=38.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+..++|..+++.. +-..-|+.|++|..||..++++|-..||.
T Consensus       158 ~rE~~vl~~l~~g~-~~~~ia~~l~is~~tV~~~~~~l~~Kl~~  200 (216)
T PRK10651        158 PRERDILKLIAQGL-PNKMIARRLDITESTVKVHVKHMLKKMKL  200 (216)
T ss_pred             HHHHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence            46677888888776 99999999999999999999999999986

>PF13309 HTH_22: HTH domain

Probab=86.93  E-value=0.37  Score=29.21  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=18.0

Q ss_pred             CHHHHHHHhCCCchHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i   37 (306)
                      +...+|+.||+|.+||-+-|
T Consensus        44 av~~vA~~L~iS~~TVY~YL   63 (64)
T PF13309_consen   44 AVEYVAEKLGISRATVYRYL   63 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHc
Confidence            77899999999999998765

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

Probab=86.88  E-value=3.5  Score=25.06  Aligned_cols=53  Identities=15%  Similarity=0.056  Sum_probs=31.9

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i   73 (306)
                      +|+..+|+.+|+|++++.+..++    .|..--.|+.+|.-..|+.=-.-+..++.+
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~----~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l   53 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERR----YGLPAPQRTDGGHRLYSEADVARLRLIRRL   53 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHh----CCCCCCCcCCCCCeecCHHHHHHHHHHHHH
Confidence            47889999999999999986543    344333454333214566544444444433

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

>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]

Probab=86.82  E-value=1  Score=33.61  Aligned_cols=93  Identities=16%  Similarity=0.226  Sum_probs=65.5

Q ss_pred             hCCCchHHHHHHHHHHHHcCce----------eEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-c
Q psy3760          26 LYTSQPGVSKAIIELEEELSID----------IFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG-N   94 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~----------Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~-~   94 (306)
                      .+|. |++-+-+...=+.-|++          +..+.++.. +++-.+..||++++.+-+.+++-.......--.... .
T Consensus        49 cyiP-PsVY~El~~fm~r~gc~~e~~~ki~twivkKtPnry-evkiPa~ifyeyV~diR~RinkGlRvAE~~i~eA~~~~  126 (221)
T COG1458          49 CYIP-PSVYRELMGFMERNGCPEEVIAKIETWIVKKTPNRY-EVKIPAAIFYEYVEDIRERINKGLRVAEEAIREASIEC  126 (221)
T ss_pred             EEeC-hHHHHHHHHHHHhCCCcHHHHHhhheeeEecCCCce-eecCcHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence            3455 88888888777766666          788888998 899999999999999999988776544433111111 0


Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCC
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPK  121 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~  121 (306)
                      ..+- ...+....+..++..|++.|-.
T Consensus       127 ~~~~-~~~i~~e~igk~I~~lR~KYR~  152 (221)
T COG1458         127 YELE-KEEIIREVVGKIIRKLREKYRE  152 (221)
T ss_pred             HHhh-hhhHHHHHHHHHHHHHHHHHHH
Confidence            1111 3455677888899999888743

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=86.53  E-value=0.56  Score=29.66  Aligned_cols=25  Identities=16%  Similarity=0.090  Sum_probs=20.1

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      .- |++.-|+..|+|++||+|-.++|
T Consensus        34 ~~-si~elA~~~~vS~sti~Rf~kkL   58 (77)
T PF01418_consen   34 FM-SISELAEKAGVSPSTIVRFCKKL   58 (77)
T ss_dssp             T---HHHHHHHCTS-HHHHHHHHHHC
T ss_pred             Hc-cHHHHHHHcCCCHHHHHHHHHHh
Confidence            56 99999999999999999988875

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed

Probab=86.45  E-value=2  Score=39.00  Aligned_cols=50  Identities=8%  Similarity=0.072  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760           5 QFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus         5 ~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      +...+..++.-+| |-..=|+.|++|.++|+++++.|+ ++|..++ .+++|.
T Consensus         8 ~~~ll~~L~dg~~hSge~l~~~lgisr~av~~~~~~~~-~~~~~i~-v~g~GY   58 (592)
T PRK13325          8 HWRVLAELADGLPQHVSQLARMADMKPQQLNGFWQQMP-AHIRGLL-RQHDGY   58 (592)
T ss_pred             HHHHHHHHhCCCccCHHHHHHHhCCCHHHHHHHHHHHH-HhCcEEE-EcCCCh
Confidence            3444444554333 779999999999999999999999 5556776 455664

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=86.35  E-value=6.6  Score=27.44  Aligned_cols=67  Identities=28%  Similarity=0.326  Sum_probs=47.2

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHH--HHHHHHHHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI--EIIMQEIEGLKKIGK   85 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a--~~il~~~~~~~~~~~   85 (306)
                      .- |...=|..+++.+-|++|.-+.||.+ | -++.+.|.|.+ .|+.|......-  ..+-+.++.+...+.
T Consensus        35 LP-SvRelA~~~~VNpnTv~raY~eLE~e-G-~i~t~rg~G~f-V~~~~~~~~~~~~~~~~~~~l~~~I~~~~  103 (125)
T COG1725          35 LP-SVRELAKDLGVNPNTVQRAYQELERE-G-IVETKRGKGTF-VTEDAKEILDQLKRELAEEELEEFIEEAK  103 (125)
T ss_pred             CC-cHHHHHHHhCCCHHHHHHHHHHHHHC-C-CEEEecCeeEE-EcCCchhhHHHHHHHHHHHHHHHHHHHHH
Confidence            45 88999999999999999999999986 3 45666778884 998888644322  223333444444444

>PHA02943 hypothetical protein; Provisional

Probab=86.33  E-value=10  Score=27.33  Aligned_cols=52  Identities=15%  Similarity=0.026  Sum_probs=39.8

Q ss_pred             HHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          10 REAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        10 ~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      +++.+.| .|.++-|+.||+|.+.+...|.-||.+=-++=..|+...++.+.+
T Consensus        17 LE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~   69 (165)
T PHA02943         17 LRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDE   69 (165)
T ss_pred             HHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEECh
Confidence            3333444 267899999999999999999999998666666666666656777

>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional

Probab=86.29  E-value=14  Score=28.94  Aligned_cols=148  Identities=11%  Similarity=0.033  Sum_probs=78.6

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC---------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCe
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD---------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL  194 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~---------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~  194 (306)
                      +++.-.-..++...+..|.+|+||+........         .+.-..++.-++++++|+++.    ..-+++||.+...
T Consensus        47 i~~~~vR~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~~v~elldLgfG~crl~vA~p~~~~----~~~~~~dl~~~~~  122 (228)
T PRK13583         47 VELLFLSASEIPRELGAGRVDLGVTGEDLVREKLADWDKRVEIVARLGFGHADLVVAVPEIWI----DVDTMADLDDVAA  122 (228)
T ss_pred             eEEEEECHHHHHHHHhCCCCcEEEeeeeeeecccccCCCCeEEEecCCCCceEEEEEEECccc----ccCCHHHhhhhhh
Confidence            444444567899999999999999853222211         122334567788999987743    1235666652221


Q ss_pred             Ee-------ecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHHhccceeeeecce-ecccccCCceeeecCCCC
Q psy3760         195 IT-------YDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVELRMGIGIIASIA-FDSNRDKNLRSISASHLF  265 (306)
Q Consensus       195 i~-------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~~~~~~l~~~~~~~~~  265 (306)
                      ..       ..-...+.+...++|.+.|+.. .++....+.+.+   ..-|.+=+++--.. -..++..+|+.+.-.. .
T Consensus       123 ~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv~l~GsvEla---P~~GlAD~IvDivsTG~TLr~NgL~~i~~~~-I  198 (228)
T PRK13583        123 DFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEGA---PANGSAEIIVDITSTGETLRANHLKILSDGV-I  198 (228)
T ss_pred             hhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEEECCCceecc---cccCcchhhhhhhchhHHHHHCCCEEecCce-E
Confidence            10       0011124467788999999884 665544555432   11121111111100 0112345677664111 3


Q ss_pred             ccceEEEEEeCCcc
Q psy3760         266 GTTISRVIIKQGTY  279 (306)
Q Consensus       266 ~~~~~~l~~~~~~~  279 (306)
                      ...+..++.++...
T Consensus       199 l~SsA~LI~n~~s~  212 (228)
T PRK13583        199 LRSQACLVRARKAD  212 (228)
T ss_pred             EEEEEEEEEecccc
Confidence            34577888877753

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

Probab=86.21  E-value=1  Score=25.85  Aligned_cols=22  Identities=27%  Similarity=0.217  Sum_probs=19.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      .+..||+.|||+.+++-+.-++
T Consensus        17 p~~eAA~~Lgv~~T~LKr~CR~   38 (52)
T PF02042_consen   17 PIKEAAKELGVSVTTLKRRCRR   38 (52)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Confidence            7899999999999888777663

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

>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins

Probab=86.16  E-value=1.2  Score=28.90  Aligned_cols=49  Identities=20%  Similarity=0.067  Sum_probs=39.0

Q ss_pred             HHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760          22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI   83 (306)
Q Consensus        22 aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~   83 (306)
                      |...||.||.++|.-++             .++..-.||+.|+..|......++.-+.....
T Consensus        33 a~~vL~rsqgtlsdlL~-------------~PKpW~~L~~~gre~y~RM~nWL~~~e~~r~~   81 (87)
T PF02376_consen   33 AKKVLNRSQGTLSDLLR-------------KPKPWNKLKPKGREPYIRMYNWLSLPEEERME   81 (87)
T ss_dssp             HHHTTSS-HHHHHHHHH-------------SCCTTCHHHHHHHHHHHHHHHHHCSTHHHHHH
T ss_pred             HHHHhccChhHHHHHhC-------------CCCCHHHcCccccHHHHHHHHHhcCCHHHHHH
Confidence            57889999999998877             55665479999999999999998876665543

The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=85.96  E-value=1.9  Score=35.06  Aligned_cols=78  Identities=13%  Similarity=0.036  Sum_probs=51.9

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCc
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGN   94 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~   94 (306)
                      .+ ++-+..+.++|+.+++--.+++|+++==..=-.+.+++..+||+.|+..+..+.+-+-.         .-...-.|.
T Consensus        20 ~~-~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~---------~~~~~WdG~   89 (280)
T TIGR02277        20 LG-SLIEFLAGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD---------PPAPAWDGK   89 (280)
T ss_pred             HH-HHHHHHHhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC---------CCCCCCCCc
Confidence            46 78899999999999999999999986322222222233348999999888775544321         112334667


Q ss_pred             EEEEeccc
Q psy3760          95 LTIATTHT  102 (306)
Q Consensus        95 l~I~~~~~  102 (306)
                      ..+.+...
T Consensus        90 W~lv~~~~   97 (280)
T TIGR02277        90 WRLLLLSG   97 (280)
T ss_pred             eEEEEeCC
Confidence            77766543

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

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

Probab=85.81  E-value=0.88  Score=25.56  Aligned_cols=21  Identities=19%  Similarity=0.077  Sum_probs=18.1

Q ss_pred             CCHHHHHHHhCCCchHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i   37 (306)
                      +|.+++|+.+|+|.++|.+.+
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~   21 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYE   21 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHH
Confidence            478999999999999988664

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

>PRK09492 treR trehalose repressor; Provisional

Probab=85.66  E-value=8.4  Score=31.79  Aligned_cols=21  Identities=14%  Similarity=0.203  Sum_probs=19.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++..-|+..|+|++||||.|.
T Consensus         6 ti~dIA~~agVS~~TVSrvLn   26 (315)
T PRK09492          6 TIKDIARLSGVGKSTVSRVLN   26 (315)
T ss_pred             cHHHHHHHhCCCHHHHhHHhC
Confidence            788999999999999999984

>PRK12423 LexA repressor; Provisional

Probab=85.51  E-value=2.4  Score=32.63  Aligned_cols=41  Identities=20%  Similarity=0.143  Sum_probs=32.8

Q ss_pred             chhhHHHHHHHHH-------hcCCHHHHHHHhC-CCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR-------QNFNLTEAAKALY-TSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~-------~~~s~~~aA~~l~-isq~~~s~~i~~LE~~   43 (306)
                      +-++-+++..+.+       .. |..+-|+.+| +|+++++++|+.|++.
T Consensus         5 t~~q~~il~~l~~~i~~~g~~P-s~~eia~~~g~~s~~~v~~~l~~L~~~   53 (202)
T PRK12423          5 TPKRAAILAFIRERIAQAGQPP-SLAEIAQAFGFASRSVARKHVQALAEA   53 (202)
T ss_pred             CHHHHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence            3455666666665       35 8999999999 5999999999999984

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=85.10  E-value=2.2  Score=30.10  Aligned_cols=37  Identities=19%  Similarity=0.222  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         6 l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      ++.+..+++.+   -|...-|+.+++|++++++.++.|++
T Consensus        12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~   51 (130)
T TIGR02944        12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL   51 (130)
T ss_pred             HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            44555555432   37888999999999999999999998

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.

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.05  E-value=5  Score=26.64  Aligned_cols=46  Identities=26%  Similarity=0.285  Sum_probs=35.9

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++|+......++++|+...-+.||+|.||+.-.+.++=..+|..
T Consensus        43 t~d~LeFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~vlramgy~   88 (122)
T COG3877          43 TSDQLEFVELFLRCRGNLKEVERELGISYPTVRTKLDEVLRAMGYN   88 (122)
T ss_pred             CHhHhHHHHHHHHHccCHHHHHHHHCCccHHHHHHHHHHHHHcCCC
Confidence            3456665555555545999999999999999999998888777753

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=84.98  E-value=2.4  Score=32.16  Aligned_cols=43  Identities=12%  Similarity=0.119  Sum_probs=36.9

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      .+..++|.-+++.. |....|+.+++|..|+..+++++-..+|+
T Consensus       152 ~~e~~vl~l~~~g~-~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~  194 (211)
T PRK15369        152 PRERQILKLITEGY-TNRDIAEQLSISIKTVETHRLNMMRKLDV  194 (211)
T ss_pred             HHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            34566676677766 99999999999999999999999999985

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=84.75  E-value=12  Score=29.93  Aligned_cols=38  Identities=16%  Similarity=0.141  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         5 ~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      +-++.-.+.+.|+ +...-|+.+++|..|+-|=|+.||+
T Consensus         9 ~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~   47 (252)
T PRK10681          9 IGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSA   47 (252)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence            3344444444441 6788999999999999999999995

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

Probab=84.74  E-value=1.5  Score=27.36  Aligned_cols=41  Identities=27%  Similarity=0.300  Sum_probs=32.4

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |-..-|..+|+|..++++.+++|+++   -++..+++.+ .+++.
T Consensus        30 t~~~iA~~~g~sr~tv~r~l~~l~~~---g~I~~~~~~i-~I~d~   70 (76)
T PF13545_consen   30 TQEEIADMLGVSRETVSRILKRLKDE---GIIEVKRGKI-IILDP   70 (76)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHHHHHT---TSEEEETTEE-EESSH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEcCCEE-EECCH
Confidence            56778999999999999999999986   3566666776 45543

...

>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []

Probab=84.68  E-value=1.6  Score=27.03  Aligned_cols=17  Identities=24%  Similarity=0.368  Sum_probs=11.9

Q ss_pred             hCCCchHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEE   42 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~   42 (306)
                      ..+||+||||-|++|..
T Consensus        34 i~vTQaTiSRDLkeL~~   50 (70)
T PF01316_consen   34 IEVTQATISRDLKELGA   50 (70)
T ss_dssp             -T--HHHHHHHHHHHT-
T ss_pred             CCcchhHHHHHHHHcCc
Confidence            57999999999998853

The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=84.65  E-value=2.4  Score=30.53  Aligned_cols=40  Identities=20%  Similarity=0.283  Sum_probs=31.9

Q ss_pred             CchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHH
Q psy3760          29 SQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus        29 sq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~   72 (306)
                      |-+-+-+.|++||+   ..|++.+.+|- .+|+.|+.++.....
T Consensus        94 sg~iiR~~LqqLE~---~glVek~~~GR-~lT~~G~~~LD~iA~  133 (150)
T PRK09333         94 SGSIIRKILQQLEK---AGLVEKTKKGR-VITPKGRSLLDNLAA  133 (150)
T ss_pred             ccHHHHHHHHHHHH---CCCeeeCCCCC-EeCHHHHHHHHHHHH
Confidence            34558899999997   46788888888 699999999887653

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=84.53  E-value=7.5  Score=25.28  Aligned_cols=68  Identities=13%  Similarity=0.134  Sum_probs=53.8

Q ss_pred             hhHHHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +++.++-.|++.+ -+  -+-|...||.---+.++++-||++   -+..-+..|.+ +|+++-.+.+....=++.
T Consensus        15 RHl~Vl~~v~eeq-PiGI~klS~~TGmp~HKVRYSLRVLEq~---~iI~PS~~GAi-~td~~~e~ie~i~~dl~e   84 (101)
T COG3388          15 RHLSVLKVVLEEQ-PIGIIKLSDETGMPEHKVRYSLRVLEQE---NIISPSRQGAI-LTDDFPEFIEEIIGDLSE   84 (101)
T ss_pred             HHHHHHHHHHHhC-CceeEeechhcCCchhhhhhhhhhhhhc---CccCccccCCc-cCccHHHHHHHHHHHHHH
Confidence            6788888899887 65  478899999999999999999985   46677788885 999987777655443333

>PRK10403 transcriptional regulator NarP; Provisional

Probab=84.47  E-value=2.6  Score=32.19  Aligned_cols=44  Identities=18%  Similarity=0.188  Sum_probs=38.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++.- |-..-|+.+++|..||..+++++-+.+|+
T Consensus       155 t~~e~~vl~~~~~g~-s~~~ia~~l~~s~~tv~~~~~~i~~kl~~  198 (215)
T PRK10403        155 TERELDVLHELAQGL-SNKQIASVLNISEQTVKVHIRNLLRKLNV  198 (215)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence            446677788888776 99999999999999999999999999875

>smart00094 TR_FER Transferrin

Probab=84.44  E-value=21  Score=29.98  Aligned_cols=75  Identities=9%  Similarity=0.118  Sum_probs=44.0

Q ss_pred             CcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--CCCCceeecccc------------ceEEEEecCCCCCCCCCCcC
Q psy3760         121 KVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQ------------WEYVIIVPLDHPLLLLNSIS  185 (306)
Q Consensus       121 ~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~------------~~~~~v~~~~~~l~~~~~i~  185 (306)
                      ...++++. .+..+.++.+.+|++|+++......  ........++..            ..-++|+.++.+     ..+
T Consensus        26 ~~~v~Cv~~~s~~~Ci~~I~~g~AD~a~ldg~~~y~A~~~~~l~pi~~E~~~~~~~~~~~Y~aVaVVkk~S~-----i~s  100 (332)
T smart00094       26 VPALECVSASSTEECIKAIQKGEADAVTLDGGDVYTAGKPYNLVPVFAENYGSEEEPETGYYAVAVVKKGSA-----IFT  100 (332)
T ss_pred             CCceEEEEcCCHHHHHHHHHCCCCCEEEECcHHHHhhcccCCceEEEEEeeccCCCCCceeEEEEEEECCCC-----CCC
Confidence            34555554 3567899999999999999731111  111111222221            123566666654     367


Q ss_pred             hhhhcCCCeEeecCC
Q psy3760         186 LKEISNYPLITYDLS  200 (306)
Q Consensus       186 ~~dl~~~~~i~~~~~  200 (306)
                      ++||.+...-....+
T Consensus       101 l~dLkGKksChtg~~  115 (332)
T smart00094      101 WNQLRGKKSCHTGVG  115 (332)
T ss_pred             HHHhCCCceecCCCC
Confidence            889988776665554

>PF14502 HTH_41: Helix-turn-helix domain

Probab=84.35  E-value=3.5  Score=23.14  Aligned_cols=38  Identities=21%  Similarity=0.174  Sum_probs=33.3

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR   55 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~   55 (306)
                      +++.=|+++++|..+|-.+|+-||+.=-+.|-.|...|
T Consensus         8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh~G   45 (48)
T PF14502_consen    8 TISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGHLG   45 (48)
T ss_pred             CHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCcCc
Confidence            78888999999999999999999999888886666555

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=84.19  E-value=3  Score=32.41  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=39.0

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |-..-|++|++|..||+.+++++=..||+.
T Consensus       150 T~RE~eVL~lla~G~-snkeIA~~L~iS~~TVk~h~~~i~~KL~v~  194 (211)
T COG2197         150 TPRELEVLRLLAEGL-SNKEIAEELNLSEKTVKTHVSNILRKLGVR  194 (211)
T ss_pred             CHHHHHHHHHHHCCC-CHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence            346777888888765 999999999999999999999999988863

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=84.14  E-value=1.3  Score=32.43  Aligned_cols=35  Identities=29%  Similarity=0.297  Sum_probs=28.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHc-CceeEEec
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEEL-SIDIFIRH   52 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~l-g~~Lf~R~   52 (306)
                      +++.-++.+|+|.|.+|..+++|++.= =.+-|.++
T Consensus        43 tl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G   78 (177)
T COG1510          43 TLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKG   78 (177)
T ss_pred             cHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccC
Confidence            778899999999999999999999753 33445553

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

Probab=83.80  E-value=1.7  Score=26.73  Aligned_cols=39  Identities=21%  Similarity=0.172  Sum_probs=30.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      |.+|+-++.--..= |+..-|+++++|+++|...|..|+.
T Consensus         2 L~~i~~~l~~~~~~-S~~eLa~~~~~s~~~ve~mL~~l~~   40 (69)
T PF09012_consen    2 LQEIRDYLRERGRV-SLAELAREFGISPEAVEAMLEQLIR   40 (69)
T ss_dssp             CHHHHHHHHHS-SE-EHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45666677766666 8999999999999999999999985

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

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=83.65  E-value=3.4  Score=30.89  Aligned_cols=54  Identities=17%  Similarity=0.119  Sum_probs=40.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +++.+|+.+|+|.+||.+..+    ..|.+ +.|+.+|.-.-|+.--..+...+.+.+.
T Consensus         2 ti~evA~~lGVS~~TLRrw~k----~g~L~-~~R~~~G~R~y~~~dl~~L~~I~~l~~~   55 (175)
T PRK13182          2 KTPFVAKKLGVSPKTVQRWVK----QLNLP-CEKNEYGHYIFTEEDLQLLEYVKSQIEE   55 (175)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH----cCCCC-CCcCCCCCEEECHHHHHHHHHHHHHHHc
Confidence            688999999999999876655    56677 5887555325788877777777777664

>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]

Probab=83.57  E-value=18  Score=27.71  Aligned_cols=198  Identities=13%  Similarity=0.061  Sum_probs=117.0

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc----------CCCCCce
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL----------SPSDKLI  159 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~----------~~~~~~~  159 (306)
                      .....|++..+.+. ...+..+...|.+. -+..+.+..++.. ....=..+++|+.++....          ..-....
T Consensus        18 ~~~adinlYGpGGP-htaL~~vA~~~~ek-tg~kVnvt~GPq~-tW~~kAkknADilfgaseqsalaia~~~~~~fs~~~   94 (252)
T COG4588          18 AANADINLYGPGGP-HTALKDVAKKYEEK-TGIKVNVTAGPQA-TWNEKAKKNADILFGASEQSALAIAEDHKDSFSEKN   94 (252)
T ss_pred             hhcceEEEecCCCC-cHHHHHHHHHHHHH-hCeEEEEecCCcc-hhhhhhhccCceeecccHHHHHHHHHhccccccccc
Confidence            34567888888774 44566666666654 5777777776553 3445567789999985211          1112334


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCC--eEeecCCCC-----cHHHHHHHHHh-------CCCceeEEEEec
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP--LITYDLSFS-----GRIKLDREFSL-------QKLTPYIVLETI  225 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~--~i~~~~~~~-----~~~~~~~~~~~-------~~~~~~~~~~~~  225 (306)
                      ..||+--+-.+++.+++|.   ..-.++||....  .+.. ++.+     -...|+...-+       ..++-|++....
T Consensus        95 i~ply~R~aiIlvkkgNPk---nIk~~eDll~~gi~ivV~-dGaG~sntsgtgvwED~agr~~~ie~v~afR~NI~~fap  170 (252)
T COG4588          95 IQPLYLRPAIILVKKGNPK---NIKGFEDLLKPGIGIVVN-DGAGVSNTSGTGVWEDIAGRKGNIETVAAFRKNIVAFAP  170 (252)
T ss_pred             cceeeeeceEEEecCCCcc---ccccHHHHhcCCceEEEe-CCCcccCCCCceehHhhhcccccHHHHHHHHhceEEEcc
Confidence            5677766778889999984   445789987643  4443 3322     11122322211       133457888888


Q ss_pred             CHHHHHHHHHhcc---ceeeeecceecccccCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         226 NSDIIKTYVELRM---GIGIIASIAFDSNRDKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       226 ~~~~~~~~v~~g~---gi~~~p~~~~~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      +..+...+-.++.   .+-.=+++....-..+.++  +++. ....+++.++..++  .++..+.|+++|++.=++.
T Consensus       171 nSgaArkaf~~~~~aDawItW~dWa~snpdig~~v--~~~~d~vIyRd~nv~~~~~--a~~ea~~F~dyl~S~EAq~  243 (252)
T COG4588         171 NSGAARKAFENQPDADAWITWADWAKSNPDIGDAV--EIEKDYVIYRDFNVALAKD--ANKEARDFADYLQSDEAQK  243 (252)
T ss_pred             CCchHHHHHhcCCCCceEEEecchhhhCCchhcee--ecccceEEeeecceeecCC--CCHHHHHHHHHHhhHHHHH
Confidence            8888888887753   3333334443221333333  4433 23455666666666  5899999999998654333

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

Probab=83.51  E-value=6  Score=28.25  Aligned_cols=54  Identities=24%  Similarity=0.190  Sum_probs=40.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE--ecCCCccccCHh
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI--RHGKRIRGLTKP   62 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~--R~~~~~~~lT~~   62 (306)
                      .+|..+.-.|.|..+||+.+++|-+|+-+.+++.+++=.. |.-  +.|+.- .+++.
T Consensus        12 ~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~~~~GrP~-kl~~~   67 (138)
T COG3415          12 RVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPKPRKGRPR-KLSEE   67 (138)
T ss_pred             HHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcccccc-ccCccCCCCCc-ccCHH
Confidence            4566665566699999999999999999999999986544 433  445554 56654

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=83.51  E-value=9.6  Score=29.61  Aligned_cols=49  Identities=24%  Similarity=0.297  Sum_probs=35.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHc--CceeEEecCCC----ccccCHhHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEEL--SIDIFIRHGKR----IRGLTKPGQAIL   67 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~l--g~~Lf~R~~~~----~~~lT~~G~~l~   67 (306)
                      |....|++|+||..++-++|..||++=  ... +.+.|.|    +++||..|...+
T Consensus        27 sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~-~~~~g~GRP~~~y~Lt~~g~~~f   81 (218)
T COG2345          27 SADELAEELGISPMAVRRHLDDLEAEGLVEVE-RQQGGRGRPAKLYRLTEKGREQF   81 (218)
T ss_pred             cHHHHHHHhCCCHHHHHHHHHHHHhCcceeee-eccCCCCCCceeeeecccchhhc
Confidence            778899999999999999999999873  333 3333222    137888887743

>PF13343 SBP_bac_6: Bacterial extracellular solute-binding protein; PDB: 2QRY_D 1XVX_A 1SI1_A 1SI0_A 1Q35_A 1Y9U_A 2OWS_A 2OWT_A 2VP1_A 2VOZ_A

Probab=83.43  E-value=10  Score=29.89  Aligned_cols=136  Identities=13%  Similarity=-0.023  Sum_probs=79.6

Q ss_pred             eeccccceEEEEecCCCCCCCC-CCcChhhhcCCC----eEeecCCCCcHHHHHHHHHh-CC----------CceeEEEE
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYP----LITYDLSFSGRIKLDREFSL-QK----------LTPYIVLE  223 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~----~i~~~~~~~~~~~~~~~~~~-~~----------~~~~~~~~  223 (306)
                      +.++.-..++++..++-- ... -+.+|+||.+-.    +...++.......+...+.. .|          +..+.. .
T Consensus        49 ~~~~~~~~~~i~yN~~~~-~~~~~P~sw~dL~~p~~~g~i~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~l~~n~~-~  126 (242)
T PF13343_consen   49 WVPYGYGPVVIAYNTDKL-KERDLPTSWADLLDPKYKGKIALPDPNSDTGLAFLLALAEAYGEDAGWEWLRELKANGA-T  126 (242)
T ss_dssp             SEEEEEEEEEEEEETTTS-SSGGTTSSGGGGGSGGGTTTEEEETTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCBS-S
T ss_pred             EEEEEEEEEEEEEEhhhc-CCCCCCccHHHHHHHHhCCCEEECCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-c
Confidence            447778888999988763 222 157999998643    44444432222211111111 00          001111 1


Q ss_pred             ecCHHHHHHHHHhc-cceeeeecceeccc--ccC-CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         224 TINSDIIKTYVELR-MGIGIIASIAFDSN--RDK-NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       224 ~~~~~~~~~~v~~g-~gi~~~p~~~~~~~--~~~-~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .. .....+.+..| ..+++.+.+.....  ... .+..+...+.......++...++......++.|++++.+.-.+.
T Consensus       127 ~~-~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~i~~v~P~eG~~~~~~~~~i~k~a~~~~~A~~fi~~lls~e~q~  204 (242)
T PF13343_consen  127 FS-SSQAAQAVASGEGAVAIGISWYSRAAQAKEKGPIKFVYPEEGTVVWPDGIAIVKGAPNPEAAKKFINFLLSPEAQK  204 (242)
T ss_dssp             SC-HHHHHHHHHTTSCSEEEEEHHHHHHHHHCTTTTEEEE-TTTGBEEEEEEEEEBTT-STHHHHHHHHHHHTSHHHHH
T ss_pred             cc-chhhhhHhhCCCceEEEEEehHHHHHHhhhcCCeEEEecCCCcEEEEEEEEEeCCCCCHHHHHHHHHHHCCHHHHH
Confidence            11 77888899999 56677776555443  221 66666666645555667777888888999999999997654333

...

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=83.21  E-value=3.3  Score=31.44  Aligned_cols=43  Identities=19%  Similarity=0.227  Sum_probs=37.6

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+..+++..+++.. |...-|+.+++|..||..++++|.+.||.
T Consensus       146 ~~E~~vl~~l~~g~-~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~  188 (204)
T PRK09958        146 KQEISVMRYILDGK-DNNDIAEKMFISNKTVSTYKSRLMEKLEC  188 (204)
T ss_pred             HHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            35566777778776 99999999999999999999999999984

>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised

Probab=83.10  E-value=1.9  Score=24.89  Aligned_cols=25  Identities=24%  Similarity=0.190  Sum_probs=21.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      |...+|++|++|+.+..+.|++|..
T Consensus        15 sa~mva~~L~vT~~~A~~li~eLg~   39 (54)
T PF11972_consen   15 SAPMVAKELGVTPQAAQRLIAELGL   39 (54)
T ss_pred             cHHHHHHHhCCCHHHHHHHHHHhhc
Confidence            6778999999999999999866554

They contain a C-terminal helix-turn-helix DNA binding domain.

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

Probab=83.08  E-value=1.8  Score=30.11  Aligned_cols=34  Identities=21%  Similarity=0.125  Sum_probs=26.7

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -.+.+.+ |+++||+..+||.+|+.+.++  ..+.|.
T Consensus        13 ~~~~~g~-s~~eaa~~F~VS~~Tv~~W~k--~~~~G~   46 (119)
T PF01710_consen   13 AYIEKGK-SIREAAKRFGVSRNTVYRWLK--RKETGD   46 (119)
T ss_pred             HHHHccc-hHHHHHHHhCcHHHHHHHHHH--hccccc
Confidence            3444445 999999999999999999999  344554

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

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=82.34  E-value=3.2  Score=29.35  Aligned_cols=54  Identities=17%  Similarity=0.180  Sum_probs=36.6

Q ss_pred             hCCCchHHHHHHHHHHHH--cCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEE--LSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~--lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ..++.++|-..|++||+.  +-...-.+ ++.+.++|+.|+..+....+--......
T Consensus        73 ~~~s~GtIYp~L~RLE~~GlI~s~~~~~-~RK~Y~ITe~Gre~L~e~~~~~~~~~~~  128 (135)
T PRK09416         73 FEGNEGSLYTLLHRLEQNRFIQSSWDHE-GAKYYQLTDKGNKMLRKAEKNATKARFI  128 (135)
T ss_pred             ccCCCccHHHHHHHHHHCCCeEEeecCC-CceEEEECHHHHHHHHHHHhCHHHhHHH
Confidence            357899999999999976  22111122 3444489999999998887644444433

>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=82.15  E-value=2.1  Score=25.84  Aligned_cols=26  Identities=31%  Similarity=0.268  Sum_probs=22.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |...=|+.+++|.+++.++++.|+++
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~   51 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAE   51 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHC
Confidence            66788999999999999999999985

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 ....

>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators

Probab=82.09  E-value=0.9  Score=25.95  Aligned_cols=17  Identities=29%  Similarity=0.302  Sum_probs=14.9

Q ss_pred             HHHHHhCCCchHHHHHH
Q psy3760          21 EAAKALYTSQPGVSKAI   37 (306)
Q Consensus        21 ~aA~~l~isq~~~s~~i   37 (306)
                      ..|+.+|+|+++||+.+
T Consensus         2 ~lA~~~gvs~~tvs~~l   18 (52)
T cd01392           2 DIARAAGVSVATVSRVL   18 (52)
T ss_pred             cHHHHHCcCHHHHHHHH
Confidence            36899999999999876

HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre

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

Probab=81.68  E-value=4  Score=25.72  Aligned_cols=33  Identities=18%  Similarity=0.232  Sum_probs=22.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++.---+++++-++.+||+..|+|.||+-+-+.
T Consensus         9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvt   41 (82)
T PF12116_consen    9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVT   41 (82)
T ss_dssp             HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHH
Confidence            333344555555999999999999999998774

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

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=81.46  E-value=3.1  Score=34.92  Aligned_cols=48  Identities=15%  Similarity=0.108  Sum_probs=38.3

Q ss_pred             CHHHHHHH--hCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHHH
Q psy3760          18 NLTEAAKA--LYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILRS   69 (306)
Q Consensus        18 s~~~aA~~--l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~~   69 (306)
                      +....|+.  +++|.+|+-+-|++||+ .|  ++.|.  +-|. -||+.|-++|..
T Consensus        23 ~s~~l~~~~~~~vS~aTiR~d~~~Le~-~G--~l~~~h~sagr-ipt~kGYR~yv~   74 (337)
T TIGR00331        23 GSKTLLEKYNLGLSSATIRNDMADLED-LG--FIEKPHTSSGR-IPTDKGYRYYVD   74 (337)
T ss_pred             CHHHHHhhcCCCCChHHHHHHHHHHHH-CC--CccCCCCCCCc-CcChhHHHHHHH
Confidence            66788999  99999999999999999 33  34444  4555 499999998874

In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.

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

Probab=81.28  E-value=7.5  Score=25.96  Aligned_cols=55  Identities=16%  Similarity=0.104  Sum_probs=37.9

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      .+++.+|+.+|||.+|+.+    .|+++|..=..|+.+|.-.-|+.--..+..++.++.
T Consensus         1 yti~EvA~~~gVs~~tLR~----ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr   55 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRY----WETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLY   55 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHH
Confidence            3789999999999998765    566666544456544431477777777777766554

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

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=81.26  E-value=1.7  Score=25.15  Aligned_cols=25  Identities=20%  Similarity=0.181  Sum_probs=19.2

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      +.|.|....|+.+|+|++++|+.++
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~~   31 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIEN   31 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHhc
Confidence            4455888999999999999998764

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=81.22  E-value=6.4  Score=25.93  Aligned_cols=56  Identities=20%  Similarity=0.208  Sum_probs=39.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC---ccccCHhHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR---IRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~---~~~lT~~G~~l~~~a~~il~~   76 (306)
                      ..++-.-..|++.....+-|+.|++. |  |+.++.+|   .+++|+.|+.|++...++-..
T Consensus        33 ~~Tri~y~aNlny~~~~~yi~~L~~~-G--li~~~~~~~~~~y~lT~KG~~fle~y~~i~~~   91 (95)
T COG3432          33 GITRIIYGANLNYKRAQKYIEMLVEK-G--LIIKQDNGRRKVYELTEKGKRFLEKYSEIREL   91 (95)
T ss_pred             CceeeeeecCcCHHHHHHHHHHHHhC-C--CEEeccCCccceEEEChhHHHHHHHHHHHHHH
Confidence            34555556677777777777777654 4  77766555   238999999998887777654

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

Probab=81.18  E-value=2.1  Score=25.68  Aligned_cols=38  Identities=24%  Similarity=0.155  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      |.++.....-- +-...|+.+++|..++.+-+..||++=
T Consensus         6 l~~i~~~~~p~-~T~eiA~~~gls~~~aR~yL~~Le~eG   43 (62)
T PF04703_consen    6 LEYIKEQNGPL-KTREIADALGLSIYQARYYLEKLEKEG   43 (62)
T ss_dssp             HHHHHHHTS-E-EHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred             HHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            44444444444 788999999999999999999999874

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=81.15  E-value=2.4  Score=38.67  Aligned_cols=42  Identities=21%  Similarity=0.161  Sum_probs=32.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcC--ceeEEecCCCccccC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELS--IDIFIRHGKRIRGLT   60 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg--~~Lf~R~~~~~~~lT   60 (306)
                      ++..=|+.|++|.+|+++-|+++++.++  ..|..|.+.|+ .+.
T Consensus        94 ~~~~La~~l~vS~sTi~~dl~~v~~~l~~~l~l~~k~~~Gi-~i~  137 (584)
T PRK09863         94 PMAQLASALNLSRTWVAERLPRLNQRYERICCIASRPGLGH-FID  137 (584)
T ss_pred             cHHHHHHHhCCCHHHHHHHHHHHHHhhhcccEEEecCCceE-EEE
Confidence            6778888888888888888888888887  77766666666 443

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

Probab=80.97  E-value=7.4  Score=25.26  Aligned_cols=38  Identities=13%  Similarity=0.144  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      .++++..+.+.|.|..+-|+.+|+|-.||||-=+.|..
T Consensus        38 R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~   75 (87)
T PF01371_consen   38 RWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLKY   75 (87)
T ss_dssp             HHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            45667645555559999999999999999988777754

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

>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=80.62  E-value=2.1  Score=30.44  Aligned_cols=36  Identities=25%  Similarity=0.245  Sum_probs=27.4

Q ss_pred             hHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHH
Q psy3760          31 PGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSI   70 (306)
Q Consensus        31 ~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a   70 (306)
                      +-+-+.+++||+   ..|+++. ++|- .+|+.|+.++..+
T Consensus        95 ~iiR~~LqqLE~---~glv~k~~~~GR-~lT~~G~~~lD~i  131 (139)
T PF01090_consen   95 SIIRKILQQLEK---AGLVEKDPKGGR-RLTPKGQRDLDRI  131 (139)
T ss_dssp             HHHHHHHHHHHH---TTSEEEETTTEE-EE-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHH---CCCEEecCCCCC-EECHHHHHHHHHH
Confidence            456778899997   5788888 6666 6999999988764

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 [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=80.61  E-value=3.9  Score=33.74  Aligned_cols=62  Identities=16%  Similarity=0.071  Sum_probs=45.1

Q ss_pred             hhHHHHHHHHH--hc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760           4 HQFRFVREAVR--QN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR   68 (306)
Q Consensus         4 ~~l~~f~~v~~--~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~   68 (306)
                      .+..|+.++.+  .|  .+...+|+.||++++++++.+..  .-+..-|+++.++|- ..|+.|..++.
T Consensus       239 ~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~--~Li~~~li~~~~~g~-~~~~~~~~~~~  304 (305)
T TIGR00635       239 IDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEP--YLLQIGFLQRTPRGR-IATELAYEHLG  304 (305)
T ss_pred             HHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhH--HHHHcCCcccCCchh-hhhHHHHHHhC
Confidence            34445655543  21  37899999999999999987741  234556678999998 59999998763

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	306
1al3_A	324	Cofactor Binding Fragment Of Cysb From Klebsiella A		9e-70
2fyi_A	228	Crystal Structure Of The Cofactor-binding Domain Of		4e-45
2hxr_A	238	Structure Of The Ligand Binding Domain Of E. Coli C		3e-08
3fzv_A	306	Crystal Structure Of Pa01 Protein, Putative Lysr Fa		3e-05
4ab6_A	222	Regulatory Domain Structure Of Nmb2055 (Metr), C103		5e-05
3jv9_A	219	The Structure Of A Reduced Form Of Oxyr From N. Men		4e-04
4ab5_A	222	Regulatory Domain Structure Of Nmb2055 (Metr) A Lys		6e-04

>pdb|1AL3|A Chain A, Cofactor Binding Fragment Of Cysb From Klebsiella Aerogenes Length = 324

Iteration: 1
 Score =  259 bits (663), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 121/301 (40%), Positives = 183/301 (60%)
Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK               R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60
Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L +ATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI E +    AD AI TE L   D L+ +PCY W   I+V  +HPL  
Sbjct: 121 RVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLAT 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S+S++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A+ +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300
Query: 301 N 301
           +
Sbjct: 301 D 301

>pdb|2FYI|A Chain A, Crystal Structure Of The Cofactor-binding Domain Of The Cbl Transcriptional Regulator Length = 228

Iteration: 1
 Score =  178 bits (451), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 86/219 (39%), Positives = 141/219 (64%)
Query: 84  GKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQA 143
           G   +   +G LTIATTHTQARY+LP++IK F   FP+V+L L+QG P++I  +++N +A
Sbjct: 5   GSHMTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEA 64
Query: 144 DIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG 203
           DI I +E LS   +L++ P ++W + ++VP DHPL  ++ ++L+ I+ +PLITY    +G
Sbjct: 65  DIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITG 124
Query: 204 RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASH 263
           R ++D  F+ + L   IVL   +SD+IKTYV L +GIG++A  +     ++NL  +   H
Sbjct: 125 RSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEEENLIRLDTRH 184
Query: 264 LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302
           LF      + +K+G   R+YV+ F++L +  L+ + I +
Sbjct: 185 LFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKR 223

>pdb|2HXR|A Chain A, Structure Of The Ligand Binding Domain Of E. Coli Cynr, A Transcriptional Regulator Controlling Cyanate Metabolism Length = 238

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/190 (23%), Positives = 89/190 (46%), Gaps = 9/190 (4%)
Query: 74  MQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQ 133
           +QE+   K+   + +    G+L IA T T   Y +  +  +F  ++P + L L + + ++
Sbjct: 11  LQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLXADFYARYPSITLQLQEXSQEK 70
Query: 134 ITEMIRNDQADIAIV-TEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY 192
           I + +  D+ D+ I    + SP  +L +IP       ++V   HPL +   ++L  + + 
Sbjct: 71  IEDXLCRDELDVGIAFAPVHSP--ELEAIPLLTESLALVVAQHHPLAVHEQVALSRLHDE 128
Query: 193 PLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL--RMGIGIIASIAFDS 250
            L+     F+ R ++D       L P +V+E   ++ I   +EL  R  +  +   A  +
Sbjct: 129 KLVLLSAEFATREQIDHYCEKAGLHPQVVIE---ANSISAVLELIRRTSLSTLLPAAIAT 185
Query: 251 NRDKNLRSIS 260
             D  L++IS
Sbjct: 186 QHD-GLKAIS 194

>pdb|3FZV|A Chain A, Crystal Structure Of Pa01 Protein, Putative Lysr Family Transcriptional Regulator From Pseudomonas Aeruginosa Length = 306

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/238 (20%), Positives = 93/238 (39%), Gaps = 21/238 (8%)
Query: 18  NLTEAAKALYTSQPGVSKAXXXXXXXXXXXXXXRHGKRIRGLTKPGQAILRSIEIIMQEI 77
           ++ EA++ LY +QP +S A              RH  +   LT  G    R  + +++  
Sbjct: 20  SVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLTPAGARFYRKAQELLRXA 79
Query: 78  EGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEM 137
              ++     +    G + I    T A   LP +I  F   +P V++ +  G  +++ + 
Sbjct: 80  HEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQG 139
Query: 138 IRNDQADIA----------IVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLK 187
           + + + D+A          I TE L P  +  +          ++P  H       +SL+
Sbjct: 140 LTSGRFDLAFLYEHDLDSTIETEPLXPPQRPHA----------LLPEGHRFAGQAQVSLR 189
Query: 188 EISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIAS 245
           ++   P I  D+  S R      F    LTP I   + + + ++  V    G  ++ +
Sbjct: 190 DLCLEPXILLDVQPS-RTYFVSLFEELGLTPNIAFSSPSIEXVRGXVGQGFGFSLLVT 246

>pdb|4AB6|A Chain A, Regulatory Domain Structure Of Nmb2055 (Metr), C103s C106s Mutant, A Lysr Family Regulator From N. Meningitidis Length = 222

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 56/111 (50%), Gaps = 9/111 (8%)
Query: 91  DTGNLTIAT-THTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT 149
           + G L IA  +HT   + +P +  EF   +P+V+L ++ G       ++   +AD+AIV+
Sbjct: 6   EAGELRIAVESHTSFDWLMPAM-GEFRPMWPQVELDIVSGFQADPVGLLLQHRADLAIVS 64
Query: 150 EILSPSDKLISI---PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
           E    ++K   I   P + +E V I   DHPL   N  + ++     LITY
Sbjct: 65  E----AEKQNGISFQPLFAYEMVGICAPDHPLAAKNVWTAEDFIGETLITY 111

>pdb|3JV9|A Chain A, The Structure Of A Reduced Form Of Oxyr From N. Meningitidis Length = 219

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 83/199 (41%), Gaps = 15/199 (7%)
Query: 93  GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL 152
           G   +    T A Y LPK+I       PK  L L +     +TE ++    D  IV E  
Sbjct: 4   GAFKLGLIFTVAPYLLPKLIVSLRRTAPKXPLXLEENYTHTLTESLKRGDVDAIIVAEPF 63
Query: 153 SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLI-------TYDLSFSGRI 205
                +++ P Y   + +IVP  H    L+++S + +    ++         D   S   
Sbjct: 64  Q-EPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRXLGEEQVLLLTEGNCXRDQVLSSCS 122
Query: 206 KLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLF 265
           +L  +  +Q LT  +   +IN+  I+  V   + I ++ + A   N D  L SI      
Sbjct: 123 ELAAKQRIQGLTNTLQGSSINT--IRHXVASGLAISVLPATALTEN-DHXLFSIIPFE-- 177
Query: 266 GTTISRVIIKQGTYLRSYV 284
           GT  SR ++    Y R++V
Sbjct: 178 GTPPSRRVVL--AYRRNFV 194

>pdb|4AB5|A Chain A, Regulatory Domain Structure Of Nmb2055 (Metr) A Lysr Family Regulator From N. Meningitidis Length = 222

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 9/111 (8%)
Query: 91  DTGNLTIAT-THTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT 149
           + G L IA   HT   +  P    EF   +P+V+L ++ G       ++   +AD+AIV+
Sbjct: 6   EAGELRIAVECHTCFDWLXPAX-GEFRPXWPQVELDIVSGFQADPVGLLLQHRADLAIVS 64
Query: 150 EILSPSDKLISI---PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197
           E    ++K   I   P + +E V I   DHPL   N  + ++     LITY
Sbjct: 65  E----AEKQNGISFQPLFAYEXVGICAPDHPLAAKNVWTAEDFIGETLITY 111

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	306
1al3_A	324	Cys regulon transcriptional activator CYSB; LYSR f	1e-126
2fyi_A	228	HTH-type transcriptional regulator CBL; Lys-R fami	1e-85
3fzv_A	306	Probable transcriptional regulator; LYSR, structur	1e-48
3fxq_A	305	LYSR type regulator of TSAMBCD; transcriptional re	3e-46
2hxr_A	238	HTH-type transcriptional regulator CYNR; CYNR tran	8e-34
1ixc_A	294	CBNR, LYSR-type regulatory protein; long alpha hel	2e-33
4ab5_A	222	Transcriptional regulator, LYSR family; transcript	2e-32
2h98_A	313	HTH-type transcriptional regulator CATM; BENM, LTT	3e-30
2h9b_A	312	HTH-type transcriptional regulator BENM; LTTR, tra	4e-30
2ql3_A	209	Probable transcriptional regulator, LYSR family P;	6e-23
3isp_A	303	HTH-type transcriptional regulator RV1985C/MT2039;	4e-18
1i6a_A	219	OXYR, hydrogen peroxide-inducible genes activator;	3e-15
3jv9_A	219	OXYR, transcriptional regulator, LYSR family; LYSR	9e-15
3ho7_A	232	OXYR; beta-alpha-barrels, DNA-binding, transcripti	3e-14
2esn_A	310	Probable transcriptional regulator; PA0477, APC582	2e-13
1uth_A	315	LYSR-type regulatory protein; transcription regula	1e-12
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	8e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
3onm_A	238	Transcriptional regulator LRHA; LYSR, ROVM, transc	6e-07
3hhg_A	306	Transcriptional regulator, LYSR family; transcript	2e-06
3mz1_A	300	Putative transcriptional regulator; structural gen	8e-06
3oxn_A	241	Putative transcriptional regulator, LYSR family; s	3e-05
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	4e-05
2y7p_A	218	LYSR-type regulatory protein; transcription regula	6e-05

>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine biosynthesis, transcription regulation; 1.80A {Klebsiella aerogenes} SCOP: c.94.1.1 Length = 324

 Score =  362 bits (931), Expect = e-126
 Identities = 128/304 (42%), Positives = 193/304 (63%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
           M L Q R++ E V  N N++  A+ LYTSQPG+SK +  LE+EL I IF R GK +  +T
Sbjct: 1   MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60

Query: 61  KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
             GQ I+R    ++ +++ +K +  E +  D G+L +ATTHTQARYALP +IK F  ++P
Sbjct: 61  PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYP 120

Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
           +V L + QG+P QI E +    AD AI TE L   D L+ +PCY W   I+V  +HPL  
Sbjct: 121 RVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLAT 180

Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
             S+S++E++ YPL+TY   F+GR +LD  F+   LTP IV    ++D+IKTYV L +G+
Sbjct: 181 KGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240

Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
           G+IAS+A D   D +L  + A+ +F  + +++  ++ T+LRSY+Y FI+  +P L R  +
Sbjct: 241 GVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300

Query: 301 NKIL 304
           +  +
Sbjct: 301 DTAV 304

>2fyi_A HTH-type transcriptional regulator CBL; Lys-R family, cofactor-binding DO cysteine biosynthesis; 2.80A {Escherichia coli K12} SCOP: c.94.1.1 Length = 228

 Score =  255 bits (654), Expect = 1e-85
 Identities = 87/227 (38%), Positives = 143/227 (62%)

Query: 80  LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR 139
           L   G   +   +G LTIATTHTQARY+LP++IK F   FP+V+L L+QG P++I  +++
Sbjct: 1   LVPRGSHMTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQ 60

Query: 140 NDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL 199
           N +ADI I +E LS   +L++ P ++W + ++VP DHPL  ++ ++L+ I+ +PLITY  
Sbjct: 61  NGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQ 120

Query: 200 SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSI 259
             +GR ++D  F+ + L   IVL   +SD+IKTYV L +GIG++A  +     ++NL  +
Sbjct: 121 GITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEEENLIRL 180

Query: 260 SASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN 306
              HLF      + +K+G   R+YV+ F++L +  L+ + I + +  
Sbjct: 181 DTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVME 227

>3fzv_A Probable transcriptional regulator; LYSR, structural genomics, PSI-2, structure initiative; 2.71A {Pseudomonas aeruginosa PA01} Length = 306

 Score =  163 bits (415), Expect = 1e-48
 Identities = 55/245 (22%), Positives = 108/245 (44%), Gaps = 6/245 (2%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
             L Q + FV     +  ++ EA++ LY +QP +S A+  LEE   + +FIRH  +   L
Sbjct: 4   YTLRQLKYFV--TTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSL 61

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  G    R  + +++     ++     +    G + I    T A   LP +I  F   +
Sbjct: 62  TPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAY 121

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE-YVIIVPLDHPL 178
           P V++ +  G  +++ + + + + D+A + E    S  + + P    +    ++P  H  
Sbjct: 122 PGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDST-IETEPLMPPQRPHALLPEGHRF 180

Query: 179 LLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238
                +SL+++   P+I  D+  S R      F    LTP I   + + ++++  V    
Sbjct: 181 AGQAQVSLRDLCLEPMILLDVQPS-RTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGF 239

Query: 239 GIGII 243
           G  ++
Sbjct: 240 GFSLL 244

>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- transcription, transcription regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A 3n6t_A 3n6u_A* Length = 305

 Score =  157 bits (399), Expect = 3e-46
 Identities = 56/263 (21%), Positives = 107/263 (40%), Gaps = 9/263 (3%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           + L   +  +   + +  +L  AA+ L+ SQP +S AI +LE+EL   + +R  + +  L
Sbjct: 2   LKLQTLQALI--CIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVS-L 58

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  GQA ++   +I+ E    ++   +      G++T A +   A  ALP  +  F  +F
Sbjct: 59  TSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREF 118

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVT-EILSPSDKLISIPCYQWEYVIIVPLDHPL 178
           P V +++  G    ++  +R+   D A+           L + P Y  + VI+    HP 
Sbjct: 119 PDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHP- 177

Query: 179 LLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TPYIVLETINSDIIKTYVELR 237
            + N+  L E+                 +   F+   L  P + L   +   +   V   
Sbjct: 178 -MANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHS 236

Query: 238 MGIGII-ASIAFDSNRDKNLRSI 259
             +  +  ++   +     L SI
Sbjct: 237 DLLTTMPRTLYERNAFKDQLCSI 259

>2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional regulator LYSR struc genomics, PSI-2, protein structure initiative; 2.05A {Escherichia coli} PDB: 3hfu_A Length = 238

 Score =  122 bits (309), Expect = 8e-34
 Identities = 39/217 (17%), Positives = 93/217 (42%), Gaps = 9/217 (4%)

Query: 67  LRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSL 126
            +     +QE+   K+   + +    G+L IA T T   Y +  ++ +F  ++P + L L
Sbjct: 4   RQYASRALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQL 63

Query: 127 LQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISL 186
            + + ++I +M+  D+ D+ I    +   + L +IP       ++V   HPL +   ++L
Sbjct: 64  QEMSQEKIEDMLCRDELDVGIAFAPVHSPE-LEAIPLLTESLALVVAQHHPLAVHEQVAL 122

Query: 187 KEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASI 246
             + +  L+     F+ R ++D       L P +V+E  +   +   +       ++ + 
Sbjct: 123 SRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAA 182

Query: 247 AFDSNRDKNLRSISASHLFGTTISR---VIIKQGTYL 280
                +   L++I    L    + R   ++ ++ ++ 
Sbjct: 183 IAT--QHDGLKAI---SLAPPLLERTAVLLRRKNSWQ 214

>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domai binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A Length = 294

 Score =  123 bits (311), Expect = 2e-33
 Identities = 47/251 (18%), Positives = 89/251 (35%), Gaps = 8/251 (3%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           M   Q + F+  AV +  N+  AAK L+ SQP +++ +  LE +L + +  R  + I  L
Sbjct: 1   MEFRQLKYFI--AVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIE-L 57

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  G A L     I++         +  +  D G L++A   T    +LP +++ F    
Sbjct: 58  TAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTST 117

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P   +SL      +  E +      +            +  +   Q +  + V       
Sbjct: 118 PTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPG-IEIVNIAQEDLYLAVHRSQSGK 176

Query: 180 LLNSISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVELR 237
              +  L ++    L  +          ++   F    + P I     ++          
Sbjct: 177 FGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG 236

Query: 238 MGIGII-ASIA 247
               I+ AS+A
Sbjct: 237 AASSIVPASVA 247

>4ab5_A Transcriptional regulator, LYSR family; transcription factors; 2.51A {Neisseria meningitidis serogroup B} PDB: 4ab6_A Length = 222

 Score =  118 bits (298), Expect = 2e-32
 Identities = 41/204 (20%), Positives = 78/204 (38%), Gaps = 7/204 (3%)

Query: 91  DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
           + G L IA         L   + EF   +P+V+L ++ G       ++   +AD+AIV+E
Sbjct: 6   EAGELRIAVECHTCFDWLMPAMGEFRPMWPQVELDIVSGFQADPVGLLLQHRADLAIVSE 65

Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
               +  +   P + +E V I   DHPL   N  + ++     LITY +         + 
Sbjct: 66  AEKQNG-ISFQPLFAYEMVGICAPDHPLAAKNVWTAEDFIGETLITYPVPDEMLDLPKKI 124

Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTIS 270
              + + P     +  +  I   V  R GI  +         +K    +    +    + 
Sbjct: 125 LIPKNINP-PRRHSELTIAIIQLVASRRGIAALPYWTVMPYLEK--GYVVHRQITADGLQ 181

Query: 271 R---VIIKQGTYLRSYVYSFIKLL 291
                 I+     +SY+ +F +++
Sbjct: 182 SKLYAAIRTEDTDKSYLNNFCQII 205

>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A {Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A* 3m1e_A Length = 313

 Score =  115 bits (290), Expect = 3e-30
 Identities = 54/253 (21%), Positives = 105/253 (41%), Gaps = 11/253 (4%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           M L   R FV   V +  ++++AA+ L  +QP +S+ I +LEEEL I +F R  +  + +
Sbjct: 1   MELRHLRYFV--TVVEEQSISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPAK-V 57

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T+ G    +    I+        + K  +   +  L I    +     LP+II  F  Q 
Sbjct: 58  TEAGMFFYQHAVQILTHTAQASSMAKRIAT-VSQTLRIGYVSSLLYGLLPEIIYLFRQQN 116

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P++ + L++   K     ++  + D+      ++    +  I  ++ +  + +   H L 
Sbjct: 117 PEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPA-IRRIMLHKEQLKLAIHKHHHLN 175

Query: 180 LLN--SISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVE 235
                 + L +I + P++ Y +S        +   F+   L P  + E     +    V 
Sbjct: 176 QFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVA 235

Query: 236 LRMGIGII-ASIA 247
              G+ I+ AS  
Sbjct: 236 AGEGVCIVPASAM 248

>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional activator, LYSR-type transcripti regulator; 1.80A {Acinetobacter SP} PDB: 2h99_A 3k1m_A 3k1n_A 3k1p_A 2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A* Length = 312

 Score =  115 bits (289), Expect = 4e-30
 Identities = 54/253 (21%), Positives = 101/253 (39%), Gaps = 11/253 (4%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           M L   R FV  AV +  + T+AA  L  +QP +S+ I  LEEEL I +  R  + ++  
Sbjct: 1   MELRHLRYFV--AVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVK-T 57

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  G    +    ++  ++ +  + K  ++ +   + I    +     LP+II  +    
Sbjct: 58  TPEGHFFYQYAIKLLSNVDQMVSMTKRIASVE-KTIRIGFVGSLLFGLLPRIIHLYRQAH 116

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
           P +++ L +   K  TE ++  + D       +S    +          ++ V   HPL 
Sbjct: 117 PNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPA-IKHSLLRNERLMVAVHASHPLN 175

Query: 180 LLN--SISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVE 235
            +    + L ++ +  ++ Y  S        +   FS   L P  + E     +    V 
Sbjct: 176 QMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVA 235

Query: 236 LRMGIGII-ASIA 247
              GI ++ AS  
Sbjct: 236 AGEGISLVPASTQ 248

>2ql3_A Probable transcriptional regulator, LYSR family P; APC7314, rhodococcus RHA1, structural genomics, PSI-2; HET: MSE; 2.05A {Rhodococcus SP} Length = 209

 Score = 93.1 bits (232), Expect = 6e-23
 Identities = 25/153 (16%), Positives = 66/153 (43%), Gaps = 3/153 (1%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
            G + +          LP ++  FT ++P+  +   +    ++   +   + D+AIV ++
Sbjct: 4   AGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL 63

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNS-ISLKEISNYPLITYDLSFSGRIKLDRE 210
               +   ++P    E ++++  +HPL  ++  + L +++ +P++  D   S    +D  
Sbjct: 64  DLSPE-WQTVPLMTREPMVVLGAEHPLAGVDGPVRLADLAEHPMVLLDAPPSTNHAMD-V 121

Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
                  P +   T N +  + +V   +G  ++
Sbjct: 122 CREAGFAPRVAYRTANFETARAFVGRGLGWTLL 154

>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped structure, DNA binding domain, regulatory domain, DNA-binding; 2.70A {Mycobacterium tuberculosis} Length = 303

 Score = 81.9 bits (203), Expect = 4e-18
 Identities = 35/245 (14%), Positives = 75/245 (30%), Gaps = 12/245 (4%)

Query: 1   MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           ++  Q   +   V   +F    AA+ L+ +   VS+ I  LE+++   + +R  K  R  
Sbjct: 6   LDGPQLAALAAVVELGSF--DAAAERLHVTPSAVSQRIKSLEQQVGQVLVVR-EKPCR-A 61

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T  G  +LR                   ++     +TIA            +        
Sbjct: 62  TTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVL 121

Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
             V++            ++R   A  A+ TE           P  +  Y+ +        
Sbjct: 122 LDVRIEDQD----HSARLLREGVAMGAVTTERNPVPG-CRVHPLGEMRYLPVASRPFVQR 176

Query: 180 LL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238
            L +  +    +  P + ++     +  L R+   ++           ++         +
Sbjct: 177 HLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKA-FRRAITRPTHFVPTTEGFTAAARAGL 235

Query: 239 GIGII 243
           G G+ 
Sbjct: 236 GWGMF 240

>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory domain, oxidized form, transcription; 2.30A {Escherichia coli} SCOP: c.94.1.1 PDB: 1i69_A Length = 219

 Score = 72.3 bits (178), Expect = 3e-15
 Identities = 23/105 (21%), Positives = 47/105 (44%), Gaps = 1/105 (0%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
           +G L I    T   Y LP II      FPK+++ L +    Q+   + + + D  I+  +
Sbjct: 4   SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV 63

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
              S+  I +P +    ++ +  DHP     ++ + +++   L+ 
Sbjct: 64  K-ESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLM 107

>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type transcriptional regulator, LTTR, redox, structural genomics, OPPF; 2.39A {Neisseria meningitidis} Length = 219

 Score = 71.2 bits (175), Expect = 9e-15
 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 1/105 (0%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
            G   +    T A Y LPK+I       PK+ L L +     +TE ++    D  IV E 
Sbjct: 3   EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP 62

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
                 +++ P Y   + +IVP  H    L+++S + +    ++ 
Sbjct: 63  F-QEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLL 106

>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio regulation; 1.58A {Porphyromonas gingivalis} Length = 232

 Score = 69.6 bits (171), Expect = 3e-14
 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 1/105 (0%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
           TG L IA   T A Y LP++   +  +   +++ + +    +    + + + D+AI+   
Sbjct: 10  TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASK 69

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
              ++ L     Y  E++  V    PL   + I   E++ + L  
Sbjct: 70  A-ETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWL 113

>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1 Length = 310

 Score = 68.4 bits (168), Expect = 2e-13
 Identities = 35/165 (21%), Positives = 67/165 (40%), Gaps = 4/165 (2%)

Query: 18  NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
           N+  AA  L  S    S A+  L + L  ++F+R G R++  T+  + +  ++   ++ +
Sbjct: 26  NVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQ-PTQRAEHLAAAVAAALRAL 84

Query: 78  EGLKKIGKEFS-AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE 136
               +  + F           A T   A   LP ++       P V+L L+    K   E
Sbjct: 85  GEGLEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVE 144

Query: 137 MIRNDQADIAI--VTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
            + + + D A+    E     + + +   +   YV++   DHP L
Sbjct: 145 ALASGRIDFALGYDEEHERLPEGIQAHDWFADRYVVVARRDHPRL 189

>1uth_A LYSR-type regulatory protein; transcription regulation, transcriptional regulator; 2.2A {Burkholderia SP} SCOP: c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A Length = 315

 Score = 66.5 bits (163), Expect = 1e-12
 Identities = 31/163 (19%), Positives = 66/163 (40%), Gaps = 3/163 (1%)

Query: 18  NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
           +++ A + L  +QP VS ++  L   L+ D+F+R  K +   T     +   +   +  +
Sbjct: 30  SVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGME-PTPYALHLAEPVIYALNTL 88

Query: 78  EGLKKIGKEFS-AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE 136
           +        F     T    +A T     Y +P +++    + P +++S L+ N   + E
Sbjct: 89  QTALTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKE 148

Query: 137 MIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
            + +   D+A+       +        ++  YV +   DHP  
Sbjct: 149 DMESGAVDLALGLLPELQTG-FFQRRLFRHRYVCMFRKDHPSA 190

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B Length = 291

 Score = 51.4 bits (124), Expect = 8e-08
 Identities = 19/127 (14%), Positives = 52/127 (40%), Gaps = 4/127 (3%)

Query: 1   MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
           M L     F       ++  T  +K        +++ I  LE+ L++ +  RH +++  L
Sbjct: 1   MKLDDLNLFRLVVENGSY--TSTSKKTMIPVATITRRIQALEDSLNLRLLNRHARKLT-L 57

Query: 60  TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
           T+ G+   +    +++ +  + +   +     +G + I+      +  +  +   F  ++
Sbjct: 58  TEAGERFYKDCSPLLERLASMTEEITDECRGASGRIRISAPSNLTKRMMMPMFNAFMEKY 117

Query: 120 PKVKLSL 126
           P + + L
Sbjct: 118 PDIHIEL 124

>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 = 51.8 bits (123), Expect = 1e-07
 Identities = 56/335 (16%), Positives = 113/335 (33%), Gaps = 85/335 (25%)

Query: 7   RFVREAVRQNFN-LTEAAKALYTSQPGVSKAIIELEEEL--SIDIFI-RHGKRIRGLTKP 62
           +FV E +R N+  L    K        +++  IE  + L     +F   +  R++   K 
Sbjct: 81  KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140

Query: 63  GQAI--LRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
            QA+  LR  + ++  I+G+   GK  +      + +    +           +   +  
Sbjct: 141 RQALLELRPAKNVL--IDGVLGSGK--TW-----VALDVCLS----------YKVQCKMD 181

Query: 121 -KVK-LSLLQGN---PKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV---IIV 172
            K+  L+L   N   P+ + EM++     I       S     I +  +  +     ++ 
Sbjct: 182 FKIFWLNL--KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 173 PLDHP--LLLLNSISLKEI-------------SNYPLITYDLSFSGRIKLDREFSLQKLT 217
              +   LL+L ++   +              + +  +T  LS +    +  +     LT
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT 299

Query: 218 PYIVLETINSDIIKTYVELR-------------MGIGII-ASIAFDSNRDKNLRSISASH 263
           P  V       ++  Y++ R               + II  SI        N +     H
Sbjct: 300 PDEVKS-----LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-----H 349

Query: 264 LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298
           +    ++  II+          S + +L P   RK
Sbjct: 350 VNCDKLTT-IIE----------SSLNVLEPAEYRK 373

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.9 bits (113), Expect = 2e-06
 Identities = 46/316 (14%), Positives = 90/316 (28%), Gaps = 108/316 (34%)

Query: 15  QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRS---I 70
           +   +T+   A  T+   +    + L  +    + +++   R + L  P + +  +   +
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL--PREVLTTNPRRL 330

Query: 71  EIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN 130
            II + I         +   +   LT              II+           SL    
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLT-------------TIIE----------SSLNVLE 367

Query: 131 PKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ--WEYVI------IVPLDHPLLLLN 182
           P +  +M       +++      P    I        W  VI      +V   H   L+ 
Sbjct: 368 PAEYRKMFD----RLSVF-----PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418

Query: 183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGI 242
               K+     +    +    ++KL+ E++L +             I+  Y   +     
Sbjct: 419 ----KQPKESTISIPSIYLELKVKLENEYALHRS------------IVDHYNIPK----- 457

Query: 243 IASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFI------------KL 290
                FDS+       +   +L                  Y YS I              
Sbjct: 458 ----TFDSD------DLIPPYLDQ----------------YFYSHIGHHLKNIEHPERMT 491

Query: 291 LSPK--LNRKFI-NKI 303
           L     L+ +F+  KI
Sbjct: 492 LFRMVFLDFRFLEQKI 507

>3onm_A Transcriptional regulator LRHA; LYSR, ROVM, transcription factor, virulence factor; 2.40A {Yersinia pseudotuberculosis} Length = 238

 Score = 48.5 bits (116), Expect = 6e-07
 Identities = 18/107 (16%), Positives = 38/107 (35%), Gaps = 11/107 (10%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
            G+L I  +   A   LP ++      +P++ + +       I +M+ + + D+AI T  
Sbjct: 26  EGSLIIGASDDTADTLLPFLLNRVATLYPRLAIDVRVKRSPFIADMLSSGEVDLAITTA- 84

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD 198
               D    +       +    +D+       +        PL+  D
Sbjct: 85  --KVDSHPHVILRTSPTLWYCSVDYQFQPGEPV--------PLVVMD 121

>3hhg_A Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B} Length = 306

 Score = 47.1 bits (113), Expect = 2e-06
 Identities = 32/140 (22%), Positives = 65/140 (46%), Gaps = 6/140 (4%)

Query: 8   FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
           FV+     +F  + AA+ L  +   VS+ +  LEE+L +++  R  +++  LT+ G    
Sbjct: 11  FVQVVESGSF--SRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQLS-LTEEGAQYF 67

Query: 68  RSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL 127
           R  + I+QE+   +           G L++ +      + L  +  +F  ++P ++LSL+
Sbjct: 68  RRAQRILQEMAAAETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLV 127

Query: 128 QGNPKQITEMIRNDQADIAI 147
                    +I   + DIA+
Sbjct: 128 SSE--GYINLI-ERKVDIAL 144

>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative, MI center for STR uctural genomics, MCSG; 1.88A {Sinorhizobium meliloti} Length = 300

 Score = 45.6 bits (109), Expect = 8e-06
 Identities = 28/125 (22%), Positives = 52/125 (41%), Gaps = 15/125 (12%)

Query: 8   FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
           F+R     NF  T A+ +L   +  V+  I  LE  L   +  R  +R+  +T  G    
Sbjct: 6   FLRVVETGNF--TRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRVL-VTPDGALYY 62

Query: 68  -RSIEII--MQEIEGLKKIGKEFSAYDT---GNLTIATTHTQARYALPKIIKEFTIQFPK 121
            R+  ++  + E++G        S   +   G L + T    A   +   + EF  ++P 
Sbjct: 63  ERAARLLSDLDELDGS------LSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPD 116

Query: 122 VKLSL 126
           +++ L
Sbjct: 117 IQIDL 121

>3oxn_A Putative transcriptional regulator, LYSR family; structural genomics, PSI-2, protein structure initiative; 2.70A {Vibrio parahaemolyticus} Length = 241

 Score = 43.5 bits (103), Expect = 3e-05
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 1/84 (1%)

Query: 96  TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
           TIATT    +  LP  +     + P V  + L     ++++ +  + AD+AI        
Sbjct: 22  TIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVE 81

Query: 156 DKLISIPCYQWEYVIIVPLDHPLL 179
             L S    +   + ++   HPL 
Sbjct: 82  P-LRSEILGRVGVLCLLSKQHPLA 104

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str} Length = 135

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 11  EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRG--LTKPGQAI 66
           + + +  +++ A +A+  S       +  L       +      GK+  G  LT  G  +
Sbjct: 33  QLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAEL 92

Query: 67  LRSIEIIMQEIE 78
           L     + + + 
Sbjct: 93  LERYRGMEERMN 104

>2y7p_A LYSR-type regulatory protein; transcription regulator, DNA-binding, transcription, transcr factor, transcription regulation; HET: SAL PEU; 1.85A {Burkholderia SP} PDB: 2y7k_A* 2y84_A 2y7w_A 2y7r_A Length = 218

 Score = 42.6 bits (101), Expect = 6e-05
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 96  TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEILSP 154
            +A T     Y +P +++    + P +++S L+ N   + E + +   D+A+ +   L  
Sbjct: 11  NLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQT 70

Query: 155 SDKLISIPCYQWEYVIIVPLDHPLL 179
                    ++  YV +   DHP  
Sbjct: 71  G--FFQRRLFRHRYVCMFRKDHPSA 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	306
1ixc_A	294	CBNR, LYSR-type regulatory protein; long alpha hel	100.0
3fxq_A	305	LYSR type regulator of TSAMBCD; transcriptional re	100.0
3fzv_A	306	Probable transcriptional regulator; LYSR, structur	100.0
2esn_A	310	Probable transcriptional regulator; PA0477, APC582	100.0
1al3_A	324	Cys regulon transcriptional activator CYSB; LYSR f	100.0
2h9b_A	312	HTH-type transcriptional regulator BENM; LTTR, tra	100.0
2h98_A	313	HTH-type transcriptional regulator CATM; BENM, LTT	100.0
1uth_A	315	LYSR-type regulatory protein; transcription regula	100.0
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	100.0
3hhg_A	306	Transcriptional regulator, LYSR family; transcript	100.0
3isp_A	303	HTH-type transcriptional regulator RV1985C/MT2039;	100.0
3mz1_A	300	Putative transcriptional regulator; structural gen	100.0
2hxr_A	238	HTH-type transcriptional regulator CYNR; CYNR tran	100.0
2fyi_A	228	HTH-type transcriptional regulator CBL; Lys-R fami	100.0
3oxn_A	241	Putative transcriptional regulator, LYSR family; s	100.0
4ab5_A	222	Transcriptional regulator, LYSR family; transcript	100.0
3ho7_A	232	OXYR; beta-alpha-barrels, DNA-binding, transcripti	100.0
2y7p_A	218	LYSR-type regulatory protein; transcription regula	100.0
2ql3_A	209	Probable transcriptional regulator, LYSR family P;	100.0
3jv9_A	219	OXYR, transcriptional regulator, LYSR family; LYSR	100.0
1i6a_A	219	OXYR, hydrogen peroxide-inducible genes activator;	99.98
3hhf_B	213	Transcriptional regulator, LYSR family; transcript	99.96
3onm_A	238	Transcriptional regulator LRHA; LYSR, ROVM, transc	99.96
2qsx_A	218	Putative transcriptional regulator, LYSR family; t	99.95
3kos_A	219	HTH-type transcriptional activator AMPR; alpha-bet	99.95
3fd3_A	208	Chromosome replication initiation inhibitor prote;	99.95
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	99.94
1twy_A	290	ABC transporter, periplasmic substrate-binding PR;	99.92
3cta_A	230	Riboflavin kinase; structural genomics, transferas	99.91
3cvg_A	294	Putative metal binding protein; PSI-II, NYSGXRC, p	99.89
1b9m_A	265	Protein (mode); DNA-binding, gene regulation, wing	99.86
4ecf_A	264	ABC-type phosphate transport system, periplasmic;	99.85
4exl_A	265	PBP 1, phosphate-binding protein PSTS 1; center fo	99.77
1ixh_A	321	Phosphate-binding protein; phosphate transport, ul	99.73
1atg_A	231	MODA, periplasmic molybdate-binding protein; tungs	99.73
1pc3_A	350	Phosphate-binding protein 1; phosphate transport r	99.69
3muq_A	237	Uncharacterized conserved protein; structural geno	99.64
3lr1_A	236	Tungstate ABC transporter, periplasmic tungstate-	99.61
3kn3_A	242	Putative periplasmic protein; alpha-beta structure	99.44
2v25_A	259	Major cell-binding factor; antigen, adhesin, aspar	99.23
2x26_A	308	Periplasmic aliphatic sulphonates-binding protein;	99.2
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	99.18
4gd5_A	279	Phosphate ABC transporter, phosphate-binding PROT;	99.17
1us5_A	314	Putative GLUR0 ligand binding core; receptor, memb	99.05
3r26_A	237	Molybdate-binding periplasmic protein; protein bin	99.02
1wdn_A	226	GLNBP, glutamine binding protein; closed form, com	98.95
3gzg_A	253	Molybdate-binding periplasmic protein; permease; m	98.92
2pyy_A	228	Ionotropic glutamate receptor bacterial homologue;	98.83
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	98.82
2pvu_A	272	ARTJ; basic amino acid binding protein, ABC transp	98.81
3cij_A	295	UPF0100 protein AF_0094; archaeal periplasmic bind	98.8
3cfx_A	296	UPF0100 protein MA_0280; ABC transporter, binding	98.8
1lst_A	239	Lysine, arginine, ornithine-binding protein; amino	98.79
1ii5_A	233	SLR1257 protein; membrane protein; HET: GLU; 1.60A	98.78
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	98.78
3cfz_A	292	UPF0100 protein MJ1186; ABC transporter, binding p	98.77
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	98.68
2hxw_A	237	Major antigenic peptide PEB3; periplasmic binding	98.64
2h09_A	155	Transcriptional regulator MNTR; transcription regu	98.61
3k6v_A	354	Solute-binding protein MA_0280; MODA, molybdate, p	98.57
3ksx_A	324	Nitrate transport protein; SSUA, alkanesulfonate-b	98.56
4f3p_A	249	Glutamine-binding periplasmic protein; ssgcid, str	98.51
3kzg_A	237	Arginine 3RD transport system periplasmic binding	98.51
4gvo_A	243	LMO2349 protein; structural genomics, IDP05245, L-	98.51
4dz1_A	259	DALS D-alanine transporter; D-alanine binding, per	98.51
3f3x_A	144	Transcriptional regulator, MARR family, putative;	98.49
3h7m_A	234	Sensor protein; histidine kinase sensor domain, ki	98.49
2y7i_A	229	STM4351; arginine-binding protein; HET: ARG; 1.90A	98.47
2yjp_A	291	Putative ABC transporter, periplasmic binding Pro	98.47
3cg1_A	296	UPF0100 protein PF0080; ABC transporter, binding p	98.46
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	98.45
2vha_A	287	Periplasmic binding transport protein; periplasmic	98.44
3del_B	242	Arginine binding protein; alpha and beta protein (	98.42
2pg4_A	95	Uncharacterized protein; structural genomics, join	98.39
3tql_A	227	Arginine-binding protein; transport and binding pr	98.39
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	98.39
2yln_A	283	Putative ABC transporter, periplasmic binding Pro	98.39
4eq9_A	246	ABC transporter substrate-binding protein-amino A	98.38
4ddd_A	327	Immunogenic protein; ssgcid, structural genomics,	98.31
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	98.31
3hv1_A	268	Polar amino acid ABC uptake transporter substrate	98.31
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	98.29
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	98.29
3kbr_A	239	Cyclohexadienyl dehydratase; pseudomonas aeruginos	98.28
2nnn_A	140	Probable transcriptional regulator; structural gen	98.26
3k4u_A	245	Binding component of ABC transporter; structural g	98.26
2q88_A	257	EHUB, putative ABC transporter amino acid-binding	98.26
3mpk_A	267	Virulence sensor protein BVGS; venus flytrap, sens	98.25
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	98.24
3qax_A	268	Probable ABC transporter arginine-binding protein;	98.24
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	98.24
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	98.22
1xt8_A	292	Putative amino-acid transporter periplasmic solut	98.2
4h5g_A	243	Amino acid ABC superfamily ATP binding cassette tr	98.18
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	98.15
4fx0_A	148	Probable transcriptional repressor protein; helix-	98.15
4i62_A	269	Amino acid ABC transporter, periplasmic amino ACI	98.15
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	98.15
3bja_A	139	Transcriptional regulator, MARR family, putative;	98.15
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	98.14
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	98.14
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	98.14
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	98.13
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	98.13
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	98.12
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	98.12
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	98.12
2gxg_A	146	146AA long hypothetical transcriptional regulator;	98.12
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	98.11
3i6v_A	232	Periplasmic His/Glu/Gln/Arg/opine family-binding;	98.1
3tmg_A	280	Glycine betaine, L-proline ABC transporter, glycin	98.09
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	98.09
3df8_A	111	Possible HXLR family transcriptional factor; APC89	98.08
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	98.08
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	98.07
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	98.07
2eth_A	154	Transcriptional regulator, putative, MAR family; M	98.07
1z91_A	147	Organic hydroperoxide resistance transcriptional;	98.06
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	98.05
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	98.05
2iee_A	271	ORF2, probable ABC transporter extracellular-bindi	98.05
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	98.03
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	98.03
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	98.03
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	98.02
1mqi_A	263	Glutamate receptor 2; GLUR2, ligand binding core,	98.02
3l6g_A	256	Betaine ABC transporter permease and substrate BI	98.01
2obp_A	96	Putative DNA-binding protein; structural genomics,	98.0
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	98.0
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.98
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.97
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.97
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.96
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.96
4h1x_A	265	PBP 2, phosphate-binding protein PSTS 2; periplasm	97.95
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.95
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	97.95
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.93
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.92
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	97.9
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	97.9
2pex_A	153	Transcriptional regulator OHRR; transcription regu	97.9
3p7i_A	321	PHND, subunit of alkylphosphonate ABC transporter;	97.89
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.89
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	97.87
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.87
4ef1_A	246	Pheromone COB1/lipoprotein, YAEC family; periplasm	97.87
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.86
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.84
3n5l_A	310	Binding protein component of ABC phosphonate TRAN;	97.84
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.82
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.8
3g3k_A	259	Glutamate receptor, ionotropic kainate 2; membrane	97.77
1yyv_A	131	Putative transcriptional regulator; reductive meth	97.77
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	97.76
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	97.73
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.73
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	97.72
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.7
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.7
3nqo_A	189	MARR-family transcriptional regulator; structural	97.7
1bja_A	95	Transcription regulatory protein MOTA; activation	97.68
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	97.68
2v3u_A	265	Glutamate receptor delta-2 subunit; postsynaptic m	97.65
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	97.65
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	97.64
3k2d_A	237	ABC-type metal ION transport system, periplasmic;	97.62
1sw5_A	275	Osmoprotection protein (PROX); binding-protein, co	97.57
3qsl_A	346	Putative exported protein; unknown, structural gen	97.57
4edp_A	351	ABC transporter, substrate-binding protein; clostr	97.54
3uif_A	348	Sulfonate ABC transporter, periplasmic sulfonate-	97.53
3un6_A	341	Hypothetical protein saouhsc_00137; structural gen	97.49
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	97.48
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	97.46
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	97.45
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.45
1yae_A	312	Glutamate receptor, ionotropic kainate 2; kainate	97.44
2g29_A	417	Nitrate transport protein NRTA; solute-binding pro	97.42
1xs5_A	241	29 kDa protein, membrane lipoprotein TPN32; peripl	97.42
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	97.41
3ix1_A	302	N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine	97.4
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.39
3tqw_A	240	Methionine-binding protein; transport and binding	97.39
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.36
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.33
3gxa_A	275	Outer membrane lipoprotein GNA1946; periplasmic, L	97.32
2rin_A	298	Putative glycine betaine-binding ABC transporter p	97.31
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.28
2fxa_A	207	Protease production regulatory protein HPR; protea	97.24
3up9_A	245	Putative uncharacterized protein; membrane lipopro	97.2
3jth_A	98	Transcription activator HLYU; transcription factor	97.15
2kko_A	108	Possible transcriptional regulatory protein (possi	97.1
3o66_A	282	Glycine betaine/carnitine/choline ABC transporter;	97.09
1pb7_A	292	N-methyl-D-aspartate receptor subunit 1; ligand bi	97.07
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	97.04
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.0
4ib2_A	252	Putative lipoprotein; putative methionine-bindning	96.99
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.94
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	96.91
1r9l_A	309	Glycine betaine-binding periplasmic protein; perip	96.9
1okr_A	123	MECI, methicillin resistance regulatory protein ME	96.85
3ir1_A	245	Outer membrane lipoprotein GNA1946; D-methionine c	96.85
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	96.83
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	96.81
4got_A	249	Methionine-binding lipoprotein METQ; NLPA lipoprot	96.79
3r6u_A	284	Choline-binding protein; substrate binding protein	96.75
1zbm_A	280	Hypothetical protein AF1704; alpha-beta protein, s	96.74
1p99_A	295	Hypothetical protein PG110; structural genomics, P	96.68
2x7q_A	321	Ca3427, possible thiamine biosynthesis enzyme; unk	96.65
2rc8_A	294	Glutamate [NMDA] receptor subunit 3A; membrane pro	96.55
1hsj_A	487	Fusion protein consisting of staphylococcus access	96.52
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	96.5
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	96.48
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.46
2a5s_A	284	N-methyl-D-aspartate receptor nmdar2A subunit, NMD	96.43
2i49_A	429	Bicarbonate transporter; alpha-beta protein, C-cla	96.42
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	96.37
3onq_A	262	Regulator of polyketide synthase expression; struc	96.29
3r0a_A	123	Putative transcriptional regulator; structural gen	96.27
3hn0_A	283	Nitrate transport protein; ABC transporter, struct	96.25
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.25
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	96.23
2o0m_A	345	Transcriptional regulator, SORC family; structural	96.21
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.2
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	96.2
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.18
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	96.16
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.11
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	96.09
2hin_A	71	GP39, repressor protein; transcription factor, dim	96.08
2f5x_A	312	BUGD; periplasmic binding protein, transport prote	95.98
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.96
2w25_A	150	Probable transcriptional regulatory protein; trans	95.94
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	95.89
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	95.89
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	95.83
3c57_A	95	Two component transcriptional regulatory protein;	95.77
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.72
3pu5_A	333	Extracellular solute-binding protein; structural g	95.7
2ozz_A	231	Hypothetical protein YHFZ; alpha-beta structure, s	95.66
1eto_A	98	FIS, factor for inversion stimulation; transcripti	95.64
1xma_A	145	Predicted transcriptional regulator; southea colla	95.64
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	95.62
2dvz_A	314	BUGE, putative exported protein; periplamsic bindi	95.58
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	95.46
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	95.43
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	95.42
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.4
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	95.38
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	95.38
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	95.37
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.37
2czl_A	272	Hypothetical protein TTHA1568; conserved hypotheti	95.35
2qpq_A	301	Protein BUG27; alpha/beta domain, venus flytrap, t	95.32
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	95.31
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.3
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	95.25
1xvx_A	312	YFUA; periplasmic iron binding protein, iron bindi	95.19
4esf_A	117	PADR-like transcriptional regulator; PADR family,	95.14
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.13
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	95.09
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	95.09
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	95.05
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.97
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	94.97
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.94
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	94.88
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.83
1nh8_A	304	ATP phosphoribosyltransferase; prtase, de novo His	94.77
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.72
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	94.68
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	94.67
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	94.66
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.64
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	94.54
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	94.52
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	94.44
1sbp_A	310	Sulfate-binding protein; 1.70A {Salmonella typhimu	94.42
4esw_A	342	Pyrimidine biosynthesis enzyme THI13; thiamin pyri	94.39
1o63_A	219	ATP phosphoribosyltransferase; structural genomics	94.32
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.29
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	94.28
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	94.27
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	94.17
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	94.14
3elk_A	117	Putative transcriptional regulator TA0346; structu	94.09
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	94.07
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	94.02
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	93.93
2g7u_A	257	Transcriptional regulator; ICLR family, structural	93.92
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	93.91
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	93.9
4i1d_A	324	ABC transporter substrate-binding protein; structu	93.84
4g6q_A	182	Putative uncharacterized protein; structural genom	93.81
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.77
1bia_A	321	BIRA bifunctional protein; transcription regulatio	93.73
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	93.72
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	93.71
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	93.6
2vd2_A	214	ATP phosphoribosyltransferase; HISG, glycosyltrans	93.52
1h3d_A	299	ATP-phosphoribosyltransferase; hisitidine biosynth	93.44
2co5_A	99	Viral protein F93; viral protein-winged helix comp	93.17
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	93.15
2vd3_A	289	ATP phosphoribosyltransferase; metal-binding, glyc	93.01
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	92.9
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	92.88
4euo_A	320	ABC transporter, substrate binding protein (polya;	92.84
2q0o_A	236	Probable transcriptional activator protein TRAR; h	92.84
3e13_X	322	Putative iron-uptake ABC transport system, peripla	92.75
1gtk_A	313	Porphobilinogen deaminase; lyase, biosynthesis of	92.75
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	92.72
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	92.7
2b4l_A	268	Glycine betaine-binding protein; substrate-binding	92.69
1u78_A	141	TC3 transposase, transposable element TC3 transpos	92.62
4h1x_A	265	PBP 2, phosphate-binding protein PSTS 2; periplasm	92.57
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	92.52
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	92.45
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	92.07
2dql_A	115	PEX protein; circadian clock associated protein, c	92.0
1z7m_E	208	ATP phosphoribosyltransferase; ATP-PRT, histidine	91.99
2nxo_A	291	Hypothetical protein SCO4506; PFAM, DUF178, NYSGXR	91.97
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	91.83
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	91.79
1ve4_A	206	ATP phosphoribosyltransferase; riken structural ge	91.77
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	91.74
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	91.34
4gl0_A	333	LMO0810 protein; structural genomics, IDP05673, sp	91.33
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	91.27
3kg2_A	823	Glutamate receptor 2; ION channel, membrane protei	91.21
2vn2_A	128	DNAD, chromosome replication initiation protein; D	91.12
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	91.05
3rpw_A	365	ABC transporter; structural genomics, PSI-biology,	90.95
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	90.94
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	90.7
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	90.34
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	90.32
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	90.29
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	90.18
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	90.1
2pfz_A	301	Putative exported protein; extracytoplasmic solute	90.06
2hzl_A	365	Trap-T family sorbitol/mannitol transporter, perip	89.96
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	89.93
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	89.85
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	89.84
2k27_A	159	Paired box protein PAX-8; paired domain, solution	89.77
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	89.7
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	89.66
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	89.15
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	89.11
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	88.71
1p6r_A	82	Penicillinase repressor; transcription regulation,	88.56
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	88.55
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	88.16
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	87.99
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	87.78
3e3m_A	355	Transcriptional regulator, LACI family; structural	87.39
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	87.35
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	87.13
3by6_A	126	Predicted transcriptional regulator; structural ge	86.96
3c9h_A	355	ABC transporter, substrate binding protein; struct	86.95
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	86.92
2pfy_A	301	Putative exported protein; extracytoplasmic solute	86.87
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	86.83
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	86.75
4eqb_A	330	Spermidine/putrescine ABC superfamily ATP binding	86.63
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	86.37
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	86.35
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	85.87
3c3w_A	225	Two component transcriptional regulatory protein;	85.19
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	85.15
3jvd_A	333	Transcriptional regulators; structural genomics, P	85.15
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	85.03
1nnf_A	309	Iron-utilization periplasmic protein; iron-binding	84.83
3o6p_A	229	Peptide ABC transporter, peptide-binding protein;	84.75
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	83.96
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	83.85
4eq9_A	246	ABC transporter substrate-binding protein-amino A	83.72
1iej_A	332	Ovotransferrin; iron, metal binding protein; 1.65A	83.71
1h45_A	334	Lactoferrin; metal transport, iron transport, meta	83.64
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	83.53
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	83.53
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	83.52
3c7j_A	237	Transcriptional regulator, GNTR family; structural	83.2
2ozz_A	231	Hypothetical protein YHFZ; alpha-beta structure, s	83.11
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	83.06
1i3j_A	116	I-TEVI, intron-associated endonuclease 1; protein-	83.03
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	82.71
2qry_A	330	Thiamine-binding periplasmic protein; thiamin bind	82.51
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	82.41
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	82.04
3g63_A	381	Pfluding; subatomic resolution, phosphate binding,	82.03
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	81.31
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	81.27
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	81.21
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	80.64
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	80.62
1yio_A	208	Response regulatory protein; transcription regulat	80.61
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	80.45
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	80.35

>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domai binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A

Probab=100.00  E-value=1.3e-60  Score=390.65  Aligned_cols=291  Identities=15%  Similarity=0.157  Sum_probs=265.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~l~~f~~v~~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (294)
T 1ixc_A            1 MEFRQLKYFIAVAEAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGI-ELTAAGHAFLEDARRILELAGRS   78 (294)
T ss_dssp             CCHHHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC-----C-CBCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcC-CHHHHHHHhCCCcchHHHHHHHHHHHHCCEEEEeCCCCe-eECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++..
T Consensus        79 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~  157 (294)
T 1ixc_A           79 GDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFF-PRHPGIEI  157 (294)
T ss_dssp             HHHHHHHHHTCCEEEEEEECSGGGGTHHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEESCC-CCCTTEEE
T ss_pred             HHHHHHHhcCCCceEEEEEccchhHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHCCCccEEEEecC-CCCCCceE
Confidence            99998877778899999999999999999999999999999999999999999999999999999999654 55788999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecC--CCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL--SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      .++++++++++++++||++.+..++++||.++|+|.+..  +...+..+++++...|+.+++.+++++..++..++.+|.
T Consensus       158 ~~l~~~~~~~v~~~~~pl~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~  237 (294)
T 1ixc_A          158 VNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGA  237 (294)
T ss_dssp             EEEEEEEEEEEEEGGGGGGTCSEECGGGGTTCEEEECCCSSSSCHHHHHHHHHHHTTCCCEEEEECSSHHHHHHHHHTTS
T ss_pred             EEEeeccEEEEEeCCCccccCCccCHHHHcCCCEEeeCCCCCchHHHHHHHHHHHCCCCcceeeecCCHHHHHHHHHcCC
Confidence            999999999999999999988899999999999999883  456678889999999999999999999999999999999


Q ss_pred             ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      |++++|.++.. ...++++.+|+++.....++|++|+++. .+|.+++|++++++.++
T Consensus       238 Gia~lp~~~~~-~~~~~l~~~~l~~~~~~~~~~l~~~~~~-~~~~~~~f~~~l~~~~~  293 (294)
T 1ixc_A          238 ASSIVPASVAA-IRWPDIAFARIVGTRVKVPISCIFRKEK-QPPILARFVEHVRRSAK  293 (294)
T ss_dssp             CBEEEEHHHHT-SCCTTEEEEEECCTTCEEEEEEEEESSS-CCHHHHHHHHHHHHHHC
T ss_pred             eEEEechhhhh-cCCCceEEEECcCCCcceeEEEEEcCCC-CCHHHHHHHHHHHHHhc
Confidence            99999998743 3567899999987556789999999986 59999999999988764

>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- transcription, transcription regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A 3n6t_A 3n6u_A*

Probab=100.00  E-value=2.4e-60  Score=391.08  Aligned_cols=295  Identities=20%  Similarity=0.235  Sum_probs=273.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         2 m~l~~L~~f~~v~~~g-s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   79 (305)
T 3fxq_A            2 LKLQTLQALICIEEVG-SLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGV-SLTSFGQAFMKHARLIVTESRRA   79 (305)
T ss_dssp             CHHHHHHHHHHHHHHS-CHHHHHHHTTCCHHHHHHHHHHHHHHHTSCSEEECSSSE-EECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEEecCCCc-cCCHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCce
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~  159 (306)
                      ...++.......|.|+||++++++..++++++..|.++||++++++....++++.+.|.+|++|++|+..+.. ..+++.
T Consensus        80 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~g~~Dlai~~~~~~~~~~~l~  159 (305)
T 3fxq_A           80 QEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLE  159 (305)
T ss_dssp             HHHHHHHHHHHHTEEEEEECHHHHHTHHHHHHHHHHHHCTTCEEEEEECCTTTTHHHHHHTSSSEEEEECCGGGSCTTEE
T ss_pred             HHHHHHHhcCCCceEEEEechHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHcCCCCEEEecCCCCCCccCee
Confidence            9988887777789999999999999999999999999999999999999888999999999999999975433 268899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC-ceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ..++++++++++++++||++..  .+++||.++|+|.+..+...+..+.+++...|+ .+++.+++++..++..++.+|.
T Consensus       160 ~~~L~~~~~~~v~~~~hpla~~--~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~v~~g~  237 (305)
T 3fxq_A          160 AQPLYVSDVVIVGQRQHPMANA--TRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHSD  237 (305)
T ss_dssp             EEEEEECCEEEEEETTCTTTTC--CSGGGGTTSEEEEECCTTSTTHHHHHHHHHTTCCCCEEEEEECCTTTHHHHHHTSS
T ss_pred             EEEeecCcEEEEEcCCCCCCCC--CCHHHHhCCCeEeeCCCCCHHHHHHHHHHHcCCCCCCceEEeCCHHHHHHHHHhCC
Confidence            9999999999999999999874  389999999999998877777788999999999 7889999999999999999999


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      |++++|.+++... ..++++.+|+++....+++|++|++++..+|+++.|++++++.+.+..
T Consensus       238 gia~lp~~~~~~~~~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~  299 (305)
T 3fxq_A          238 LLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWIQHHALQTG  299 (305)
T ss_dssp             CEEEEEHHHHHSSTTGGGEEECCCSSCCCCCEEEEEEETTSCCCHHHHHHHHHHHHHCC---
T ss_pred             EEEEeeHHHHhhhhhcCCEEEeeCCCCCCCCceEEEEeCCCCCCHHHHHHHHHHHHHHhhcc
Confidence            9999999998765 789999999988777789999999999999999999999999876543

>3fzv_A Probable transcriptional regulator; LYSR, structural genomics, PSI-2, structure initiative; 2.71A {Pseudomonas aeruginosa PA01}

Probab=100.00  E-value=8.2e-60  Score=388.04  Aligned_cols=294  Identities=20%  Similarity=0.321  Sum_probs=263.8

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      ||+++|++|++|+++| ||++||++||+||||+|++|++||++||++||+|+ ++|+ +||++|+.|+++++++++.+++
T Consensus         4 ~~l~~l~~f~~v~~~~-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~G~~l~~~a~~~l~~~~~   81 (306)
T 3fzv_A            4 YTLRQLKYFVTTVECG-SVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGV-SLTPAGARFYRKAQELLRMAHE   81 (306)
T ss_dssp             CCHHHHHHHHHHHHSS-SHHHHHHHHTCCC-CHHHHHHHHHHHC-CCCC----------CCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCeeEeecCCCCc-eECHhHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 99999999999999999999999999999999996 8998 8999999999999999999999


Q ss_pred             HHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760          80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI  159 (306)
Q Consensus        80 ~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~  159 (306)
                      +...+........|.|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.
T Consensus        82 ~~~~~~~~~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~  160 (306)
T 3fzv_A           82 FEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEH-DLDSTIE  160 (306)
T ss_dssp             HHHC-CCCCCCCCEEEEEEEEGGGHHHHHHHHHHHHHHHCTTEEEEEEEECHHHHHHHHHHTSCSEEEECSS-SCCTTEE
T ss_pred             HHHHHHHhccCCCceEEEEechhhhHHHHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEecc-ccccccc
Confidence            998888777778899999999999999999999999999999999999999999999999999999999755 5667899


Q ss_pred             eeccc-cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 SIPCY-QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~~~l~-~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ..+++ .++++++++++||++.+..++++||.++|+|.+..+.. +..+..++...|+.+++.+++++..++..++.+|.
T Consensus       161 ~~~l~~~~~~~~v~~~~~pl~~~~~~~~~dL~~~~~i~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~  239 (306)
T 3fzv_A          161 TEPLMPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQPS-RTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGF  239 (306)
T ss_dssp             EEESSCCBCCEEEEETTCTTTTSSEECHHHHTTSCEEEECCTTH-HHHHHHHHHHTTCCCCEEEEESCHHHHHHHHHTTS
T ss_pred             eeeeeeccccEEEecCCCcccCCCCCCHHHHcCCCEEEecCCcc-hHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHcCC
Confidence            99999 99999999999999999899999999999999987654 77888999999999999999999999999999999


Q ss_pred             ceeeeecceeccc-ccCC-ceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         239 GIGIIASIAFDSN-RDKN-LRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~-l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      |++++|...+... ..+. ++.+|++++....++|++|++++..+|.+++|++++++.+++.
T Consensus       240 Gia~lp~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~  301 (306)
T 3fzv_A          240 GFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGKL  301 (306)
T ss_dssp             CBEEECCCCSCSBCTTSCBEEEEEESSCCCBCCCEEEEETTSCCCHHHHHHHHHHHHHHHC-
T ss_pred             CEEEEecccccccccCCCceEEEECCCCCccceEEEEEeCCcccCHHHHHHHHHHHHHHHHh
Confidence            9999999888765 4554 9999998866778999999999999999999999999988653

>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1

Probab=100.00  E-value=4.5e-60  Score=390.33  Aligned_cols=293  Identities=16%  Similarity=0.126  Sum_probs=267.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus        10 m~l~~L~~f~~v~~~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   87 (310)
T 2esn_A           10 LDLNLLLVFDALYRHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRM-QPTQRAEHLAAAVAAALRALGEG   87 (310)
T ss_dssp             SCTTHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEEETTEE-EECHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHhhCCcceeecCCCc-cccHHHHHHHHHHHHHHHHHHhh
Confidence            7899999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhc-cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEc---cccCCCC
Q psy3760          81 KKIGKEFS-AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT---EILSPSD  156 (306)
Q Consensus        81 ~~~~~~~~-~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~---~~~~~~~  156 (306)
                      ...++... ....|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+.   .+ ...+
T Consensus        88 ~~~~~~~~~~~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~  166 (310)
T 2esn_A           88 LEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALGYDEEHE-RLPE  166 (310)
T ss_dssp             TGGGSCCCTTTCCCEEEEECCHHHHHHHHHHHHHHHHHHSTTCEEEEECCSSSCCHHHHHHTSSSEEEECCSTTC-CCCT
T ss_pred             hccccCCChhhcCceEEEEeChHHHHHHHHHHHHHHHHHCCCeEEEEEeCCcccHHHHHHcCCCCEEEecCcccc-cCCc
Confidence            98776654 3567899999999999999999999999999999999999988889999999999999996   44 5678


Q ss_pred             CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         157 KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       157 ~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      ++...++++++++++++++||++. .+++++||.++|++.+..+...+..++.++...|+.+++.+++++..++..+|.+
T Consensus       167 ~l~~~~l~~~~~~~v~~~~~pl~~-~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~  245 (310)
T 2esn_A          167 GIQAHDWFADRYVVVARRDHPRLA-GAPTLEGYLAERHAVVTPWNEDSGVIDRLLARSGLRREVAVQLPTVLAALFLAGS  245 (310)
T ss_dssp             TEEEEEEEEECEEEEEESSCTTCS-SSCCHHHHHTSEEEEECTTCCSSCHHHHHHHHTTCCCEEEEEESCHHHHHHHHHT
T ss_pred             CcceeeeeccceEEEEeCCCCCcC-CCCCHHHHhcCCcEEEeCCCCcccHHHHHHHhCCCCeeEEEeCCCHHHHHHHHhc
Confidence            899999999999999999999985 7899999999999999877666678899999999999999999999999999999


Q ss_pred             ccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         237 RMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       237 g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      |.|++++|.+.+... ..++++.+|++......++|++|++++..+|.+++|++++++.+..
T Consensus       246 g~Gia~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~s  307 (310)
T 2esn_A          246 TDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQLKGLDIS  307 (310)
T ss_dssp             SSCEEEEEHHHHHHHHHHHTEEEECCSSCCCCEEEEEEEECC--CCHHHHHHHHHSCCCC--
T ss_pred             CCeEEEcHHHHHHHHhhcCCceEecCCCCCCCeeEEEEEeCcccCCHHHHHHHHHHHHhccc
Confidence            999999999988765 5678999999876667899999999999999999999999877543

>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine biosynthesis, transcription regulation; 1.80A {Klebsiella aerogenes} SCOP: c.94.1.1

Probab=100.00  E-value=1.1e-59  Score=390.25  Aligned_cols=302  Identities=42%  Similarity=0.777  Sum_probs=195.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++|+||++||++||+||||||++|++||++||++||+|+++|+++||++|+.|+++++++++.++++
T Consensus         1 M~l~~L~~F~~v~~~gls~s~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~~l~~~~~~   80 (324)
T 1al3_A            1 MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGQEIIRIAREVLSKVDAI   80 (324)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCHHHHHHHHHHHHcccCHHHHHHHhCCCchHHHHHHHHHHHHhCCEEEEECCCCcceeCHhHHHHHHHHHHHHHHHHHH
Confidence            89999999999999966999999999999999999999999999999999999997139999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...+........|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+.......+++..
T Consensus        81 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dlai~~~~~~~~~~l~~  160 (324)
T 1al3_A           81 KSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVM  160 (324)
T ss_dssp             -------CCCCEEEEEEEECHHHHHHTSHHHHHHHHHHCTEEEEEEEECCHHHHHHHHHTTCCSEEEESSCCCTTSCEEE
T ss_pred             HHHHHHhhcCCCCeEEEEechhhhhhHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCceEEEEecCCCCCCCeeE
Confidence            98888777777899999999999999999999999999999999999999999999999999999999644345688999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++.+.+++++||.++|+|.+..+...+..+++++...|+.+++.+++++..++..+|.+|.|+
T Consensus       161 ~~L~~~~~~~v~~~~~pl~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~lv~~G~Gi  240 (324)
T 1al3_A          161 LPCYHWNRSIVVTPEHPLATKGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV  240 (324)
T ss_dssp             EEEEEECEEEEECTTSTTTTTSCCCHHHHHTSEEEEECTTSTTHHHHHHHHHHHTCCCEEEEEESSHHHHHHHHHHTSCE
T ss_pred             EEecCCceEEEEcCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCCCe
Confidence            99999999999999999998889999999999999998877777788899999999999999999999999999999999


Q ss_pred             eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      +++|.+.+.....++++.+|+++......+|++|+++...++.++.|++++++.+.+...++
T Consensus       241 ailp~~~~~~~~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~~~~~~~~~  302 (324)
T 1al3_A          241 GVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVVDT  302 (324)
T ss_dssp             EEEEGGGCCTTTCTTSEEEECBTTBCCEEEEEEEETTCCCCHHHHHHHHHHCTTCCHHHHHH
T ss_pred             EEechhhhhhhccCCeEEEECCCCCcceEEEEEEeCCCCCCHHHHHHHHHHHHHhccchhhh
Confidence            99999887655457799999987666789999999999999999999999999887766654

>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional activator, LYSR-type transcripti regulator; 1.80A {Acinetobacter SP} PDB: 2h99_A 3k1m_A 3k1n_A 3k1p_A 2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A*

Probab=100.00  E-value=5.6e-59  Score=384.03  Aligned_cols=292  Identities=18%  Similarity=0.255  Sum_probs=183.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~F~~va~~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~   78 (312)
T 2h9b_A            1 MELRHLRYFVAVVEEQ-SFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPV-KTTPEGHFFYQYAIKLLSNVDQM   78 (312)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CcHHHHHHHHHHHHhC-CHHHHHHHhcCCccHHHHHHHHHHHHhCCEeEeeCCCCc-eECHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++....... .|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++..
T Consensus        79 ~~~~~~~~~~~~-~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dlai~~~~-~~~~~l~~  156 (312)
T 2h9b_A           79 VSMTKRIASVEK-TIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLK-ISDPAIKH  156 (312)
T ss_dssp             ----------CC-EEEEEECGGGGGTTHHHHHHHHHHTCTTCEEEEEECCHHHHHHHHHTTSCSEEEESSC-CCCTTEEE
T ss_pred             HHHHHHHhCCCC-eEEEEechhhhHhhHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCCCEEEEeCC-CCCCCceE
Confidence            998887766667 9999999999999999999999999999999999999999999999999999999654 56678999


Q ss_pred             eccccceEEEEecCCCCCCC-CCC-cChhhhcCCCeEeecCC--CCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNS-ISLKEISNYPLITYDLS--FSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~-i~~~dl~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      .++++++++++++++||++. +.. ++++||.++|+|.+...  ...+..+..++...|+.+++.+++++..++..+|.+
T Consensus       157 ~~L~~~~~~~v~~~~hpla~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~  236 (312)
T 2h9b_A          157 SLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAA  236 (312)
T ss_dssp             EEEEEEEEEEEEETTSGGGGGTTTCBCGGGSTTSEEEECCCSSSSSHHHHHHHHHHTTTCCCSEEEECSSHHHHHHHHHT
T ss_pred             EEeecceEEEEEcCCCccccccCCCCCHHHHcCCCEEEeCCCCCchHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHc
Confidence            99999999999999999987 666 99999999999997654  346778889999999999999999999999999999


Q ss_pred             ccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         237 RMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       237 g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      |.|++++|.+.+.. ..++++.+|+++.....++|++|+++. .+|.++.|++++++.+.+.
T Consensus       237 g~Gia~lp~~~~~~-~~~~l~~~~l~~~~~~~~~~l~~~~~~-~~~~~~~f~~~l~~~~~~~  296 (312)
T 2h9b_A          237 GEGISLVPASTQSI-QLFNLSYVPLLDPDAITPIYIAVRNME-ESTYIYSLYETIRQIYAYE  296 (312)
T ss_dssp             TSCBEEEEGGGGGB-CCTTEEEEEBCSTTCEEEEEEEEETTC-CCHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEecchhhhc-CCCCeEEEECCCCcccceEEEEEcCCC-CCHHHHHHHHHHHHhhccc
Confidence            99999999988754 346788999987666789999999987 6999999999999987654

>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A {Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A* 3m1e_A

Probab=100.00  E-value=9.8e-59  Score=382.44  Aligned_cols=293  Identities=19%  Similarity=0.252  Sum_probs=183.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~L~~F~~vae~g-S~s~AA~~L~isq~avS~~I~~LE~~lG~~Lf~R~~r~v-~lT~~G~~l~~~a~~il~~~~~~   78 (313)
T 2h98_A            1 MELRHLRYFVTVVEEQ-SISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPA-KVTEAGMFFYQHAVQILTHTAQA   78 (313)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCCccHHHHHHHHHHHHhCCeeEEcCCCCe-EECHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++....... .|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++..
T Consensus        79 ~~~~~~~~~~~~-~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dlai~~~~-~~~~~l~~  156 (313)
T 2h98_A           79 SSMAKRIATVSQ-TLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLK-ITDPAIRR  156 (313)
T ss_dssp             ----------CC-EEEEEECGGGGGTTHHHHHHHHHHHCTTSEEEEEECCHHHHHHHHHHTSCSEEEESSC-CCCTTEEE
T ss_pred             HHHHHHhhCCCc-EEEEEechHhHHhHHHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHcCCCCEEEEeCC-CCCCCeeE
Confidence            998887766667 9999999999999999999999999999999999999999999999999999999654 56678999


Q ss_pred             eccccceEEEEecCCCCCCC-CCC-cChhhhcCCCeEeecCC--CCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNS-ISLKEISNYPLITYDLS--FSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~-i~~~dl~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      .++++++++++++++||++. +.. ++++||.++|+|.+...  ...+..+.+++...|+.+++.+++++..++..++.+
T Consensus       157 ~~L~~~~~~~v~~~~hpl~~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (313)
T 2h98_A          157 IMLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAA  236 (313)
T ss_dssp             EEEEEEEEEEEEETTSGGGGGTTSCBCGGGGTTSCEEECCCSSSSSHHHHHHHHHHHTTCCCSCEEECSCHHHHHHHHHT
T ss_pred             EEeeeCcEEEEEcCCCcccccCCCCcCHHHHcCCCEEEecCCCCchHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHc
Confidence            99999999999999999987 666 99999999999997654  346677889999999999999999999999999999


Q ss_pred             ccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         237 RMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       237 g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      |.|++++|.+++.. ..+++..+|+++.....++|++|+++. .+|.+++|++++++.+.+..
T Consensus       237 g~Gia~lp~~~~~~-~~~~l~~~~l~~~~~~~~~~l~~~~~~-~~~~~~~f~~~l~~~~~~~~  297 (313)
T 2h98_A          237 GEGVCIVPASAMDI-GVKNLLYIPILDDDAYSPISLAVRNMD-HSNYIPKILACVQEVFATHH  297 (313)
T ss_dssp             TSCBEEEEGGGGGS-CCTTEEEEEBCSTTCEEEEEEEEETTC-CCTHHHHHHHHHHHHHHHTT
T ss_pred             CCcEEEeehhhhhc-CCCCeEEEECCCCCccceEEEEEcCCC-CCHHHHHHHHHHHHHhcccc
Confidence            99999999988754 346788899987566789999999987 68999999999998876544

>1uth_A LYSR-type regulatory protein; transcription regulation, transcriptional regulator; 2.2A {Burkholderia SP} SCOP: c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A

Probab=100.00  E-value=1.9e-59  Score=387.25  Aligned_cols=295  Identities=15%  Similarity=0.167  Sum_probs=191.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus        14 m~l~~L~~f~~v~~~g-s~t~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~   91 (315)
T 1uth_A           14 IDLNLLVVFNQLLLDR-SVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGM-EPTPYALHLAEPVIYALNTLQTA   91 (315)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCcceeecCCCc-cCCHHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhcc-CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760          81 KKIGKEFSA-YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI  159 (306)
Q Consensus        81 ~~~~~~~~~-~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~  159 (306)
                      ...++.... ...|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++.
T Consensus        92 ~~~~~~~~~~~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~  170 (315)
T 1uth_A           92 LTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLP-ELQTGFF  170 (315)
T ss_dssp             --CCSSCCTTTCCCEEEEECCHHHHHHHHHHHHHHHHHHCTTCEEEEECTTSSCHHHHHHHTSCCEEEECCT-TCCTTEE
T ss_pred             hccCCCCCccccceEEEEEechHHHHHHHHHHHHHHHHHCCCcEEEEEeCCcccHHHHHHCCCCCEEEecCC-CCCCCce
Confidence            876665433 35789999999998889999999999999999999999999889999999999999999654 4567899


Q ss_pred             eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      ..++++++++++++++||++. .+++++||.++|++.+......+..+++++...|+.+++.+++++..++..+|.+|.|
T Consensus       171 ~~~l~~~~~~~v~~~~hpl~~-~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~g  249 (315)
T 1uth_A          171 QRRLFRHRYVCMFRKDHPSAK-SPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDL  249 (315)
T ss_dssp             EEEEEEECEEEEEETTCSSCC-SSCCHHHHHHSEEEEECCTTSGGGGHHHHHHHTTCCCEEEEEESSSTTHHHHHHTSSC
T ss_pred             EEEeeccceEEEEeCCCCCcC-CCCCHHHHhcCCeEEEecCCCCCCchhHHHHhcCCCceEEEECCcHHHHHHHHhcCCE
Confidence            999999999999999999987 7899999999999988765555667889999999999999999999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      ++++|.+++... ..++++.+|++...+..++|++|++++..+|.+++|++++++.+++..
T Consensus       250 iailp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~  310 (315)
T 1uth_A          250 IATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEAH  310 (315)
T ss_dssp             BEEEEHHHHHHHTTTTTEEEEECSSCCCCEEEEEEEEGGGTTCHHHHHHHHHHHHHHCCTT
T ss_pred             EEEcHHHHHHHHhhcCCceEeCCCCCCCCccEEEEECCccCCChHHHHHHHHHHHHHHHhh
Confidence            999999888664 567899999987666789999999999999999999999999886543

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B

Probab=100.00  E-value=1e-58  Score=378.69  Aligned_cols=289  Identities=11%  Similarity=0.183  Sum_probs=260.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||+|++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus         1 m~l~~l~~f~~v~~~~-s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   78 (291)
T 3szp_A            1 MKLDDLNLFRLVVENG-SYTSTSKKTMIPVATITRRIQALEDSLNLRLLNRHARKL-TLTEAGERFYKDCSPLLERLASM   78 (291)
T ss_dssp             CCHHHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCEEEETTEE-EECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEeecCCCc-ccCHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.|+||++++++..++++++..|.+.||++++++...+.   .+.|.+|++|++|+..+ ...+++..
T Consensus        79 ~~~~~~~~~~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~---~~~l~~~~~Dl~i~~~~-~~~~~l~~  154 (291)
T 3szp_A           79 TEEITDECRGASGRIRISAPSNLTKRMMMPMFNAFMEKYPDIHIELMMSNQ---ADDLDPTEWDVIFRVGP-QRDSSLIA  154 (291)
T ss_dssp             HHHHHTSCCSSCEEEEEEEETTTHHHHTHHHHHHHHHHCTTEEEEEEEECS---CSCCCGGGCSEEEEESC-CCCTTCEE
T ss_pred             HHHHHhcccCCceEEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEEecC---ccCccccCceEEEEecC-CCCCCeeE
Confidence            999998878888999999999999999999999999999999999996543   46888999999999765 56789999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||++.+.+++++||.++|++. ..+...+......+...+..+++.+++++..++..+|.+|.|+
T Consensus       155 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~~~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi  233 (291)
T 3szp_A          155 RKIGEVKDILVASPQYLSSHPQPTHAEELHQHQLLK-GYPLLKWQLTNSQGETVVNSDRGRFQASALNVVRSACSEGLGI  233 (291)
T ss_dssp             EEEEEECEEEEECHHHHHHSCCCSSGGGGGGSCEEE-ETTBCSEEEECTTSCEEEECCCCSEEESSHHHHHHHHHTTCCE
T ss_pred             EEecccceEEEECHHHHHhcCCCCCHHHHhcCCeee-cCCCCceeEEcCCCceeEEeccCceEECcHHHHHHHHHcCCcE
Confidence            999999999999999998888899999999999999 4432322333333556677788899999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      +++|.+.+... ..+.++.++.+.....+++|++|++++..+|.+++|++++++.+.
T Consensus       234 ailp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~  290 (291)
T 3szp_A          234 TLMPDVMLREFLEDGSLVQVLSDWSSNPRDIYMLYNHKDHQPEKVRLFIDFVIGYHL  290 (291)
T ss_dssp             EEEEGGGTHHHHHTTTSEECCTTCBCCCEEEEEEECCGGGCCHHHHHHHHHHHHSCC
T ss_pred             EEccHHHHHHHHhCCCeEEecCCccCCCCcEEEEECCCCCCCHHHHHHHHHHHHHhc
Confidence            99999999876 778888886665566789999999999999999999999998753

>3hhg_A Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B}

Probab=100.00  E-value=1.3e-57  Score=374.97  Aligned_cols=295  Identities=15%  Similarity=0.190  Sum_probs=254.7

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus         3 ~~l~~l~~f~~v~~~g-s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~il~~~~~~   80 (306)
T 3hhg_A            3 TNSEELTVFVQVVESG-SFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQL-SLTEEGAQYFRRAQRILQEMAAA   80 (306)
T ss_dssp             CCHHHHHHHHHHHHSS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEETTSSSC-EECHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEeecCCCe-eECHhHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      .+.+........|.|+||++++++..++++++..|.+.||++++++...   +....+.+|++|++|+..+ ...+++.+
T Consensus        81 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~---~~~~~l~~~~~Dl~i~~~~-~~~~~l~~  156 (306)
T 3hhg_A           81 ETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLVSS---EGYINLIERKVDIALRAGE-LDDSGLRA  156 (306)
T ss_dssp             HHHHHTTSSCCCEEEEEEBCHHHHHHTHHHHHHHHHHHCTTEEEEEECC---SSSHHHHTTSSSCEEESCC-CCCSSCEE
T ss_pred             HHHHHhcccCCCCcEEEEccHHHHHHHHHHHHHHHHHHCCCeEEEEEec---cchhhHhhcCccEEEEeCC-CCCCCeEE
Confidence            9999988778899999999999999999999999999999999999833   3455788999999999755 66789999


Q ss_pred             eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      .++++++++++++++||+..+.+++++||.++|+|.+..+..........+...+..+++.+++++..++.+++.+|.|+
T Consensus       157 ~~L~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Gi  236 (306)
T 3hhg_A          157 RHLFDSRFRVIASPEYLAKHGTPQSTEELAGHQCLGFTEPGSLNTWAVLDAQGNPYKISPHFTASSGEILRSLCLSGCGI  236 (306)
T ss_dssp             EEEEEEEEEEEECHHHHHHHCCCSSTTGGGGSCBCEESSTTTSCEEEEECSSSCEEECCCSSEESSHHHHHHHHHTTSCE
T ss_pred             EEeeeeEEEEEECHHHHHhcCCCCCHHHHhcCCEEEecCCCCCcceEEEcCCCcEEeccCeEEECCHHHHHHHHHhCCCe
Confidence            99999999999999998888888999999999999887755432221112222344566678999999999999999999


Q ss_pred             eeeecceeccc-ccCCceeeecCCCCc-cceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLFG-TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN  301 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  301 (306)
                      +++|.+.+... ..+.++.+......+ ..++|++|+++...+|++++|++++++.+++....
T Consensus       237 a~lp~~~~~~~~~~g~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~~  299 (306)
T 3hhg_A          237 VCLSDFLVDNDIAEGKLIPLLAEQTSDKTHPFNAVYYSDKAVNLRLRVFLDFLVEELGNNLCG  299 (306)
T ss_dssp             EEEEHHHHHHHHHHTSSEECSTTTBCCCEEEEEEEECSGGGGCHHHHHHHHHHHHHCC-----
T ss_pred             EeccHHHHHHHHhCCCcEEeCCCCcCCCCccEEEEecCCCcCCHHHHHHHHHHHHHccccccc
Confidence            99999998876 677888763333222 56999999999999999999999999998765543

>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped structure, DNA binding domain, regulatory domain, DNA-binding; 2.70A {Mycobacterium tuberculosis}

Probab=100.00  E-value=6.9e-55  Score=358.22  Aligned_cols=285  Identities=13%  Similarity=0.083  Sum_probs=256.0

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+ +|+ +||++|+.|+++++++++.++++
T Consensus         6 m~l~~L~~f~~v~~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~-~~~-~lT~~G~~l~~~a~~~l~~~~~~   82 (303)
T 3isp_A            6 LDGPQLAALAAVVELG-SFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVRE-KPC-RATTAGIPLLRLAAQTALLESEA   82 (303)
T ss_dssp             CCSHHHHHHHHHHHHT-CHHHHHTTTTCCHHHHHHHHHHHHHHHTSCCEECS-SSC-EECGGGHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeeEEcC-CCC-eeCchHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 99999999999999999999999999999999998 598 79999999999999999999999


Q ss_pred             HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760          81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS  160 (306)
Q Consensus        81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~  160 (306)
                      ...++.......|.|+||+++++...++++++..|  +  ++.+++...++.++.+.|.+|++|++|+..+ ...+++..
T Consensus        83 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f--~--~v~i~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~l~~  157 (303)
T 3isp_A           83 LAEMGGNASLKRTRITIAVNADSMATWFSAVFDGL--G--DVLLDVRIEDQDHSARLLREGVAMGAVTTER-NPVPGCRV  157 (303)
T ss_dssp             TTTTC--CTTCCEEEEEEECHHHHHTTGGGGGTTC--C--SEEEEEEECCHHHHHHHHHTTSCSEEEESCC-SCCTTEEE
T ss_pred             HHHhhhccccCCceEEEeechhHHHHHHHHHHHhh--c--cceEEEEecChHHHHHHHHcCcceEEEecCC-CCCCCeEE
Confidence            88777766778899999999999999999999999  3  9999999999999999999999999999654 56689999


Q ss_pred             eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      .++++++++++++++||+.. ++.++++||.++|+|.+..+...+..+...+...++.+ +.+++++..++..+|.+|.|
T Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~G  236 (303)
T 3isp_A          158 HPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITR-PTHFVPTTEGFTAAARAGLG  236 (303)
T ss_dssp             EEEEEEEEEEEECHHHHHHHCTTCSCTTTTTTSCBCCSSTTCCHHHHHHHHHHSSCCCC-CBCCCCSHHHHHHHHHTTSC
T ss_pred             EEccceeEEEEecchHhhhccccCCCHhHhccCCceecCCCCcHHHHHHHHHhhcccCC-ceEEECCHHHHHHHHHhCCe
Confidence            99999999999999999876 45789999999999999887777777777777778887 78899999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      ++++|.+.+... ..+.++.++  ...  .+++++|++++..+|.+++|++++++.+++.
T Consensus       237 i~~lp~~~~~~~~~~~~l~~l~--~~~--~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~  292 (303)
T 3isp_A          237 WGMFPEKLAASPLADGSFVRVC--DIH--LDVPLYWQCWKLDSPIIARITDTVRAAASGL  292 (303)
T ss_dssp             BEEEEHHHHHHHHHHSSCEESS--SCC--EEEEEEEEEESSCCHHHHHHHHHHHHHTTTS
T ss_pred             EEeccHHHHhhhhcCCCeEEec--CCC--CccceEEecCCCCChHHHHHHHHHHHHHHHh
Confidence            999999988776 566665544  322  7999999999999999999999999988654

>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative, MI center for STR uctural genomics, MCSG; 1.88A {Sinorhizobium meliloti}

Probab=100.00  E-value=6.4e-56  Score=363.62  Aligned_cols=290  Identities=14%  Similarity=0.153  Sum_probs=175.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI   83 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~   83 (306)
                      ++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++...
T Consensus         1 ~~L~~f~~v~~~~-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~~~~   78 (300)
T 3mz1_A            1 QGMRAFLRVVETG-NFTRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRV-LVTPDGALYYERAARLLSDLDELDGS   78 (300)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CcHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEecCCCce-eeCHhHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999 999999999999999999999999999999999999999 89999999999999999999999998


Q ss_pred             HHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecc
Q psy3760          84 GKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPC  163 (306)
Q Consensus        84 ~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l  163 (306)
                      ++.......|.|+||++++++..++++++..|.+.||++++++...+..   ..+.+|++|++|+..+ ...+++.+.++
T Consensus        79 ~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~~---~~l~~~~~Dl~i~~~~-~~~~~l~~~~l  154 (300)
T 3mz1_A           79 LSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRT---IDYLAENVDCAIRAGT-LTDQSLIARRI  154 (300)
T ss_dssp             ------CCCEEEEEEECHHHHHHTHHHHHHHHHHHCTTEEEEEEECCCC-----CCCTTCCEEEEESS-CSCTTSEEEEE
T ss_pred             HHhhccCCCceEEEEecHHHHHHHHHHHHHHHHHHCCCcEEEEEeCCCc---ccccccCCcEEEEecc-CCCCCeEEEEe
Confidence            8887777889999999999999999999999999999999999875442   3688999999999755 66789999999


Q ss_pred             ccceEEEEecCCCCCCCCCCcChhhhcCCCeEe-ecCCCC---cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT-YDLSFS---GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~-~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      ++++++++++++||+..+.+++++||.++|++. +.....   ....+...+...++.+++.+++++..++..++.+|.|
T Consensus       155 ~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~G  234 (300)
T 3mz1_A          155 TEMKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTMAANESTTYLAAARAGLG  234 (300)
T ss_dssp             EEECEEEEEEHHHHHHSCCCSSGGGGGTTSCEEEEBCCC--CBCCEEEEETTEEEEECCCEEEEESSHHHHHHHHHTTCC
T ss_pred             ecceeEEEECHHHHHhCCCCCCHHHHHhChhhhhccccccCcCcceEEecCCceEEEeccceEEECCHHHHHHHHHhCCC
Confidence            999999999999998888889999999999998 654321   1112233334445788999999999999999999999


Q ss_pred             eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      ++++|.+.+... ..+.++.++.+.....++++++|++++..+|.+++|++++++.+++..
T Consensus       235 i~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~  295 (300)
T 3mz1_A          235 VIQAPLFMVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWVVKVMAQSQ  295 (300)
T ss_dssp             BEEEEHHHHHHHHHHTSEEECCTTCBCCCEEEEEEECTTCCCCHHHHHHHHHHHHHHHHHT
T ss_pred             EEeccHHHHHHHHhCCCeEEeCCCcCCCCccEEEEEcCcccCcHHHHHHHHHHHHHhhhhh
Confidence            999999998776 678888887776677889999999999999999999999999987653

>2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional regulator LYSR struc genomics, PSI-2, protein structure initiative; 2.05A {Escherichia coli} PDB: 3hfu_A

Probab=100.00  E-value=3.6e-35  Score=232.36  Aligned_cols=231  Identities=18%  Similarity=0.281  Sum_probs=184.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCee
Q psy3760          65 AILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQAD  144 (306)
Q Consensus        65 ~l~~~a~~il~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~D  144 (306)
                      .|+++|+++++.++++.+.++.......|+|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|
T Consensus         2 ~l~~~a~~il~~~~~~~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~~g~~D   81 (238)
T 2hxr_A            2 VWRQYASRALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELD   81 (238)
T ss_dssp             -----------------------------CEEEEECHHHHTTTHHHHHHHHHHHCTTSCEEEEECCHHHHHHHHHTTSCS
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhcccCCeEEEeechhhHHHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCCc
Confidence            47899999999999999988887777789999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccccCCCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEe
Q psy3760         145 IAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLET  224 (306)
Q Consensus       145 i~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (306)
                      ++|+..+ ...+++.+.++++++++++++++||++.+..++++||.++|+|.+..+...+..+..++...|+.+++.+++
T Consensus        82 l~i~~~~-~~~~~l~~~~l~~~~~~~v~~~~hpl~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (238)
T 2hxr_A           82 VGIAFAP-VHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEA  160 (238)
T ss_dssp             EEEEESS-CCCTTEEEEEEEEEEEEEEEETTSGGGGCSEECGGGGGGCEEEEECTTSHHHHHHHHHHHHTTCCCEEEEEE
T ss_pred             EEEEcCC-CCcccceeeeeccCcEEEEEcCCCcccccCCCCHHHHhcCCeEEecCCccHHHHHHHHHHHcCCCCCeEEEe
Confidence            9999654 456789999999999999999999999888899999999999999887666777889999999999999999


Q ss_pred             cCHHHHHHHHHhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         225 INSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       225 ~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      ++..+++++|.+|.|++++|.+.+.  ..++++.+|++.....+.++++|+++...++.+++|++++++.+.+.
T Consensus       161 ~~~~~~~~~v~~g~Gi~~lp~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~  232 (238)
T 2hxr_A          161 NSISAVLELIRRTSLSTLLPAAIAT--QHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCAVV  232 (238)
T ss_dssp             SCHHHHHHHHHHSSCBEEEETHHHH--HCTTEEEEEESSCSCEEEEEEEEETTSCCCHHHHHHHHHHHHHHC--
T ss_pred             CCHHHHHHHHHcCCcEEEecHHHhc--cCCCeEEEecCCCCeeEEEEEEEeCCCccCHHHHHHHHHHHHhcccC
Confidence            9999999999999999999998876  46789999987656677999999999999999999999999877543

>2fyi_A HTH-type transcriptional regulator CBL; Lys-R family, cofactor-binding DO cysteine biosynthesis; 2.80A {Escherichia coli K12} SCOP: c.94.1.1

Probab=100.00  E-value=9.7e-33  Score=217.01  Aligned_cols=216  Identities=39%  Similarity=0.718  Sum_probs=192.9

Q ss_pred             HhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccc
Q psy3760          85 KEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY  164 (306)
Q Consensus        85 ~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~  164 (306)
                      +.......|+|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+.......+++...+++
T Consensus         6 ~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~~~l~   85 (228)
T 2fyi_A            6 SHMTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWF   85 (228)
T ss_dssp             CCTTTTCCEEEEEEECHHHHHHTHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEESSSSTTCTTEEEEEEE
T ss_pred             HHhcCCCcceEEEeeccchHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecccCCCCCceEEEee
Confidence            34455678899999999999999999999999999999999999999999999999999999996443346789999999


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeee
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIA  244 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p  244 (306)
                      +++++++++++||++.+..++++||.++|+|.+..+...+..+..++...|+.+++.+++++..++..+|.+|.|++++|
T Consensus        86 ~~~~~~v~~~~hpla~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~~G~Gia~lp  165 (228)
T 2fyi_A           86 RWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVA  165 (228)
T ss_dssp             EECEEEEEETTCGGGTSSSCCHHHHTTSCEEEECTTSTTHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTSCEEEEE
T ss_pred             ecceEEEecCCCCccccCccCHHHHcCCCeEEecCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhCCCEEEee
Confidence            99999999999999988889999999999999988777777888999999999999999999999999999999999999


Q ss_pred             cceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         245 SIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       245 ~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      .+.+.....++++.+|+++......++++|++++..++.++.|++++++.+.+...
T Consensus       166 ~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~  221 (228)
T 2fyi_A          166 EQSSGEQEEENLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDI  221 (228)
T ss_dssp             GGGGSTTCCTTEEEECCTTTSCCEEEEEEEETTCCBCHHHHHHHHHHCSSSCHHHH
T ss_pred             hHhhhhcccCCeEEEECCCcccceEEEEEEeCCCcCCHHHHHHHHHHHHhhhhhHH
Confidence            98775543567999998875556799999999999999999999999988766544

>3oxn_A Putative transcriptional regulator, LYSR family; structural genomics, PSI-2, protein structure initiative; 2.70A {Vibrio parahaemolyticus}

Probab=100.00  E-value=1.8e-32  Score=217.21  Aligned_cols=220  Identities=15%  Similarity=0.081  Sum_probs=192.0

Q ss_pred             HHHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCC
Q psy3760          78 EGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK  157 (306)
Q Consensus        78 ~~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~  157 (306)
                      +++............|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...++
T Consensus         4 ~~l~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~   82 (241)
T 3oxn_A            4 RQLLSPVEFDPQQCDQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPT-GPVEP   82 (241)
T ss_dssp             ----------CCSCCCEEEEEECSHHHHHTHHHHHHHHHHHCTTCEEEEEECCGGGHHHHHHTSCCSEEEECCS-SCCTT
T ss_pred             hhcCCCCCcCcccCCceEEEEechHHHHHHHHHHHHHHHHHCCCCEEEEEECCcccHHHHHHcCCCCEEEecCC-CCCcc
Confidence            33343333334567899999999999999999999999999999999999999999999999999999999654 57789


Q ss_pred             ceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         158 LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       158 ~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      +.+.++++++++++++++||++. ..++++||.++|+|.+..+...+..+++++... +.+++.+++++..++.++|.+|
T Consensus        83 ~~~~~l~~~~~~~v~~~~hpl~~-~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g  160 (241)
T 3oxn_A           83 LRSEILGRVGVLCLLSKQHPLAN-QEMSLDDYLSHPHAMIAISDGVKALIEQALIDK-PQRKMVLRAYHLEAALAIVDTL  160 (241)
T ss_dssp             EEEEEEECCCEEEEEETTSGGGG-SCCCHHHHHTSEEEECSCCHHHHHHHHHHSTTS-CCCEEEEECSSTHHHHHHC--C
T ss_pred             ceeEEeecccEEEEEeCCCCccc-CCCCHHHHhcCCeEEEecCCCccchhHHHHHhh-ccceEEEECCcHHHHHHHHhCC
Confidence            99999999999999999999998 889999999999999988877788889999999 9999999999999999999999


Q ss_pred             cceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         238 MGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       238 ~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      .|++++|.+.+... ..++++.+|++.....+.++++|+++...++.+++|++++++.+++...
T Consensus       161 ~giailp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  224 (241)
T 3oxn_A          161 PIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIA  224 (241)
T ss_dssp             CCEEEEEHHHHHHHHHHTTEEEECCSSCCCCCCEEEEEEGGGTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEcHHHHHHHhcccCCceEeCCCCCCCcccEEEEEcCcCCCCchhHHHHHHHHHHHHHHHH
Confidence            99999999998876 5689999999876677899999999999999999999999999876543

>4ab5_A Transcriptional regulator, LYSR family; transcription factors; 2.51A {Neisseria meningitidis serogroup B} PDB: 4ab6_A

Probab=100.00  E-value=2.1e-32  Score=213.91  Aligned_cols=209  Identities=19%  Similarity=0.193  Sum_probs=193.6

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~  168 (306)
                      .+..|+|+||+++++...++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.+++++++
T Consensus         4 ~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~~~~~~l~~~~~   82 (222)
T 4ab5_A            4 EGEAGELRIAVECHTCFDWLMPAMGEFRPMWPQVELDIVSGFQADPVGLLLQHRADLAIVSEA-EKQNGISFQPLFAYEM   82 (222)
T ss_dssp             -CTTEEEEEECCCTTTHHHHHHHHHHHHHHSTTEEEEEECCCCSCTHHHHHTTSCSEEEESCC-CCCTTEEEEEEEEEEE
T ss_pred             CCccceEEEEEehHHHHHHHHHHHHHHHHHCCCcEEEEecCCHHHHHHHHHcCCcCEEEecCC-CCcCCeEEEEeecCcE
Confidence            456789999999999999999999999999999999999999999999999999999999654 5678899999999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++++||++.+..++++||.++|++.+..+...+..+.+++...++.++ .+++++..++..++.+|.|++++|.+.+
T Consensus        83 ~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g~gi~~~p~~~~  161 (222)
T 4ab5_A           83 VGICAPDHPLAAKNVWTAEDFIGETLITYPVPDEMLDLPKKILIPKNINPP-RRHSELTIAIIQLVASRRGIAALPYWTV  161 (222)
T ss_dssp             EEEECTTSGGGGCSEECGGGGSSSCEEECSSCGGGCHHHHHTTGGGTCCCC-EEECSCHHHHHHHHHTTSCBEEEEHHHH
T ss_pred             EEEecCCChhhccCCcCHHHHcCCCEEecCCCcHHHHHHHHHHHHcCCCCC-eEecCCHHHHHHHHHcCCeEEEcchHHh
Confidence            999999999999999999999999999999887888899999999999999 9999999999999999999999999988


Q ss_pred             ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      ... ..++++.+|+++....+.++++|++++..++.+++|++++++.+.+..
T Consensus       162 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~  213 (222)
T 4ab5_A          162 MPYLEKGYVVHRQITADGLQSKLYAAIRTEDTDKSYLNNFCQIIRERGFADL  213 (222)
T ss_dssp             HHHHHTTSCEEEEESTTCCEEEEEEEEEGGGTTCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHhhcCcEEEEecCCCccceEEEEEEeCCcccCHHHHHHHHHHHhhhhccc
Confidence            765 678899999998677889999999999999999999999999876643

>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio regulation; 1.58A {Porphyromonas gingivalis}

Probab=100.00  E-value=1.4e-32  Score=216.41  Aligned_cols=212  Identities=18%  Similarity=0.167  Sum_probs=192.7

Q ss_pred             hhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecccc
Q psy3760          86 EFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ  165 (306)
Q Consensus        86 ~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~  165 (306)
                      ..+....|.|+||+++++...++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.++++
T Consensus         4 ~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~~~l~~   82 (232)
T 3ho7_A            4 EEQQSLTGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASK-AETEGLEDDLLYY   82 (232)
T ss_dssp             ------CEEEEEEECTTTHHHHHHHHHHHHHHHSTTEEEEEEECCHHHHHHHHHHTSCSEEEESSC-CCCTTEEEEEEEE
T ss_pred             hhhcccceeEEEEeccccchhhhHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCCCEEEEcCC-CCCCCeEEEEecc
Confidence            344567789999999999999999999999999999999999999999999999999999999765 5568999999999


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-eeEEEEecCHHHHHHHHHhccceeeee
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-PYIVLETINSDIIKTYVELRMGIGIIA  244 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p  244 (306)
                      ++++++++++||++.+..++++||.++|+|.+..+...+..+.+++...++. +++.+++++..++..++.+|.|++++|
T Consensus        83 ~~~~~v~~~~hpl~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p  162 (232)
T 3ho7_A           83 EEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIP  162 (232)
T ss_dssp             EEEEEEECTTSGGGGSSSBCGGGCCGGGBCCCTTTTTTTSTTHHHHTCTTTTCSSEEEESCCHHHHHHHHHTTCCEEEEE
T ss_pred             cCEEEEEcCCCccccCCCcCHHHhcCCCEEEecCCCcHHHHHHHHHHHcCCCcCceeEEeCCHHHHHHHHHcCCcEEEec
Confidence            9999999999999999999999999999999988877888899999999997 999999999999999999999999999


Q ss_pred             cceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         245 SIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       245 ~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .+.+... ..++++.+|+++....+.++++|++++..++.+++|++++++.+++.
T Consensus       163 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  217 (232)
T 3ho7_A          163 QLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSD  217 (232)
T ss_dssp             GGGGGGSCHHHHTTEECBCSSEEEEEEEEEEETTCSCHHHHHHHHHHHHTTSCGG
T ss_pred             HHHhhhhcccCceEEEEccCCCceEEEEEEEeCCCccCHHHHHHHHHHHHHhccc
Confidence            9999866 66789999998767788999999999989999999999999988654

>2y7p_A LYSR-type regulatory protein; transcription regulator, DNA-binding, transcription, transcr factor, transcription regulation; HET: SAL PEU; 1.85A {Burkholderia SP} PDB: 2y7k_A* 2y84_A 2y7w_A 2y7r_A

Probab=100.00  E-value=3.7e-32  Score=212.20  Aligned_cols=207  Identities=13%  Similarity=0.115  Sum_probs=184.8

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV  169 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~  169 (306)
                      ...|+|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.++++++++
T Consensus         5 ~~~g~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~l~~~L~~g~iDl~i~~~~-~~~~~l~~~~l~~~~~~   83 (218)
T 2y7p_A            5 ASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLP-ELQTGFFQRRLFRHRYV   83 (218)
T ss_dssp             TCCCEEEEECCHHHHHHHHHHHHHHHHHHCTTCEEEEECCCTTTHHHHHHHTSSCEEEECCT-TCCTTEEEEEEEEECEE
T ss_pred             ccceEEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEEeCCcccHHHHHhCCCceEEEecCC-CCCcceeEEEeeeccEE
Confidence            45789999999999999999999999999999999999999999999999999999998643 44578999999999999


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++++++||++. ..++++||.++|++........+..+++++...|+.+++.+++++..++..+|.+|.|++++|...+.
T Consensus        84 ~v~~~~hpla~-~~i~l~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~lv~~g~Giailp~~~~~  162 (218)
T 2y7p_A           84 CMFRKDHPSAK-SPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAV  162 (218)
T ss_dssp             EEEETTCSSCC-SSCCHHHHHHSEEEEECCTTSGGGGHHHHHHHTTCCCEEEEEESSSTTHHHHHHTSSCBEEEEHHHHH
T ss_pred             EEEcCCCCCCC-CCCCHHHHhhCCCEEeecCCCccCHHHHHHHhcCCcceEEEEcCcHHHHHHHHhCCCEEEEcHHHHHH
Confidence            99999999997 78999999999999876555556778999999999999999999999999999999999999998765


Q ss_pred             cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .. ..++++.+|++.......++++|++++..+|+.++|++.+++.+++.
T Consensus       163 ~~~~~~~l~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  212 (218)
T 2y7p_A          163 RCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEA  212 (218)
T ss_dssp             HHHHHHTEEEEECSSCCCCEEEEEEEEGGGTTCHHHHHHHHHHHHHHCCT
T ss_pred             HhhhcCCceEecCCCCCCCccEEEEEccccCCChHHHHHHHHHHHHHHhh
Confidence            43 45679999998655567999999999989999999999999887654

>2ql3_A Probable transcriptional regulator, LYSR family P; APC7314, rhodococcus RHA1, structural genomics, PSI-2; HET: MSE; 2.05A {Rhodococcus SP}

Probab=100.00  E-value=4.7e-31  Score=204.50  Aligned_cols=201  Identities=14%  Similarity=0.263  Sum_probs=179.6

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~  170 (306)
                      ..|+|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+... ...+++...+++++++++
T Consensus         3 ~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~l~~~l~~g~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~   81 (209)
T 2ql3_A            3 VAGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL-DLSPEWQTVPLMTREPMV   81 (209)
T ss_dssp             CCEEEEEEECGGGTTTTHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHTTSCSEEEEESS-SCCTTEEEEEEEEECCEE
T ss_pred             cceeEEEeechhhhhhhHHHHHHHHHHHCCCceEEEEECcHHHHHHHHHcCCccEEEEecC-CCCCCceEEEeecCceEE
Confidence            4689999999999999999999999999999999999999999999999999999998654 456789999999999999


Q ss_pred             EecCCCCCCCCC-CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce--
Q psy3760         171 IVPLDHPLLLLN-SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA--  247 (306)
Q Consensus       171 v~~~~~~l~~~~-~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~--  247 (306)
                      +++++||++.+. .++++||.++|+|.+.. ...+..+.+++...|+.+++.+++++..+++++|.+|.|++++|...  
T Consensus        82 v~~~~hpl~~~~~~~~~~~l~~~~~i~~~~-~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~  160 (209)
T 2ql3_A           82 VLGAEHPLAGVDGPVRLADLAEHPMVLLDA-PPSTNHAMDVCREAGFAPRVAYRTANFETARAFVGRGLGWTLLLQRPRV  160 (209)
T ss_dssp             EEETTCGGGGCCSCBCGGGGTTSCEEEECC-TTHHHHHHHHHHHHTCCCCEEEEESCHHHHHHHHHHTSCBEEESCCCSS
T ss_pred             EEeCCCccccCCCCcCHHHHhCCCEEeeCC-hhHHHHHHHHHHHcCCCCceEEEECCHHHHHHHHHcCCeEEEeeCCccc
Confidence            999999998877 89999999999999887 56667788899999999999999999999999999999999999853  


Q ss_pred             ecccccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         248 FDSNRDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       248 ~~~~~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ......++++.+|+++.. ....++++|++++..++++++|++++++
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~  207 (209)
T 2ql3_A          161 DVTYEGLPVVVKPIAEPKPASVAVVVAWHQEATLSRVARAFIRFVTA  207 (209)
T ss_dssp             CBCTTSCBEEEEEBCSSCCCCEEEEEEEETTCCCCHHHHHHHHHHTC
T ss_pred             ccccCCCceEEEECCCCCcceEEEEEEEeCCCCCCHHHHHHHHHHhc
Confidence            222245789999988755 6679999999998889999999998864

>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type transcriptional regulator, LTTR, redox, structural genomics, OPPF; 2.39A {Neisseria meningitidis}

Probab=100.00  E-value=6.7e-32  Score=210.53  Aligned_cols=206  Identities=17%  Similarity=0.189  Sum_probs=189.6

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~  170 (306)
                      ..|+|+||+++++...++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.+++++++++
T Consensus         2 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~   80 (219)
T 3jv9_A            2 LEGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP-FQEPGIVTEPLYDEPFFV   80 (219)
T ss_dssp             -CCCEEEEEETTTHHHHHHHHHHHHHHHSTTCCEEEEEECHHHHHHHHHHTSSSEEEEESS-CCCTTEEEEEEEEEEEEE
T ss_pred             cCCcEEEEEcchhhHHHHHHHHHHHHHHCCCcEEEEEeCCcHHHHHHHHcCCCCEEEEcCC-CCCCCeeEEEeeeceEEE
Confidence            4689999999999999999999999999999999999999999999999999999999764 567899999999999999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHh-----CCCceeEEEEecCHHHHHHHHHhccceeeeec
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSL-----QKLTPYIVLETINSDIIKTYVELRMGIGIIAS  245 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~  245 (306)
                      +++++||++.+..++++||.++|++.+..+...+..+..++..     .++.++..+++++..++..++.+|.|++++|.
T Consensus        81 v~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~  160 (219)
T 3jv9_A           81 IVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCSELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPA  160 (219)
T ss_dssp             EEETTCGGGTSSSCCSSTTSSSCEEEECTTCHHHHHHHHHCSTTHHHHHHHTTTSSCEESSHHHHHHHHHHTSCEEEEEG
T ss_pred             EEeCCCCcccCCCCCHHHhcCCcEEEecCCccHHHHHHHHHHhhhhhhccCCCCceEEeCCHHHHHHHHHcCCcEEehhH
Confidence            9999999999999999999999999998887778888888877     66778888999999999999999999999999


Q ss_pred             ceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         246 IAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       246 ~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      +.+..+..++++.+|+++......++++|++++..++.+++|++++++.+.+
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  212 (219)
T 3jv9_A          161 TALTENDHMLFSIIPFEGTPPSRRVVLAYRRNFVRPKALSAMKAAIMQSQLH  212 (219)
T ss_dssp             GGCCTTCTTTEEEECCSSSCCEEEEEEEEETTCSCHHHHHHHHHHHHTSCCS
T ss_pred             HHHHhccCCcEEEEecCCCCcceeEEEEEecCccccHHHHHHHHHHHhhccc
Confidence            9988766778999999887778899999999999999999999999987643

>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory domain, oxidized form, transcription; 2.30A {Escherichia coli} SCOP: c.94.1.1 PDB: 1i69_A

Probab=99.98  E-value=3.4e-32  Score=212.53  Aligned_cols=206  Identities=16%  Similarity=0.254  Sum_probs=182.7

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~  170 (306)
                      ..|+|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...+++++++++
T Consensus         3 ~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~   81 (219)
T 1i6a_A            3 MSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV-KESEAFIEVPLFDEPMLL   81 (219)
T ss_dssp             TCEEEEEEECTTTHHHHHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEEECC-GGGTTSEEEEEEEEEEEE
T ss_pred             CceEEEEEeccchhhhhhhHHHHHHHHHCCCeEEEEEECChHHHHHHHHcCCeeEEEecCC-CCCCCcceeeeecccEEE
Confidence            4689999999999999999999999999999999999999999999999999999998644 345789999999999999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++++||++.+..++++||.++|+|....+...+..+.+++...|+.+++.+++++..+++.+|.+|.|++++|.+.+..
T Consensus        82 v~~~~hpla~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~~g~Gia~lp~~~~~~  161 (219)
T 1i6a_A           82 AIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPP  161 (219)
T ss_dssp             EEETTSGGGGCSCEEGGGGTTSEEECCTTTTCSSCTTSSCSSCTTSEEECTTTTSCHHHHHHHHHTTSCBEEEEGGGSCS
T ss_pred             EEcCCCccccCCccCHHHhcCCcEEEecCCCcHHHHHHHHHHHCCCCCCceEeeCCHHHHHHHHHhCCCEEEeehhhhhh
Confidence            99999999988889999999999999887665555556667777888888889999999999999999999999998765


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      . ..++++.+|+++......++++|+++...++.+++|++++++.+.+
T Consensus       162 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~  209 (219)
T 1i6a_A          162 ERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDG  209 (219)
T ss_dssp             SSEETTEEEECEESSCCEEEEEEEECTTCTTHHHHHHHHHHHHHHHTT
T ss_pred             hccCCcEEEEECCCCcceEEEEEEECCCCCCCHHHHHHHHHHHHHHHH
Confidence            4 5678999998765566789999999998999999999999887654

>3hhf_B Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 2.30A {Neisseria meningitidis serogroup B}

Probab=99.96  E-value=2.3e-30  Score=200.97  Aligned_cols=206  Identities=13%  Similarity=0.123  Sum_probs=172.8

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~  168 (306)
                      ....|+|+||++++++..++++++..|.++||++++++...+  . ...|.+|++|++|+..+ ...+++.+.+++++++
T Consensus         3 ~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~~--~-~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~   78 (213)
T 3hhf_B            3 EIPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLVSSE--G-YINLIERKVDIALRAGE-LDDSGLRARHLFDSRF   78 (213)
T ss_dssp             --CCEEEEEEECHHHHHHTHHHHHHHHHHHCTTEEEEEECCS--T-THHHHTTSSSEEEECC---CCSSEEEEEEEEECE
T ss_pred             CCCCceEEEecCHHHHHHHHHHHHHHHHHHCCCcEEEEEeCC--c-HHHHHhCCccEEEEEec-CCCccceEEeeecceE
Confidence            346789999999999999999999999999999999999533  3 34599999999999754 5678899999999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++++||++.+..++++||.++|+|.+..+...+..+...+...+..+++.+++++..++..+|.+|.|++++|.+.+
T Consensus        79 ~~v~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~  158 (213)
T 3hhf_B           79 RVIASPEYLAKHGTPQSTEELAGHQCLGFTEPGSLNTWAVLDAQGNPYKISPHFTASSGEILRSLCLSGCGIVCLSDFLV  158 (213)
T ss_dssp             EEEECHHHHHHHCCCSSGGGGGGSCBCEESSCGGGGEEEEECTTSCEEECCCSSEESSHHHHHHHHHTTSCBEEEEHHHH
T ss_pred             EEEeCHHHHHhcCCCCCHHHhcCCCeEEecCCCCccchhhhhCCCccccccCceeeCCHHHHHHHHHcCCcEEEeeHHHh
Confidence            99999999999888999999999999999887665554455556667778888999999999999999999999999998


Q ss_pred             ccc-ccCCceeeecCCCCc-cceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         249 DSN-RDKNLRSISASHLFG-TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      ... ..+.++.+......+ .++++++|++++..++.+++|++++++.+++.
T Consensus       159 ~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  210 (213)
T 3hhf_B          159 DNDIAEGKLIPLLAEQTSDKTHPFNAVYYSDKAVNLRLRVFLDFLVEELGNN  210 (213)
T ss_dssp             HHHHHHTSSEEECTTTBCCCCEEEEEEEEGGGGGCHHHHHHHHHHHHHC---
T ss_pred             hHHHhcCCcEEecCCCCCCceeeEEEEEcCCCCCChHHHHHHHHHHHHhhhh
Confidence            765 667788773333333 67999999999999999999999999988754

>3onm_A Transcriptional regulator LRHA; LYSR, ROVM, transcription factor, virulence factor; 2.40A {Yersinia pseudotuberculosis}

Probab=99.96  E-value=4.7e-27  Score=185.70  Aligned_cols=195  Identities=14%  Similarity=0.145  Sum_probs=170.2

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~  168 (306)
                      ....|.|+||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+   .+++.+.+++++++
T Consensus        23 ~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~~l~~~~~   99 (238)
T 3onm_A           23 SNMEGSLIIGASDDTADTLLPFLLNRVATLYPRLAIDVRVKRSPFIADMLSSGEVDLAITTAK---VDSHPHVILRTSPT   99 (238)
T ss_dssp             ----CCEEEEECHHHHTTHHHHHHHHHHHHCTTCCEEEEECCHHHHHHHHHHTSCSEEEECSC---C-CCCEEEEEEECE
T ss_pred             cCCceeEEEeccchhhHHHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHCCCccEEEEecC---CCCcceEEeecCCE
Confidence            456789999999999999999999999999999999999999999999999999999999754   23599999999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++++||++.+..        .|++.+..+...+..+.+++...++.+++.+++++..+++++|.+|.|++++|.+++
T Consensus       100 ~~v~~~~~~l~~~~~--------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Giailp~~~~  171 (238)
T 3onm_A          100 LWYCSVDYQFQPGEP--------VPLVVMDEPSLYREMAIEHLTQAGVPWRIAYVASSLSAIRAAVRAGLGVTARPIEMM  171 (238)
T ss_dssp             EEEEETTCCCCTTSC--------EEEEEESSSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCBEEEEGGGC
T ss_pred             EEEEcCCCCcccCCC--------cceEECCCchhHHHHHHHHHHHCCCCeEEEEEeCCHHHHHHHHHcCCeEEEechHHc
Confidence            999999999887653        489999888778888999999999999999999999999999999999999999987


Q ss_pred             cccccCCceeeecCC--CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         249 DSNRDKNLRSISASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       249 ~~~~~~~l~~~~~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      .    +++..+++..  +.....++++|++++..++.+++|++++++.+++.
T Consensus       172 ~----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~  219 (238)
T 3onm_A          172 S----PDLRVLGETEGLPGLPETRYVLCKDKQCDNELALAIFSALQNSYQHT  219 (238)
T ss_dssp             C----TTEEEECGGGTCCCCCCEEEEEECCTTCCCHHHHHHHHHHHTTCC--
T ss_pred             c----chheecccccCCCCccceeeEEEecccccCHHHHHHHHHHHHHHHHH
Confidence            5    3566677654  33467899999999999999999999999987654

>2qsx_A Putative transcriptional regulator, LYSR family; the putative transcriptional regulator, PSI-2, structure initiative, MCSG; 1.64A {Vibrio parahaemolyticus}

Probab=99.95  E-value=2.5e-28  Score=190.52  Aligned_cols=194  Identities=16%  Similarity=0.153  Sum_probs=150.5

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcc--ccCCCCCceeeccccceE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE--ILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~--~~~~~~~~~~~~l~~~~~  168 (306)
                      ..|.|+||++++++..++++.+..|.++||++++++...++.  . .+.+|++|++|..+  . ...+  ...+++++++
T Consensus        17 ~~G~lrI~~~~~~~~~~L~~~l~~f~~~~P~i~l~l~~~~~~--~-~l~~~~~Dlai~~~~~~-~~~~--~~~~l~~~~~   90 (218)
T 2qsx_A           17 DQELLVVDVTPSFASLWLVPNINDFHQRHPNIRVKILTGDGA--V-KNIHGESDLHVRCLPLS-THYE--YSQLLCEETL   90 (218)
T ss_dssp             --CEEEEEECHHHHHHTHHHHHHHHHHHCTTCEEEEEECCSC--C------CCSEEEEEEECC-SCCS--SEEEEEEEEE
T ss_pred             CCCcEEEecCHHHHHHHHHHHHHHHHHHCCCeEEEEEecCCc--c-cccCCCCCEEEEcCCCC-CCCc--cceeccCCCE
Confidence            468999999999999999999999999999999999998765  3 78899999999865  3 2223  8899999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHHHHhccceeeeec
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTYVELRMGIGIIAS  245 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~~g~gi~~~p~  245 (306)
                      ++|++++|+ +   +++++||.++|+|....+.   ..+..|+...|..+   +..+++++..++++++.+|.|++++|.
T Consensus        91 ~~v~sp~~~-~---~~~~~dL~~~~~i~~~~~~---~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~v~~G~Gia~lp~  163 (218)
T 2qsx_A           91 LLIGNTNLP-K---LSDNQAISHYPFIPQTTRP---QLWEQFKQENDLECPITYHSVGFEHFYLACEAVRMEKGLALLPD  163 (218)
T ss_dssp             EEEEETTCC-----------CTTSCBCCCTTCT---THHHHHHTCC-----CCBCSBCCSSHHHHHHHHHTTCCBEEEEH
T ss_pred             EEEEChhhc-c---CCCHHHHhcCCeEecCCCc---hHHHHHHHHcCCCcccCCCCceeccHHHHHHHHHhCCCEEEecH
Confidence            999999997 3   5789999999999876542   34677887777643   567889999999999999999999999


Q ss_pred             ceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         246 IAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       246 ~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      +++... ..+.|+.++.+.......+|++|++++..++.++.|++++++.+.+
T Consensus       164 ~~~~~~l~~g~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~  216 (218)
T 2qsx_A          164 FMAQFSILRGDIQHIGNLKLHSGYGYYVVIPNFRLTSRKVALFHDWLKDKLTH  216 (218)
T ss_dssp             HHHHHHHHTTSEEEEEEEEEEEEEEEEEECCTTCTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHCCCccccCccccCCCceEEEEeccccCCCHHHHHHHHHHHHHhhc
Confidence            888665 6788888765433345789999999999999999999999987654

>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich, DNA-binding, transcription regulation; HET: MES; 1.83A {Citrobacter freundii} PDB: 3kot_A

Probab=99.95  E-value=9.6e-28  Score=187.14  Aligned_cols=204  Identities=12%  Similarity=0.009  Sum_probs=167.1

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY  168 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~  168 (306)
                      .+..|.|+||++++++..++++++..|.++||++++++...+..   ..|.+|++|++|+..+ ...+++...+++++++
T Consensus         8 ~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~---~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~   83 (219)
T 3kos_A            8 KQTQEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNR---VDPAAEGLDYTIRYGG-GAWHDTDAQYLCSALM   83 (219)
T ss_dssp             ---CEEEEEEEEHHHHHHTHHHHHHHHHHHCTTEEEEEEEECSC---CCHHHHTCSEEEEEEC-SCCTTEEEEEEEECCE
T ss_pred             cCcCCcEEEEeCHHHHHHHHHhHHHHHHHHCCCceEEEEeccCc---cccccCCccEEEEeCC-CCCCCceEEEecccce
Confidence            34578999999999999999999999999999999999886653   3678999999999654 5668899999999999


Q ss_pred             EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760         169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF  248 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~  248 (306)
                      +++++++|.   ...++++||.++|||.+..+..+...+...+...+..++..+++++..+++++|.+|.|++++|.+.+
T Consensus        84 ~~v~~p~~~---~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~  160 (219)
T 3kos_A           84 SPLCSPTLA---SQIQTPADILKFPLLRSYRRDEWALWMQTVGEAPPSPTHNVMVFDSSVTMLEAAQAGMGVAIAPVRMF  160 (219)
T ss_dssp             EEEBCHHHH---TTCSSGGGGGGSCEEEESCTTHHHHHHHHTTCCCCCTTSCEEEESCHHHHHHHHHTTSCBEEEEGGGC
T ss_pred             EEEeChHHh---hccCCHHHHhcCceeccCCccCHHHHHHHcCCCCCccccceeEEccHHHHHHHHHcCCCeEeehHHhh
Confidence            999998872   35799999999999999866544444444444445556788999999999999999999999999998


Q ss_pred             ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      ... ..+.++. ++........++++|+++...++.+++|++++++.+.+...
T Consensus       161 ~~~~~~~~l~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~  212 (219)
T 3kos_A          161 THLLSSERIVQ-PFLTQIDLGSYWITRLQSRPETPAMREFSRWLTGVLHKTSG  212 (219)
T ss_dssp             HHHHHTTSSBC-CCCCCBCSCEEEEEEETTSCCCHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHcCCeec-cccCCccCCcEEEEecccccCCHHHHHHHHHHHHhhccccc
Confidence            766 5666764 44444556799999999999999999999999999876554

>3fd3_A Chromosome replication initiation inhibitor prote; structural genomics, LYSR, PSI-2, structure initiative; HET: MSE P33 PG4; 1.70A {Agrobacterium tumefaciens str}

Probab=99.95  E-value=7.1e-27  Score=180.56  Aligned_cols=200  Identities=11%  Similarity=0.010  Sum_probs=171.7

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEE
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVII  171 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v  171 (306)
                      .|+|+||++++++..++++++..|.++| ++++++...++.++.+.+.+|..|+++...+ ...+++.+.++++++++++
T Consensus         1 ~g~l~Ig~~~~~~~~~l~~~l~~f~~~~-~v~l~l~~~~~~~~~~~l~~g~d~~~i~~~~-~~~~~l~~~~l~~~~~~~v   78 (208)
T 3fd3_A            1 RVTLNIATNADSLGTWFLDAVSKFTGGS-DYLVNIAVDDQDHTVEWLRGGRVLAAVTAHD-KPVQGCRVTPLGVLRYHAT   78 (208)
T ss_dssp             CCEEEEEECHHHHTTTHHHHHHHHHHTS-SCEEEEEECCSSCHHHHHHTTSCSEEEESCC-SCCTTCEEEEEEEEEEEEE
T ss_pred             CceEEEEecHHHHHHHHHHHHHHHHhhc-CeEEEEEeCCcHhHHHHHhcCcceEEEecCC-CCCCCceEEEccceEEEEE
Confidence            4789999999999999999999999999 6999999999989999999995555566433 5668899999999999999


Q ss_pred             ecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         172 VPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       172 ~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      ++++|+... ..+++++||.++|+|.+..+...+..+...+...++.+ +.+++++.++++++|.+|.|++++|.+.+..
T Consensus        79 ~~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~  157 (208)
T 3fd3_A           79 ASPDFMARHFADGVTPAALARAPGLTFNQKDRLQASWIRTALGEDVSY-PTHWLPSTDGFVKASLAGMGWGLNPVQLVAE  157 (208)
T ss_dssp             ECHHHHHHHCTTCSCHHHHTTSCEEESSTTCCHHHHHHHHHHSSCCCC-CEEECCCHHHHHHHHHTTSCBEEEEHHHHHH
T ss_pred             EChHHhhhhccCCCCHHHHhcCCeEEeCCCchhHHHHHHHhcCCCCCc-ceEEECCHHHHHHHHHhCCCeecccHHHHHh
Confidence            999996665 57899999999999999887776667776677778888 9999999999999999999999999998876


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      . ..+.++.+. ++  ...+++++|++++..++++++|++++++.+++
T Consensus       158 ~~~~~~l~~~~-~~--~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~  202 (208)
T 3fd3_A          158 HLAAGRLVELM-PG--TPLDIPLYWQVNRLAAERLAGLTANMVGTARV  202 (208)
T ss_dssp             HHHHTSSEESS-TT--CCEEEEEEEEECTTTTTTTHHHHHHHHHHHHH
T ss_pred             hccCCceEEec-CC--CCccEEEEecCCCccCHHHHHHHHHHHHhhhh
Confidence            5 566666552 22  23579999999999999999999999987654

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=99.94  E-value=3.5e-27  Score=164.88  Aligned_cols=102  Identities=9%  Similarity=0.012  Sum_probs=79.9

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ||+++|++|++|+++| ||++||+.||+|||++|++|++||++||++||+|++     +++ +||++|+.|+++++++++
T Consensus        24 ~~~~~L~~f~av~e~g-S~s~AA~~L~iSqsavS~~I~~LE~~lG~~Lf~R~~~G~~grg~-~LT~~G~~ll~~a~~il~  101 (135)
T 2ijl_A           24 LGHGKVELMQLIAETG-SISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGA-ALTVFGAELLERYRGMEE  101 (135)
T ss_dssp             ESHHHHHHHHHHHHHS-CHHHHHHHTTCCHHHHHHHHHHHHHHBSSCSEEECCC------E-EECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCCeeEEecCCCCCCCce-eECHHHHHHHHHHHHHHH
Confidence            6899999999999999 999999999999999999999999999999999996     588 799999999999999999


Q ss_pred             HHHHH----HHHHHhhccCCCCcEEEEecccch
Q psy3760          76 EIEGL----KKIGKEFSAYDTGNLTIATTHTQA  104 (306)
Q Consensus        76 ~~~~~----~~~~~~~~~~~~~~l~I~~~~~~~  104 (306)
                      .++++    .+.+...-....+.+||..+..++
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~  134 (135)
T 2ijl_A          102 RMNEALREDIDWLEANRNPQDALNRDREPPTLG  134 (135)
T ss_dssp             HHHHHTHHHHHHHHHHBCCC-------------
T ss_pred             HHHHHHHHHHHHHHHhhhcccCceeecCCCccC
Confidence            99887    344444456788999999887654

>1twy_A ABC transporter, periplasmic substrate-binding PR; nysgxrc target, structural genomics, protei structure initiative, PSI; 1.65A {Vibrio cholerae o1 biovar eltor} SCOP: c.94.1.1

Probab=99.92  E-value=1.8e-23  Score=169.96  Aligned_cols=205  Identities=17%  Similarity=0.222  Sum_probs=166.9

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC---CCceeecccc
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS---DKLISIPCYQ  165 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~---~~~~~~~l~~  165 (306)
                      ....|.|+||++.++. .++++++..|.++||++++++...++.++.+.|.+|++|++|+..+....   +++...+++.
T Consensus        24 ~~~~g~l~Ig~~~~~~-~~l~~~l~~f~~~~P~i~v~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~~~~~~~~~~l~~  102 (290)
T 1twy_A           24 FVQASEITISGSTSVA-RIMDVLAEKYNQQHPETYVAVQGVGSTAGISLLKKGVADIAMTSRYLTESEAQNTLHTFTLAF  102 (290)
T ss_dssp             ----CEEEEEECHHHH-HHHHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHTTSCSEEEESSCCCTTTCCTTCEEEEEEE
T ss_pred             cccCCCEEEecCcchH-HHHHHHHHHHHhhCCCceEEEEecCcHHHHHHHhcCCCcEEEecCCCchhhhhcCceEEEEEe
Confidence            3456899999999888 79999999999999999999999999999999999999999996542222   5789999999


Q ss_pred             ceEEEEecCCCCCCCCCC-----------cChhhhcC----CCeEeecCCCCcHHHHHHHHHhCC--------CceeEEE
Q psy3760         166 WEYVIIVPLDHPLLLLNS-----------ISLKEISN----YPLITYDLSFSGRIKLDREFSLQK--------LTPYIVL  222 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~-----------i~~~dl~~----~~~i~~~~~~~~~~~~~~~~~~~~--------~~~~~~~  222 (306)
                      ++++++++++||++....           ++++||.+    .+++....+...+..+..++...+        ..++..+
T Consensus       103 ~~~~~v~~~~~pl~~~~~~~l~~~~~~~~~~~~dL~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (290)
T 1twy_A          103 DGLAIVVNQANPVTNLTREQLYGIYKGQITNWKQVGGNDQKIAVVTREASSGTRYSFESLMGLTKTVKDREVSDVAPTAL  182 (290)
T ss_dssp             EEEEEEECTTCCCCEECHHHHHHHHHTSCCBGGGGTSCSCBCEEEEECTTCHHHHHHHHHHTCEEEETTEEEECSCTTSE
T ss_pred             eeEEEEECCCCCccccCHHHHHHHhcCCCCCccccCCCCCeeEEEecCCCchHHHHHHHHHhcccccccccccccCcccc
Confidence            999999999999875443           78999988    889988776666777777776222        2455678


Q ss_pred             EecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCC------------CccceEEEEEeCCccccHHHHHHHH
Q psy3760         223 ETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHL------------FGTTISRVIIKQGTYLRSYVYSFIK  289 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~------------~~~~~~~l~~~~~~~~~~~~~~~~~  289 (306)
                      ++++...+.++|.+| .|++++|...+.    ++++.+++...            .....++++|+++ ..++.++.|++
T Consensus       183 ~~~~~~~~~~~v~~g~~gi~~~p~~~~~----~~l~~~~l~~~~p~~~~i~~~~~~~~~~~~l~~~~~-~~~~~~~~f~~  257 (290)
T 1twy_A          183 VVNSNSMMKTLVNHNTQAVGFISIGSVD----KSVKAIQFEKADPTSDNIAKHTYQLSRPFLILHYSD-NADEQTKEFIA  257 (290)
T ss_dssp             EESSHHHHHHHHHHCTTEEEEEEGGGCC----TTSEECEETTBCCCHHHHHTTCSCCEEEEEEEECTT-TCCHHHHHHHH
T ss_pred             ccCChHHHHHHHhcCCCcEEEeeHHHhh----CCceEeEecCCCCCHHHHhcCCCccEEEEEEEEcCC-CCCHHHHHHHH
Confidence            899999999999999 999999998763    46777777641            2356899999888 78999999999


Q ss_pred             HHhHHhhHHH
Q psy3760         290 LLSPKLNRKF  299 (306)
Q Consensus       290 ~l~~~~~~~~  299 (306)
                      ++++...+..
T Consensus       258 ~l~~~~~q~~  267 (290)
T 1twy_A          258 FLKSESAKKL  267 (290)
T ss_dssp             HHHSHHHHHH
T ss_pred             HHhCHHHHHH
Confidence            9987644433

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=99.91  E-value=7.7e-25  Score=170.97  Aligned_cols=185  Identities=18%  Similarity=0.157  Sum_probs=131.0

Q ss_pred             chhhHHHHHHHHHhcCC--------HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec----CCCccccCHhHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFN--------LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH----GKRIRGLTKPGQAILRS   69 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s--------~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~----~~~~~~lT~~G~~l~~~   69 (306)
                      +-+++++|..+++.| +        +++||+.|++||||+|++|++||+   ..||.|+    ++++ +||++|+.+++.
T Consensus         6 ~~~~l~~l~~l~~~~-~l~~~~~~s~s~aA~~L~isq~avSr~I~~LE~---~~L~~R~~~~R~~~v-~LT~~G~~l~~~   80 (230)
T 3cta_A            6 DDQYYRAIKKIKEAA-EASNRAYLTSSKLADMLGISQQSASRIIIDLEK---NGYITRTVTKRGQIL-NITEKGLDVLYT   80 (230)
T ss_dssp             -CHHHHHHHHHHHHT-TTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHH---TTSEEEEEETTEEEE-EECHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhc-ccccCCCcCHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEEEcCCeEEE-EECHHHHHHHHH
Confidence            458999999999999 9        999999999999999999999999   7799999    8888 899999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhccCCCCcEEEEecccchhhh--hHHHHHHHHHh-----CCCcEEEEEeCChhHHHHHHHcCC
Q psy3760          70 IEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYA--LPKIIKEFTIQ-----FPKVKLSLLQGNPKQITEMIRNDQ  142 (306)
Q Consensus        70 a~~il~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~~~--l~~~l~~~~~~-----~p~~~i~~~~~~~~~~~~~l~~~~  142 (306)
                      +.+++..+.+..     ......+.+++|++.  ....  +++++..|.+.     ||+ ++++...++......+.++.
T Consensus        81 ~~~~~~~~~~~~-----~~~~~~~~l~~~~~~--~~~~~~l~~~l~~f~~~Lg~~P~P~-~l~l~~~~~~~~~~~~~~~~  152 (230)
T 3cta_A           81 EFADLSRILAIK-----NNVVITGTVTSGMGE--GRYYVARKQYIIQFQEKLGIIPYLG-TLNIKVDQASLPELRKIRGF  152 (230)
T ss_dssp             HHHHHHHHTTCC-----CCEEEEEEECC--------------CCHHHHHHHSCSCCCC----EEEECGGGHHHHHHHHHS
T ss_pred             HHHHHHHHhhhh-----hHHHHHHHHHhcCCH--HHHHHHHHHHHHHHHHHhCCCCCCC-cEEEEecCchhHHHHHHhcC
Confidence            999998776632     233456788888844  3445  89999999999     999 99999998888888888888


Q ss_pred             eeEEEEccc--cCCCCCceeecc--ccceEEEEecC-CCCCCCCCCcChhhhcCCCeEeecCCC
Q psy3760         143 ADIAIVTEI--LSPSDKLISIPC--YQWEYVIIVPL-DHPLLLLNSISLKEISNYPLITYDLSF  201 (306)
Q Consensus       143 ~Di~i~~~~--~~~~~~~~~~~l--~~~~~~~v~~~-~~~l~~~~~i~~~dl~~~~~i~~~~~~  201 (306)
                      .|+++....  .....++.+.++  .+++.++++|+ .|+++..+.+++.+|.+.  +.+.++.
T Consensus       153 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~vv~p~~~~~~~~~~~i~~~~L~~~--l~l~~g~  214 (230)
T 3cta_A          153 RGIHIEGFKTEDRTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISDKYLREE--INLHDGD  214 (230)
T ss_dssp             CCEEECCEEC--CEECCEEEEEEEETTEEEEEEEESSCCCCSEEEEECC--------------C
T ss_pred             CCeecCCccCCCCcEEeEEEEEEEECCEEEEEEEecccCCCCEEEEECCcchHhh--cCCCCCC
Confidence            898776321  122345667555  66999999995 344665778899999877  5555543

>3cvg_A Putative metal binding protein; PSI-II, NYSGXRC, periplasmic, structural GENO protein structure initiative; 1.97A {Coccidioides immitis}

Probab=99.89  E-value=4.6e-22  Score=161.52  Aligned_cols=212  Identities=12%  Similarity=0.064  Sum_probs=166.6

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHh---C--CCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC----CC--c
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQ---F--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS----DK--L  158 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~---~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~----~~--~  158 (306)
                      ...|+|+||++.+.+..+++.++..|.++   |  |++++++...++.++.++|.+|++|++++.......    ++  +
T Consensus        17 ~~~g~L~Ig~~~~~~~~~lp~ll~~F~~~~~~~~~P~v~v~l~~~~s~~l~~~l~~G~~Dl~i~~~~~~~~~l~~~~~~~   96 (294)
T 3cvg_A           17 HSPVQLRIGNGGAGQSGLVKELADAFIKSKVDSGSAPFKVAWYKSDTTVTINYLKDGIVDVGITYSPVAERISIKHGISE   96 (294)
T ss_dssp             --CEEEEEEESHHHHHTHHHHHHHHHHHHHHSCC---CEEEEEECCHHHHHHHHHTTSCSEEEESCHHHHHHHHHTTSBC
T ss_pred             CCCceEEEEeccchhHHHHHHHHHHHHhhhcccCCCCeEEEEEeCCHHHHHHHHHcCCCcEEEEcCchhhhHHHhCCccc
Confidence            46789999999888889999999999999   9  999999999999999999999999999996432110    12  2


Q ss_pred             eee-ccccceEEEEecCCCC--CCCCCCc--ChhhhcC----------CCeEeecCCCCcHHHHHHHHHhCCCceeE---
Q psy3760         159 ISI-PCYQWEYVIIVPLDHP--LLLLNSI--SLKEISN----------YPLITYDLSFSGRIKLDREFSLQKLTPYI---  220 (306)
Q Consensus       159 ~~~-~l~~~~~~~v~~~~~~--l~~~~~i--~~~dl~~----------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~---  220 (306)
                      ... +++.++++++++++||  ++....+  ++++|..          .|||....++..+..+..++...++.+++   
T Consensus        97 ~~~~~l~~d~lvlv~~~~hp~~l~~~~~~~~~l~~L~~~~~~g~~~~~~p~i~~~~~s~~r~~~~~~~~~~g~~~~~~~~  176 (294)
T 3cvg_A           97 SPSYYAFRDHFMLIGPPSNPAKLSGDSDIADMFSKMHDAAEAGNTKPPVRFLSRYDKSATNIKEAELWLSIGQVPWATAY  176 (294)
T ss_dssp             SSCEEEEEEEEEEEECTTCTTCCCTTSCHHHHHHHHHHHHHHCCSSSCCCEEECCSSSHHHHHHHHHHHHTTCCTTSSSC
T ss_pred             ceeeeEEeccEEEEecCCChhhccccccHHHHHHHHhcCcccCCCCccceeEeCCCCCcHHHHHHHHHHhcCCCcccccc
Confidence            345 8999999999999999  4444332  4889988          99999998888888899999999888874   


Q ss_pred             ---EEEe-cCHHHHHHHHHhccceeeeecceeccc-c--cCCceeeecC----CCCccceEEEEEeCCccccHHHHHHHH
Q psy3760         221 ---VLET-INSDIIKTYVELRMGIGIIASIAFDSN-R--DKNLRSISAS----HLFGTTISRVIIKQGTYLRSYVYSFIK  289 (306)
Q Consensus       221 ---~~~~-~~~~~~~~~v~~g~gi~~~p~~~~~~~-~--~~~l~~~~~~----~~~~~~~~~l~~~~~~~~~~~~~~~~~  289 (306)
                         ...+ ++...++.++..|.|++++|....... .  .+.++.+++.    +....+.++++|+++...+++++.|++
T Consensus       177 ~~~~~~~~~~~~~~~~~v~~g~g~ai~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~s~aa~~Fi~  256 (294)
T 3cvg_A          177 STWYHQYITFPIQALTAAILLREYTITDYGTYLSIPRGLRDQMVIYKKGTNDADDPLLNPAHLLVGARAKNAEMAKEFAK  256 (294)
T ss_dssp             CTTEEECCSCHHHHHHHHHHTTCEEEEEHHHHTTSCHHHHTTCEEEEECCSCTTCTTEEEEEEEEBSSCSSHHHHHHHHH
T ss_pred             cceeEEecCCchhhhhhhhcCCCeeeeeeeeEEEeccccCCceEEEecCCCCCCcceeeEEEEEEeCCCCCHHHHHHHHH
Confidence               4455 478899999999999999987432221 1  3568888764    445677899999988888999999999


Q ss_pred             HHhHHh-hHHHHH
Q psy3760         290 LLSPKL-NRKFIN  301 (306)
Q Consensus       290 ~l~~~~-~~~~~~  301 (306)
                      ++++.- .+..+.
T Consensus       257 ~l~s~e~gq~i~~  269 (294)
T 3cvg_A          257 WLVSKEGGQKVIE  269 (294)
T ss_dssp             HHHSTTTHHHHHH
T ss_pred             HHcCcHHHHHHHH
Confidence            998764 444443

>1b9m_A Protein (mode); DNA-binding, gene regulation, winged helix turn helix, molybdate, OB fold, transcription; 1.75A {Escherichia coli} SCOP: a.4.5.8 b.40.6.2 b.40.6.2 PDB: 1b9n_A 1o7l_A 1h9s_A 1h9r_A 1h9s_B

Probab=99.86  E-value=6.5e-24  Score=169.97  Aligned_cols=127  Identities=13%  Similarity=0.098  Sum_probs=101.4

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      |++++|++|.+++++| ||++||++||+|||++|++|++||+.+|.+||+|++     +++ +||++|+.|+++++.+++
T Consensus        20 ~~~~~l~~f~~v~~~g-s~~~aa~~l~~s~~~~s~~i~~le~~lg~~L~~R~~~~lsg~~~-~lt~~g~~l~~~~~~~~~   97 (265)
T 1b9m_A           20 ADPRRISLLKHIALSG-SISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGA-VLTRYGQRLIQLYDLLAQ   97 (265)
T ss_dssp             ECHHHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEECCCC-----E-EECHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCce-EECHHHHHHHHHHHHHHH
Confidence            5789999999999999 999999999999999999999999999999999997     477 899999999999999999


Q ss_pred             HHHHHHHHHHhhccCC----CCcE-EEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCC
Q psy3760          76 EIEGLKKIGKEFSAYD----TGNL-TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN  130 (306)
Q Consensus        76 ~~~~~~~~~~~~~~~~----~~~l-~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~  130 (306)
                      .++.+.+.+.......    .+.+ +++...+ ...+++..+..|...+|++.+++...+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s-a~n~L~~~v~~~~~~~p~~~v~l~l~~  156 (265)
T 1b9m_A           98 IQQKAFDVLSDDDALPLNSLLAAISRFSLQTS-ARNQWFGTITARDHDDVQQHVDVLLAD  156 (265)
T ss_dssp             HHHHHHHHHHHCCSSCTTCHHHHHHHHTEEES-SSEEEEEEECCCSSSSCCSEEEEEETT
T ss_pred             HHHHHHHHHHhccCCchHHHHHHHhhccCccc-ceeEeccEEEEEEeCCccEEEEEEECC
Confidence            9999998887633111    1233 3333222 334556666777778888888777543

>4ecf_A ABC-type phosphate transport system, periplasmic; ABC transporter, phosphate transport receptor; HET: MSE; 1.55A {Lactobacillus brevis}

Probab=99.85  E-value=6.6e-20  Score=146.16  Aligned_cols=194  Identities=12%  Similarity=0.063  Sum_probs=159.9

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC-----CCceeecccc
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS-----DKLISIPCYQ  165 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~-----~~~~~~~l~~  165 (306)
                      ..|.|+|+.+.++. .+++.++..|.++||++++.+...++.+.++.|.+|++|++++..+....     .++...++..
T Consensus         2 ~~G~l~i~gs~t~~-~~l~~~~~~f~~~~P~v~i~v~~~~S~~~~~~l~~g~~Dig~~~~~~~~~e~~~~~~l~~~~i~~   80 (264)
T 4ecf_A            2 AGESITAVGSTALQ-PLVEAAGEQYTGEHLGTFINVQGGGTGTGLSQIQEGAVQIGNSDLFAGEQKGINARQLVDHRVAV   80 (264)
T ss_dssp             CCEEEEEEECTTTH-HHHHHHHHHHHHHSTTEEEEEEEECHHHHHHHHHHTSSSEEEESSCGGGSTTCCGGGEECCEEEE
T ss_pred             CCceEEEEecChHH-HHHHHHHHHHHHHCCCceEEEEeCCCHHHHHHHHcCCCchhhccCCCChhHHhhccCCEEEEEEE
Confidence            35799999998874 79999999999999999999999999999999999999999986442221     4788999999


Q ss_pred             ceEEEEecCCCCCCCCCCcChhhhcC----------------C--CeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760         166 WEYVIIVPLDHPLLLLNSISLKEISN----------------Y--PLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS  227 (306)
Q Consensus       166 ~~~~~v~~~~~~l~~~~~i~~~dl~~----------------~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (306)
                      +.++++++++||+.   .++.++|.+                .  +++....+++.+..+.+.+...+ .....++.++.
T Consensus        81 d~lvvvv~~~~p~~---~lt~~~L~~if~G~i~~W~~l~~~~~~i~~i~r~~gSgtr~~f~~~l~~~~-~~~~~~~~~s~  156 (264)
T 4ecf_A           81 VGITPIVNKKVGVK---NLSTNQLIKIFTGQITNWKEVGGADQSIVLINRAQGSGTRATFEQFGLANH-RSKTAQEQDSS  156 (264)
T ss_dssp             EEEEEEECTTSSCS---EECHHHHHHHHTTSCCBGGGGTSCSCBCEEEEECTTCHHHHHHHHHTSTTC-CCCSCEEESSH
T ss_pred             EEEEEEEcCCCccc---ccCHHHHHHHHCCCCcccccCCCCCCeeEEeccCCCCcHHHHHHHHhccCC-CCCcccccCCH
Confidence            99999999999973   466666653                3  47777888888999998886665 33456789999


Q ss_pred             HHHHHHHHhcc-ceeeeecceecccccCCceeeecCC------------CCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         228 DIIKTYVELRM-GIGIIASIAFDSNRDKNLRSISASH------------LFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       228 ~~~~~~v~~g~-gi~~~p~~~~~~~~~~~l~~~~~~~------------~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      +.++++|.++. ||++++...+.    +.++.++++.            .+..+++|+++++.  .++.++.|++++.+.
T Consensus       157 ~~i~~~V~~~~~aIg~~~~~~~~----~~l~~l~i~~v~pt~~~i~~g~ypl~r~~~~~~~~~--~~~~~~~F~~~~~s~  230 (264)
T 4ecf_A          157 GMVRSIVATTPGAISYVAFSYVN----KTVQALSLNHVAPTEVNVTTNDWRIWSYEHLYTKGH--PTGLTKAFITYVQSP  230 (264)
T ss_dssp             HHHHHHHHHSTTEEEEEEGGGCC----TTSEECEETTBCCCHHHHHTTSSCCEEEEEEEEESS--CCHHHHHHHHHHHSH
T ss_pred             HHHHHHHhcCCCcEEEEEhHHhh----CCceEEEEccccCCHHHhhcCCCCceeEEEEEEcCC--CcHHHHHHHHHHhCc
Confidence            99999999996 79999988774    3688888762            24567899999764  589999999999875


Q ss_pred             h
Q psy3760         295 L  295 (306)
Q Consensus       295 ~  295 (306)
                      -
T Consensus       231 ~  231 (264)
T 4ecf_A          231 A  231 (264)
T ss_dssp             H
T ss_pred             h
Confidence            4

>4exl_A PBP 1, phosphate-binding protein PSTS 1; center for structural genomics of infectious diseases (csgid national institute of allergy and infectious diseases; 1.70A {Streptococcus pneumoniae}

Probab=99.77  E-value=7.2e-17  Score=128.59  Aligned_cols=195  Identities=10%  Similarity=0.069  Sum_probs=155.5

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeeccccc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPCYQW  166 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l~~~  166 (306)
                      .+.|+|+.+.++. .+++.++..|.+.||++++++...++...++.+.+|++||+++....     ....++...++..+
T Consensus         3 ~~~l~i~gStt~~-~~~~~~~~~F~~~~P~v~i~v~~~gS~~gi~~l~~g~~Dig~~~~~~~~~~~~~~~~l~~~~ia~d   81 (265)
T 4exl_A            3 GESITAVGSTALQ-PLVEVAADEFGTIHVGKTVNVQGGGSGTGLSQVQSGAVDIGNSDVFAEEKDGIDASALVDHKVAVA   81 (265)
T ss_dssp             CCEEEEEECTTHH-HHHHHHHHHHHHHSTTCEEEEEEECHHHHHHHHHTTSSSEEEESSCGGGSTTCCGGGEECCEEEEE
T ss_pred             CceEEEEeeCcHH-HHHHHHHHHHHHHCCCceEEEeeCCcHHHHHHHHcCCCccccccCCcchhhcccccCceEeeEEEE
Confidence            4789999999875 78999999999999999999999999999999999999999984221     12357889999999


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhcC----------------C--CeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEISN----------------Y--PLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD  228 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~~----------------~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (306)
                      .++++++++||+.   .++.++|.+                .  +++....+++.+..+.+.+...+. .....+.++..
T Consensus        82 ~lvvvv~~~~~~~---~lt~~~L~~If~G~i~~W~~lg~p~~~I~~v~R~~gSGTr~~f~~~l~~~~~-~~~~~~~~s~~  157 (265)
T 4exl_A           82 GLALIVNKEVDVD---NLTTEQLRQIFIGEVTNWKEVGGKDLPISVINRAAGSGSRATFDTVIMEGQS-AMQSQEQDSNG  157 (265)
T ss_dssp             EEEEEECTTCCCC---EECHHHHHHHHTTSCCBGGGBTSCSCBCEEEEECTTSHHHHHHHHHTTTTCC-CCSCEEECCHH
T ss_pred             EEEEEECCCCccc---cCCHHHHHHHHcCCCCcccccCCCCCeeEEEecCCCCcHHHHHHHHHccCCC-CccccccCChH
Confidence            9999999999963   456666643                2  467778888889999998876654 33457889999


Q ss_pred             HHHHHHHhc-cceeeeecceecccccCCceeeecCC------------CCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         229 IIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASH------------LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       229 ~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~------------~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      .+.++|.++ .||++++...+..    .++.++++.            .+..+.+|++++..  .++.++.|++++.+.-
T Consensus       158 ~v~~~V~~~~~aIGy~~~~~~~~----~lk~l~i~gv~pt~~~i~~g~YPl~r~~~~~~~~~--~~~~~~~F~~~~~s~~  231 (265)
T 4exl_A          158 AVKSIVSKSPGAISYLSLTYIDD----SVKSMKLNGYDLSPENISSNNWPLWSYEHMYTLGQ--PNELAAEFLNFVLSDE  231 (265)
T ss_dssp             HHHHHHHHSTTEEEEEEGGGCCT----TSEECEETTBCCCHHHHHTTSSCCEEEEEEEEESS--CCHHHHHHHHHHHSHH
T ss_pred             HHHHHHhcCCCeEEEEEHHHhhC----cccEeEECCcCCCHHHhccCCCCCeeeEEEEECCC--chHHHHHHHHHHhCcc
Confidence            999999875 8999999877643    488888764            23456778876653  5899999999998754


Q ss_pred             hH
Q psy3760         296 NR  297 (306)
Q Consensus       296 ~~  297 (306)
                      .+
T Consensus       232 gq  233 (265)
T 4exl_A          232 TQ  233 (265)
T ss_dssp             HH
T ss_pred             hH
Confidence            33

>1ixh_A Phosphate-binding protein; phosphate transport, ultra high resolution, phosphate bindin protein; 0.98A {Escherichia coli} SCOP: c.94.1.1 PDB: 2abh_A 1a54_A* 1a55_A 1ixi_A 1quk_A 1ixg_A 1oib_A 1pbp_A 1qul_A 1qui_A 1quj_A 1a40_A 2z22_X

Probab=99.73  E-value=1e-16  Score=131.43  Aligned_cols=197  Identities=13%  Similarity=0.025  Sum_probs=152.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCC-----ceeeccccceE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK-----LISIPCYQWEY  168 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~-----~~~~~l~~~~~  168 (306)
                      .|+|+.+.++ ..+++.++..|.+ ||++++++...++...++.+.+|.+|++++..+ ...+.     +...++..+.+
T Consensus         3 ~l~i~gs~t~-~~~l~~~~~~f~~-~p~v~i~v~~~gS~~~~~~l~~g~~Di~~~~~~-~~~~e~~~~~l~~~~~~~d~l   79 (321)
T 1ixh_A            3 SLTGAGATFP-APVYAKWADTYQK-ETGNKVNYQGIGSSGGVKQIIANTVDFGASDAP-LSDEKLAQEGLFQFPTVIGGV   79 (321)
T ss_dssp             EEEEEECSTT-HHHHHHHHHHHHH-HHCCEEEEEECCHHHHHHHHHTTCSSEEEESSC-CCHHHHHHHTEEEEEEEEEEE
T ss_pred             eEEEEEeCcH-HHHHHHHHHHHHh-cCCceEEEecCCCHHHHHHHHcCCCcEEecccC-CChhhHhhCCCEEeeeeeeeE
Confidence            6999999985 6799999999998 999999999999999999999999999999755 33333     58899999999


Q ss_pred             EEEecCCCCCCCCCCcC--------------hhh-----------hcCCC--eEeecCCCCcHHHHHHHHHhCCC-----
Q psy3760         169 VIIVPLDHPLLLLNSIS--------------LKE-----------ISNYP--LITYDLSFSGRIKLDREFSLQKL-----  216 (306)
Q Consensus       169 ~~v~~~~~~l~~~~~i~--------------~~d-----------l~~~~--~i~~~~~~~~~~~~~~~~~~~~~-----  216 (306)
                      +++++++|+...+..++              |+|           +.+.|  ++....+++.+..+.+.+...+.     
T Consensus        80 vvvv~~~~~~~~~~~lt~~~l~~If~g~i~~W~d~~i~~~np~~~l~~~~I~~v~r~~~Sgt~~~f~~~l~~~~~~~~~~  159 (321)
T 1ixh_A           80 VLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWDDEAIAKLNPGLKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKNN  159 (321)
T ss_dssp             EEEECCTTCCTTCCEECHHHHHHHHTTCCCBTTCHHHHHHCTTCCCCCCBCEEEEESSCCHHHHHHHHHHHHHCHHHHHH
T ss_pred             EEEEeCCCCccccccCCHHHHHHHhcCCCCcCCChhhhhhCCCCCCCCCeEEEEecCCCCcHHHHHHHHHHhcCcchhhc
Confidence            99999999876433444              666           66778  88888888889898988876432     


Q ss_pred             -------ceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc---------ccCCceeeec------------------
Q psy3760         217 -------TPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN---------RDKNLRSISA------------------  261 (306)
Q Consensus       217 -------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~---------~~~~l~~~~~------------------  261 (306)
                             .....+..++.+.+.++|.+| .||++++...+...         ..+.++....                  
T Consensus       160 ~~~g~~~~~~~~~~~~~~~~v~~~V~~~~~~Ig~v~~~~~~~~~l~~~~l~~~~G~~v~p~~~~i~~a~~~~~~~~~~~~  239 (321)
T 1ixh_A          160 VGTGSTVKWPIGLGGKGNDGIAAFVQRLPGAIGYVEYAYAKQNNLAYTKLISADGKPVSPTEENFANAAKGADWSKTFAQ  239 (321)
T ss_dssp             TCCCSSCCCSSCEEESHHHHHHHHHHHSTTEEEEEEHHHHHTTTCEECEEECTTSCEECCCHHHHHHHTTTCCTTTCSCC
T ss_pred             cCcCccccCCcccccCCcHHHHHHHhcCCCeEEEechHHhhhcCCcEEEEEcCCCCEeCCCHHHHHHHHhcCccccccce
Confidence                   222247899999999999999 48999998765431         0222211111                  


Q ss_pred             -------CC-CCccceEEEEEeCCcc---ccHHHHHHHHHHhH
Q psy3760         262 -------SH-LFGTTISRVIIKQGTY---LRSYVYSFIKLLSP  293 (306)
Q Consensus       262 -------~~-~~~~~~~~l~~~~~~~---~~~~~~~~~~~l~~  293 (306)
                             +. .+..+.+|++++++..   .++.++.|++++.+
T Consensus       240 ~~~~~~~~~~YPi~r~~~~~~~~~~~~~~~~~~~~~Fl~~~~s  282 (321)
T 1ixh_A          240 DLTNQKGEDAWPITSTTFILIHKDQKKPEQGTEVLKFFDWAYK  282 (321)
T ss_dssp             CCBSCCSTTCCSBEEEEEEEEESBCSSHHHHHHHHHHHHHHHH
T ss_pred             eccCCCCCCCccccceEEEEEECCcCchhhHHHHHHHHHHHHh
Confidence                   12 2345678899888754   58899999999987

>1atg_A MODA, periplasmic molybdate-binding protein; tungstate, ABC transporter; 1.20A {Azotobacter vinelandii} SCOP: c.94.1.1

Probab=99.73  E-value=4.6e-16  Score=121.68  Aligned_cols=196  Identities=9%  Similarity=0.037  Sum_probs=145.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCCc----eeeccc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDKL----ISIPCY  164 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~~----~~~~l~  164 (306)
                      +|+|+++.++ ..+++.++..|.++ |++++++...++.++.+.|.+|. +|+++......    ...++    ...++.
T Consensus         1 ~l~i~~~~~~-~~~l~~~~~~F~~~-p~i~v~~~~~~s~~l~~~l~~g~~~Dv~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (231)
T 1atg_A            1 ELKVVTATNF-LGTLEQLAGQFAKQ-TGHAVVISSGSSGPVYAQIVNGAPYNVFFSADEKSPEKLDNQGFALPGSRFTYA   78 (231)
T ss_dssp             CEEEEEEGGG-HHHHHHHHHHHHHH-HCCCEEEEEECHHHHHHHHHTTCCCSEEECSSSHHHHHHHHTTCBCTTCCEEEE
T ss_pred             CeEEEEEcch-HHHHHHHHHHHHhc-cCCeEEEEECCcHHHHHHHHcCCCCCEEEeCChhHHHHHHhcCCCcCCceeEee
Confidence            4899998876 66899999999999 99999999999999999999998 99998843210    02333    478889


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCC---CeEeecCC-CCcHHHHHHHHHhCCCcee-----EEEEecCHHHHHHHHH
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNY---PLITYDLS-FSGRIKLDREFSLQKLTPY-----IVLETINSDIIKTYVE  235 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~---~~i~~~~~-~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~v~  235 (306)
                      .++++++++++||+..    +++||.+.   +++..++. ...+....+.+...|+.+.     .....++...+.+++.
T Consensus        79 ~~~~vlv~~~~~~~~~----~~~dL~~~~~~~i~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~v~  154 (231)
T 1atg_A           79 IGKLVLWSAKPGLVDN----QGKVLAGNGWRHIAISNPQIAPYGLAGTQVLTHLGLLDKLTAQERIVEANSVGQAHSQTA  154 (231)
T ss_dssp             ECCEEEEESSTTTSCT----TSGGGGSSSCSCEEEECTTTCHHHHHHHHHHHHTTCHHHHHHTTCEEEESSHHHHHHHHH
T ss_pred             eeeEEEEEcCCCCCCc----chhhhccCCCCEEEecCCCCCchhHHHHHHHHHCCCcccccccceEEecCCHHHHHHHHH
Confidence            9999999999998643    78999887   78777665 4566677888888887532     2347889999999999


Q ss_pred             hcc-ceeeeecceeccc-ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         236 LRM-GIGIIASIAFDSN-RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       236 ~g~-gi~~~p~~~~~~~-~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      +|. ++++++...+... .......++++.. .......+...++...++.+++|++++.+.-
T Consensus       155 ~G~~~i~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~i~~~~~~~~~a~~fi~~l~s~~  217 (231)
T 1atg_A          155 SGAADLGFVALAQIIQAAAKIPGSHWFPPANYYEPIVQQAVITKSTAEKANAEQFMSWMKGPK  217 (231)
T ss_dssp             TTSSSEEEEEGGGTCCTTSCCSSEEECCCGGGSCCCEEEEEEBTTCSCHHHHHHHHHHTTSHH
T ss_pred             cCCCCEEEEEHHHhhhccccccCeEEEeCcccCccceEeEEEecCCCChHHHHHHHHHHcCHH
Confidence            995 8999998765432 1111344455442 1223334444577778999999999987653

>3muq_A Uncharacterized conserved protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.05A {Vibrio parahaemolyticus}

Probab=99.64  E-value=1.6e-14  Score=111.67  Aligned_cols=206  Identities=14%  Similarity=0.105  Sum_probs=151.9

Q ss_pred             CcEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCC-------ceeeccc
Q psy3760          93 GNLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK-------LISIPCY  164 (306)
Q Consensus        93 ~~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~-------~~~~~l~  164 (306)
                      ..|+|++..+.. ..+++.++..|.++| ++++.+...++.++++++.+|.+|++++..+ .....       ....++.
T Consensus         5 ~~L~vaaatS~~~~~ll~~L~~~Fek~~-gv~V~~~~~gSg~ll~qi~~G~aDv~isa~~-~~~~~l~~~g~~~~~~~~a   82 (237)
T 3muq_A            5 EHVRLATTTSTYHSGLLDYLLPQFEKDT-GYKVDVIAAGTGKALKMGENGDVDLVMTHAP-KAEGTFVEKGYGVLPRKLM   82 (237)
T ss_dssp             CEEEEEEEHHHHHHTHHHHHHHHHHHHH-CCEEEEEEECHHHHHHHHHTTSSSEEEECCH-HHHHHHHHTTSEEEEEEEE
T ss_pred             CEEEEEEECCcchhhHHHHHHHHHHHHh-CceEEEEEcChHHHHHHHhcCCCCEEEecCc-hhHHHHHhcCCccccEEEE
Confidence            479999987664 578999999999999 7999999999999999999999999999644 22222       3567888


Q ss_pred             cceEEEEecCCCCCCCCCCcChh----hhc--CCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEe-cCHHHHHHHHH
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLK----EIS--NYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLET-INSDIIKTYVE  235 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~----dl~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~v~  235 (306)
                      .+++++|+|++||+.-+...++.    .+.  +.|||+..++++.+....++|++.|+.|..  ..++ ..+...+.++.
T Consensus        83 ~N~lVlV~P~~~P~~i~~~~dl~~~l~~Ia~~~~~fisRedgSGTr~~~~~~~~~~gi~p~~~wy~~~g~gm~~~l~~a~  162 (237)
T 3muq_A           83 YNDFVIVGPKADPAKIKDDESVLDVFKEIANKNATFISRGDDSGTHKKEMGFWAQTKIEPNFGGYRSVGQGMGPTLNMAS  162 (237)
T ss_dssp             EEEEEEEECTTCTTCCTTCSSHHHHHHHHHHTTCCEEECCSCCHHHHHHHHHHHHHTCCSCSTTEEECCCCHHHHHHHHH
T ss_pred             eCCEEEEEeCCChhhccchhhHHHHHHHHhhcCCcEEEccCCCcHHHHHHHHHHHcCCCCCCCchhhhCcCHHHHHHHHH
Confidence            99999999999997644333443    344  999999999999999999999999998753  2233 46678888888


Q ss_pred             hccceeeeecceeccc-ccCCceeeecCCCCccceEEEEE-eCCc---cccHHHHHHHHHHhHHhhHHHH
Q psy3760         236 LRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVII-KQGT---YLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       236 ~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~-~~~~---~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      ...++++..+...-.+ ...+|..+--.++....+|.++. .+.+   ......++|++|+.+.=.+..+
T Consensus       163 ~~~~y~l~dr~t~l~~~~~~~l~i~~~gd~~l~n~y~v~~v~p~~~~~~~~~~a~~f~~wl~s~~gQ~~i  232 (237)
T 3muq_A          163 EMQGYTMSDRGTWLAYQNKLDLEILFQGDEKLFNPYQVILVNPERYPTINYQGAKAFSDWLVNPRGQELI  232 (237)
T ss_dssp             HTTCBEEEEHHHHHHHGGGCSCEEEECCCGGGEEEEEEEEECTTTCTTSCHHHHHHHHHHHHSHHHHHHH
T ss_pred             hcCCEEEEechHHhhccccCCeEEEEcCCCceeeeeEEEEECcccCCccCHHHHHHHHHHHcCHHHHHHH
Confidence            8899999886443233 34567765544534333444333 2222   1467899999999765444443

>3lr1_A Tungstate ABC transporter, periplasmic tungstate- binding protein; the tungstate ABC transporter, structural genomics, PSI, MCSG; 1.80A {Geobacter sulfurreducens}

Probab=99.61  E-value=5.2e-14  Score=108.61  Aligned_cols=208  Identities=12%  Similarity=0.063  Sum_probs=150.8

Q ss_pred             CCCcEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC------CCCceeecc
Q psy3760          91 DTGNLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP------SDKLISIPC  163 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~------~~~~~~~~l  163 (306)
                      ..|.|+|++..+.. ..+++.++..|.++| ++++.+...++.++++++.+|.+|++++..+...      .-.....++
T Consensus         3 ~~g~L~vaaa~S~~~~~ll~~L~~~Fek~~-gv~V~~~~~gSg~ll~qi~~G~aDV~isa~~~~~~~l~~~g~~~~~~~~   81 (236)
T 3lr1_A            3 AEERLKMSTTTSTQDSGLLKVLLPPFEKKN-NVKVDVIAVGTGQALKLGEAGDVDVVFVHARKLEDKFVADGFGVNRKDV   81 (236)
T ss_dssp             CSCEEEEEEEHHHHHHCHHHHHHHHHHHHH-TCEEEEEEECHHHHHHHHHTTSCSEEEECCHHHHHHHHHTTSEEEEEEE
T ss_pred             CCcEEEEEEECCccchHHHHHHHHHHHHHh-CCeEEEEEcChHHHHHHHhcCCCCEEeecCchhHHHHHhcCCCcceEEE
Confidence            46899999998765 478999999999998 9999999999999999999999999999644221      112466789


Q ss_pred             ccceEEEEecCCCCCCCCCCcCh----hhh--cCCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEe-cCHHHHHHHH
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISL----KEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLET-INSDIIKTYV  234 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~----~dl--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~v  234 (306)
                      ..+++++++|++||+.-+...++    ..+  .+.|||...++++.+....+.|+..|+.|.-  ..++ ..+...+.++
T Consensus        82 ~~n~lVlV~P~~~P~~i~~~~dl~~~l~~IA~a~~~fisRed~SGT~~~~~~l~~~aGi~p~~~wy~~~g~gm~~~l~~a  161 (236)
T 3lr1_A           82 MYNDFVIVGPKNDPAGIAKAKTAAEALKLLATKGATFISRGDKSGTHTKELDLWKSAGVDPKGNWYVEAGQGMGPVITMA  161 (236)
T ss_dssp             EECCEEEEECTTCTTCGGGCSSHHHHHHHHHHHTCCEEECCSSSHHHHHHHHHHHHTTCCCCSSSEEECCSCHHHHHHHH
T ss_pred             EcCcEEEEEECCChhhccchhhHHHHHHHHhhCCCcEEEccCCcchHHHHHHHHHHcCCCCCCCchhhcCcCHHHHHHHH
Confidence            99999999999999754332233    333  5899999999999999999999999998753  2233 4667888888


Q ss_pred             Hhccceeeeecceeccc--ccCCceeeecCCCCccceEEEEE-eCCc---cccHHHHHHHHHHhHHhhHHH
Q psy3760         235 ELRMGIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVII-KQGT---YLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       235 ~~g~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~-~~~~---~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      ....++++..+...-.+  ...+|..+--.++....+|.++. .+.+   ......++|++||.+.=.+..
T Consensus       162 ~~~~~y~ltdr~t~l~~~~~~~~l~i~~~~d~~l~n~y~~~~v~p~~~~~~~~~~a~~f~~~l~s~~~q~~  232 (236)
T 3lr1_A          162 TERRAYTLTDRGTYNAFKGAKTDLVILFQGEKGLFNPYGIMAVNPKKFPHVKYDLAMKLIDYVTGPEGLKI  232 (236)
T ss_dssp             HHHTCEEEEEHHHHHHHBTTTBCCEEEEEC---CCEEEEEEEECTTTCTTSCHHHHHHHHHHHTSHHHHHH
T ss_pred             HHcCCEEEecchhhhhcccCCCCeEEEEcCCcceeeceeEEEECcccCCccCHHHHHHHHHHhcCHHHHHH
Confidence            88899998887333222  24456665444433333443332 2221   246789999999976544433

>3kn3_A Putative periplasmic protein; alpha-beta structure, periplasmic binding protein fold, STRU genomics, PSI-2, protein structure initiative; HET: GSH CIT; 2.41A {Wolinella succinogenes}

Probab=99.44  E-value=1.6e-12  Score=100.32  Aligned_cols=207  Identities=12%  Similarity=0.053  Sum_probs=150.8

Q ss_pred             CCCcEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-------Cceeec
Q psy3760          91 DTGNLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-------KLISIP  162 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-------~~~~~~  162 (306)
                      ..+.|+|++..++. ..+++.+...|.+.+ ++++.+...++..+++++.+|.+|+.++..+ ....       .....+
T Consensus         3 ~~~~L~vaaaaS~~~s~ll~eL~~~Fek~~-gv~V~~~~~gSg~ll~qi~~G~aDVfisa~~-~~~~~l~~~G~~~~~~~   80 (242)
T 3kn3_A            3 AAAELRMATTTSTDNTGLLDVLAPAYKKDT-GVDLKWVAVGTGNALKLGENCDVDVVFVHAP-KVELEYVEKGFGIDRTP   80 (242)
T ss_dssp             -CCEEEEEEEHHHHHHTHHHHHHHHHHHHH-SCEEEEEEECHHHHHHHHHTTCCSEEEECCH-HHHHHHHHHTSEEEEEE
T ss_pred             CCceEEEEEECCcccchHHHHHHHHHHHHh-CCeEEEEEcCcHHHHHHHhcCCCCEEEecCh-HhHHHHHhcCCCccceE
Confidence            35789999998765 568999999999998 7999999999999999999999999999643 2212       135678


Q ss_pred             cccceEEEEecCCCCCCCCCCcChhhh------cCCCeEeecCCCCcHHHHHHHHHhCCCc-eeE---EEEe-cCHHHHH
Q psy3760         163 CYQWEYVIIVPLDHPLLLLNSISLKEI------SNYPLITYDLSFSGRIKLDREFSLQKLT-PYI---VLET-INSDIIK  231 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~~~~i~~~dl------~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~-~~~~~~~  231 (306)
                      +...++++|+|++||..-. ..++.+.      .+.|||+..++++.+....+.++..|+. |..   ..++ ..+...+
T Consensus        81 ~a~N~LVLV~P~~~Pa~i~-~~dl~~~~~~IA~a~~~FvsR~d~SGT~~~e~~lw~~~gi~~p~~~~wy~~~g~gm~~~l  159 (242)
T 3kn3_A           81 VMYNDFVIIGNPSFKQKFT-GMSVAEAFKLIEKEQVKFVSRGDKSGTHSKEREVWKEALGKIPEKESWYIEAGQGMLATI  159 (242)
T ss_dssp             EECSCEEEEECTHHHHHHT-TCCHHHHHHHHHHHTCCEEECCSSCHHHHHHHHHHHHHHSSCCTTCTTEEECCSCHHHHH
T ss_pred             EEcceEEEEEeCCCccccc-hhhHHHHHHHHHhcCCcEEECCCCccHHHHHHHHHHHcCCCCCCCCCchhhcCcCHHHHH
Confidence            8899999999999984333 3344332      5899999999999999999999999998 742   3333 4667888


Q ss_pred             HHHHhccceeeeecceeccc-----ccCCceeeecCCCCccceEEEE-EeCCc---cccHHHHHHHHHHhHHhhHHHH
Q psy3760         232 TYVELRMGIGIIASIAFDSN-----RDKNLRSISASHLFGTTISRVI-IKQGT---YLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       232 ~~v~~g~gi~~~p~~~~~~~-----~~~~l~~~~~~~~~~~~~~~l~-~~~~~---~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      .+...-.++++..+...-.+     ...+|..+--.++....+|.++ ..+.+   ......+.|++||.+.=.+..+
T Consensus       160 ~~a~~~~~Y~l~dr~t~l~~~~~~~~~~~l~i~~~gd~~l~n~y~~~~v~p~~~~~~~~~~a~~f~~~l~s~~~q~~i  237 (242)
T 3kn3_A          160 NIAEEQKGLTLTDRGTFIKYESNHKGKPPMVIVLEGDNTLKNFYSIMAVNPKRCEKADYKGAKQFIDWIVSEKMQAEI  237 (242)
T ss_dssp             HHHHHTTCEEEEEHHHHHHHHHHSCSSCSCEEEECCCGGGCCEEEEEEECTTTCTTSCHHHHHHHHHHHHSHHHHHHH
T ss_pred             HHHHHcCCEEEeeehhhhhcchhhcCCCCeEEEEcCCcceEeeeEEEEECcccCCccCHHHHHHHHHHHcCHHHHHHH
Confidence            88888899999887543222     2345776654443333344333 23222   3567899999999765444443

>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate, transport, ABC transport, virulence factor, receptor; 1.49A {Campylobacter jejuni}

Probab=99.23  E-value=2.1e-10  Score=90.89  Aligned_cols=189  Identities=12%  Similarity=0.076  Sum_probs=129.6

Q ss_pred             CCcEEEEecccchh------------hhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCC
Q psy3760          92 TGNLTIATTHTQAR------------YALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPS  155 (306)
Q Consensus        92 ~~~l~I~~~~~~~~------------~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~  155 (306)
                      .++|+||+......            .+...++..+.++.  |++++++...+..++.+.|.+|++|+++.....  ...
T Consensus        37 ~~~l~vg~~~~~~p~~~~~~~~g~~~G~~~~l~~~~~~~~~~pg~~v~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~  116 (259)
T 2v25_A           37 KGQLIVGVKNDVPHYALLDQATGEIKGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERK  116 (259)
T ss_dssp             HTCEEEEECSEETTTEEEETTTTEEESHHHHHHHHHHHHHHSCTTSEEEEECCTTTHHHHHHTTSCSEECSSCBCCHHHH
T ss_pred             CCeEEEEECCCCCCeEEEECCCCeEEEeeHHHHHHHHHHhcCCCcceEEEEcCHHHHHHHHhCCCCCEEEecCccCHHHH
Confidence            36799998654322            34467888888888  999999999888999999999999999853211  112


Q ss_pred             CCceee-ccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHH
Q psy3760         156 DKLISI-PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYV  234 (306)
Q Consensus       156 ~~~~~~-~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  234 (306)
                      ..+.+. ++....+++++++++++     -+++||.+.++.. ..+......+...+...|+.+++ ..+++...+..++
T Consensus       117 ~~~~~~~p~~~~~~~~~~~~~~~i-----~~~~dL~g~~i~~-~~g~~~~~~~~~~~~~~g~~~~~-~~~~~~~~~~~~l  189 (259)
T 2v25_A          117 RIYNFSEPYYQDAIGLLVLKEKKY-----KSLADMKGANIGV-AQAATTKKAIGEAAKKIGIDVKF-SEFPDYPSIKAAL  189 (259)
T ss_dssp             TTEEECSCSEEEEEEEEEEGGGCC-----CSGGGCTTCEEEE-ETTCSHHHHHHHHHHHTTCCCEE-EEESSHHHHHHHH
T ss_pred             hcCcccccceeCceEEEEeCCCCC-----CCHHHhCCCEEEE-ecCCchHHHHHHHHHhcCCceeE-EEeCCHHHHHHHH
Confidence            345554 78889999999999875     3789999998655 45666677778888888886654 4788999999999


Q ss_pred             Hhccc-eeeeecceeccc-c-cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         235 ELRMG-IGIIASIAFDSN-R-DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       235 ~~g~g-i~~~p~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .+|.. .++.+...+... . .+.  .  .........++++.+++.  ......+-+.+.+
T Consensus       190 ~~g~vDa~~~~~~~~~~~~~~~~~--~--~~~~~~~~~~~~~~~k~~--~~l~~~~~~~l~~  245 (259)
T 2v25_A          190 DAKRVDAFSVDKSILLGYVDDKSE--I--LPDSFEPQSYGIVTKKDD--PAFAKYVDDFVKE  245 (259)
T ss_dssp             HTTSSSEEEEEHHHHTTTCCTTEE--E--CSCCCSEEEECCEEETTC--HHHHHHHHHHHHH
T ss_pred             HcCCCcEEEecHHHHHHHHHhCCC--c--cccccccceeEEEEcCCC--HHHHHHHHHHHHH
Confidence            99944 444444444333 2 222  1  222233457778888774  3334444444433

>2x26_A Periplasmic aliphatic sulphonates-binding protein; transport protein; 1.75A {Escherichia coli}

Probab=99.20  E-value=5.2e-10  Score=91.28  Aligned_cols=197  Identities=13%  Similarity=0.087  Sum_probs=130.3

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcCCeeEEEEccccC---CCCCce-----eec
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAIVTEILS---PSDKLI-----SIP  162 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~~~Di~i~~~~~~---~~~~~~-----~~~  162 (306)
                      .++||||+.+.....+++.....|.+.+|++++++...++ .++.+.|.+|++|++++.....   ...+..     ..+
T Consensus         2 ~~~lrig~~~~~~~~~~a~~~g~~~~~~~g~~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~~~~~~   81 (308)
T 2x26_A            2 PEALRIGYQKGSIGMVLAKSHQLLEKRYPESKISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVEP   81 (308)
T ss_dssp             CSEEEEEECTTCHHHHHHHHTTHHHHHCTTSEEEEEECSSHHHHHHHHHHTSCSEEEECSHHHHHHHHTTCCEEEEEEEC
T ss_pred             CeEEEEEccCCchHHHHHHhcChHhHhcCCCceEEEECCCcHHHHHHHHCCCCCEEcccCcHHHHHHhcCCCeEEEEEec
Confidence            4689999998876677787778889999999999988765 7899999999999999742211   011222     222


Q ss_pred             cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHHhc-cce
Q psy3760         163 CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELR-MGI  240 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g-~gi  240 (306)
                      ......++++++++++     -+++||.+.++.. ..+......+..++...|+.+. +.+...+...+..++.+| ...
T Consensus        82 ~~~~~~~lv~~~~~~i-----~s~~dL~Gk~i~~-~~gs~~~~~l~~~l~~~Gl~~~~v~~~~~~~~~~~~al~~G~vDa  155 (308)
T 2x26_A           82 PKPKAEVILVAENSPI-----KTVADLKGHKVAF-QKGSSSHNLLLRALRQAGLKFTDIQPTYLTPADARAAFQQGNVDA  155 (308)
T ss_dssp             CCGGGEEEEEETTCSC-----CSGGGGTTSEEEE-CTTSHHHHHHHHHHHHTTCCGGGSEEEECCHHHHHHHHHTTSSSE
T ss_pred             CCCCceEEEEeCCCCC-----CCHHHcCCCEEee-eCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCCCCE
Confidence            2345788999998864     3789999998777 4555556677788999998764 334445677788888888 334


Q ss_pred             eeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCC-ccccHHHHHHHHHHhHH
Q psy3760         241 GIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQG-TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       241 ~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~-~~~~~~~~~~~~~l~~~  294 (306)
                      ++++....... ..++++.+...... ....++++.++- ...+..++.|.+.+.+.
T Consensus       156 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~al~~a  212 (308)
T 2x26_A          156 WAIWDPYYSAALLQGGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQGVLATFSEA  212 (308)
T ss_dssp             EEEETTHHHHHHHHSSEEEEEESTTSCCCCEEEEEEHHHHHHTHHHHHHHHHHHHHH
T ss_pred             EEecchhHHHHHhcCCcEEEecCCCcCCcceEEEEcHHHHHHCHHHHHHHHHHHHHH
Confidence            55555444333 33556665433222 233433333221 22356788888877664

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

Probab=99.18  E-value=6.6e-11  Score=82.14  Aligned_cols=76  Identities=16%  Similarity=0.145  Sum_probs=69.4

Q ss_pred             CchhhHHHHHHHHH-hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVR-QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         1 m~~~~l~~f~~v~~-~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      ++..++++|..+.+ .. |++.+|+.+++|+|++|++|+.||+ .|..++.|.++++ .+|..|..+.+.+..+++.++.
T Consensus        30 ~~~~~~~il~~L~~~~~-s~~ela~~l~is~stvsr~l~~Le~-~Glv~~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~  106 (119)
T 2lkp_A           30 ATPSRLMILTQLRNGPL-PVTDLAEAIGMEQSAVSHQLRVLRN-LGLVVGDRAGRSI-VYSLYDTHVAQLLDEAIYHSEH  106 (119)
T ss_dssp             CCHHHHHHHHHHHHCCC-CHHHHHHHHSSCHHHHHHHHHHHHH-HCSEEEEEETTEE-EEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHHHHHH-CCCEEEEecCCEE-EEEEchHHHHHHHHHHHHHHhh
Confidence            46778999999998 77 9999999999999999999999999 9999999999998 6999999999998888887765

>4gd5_A Phosphate ABC transporter, phosphate-binding PROT; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.70A {Clostridium perfringens}

Probab=99.17  E-value=5e-09  Score=84.11  Aligned_cols=207  Identities=14%  Similarity=0.117  Sum_probs=141.6

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC---CCCCceeeccccc
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS---PSDKLISIPCYQW  166 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~l~~~  166 (306)
                      ...++|+|..+.++ ..++..+...|.+.||++++++...++...++++.+|.+|++....+..   ....+...++..+
T Consensus        34 ~~~~~i~i~GSss~-~p~~~~~a~~f~~~~p~v~v~~~~~GSg~g~~~~~~G~~di~~as~~~~~~e~~~~~~~~~ia~d  112 (279)
T 4gd5_A           34 KSTNSVSISGSTSV-GPVMEAEAEAFKTKKPDVSIEINQIGSSAGIKNAMEGVSEIGMASRDLKGEEKQAGLKEVEIAYD  112 (279)
T ss_dssp             ---CEEEEEECTTT-HHHHHHHHHHHHHHSTTCEEEEEECCHHHHHHHHHHTSSSEEEESSCCCHHHHTTCCEEEEEEEE
T ss_pred             cCCCeEEEEEeCcH-HHHHHHHHHHHHHHCCCceEEEeeCCcHHHHHHHHcCCCcEEEecchhhhhHhhcCceEEEEEee
Confidence            34578999988775 5688899999999999999999999999999999999999999864422   1345778889999


Q ss_pred             eEEEEecCCCCCCC-----------CCCcChhhhcC--CC--eEeecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHH
Q psy3760         167 EYVIIVPLDHPLLL-----------LNSISLKEISN--YP--LITYDLSFSGRIKLDREFSLQKLTP-YIVLETINSDII  230 (306)
Q Consensus       167 ~~~~v~~~~~~l~~-----------~~~i~~~dl~~--~~--~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  230 (306)
                      .+++++++++|...           .+..+|.|+..  .+  .+..+.+.+.+..+.+.+...+... .......+...+
T Consensus       113 ~~~vivn~~n~~~~lt~~~l~~i~~g~i~~W~~l~~~~~~i~~~~r~~~sgt~~~f~~~~~~~~~~~~~~~~~~~~~~~~  192 (279)
T 4gd5_A          113 GIALITHKNNPVKDLTLVQIKDIYTGKITNWKELGGNDAPIVVVSREDGSGTRDAFQEIVGFKAEELTVNSQISDGSGNI  192 (279)
T ss_dssp             EEEEEEETTCSCCEECHHHHHHHHTTSCCBGGGGTSCSSBCEEEEECTTCHHHHHHHHHHTCCGGGSCTTCEEESSHHHH
T ss_pred             ceeeeeccCCccccccHHHHHHHhcccccchhhcCCCccceeEEeCCCCchHHHHHHHHHhccCcccCccccccCCcccc
Confidence            99999999998543           22334555532  23  4444556667777777764333221 123345677778


Q ss_pred             HHHHHhc-cceeeeecceecccccCCceeeecCC------------CCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         231 KTYVELR-MGIGIIASIAFDSNRDKNLRSISASH------------LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       231 ~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~------------~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      ...|..+ .+++++......    ..+..++++.            .+..++++++++... .++.+++|++++.+.-.+
T Consensus       193 ~~~V~~~~~aiGy~~~~~~~----~~~~~~~v~gv~pt~~~i~~g~YPl~rp~~~v~~~~~-~~~~ak~F~~f~~S~egQ  267 (279)
T 4gd5_A          193 KSLVQGNENAIGYISFSYVD----DSVSAVKVDGVEATPENVLNKSYKVSRPFLAVYKEEN-LTESGKSFIDFILSEEGQ  267 (279)
T ss_dssp             HHHHHHCTTEEEEEEGGGCC----TTEEECEETTBCCCHHHHHTTCSCCEEEEEEEECTTT-CCHHHHHHHHHHHSHHHH
T ss_pred             eeEEeecCccceecchhhhh----ccccEeeecCccCCHHHhhcCCCCcEEEEEEEEcCCC-CCHHHHHHHHHHcCHHHH
Confidence            8888876 678887654432    3455444432            123456777776544 578999999999865444


Q ss_pred             HHHHh
Q psy3760         298 KFINK  302 (306)
Q Consensus       298 ~~~~~  302 (306)
                      ..+++
T Consensus       268 ~ii~~  272 (279)
T 4gd5_A          268 DIVAK  272 (279)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>1us5_A Putative GLUR0 ligand binding core; receptor, membrane protein, glutamate receptor, L-glutamate; HET: GLU; 1.5A {Thermus thermophilus} SCOP: c.94.1.1 PDB: 1us4_A*

Probab=99.05  E-value=6.9e-09  Score=84.79  Aligned_cols=166  Identities=9%  Similarity=0.078  Sum_probs=115.1

Q ss_pred             CCcEEEEecccchhh-hhHHHHHHHHHh-CCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc------------C---
Q psy3760          92 TGNLTIATTHTQARY-ALPKIIKEFTIQ-FPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL------------S---  153 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~-~l~~~l~~~~~~-~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~------------~---  153 (306)
                      .+.|+|++....+.. .++..+.++..+ +|++++++.. .+.....+.|.+|++|++++....            .   
T Consensus        18 ~~~i~i~~~~~~g~~~~~~~~la~~~~~~~~g~~v~v~~~~~~~~~~~~l~~g~~Dl~~~~~~~~~~~~~~~~~~~~~~~   97 (314)
T 1us5_A           18 QEFITIGSGSTTGVYFPVATGIAKLVNDANVGIRANARSTGGSVANINAINAGEFEMALAQNDIAYYAYQGCCIPAFEGK   97 (314)
T ss_dssp             CEEEEEECCCTTSSHHHHHHHHHHHHHHHTSSEEEEEECCSCHHHHHHHHHTTSCSEEEEEHHHHHHHHHTCSSTTTTTC
T ss_pred             CceEEEEeCCCCchhHHHHHHHHHHHHhcCCCceEEEEecCcHHHHHHHHHcCCCcEEEEccHhHHHHhcCCCCCCCCCC
Confidence            468999998654433 477888887775 8999999985 567789999999999999975211            0   


Q ss_pred             CCCCceee-ccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEecCHHHH
Q psy3760         154 PSDKLISI-PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LETINSDII  230 (306)
Q Consensus       154 ~~~~~~~~-~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~  230 (306)
                      ...++... .+..+++++++++++|+     .+++||.+.++.....+...+..+..+++..|+.++.+  ....+...+
T Consensus        98 ~~~~~~~v~~~~~~~~~lvv~~~~~i-----~sl~dL~g~~i~~~~~gs~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~  172 (314)
T 1us5_A           98 PVKTIRALAALYPEVVHVVARKDAGI-----RTVADLKGKRVVVGDVGSGTEQNARQILEAYGLTFDDLGQAIRVSASQG  172 (314)
T ss_dssp             CCTTEEEEEEEEEEEEEEEEETTSSC-----SSGGGGTTSEEECCCTTCHHHHHHHHHHHHTTCCGGGSSEEECCCHHHH
T ss_pred             CccchhehhhcCcceEEEEEECCCCC-----CcHHHhCCCEeecCCCCchHHHHHHHHHHHcCCCHHHcCceecCCHHHH
Confidence            12456554 67788999999999874     38999999988876666666667778889999876522  233355566


Q ss_pred             HHHHHhc-cceeee----ecceeccc-ccCCceeeecC
Q psy3760         231 KTYVELR-MGIGII----ASIAFDSN-RDKNLRSISAS  262 (306)
Q Consensus       231 ~~~v~~g-~gi~~~----p~~~~~~~-~~~~l~~~~~~  262 (306)
                      ...+.+| ...++.    |...+... ..++++.+++.
T Consensus       173 ~~al~~G~vda~~~~~~~p~~~~~~~~~~g~l~~l~v~  210 (314)
T 1us5_A          173 IQLMQDKRADALFYTVGLGASAIQQLALTTPIALVAVD  210 (314)
T ss_dssp             HHHHHTTSCSEEEEEECTTCHHHHHHHHHSCEEECCCC
T ss_pred             HHHHHcCCccEEEEccCCCcHHHHHHHhcCCeEEEeCC
Confidence            6666766 344442    33233332 45667666553

>3r26_A Molybdate-binding periplasmic protein; protein binding; 1.70A {Escherichia coli} SCOP: c.94.1.1 PDB: 3axf_A 1amf_A 1wod_A

Probab=99.02  E-value=9.8e-08  Score=74.57  Aligned_cols=203  Identities=14%  Similarity=0.111  Sum_probs=136.5

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCCc----eeec
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDKL----ISIP  162 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~~----~~~~  162 (306)
                      .++|+|.+..++ ...+..++..|.++ |++++++...++.++..++.+|. +|+.+......    ...++    ...+
T Consensus         6 a~~l~v~~a~s~-~~~~~~l~~~Fe~~-~gi~V~~~~~~s~~l~~~i~~g~~~Dv~~~a~~~~~~~l~~~g~~~~~~~~~   83 (237)
T 3r26_A            6 EGKITVFAAASL-TNAMQDIATQFKKE-KGVDVVSSFASSSTLARQIEAGAPADLFISADQKWMDYAVDKKAIDTATRQT   83 (237)
T ss_dssp             -CEEEEEEEGGG-HHHHHHHHHHHHHH-HCCEEEEEEECHHHHHHHHHHTCCCSEEECSSHHHHHHHHHTTCBCGGGCEE
T ss_pred             CCcEEEEEccch-HHHHHHHHHHHHhc-cCCeEEEEECCHHHHHHHHHcCCCceEEEECCHHHHHHHHHCCCCCCCceee
Confidence            468999998775 45678899999886 99999999999999999999987 99999853210    01222    2467


Q ss_pred             cccceEEEEecCCCCCCC---CCCcChhhhcC-CCeEeecCCC-CcHHHHHHHHHhCCC----ceeEEEEecCHHHHHHH
Q psy3760         163 CYQWEYVIIVPLDHPLLL---LNSISLKEISN-YPLITYDLSF-SGRIKLDREFSLQKL----TPYIVLETINSDIIKTY  233 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~---~~~i~~~dl~~-~~~i~~~~~~-~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~  233 (306)
                      +....++++++++++...   ...-+|.++.. ..+...++.. .......+.++..|+    .++.+ ...+...+.++
T Consensus        84 ~~~~~lvl~~~~~~~~~~~~i~~~~~l~~l~~~~~iai~~p~~~p~G~~a~~~l~~~g~~~~l~~~~~-~~~~~~~~~~~  162 (237)
T 3r26_A           84 LLGNSLVVVAPKASVQKDFTIDSKTNWTSLLNGGRLAVGDPEHVPAGIYAKEALQKLGAWDTLSPKLA-PAEDVRGALAL  162 (237)
T ss_dssp             EEEECEEEEEESSCCCCCCCCSTTCCHHHHHTTCCEEEECTTTCHHHHHHHHHHHHTTCHHHHGGGEE-EESSHHHHHHH
T ss_pred             eEcceEEEEEeCCCCcccccccchHhHHHhcCCCeEEEeCCCCCChHHHHHHHHHHcCCHHHhhhcEE-ecCCHHHHHHH
Confidence            888899999999986432   12235777653 5666666653 344455677777776    45554 66788899999


Q ss_pred             HHhc-cceeeeecceecccccCCceee-ecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         234 VELR-MGIGIIASIAFDSNRDKNLRSI-SASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       234 v~~g-~gi~~~p~~~~~~~~~~~l~~~-~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      +..| ..++++....+..  .+++..+ .++.. .....+.+...++... +..++|++++.+.-.+...
T Consensus       163 v~~Ge~d~gi~~~s~a~~--~~~~~~v~~~P~~~~~~~~~~~ai~k~~~~-~~A~~Fi~fl~S~eaq~i~  229 (237)
T 3r26_A          163 VERNEAPLGIVYGSDAVA--SKGVKVVATFPEDSHKKVEYPVAVVEGHNN-ATVKAFYDYLKGPQAAEIF  229 (237)
T ss_dssp             HHTTSSSEEEEEHHHHHH--CSSEEEEEECCGGGSCCEEEEEEEBTTCCS-HHHHHHHHHHTSHHHHHHH
T ss_pred             HHcCCCCEEEEEeccccc--CCCCeEEEECCcccCCeeeeeEEEEcCCCC-HHHHHHHHHHcCHHHHHHH
Confidence            9988 5566665543322  3345443 44432 2333445555566654 7899999999765444333

>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide, complex (binding protein/peptide); 1.94A {Escherichia coli} SCOP: c.94.1.1 PDB: 1ggg_A

Probab=98.95  E-value=2.6e-08  Score=76.94  Aligned_cols=197  Identities=9%  Similarity=0.019  Sum_probs=122.7

Q ss_pred             CCcEEEEecccchh----------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCCce
Q psy3760          92 TGNLTIATTHTQAR----------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDKLI  159 (306)
Q Consensus        92 ~~~l~I~~~~~~~~----------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~~~  159 (306)
                      .+.|+||+......          .+...++..+.++. ++++++...+..++.+.+.+|++|+++....  ......+.
T Consensus         2 ~~~l~v~~~~~~~P~~~~~~g~~~G~~~dl~~~~~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~   80 (226)
T 1wdn_A            2 DKKLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKEL-KLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAID   80 (226)
T ss_dssp             --CEEEEEESSBTTTBEEETTEEESHHHHHHHHHHHHH-TCCEEEEEECGGGHHHHHHTTSSSEEEEEEECCHHHHTTSE
T ss_pred             CceEEEEECCCCCCeeEecCCcEEEeeHHHHHHHHHHh-CCEEEEEECCHHHHHHHHhCCCCCEEEEcCcCCHHHhCccc
Confidence            36799999743333          46688888888776 7888888888999999999999999985311  11123344


Q ss_pred             e-eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 S-IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 ~-~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      + .++.....+++++++++    ...+++||.+.++.... +.....    ++.... .......+++...+..++.+|.
T Consensus        81 ~~~p~~~~~~~~~~~~~~~----~i~~~~dL~g~~i~~~~-g~~~~~----~l~~~~-~~~~~~~~~~~~~~~~~l~~g~  150 (226)
T 1wdn_A           81 FSDGYYKSGLLVMVKANNN----DVKSVKDLDGKVVAVKS-GTGSVD----YAKANI-KTKDLRQFPNIDNAYMELGTNR  150 (226)
T ss_dssp             ECSCCEEEEEEEEEETTCC----SCSSSTTTTTCEEEEET-TSHHHH----HHHHHC-CCSEEEEESSHHHHHHHHHTTS
T ss_pred             cccchhcCceEEEEeCCCC----CCCCHHHhCCCEEEEEc-CCcHHH----HHHHhC-CCceEEEeCCHHHHHHHHHcCC
Confidence            3 47888999999999986    23478999998866643 333322    333321 1223457789999999999995


Q ss_pred             ceeeee-cceeccc-cc---CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         239 GIGIIA-SIAFDSN-RD---KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       239 gi~~~p-~~~~~~~-~~---~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      .=+++. ....... ..   ..+..++.  ......++++++++.  ......|-+.+.+.-+....+++
T Consensus       151 vDa~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~~--~~l~~~~~~~l~~l~~~g~~~~i  216 (226)
T 1wdn_A          151 ADAVLHDTPNILYFIKTAGNGQFKAVGD--SLEAQQYGIAFPKGS--DELRDKVNGALKTLRENGTYNEI  216 (226)
T ss_dssp             CSEEEEEHHHHHHHHHTTTTTTEEEEEE--EEEEEEEEEEECTTC--HHHHHHHHHHHHHHHHTSHHHHH
T ss_pred             cCEEEeCcHHHHHHHHhCCCCceEEecC--CcccCceEEEEeCCC--HHHHHHHHHHHHHHHhCChHHHH
Confidence            544444 3333322 22   23444432  223457788888773  34444444444444333344444

>3gzg_A Molybdate-binding periplasmic protein; permease; molybdate complex, mutant K127S, metal binding protein; 1.55A {Xanthomonas axonopodis PV} PDB: 2h5y_A

Probab=98.92  E-value=3.8e-07  Score=71.82  Aligned_cols=204  Identities=10%  Similarity=0.072  Sum_probs=137.2

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCCc----eee
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDKL----ISI  161 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~~----~~~  161 (306)
                      ..++|+|.+..++ ...+..++..|.+++ ++++++...++.++..++.+|. +|+.+......    ...++    ...
T Consensus        21 aa~~L~V~~a~s~-~~~~~~l~~~Fe~~~-gi~V~~~~~~Sg~l~~qi~~g~~~DV~~sa~~~~~~~l~~~gl~~~~~~~   98 (253)
T 3gzg_A           21 MTAPVTVFAAASL-KESMDEAATAYEKAT-GTPVRVSYAASSALARQIEQGAPADVFLSADLEWMDYLQQHGLVLPAQRH   98 (253)
T ss_dssp             -CCCEEEEEEGGG-HHHHHHHHHHHHHHH-SCCEEEEEECHHHHHHHHHTTCCCSEEECSSHHHHHHHHHTTSSCGGGEE
T ss_pred             cCCCEEEEEecCh-HHHHHHHHHHHHHHh-CCeEEEEECChHHHHHHHHcCCCceEEEECCHHHHHHHHHCCCcCCCcce
Confidence            3567999998775 446788999999998 8999999999999999999986 99999853210    11222    346


Q ss_pred             ccccceEEEEecCCCCCCCCCC--cChhhhcC--CCeEeecCCC-CcHHHHHHHHHhCCC----ceeEEEEecCHHHHHH
Q psy3760         162 PCYQWEYVIIVPLDHPLLLLNS--ISLKEISN--YPLITYDLSF-SGRIKLDREFSLQKL----TPYIVLETINSDIIKT  232 (306)
Q Consensus       162 ~l~~~~~~~v~~~~~~l~~~~~--i~~~dl~~--~~~i~~~~~~-~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~  232 (306)
                      .+....+++++++++|......  -+|.++..  ..++..++.. .......++++..|+    .++. ...++...+..
T Consensus        99 ~~a~~~lvl~~~~~~~~~~~~i~~~dl~~l~~~~~~iai~dP~~~p~G~~a~~~l~~~g~~~~l~~~~-v~~~~~~~~~~  177 (253)
T 3gzg_A           99 NLLGNTLVLVAPASSKLRVDPRAPGAIAKALGENGRLAVGQTASVPAGSYAAAALRKLGQWDSVSNRL-AESESVRAALM  177 (253)
T ss_dssp             EEEEECEEEEEETTCCCCCCTTSTTHHHHHTTTTCCEEEECTTTSHHHHHHHHHHHHTTCHHHHTTSE-EEESSHHHHHH
T ss_pred             eEEeeEEEEEEECCCCcccCCCCHHHHHHhhcCCCEEEEeCCCCCchHHHHHHHHHHcCcHHHHhhce-eecCCHHHHHH
Confidence            7788899999999987430111  23666533  5677766643 344555677777776    3555 45788889999


Q ss_pred             HHHhc-cceeeeecceecccccCCceee-ecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         233 YVELR-MGIGIIASIAFDSNRDKNLRSI-SASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       233 ~v~~g-~gi~~~p~~~~~~~~~~~l~~~-~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      ++..| ..++++....+..  .+++..+ .++.. .....+.+...++. ..+..++|+++|.+.-.+...
T Consensus       178 ~v~~Gead~giv~~s~a~~--~~~v~~v~~~P~~~~~~i~~~~ai~k~~-~~~~A~~Fi~fl~S~eaq~i~  245 (253)
T 3gzg_A          178 LVSRGEAPLGIVYGSDARA--DAKVRVVATFPDDSHDAIVYPVAALKNS-NNPATAAFVSWLGSKPAKAIF  245 (253)
T ss_dssp             HHHTTSSSEEEEEHHHHHH--CTTEEEEEECCGGGSCCEEEEEEECTTC-CCTTHHHHHHHTTSHHHHHHH
T ss_pred             HHHcCCCCEEEEEhhcccc--CCCceEEEECCcccCceeEEEEEEECCC-ChHHHHHHHHHHcCHHHHHHH
Confidence            99988 5566666544332  3445544 34432 23345555555665 578999999999765444433

>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand binding domain, transport protein; HET: GLU; 2.10A {Nostoc punctiforme}

Probab=98.83  E-value=3.3e-08  Score=76.49  Aligned_cols=189  Identities=10%  Similarity=0.080  Sum_probs=119.0

Q ss_pred             CCcEEEEecccchh---------hhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC--CCCCce
Q psy3760          92 TGNLTIATTHTQAR---------YALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS--PSDKLI  159 (306)
Q Consensus        92 ~~~l~I~~~~~~~~---------~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~  159 (306)
                      .++|+||+.+..+.         .+...++..+.++. ++++++... +...+++.|.+|++|+++......  ....+.
T Consensus         2 ~~~l~v~~~~~~P~~~~~~g~~~G~~~dl~~~~~~~~-g~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~   80 (228)
T 2pyy_A            2 QQPLLVATRVIPPFVLSNKGELSGFSIDLWRSIATQI-GIESKLIEYSSVPELISAIKDNKVNLGIAAISITAEREQNFD   80 (228)
T ss_dssp             --CEEEEECCBTTTBBCC---CBSHHHHHHHHHHHHH-TCCEEEEECSSHHHHHHHHHTTSCSEECSSCBCCHHHHHHSE
T ss_pred             CceEEEEecCCCCeEEecCCceEEEeHHHHHHHHHHh-CCcEEEEEcCCHHHHHHHHHCCCcCEEEeccccCHHHHccce
Confidence            36799999764322         23445777777775 889999988 678899999999999997531111  112233


Q ss_pred             -eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         160 -SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       160 -~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                       +.++.....++++++++|... ...+++||.+.++..... ..    ...++...+.   ....+++...+..++.+|.
T Consensus        81 ~~~p~~~~~~~~~~~~~~~~~~-~~~~~~dL~g~~i~~~~g-~~----~~~~l~~~~~---~~~~~~~~~~~~~~l~~g~  151 (228)
T 2pyy_A           81 FSLPIFASGLQIMVRNLESGTG-DIRSIDDLPGKVVATTAG-ST----AATYLREHHI---SVLEVPKIEEAYKALQTKK  151 (228)
T ss_dssp             ECSCSEEEEEEEEEEC-----C-CCCSGGGCTTCEEEEETT-SH----HHHHHHHTTC---EEEEESSHHHHHHHHHTTS
T ss_pred             ecccchhcceEEEEECCccccC-CcCCHHHcCCCeEEEEcC-cH----HHHHHHHcCC---ceEecCCHHHHHHHHHcCC
Confidence             347888899999999986532 245899999988776543 22    3445555554   2456789999999999994


Q ss_pred             c-eeeeecceeccc-cc---CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         239 G-IGIIASIAFDSN-RD---KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       239 g-i~~~p~~~~~~~-~~---~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      . ..+.+....... ..   ..+...+..  ....+++++++++....+.+.++++.++
T Consensus       152 ~D~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~l~~l~  208 (228)
T 2pyy_A          152 ADAVVFDAPVLLFYAANEGKGKVEIVGSI--LREESYGIILPNNSPYRKPINQALLNLK  208 (228)
T ss_dssp             SSEEEEEHHHHHHHHHTTTTTTEEEEEEE--EEEEEECCEECTTCTTHHHHHHHHHHHH
T ss_pred             CCEEEecHHHHHHHHHhCCCCcEEEeccc--ccceeEEEEEeCChHHHHHHHHHHHHHH
Confidence            4 666666544332 22   234444322  2345778888877655555555555554

>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=98.82  E-value=4e-09  Score=70.40  Aligned_cols=80  Identities=16%  Similarity=0.103  Sum_probs=62.7

Q ss_pred             CchhhHHHHHHHHHhcCCHHH---H---HHHhCCCchHHHHHHHHHHHH-cCceeEEecCCCccccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTE---A---AKALYTSQPGVSKAIIELEEE-LSIDIFIRHGKRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~---a---A~~l~isq~~~s~~i~~LE~~-lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i   73 (306)
                      ++..++.++..+.+.+ .++.   +   |+.+++|++++|+.|++||+. |-.+......+.+ .||+.|+.+++.+.++
T Consensus         6 lt~~q~~iL~~l~~~~-~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~-~LT~~G~~~~~~~~~~   83 (99)
T 1tbx_A            6 FFYPEAIVLAYLYDNE-GIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRL-YLTEKGKLFAISLKTA   83 (99)
T ss_dssp             SBCHHHHHHHHHTTCT-TCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEE-EECHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC-CcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEE-EECHHHHHHHHHHHHH
Confidence            3567889999999877 7666   6   999999999999999999995 3222222234555 8999999999999999


Q ss_pred             HHHHHHHHH
Q psy3760          74 MQEIEGLKK   82 (306)
Q Consensus        74 l~~~~~~~~   82 (306)
                      ++.+.+-..
T Consensus        84 ~~~~~~~~~   92 (99)
T 1tbx_A           84 IETYKQIKK   92 (99)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888776443

>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER bacterium, transport protein; HET: LYS; 1.79A {Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*

Probab=98.81  E-value=1.1e-07  Score=75.82  Aligned_cols=200  Identities=11%  Similarity=0.063  Sum_probs=124.9

Q ss_pred             CCCCcEEEEecccchh----------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          90 YDTGNLTIATTHTQAR----------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~----------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ...+.|+||+......          .+...++..+.++. ++++++...+..++++.|.+|++|+++......  ....
T Consensus        39 ~~~~~l~v~~~~~~~P~~~~~~g~~~G~~~dl~~~i~~~~-g~~v~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~  117 (272)
T 2pvu_A           39 ATKKKVVVGTDAAFAPFEYMQKGKIVGFDVDLLDAVMKAA-GLDYELKNIGWDPLFASLQSKEVDMGISGITITDERKQS  117 (272)
T ss_dssp             CCCCCEEEEECCCBTTTBEEETTEEESHHHHHHHHHHHHH-TCCEEEEECCHHHHHHHHHHTSSSEECSSCBCCHHHHTT
T ss_pred             ccCCeEEEEECCCCCCeEEecCCeEEEEHHHHHHHHHHHh-CCceEEEECCHHHHHHHHhCCCCCEEEeCCcCCHHHHhc
Confidence            3467899999743222          36677888887765 888999888899999999999999998521111  1123


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. +.++.....+++++++++     ..+++||.+.++.... +......+.+.+   + .......+++...++.++.+
T Consensus       118 ~~~s~p~~~~~~~l~~~~~~~-----i~~~~dL~g~~i~~~~-g~~~~~~l~~~~---~-~~~~i~~~~~~~~~~~~l~~  187 (272)
T 2pvu_A          118 YDFSDPYFEATQVILVKQGSP-----VKNALDLKGKTIGVQN-ATTGQEAAEKLF---G-KGPHIKKFETTVVAIMELLN  187 (272)
T ss_dssp             EEECSCCEEECEEEEEETTCC-----CCSGGGGTTSCEEEET-TSHHHHHHHHHH---C-SSTTEEEESSHHHHHHHHHT
T ss_pred             CccchhhhccceEEEEECCCC-----CCCHHHhCCCeEEEEc-CchHHHHHHHhc---C-CCCeEEEcCCHHHHHHHHHc
Confidence            33 367888899999999986     2478999999876654 433333333333   2 12223467899999999999


Q ss_pred             ccc-eeeeecceeccc-c-cC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         237 RMG-IGIIASIAFDSN-R-DK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       237 g~g-i~~~p~~~~~~~-~-~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      |.. .++.+...+... . .+  ++..++.........++++.+++   ......|-+.|.+..+....+++
T Consensus       188 G~vDa~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~k~---~~l~~~l~~~l~~l~~~g~~~~i  256 (272)
T 2pvu_A          188 GGVDAVITDNAVANEYVKNNPNKKLQVIEDPKNFASEYYGMIFPKN---SELKAKVDEALKNVINSGKYTEI  256 (272)
T ss_dssp             TSCSEEEEEHHHHHHHHHHCGGGCEEEECCTTTSCCEEECCEEETT---CTTHHHHHHHHHHHHHTTHHHHH
T ss_pred             CCccEEEeCHHHHHHHHHhCCCCceEEeccccccCCceEEEEEeCC---HHHHHHHHHHHHHHHhCChHHHH
Confidence            944 445554443332 1 22  25555433212345778888887   33444444444444333334443

>3cij_A UPF0100 protein AF_0094; archaeal periplasmic binding protein, unknown function, metal binding protein, transport protein; 1.07A {Archaeoglobus fulgidus} PDB: 2ons_A 2onk_E 2onr_A

Probab=98.80  E-value=4.3e-07  Score=73.41  Aligned_cols=200  Identities=11%  Similarity=0.045  Sum_probs=127.2

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc-CC-eeEEEEccccC----CCCCc--eeecc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN-DQ-ADIAIVTEILS----PSDKL--ISIPC  163 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~-~~-~Di~i~~~~~~----~~~~~--~~~~l  163 (306)
                      .++|+|.+..++ ...+..++..|.++||++++++...++.++..++.+ |. +|+.+......    ...++  ...++
T Consensus         4 ~~~l~v~~a~s~-~~~~~~l~~~F~~~~~gi~V~~~~~~s~~l~~~i~~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~   82 (295)
T 3cij_A            4 NVKLKVFHAGSL-TEPMKAFKRAFEEKHPNVEVQTEAAGSAATIRKVTELGRKADVIATADYTLIQKMMYPEFANWTIMF   82 (295)
T ss_dssp             -CEEEEEEEGGG-HHHHHHHHHHHHHHCTTCEEEEEEECHHHHHHHHHTSCCCCSEEEESSTHHHHHHHTTTTCCCCEEE
T ss_pred             CceEEEEecCCH-HHHHHHHHHHHHHHCCCceEEEEeCcHHHHHHHHHhCCCCCCEEEEcChhhHHHHHhCCCcceeeEE
Confidence            467999887654 457888999999999999999999999999999998 74 99999853210    12233  24567


Q ss_pred             ccceEEEEecCCCCCCC-CCCcChhh-hc--CCCeEeecCCCC-cHHHHHH----------------HHHhC--C-----
Q psy3760         164 YQWEYVIIVPLDHPLLL-LNSISLKE-IS--NYPLITYDLSFS-GRIKLDR----------------EFSLQ--K-----  215 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~-~~~i~~~d-l~--~~~~i~~~~~~~-~~~~~~~----------------~~~~~--~-----  215 (306)
                      ....++++++++++... ..+.+|.| |.  ..+++..++... .......                .+...  .     
T Consensus        83 ~~~~lvl~~~~~~~~~~~i~~~~w~dll~~~~~~I~~~~p~~~~~G~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~  162 (295)
T 3cij_A           83 AKNQIVLAYRNDSRYADEINSQNWYEILKRPDVRFGFSNPNDDPCGYRSLMAIQLAELYYNDPTIFDELVAKNSNLRFSE  162 (295)
T ss_dssp             EECCEEEEECTTSTTTTTCCTTTHHHHHTSTTCCEEEECTTTCHHHHHHHHHHHHHHHHTTCTTHHHHHTGGGBSCCEEE
T ss_pred             EeeeEEEEEeCCCccccccCcccHHHHhcCCCcEEEEeCCCcCCccHHHHHHHHHHHHhccCCcHHHHHhhccccccccc
Confidence            78899999999987542 23458999 43  345776665422 2111111                11111  0     


Q ss_pred             -------C-------ce--eEEEEecCHHHHHHHHHhcc-ceeeeecceecccccCCceeeecCCCC-------------
Q psy3760         216 -------L-------TP--YIVLETINSDIIKTYVELRM-GIGIIASIAFDSNRDKNLRSISASHLF-------------  265 (306)
Q Consensus       216 -------~-------~~--~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~~~~~l~~~~~~~~~-------------  265 (306)
                             +       .+  +......+...+..++.+|. .++++....+...   ++..+.++...             
T Consensus       163 ~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~Ge~d~~i~~~s~a~~~---~~~~~~~P~~~~~~~~~~~~~y~~  239 (295)
T 3cij_A          163 DNGSYVLRMPSSERIEINKSKIMIRSMEMELIHLVESGELDYFFIYKSVAKQH---GFNFVELPVEIDLSSPDYAELYSK  239 (295)
T ss_dssp             ETTEEEEECCCGGGCCBCTTTEEEESSTHHHHHHHHTTSCSEEEEEHHHHHHT---TCEEEECCTTTSSCCGGGHHHHTT
T ss_pred             cCCcccccccccccccccccceeecccHHHHHHHHhCCCCCEEEEEeehhhhC---CCCEEECchhhccCCccccccccc
Confidence                   0       01  11234456668889999994 6677665444321   23333343321             


Q ss_pred             -------------ccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         266 -------------GTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       266 -------------~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                                   ....+.+...++......+++|+++|.+.=
T Consensus       240 ~~~~~~~~~~~~~~~i~~~~~i~k~a~~~~~A~~Fi~fl~S~e  282 (295)
T 3cij_A          240 VKVVLANGKEVTGKPIVYGITIPKNAENRELAVEFVKLVISEE  282 (295)
T ss_dssp             EEEECTTSCEEECCCCEEEEECCTTCSCHHHHHHHHHHHHSHH
T ss_pred             eEEeccCCccccCCceEEEEEeecCCCCHHHHHHHHHHHhChh
Confidence                         123456667777777889999999998653

>3cfx_A UPF0100 protein MA_0280; ABC transporter, binding protein, molybdate, tungstate, LIGA unknown function, transport protein; 1.60A {Methanosarcina acetivorans}

Probab=98.80  E-value=1.1e-06  Score=70.95  Aligned_cols=202  Identities=11%  Similarity=0.052  Sum_probs=127.8

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc-CC-eeEEEEccccC----CCCCc--eeecc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN-DQ-ADIAIVTEILS----PSDKL--ISIPC  163 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~-~~-~Di~i~~~~~~----~~~~~--~~~~l  163 (306)
                      .++|+|.+..++ ...+..++..|.++||++++++...++.++..++.+ |. +|+.+......    ...++  ...++
T Consensus         4 ~~~l~v~~a~s~-~~~~~~l~~~F~~~~~gi~V~~~~~~s~~l~~~i~~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~   82 (296)
T 3cfx_A            4 GEVLTVFHAGSL-SVPFEELEAEFEAQHPGVDVQREAAGSAQSVRKITELGKKADVLASADYALIPSLMVPEYADWYAAF   82 (296)
T ss_dssp             CCEEEEEECGGG-HHHHHHHHHHHHHHSTTCEEEEEECCHHHHHHHHHTSCCCCSEEEESSTTHHHHHTTTTTCSCEEEE
T ss_pred             CceEEEEecccH-HHHHHHHHHHHHHHCCCceEEEEeCchHHHHHHHHhCCCCCcEEEECChhhHHHHHhCCCccceeee
Confidence            467999987654 457888999999999999999999999999999998 74 99999853210    12333  24567


Q ss_pred             ccceEEEEecCCCCCCCC-CCcChhh-hc--CCCeEeecCCC-CcHH----HHH------------HHHHhC--C-----
Q psy3760         164 YQWEYVIIVPLDHPLLLL-NSISLKE-IS--NYPLITYDLSF-SGRI----KLD------------REFSLQ--K-----  215 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~-~~i~~~d-l~--~~~~i~~~~~~-~~~~----~~~------------~~~~~~--~-----  215 (306)
                      ....++++++++++.... .+.+|.| |.  ..++...++.. ....    .+.            +.+...  +     
T Consensus        83 ~~~~l~i~~~~~~~~~~~~~~~~w~dll~~~~~~I~~~~p~~~~~G~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~l~~  162 (296)
T 3cfx_A           83 ARNQMILAYTNESKYGDEINTDNWYEILRRPDVRYGFSNPNDDPAGYRSQMVTQLAESYYNDDMIYDDLMLANTGMTLTT  162 (296)
T ss_dssp             EECCEEEEECTTSTTTTTCCTTTHHHHHHSTTCCEEEECTTTCHHHHHHHHHHHHHHHHTTCTTHHHHHTGGGSSCEEEE
T ss_pred             EeeeEEEEEeCCCccccCCCcccHHHHhCCCCeEEEEeCCCCCCCcHHHHHHHHHHHHhhcCccHHHHHhhccccccccc
Confidence            778899999999875422 3458999 53  34566666542 2211    111            111111  0     


Q ss_pred             ---------------Ccee--EEEEecCHHHHHHHHHhccc-eeeeecceecccccCCceeeecCCCC------------
Q psy3760         216 ---------------LTPY--IVLETINSDIIKTYVELRMG-IGIIASIAFDSNRDKNLRSISASHLF------------  265 (306)
Q Consensus       216 ---------------~~~~--~~~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~~~~~~l~~~~~~~~~------------  265 (306)
                                     ..|+  ......+...+..++.+|.+ ++++....+...   ++..+.++...            
T Consensus       163 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~Ge~d~~i~~~s~a~~~---~~~~~~~P~~~~~~~~~~~~~y~  239 (296)
T 3cfx_A          163 EENGTALIHVPASEEISPNTSKIMLRSMEVELSSALETGEIDYLYIYRSVAEQH---GFEYVALPPAIDLSSLEYADNYS  239 (296)
T ss_dssp             CTTSCEEEECCCGGGCCCCTTTEEEESSGGGGHHHHHTTSCSEEEEEHHHHHHH---TCEEECCCTTTSSCCGGGHHHHT
T ss_pred             ccCCcccccccccccccccccceeecccHHHHHHHHHcCCCCEEEeehhhHhhC---CCCEEECChhhcccCcccccccc
Confidence                           0111  12344566678899999954 666665443221   22333333211            


Q ss_pred             --------------ccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         266 --------------GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       266 --------------~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                                    ......+...++....+.+++|+++|.+.=.+
T Consensus       240 ~v~~~~~~g~~~~~~~i~~~~~i~k~a~~~~~A~~Fi~fllS~e~q  285 (296)
T 3cfx_A          240 KVQVEMVNGEVVTGSPIVYGVTIPNNAENSELATEFVALLLGETGQ  285 (296)
T ss_dssp             TEEEECTTSCEEECCCCEEEEECCTTCSCHHHHHHHHHHHHSHHHH
T ss_pred             ceeeeccCCccccCCceEEEEEeecCCCCHHHHHHHHHHHhChHHH
Confidence                          11345666777777788999999999865333

>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP: c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A* 1hpb_P*

Probab=98.79  E-value=1.3e-07  Score=73.79  Aligned_cols=202  Identities=13%  Similarity=0.076  Sum_probs=124.3

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .+.|+||+.....           ..+...++..+.++. ++++++...+...++..|.+|++|+++......  ....+
T Consensus         3 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~   81 (239)
T 1lst_A            3 PQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRM-QVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEI   81 (239)
T ss_dssp             CSEEEEEECSCBTTTBEECTTCCEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHHHC
T ss_pred             cceEEEEECCCcCCeeEECCCCCEeeEHHHHHHHHHHHH-CCeEEEEeCCHHHHHHHHhCCCCCEEEECcCcCHHHhhce
Confidence            4789999843221           235568888888876 899999999999999999999999997621111  11222


Q ss_pred             e-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 I-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 ~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      . +.++.....+++++++++..    .+++||.+.++.. ..+......+.+.+...+.   ....+++...++.++.+|
T Consensus        82 ~~s~p~~~~~~~l~~~~~~~~~----~~~~dL~g~~v~~-~~g~~~~~~l~~~~~~~~~---~~~~~~~~~~~~~~l~~G  153 (239)
T 1lst_A           82 AFSDKLYAADSRLIAAKGSPIQ----PTLESLKGKHVGV-LQGSTQEAYANDNWRTKGV---DVVAYANQDLIYSDLTAG  153 (239)
T ss_dssp             EECSCSBCCCEEEEEETTCCCC----SSHHHHTTCEEEE-ETTSHHHHHHHHHTGGGTC---EEEEESSHHHHHHHHHTT
T ss_pred             eecccceeCceEEEEeCCCCCC----CCHHHhCCCEEEE-EcCccHHHHHHHhcccCCC---eEEEcCCHHHHHHHHHcC
Confidence            2 34788899999999998743    4799999988554 4454444445544433333   345688999999999999


Q ss_pred             cc-eeeeecceecc--c-c--cCCceeeecCCCCc---cceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         238 MG-IGIIASIAFDS--N-R--DKNLRSISASHLFG---TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       238 ~g-i~~~p~~~~~~--~-~--~~~l~~~~~~~~~~---~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .. .++.+...+..  . .  ..++..++.+....   ..+++++++++.  ......|-+.|.+.-+....+++.
T Consensus       154 ~vDa~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~--~~l~~~~~~~l~~l~~~G~~~~i~  227 (239)
T 1lst_A          154 RLDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDD--TELKAAFDKALTELRQDGTYDKMA  227 (239)
T ss_dssp             SCSEEEEEHHHHHHHTTTSGGGTTEEECSSCBCCHHHHCSSBCCEECTTC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             CCCEEEeCcHHHHHHHHhccCCCceEEeccccccccccCcceEEEEeCCC--HHHHHHHHHHHHHHHHCccHHHHH
Confidence            44 34444433221  1 1  12344443222111   125677777652  334444444444444443455544

>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A

Probab=98.78  E-value=7.5e-07  Score=69.00  Aligned_cols=188  Identities=11%  Similarity=0.036  Sum_probs=120.2

Q ss_pred             CCCcEEEEecccchhh------------hhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC--CC
Q psy3760          91 DTGNLTIATTHTQARY------------ALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS--PS  155 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~------------~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~--~~  155 (306)
                      ..+.|+||+.+.....            +...++..+.++. ++++++... +..++++.+.+|++|+++......  ..
T Consensus         2 ~~~~l~v~~~~~~P~~~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~   80 (233)
T 1ii5_A            2 SAMALKVGVVGNPPFVFYGEGKNAAFTGISLDVWRAVAESQ-KWNSEYVRQNSISAGITAVAEGELDILIGPISVTPERA   80 (233)
T ss_dssp             CSCCEEEEECCCTTTCEEC-----CEESHHHHHHHHHHHHH-TCCEEEEECSCHHHHHHHHHTTSCSEEEEEEECCHHHH
T ss_pred             CCceEEEEecCCCCeEEEecCCCCCEEEEeHHHHHHHHHHc-CCcEEEEEeCCHHHHHHHHHCCCcCEEEeeeecCcccc
Confidence            3568999997642222            2345777777665 899999998 999999999999999998531111  11


Q ss_pred             --CCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHH
Q psy3760         156 --DKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKT  232 (306)
Q Consensus       156 --~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (306)
                        ..+. +.++.....+++++++++   ....+++||.+.++...... ..    ..++...+.   ....+++...++.
T Consensus        81 ~~~~~~~s~p~~~~~~~~~~~~~~~---~~i~~~~dL~g~~v~~~~g~-~~----~~~l~~~~~---~~~~~~~~~~~~~  149 (233)
T 1ii5_A           81 AIEGITFTQPYFSSGIGLLIPGTAT---PLFRSVGDLKNKEVAVVRDT-TA----VDWANFYQA---DVRETNNLTAAIT  149 (233)
T ss_dssp             TSTTEEECCCCEEEEEEEEEEGGGT---TTCSSGGGGTTCEEEEETTS-HH----HHHHHHTTC---EEEEESSHHHHHH
T ss_pred             ccceeEEccceeecCeEEEEECCCC---CCCCCHHHhCCCeEEEECCc-cH----HHHHHHcCC---CeEEcCCHHHHHH
Confidence              3344 347888899999999885   12457899999887765432 22    334444443   3456789999999


Q ss_pred             HHHhccceeeee-cceeccc-c-cC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         233 YVELRMGIGIIA-SIAFDSN-R-DK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       233 ~v~~g~gi~~~p-~~~~~~~-~-~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      ++.+|..=+++. ...+... . .+  .+..++.  ......++++.+++......+.++++.++
T Consensus       150 ~l~~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~k~~~l~~~~~~~l~~l~  212 (233)
T 1ii5_A          150 LLQKKQVEAVMFDRPALIYYTRQNPNLNLEVTEI--RVSLEPYGFVLKENSPLQKTINVEMLNLL  212 (233)
T ss_dssp             HHHTTSCSEEEEEHHHHHHHHHHCGGGCEEECSC--CSEEEEEEEEEETTCTTHHHHHHHHHHHH
T ss_pred             HHHcCCccEEEeCHHHHHHHHHhCCCCcEEEeCc--cccccceEEEEcCCchHHHHHHHHHHHHH
Confidence            999997644444 3333322 1 22  3444332  23345788888887544444555544443

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=98.78  E-value=1.2e-09  Score=65.90  Aligned_cols=45  Identities=24%  Similarity=0.314  Sum_probs=37.0

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC--HhHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT--KPGQAILR   68 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT--~~G~~l~~   68 (306)
                      +..+++.+ ||++||+.||||||+||++|             |.++++ .||  +.|+.+++
T Consensus         7 L~~~~~~~-s~t~aA~~L~vtQ~AVS~~i-------------r~~r~v-~Lt~~~~G~~~~~   53 (66)
T 2ovg_A            7 LKDYAMRF-GQTKTAKDLGVYPSSINQAI-------------HAGRKI-FLTINADGSVYAE   53 (66)
T ss_dssp             HHHHHHHH-CHHHHHHHHTSCHHHHHHHH-------------HHTCEE-EEEECTTSCEEEE
T ss_pred             HHHHHHHC-CHHHHHHHhCCCHHHHHHHH-------------HhCCCc-eeEecCCcceeHH
Confidence            34568888 99999999999999999998             467787 688  88876543

>3cfz_A UPF0100 protein MJ1186; ABC transporter, binding protein, molybdate, tungstate, ligand, unknown function, transport protein; 1.70A {Methanocaldococcus jannaschii}

Probab=98.77  E-value=9.4e-07  Score=71.30  Aligned_cols=197  Identities=12%  Similarity=0.028  Sum_probs=126.8

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc-CC-eeEEEEccccC----CCCCc--eeecc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN-DQ-ADIAIVTEILS----PSDKL--ISIPC  163 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~-~~-~Di~i~~~~~~----~~~~~--~~~~l  163 (306)
                      .++|+|.+..++ ...+..++..|.++||++++++...++.++..++.+ |. +|+.+......    ...++  ...++
T Consensus         4 ~~~l~v~~a~s~-~~~~~~l~~~F~~~~~gi~V~~~~~~s~~l~~~i~~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~   82 (292)
T 3cfz_A            4 KIVLKIFHAGSL-SVPFEEYEKMFEKEHPNVDVEREPAGSVACVRKIIDLGKKADILASADYSLIPQMMMPKYADWYVMF   82 (292)
T ss_dssp             CEEEEEEEEGGG-HHHHHHHHHHHHHHCTTEEEEEEEECHHHHHHHHHTSCCCCSEEEESSTTHHHHHTTTTTCSCCEEE
T ss_pred             CceEEEEEccch-HHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHhcCCCCcEEEECChHHHHHHHhCCCccceeee
Confidence            457999877664 457889999999999999999999999999999998 74 99999853210    12233  24567


Q ss_pred             ccceEEEEecCCCCCCCC-CCcChhhhc---CCCeEeecCCCC-cHHHHHH-------------HHHhCCCc--------
Q psy3760         164 YQWEYVIIVPLDHPLLLL-NSISLKEIS---NYPLITYDLSFS-GRIKLDR-------------EFSLQKLT--------  217 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~-~~i~~~dl~---~~~~i~~~~~~~-~~~~~~~-------------~~~~~~~~--------  217 (306)
                      ....++++++++++.... .+.+|.||.   ..++...++... .......             ++......        
T Consensus        83 ~~~~lvi~~~~~~~~~~~i~~~~w~dll~~p~~~I~~~dp~~~~~G~~~~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~  162 (292)
T 3cfz_A           83 ARNEIVLAYTDKSKYKDEINSTNWYKILQRPDVKIGFSNPNDDPCGYRTQMVLQLAELYYKDPTIYDNLVLKHSNIKVEE  162 (292)
T ss_dssp             EECCEEEEECTTSTTTTTCCTTTHHHHTTSTTCCEEEECTTTCHHHHHHHHHHHHHHHHHTCTTHHHHHTGGGBSCEEEE
T ss_pred             EeccEEEEEcCCCccccCCCcccHHHHhcCCCcEEEeCCCCCCCCcHHHHHHHHHHHHhccCCcHHHHHhcccccccccc
Confidence            788999999999875422 345899943   345776665422 2111111             11111100        


Q ss_pred             ----------------eeEEEEecCHHHHHHHHHhcc-ceeeeecceecccccCCceeeecCCCC---------------
Q psy3760         218 ----------------PYIVLETINSDIIKTYVELRM-GIGIIASIAFDSNRDKNLRSISASHLF---------------  265 (306)
Q Consensus       218 ----------------~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~~~~~l~~~~~~~~~---------------  265 (306)
                                      .+......+...+..++.+|. .++++..+.+..   .++..+.++...               
T Consensus       163 ~~g~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~Ge~d~gi~~~s~a~~---~~~~~~~~P~~~~~~~~~~~~~~~~~~  239 (292)
T 3cfz_A          163 NNGTYLILVPKELDVDTNKLFVRSKETDLLAPLEAGAFDYLFIYKSVANQ---HHLKYIELPKEINLGYYEYADTYKKVA  239 (292)
T ss_dssp             ETTEEEEEECSSCCBCTTTEEEESSGGGGHHHHHTTSSSEEEEEHHHHHH---TTCEEECCCTTTSSCCGGGHHHHTTEE
T ss_pred             cCCcccccccccccccccceeecccHHHHHHHHHCCCCCEEEEEehhhhh---CCCCEEECChhhcccCccccchhhcee
Confidence                            001244566678889999984 677776554422   133334333321               


Q ss_pred             ------------ccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         266 ------------GTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       266 ------------~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                                  ......+...++......+++|+++|.
T Consensus       240 ~~~~~~~~~~~~~~i~~~~~i~k~a~~~~~A~~Fi~fl~  278 (292)
T 3cfz_A          240 LKIIAKNKTINAKPIVYGMTVPTNAPHKKEAIEFVKFVL  278 (292)
T ss_dssp             EEEGGGTEEEECCCCEEEEECCTTCTTHHHHHHHHHHHH
T ss_pred             eeeccccccccCCceeEEEEeecCCCCHHHHHHHHHHHH
Confidence                        113456677777777889999999998

>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=98.68  E-value=3.8e-08  Score=68.04  Aligned_cols=73  Identities=15%  Similarity=0.265  Sum_probs=60.6

Q ss_pred             chhhHHHHHHHHH-hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR-QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus         2 ~~~~l~~f~~v~~-~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      |...+++|..+.+ .. +++..|+.+++|||++|++|+.||+ .|...+.|.|++. ..+..+..+.+.++.+++.+
T Consensus        45 ~~~rl~IL~~L~~~~~-s~~ela~~lgis~stvs~~L~~Le~-~Glv~~~~~gr~~-~y~l~~~~l~~~~~~l~~~~  118 (122)
T 1r1t_A           45 DPNRLRLLSLLARSEL-CVGDLAQAIGVSESAVSHQLRSLRN-LRLVSYRKQGRHV-YYQLQDHHIVALYQNALDHL  118 (122)
T ss_dssp             CHHHHHHHHHHTTCCB-CHHHHHHHHTCCHHHHHHHHHHHHH-TTSEEEEEETTEE-EEEESSHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHH-CCCeEEEEeCCEE-EEEEChHHHHHHHHHHHHHH
Confidence            3456778888876 45 9999999999999999999999999 9999999998886 46666667777777777654

>2hxw_A Major antigenic peptide PEB3; periplasmic binding protein, N-glycosylation, structural genomics; HET: FLC; 1.60A {Campylobacter jejuni} PDB: 3fjm_A 3fjg_A 3fir_A* 3fj7_A*

Probab=98.64  E-value=9.5e-07  Score=68.90  Aligned_cols=191  Identities=19%  Similarity=0.133  Sum_probs=122.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc----CCCCC---c---eeecc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL----SPSDK---L---ISIPC  163 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~----~~~~~---~---~~~~l  163 (306)
                      .|+|.+..++ ...+..++..|.+++ ++++++...++.++..++. +.+|+++.....    ....+   +   ....+
T Consensus         2 ~l~v~~~~~~-~~~~~~~~~~F~~~~-gi~V~~~~~~s~~l~~~l~-~~~Dv~~~~~~~~~~~l~~~~~~~~~~~~~~~~   78 (237)
T 2hxw_A            2 DVNLYGPGGP-HTALKDIANKYSEKT-GVKVNVNFGPQATWFEKAK-KDADILFGASDQSALAIASDFGKDFNVSKIKPL   78 (237)
T ss_dssp             CEEEEECSST-HHHHHHHHHHHHHHH-CCCEEEEESSHHHHHHHHH-HHCSEEEESSHHHHHHHHTTSGGGCCGGGCEEE
T ss_pred             eEEEEeccch-HHHHHHHHHHHHHHh-CceEEEEeCChHHHHHHhc-cCCCEEEeCCHHHHHHHHHhcccccCccccccc
Confidence            3778777664 446788999999885 9999999899999999999 899999986410    01111   2   35567


Q ss_pred             ccceEEEEecCCCCCCCCCCcChhhhc--CCCeEeecCC-----CCcHHHHHHHHHhCC-------CceeEEEEecCHHH
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISLKEIS--NYPLITYDLS-----FSGRIKLDREFSLQK-------LTPYIVLETINSDI  229 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~~dl~--~~~~i~~~~~-----~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~  229 (306)
                      ....+++++++++|.   ...+|+||.  +.+++..++.     .+........+ ..+       +.++.....++...
T Consensus        79 ~~~~~~l~~~~~~~~---~~~sw~dL~~~~~~i~~~d~~~~~~~~~~g~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~  154 (237)
T 2hxw_A           79 YFREAIILTQKGNPL---KIKGLKDLANKKVRIVVPEGAGKSNTSGTGVWEDMIG-RTQDIKTIQNFRNNIVAFVPNSGS  154 (237)
T ss_dssp             EEEEEEEEESTTCTT---CCCSHHHHHHSCCCEEECCCTTSSCCTTTTHHHHHHH-TTCCHHHHHHHHHTEEEECCCCTT
T ss_pred             ccCceEEEEeCCCCC---CCCCHHHhcCCCcEEEecCCCCCCcccchHHHHHHHH-HccCHHHHHHHhhceEEEcCCHHH
Confidence            788999999998763   346899997  4566655431     11211222222 111       34565445566666


Q ss_pred             HHH-HHHhccceeeeecceecccccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         230 IKT-YVELRMGIGIIASIAFDSNRDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       230 ~~~-~v~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      +.+ ++..+..++++....+.. ..+.+..+|++... ....+.++..++.  .+.+++|++++.+.
T Consensus       155 ~~~~~~~g~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~--~~~A~~Fi~fl~s~  218 (237)
T 2hxw_A          155 ARKLFAQDQADAWITWIDWSKS-NPDIGTAVAIEKDLVVYRTFNVIAKEGA--SKETQDFIAYLSSK  218 (237)
T ss_dssp             C--CTTTTTCSEEEEEHHHHHH-STTSSEEEECCTTTCCEEEEEEEECTTC--CHHHHHHHHHTTSH
T ss_pred             HHHHHHcCCeeEEEEechhhhc-CCCceEEEecCCceeEEeeeeEEEccCC--hHHHHHHHHHHcCH
Confidence            665 666667777777654432 22456667766532 3445566666665  78999999999765

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=98.61  E-value=2.6e-07  Score=67.04  Aligned_cols=70  Identities=20%  Similarity=0.152  Sum_probs=56.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      ..++.-.... |.+..|+.+++|++++|+.|++||+. |  |+.|. ++++ .+|+.|+.++..+......++...
T Consensus        46 ~~~l~~~~~~-~~~~la~~l~vs~~tvs~~l~~Le~~-G--lv~r~~~~~~-~lT~~g~~~~~~~~~~~~~~~~~~  116 (155)
T 2h09_A           46 SDLIREVGEA-RQVDMAARLGVSQPTVAKMLKRLATM-G--LIEMIPWRGV-FLTAEGEKLAQESRERHQIVENFL  116 (155)
T ss_dssp             HHHHHHHSCC-CHHHHHHHHTSCHHHHHHHHHHHHHT-T--CEEEETTTEE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCc-CHHHHHHHhCcCHHHHHHHHHHHHHC-C--CEEEecCCce-EEChhHHHHHHHHHHHHHHHHHHH
Confidence            3344434556 99999999999999999999999998 7  45554 6777 799999999999888877766655

>3k6v_A Solute-binding protein MA_0280; MODA, molybdate, periplasmic BIN protein, ABC transporter, transport protein, ligand, metal- protein; HET: CIT; 1.69A {Methanosarcina acetivorans} PDB: 3k6u_A* 3k6w_A 3k6x_A

Probab=98.57  E-value=2.2e-05  Score=64.61  Aligned_cols=206  Identities=10%  Similarity=0.033  Sum_probs=132.3

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH-cC-CeeEEEEccccC----CCCCc--eeec
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR-ND-QADIAIVTEILS----PSDKL--ISIP  162 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~-~~-~~Di~i~~~~~~----~~~~~--~~~~  162 (306)
                      ..++|+|.+..++. ..+..+...|.+++|++++++...++..+..++. .| .+|+.++.....    ...++  ....
T Consensus        41 ~a~~L~V~~a~sl~-~~~~~l~~~Fe~~~pgv~V~~~~ggSg~l~~qi~e~G~~aDVf~sad~~~~~~l~~~g~~~~~~~  119 (354)
T 3k6v_A           41 EGEVLTVFHAGSLS-VPFEELEAEFEAQHPGVDVQREAAGSAQSVRKITELGKKADVLASADYALIPSLMVPEYADWYAA  119 (354)
T ss_dssp             --CEEEEEEEGGGH-HHHHHHHHHHHHHSTTCEEEEEEECHHHHHHHHHTSCCCCSEEEESSTTHHHHHTTTTTCSCEEE
T ss_pred             CCCcEEEEEecchH-HHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHhcCCCccEEEECCHHHHHHHHhCCCCCCceE
Confidence            34579999988754 4678899999999999999999999999999995 34 799999853210    12232  3567


Q ss_pred             cccceEEEEecCCCCCCCC-CCcC-hhhhc--CCCeEeecCCCC-cHHHHHHHHH-------------hC-----CCc--
Q psy3760         163 CYQWEYVIIVPLDHPLLLL-NSIS-LKEIS--NYPLITYDLSFS-GRIKLDREFS-------------LQ-----KLT--  217 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~~-~~i~-~~dl~--~~~~i~~~~~~~-~~~~~~~~~~-------------~~-----~~~--  217 (306)
                      +....+++++++++|.... ..-+ +++|.  +..+...++... ....-.+.++             ..     ++.  
T Consensus       120 ~a~n~lVliv~~~~p~~~~I~~~~~~~~L~~~~~riai~~P~~~P~G~~a~~~l~~a~~~~~~~gl~~~l~~~~~~v~l~  199 (354)
T 3k6v_A          120 FARNQMILAYTNESKYGDEINTDNWYEILRRPDVRYGFSNPNDDPAGYRSQMVTQLAESYYNDDMIYDDLMLANTGMTLT  199 (354)
T ss_dssp             EEECCEEEEECTTSTTTTTCCTTTHHHHHHSTTCCEEEECTTTCHHHHHHHHHHHHHHHHHTCTTHHHHHTGGGSSCEEE
T ss_pred             eECCeEEEEEECCCccccccCcccHHHHhcCCCCEEEEcCCCCCChHHHHHHHHHHHHhhcccccHHHHHhhhccccccc
Confidence            8888999999999875311 1113 46776  356777776542 2221111111             11     110  


Q ss_pred             --------------------eeEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCCC-----------
Q psy3760         218 --------------------PYIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHLF-----------  265 (306)
Q Consensus       218 --------------------~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~~-----------  265 (306)
                                          .+......+...+...+..| .-++++..+.+..   .++.+++++...           
T Consensus       200 ~~~~g~~~~~~p~~~~~~~~~~k~v~~~~v~~~l~~v~~G~aDag~vy~S~a~~---~~l~~v~lP~~~n~~~~~~~~~y  276 (354)
T 3k6v_A          200 TEENGTALIHVPASEEISPNTSKIMLRSMEVELSSALETGEIDYLYIYRSVAEQ---HGFEYVALPPAIDLSSLEYADNY  276 (354)
T ss_dssp             ECTTSCEEEECCCHHHHCCCTTTEEEESSHHHHHHHHHHTSCSEEEEEHHHHHH---HTCEEEECCTTTSSCCGGGHHHH
T ss_pred             cccCcccccccccccccccccceeEeCCCHHHHHHHHHcCCCCEEEEEhhhhhh---cCCcEEeCChhhccccccccccc
Confidence                                12345678899999999998 4455555544433   135666665421           


Q ss_pred             ---------------ccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         266 ---------------GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       266 ---------------~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                                     ....+.+...++....+..++|+++|.+.-.+...
T Consensus       277 ~~v~v~~~~~~~~~~~Pi~y~~ai~k~a~~~~~A~~Fi~fL~S~eaq~i~  326 (354)
T 3k6v_A          277 SKVQVEMVNGEVVTGSPIVYGVTIPNNAENSELATEFVALLLGETGQQIF  326 (354)
T ss_dssp             TTEEEECTTSCEEECCCCEEEEECCTTCTTHHHHHHHHHHHHSHHHHHHH
T ss_pred             cceeeeccccccccCCceeEeEEeecCCCCHHHHHHHHHHHcCHHHHHHH
Confidence                           12356666677777778999999999865444333

>3ksx_A Nitrate transport protein; SSUA, alkanesulfonate-binding protein, periplasmic-binding P transport protein; HET: MPO; 1.70A {Xanthomonas axonopodis PV} PDB: 3e4r_A* 3ksj_A*

Probab=98.56  E-value=8.1e-06  Score=66.81  Aligned_cols=200  Identities=14%  Similarity=0.111  Sum_probs=124.3

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeecc
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPC  163 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l  163 (306)
                      ....+||||+.+.....++......|.+..+++++++... +...+.+.|.+|++|++++....     .....+.....
T Consensus        26 ~~~~~lrig~~~~~~p~~~a~~~g~~~~~~~g~~v~~~~~~~~~~~~~al~~G~~D~~~~~~~~~~~~~~~g~~~~~v~~  105 (324)
T 3ksx_A           26 AEPAQLRIGYQKAVSSLVLAKQHRLLEQRFPRTKITWVEFPAGPQLLEALNVGSIDLGGAGDIPPLFAQAAGADLLYVGW  105 (324)
T ss_dssp             CCCSEEEEEEETTCHHHHHHHHHTHHHHHCTTSEEEEEEESSHHHHHHHHHTTSCSEEEEESHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCeEEEEecCCchhHHHHHhhCHHHHhcCCCceEEEECCCHHHHHHHHHCCCCCEEeecCHHHHHHHhcCCCEEEEEE
Confidence            3456899999987665666666677888888999999874 66788999999999999874211     11222222211


Q ss_pred             ---ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHHhcc-
Q psy3760         164 ---YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRM-  238 (306)
Q Consensus       164 ---~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~-  238 (306)
                         ......++++++.+.     -+++||.+.++... .+......+..++...|+.+. +.+..-+...+..++.+|. 
T Consensus       106 ~~~~~~~~~lvv~~~s~I-----~s~~DLkGk~i~v~-~gs~~~~~~~~~l~~~Gl~~~~v~~v~~~~~~~~~al~~G~v  179 (324)
T 3ksx_A          106 VPPTPKAETILVPSKSAL-----RTVADLKGKRIAFQ-KGSSAHNLLLRVLAKSGLSMRDITPLYLSPANARAAFAAGQV  179 (324)
T ss_dssp             ECCCGGGEEEEEETTCSC-----CSGGGGTTCEEEEC-TTSHHHHHHHHHHHHTTCCGGGSEEEECCHHHHHHHHHTTCC
T ss_pred             ecCCCCceEEEEeCCCCC-----CCHHHhCCCEEEec-CCChHHHHHHHHHHHcCCCHHHeEEEeCCHHHHHHHHHcCCC
Confidence               123577888887653     37899998887665 555555567788999998763 2333336778888888883 


Q ss_pred             ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                      -.++++....... ..+..+.+...........+++.+++.  ..+..++.|++.+.+..
T Consensus       180 Da~~~~~p~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a~  239 (324)
T 3ksx_A          180 DAWAIWDPWYSALTLDGSARLLANGEGLGLTGGFFLSSRRYATAWGPFVQQVMGTLNQAD  239 (324)
T ss_dssp             SEEEEETTHHHHHHHTTSEEEEEESTTSCCCCEEEEEEHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             CEEEEccHHHHHHHhcCCcEEEecccccCCCccEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence            2233444333222 334555443222222222334444432  23567788887776554

>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics, GLUT seattle structural genomics center for infectious disease; 2.40A {Burkholderia pseudomallei}

Probab=98.51  E-value=6.5e-06  Score=64.51  Aligned_cols=198  Identities=10%  Similarity=0.006  Sum_probs=124.1

Q ss_pred             CCCcEEEEecccch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          91 DTGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        91 ~~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      ..+.|+||+.....          ..+...++..+.++. ++++++...+..+++..+.+|++|+++......  ....+
T Consensus        22 ~~~~l~v~~~~~~~P~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~  100 (249)
T 4f3p_A           22 MAKELVVGTDTSFMPFEFKQGDKYVGFDLDLWAEIAKGA-GWTYKIQPMDFAGLIPALQTQNIDVALSGMTIKEERRKAI  100 (249)
T ss_dssp             --CCEEEEEESCBTTTBEEETTEEESHHHHHHHHHHHHH-TCCEEEEEECGGGHHHHHHTTSCSEEEEEEECCHHHHTTE
T ss_pred             cCceEEEEeCCCCCCeEEecCCeEEEEhHHHHHHHHHHc-CCceEEEecCHHHHHHHHHCCCCCEEEeccccCHHHHcCc
Confidence            45789999973221          246777888877764 788888888899999999999999977431111  11222


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                       -+.++.....+++++++.+    ..-+++||.+..+.... +...    ..++..... ......+++...++.++.+|
T Consensus       101 ~~s~p~~~~~~~~~~~~~~~----~i~~~~dL~g~~i~v~~-g~~~----~~~l~~~~~-~~~~~~~~~~~~~~~~L~~G  170 (249)
T 4f3p_A          101 DFSDPYYDSGLAAMVQANNT----TIKSIDDLNGKVIAAKT-GTAT----IDWIKAHLK-PKEIRQFPNIDQAYLALEAG  170 (249)
T ss_dssp             EECSCCEEEEEEEEEETTCC----SCCSSGGGTTSEEEEET-TSHH----HHHHHHHCC-CSEEEEESSHHHHHHHHHTT
T ss_pred             ceecceeeccEEEEEECCCC----CcCChHHhCCCEEEEeC-CChH----HHHHHhcCC-CceEEEcCCHHHHHHHHHcC
Confidence             2457888899999998874    23578999888766554 3322    333433322 23456778999999999999


Q ss_pred             cc-eeeeecceeccc--c--cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         238 MG-IGIIASIAFDSN--R--DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       238 ~g-i~~~p~~~~~~~--~--~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .. ..+.+...+...  .  ...+...+..  ....+++++.+++..   ....|-+.|++.-+....+++.
T Consensus       171 rvDa~i~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~k~~~---l~~~l~~~l~~l~~~g~~~~i~  237 (249)
T 4f3p_A          171 RVDAAMHDTPNVLFFVNNEGKGRVKVAGAP--VSGDKYGIGFPKGSP---LVAKVNAELARMKADGRYAKIY  237 (249)
T ss_dssp             SSSEEEEEHHHHHHHHHTTTTTTEEEEEEE--EEEEEEEEEEETTCT---HHHHHHHHHHHHHHHTHHHHHH
T ss_pred             CeeEEEeCcHHHHHHHHhCCCCceEEecCC--CCCccEEEEEcCCch---HHHHHHHHHHHHHhCCcHHHHH
Confidence            54 344444433332  1  2335554432  234577888888763   5555555555544444555543

>3kzg_A Arginine 3RD transport system periplasmic binding protein; arginine transport system, protein structure initiative II(PSI II); 2.06A {Legionella pneumophila subsp} SCOP: c.94.1.0

Probab=98.51  E-value=2.2e-06  Score=66.72  Aligned_cols=199  Identities=10%  Similarity=0.014  Sum_probs=126.2

Q ss_pred             CCcEEEEecccch------------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          92 TGNLTIATTHTQA------------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        92 ~~~l~I~~~~~~~------------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      .++|+||+.....            ..+...++..+.++. ++.+++...+..++++.+.+|++|+++......  ....
T Consensus         2 ~~~l~v~~~~~~~P~~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~   80 (237)
T 3kzg_A            2 SLNLTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRL-HATCTFEAYIFDDLFPALKNREVDLVIASMIITDERKKH   80 (237)
T ss_dssp             CCEEEEEEESEETTTEECCCTTSCCBSHHHHHHHHHHHHT-TCEEEEEEECGGGHHHHHHTTSSSEECSSCBCCTTGGGT
T ss_pred             CceEEEEECCCCCCeEEEeCCCCCEeeehHHHHHHHHHHh-CCceEEEEcCHHHHHHHHhCCCCCEEEEccccChhHhcc
Confidence            4678888865211            245567888887774 799999988999999999999999887532211  1223


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. +.++.....+++++++.+     .-+++||.+..+.... +......    +...... .....+++...++.++.+
T Consensus        81 ~~fs~p~~~~~~~~~~~~~~~-----~~~~~dL~g~~i~~~~-g~~~~~~----~~~~~~~-~~~~~~~~~~~~~~~l~~  149 (237)
T 3kzg_A           81 FIFSLPYMESNSQYITTVDSK-----ISTFDDLHGKKIGVRK-GTPYARQ----VLSENRN-NQVIFYELIQDMLLGLSN  149 (237)
T ss_dssp             CEECCCSBCCEEEEEEETTCS-----CCSGGGGTTCEEEEET-TSTHHHH----HHHTCSS-CEEEEESSHHHHHHHHHT
T ss_pred             ceeeeeeeecceEEEEECCCC-----CCCHHHhCCCEEEEec-CCHHHHH----HHHhCCC-CcEEEeCCHHHHHHHHHc
Confidence            33 457889999999999886     3478999987766654 3332222    2222211 345678899999999999


Q ss_pred             ccce-eeeecceeccc--ccC--------CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         237 RMGI-GIIASIAFDSN--RDK--------NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       237 g~gi-~~~p~~~~~~~--~~~--------~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      |..= .+.+...+...  ..+        ++..++.+. ....+++++.+++  .......|-+.|++.-+....+++.+
T Consensus       150 G~vDa~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-~~~~~~~~~~~k~--~~~l~~~l~~~l~~l~~~G~~~~i~~  226 (237)
T 3kzg_A          150 NQVDASLMDYEAAKYWMASEPYAYKLIGKKYKLIGKKI-SIGEGYSIMANPD--QFVLIKKINKILLEMEADGTYLRLYS  226 (237)
T ss_dssp             TSSSEEEEEHHHHHHHHTTSSTTHHHHCCSEEEEEEEE-ECTTCBCCEECGG--GHHHHHHHHHHHHHHHHSSHHHHHHH
T ss_pred             CCCCEEEeCcHHHHHHHHhCCccccccCCceEEecCcc-ccCccEEEEEcCC--CHHHHHHHHHHHHHHHHCCcHHHHHH
Confidence            9543 34444333332  223        555554322 1334667777776  24555666666666555556665543

>4gvo_A LMO2349 protein; structural genomics, IDP05245, L-cystine, ABC transporter, periplasmic binding protein, niaid; HET: HIS; 1.45A {Listeria monocytogenes} PDB: 2o1m_A

Probab=98.51  E-value=1.7e-06  Score=67.77  Aligned_cols=208  Identities=13%  Similarity=0.098  Sum_probs=123.1

Q ss_pred             CCCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CC
Q psy3760          90 YDTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SD  156 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~  156 (306)
                      ...++|+||+...+.           ..+...++..+.++.+++++++...+...++..|.+|++|+++......+  ..
T Consensus         6 ~~~~tl~vg~~~~~pP~~~~d~~G~~~G~~vdl~~~ia~~l~g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR~~   85 (243)
T 4gvo_A            6 QKVQTITVGTGTQFPNVCFLDENGKLTGYDVELVKEIDKRLPGYKFKFKTMDFSNLLVSLGAGKVDIVAHQMEKSKEREK   85 (243)
T ss_dssp             --CEEEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHTCTTEEEEEEECCGGGHHHHHHTTSCSEECSCCBCCHHHHH
T ss_pred             ccCCeEEEEECCCCCCeEEECCCCcEEEhHHHHHHHHHHhccCCeEEEEECCHHHHHHHHHCCCCCEecccCCCCHHHhh
Confidence            346789999864322           23567788888887779999999999999999999999999875311111  11


Q ss_pred             Cce-eeccc-cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHH
Q psy3760         157 KLI-SIPCY-QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYV  234 (306)
Q Consensus       157 ~~~-~~~l~-~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  234 (306)
                      .+. +.+.+ .....+++.++.+    ..-+++||.+....... +......+..+....+......+...+...++.++
T Consensus        86 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~~dL~g~~v~v~~-gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L  160 (243)
T 4gvo_A           86 KFLFNDVAYNNFPLQLTVLDSNN----SINSTKDLAGKRVITSA-TSNGALVLKKINEEQGNNFEIAYEGQGSNDTANQL  160 (243)
T ss_dssp             HSEECSSCCEECCEEEEEETTCC----SCSSGGGGTTCEEEECT-TCHHHHHHHHHHHHTTSCSEEEECCSGGGSHHHHH
T ss_pred             hhhhhhhhcccccceEEEecccc----ccCchHHhcCCeEEEec-CchHHHHHHHHHHhccccceeccccCChHHHHHHH
Confidence            233 23433 3455566655543    23478999888776554 33333455566666666566666778888899999


Q ss_pred             Hhccceeeeeccee-ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         235 ELRMGIGIIASIAF-DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       235 ~~g~gi~~~p~~~~-~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ..|..=+++..... ... ....+....+.......++++..+++.  +.....|=+.|++.-+....+++.
T Consensus       161 ~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~--~~l~~~in~~l~~l~~~G~~~~i~  230 (243)
T 4gvo_A          161 KTGRADATISTPFAVDFQNKTSAIKEKVVGDVLSNAKVYFMLGKDE--TKLSKKVDEALQSIIDDGTLKKLS  230 (243)
T ss_dssp             HHTSCSBEEECHHHHHHHHHTCSSCEEEEEEEEECCEECCEECTTC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             HcCCccEEEccHHHHHHHHhhCCCceEEeccCCCCCcEEEEEeCCC--HHHHHHHHHHHHHHHhCcHHHHHH
Confidence            99955444443222 222 223332222222233446777777763  334444444444443333444443

>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic, transport protein; 1.90A {Salmonella enterica} PDB: 3r39_A 4f3s_A

Probab=98.51  E-value=6.8e-06  Score=64.88  Aligned_cols=202  Identities=12%  Similarity=0.071  Sum_probs=128.3

Q ss_pred             CCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          91 DTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ..+.|+||+.....           ..+...++..+.++. ++++++...+..++.+.+.+|++|+++......  ....
T Consensus        27 ~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~  105 (259)
T 4dz1_A           27 EGRTLNVAVSPASPPMLFKSADGKLQGIDLELFSSYCQSR-HCKLNITEYAWDGMLGAVASGQADVAFSGISITDKRKKV  105 (259)
T ss_dssp             TTCEEEEEECCCBTTTBEECTTCCEESHHHHHHHHHHHHH-TCEEEEEECCHHHHHHHHHHTSSSEEEEEEECCHHHHTT
T ss_pred             cCCeEEEEECCCCCCeEEECCCCCEEEeHHHHHHHHHHHh-CCeEEEEEcCHHHHHHHHhCCCCCEEEECCcCCHHHhhc
Confidence            45789999974311           235556777776654 789999999999999999999999977531111  1222


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHH
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVE  235 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~  235 (306)
                      +. +.+++....++++.++.+.   ..-+++||.+....... +......+.+.+...|+.+ .....+++...++.++.
T Consensus       106 ~~fs~p~~~~~~~~~~~~~~~~---~i~~~~dL~g~~v~v~~-g~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~  181 (259)
T 4dz1_A          106 IDFSEPYYINSFYLVSMANHKI---TLNNLNELNKYSIGYPR-GMAYSDLIKNDLEPKGYYSLSKVKLYPTYNETMADLK  181 (259)
T ss_dssp             EEECCCSEEEEEEEEEETTSCC---CCCSGGGGGGSCEEEET-TSTHHHHHHHHTGGGTSCCGGGCEEESSHHHHHHHHH
T ss_pred             cccccchhhCceEEEEEcCCCC---CCCCHHHhCCCEEEEeC-CcHHHHHHHHhcccccccccceeEecCCHHHHHHHHH
Confidence            32 4578888888888776531   23478999998877654 4445566666666666654 34556789999999999


Q ss_pred             hcccee-eeecceeccc-c--cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         236 LRMGIG-IIASIAFDSN-R--DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       236 ~g~gi~-~~p~~~~~~~-~--~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      +|..=+ +.....+..+ .  ...+.....  .....++++..+++.   +....|-+.|++ -....++++
T Consensus       182 ~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~k~~---~l~~~ln~~l~~-~g~~~l~~~  247 (259)
T 4dz1_A          182 NGNLDLAFIEEPVYFTFKNKKKMPIESRYV--FKNVDQLGIAFKKGS---PVRDDFNLWLKE-QGPQKISGI  247 (259)
T ss_dssp             HTSCSEEEEEHHHHHHHHHTSCCCEEEEEE--EEEEEEEEEEEETTC---HHHHHHHHHHHH-HCHHHHHHH
T ss_pred             cCCCCEEEecHHHHHHHhccCCCceEeecc--cCCCceEEEEEeCCh---HHHHHHHHHHHh-CCCeehHHH
Confidence            994433 3444333222 1  223333222  123457888888875   466666666665 333333433

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=98.49  E-value=6.9e-07  Score=63.92  Aligned_cols=77  Identities=16%  Similarity=0.315  Sum_probs=63.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-----CccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-----RIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-----~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ++..++.++..+.+.+.|++.-|+.+++|+|++|+.|++||+. |.--..+++.     .+ .||+.|+.+++.+.....
T Consensus        35 lt~~~~~iL~~l~~~~~~~~~la~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~~~~~  112 (144)
T 3f3x_A           35 LSYLDFSILKATSEEPRSMVYLANRYFVTQSAITAAVDKLEAK-GLVRRIRDSKDRRIVIV-EITPKGRQVLLEANEVLR  112 (144)
T ss_dssp             CCHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEE-EECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEeccCCCCCceEEE-EECHHHHHHHHHHHHHHH
Confidence            3567888999998876589999999999999999999999998 6655554432     35 899999999999888877


Q ss_pred             HHHH
Q psy3760          76 EIEG   79 (306)
Q Consensus        76 ~~~~   79 (306)
                      .+.+
T Consensus       113 ~~~~  116 (144)
T 3f3x_A          113 NLVN  116 (144)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>3h7m_A Sensor protein; histidine kinase sensor domain, kinase, phosphoprotein, transferase; 2.40A {Geobacter sulfurreducens} SCOP: c.94.1.0

Probab=98.49  E-value=1.4e-05  Score=61.67  Aligned_cols=201  Identities=9%  Similarity=0.033  Sum_probs=126.9

Q ss_pred             cCCCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCC
Q psy3760          89 AYDTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSD  156 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~  156 (306)
                      ....++|+||+.....           ..+...++..+.++. ++++++...+..++...+.+|++|++...... ....
T Consensus         7 ~~~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~r~~   85 (234)
T 3h7m_A            7 RDRHRTIVVGGDRDYPPYEFIDQNGKPAGYNVELTRAIAEVM-GMTVEFRLGAWSEMFSALKSGRVDVLQGISWSEKRAR   85 (234)
T ss_dssp             CCSSSCEEEEEETEETTTEEECTTSCEESHHHHHHHHHHHHH-TCCEEEEEECGGGHHHHHHTTSSSEEEEEECCHHHHT
T ss_pred             cCCCCEEEEEecCCCCCeEEECCCCCEeeeEHHHHHHHHHHc-CCceEEEeCCHHHHHHHHhCCCeeEEEeccCCHhHHh
Confidence            3456789999853221           246677777777664 78888888899999999999999996432211 1112


Q ss_pred             Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+ -+.++.....+++++++.+    ..-+++||.+..+......     ....++...+... ....+++...++.++.
T Consensus        86 ~~~~s~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~i~~~~g~-----~~~~~l~~~~~~~-~~~~~~~~~~~~~~l~  155 (234)
T 3h7m_A           86 QIDFTPPHTIVYHAIFARRDSP----PAAGLEDLRGRKVALHRDG-----IMHEYLAERGYGK-DLVLTPTPADALRLLA  155 (234)
T ss_dssp             TEEEEEEEEEEEEEEEEESSSC----CCSSGGGGTTSCEEEETTS-----HHHHHHHTTTCGG-GEEEESSHHHHHHHHH
T ss_pred             hcCCCccccccceEEEEECCCC----CCCCHHHhCCCEEEEEeCc-----hHHHHHHhcCCCc-eEEEeCCHHHHHHHHH
Confidence            22 3567788889999999876    2347899999988776532     2345566655433 3456789999999999


Q ss_pred             hccc-eeeeecceeccc-c---cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMG-IGIIASIAFDSN-R---DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~-~---~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|.. ..+.+....... .   ...+...+..  ....++++..+++.  ......|-+.|.+.-+....+++.
T Consensus       156 ~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~~l~~~l~~~l~~l~~~g~~~~i~  225 (234)
T 3h7m_A          156 AGGCDYAVVAMVPGMYIIRENRLTNLVPVARS--IAAQRYGYAVRQGD--AELLARFSEGLAILRKTGQYEAIR  225 (234)
T ss_dssp             TTSSSEEEEEHHHHHHHHHHTTCTTEEEEEEE--EEEEEEEEEEETTC--HHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             cCCceEEEeccHHHHHHHHhcCCCceEEeccc--cCCCceEEEEeCCC--HHHHHHHHHHHHHHHHcCcHHHHH
Confidence            9944 334444333222 1   2334444322  23456777777763  345555555555554444555554

>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella enterica subsp}

Probab=98.47  E-value=1e-05  Score=62.34  Aligned_cols=199  Identities=9%  Similarity=-0.000  Sum_probs=121.9

Q ss_pred             CCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          91 DTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ..+.|+||+.....           ..+...++..+.++. ++++++...+..++...+.+|++|+++......  ....
T Consensus         4 ~a~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~   82 (229)
T 2y7i_A            4 SARTLHFGTSATYAPYEFVDADNKIVGFDIDVANAVCKEM-QAECSFTNQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQ   82 (229)
T ss_dssp             SCCEEEEEECCCBTTTBEECTTSCEESHHHHHHHHHHHHT-TCEEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHTT
T ss_pred             cCCcEEEEeCCCcCCceEECCCCCCcceeHHHHHHHHHHh-CCeEEEEEcCHHHHHHHHhCCCceEEEecCccCHHHhcc
Confidence            35689999863211           235667888888876 889999998999999999999999998421111  1123


Q ss_pred             ce-eeccccc-eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         158 LI-SIPCYQW-EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       158 ~~-~~~l~~~-~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      +. +.++... ..++++++++      .-+++||.+.++.... +....    .++...... .....+++...++.++.
T Consensus        83 ~~~s~p~~~~~~~~~~~~~~~------~~~~~dL~g~~v~~~~-g~~~~----~~l~~~~~~-~~~~~~~~~~~~~~~l~  150 (229)
T 2y7i_A           83 VSFSQPYYEGLSAVVVTRKGA------YHTFADLKGKKVGLEN-GTTHQ----RYLQDKQQA-ITPVAYDSYLNAFTDLK  150 (229)
T ss_dssp             SEECSCSBCCCCEEEEEETTS------CCSTGGGTTCEEEEET-TSHHH----HHHHHHCTT-SEEEEESCHHHHHHHHH
T ss_pred             eeeccccccCCcEEEEEeCCC------CCCHHHHCCCEEEEec-CCcHH----HHHHHhCCC-CeEEecCCHHHHHHHHH
Confidence            33 4478888 9999999886      3478999988866544 33332    233332211 23456789999999999


Q ss_pred             hccceee-eecceeccc--ccCCceeeecCCCCc---cceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMGIGI-IASIAFDSN--RDKNLRSISASHLFG---TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~gi~~-~p~~~~~~~--~~~~l~~~~~~~~~~---~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|..=++ .+.......  ..+++..++......   ..+++++.+++.  ......|-+.|.+.-+....+++.
T Consensus       151 ~grvDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~~l~~l~~~g~~~~i~  223 (229)
T 2y7i_A          151 NNRLEGVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDN--DALLQEINAALDKVKASPEYAQMQ  223 (229)
T ss_dssp             TTSCSEEEEEHHHHHHHHTTCTTEEECSCCBCCTTTSCCCBCCEECTTC--HHHHHHHHHHHHHHHTSHHHHHHH
T ss_pred             cCCcCEEEechHHHHHHHHhCCCeEEeccccccccccccceEEEEeCCC--HHHHHHHHHHHHHHHhCChHHHHH
Confidence            9954444 333333222  234566554322111   236677777662  345555555555544444455443

>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid; transport protein, solute-binding protein; 2.26A {Neisseria gonorrhoeae}

Probab=98.47  E-value=4.1e-06  Score=67.46  Aligned_cols=196  Identities=9%  Similarity=0.090  Sum_probs=119.4

Q ss_pred             CcEEEEecccch-----------hhhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          93 GNLTIATTHTQA-----------RYALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        93 ~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      +.|+||+.....           ..+...++..+.++.  |++++++...+..++.+.|.+|++|+++......  ....
T Consensus        55 ~~l~vg~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~~~~g~~v~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~  134 (291)
T 2yjp_A           55 GVIRIGVFGDKPPFGYVDANGKNQGFDVEIAKDLAKDLLGSPDKVEFVLTEAANRVEYVRSGKVDLILANFTQTPERAEA  134 (291)
T ss_dssp             TCEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHHHSCGGGEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHTT
T ss_pred             CeEEEEEcCCCCCceEECCCCCEeehHHHHHHHHHHHhccCCceEEEEEccHHHHHHHHhCCCeeEEEeCCCCChHHHcc
Confidence            579999853211           235566777777665  7899999998899999999999999998532111  1122


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. ..++.....+++++++.+     .-+++||.+..+... .+......+...    ... .....+++...+..++.+
T Consensus       135 ~~~~~p~~~~~~~l~~~~~~~-----i~sl~dL~gk~v~~~-~g~~~~~~l~~~----~~~-~~~~~~~~~~~~~~~l~~  203 (291)
T 2yjp_A          135 VDFADPYMKVALGVVSPKNKP-----ITDMAQLKDQTLLVN-KGTTADAFFTKS----HPE-VKLLKFDQNTETFDALKD  203 (291)
T ss_dssp             EEECCCCEEECEEEEEETTSC-----CCSGGGGTTSEEEEE-TTSHHHHHHHHH----CTT-SEEEEESSHHHHHHHHHT
T ss_pred             ceeccCeeecceEEEEeCCCC-----CCCHHHhCCCEEEEe-cCCcHHHHHHHh----CCC-ceEEEeCCHHHHHHHHHc
Confidence            33 356777888999998873     347899998876654 443333333322    211 234567899999999999


Q ss_pred             ccce-eeeecceeccc--ccCCceeeecCCCCccceE-EEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         237 RMGI-GIIASIAFDSN--RDKNLRSISASHLFGTTIS-RVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       237 g~gi-~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      |..= ++.+...+...  ..+.+..++...  ....+ +++.+++.  ....+.|-+.|.+.-+....+++
T Consensus       204 G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~k~~--~~l~~~l~~al~~l~~~g~~~~i  270 (291)
T 2yjp_A          204 GRGVALAHDNALLWAWAKENPNFEVAIGNL--GPAEFIAPAVQKGN--ADLLNWVNGEIAAMKKDGRLKAA  270 (291)
T ss_dssp             TSSSEEEEEHHHHHHHHHHCTTEEEEECCS--SSCEEECCEEETTC--HHHHHHHHHHHHHHHHHSHHHHH
T ss_pred             CCccEEEecHHHHHHHHHhCCCeEEcCCcc--cCCcceEEEEeCCC--HHHHHHHHHHHHHHHhCChHHHH
Confidence            9443 34444433332  334555554322  23355 67777763  33455555555444444344444

>3cg1_A UPF0100 protein PF0080; ABC transporter, binding protein, molybdate, tungstate, ligand, unknown function, transport protein; 1.60A {Pyrococcus furiosus} PDB: 3cg3_A

Probab=98.46  E-value=2.5e-06  Score=68.92  Aligned_cols=199  Identities=14%  Similarity=0.052  Sum_probs=124.2

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHH---HhCCCcEEEE--EeCChhHHHHHHHc-C-CeeEEEEccccC----CCCCc--
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFT---IQFPKVKLSL--LQGNPKQITEMIRN-D-QADIAIVTEILS----PSDKL--  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~---~~~p~~~i~~--~~~~~~~~~~~l~~-~-~~Di~i~~~~~~----~~~~~--  158 (306)
                      .++|+|.+..++ ...+..++..|.   ++||++++++  ...++.++..++.+ | .+|+.+......    ...++  
T Consensus         4 ~~~l~v~~~~~~-~~~~~~~~~~F~~~~~~~~gi~V~~~~~~~~s~~l~~~i~~~g~~~Dv~~~~~~~~~~~l~~~g~~~   82 (296)
T 3cg1_A            4 EVTLIVFHAGSL-SVPFQEVEKEFSEYAERNLGIKVSFQDEASGSVMAVRKVTDLGRKADVIGVADYTLIPQLLIPNYTD   82 (296)
T ss_dssp             CEEEEEEEEGGG-HHHHHHHHHHHHHHHHHHHSCCEEEEEEEECHHHHHHHHHTSCCCCSEEEESSTTHHHHHTTTTTCS
T ss_pred             ccEEEEEEccch-HHHHHHHHHHHHHHHHhCCCceEEEEeecCCHHHHHHHHHhCCCCCCEEEECChhHHHHHhcCCCCC
Confidence            457999887664 446788999999   8899999999  88899999999988 5 699999853211    12222  


Q ss_pred             eeeccccceEEEEecCCCCCCC---CCCcChhhhcC---CCeEeecCCCC-cHH----HHH--------HHHHhCC-C--
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLL---LNSISLKEISN---YPLITYDLSFS-GRI----KLD--------REFSLQK-L--  216 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~---~~~i~~~dl~~---~~~i~~~~~~~-~~~----~~~--------~~~~~~~-~--  216 (306)
                      ...++....+++++++++|...   ..+.+|.||..   .++.+.++... ...    .+.        .+++... .  
T Consensus        83 ~~~~~~~~~~vi~~~~~~~~~~~i~~~p~sw~dll~~p~~~i~~~~p~~~~~G~~~~~~~~~~~~~~~~~~~~~l~~~~~  162 (296)
T 3cg1_A           83 FYVLFATNEIVIAFTDKSRYVEEMKSNPDKWYEILAREDVRFGFSDPNQDPCGYRSLMVIKLADLYYGKEIFKELIEENT  162 (296)
T ss_dssp             CCEEEEECCEEEEECTTSTTHHHHHHCGGGHHHHHTSTTCCEEEECTTTCHHHHHHHHHHHHHHHHHTSCHHHHHTTTTB
T ss_pred             cceecccccEEEEEcCCCchhcccCCCCCCHHHHhcCCCcEEEeCCCCCCchhHHHHHHHHHHHHhcchhHHHHHHhccc
Confidence            3567778899999999987421   23468999642   34666655421 211    111        1121111 1  


Q ss_pred             -----------------ceeEEEEecCHHHHHHHHHhcc-ceeeeecceecccccCCceeeecCCC--------------
Q psy3760         217 -----------------TPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSNRDKNLRSISASHL--------------  264 (306)
Q Consensus       217 -----------------~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~~~~~l~~~~~~~~--------------  264 (306)
                                       .++......+...+.+++.+|. .++++....+...   .+..++++..              
T Consensus       163 ~~~~g~~~~l~~~~~~~~~~~~~~~~~~~~~~~~v~~Ge~~~~i~~~s~a~~~---~~~~~~~p~~~~~~~~~~~~~~~~  239 (296)
T 3cg1_A          163 NIYSNGTQIYAPKEITVNPGKIVIRPKETDLLGLVESGSIDYIFIYKSVAKQH---NLSYITLPSEINLGDFSKEKFYGQ  239 (296)
T ss_dssp             SCEEETTEEEECSSCCBCTTTEEEESSGGGGHHHHHHTSSSEEEEEHHHHHHT---TCEEEECCTTTSSCCGGGHHHHTT
T ss_pred             ccccCccccccccccccccccceecCchHHHHHHHhCCCCCEEEEEhhHHHHc---CCCeEecChhhccccccccccccc
Confidence                             0112344556667888899884 6666655443221   2222222211              


Q ss_pred             -------------CccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         265 -------------FGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       265 -------------~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                                   .......+...++......+++|+++|.+.
T Consensus       240 v~~~~p~~g~~~~~~~~~~~~~i~k~a~~~~~A~~Fi~fl~s~  282 (296)
T 3cg1_A          240 ISITLGSTGKTIKAKPIVYGVTVLKDAPNREVAIEFLRYLLSE  282 (296)
T ss_dssp             CEEEETTTCCEEECCCCEEEEEECTTCTTHHHHHHHHHHHHSH
T ss_pred             eeEEecCCcccccCceeeeeEEEeCCCCCHHHHHHHHHHHhCh
Confidence                         112355666777777788999999999764

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

Probab=98.45  E-value=4.9e-07  Score=65.04  Aligned_cols=75  Identities=19%  Similarity=0.250  Sum_probs=59.7

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .|.+..|+.+++|+|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+.+
T Consensus        38 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-G--lv~r~~~~~D~R~~~~-~lT~~G~~~~~~~~~  113 (148)
T 3nrv_A           38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK-K--YIEVNGHSEDKRTYAI-NLTEMGQELYEVASD  113 (148)
T ss_dssp             CCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEC---------CCB-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEeecCCCCcceeEe-EECHhHHHHHHHHHH
Confidence            4567889999998865 256678999999999999999999998 4  44444       4566 899999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       114 ~~~~~~~  120 (148)
T 3nrv_A          114 FAIEREK  120 (148)
T ss_dssp             HTHHHHH
T ss_pred             HHHHHHH
Confidence            7776544

>2vha_A Periplasmic binding transport protein; periplasmic binding protein, ligand binding, ultrahigh resolution; HET: GLU; 1.00A {Shigella flexneri} PDB: 2ia4_A*

Probab=98.44  E-value=1.4e-05  Score=63.98  Aligned_cols=201  Identities=6%  Similarity=0.065  Sum_probs=124.6

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHh----C--CCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQ----F--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-  153 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~----~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-  153 (306)
                      .+.|+||+.....           ..+...++..+.+.    .  |++++++...+..+++..+.+|++|+++...... 
T Consensus        16 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~ia~~l~~~~G~~~~~v~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~   95 (287)
T 2vha_A           16 NGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNV   95 (287)
T ss_dssp             HTEEEEEECSEETTTEEECSSSCEESHHHHHHHHHHHHHHHHTTCTTCEEEEEECCTTTHHHHHHTTSCSEECSSCBCCH
T ss_pred             CCeEEEEEcCCCCCceEECCCCCcccccHHHHHHHHHHHHHhcCCCCceEEEEECCHHHHHHHHHCCCeeEEeccccCCc
Confidence            3579999864211           13445566555442    3  4699999998888999999999999997531111 


Q ss_pred             -CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHH
Q psy3760         154 -PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIK  231 (306)
Q Consensus       154 -~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (306)
                       ....+. +.++.....+++++++++.     -+++||.+.++... .+......+...+...+...+ ...+++...++
T Consensus        96 ~r~~~~~~s~p~~~~~~~l~~~~~~~i-----~sl~dL~g~~v~~~-~g~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~  168 (287)
T 2vha_A           96 ERQKQAAFSDTIFVVGTRLLTKKGGDI-----KDFADLKGKAVVVT-SGTTSEVLLNKLNEEQKMNMR-IISAKDHGDSF  168 (287)
T ss_dssp             HHHTTCEEEEEEEEEEEEEEEETTSSC-----CSGGGGTTCEEEEE-TTSHHHHHHHHHHHHTTCCCE-EEEESSHHHHH
T ss_pred             chhhcccccceeeecceEEEEECCCCC-----CCHHHcCCCEEEEe-CCCcHHHHHHHHhhccCCCce-EEEcCCHHHHH
Confidence             122344 3778888999999998753     47899998876554 454555566666665554433 44678899999


Q ss_pred             HHHHhcccee-eeecceeccc-cc----CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         232 TYVELRMGIG-IIASIAFDSN-RD----KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       232 ~~v~~g~gi~-~~p~~~~~~~-~~----~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      .++.+|..=+ +.+...+... ..    +.+..++.+  .....++++.+++  .......|-+.|.+..+....+++
T Consensus       169 ~~L~~G~vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~k~--~~~l~~~l~~~l~~l~~~g~~~~i  242 (287)
T 2vha_A          169 RTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKP--QSQEAYGCMLRKD--DPQFKKLMDDTIAQVQTSGEAEKW  242 (287)
T ss_dssp             HHHHTTSCSEEEEEHHHHHHHHTTSSSGGGEEEESCC--SCEEEEEEEECTT--CHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHcCCeeEEEeChHHHHHHHHhCCCCCceEecCCc--cccCceEEEEeCC--CHHHHHHHHHHHHHHHhCchHHHH
Confidence            9999995433 3443333222 21    234444432  2345777887776  234555555555554444444444

>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic protein, arginine protein binding, transport protein; 1.92A {Chlamydia trachomatis} SCOP: c.94.1.0

Probab=98.42  E-value=1.5e-05  Score=62.05  Aligned_cols=199  Identities=7%  Similarity=-0.009  Sum_probs=123.2

Q ss_pred             CCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          91 DTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ..+.|+||+.....           ..+...++..+.++. ++++++...+...++..|.+|++|+++......  ....
T Consensus         9 ~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~   87 (242)
T 3del_B            9 NSEKFIVGTNATYPPFEFVDKRGEVVGFDIDLAREISNKL-GKTLDVREFSFDALILNLKQHRIDAVITGMSITPSRLKE   87 (242)
T ss_dssp             --CEEEEEECSCBTTTBEECTTSCEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHTTSSSEECSSBBCCHHHHTT
T ss_pred             cCCcEEEEeCCCCCCeeEECCCCCEEEeeHHHHHHHHHHc-CCceEEEEcCHHHHHHHHhCCCcCEEEecCcCCHHHHhc
Confidence            45789999963211           245667787777764 699999999999999999999999997421111  1233


Q ss_pred             ceeeccc--cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         158 LISIPCY--QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       158 ~~~~~l~--~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      +.+.++.  ....+++++++.+     .-+++||.+..+.... +...    ..++...  .......+++...++.++.
T Consensus        88 ~~~~p~~~~~~~~~~~~~~~~~-----i~~~~dL~g~~i~v~~-g~~~----~~~l~~~--~~~~~~~~~~~~~~~~~L~  155 (242)
T 3del_B           88 ILMIPYYGEEIKHLVLVFKGEN-----KHPLPLTQYRSVAVQT-GTYQ----EAYLQSL--SEVHIRSFDSTLEVLMEVM  155 (242)
T ss_dssp             EEEEEEEEEEESEEEEEEESCC-----SCCCCGGGSSCEEEET-TSHH----HHHHHHS--TTCCEEEESSHHHHHHHHH
T ss_pred             ccceeeeecCCceEEEEeCCCC-----CCCHHHhCCCEEEEEc-CcHH----HHHHHhC--CCceEEEECCHHHHHHHHH
Confidence            4347777  7778888888832     3478899988876654 3322    2333332  1233456789999999999


Q ss_pred             hccc-eeeeecceeccc--ccCCceeeecCCCC--ccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMG-IGIIASIAFDSN--RDKNLRSISASHLF--GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~--~~~~l~~~~~~~~~--~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|.. .++.+...+...  ..+.+..++.+...  ....+++..+++  .......|-+.|.+.-+....+++.
T Consensus       156 ~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~l~~~l~~~l~~l~~~g~~~~i~  227 (242)
T 3del_B          156 HGKSPVAVLEPSIAQVVLKDFPALSTATIDLPEDQWVLGYGIGVASD--RPALALKIEAAVQEIRKEGVLAELE  227 (242)
T ss_dssp             TTSSSEEEECHHHHHHHGGGCTTEEEEEEECCGGGCEEEEEEEEETT--CHHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             cCCCCEEEecHHHHHHHHHhCCCeEEecCccCcccccceEEEEEeCC--CHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            9944 444444333332  33445555432211  122377877877  2445666666666655555555554

>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=98.39  E-value=5.2e-07  Score=59.45  Aligned_cols=73  Identities=16%  Similarity=0.102  Sum_probs=56.2

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchH-HHHHHHHHHHH--cCceeEEecCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPG-VSKAIIELEEE--LSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~-~s~~i~~LE~~--lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +.+.++..+.+.+  .+++.-|+.+++|+|+ +|+.|++||+.  +...--+|....+ .||+.|+.+++.+.+..+.+
T Consensus        16 ~~l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~-~LT~~G~~~~~~~~~~~~~l   93 (95)
T 2pg4_A           16 RILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTL-KLTEKGRRLAECLEKCRDVL   93 (95)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEE-EECHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEE-EECHhHHHHHHHHHHHHHHh
Confidence            4566777776653  4999999999999999 99999999987  3211222334555 89999999999998887654

>3tql_A Arginine-binding protein; transport and binding proteins, transport protein; HET: MSE ARG; 1.59A {Coxiella burnetii} SCOP: c.94.1.0

Probab=98.39  E-value=1.4e-05  Score=61.36  Aligned_cols=200  Identities=11%  Similarity=0.042  Sum_probs=123.8

Q ss_pred             CcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc-
Q psy3760          93 GNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL-  158 (306)
Q Consensus        93 ~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~-  158 (306)
                      ++|+||+.....           ..+...++..+.++. ++++++...+..++...+.+|++|+++......  ....+ 
T Consensus         2 ~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~   80 (227)
T 3tql_A            2 DTIKFATEATYPPYVYMGPSGQVEGFGADIVKAVCKQM-QAVCTISNQPWDSLIPSLKLGKFDALFGGMNITTARQKEVD   80 (227)
T ss_dssp             CEEEEEECSCBTTTBEEC--CCEESHHHHHHHHHHHHT-TCEEEEEECCHHHHHHHHHHTSCSEECSSCBCCTTGGGTEE
T ss_pred             ceEEEEEcCCCCCeeEECCCCCcccchHHHHHHHHHHh-CCeEEEEeCCHHHHHHHHhCCCCCEEEecCcCCHhHHhhee
Confidence            578888865211           236677888887764 899999999999999999999999997432111  12222 


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      -+.++.....+++++++.+..    -+++||.+..+..... ......+.......    .....+++...++.++.+|.
T Consensus        81 ~s~p~~~~~~~l~~~~~~~~~----~~~~dL~g~~v~~~~g-~~~~~~l~~~~~~~----~~~~~~~~~~~~~~~l~~gr  151 (227)
T 3tql_A           81 FTDPYYTNSVSFIADKNTPLT----LSKQGLKGKIIGVQGG-TTFDSYLQDSFGNS----ITIQRYPSEEDALMDLTSGR  151 (227)
T ss_dssp             ECSCSBCCEEEEEEETTSCCC----CSTTTTTTCEEEEETT-SHHHHHHHHHHGGG----SEEEEESSHHHHHHHHTTTS
T ss_pred             cccceeccceEEEEeCCCCCC----CCHHHhCCCEEEEEec-ccHHHHHHHhcccc----ceEEEcCCHHHHHHHHHcCC
Confidence            245788889999999988643    3788998887766543 33333333333221    34567889999999999994


Q ss_pred             c-eeeeecceeccc--ccC--Cceeee--cCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         239 G-IGIIASIAFDSN--RDK--NLRSIS--ASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       239 g-i~~~p~~~~~~~--~~~--~l~~~~--~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      . ..+.+...+...  ..+  ++..+.  +... .....+++..+++.  ......|-+.|.+.-+....+++.
T Consensus       152 vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~~l~~l~~~g~~~~i~  223 (227)
T 3tql_A          152 VDAVVGDTPLIKQWLKQNGRREYVLIGKPVNDPNYFGKGVGIAVKKGN--QALLLKLNKALAAIKANGVYAAIV  223 (227)
T ss_dssp             SSEEESCHHHHHHHHHHTTCCSEEEEEEECCCGGGCCSCBCCEEETTC--HHHHHHHHHHHHHHHHTSHHHHHH
T ss_pred             cCEEEeChHHHHHHHHhCCCCCEEEecCcccCccccccceEEEEcCCC--HHHHHHHHHHHHHHHhCChHHHHH
Confidence            4 334444333322  222  255543  2221 11235577777762  345555555555554444555554

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=98.39  E-value=2.4e-06  Score=60.66  Aligned_cols=60  Identities=20%  Similarity=0.231  Sum_probs=50.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      |++..|+.+++|+|++|+.|++||+. |  |+.|.++++ .||+.|+.+...+......++...
T Consensus        33 s~~ela~~l~is~~tv~~~l~~Le~~-G--li~r~~~~~-~Lt~~g~~~~~~~~~~~~~~~~~~   92 (139)
T 2x4h_A           33 KINRIAKDLKIAPSSVFEEVSHLEEK-G--LVKKKEDGV-WITNNGTRSINYLIKAHRVIEILL   92 (139)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEETTEE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHC-C--CEEecCCeE-EEChhHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999998 5  677777777 799999998877766555544444

>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid; transport protein, solute-BIND protein; HET: CYS GOL; 1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A

Probab=98.39  E-value=9.5e-06  Score=65.02  Aligned_cols=196  Identities=14%  Similarity=0.099  Sum_probs=121.0

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CC--CCC
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SP--SDK  157 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~--~~~  157 (306)
                      .+.|+||+.....           ..+...++..+.++. ++++++...+...+.+.|.+|++|+++..... ..  ...
T Consensus        56 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-G~~v~~~~~~~~~~~~~l~~G~~D~~~~~~~~~t~~r~~~  134 (283)
T 2yln_A           56 KGTVTVGTEGTYAPFTYHDKDGKLTGYDVEVTRAVAEKL-GVKVEFKETQWDSMMAGLKAGRFDVVANQVGLTSPERQAT  134 (283)
T ss_dssp             TCEEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHHTSCSEECSSCCCCSHHHHHH
T ss_pred             CCeEEEEECCCCCCeeEECCCCCEeeehHHHHHHHHHHc-CCceEEEECCHHHHHHHHHCCCcCEEEecCccCChhhhcc
Confidence            4689999975221           245567777777765 88999999889999999999999999853221 11  112


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. ..++......++++++.+     .-+++||.+..+.. ..+...    ..++...+.   ....+++...++.++..
T Consensus       135 ~~~~~p~~~~~~~l~~~~~~~-----i~s~~dL~G~~v~v-~~g~~~----~~~l~~~~~---~~~~~~~~~~~~~~l~~  201 (283)
T 2yln_A          135 FDKSEPYSWSGAVLVAHNDSN-----IKSIADIKGVKTAQ-SLTSNY----GEKAKAAGA---QLVPVDGLAQSLTLIEQ  201 (283)
T ss_dssp             EEECSCSEEECEEEEEETTCS-----CCSGGGCTTSEEEE-CTTSHH----HHHHHHTTC---EEEECSSHHHHHHHHHT
T ss_pred             eEeccCeeeecEEEEEECCCC-----CCCHHHhCCCEEEE-ecCchH----HHHHHHcCC---eEEEeCCHHHHHHHHHc
Confidence            22 336777888999999876     34789998877665 333322    334444453   23466788999999999


Q ss_pred             ccc-eeeeecceeccc--ccC--Cceeee-cCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         237 RMG-IGIIASIAFDSN--RDK--NLRSIS-ASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       237 g~g-i~~~p~~~~~~~--~~~--~l~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      |.. .++.+...+...  ..+  .+..++ ... .....++++.+++.  ......|-+.|.+..+....+++.
T Consensus       202 g~vDa~i~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~~~~i~~~k~~--~~l~~~i~~al~~l~~~g~~~~i~  272 (283)
T 2yln_A          202 KRADATLNDELAVLDYLKKNPNAGVKIVWSAPA-DEKVGSGLIVNKGN--DEAVAKFSTAINELKADGTLKKLG  272 (283)
T ss_dssp             TSCCEEEEEHHHHHHHHHHSTTSSEEEEEECCG-GGCEEECCEEESSC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             CCCCEEEecHHHHHHHHHhCCCCcEEEccCccc-CCcccEEEEEeCCC--HHHHHHHHHHHHHHHHCCcHHHHH
Confidence            944 444444433322  122  255555 322 11447778888773  334555555555444444444443

>4eq9_A ABC transporter substrate-binding protein-amino A transport; structural genomics, niaid; HET: GSH; 1.40A {Streptococcus pneumoniae}

Probab=98.38  E-value=9.7e-06  Score=63.23  Aligned_cols=205  Identities=13%  Similarity=0.076  Sum_probs=128.7

Q ss_pred             CCCcEEEEecccc----------hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCc
Q psy3760          91 DTGNLTIATTHTQ----------ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKL  158 (306)
Q Consensus        91 ~~~~l~I~~~~~~----------~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~  158 (306)
                      ..+.|+||+....          ...+...++..+.++..++++++...+...++..|.+|++|+++.......  ...+
T Consensus         6 ~~~~l~v~~~~~~~P~~~~~~g~~~G~~~dl~~~i~~~~g~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~   85 (246)
T 4eq9_A            6 SKKEIIVATNGSPRPFIYEENGELTGYEIEVVRAIFKDSDKYDVKFEKTEWSGVFAGLDADRYNMAVNNLSYTKERAEKY   85 (246)
T ss_dssp             -CEEEEEEECCCSTTTSEEETTEEESHHHHHHHHHHTTCSSEEEEEEECCHHHHHHHHHTTSCSEECSSCCCCHHHHHHE
T ss_pred             CCCEEEEEeCCCcCCeEEcCCCCCcccHHHHHHHHHHHcCCceEEEEeCCHHHHHHHHhCCCcCEEecccccChhhhhce
Confidence            4578999997421          135677888888887644999999999999999999999999885311111  1122


Q ss_pred             -eeeccccceEEEEecC-CCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHH
Q psy3760         159 -ISIPCYQWEYVIIVPL-DHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVE  235 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~-~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~  235 (306)
                       -+.++.....++++++ +.+     .-+++||.+..+... .+......+..+....+... .+.+...+...++.++.
T Consensus        86 ~~s~p~~~~~~~~~~~~~~~~-----i~~~~dL~g~~i~~~-~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~  159 (246)
T 4eq9_A           86 LYAAPIAQNPNVLVVKKDDSS-----IKSLDDIGGKSTEVV-QATTSAKQLEAYNAEHTDNPTILNYTKADFQQIMVRLS  159 (246)
T ss_dssp             EECCCCEECCEEEEEETTCCS-----CSSGGGCTTCEEEEC-TTCHHHHHHHHHHHHCTTSCCEEEECCCCHHHHHHHHH
T ss_pred             eeccceecCceEEEEECCCCC-----CCCHHHhCCCEEEEe-cCccHHHHHHHHHhhCCCcceEEEecCCCHHHHHHHHH
Confidence             2467888899999998 443     347899988877654 44444555556555555432 33334468999999999


Q ss_pred             hccc-eeeeecceeccc----ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMG-IGIIASIAFDSN----RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~----~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|.. ..+.....+...    ...++........ ....++++.+++.  ......|-+.|++.-+....+++.
T Consensus       160 ~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~k~~--~~l~~~ln~~l~~l~~~g~~~~i~  230 (246)
T 4eq9_A          160 DGQFDYKIFDKIGVETVIKNQGLDNLKVIELPSD-QQPYVYPLLAQGQ--DELKSFVDKRIKELYKDGTLEKLS  230 (246)
T ss_dssp             TTSSSEEEEEHHHHHHHHHHHTCTTEEEEECCCS-SCCEECCEEETTC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             cCCceEEEecHHHHHHHHHhCCCCCceEecCcCC-CCCcEEEEEcCCC--HHHHHHHHHHHHHHHhCCcHHHHH
Confidence            9954 344444333322    2234666664432 2224677777764  345555555555544444555544

>4ddd_A Immunogenic protein; ssgcid, structural genomics, seattle structural genomics CEN infectious disease, immune system; 1.90A {Ehrlichia chaffeensis}

Probab=98.31  E-value=2.9e-05  Score=63.53  Aligned_cols=200  Identities=14%  Similarity=0.122  Sum_probs=126.4

Q ss_pred             CCCCcEEEEecccchhh-hhHHHHHHHHHhC----CCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc-----------
Q psy3760          90 YDTGNLTIATTHTQARY-ALPKIIKEFTIQF----PKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL-----------  152 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~-~l~~~l~~~~~~~----p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~-----------  152 (306)
                      ...+.|+|++...-+.+ .+...+.++..+.    +++++.+.. .++...+..+.+|++|++++....           
T Consensus        29 ~~~~~i~i~~g~~gG~~~~~~~~la~~l~~~~~~~~g~~v~v~~~~g~~~~i~~l~~g~~D~~~~~~~~~~~a~~g~~~f  108 (327)
T 4ddd_A           29 LNREYILIGTGSMTGVYYPIGGSICRFIASDYGKDNKIICSISSTTGSVYNLNSIRYSNMDISIVQSDLEYYAYNGLGFY  108 (327)
T ss_dssp             CCCEEEEEECCCTTSSHHHHHHHHHHHHHHHHGGGTSEEEEEECCCCHHHHHHHHHTTSCSEEEEEHHHHHHHHHTCGGG
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccCCCCCeEEEEEecCcHHHHHHHHHcCCCcEEEECcHHHHHHHhCcCcc
Confidence            34568999998654443 5777777776665    899999988 466788899999999999975221           


Q ss_pred             C---CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEecC
Q psy3760         153 S---PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLETIN  226 (306)
Q Consensus       153 ~---~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~  226 (306)
                      .   ...++. ...++...++++++++.+.     -+++||.+.++.....+...+.....+++..|+.+..  .+...+
T Consensus       109 ~~~~~~~d~~~v~~~~~~~~~lvv~~ds~i-----~sl~DL~gk~v~~~~~Gs~~~~~~~~~l~~~Gi~~~~v~~v~~~g  183 (327)
T 4ddd_A          109 EKMLPMDNLRMLASLHKEYLTIVVKKSSNI-----SVIDDIKGKRVNIGSPGTGVRVAMLKLLGEKGWTKKDFSVMAELK  183 (327)
T ss_dssp             TTSCCCTTEEEEEEEEEEEEEEEEETTSSC-----CSGGGGTTSEEECCSTTSHHHHHHHHHHHHHTCCGGGCSEEECCC
T ss_pred             cccCCCcchhehhccCCccEEEEEECCCCC-----CCHHHhCCCEEecCCCCccHHHHHHHHHHHcCCChHhcchhhcCC
Confidence            1   123444 3456778899999998763     3789998877665455555555667778888887631  234456


Q ss_pred             HHHHHHHHHhcc-ceeee----ecceeccc-ccCCceeeecCCC---------------------C--------ccceEE
Q psy3760         227 SDIIKTYVELRM-GIGII----ASIAFDSN-RDKNLRSISASHL---------------------F--------GTTISR  271 (306)
Q Consensus       227 ~~~~~~~v~~g~-gi~~~----p~~~~~~~-~~~~l~~~~~~~~---------------------~--------~~~~~~  271 (306)
                      ...+...+.+|. -..+.    |...+..+ ..++++.+++...                     .        ......
T Consensus       184 ~~~a~~aL~~G~vDa~~~~~~~p~~~~~~~~~~g~lr~L~v~~~~r~~~~p~~Pt~~~~~ip~g~~~~~~dv~t~~~~~~  263 (327)
T 4ddd_A          184 SSEQAQALCDNKIDVMVDVIGHPNASIQEASATCDIKFIPLDDRLIDDLHAKYPYYQKDIISGGLYNDSPDIQTVSVKAS  263 (327)
T ss_dssp             HHHHHHHHHTTSCSBEEEEECSSCHHHHHHHHHSCEEECCCCHHHHHHHHHHCTTCEEEEECSCSSSSCCCEEEEEEEEE
T ss_pred             HHHHHHHHHcCCCCEEEEccCCCcHHHHHHHhcCCeEEEeCCHHHHHHHHHhCCCceEEEeCCCCCCCCCCcceeeeeeE
Confidence            666777777772 22222    11122233 4566666544320                     1        011223


Q ss_pred             EEEeCCccccHHHHHHHHHHhHHh
Q psy3760         272 VIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       272 l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      ++.+++.+ .+.+.++.+.+.+.+
T Consensus       264 l~ap~~~p-~~vv~~l~~a~~e~~  286 (327)
T 4ddd_A          264 LVTTTELS-NDLAYKIVKSIATHL  286 (327)
T ss_dssp             EEEETTSC-HHHHHHHHHHHHHTH
T ss_pred             EEEcCCCC-HHHHHHHHHHHHhCH
Confidence            55577764 667777777776654

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

Probab=98.31  E-value=2e-06  Score=62.85  Aligned_cols=75  Identities=17%  Similarity=0.296  Sum_probs=59.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+..|+.+++|++++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+..
T Consensus        47 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~---glv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  122 (162)
T 2fa5_A           47 MAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLER---GFIRRETHGDDRRRSML-ALSPAGRQVYETVAP  122 (162)
T ss_dssp             CCHHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEC---------CCC-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEeeecCCCCCCeeEE-EECHHHHHHHHHHHH
Confidence            3567788888888644 266779999999999999999999998   5666643       456 799999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       123 ~~~~~~~  129 (162)
T 2fa5_A          123 LVNEMEQ  129 (162)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7765543

>3hv1_A Polar amino acid ABC uptake transporter substrate binding protein; protein structure initiative II(PSI II), nysgxrc; 1.90A {Streptococcus thermophilus lmg 18311}

Probab=98.31  E-value=3.6e-05  Score=60.94  Aligned_cols=202  Identities=9%  Similarity=-0.027  Sum_probs=124.5

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .+.|+||+.....           ..+...++..+.+.. ++++++...+..+++..|.+|++|+++......  ....+
T Consensus        20 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~   98 (268)
T 3hv1_A           20 EKKIKIGFDATFVPMGYEEKDGSYIGFDIDLANAVFKLY-GIDVEWQAIDWDMKETELKNGTIDLIWNGYSVTDERKQSA   98 (268)
T ss_dssp             HTEEEEEECTEETTTEEECTTSCEECHHHHHHHHHHHTT-TCEEEEEECCGGGHHHHHHHTSCSEECSSCBCCHHHHTTC
T ss_pred             CCcEEEEECCCCCCceEECCCCCEEEehHHHHHHHHHHh-CCcEEEEECCHHHHHHHHHCCCCCEEEecCccCHHHHhcC
Confidence            4689999974321           246677888887764 899999999999999999999999988422111  11222


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhC--CCceeEEEEecCHHHHHHHHH
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ--KLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~v~  235 (306)
                       -+.++.....+++++++.+     .-+++||.+..+...... .....+.......  .........+++...++.++.
T Consensus        99 ~fs~p~~~~~~~~~~~~~~~-----i~~~~dL~g~~i~v~~g~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~  172 (268)
T 3hv1_A           99 DFTEPYMVNEQVLVTKKSSG-----IDSVAGMAGKTLGAQAGS-SGYDAFNASPKILKDVVANQKVVQYSTFTQALIDLN  172 (268)
T ss_dssp             EECCCCEEECEEEEEEGGGC-----CCSSGGGTTCCEEEETTC-HHHHHHHHCTTTTTTTSGGGCEEEESSHHHHHHHHH
T ss_pred             cCcHHHeeCceEEEEECCCC-----CCCHHHhCCCEEEEEeCC-chHHHHHHhhHHHhhhcccceEEEeCCHHHHHHHHH
Confidence             2457888889999988763     347899998887776532 2222222211111  122234667889999999999


Q ss_pred             hccc-eeeeecceeccc-c-c---CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMG-IGIIASIAFDSN-R-D---KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~-~-~---~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|.. ..+.....+... . .   +.+..++..  ....+++++.+++.  ......|-+.|.+.-+....+++.
T Consensus       173 ~GrvDa~i~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~k~~--~~l~~~ln~~l~~l~~~g~~~~i~  243 (268)
T 3hv1_A          173 SGRIDGLLIDRVYANYYLEKSGVLDQYNVMPAG--YEGESFAVGARKVD--KTLIKKINQGFETLYKNGEFQKIS  243 (268)
T ss_dssp             HTSCSEEEEEHHHHHHHHHHTTCGGGEEEEECS--SCCEEECCEECTTC--HHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             cCCCCEEEeCHHHHHHHHHhCCCCCceEECCCC--CCCCcEEEEEcCCC--HHHHHHHHHHHHHHHhCCHHHHHH
Confidence            9954 344444333322 1 2   345555443  23456777777652  344555555555544444455543

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=98.29  E-value=1.1e-07  Score=58.21  Aligned_cols=51  Identities=20%  Similarity=0.266  Sum_probs=42.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcccc--CHhHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL--TKPGQAILRSIEI   72 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~l--T~~G~~l~~~a~~   72 (306)
                      +++..+.+.| |++++|+.+|+|||+||+.+             |.++++ .+  |+.|+.++++++.
T Consensus         5 ~l~~~~~~~g-s~~~~A~~lgis~~~vs~~~-------------~~~~~~-~l~~t~~G~~~~~~~~~   57 (67)
T 2pij_A            5 PLSKYLEEHG-TQSALAAALGVNQSAISQMV-------------RAGRSI-EITLYEDGRVEANEIRP   57 (67)
T ss_dssp             EHHHHHHHTC-CHHHHHHHHTSCHHHHHHHH-------------HTTCCE-EEEECTTSCEEEEEEEE
T ss_pred             HHHHHHHHcC-CHHHHHHHHCcCHHHHHHHH-------------cCCCCC-CeEEccCceEehHhhcC
Confidence            4567889999 99999999999999999998             567777 78  9999877665443

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=98.29  E-value=3.5e-07  Score=54.72  Aligned_cols=27  Identities=30%  Similarity=0.278  Sum_probs=24.1

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      ..+.+.+ |++++|+.||+|||+||+.+
T Consensus         8 k~l~~~~-sq~~~A~~Lgvsq~aVS~~~   34 (65)
T 2cw1_A            8 KKFVEDK-NQEYAARALGLSQKLIEEVL   34 (65)
T ss_dssp             HHHHTTS-CHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHHHc-CHHHHHHHhCCCHHHHHHHH
Confidence            3457778 99999999999999999988

>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural genomics, PSI-2, protein structure initiative; HET: EPE; 1.66A {Pseudomonas aeruginosa}

Probab=98.28  E-value=1.5e-05  Score=61.84  Aligned_cols=200  Identities=12%  Similarity=0.068  Sum_probs=124.5

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .+.|+||+.....           ..+...++..+.+.. ++++++...+..+++..|.+|++|+++......  ....+
T Consensus        14 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~   92 (239)
T 3kbr_A           14 SGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESL-GAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQA   92 (239)
T ss_dssp             HTEEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHT-TCEEEEEECCTTTHHHHHHTTCCSEECSSCBCCHHHHTTC
T ss_pred             CCeEEEEECCCCCCeeEECCCCCEEeehHHHHHHHHHHH-CCceEEEEeCHHHHHHHHHCCCcCEEEeCCcCCHHHcCcc
Confidence            4689999963211           146677888888775 899999999999999999999999996432111  11223


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhhc--CCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEIS--NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                       -+.++.....+++++++.+.   ..-+++||.  +..+.. ..+....    .++.... .......+++...++.++.
T Consensus        93 ~fs~p~~~~~~~~~~~~~~~~---~i~~~~dL~~~g~~v~~-~~g~~~~----~~l~~~~-~~~~~~~~~~~~~~~~~l~  163 (239)
T 3kbr_A           93 YFSIPYLRDGKTPITLCSEEA---RFQTLEQIDQPGVTAIV-NPGGTNE----KFARANL-KKARILVHPDNVTIFQQIV  163 (239)
T ss_dssp             EECSCSEEECEEEEEEGGGGG---GGSSHHHHSSTTCEEEE-CTTSHHH----HHHHHHC-SSSEEEECCCTTTHHHHHH
T ss_pred             ccchHHhccCcEEEEECCccc---ccCCHHHhcCCCcEEEE-cCCCcHH----HHHHHhC-CCCceEEeCCHHHHHHHHH
Confidence             24578888889999887531   234789998  444443 3443332    2333321 1233456778889999999


Q ss_pred             hccc-eeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMG-IGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|.. ..+.....+...  ..+++..+....+....+++++.++   .......|-+.|.+..+....+++.
T Consensus       164 ~grvDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k---~~~l~~~ln~~l~~l~~~g~~~~i~  232 (239)
T 3kbr_A          164 DGKADLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPR---DEAFKRYVDQWLHIAEQSGLLRQRM  232 (239)
T ss_dssp             TTSCSEEEEEHHHHHHHHHHCTTEEECCCC-CCCCEEECCEECS---CHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             cCCcCEEEEchHHHHHHHHhCCCcEEecCCCCccccceEEEEcC---CHHHHHHHHHHHHHHHHCCcHHHHH
Confidence            9954 344444444333  3455666554443445577777777   3555666666666655555555554

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

Probab=98.26  E-value=3e-06  Score=60.15  Aligned_cols=78  Identities=12%  Similarity=0.054  Sum_probs=58.9

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE----EecCCCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIF----IRHGKRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf----~R~~~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      |+..++.++..+.+.+ .|.+..|+.+++|+|++|+.|++||+.=-+.-.    +|....+ .||+.|+.++..+.....
T Consensus        36 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~~  114 (140)
T 2nnn_A           36 LTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLV-SLSPAGRAELEAGLAAAR  114 (140)
T ss_dssp             CCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEE-EECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeee-EECHhHHHHHHHHHHHHH
Confidence            4567888888887654 267788999999999999999999988333332    1223345 799999999999888776


Q ss_pred             HHHH
Q psy3760          76 EIEG   79 (306)
Q Consensus        76 ~~~~   79 (306)
                      .+..
T Consensus       115 ~~~~  118 (140)
T 2nnn_A          115 EINR  118 (140)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>3k4u_A Binding component of ABC transporter; structural genomics, protein structure INI NEW YORK structural genomix research consortium, nysgxrc; HET: LYS; 2.62A {Wolinella succinogenes} SCOP: c.94.1.0

Probab=98.26  E-value=7.2e-05  Score=58.27  Aligned_cols=199  Identities=13%  Similarity=0.010  Sum_probs=120.2

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .+.|+||+.....           ..+...++..+.+.. ++++++...+...++..|.+|++|+++......  ....+
T Consensus         4 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~   82 (245)
T 3k4u_A            4 RGELRVGLEPGYLPFEMKDKKGNVIGFDVDLAREMAKAM-GVKLKLVPTSWDGLIPGLVTEKFDIIISGMTISQERNLRV   82 (245)
T ss_dssp             CSEEEEEECTTSTTTCEEETTTEEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHTTS
T ss_pred             CCeEEEEECCCcCCeeEECCCCCCccchHHHHHHHHHHh-CCeEEEEEccHHHHHHHHhCCCcCEEEecCcCCHHHHhhc
Confidence            5689999982211           245567777777664 789999999999999999999999987421111  11222


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhhc--CCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEIS--NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                       -+.++.....+++++++.+   ...-+++||.  +..+.... +....    ..+.... .......+++...++.++.
T Consensus        83 ~~s~p~~~~~~~~~~~~~~~---~~i~~~~dL~~~g~~i~v~~-g~~~~----~~l~~~~-~~~~~~~~~~~~~~~~~L~  153 (245)
T 3k4u_A           83 NFVEPYIVVGQSLLVKKGLE---KGVKSYKDLDKPELTLVTKF-GVSAE----YAAKRLF-KNAKLKTYDTEAEAVQEVL  153 (245)
T ss_dssp             EECSCSEEECEEEEEETTTT---TTCCSGGGGCCSSCEEEEET-TSHHH----HHHHHHC-SSSEEEEESSHHHHHHHHH
T ss_pred             CcchhhheeceEEEEECCcc---cccCCHHHhccCCcEEEEeC-CcHHH----HHHHhhC-CcCCEEEeCCHHHHHHHHH
Confidence             3457888899999998853   2234789998  55555543 33332    2333221 1234557789999999999


Q ss_pred             hccceee-eecceeccc----ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMGIGI-IASIAFDSN----RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~gi~~-~p~~~~~~~----~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|..=++ .....+...    ....+...+.+  ....+++++.+++.  ......|-+.|.+.-+....+++.
T Consensus       154 ~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~k~~--~~l~~~ln~~l~~l~~~g~~~~i~  223 (245)
T 3k4u_A          154 NGKADMFIFDLPFNVAFMAQKGQGYLVHLDTS--LTYEPLGWAIKKGD--PDFLNWLNHFLAQIKHDGSYDELY  223 (245)
T ss_dssp             SSSSEEEEEEHHHHHHHHHHTTTTTEEEECCC--CSCEEECCEECTTC--HHHHHHHHHHHHHHHHHSHHHHHH
T ss_pred             cCCCcEEEEcHHHHHHHHhcCCccceeecCCC--cccccEEEEEcCCC--HHHHHHHHHHHHHHHhCcHHHHHH
Confidence            9955444 333333222    22334433332  33557788888763  334555555555544444455443

>2q88_A EHUB, putative ABC transporter amino acid-binding prote; substrate-binding protein, compatible solues, ABC-transporte osmoprotection; HET: 4CS; 1.90A {Sinorhizobium meliloti} PDB: 2q89_A*

Probab=98.26  E-value=3.3e-05  Score=60.70  Aligned_cols=200  Identities=11%  Similarity=0.027  Sum_probs=120.7

Q ss_pred             CcEEEEecccch----------hhhhHHHHHHHHHhCCCcE-EEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCce
Q psy3760          93 GNLTIATTHTQA----------RYALPKIIKEFTIQFPKVK-LSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLI  159 (306)
Q Consensus        93 ~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~-i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~  159 (306)
                      +.|+||+.....          ..+...++..+.++. ++. +++...+...++..+.+|++|+++......  ....+.
T Consensus        13 ~~l~v~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~~   91 (257)
T 2q88_A           13 GFARIAIANEPPFTAVGADGKVSGAAPDVAREIFKRL-GVADVVASISEYGAMIPGLQAGRHDAITAGLFMKPERCAAVA   91 (257)
T ss_dssp             TEEEEEECCCTTTCEECTTCCEESHHHHHHHHHHHHT-TCCEEEEEECCGGGHHHHHHTTSCSEECSCCBCCHHHHTTSE
T ss_pred             CeEEEEcCCCCCeeEECCCCCcccccHHHHHHHHHHc-CCCeeeEEeCCHHHHHHHHHCCCcCEEEecccCCHHHHhccc
Confidence            579999874321          235567888887765 676 888888889999999999999997321111  112232


Q ss_pred             -eeccccceEEEEecCCCCCCCCCCcChhhhc---CCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         160 -SIPCYQWEYVIIVPLDHPLLLLNSISLKEIS---NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       160 -~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~---~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                       +.++.....+++++++.+..   .-+++||.   +..+.... +..    ....+...+........+++...++.++.
T Consensus        92 ~s~p~~~~~~~~~~~~~~~~~---i~~~~dL~~~~g~~i~~~~-g~~----~~~~l~~~~~~~~~~~~~~~~~~~~~~l~  163 (257)
T 2q88_A           92 YSQPILCDAEAFALKKGNPLG---LKSYKDIADNPDAKIGAPG-GGT----EEKLALEAGVPRDRVIVVPDGQSGLKMLQ  163 (257)
T ss_dssp             ECSCCCEECEEEEEETTCTTC---CCBHHHHHHCTTCCEEECT-TSH----HHHHHHHTTCCGGGEEECSSHHHHHHHHH
T ss_pred             cccchhcCceEEEEECCCccC---CCCHHHHhccCCceEEEEC-Ccc----cHHHHHhcCCCCceEEEcCCHHHHHHHHH
Confidence             45788888999999987521   24789999   77776543 322    23455666654334567889999999999


Q ss_pred             hccce-eeeecceeccc--ccC--Cceee-ecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMGI-GIIASIAFDSN--RDK--NLRSI-SASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~gi-~~~p~~~~~~~--~~~--~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|..= .+.....+..+  ..+  .+..+ |+.. .+...++++.+++  .......|-+.|.+..+....+++.
T Consensus       164 ~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~k~--~~~l~~~l~~~l~~~~~~g~~~~i~  235 (257)
T 2q88_A          164 DGRIDVYSLPVLSINDLVSKANDPNVEVLAPVEG-APVYCDGAAFRKG--DEALRDAFDVELAKLKESGEFAKII  235 (257)
T ss_dssp             HTSCSEEEEEHHHHHHHHHHHCCTTEEEECSCBT-CCCEEBCCEECGG--GHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             cCCCcEEEcCHHHHHHHHHhCCCcceeeecccCC-ccccceEEEEcCC--CHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            99443 33443333222  112  23332 2222 1223555666665  2445555555555544444555544

>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain, signaling protein; 2.04A {Bordetella pertussis} PDB: 3mpl_A

Probab=98.25  E-value=0.00025  Score=56.13  Aligned_cols=199  Identities=12%  Similarity=0.072  Sum_probs=122.9

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc-CCCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL-SPSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~  158 (306)
                      .+.|+||+.....           ..+...++..+.++. ++++++.. .+..++.+.+.+|++|++...... .....+
T Consensus        31 ~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~~l~~G~~D~~~~~~~t~~r~~~~  109 (267)
T 3mpk_A           31 HPVVKVAVLNLFAPFTLFRTDEQFGGISAAVLQLLQLRT-GLDFEIIGVDTVEELIAKLRSGEADMAGALFVNSARESFL  109 (267)
T ss_dssp             CSEEEEEEETEETTTEECCTTCCCBSHHHHHHHHHHHHH-CCEEEEEEESSHHHHHHHHHHTSCSEEEEEECCGGGTTTE
T ss_pred             CCcEEEEeCCCCCCeEEECCCCcEeeeHHHHHHHHHHHH-CCeEEEEecCCHHHHHHHHHCCCccEEecccCChhhhcce
Confidence            4689999976321           245667777777764 78999985 468899999999999997643211 122333


Q ss_pred             e-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 I-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 ~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                      . +.++.....+++++++.+.    .-+++||.+..+..... .....    ++..... ......+++...++.++.+|
T Consensus       110 ~fs~p~~~~~~~l~~~~~~~~----i~~~~dL~g~~i~v~~g-~~~~~----~l~~~~~-~~~~~~~~~~~~~l~~L~~G  179 (267)
T 3mpk_A          110 SFSRPYVRNGMVIVTRQDPDA----PVDADHLDGRTVALVRN-SAAIP----LLQRRYP-QAKVVTADNPSEAMLMVANG  179 (267)
T ss_dssp             EECSCSEEECEEEEEESSTTS----CSSGGGCTTCEEEEETT-CTHHH----HHHHHCT-TSEEEEESSHHHHHHHHHHT
T ss_pred             EechhhccCceEEEEECCCCC----CCCHHHHCCCEEEEeCC-chhHH----HHHHhCC-CcEEEEeCCHHHHHHHHHcC
Confidence            3 4678888999999988542    35789999887776654 33323    3332221 23355678999999999999


Q ss_pred             cc-eeeeecceeccc----ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         238 MG-IGIIASIAFDSN----RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       238 ~g-i~~~p~~~~~~~----~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      .. .++.+...+...    ..+.+...+... .....++++.+++.  ......|-+.|.+ +.+...+++.+
T Consensus       180 rvDa~i~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~k~~--~~l~~~ln~~l~~-l~~~~~~~i~~  248 (267)
T 3mpk_A          180 QADAVVQTQISASYYVNRYFAGKLRIASALD-LPPAEIALATTRGQ--TELMSILNKALYS-ISNDELASIIS  248 (267)
T ss_dssp             SCSEEEEEHHHHHHHHHHHCTTTEEEEEECS-SCCEEEEEEEETTC--HHHHHHHHHHHHT-SCHHHHHHHHH
T ss_pred             CCCEEEecHHHHHHHHHhcCCCceEEEeccC-CCceeEEEEEcCCC--HHHHHHHHHHHHh-CCHHHHHHHHH
Confidence            44 444444333222    134566665533 23457788888762  2344444444443 33334655543

>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=98.24  E-value=6.9e-06  Score=58.48  Aligned_cols=60  Identities=20%  Similarity=0.320  Sum_probs=48.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      +.+..|+.+++|+|++|+.|++||+.   -|+.|.+ +++ .||+.|..++..+......++.+.
T Consensus        24 ~~~ela~~l~vs~~tvs~~l~~Le~~---Glv~r~~~~~~-~LT~~g~~~~~~~~~~~~~~~~~l   84 (142)
T 1on2_A           24 RVSDIAEALAVHPSSVTKMVQKLDKD---EYLIYEKYRGL-VLTSKGKKIGKRLVYRHELLEQFL   84 (142)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHT---TSEEEETTTEE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHC---CCEEEeeCceE-EEchhHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999983   4556554 556 899999999988777655555544

>3qax_A Probable ABC transporter arginine-binding protein; periplasmic, transport PR; HET: ARG; 2.00A {Chlamydophila pneumoniae} PDB: 3g41_A* 3n26_A*

Probab=98.24  E-value=6.3e-05  Score=59.36  Aligned_cols=200  Identities=8%  Similarity=-0.018  Sum_probs=120.7

Q ss_pred             CCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          91 DTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      ..+.|++|+.....           ..+...++..+.++. ++++++...+..+..+.+.+|++|+++......  ....
T Consensus        29 ~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~  107 (268)
T 3qax_A           29 RNRIWIVGTNATYPPFEYVDAQGEVVGFDIDLAKAISEKL-GKQLEVREFAFDALILNLKKHRIDAILAGMSITPSRQKE  107 (268)
T ss_dssp             --CEEEEEECSCBTTTBEECTTSCEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHHTSSSEECSCCBCCHHHHTT
T ss_pred             cCCeEEEEECCCCCCceEECCCCCEEEEEHHHHHHHHHHh-CCeEEEEecCHHHHHHHHhCCCccEEeecCccCHhHhcc
Confidence            45689999974321           234566777776664 689999988999999999999999997421111  1223


Q ss_pred             ceeeccc--cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         158 LISIPCY--QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       158 ~~~~~l~--~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      +...++.  ....+++++++..    ..-+++||.+..+.... +...    ...+...  .......+++...+..++.
T Consensus       108 ~~~~p~~~~~~~~~~~~~~~~~----~i~~~~dL~g~~i~~~~-g~~~----~~~l~~~--~~~~~~~~~~~~~~~~~l~  176 (268)
T 3qax_A          108 IALLPYYGDEVQELMVVSKRSL----ETPVLPLTQYSSVAVQT-GTYQ----EHYLLSQ--PGICVRSFDSTLEVIMEVR  176 (268)
T ss_dssp             SEEEEEECCCBCEEEEEEETTS----CSCCCCGGGSSCEEEET-TSHH----HHHHHTS--TTCCEEEESCHHHHHHHHH
T ss_pred             eeeecceecccceEEEEECCCC----CCCCHHHhCCCEEEEec-CcHH----HHHHHhC--CCceEEecCCHHHHHHHHH
Confidence            3337777  7788889888752    23478999998877654 3222    3333332  1223446789999999999


Q ss_pred             hccce-eeeecceeccc--ccCCceeeecCCC--CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         236 LRMGI-GIIASIAFDSN--RDKNLRSISASHL--FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       236 ~g~gi-~~~p~~~~~~~--~~~~l~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      +|..= .+.....+...  ..+.+..++.+..  .....+++..+++.  ......|-+.+.+..+....+++.
T Consensus       177 ~G~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~--~~l~~~l~~~l~~l~~~g~~~~i~  248 (268)
T 3qax_A          177 YGKSPVAVLEPSVGRVVLKDFPNLVATRLELPPECWVLGCGLGVAKDR--PEEIQTIQQAITDLKSEGVIQSLT  248 (268)
T ss_dssp             TTSSSEEEECHHHHHHHGGGCTTEEEEEEECCGGGCBCCEEEEECTTC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             cCCCCEEEecHHHHHHHHHhCCCcEEecCccCcccccccEEEEEeCCC--HHHHHHHHHHHHHHHHCCcHHHHH
Confidence            99443 33443333322  3445555542221  11223788888762  345555555555554444555443

>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=98.24  E-value=7.3e-06  Score=54.42  Aligned_cols=68  Identities=12%  Similarity=0.108  Sum_probs=49.1

Q ss_pred             hhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe---cC--CCccccCHhHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR---HG--KRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         4 ~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R---~~--~~~~~lT~~G~~l~~~a~~il   74 (306)
                      .+++++..+.  ... |++..|+.+++|+|++|++|++||+. |.--..+   ++  ..+ .+|+.|...+......+
T Consensus        17 ~~~~iL~~L~~~~~~-~~~ela~~l~is~~tvs~~l~~L~~~-gli~~~~~~~~~r~~~~-~lt~~g~~~~~~~~~~~   91 (100)
T 1ub9_A           17 VRLGIMIFLLPRRKA-PFSQIQKVLDLTPGNLDSHIRVLERN-GLVKTYKVIADRPRTVV-EITDFGMEEAKRFLSSL   91 (100)
T ss_dssp             HHHHHHHHHHHHSEE-EHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEE-EECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCCcceEEE-EECHHHHHHHHHHHHHH
Confidence            4566676665  445 89999999999999999999999998 4433333   22  234 89999987665544433

>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=98.22  E-value=4.7e-06  Score=59.46  Aligned_cols=77  Identities=18%  Similarity=0.156  Sum_probs=59.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ -|++..|+.+++|+|++|+.|++||+. |.--..++     ...+ .||+.|+.++..+....
T Consensus        27 lt~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~-gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~  104 (144)
T 1lj9_A           27 LTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ-GFIYRQEDASNKKIKRI-YATEKGKNVYPIIVREN  104 (144)
T ss_dssp             CTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHC-CCEEeecCCCCCceeee-EEChhHHHHHHHHHHHH
Confidence            4567888888888754 278999999999999999999999998 44333332     1225 79999999999888877


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+..
T Consensus       105 ~~~~~  109 (144)
T 1lj9_A          105 QHSNQ  109 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66543

>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC transport, cysteine uptake; 2.00A {Campylobacter jejuni} SCOP: c.94.1.1

Probab=98.20  E-value=2.4e-05  Score=62.90  Aligned_cols=196  Identities=11%  Similarity=0.100  Sum_probs=118.1

Q ss_pred             CcEEEEecccc-----------hhhhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760          93 GNLTIATTHTQ-----------ARYALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK  157 (306)
Q Consensus        93 ~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~  157 (306)
                      +.|+||+....           ...+...++..+.++.  |++++++...+..++.+.+.+|++|+++......  ....
T Consensus        44 ~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~~~~g~~~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~  123 (292)
T 1xt8_A           44 GVVRIGVFGDKPPFGYVDEKGNNQGYDIALAKRIAKELFGDENKVQFVLVEAANRVEFLKSNKVDIILANFTQTPQRAEQ  123 (292)
T ss_dssp             SSEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHHHSCTTCEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHTT
T ss_pred             CeEEEEECCCCCCeeEECCCCCEeeEhHHHHHHHHHHhccCCceEEEEEcCHHHHHHHHhCCCeeEEeecCCCCcchhcc
Confidence            57999985321           1345567777777765  6899999998889999999999999997532111  1123


Q ss_pred             ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760         158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL  236 (306)
Q Consensus       158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  236 (306)
                      +. +.++.....+++++++.+     .-+++||.+..+... .+......+.+    ..... ....+++...+..++.+
T Consensus       124 ~~~s~p~~~~~~~~~~~~~~~-----i~~~~dL~g~~i~~~-~g~~~~~~l~~----~~~~~-~~~~~~~~~~~~~~L~~  192 (292)
T 1xt8_A          124 VDFCSPYMKVALGVAVPKDSN-----ITSVEDLKDKTLLLN-KGTTADAYFTQ----NYPNI-KTLKYDQNTETFAALMD  192 (292)
T ss_dssp             EEECCCCEEEEEEEEEETTCC-----CCSSGGGTTSEEEEE-TTSHHHHHHHH----HCTTS-EEEEESSHHHHHHHHHT
T ss_pred             eeeeccceecceEEEEECCCC-----CCCHHHhCCCEEEEe-CCCcHHHHHHH----hCCCc-eEEEcCCHHHHHHHHHc
Confidence            33 357888889999998873     347899988876654 34333333332    22122 34567899999999999


Q ss_pred             ccceee-eecceeccc--ccCCceeeecCCCCccceE-EEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         237 RMGIGI-IASIAFDSN--RDKNLRSISASHLFGTTIS-RVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       237 g~gi~~-~p~~~~~~~--~~~~l~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      |..=++ .........  ..+++..++..  ....++ +++.+++.  ......+-+.|.+.-+....+++
T Consensus       193 G~vDa~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~k~~--~~l~~~l~~~l~~l~~~g~~~~i  259 (292)
T 1xt8_A          193 KRGDALSHDNTLLFAWVKDHPDFKMGIKE--LGNKDVIAPAVKKGD--KELKEFIDNLIIKLGQEQFFHKA  259 (292)
T ss_dssp             TSSSEEEEEHHHHHHHHHHCTTEEEEEEE--EEEEEEECCEEETTC--HHHHHHHHHHHHHHHTTTHHHHH
T ss_pred             CCccEEEecHHHHHHHHHhCCCeEEcccc--cccCceeEEEEeCCC--HHHHHHHHHHHHHHHhCcHHHHH
Confidence            954443 333333222  23445554422  223344 66777663  33444444444444333344444

>4h5g_A Amino acid ABC superfamily ATP binding cassette transporter, binding protein; center for structural genomics of infectious diseases (csgid national institute of allergy and infectious diseases; HET: ARG; 1.78A {Streptococcus pneumoniae} PDB: 4h5f_A*

Probab=98.18  E-value=5.1e-05  Score=59.21  Aligned_cols=201  Identities=13%  Similarity=0.060  Sum_probs=120.9

Q ss_pred             CCcEEEEecccchh--------------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CC
Q psy3760          92 TGNLTIATTHTQAR--------------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PS  155 (306)
Q Consensus        92 ~~~l~I~~~~~~~~--------------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~  155 (306)
                      +|.|+||+......              .+-..++..+.++. ++++++...+...++..|.+|++|+++......  ..
T Consensus        11 ~g~L~Vg~~~~~pP~~~~~~~d~~g~~~G~~vdl~~~ia~~l-g~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~eR~   89 (243)
T 4h5g_A           11 KGKLVVATSPDYAPFEFQSLVDGKNQVVGADIDMAQAIADEL-GVKLEILSMSFDNVLTSLQTGKADLAVAGISATDERK   89 (243)
T ss_dssp             HTEEEEEECCCBTTTBEEEEETTEEEEESHHHHHHHHHHHHH-TSEEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHH
T ss_pred             CCEEEEEECCCCCCcEeeeccCCCCcEEEeHHHHHHHHHHHh-CCceEEecccHHHHHHHHHcCCCCcccccccCChhHc
Confidence            47899999653321              45667787777663 789999999999999999999999988632211  12


Q ss_pred             CCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHH
Q psy3760         156 DKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYV  234 (306)
Q Consensus       156 ~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  234 (306)
                      ..+. +.+++....++++.++.+.   ..-+++||.+........ ..    ....+..... ......+++...++.++
T Consensus        90 ~~~~fs~py~~~~~~~~v~~~~~~---~~~~~~dl~g~~i~v~~g-~~----~~~~l~~~~~-~~~i~~~~~~~~~~~~l  160 (243)
T 4h5g_A           90 EVFDFSIPYYENKISFLVHKADVE---KYKDLTSLESANIAAQKG-TV----PESMVKEQLP-KAQLTSLTNMGEAVNEL  160 (243)
T ss_dssp             TTEEECSCSBCCCEEEEEEGGGTT---TCCSHHHHHTSEEEEETT-SH----HHHHHHHHCT-TSEEEEESCHHHHHHHH
T ss_pred             cEEEccCccccCcccccccccccc---cccccccCCCCEEEecCC-cH----HHHHHHHhcc-cceeEEeCCHHHHHHHH
Confidence            2333 4778888888888776532   234789999888766543 22    2333333322 23355788999999999


Q ss_pred             Hhccc-eeeeecceeccc--ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         235 ELRMG-IGIIASIAFDSN--RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       235 ~~g~g-i~~~p~~~~~~~--~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .+|.. ..+.....+..+  ..+++....+... .....+++..+++.  ......|=+.|.+.-+....+++.
T Consensus       161 ~~GrvD~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~~--~~L~~~~n~aL~~l~~dG~~~~i~  232 (243)
T 4h5g_A          161 QAGKIDAVHMDEPVALSYAAKNAGLAVATVSLKMKDGDANAVALRKNS--DDLKEVVDKVIQKLKDEGTYQSYL  232 (243)
T ss_dssp             HHTSCSEEEEEHHHHHHHHHHCTTEEECSCCCCCCSSCCBCCEEESSC--HHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             HcCCccEEEecHHHHHHHHHHCCCCceeeccCCcccCceEEEEEeCCC--HHHHHHHHHHHHHHHHCCHHHHHH
Confidence            99955 344444333322  3444443333221 22335667777763  233333333444433344455554

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

Probab=98.15  E-value=1.2e-05  Score=57.78  Aligned_cols=77  Identities=16%  Similarity=0.202  Sum_probs=59.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ .+.+..|+.+++|+|++|+.|++||+. |.--..++     ...+ .||+.|+.++..+....
T Consensus        40 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~  117 (150)
T 2rdp_A           40 ITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERN-GLVARVRDEHDRRVVRI-RLLEKGERIIEEVIEKR  117 (150)
T ss_dssp             SCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECCC---CEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC-CCeeecCCCCCcceeEe-EECHhHHHHHHHHHHHH
Confidence            3556788888887643 388999999999999999999999997 44433322     2235 79999999999988877


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      .....
T Consensus       118 ~~~~~  122 (150)
T 2rdp_A          118 QRDLA  122 (150)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66543

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=98.15  E-value=9.7e-06  Score=58.11  Aligned_cols=75  Identities=16%  Similarity=0.242  Sum_probs=55.4

Q ss_pred             CchhhHHHHHHHHHhc------CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec------CCCccccCHhHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN------FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH------GKRIRGLTKPGQAILR   68 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~------~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~------~~~~~~lT~~G~~l~~   68 (306)
                      ++..++.++..+.+..      .|.+.-|+.+++++|++|+.|++||+. |.  +.+.      ...+ .||+.|+.++.
T Consensus        31 Lt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~-gl--Vr~~~~~DrR~~~v-~LT~~G~~~~~  106 (148)
T 4fx0_A           31 LTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRD-GL--VRVMAGADARCKRI-ELTAKGRAALQ  106 (148)
T ss_dssp             CCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHT-TS--BC-----------C-CBCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CC--EEeeCCCCCCeeEE-EECHHHHHHHH
Confidence            3456778888887653      167899999999999999999999987 64  3332      2345 89999999999


Q ss_pred             HHHHHHHHHHH
Q psy3760          69 SIEIIMQEIEG   79 (306)
Q Consensus        69 ~a~~il~~~~~   79 (306)
                      .+.+.....++
T Consensus       107 ~~~~~~~~~~~  117 (148)
T 4fx0_A          107 KAVPLWRGVQA  117 (148)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99887666543

>4i62_A Amino acid ABC transporter, periplasmic amino ACI protein, putative; center for structural genomics of infectious diseases (csgid national institute of allergy and infectious diseases (NIAI niaid; HET: ARG; 1.05A {Streptococcus pneumoniae}

Probab=98.15  E-value=8.3e-05  Score=58.68  Aligned_cols=201  Identities=13%  Similarity=0.060  Sum_probs=121.3

Q ss_pred             CCcEEEEecccchh--------------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CC
Q psy3760          92 TGNLTIATTHTQAR--------------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PS  155 (306)
Q Consensus        92 ~~~l~I~~~~~~~~--------------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~  155 (306)
                      .+.|+||+......              .+...++..+.+.. ++++++...+..++.+.+.+|++|+++......  ..
T Consensus        38 ~~~l~v~~~~~~~P~~~~~~~~~~g~~~G~~~dl~~~~~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~  116 (269)
T 4i62_A           38 KGKLVVALNPDFAPFEYQKVVDGKNQIVGSDIELAKAIATEL-GVELELSPMSFDNVLASVQSGKADLAISGVSKTDERS  116 (269)
T ss_dssp             HTEEEEEECSCBTTTBEEEEETTEEEEESHHHHHHHHHHHHH-TCEEEEEECCHHHHHHHHHTTSCSEECSSCBCCHHHH
T ss_pred             CCeEEEEecCCCCCceeecccCCCCcEeeecHHHHHHHHHHH-CCceEEEEcCHHHHHHHHhCCCccEEecCCcCCHhHh
Confidence            35899999643221              34556777776664 789999999999999999999999987531111  11


Q ss_pred             CCc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHH
Q psy3760         156 DKL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYV  234 (306)
Q Consensus       156 ~~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  234 (306)
                      ..+ -+.++.....+++++++.+   ...-+++||.+.++..... ...    ..++...... .....+++...+..++
T Consensus       117 ~~~~~s~p~~~~~~~~~~~~~~~---~~i~~~~dL~g~~i~~~~g-~~~----~~~l~~~~~~-~~~~~~~~~~~~~~~l  187 (269)
T 4i62_A          117 KVFDFSTPYYTAKNKLIVKKSDL---ATYQSVNDLAQKKVGAQKG-SIQ----ETMAKDLLQN-SSLVSLPKNGNLITDL  187 (269)
T ss_dssp             TTEEECSCCEECCEEEEEEGGGT---TTCSSGGGGC-CEEEEETT-SHH----HHHHHHHCTT-SEEEEESCHHHHHHHH
T ss_pred             hceecccchhhcceEEEEECCcc---ccccCHHHhCCCeEEEecC-chH----HHHHHHhCCC-CcEEecCCHHHHHHHH
Confidence            222 2457788888999988742   1234789999888776543 222    2333332212 2345678999999999


Q ss_pred             Hhcccee-eeecceeccc--ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         235 ELRMGIG-IIASIAFDSN--RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       235 ~~g~gi~-~~p~~~~~~~--~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .+|..=+ +.+...+...  ..+.+........ .....++++.+++.  ......|-+.+++.-+....+++.
T Consensus       188 ~~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~~l~~l~~~g~~~~i~  259 (269)
T 4i62_A          188 KSGQVDAVIFEEPVAKGFVENNPDLAIADLNFEKEQDDSYAVAMKKDS--KELKEAVDKTIQKLKESGELDKLI  259 (269)
T ss_dssp             HTTSSSEEEEEHHHHHHHHHHCTTEEECSCCCCC-CCCEECCEEESSC--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             HcCCCCEEEeChHHHHHHHHhCCCCeEEeeccCCCcccceEEEEeCCC--HHHHHHHHHHHHHHHhCChHHHHH
Confidence            9994433 3444433322  3455555444332 22456777777763  335555555555554444555443

>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=98.15  E-value=7.3e-06  Score=58.07  Aligned_cols=75  Identities=27%  Similarity=0.356  Sum_probs=59.7

Q ss_pred             CchhhHHHHHHHHHh---cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ---NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~---~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a   70 (306)
                      ++..++.++..+.+.   +-|.+.-|+.+++|+|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+
T Consensus        29 lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-G--li~r~~~~~D~R~~~~-~LT~~G~~~~~~~  104 (139)
T 3eco_A           29 ITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERK-K--LIYRYVDAQDTRRKNI-GLTTSGIKLVEAF  104 (139)
T ss_dssp             CCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEEECCC--CCEEE-EECHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHC-C--CEeecCCCCCCCeeee-EECHHHHHHHHHH
Confidence            356788888888874   3389999999999999999999999997 3  44443       2334 7999999999988


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      .+....+..
T Consensus       105 ~~~~~~~~~  113 (139)
T 3eco_A          105 TSIFDEMEQ  113 (139)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            887766544

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

Probab=98.15  E-value=9e-06  Score=57.57  Aligned_cols=77  Identities=9%  Similarity=0.215  Sum_probs=58.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---C--CCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---G--KRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~--~~~~~lT~~G~~l~~~a~~il   74 (306)
                      |+..++.++..+.+.+ .|.+..|+.+++|+|++|+.|++||+. |.---.++   +  ..+ .||+.|+.+++.+.+..
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~-gli~r~~~~~d~r~~~~-~lT~~G~~~~~~~~~~~  108 (139)
T 3bja_A           31 ISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRD-GYVMTEKNPNDQRETLV-YLTKKGEETKKQVDVQY  108 (139)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHT-TSEEEEECSSCTTCEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHC-CCeeeccCCCCCceeEE-EECHHHHHHHHHHHHHH
Confidence            4567888888888743 278899999999999999999999997 43332222   1  224 79999999999888776


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+..
T Consensus       109 ~~~~~  113 (139)
T 3bja_A          109 SDFLK  113 (139)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>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=98.14  E-value=1.3e-05  Score=56.66  Aligned_cols=74  Identities=16%  Similarity=0.163  Sum_probs=57.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++|+|++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+.+
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~---gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  107 (138)
T 1jgs_A           32 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLV-KLTTGGAAICEQCHQ  107 (138)
T ss_dssp             SCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEEECTTCSSCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHC---CCEEecCCcccCceeEe-EEChhHHHHHHHHHH
Confidence            3556788888887643 278999999999999999999999987   3445432       125 799999999998888


Q ss_pred             HHH-HHH
Q psy3760          73 IMQ-EIE   78 (306)
Q Consensus        73 il~-~~~   78 (306)
                      ... .+.
T Consensus       108 ~~~~~~~  114 (138)
T 1jgs_A          108 LVGQDLH  114 (138)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            775 443

>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=98.14  E-value=3e-06  Score=60.33  Aligned_cols=77  Identities=16%  Similarity=0.153  Sum_probs=58.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CC--CccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GK--RIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~--~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|++++|+.|++||+. |.--..++   ++  .+ .||+.|+.++..+.+..
T Consensus        35 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~-gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~  112 (142)
T 2bv6_A           35 LTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQV-DLIKRERSEVDQREVFI-HLTDKSETIRPELSNAS  112 (142)
T ss_dssp             CCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHT-TSEEEEECSSSTTCEEE-EECHHHHHHHHHHTTHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeecCCCCcceEEE-EEChHHHHHHHHHHHHH
Confidence            3566788888888754 256677999999999999999999998 54443332   22  34 79999999999988777


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+..
T Consensus       113 ~~~~~  117 (142)
T 2bv6_A          113 DKVAS  117 (142)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66553

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=98.14  E-value=5.7e-06  Score=55.47  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=51.0

Q ss_pred             CchhhHHHHHHHHH--hcCCHHHHHHHh--CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760           1 MNLHQFRFVREAVR--QNFNLTEAAKAL--YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR   68 (306)
Q Consensus         1 m~~~~l~~f~~v~~--~~~s~~~aA~~l--~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~   68 (306)
                      |+.-+.+++..+.+  .. |.+.-|+.+  ++|+++++++|++||+.   -|+.+.+++++++|+.|+.+++
T Consensus        11 md~~d~~IL~~L~~~g~~-s~~eLA~~l~~giS~~aVs~rL~~Le~~---GLV~~~~rg~Y~LT~~G~~~l~   78 (111)
T 3b73_A           11 MTIWDDRILEIIHEEGNG-SPKELEDRDEIRISKSSVSRRLKKLADH---DLLQPLANGVYVITEEGEAYLN   78 (111)
T ss_dssp             CCHHHHHHHHHHHHHSCB-CHHHHHTSTTCCSCHHHHHHHHHHHHHT---TSEEECSTTCEEECHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHcCCC-CHHHHHHHHhcCCCHHHHHHHHHHHHHC---CCEEecCCceEEECchHHHHHH
Confidence            45556667777765  45 889999999  99999999999999985   3555566776699999999886

>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=98.13  E-value=1.1e-05  Score=57.79  Aligned_cols=74  Identities=20%  Similarity=0.232  Sum_probs=57.9

Q ss_pred             chhhHHHHHHHHH-h-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR-Q-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         2 ~~~~l~~f~~v~~-~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      +..++.++..+.+ . +.+.+..|+.+++|+|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+..
T Consensus        34 ~~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~-g--lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  109 (147)
T 2hr3_A           34 QFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERG-G--LIVRHADPQDGRRTRV-SLSSEGRRNLYGNRA  109 (147)
T ss_dssp             HHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-T--SEEEEC------CCEE-EECHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-C--CEeeCCCCCCCCceee-EECHHHHHHHHHHHH
Confidence            3467888888886 2 2389999999999999999999999997 2  33332       2335 799999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      .......
T Consensus       110 ~~~~~~~  116 (147)
T 2hr3_A          110 KREEWLV  116 (147)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776544

>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=98.13  E-value=6.5e-06  Score=54.09  Aligned_cols=76  Identities=21%  Similarity=0.190  Sum_probs=54.5

Q ss_pred             chhhHHHHHHHHHh-c----CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ-N----FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         2 ~~~~l~~f~~v~~~-~----~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~l~~~a~~il   74 (306)
                      +-+.+.++..+... +    .+.+.-|+.+++++|++|+.|++||+. |.---..++  +.+ .||+.|+.++..+.+..
T Consensus        11 ~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~-Glv~~~~d~R~~~v-~LT~~G~~~~~~~~~~~   88 (95)
T 2qvo_A           11 KEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEA-KMVECELEGRTKII-RLTDKGQKIAQQIKSII   88 (95)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHT-TSEEEEEETTEEEE-EECHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-cCccCCCCCCeEEE-EEChhHHHHHHHHHHHH
Confidence            34566666666542 2    268999999999999999999999975 433222223  245 89999999999988887


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+++
T Consensus        89 ~~~e~   93 (95)
T 2qvo_A           89 DIMEN   93 (95)
T ss_dssp             HHC--
T ss_pred             HHHhc
Confidence            76553

>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=98.12  E-value=1e-05  Score=58.51  Aligned_cols=75  Identities=15%  Similarity=0.207  Sum_probs=58.5

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-------CccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-------RIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-------~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .|.+..|+.+++|+|++|+.|++||+. |  |+.|...       .+ .||+.|+.++..+.+
T Consensus        35 l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~-g--lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  110 (155)
T 1s3j_A           35 VTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQK-N--LIARTHNTKDRRVIDL-SLTDEGDIKFEEVLA  110 (155)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHT-T--SEEEEECSSCTTSEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEeecCCCCCCceEEE-EECHHHHHHHHHHHH
Confidence            4566788888888743 278899999999999999999999997 4  4444322       35 799999999998887


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       111 ~~~~~~~  117 (155)
T 1s3j_A          111 GRKAIMA  117 (155)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7765443

>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=98.12  E-value=1e-05  Score=54.35  Aligned_cols=71  Identities=14%  Similarity=0.179  Sum_probs=53.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHhHHHHHHHHHHHHHH
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~G~~l~~~a~~il~~   76 (306)
                      ...++++..+.+.+.+++.-|+.+++|+|++|++|+.|| +.|.-...|.|+.+. ++|+.+  +.+.+..+++.
T Consensus        26 ~~r~~IL~~L~~~~~~~~ela~~l~is~stvs~~L~~L~-~~Glv~~~~~gr~~~y~l~~~~--~~~~~~~l~~~   97 (106)
T 1r1u_A           26 YNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLK-SVHLVKAKRQGQSMIYSLDDIH--VATMLKQAIHH   97 (106)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHH-HTTSEEEEEETTEEEEEESSHH--HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH-HCCCeEEEEeCCEEEEEEChHH--HHHHHHHHHHH
Confidence            345677777765444899999999999999999999999 789998888877542 567654  44445554443

>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=98.12  E-value=8e-06  Score=58.13  Aligned_cols=75  Identities=21%  Similarity=0.323  Sum_probs=55.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|+|++|+.|++||+.   -|+.|.       ...+ .||+.|+.++..+.+
T Consensus        35 lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~---Glv~r~~~~~DrR~~~~-~LT~~G~~~~~~~~~  110 (142)
T 3ech_A           35 LTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR---NLVRRERNPSDQRSFQL-FLTDEGLAIHLHAEL  110 (142)
T ss_dssp             CCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHT---TSEEC----------CC-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC---CCEeeccCCCCCCeeee-EECHHHHHHHHHHHH
Confidence            3567888888888754 366788999999999999999999985   455553       2335 799999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       111 ~~~~~~~  117 (142)
T 3ech_A          111 IMSRVHD  117 (142)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7666544

>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=98.12  E-value=1.2e-05  Score=57.51  Aligned_cols=77  Identities=16%  Similarity=0.239  Sum_probs=56.3

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---C--CCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---G--KRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~--~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ++..++.++..+...+.+.+.-|+.+++|+|++|+.|++||+. |.--..++   +  ..+ .||+.|+.++..+.....
T Consensus        35 l~~~~~~iL~~l~~~~~~~~ela~~l~~s~~tvs~~l~~Le~~-glv~r~~~~~d~r~~~~-~lT~~G~~~~~~~~~~~~  112 (146)
T 2gxg_A           35 LSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEM-GLVVRVRDREDRRKILI-EITEKGLETFNKGIEIYK  112 (146)
T ss_dssp             CCHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEE-EECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCcCHHHHHHHhCCCchhHHHHHHHHHHC-CCEEeecCCCCCceEEE-EECHHHHHHHHHHHHHHH
Confidence            3556777777777222366777999999999999999999998 44333332   1  235 799999999998887766


Q ss_pred             HHHH
Q psy3760          76 EIEG   79 (306)
Q Consensus        76 ~~~~   79 (306)
                      ....
T Consensus       113 ~~~~  116 (146)
T 2gxg_A          113 KLAN  116 (146)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>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=98.11  E-value=9.3e-06  Score=57.65  Aligned_cols=75  Identities=13%  Similarity=0.126  Sum_probs=59.5

Q ss_pred             CchhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a   70 (306)
                      ++..++.++..+.+.+   -+.+.-|+.+++|++++|+.|++||+. |  |+.|..       ..+ .||+.|+.++..+
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~-G--li~r~~~~~d~R~~~i-~lT~~G~~~~~~~  107 (141)
T 3bro_A           32 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIK-K--LLYRKVSGKDSRQKCL-KLTKKANKLETII  107 (141)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEEECSSCTTSEEE-EECHHHHTTHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHC-C--CEEeeCCCcCCCeeee-EECHHHHHHHHHH
Confidence            3556788888888764   389999999999999999999999997 3  444431       234 7999999999988


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      ......+.+
T Consensus       108 ~~~~~~~~~  116 (141)
T 3bro_A          108 LSYMDSDQS  116 (141)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            887766554

>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding; structural genomics, transporter, PSI-2, protein structure initiative; HET: LYS; 2.00A {Silicibacter pomeroyi} SCOP: c.94.1.0

Probab=98.10  E-value=6e-05  Score=58.30  Aligned_cols=191  Identities=6%  Similarity=-0.054  Sum_probs=115.7

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~  158 (306)
                      .++|+||+.....           ..+...++..+.++. ++++++...+...++..|.+|++|+++......  ....+
T Consensus         4 a~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~r~~~~   82 (232)
T 3i6v_A            4 ADTVRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRA-GLTCEWVKNDWDSIIPNLVSGNYDTIIAGMSITDERDEVI   82 (232)
T ss_dssp             --CEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHH-TCCEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHTTS
T ss_pred             CCEEEEEECCCCCCeeEECCCCCEeeehHHHHHHHHHHc-CCceEEEECCHHHHHHHHHCCCCCEEEeCCcCCHHHHhhc
Confidence            4678998873211           245667777777664 888999989999999999999999987532111  11222


Q ss_pred             -eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                       -+.++.....+++++++.         ++||.+ .+.. ..+...    ..++...+   .....+++...++.++.+|
T Consensus        83 ~fs~p~~~~~~~~~~~~~~---------~~dL~g-~igv-~~g~~~----~~~l~~~~---~~~~~~~~~~~~~~~L~~G  144 (232)
T 3i6v_A           83 DFTQNYIPPTASSYVATSD---------GADLSG-IVAA-QTATIQ----AGYIAESG---ATLVEFATPEETIAAVRNG  144 (232)
T ss_dssp             EEEEEEECCCEEEEEESST---------TCCTTS-EEEE-ETTSHH----HHHHHHSS---SEEEEESSHHHHHHHHHTT
T ss_pred             CcccccccCCeEEEEECCC---------hHHhCC-CEEE-ecCchH----HHHHHhcC---CeEEEeCCHHHHHHHHHcC
Confidence             356788888899988875         677888 4444 444332    34444443   3355678999999999999


Q ss_pred             cce-eeeecceeccc--cc-CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         238 MGI-GIIASIAFDSN--RD-KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       238 ~gi-~~~p~~~~~~~--~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ..= .+.....+..+  .. +++..++.+. .....++++.+++.  ......|-+.|++.-+....+++.
T Consensus       145 rvDa~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~k~~--~~l~~~ln~~l~~l~~~G~~~~i~  212 (232)
T 3i6v_A          145 EADAVFADRDYLVPIVAESGGELMFVGDDV-PLGGGVGMGLRESD--GELRGKFDAAITSMKEDGTLNTMI  212 (232)
T ss_dssp             SSSEEEEEHHHHHHHHHHTTTSSEEEEEEE-ECSSCEEEEECTTC--HHHHHHHHHHHHHHHHTSHHHHHH
T ss_pred             CcCEEEEChHHHHHHHHhCCCCeEEecCCC-CCCCcEEEEEeCCC--HHHHHHHHHHHHHHHHCChHHHHH
Confidence            543 33444333322  22 5566655322 23346788877652  334444444444443333444443

>3tmg_A Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein...; ssgcid, structural genomics; 1.90A {Borrelia burgdorferi}

Probab=98.09  E-value=0.00063  Score=54.22  Aligned_cols=192  Identities=11%  Similarity=0.109  Sum_probs=126.4

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC--------CCceee-
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS--------DKLISI-  161 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~--------~~~~~~-  161 (306)
                      ..+.|+||....-...++..++..+.+. -++++++...+...+.+.|.+|++|+......+...        ..+... 
T Consensus        14 ~~~~I~Ig~~~~te~~i~~~i~~~~Le~-~G~~Ve~~~~~~~~~~~AL~~G~iD~~~e~w~~~~~~~~~~~~~~~l~~l~   92 (280)
T 3tmg_A           14 NLKSVKIGYVNWGGETAATNVLKVVFEK-MGYNAEIFSVTTSIMYQYLASGKIDGTVSSWVPTADKFYYEKLKTKFVDLG   92 (280)
T ss_dssp             -CEEEEEEECCCHHHHHHHHHHHHHHHH-TTEEEEEEECCHHHHHHHHHTTSSSEEEEEEETTTTHHHHHHHGGGEEEEE
T ss_pred             CCCCEEEEcCCCchHHHHHHHHHHHHHH-CCCceEEEECCcHHHHHHHHCCCCcEEEeccCCcccHHHHHHhcCcEEEcc
Confidence            4568999998887777888888888877 589999988888788999999999999864221111        122211 


Q ss_pred             c-cccceEEEEecCCCCCCCCCCcChhhhcCCC------eEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH----HH
Q psy3760         162 P-CYQWEYVIIVPLDHPLLLLNSISLKEISNYP------LITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD----II  230 (306)
Q Consensus       162 ~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  230 (306)
                      + .....+.+++++..+     --+++||.++.      ++..+++..........++..|+.........+..    .+
T Consensus        93 ~~~~~~~~~l~V~~~~~-----i~sisDL~~~~~~f~~~~~g~~~G~~~~~~~~~~l~~yGL~~~~~~v~~s~~~m~~~l  167 (280)
T 3tmg_A           93 ANYEGTIQGFVVPSYVP-----ISSISELKGKGDKFKNKMIGIDAGAGTQIVTEQALNYYGLSKEYELVPSSESVMLASL  167 (280)
T ss_dssp             EEEEEEEEEEEEETTSC-----CCBGGGGTTCGGGGTTEEECCSTTCHHHHHHHHHHHHTTCTTTSEEECCCHHHHHHHH
T ss_pred             ccCCCceEEEEECCCCC-----CCCHHHHHhhHHHcCCeEEecCCCchhHHHHHHHHHhcCCCCceEEEeCCHHHHHHHH
Confidence            1 223457888888763     34788888764      67677776656666778888898511222233333    24


Q ss_pred             HHHHHhccc---eeeeecceecccccCCceeeecCCCC--ccceEEEEEeCCc-cccHHHHHHHHHH
Q psy3760         231 KTYVELRMG---IGIIASIAFDSNRDKNLRSISASHLF--GTTISRVIIKQGT-YLRSYVYSFIKLL  291 (306)
Q Consensus       231 ~~~v~~g~g---i~~~p~~~~~~~~~~~l~~~~~~~~~--~~~~~~l~~~~~~-~~~~~~~~~~~~l  291 (306)
                      .+++.+|.-   .+.-|.+....   .+++.+.-+...  +....+.+.+++- ...|.+.+|++-+
T Consensus       168 ~~A~~~g~~~v~~~w~p~~~~~~---~~l~~LeD~k~~~~p~~~~~~vvr~~~~~~~P~~~~~L~~l  231 (280)
T 3tmg_A          168 DSSIKRNEWILVPLWKPHWAFSR---YDIKFLDDPDLIMGGIESVHTLVRLGLENDDFDAYYVFDHF  231 (280)
T ss_dssp             HHHHHTTCCCCEEEEESCTHHHH---SCEEECBCTTCTTCSSEEEEEEEETTHHHHCHHHHHHHHHC
T ss_pred             HHHHHCCCCEEEEEecCchhhhc---CCeEEecCccccCCCcceEEEEeccchhhHChHHHHHHHhC
Confidence            567777743   45566666544   368887665432  4456666666652 3457888888877

>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=98.09  E-value=1.3e-05  Score=57.72  Aligned_cols=74  Identities=15%  Similarity=0.189  Sum_probs=54.9

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE-------ecCCCccccCHhHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI-------RHGKRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~-------R~~~~~~~lT~~G~~l~~~a~~i   73 (306)
                      +..++.++..+ +.+ .|.+.-|+.+++|+|++|+.|++||+. |.---.       |....+ .||+.|+.++..+.+.
T Consensus        37 t~~q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~-Glv~r~~~~~~~D~R~~~~-~lT~~G~~~~~~~~~~  113 (151)
T 3kp7_A           37 SAEQSHVLNML-SIEALTVGQITEKQGVNKAAVSRRVKKLLNA-ELVKLEKPDSNTDQRLKII-KLSNKGKKYIKERKAI  113 (151)
T ss_dssp             CHHHHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHT-TSEEC-----------CCB-EECHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCCCCCCCCeeEE-EECHhHHHHHHHHHHH
Confidence            45677777777 554 356777999999999999999999987 544332       223445 7999999999998888


Q ss_pred             HHHHH
Q psy3760          74 MQEIE   78 (306)
Q Consensus        74 l~~~~   78 (306)
                      ...+.
T Consensus       114 ~~~~~  118 (151)
T 3kp7_A          114 MSHIA  118 (151)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66653

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=98.08  E-value=1.3e-05  Score=54.19  Aligned_cols=71  Identities=17%  Similarity=0.174  Sum_probs=53.5

Q ss_pred             HHHHHHHHHhcCC--HHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEec---CCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFN--LTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRH---GKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         6 l~~f~~v~~~~~s--~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      +.++..+.+...+  ++.=|+.+ ++|++++|++|+.||+.   -|+.|.   ...+ +||+.|+.+.+....+.+-.+.
T Consensus        30 l~IL~~L~~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~---GlV~r~~~r~~~y-~LT~~G~~l~~~l~~l~~w~~~  105 (111)
T 3df8_A           30 MLIISVLGNGSTRQNFNDIRSSIPGISSTILSRRIKDLIDS---GLVERRSGQITTY-ALTEKGMNVRNSLMPLLQYISV  105 (111)
T ss_dssp             HHHHHHHTSSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHT---TSEEEEESSSEEE-EECHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHC---CCEEEeecCcEEE-EECccHHHHHHHHHHHHHHHHH
Confidence            4445555533225  89999999 99999999999999985   466665   2344 8999999999998888775444


Q ss_pred             H
Q psy3760          80 L   80 (306)
Q Consensus        80 ~   80 (306)
                      +
T Consensus       106 ~  106 (111)
T 3df8_A          106 L  106 (111)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=98.08  E-value=1.4e-05  Score=57.49  Aligned_cols=75  Identities=17%  Similarity=0.240  Sum_probs=58.2

Q ss_pred             CchhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-------CccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-------RIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-------~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.+  .+.+.-|+.+++++|++|+.|++||+.   -|+.|...       .+ .||+.|+.++..+.
T Consensus        37 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~---Glv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~  112 (150)
T 3fm5_A           37 LRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEER---GLVVRTLDPSDRRNKLI-AATEEGRRLRDDAK  112 (150)
T ss_dssp             CCHHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHTT---TSEEC-----------C-EECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHHC---CCEEeeCCccccchhee-eECHHHHHHHHHHH
Confidence            3567888888887643  288999999999999999999999985   55666432       25 79999999999888


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      +....+..
T Consensus       113 ~~~~~~~~  120 (150)
T 3fm5_A          113 ARVDAAHG  120 (150)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            87766544

>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=98.07  E-value=1.1e-05  Score=58.08  Aligned_cols=75  Identities=17%  Similarity=0.145  Sum_probs=57.2

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|++++|+.|++||+.=   |+.|.       ...+ .||+.|+.++..+..
T Consensus        38 lt~~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~G---lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  113 (152)
T 3bj6_A           38 VTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAG---LIERRTNPEHARSHRY-WLTPRGEAIITAIRA  113 (152)
T ss_dssp             CCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTT---SEEEECCSSSTTSCEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC---CeeecCCcccccceee-EEChhhHHHHHHHHH
Confidence            3567888899998865 1345559999999999999999999873   33432       2244 799999999998887


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       114 ~~~~~~~  120 (152)
T 3bj6_A          114 DEMAKLA  120 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766544

>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=98.07  E-value=6.3e-06  Score=56.92  Aligned_cols=68  Identities=15%  Similarity=0.138  Sum_probs=47.8

Q ss_pred             hhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         4 ~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~l~~~a~~il~   75 (306)
                      ..++++..+.  ... |++..|+.+|+|+|++|++|+.|| +.|.-...|.|+.. +++|+.|  +...+..+.+
T Consensus        43 ~rl~IL~~L~~~~~~-s~~eLa~~l~is~stvs~~L~~L~-~~Glv~~~~~gr~~~y~l~~~~--~~~~~~~l~~  113 (122)
T 1u2w_A           43 NRAKITYALCQDEEL-CVCDIANILGVTIANASHHLRTLY-KQGVVNFRKEGKLALYSLGDEH--IRQIMMIALA  113 (122)
T ss_dssp             HHHHHHHHHHHSSCE-EHHHHHHHHTCCHHHHHHHHHHHH-HTTSEEEC----CCEEEESCHH--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCc-CHHHHHHHHCcCHHHHHHHHHHHH-HCCCeEEEEECCEEEEEECHHH--HHHHHHHHHH
Confidence            4567787777  344 899999999999999999999999 78998888887644 2677654  3333444433

>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=98.07  E-value=1.7e-05  Score=57.27  Aligned_cols=77  Identities=18%  Similarity=0.168  Sum_probs=57.9

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      |+..++.++..+.+.+ .|.+..|+.+++|+|++|+.|++||+. |.--..+.     ...+ .||+.|+.++..+.+..
T Consensus        42 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~  119 (154)
T 2eth_A           42 MKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKR-GLVVREMDPVDRRTYRV-VLTEKGKEIFGEILSNF  119 (154)
T ss_dssp             SBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHT-TSEEEEECTTTSSCEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCCCCcceeEE-EECHHHHHHHHHHHHHH
Confidence            3567888888888742 388999999999999999999999997 33222221     2234 79999999999887776


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      .....
T Consensus       120 ~~~~~  124 (154)
T 2eth_A          120 ESLLK  124 (154)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65443

>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=98.06  E-value=2e-06  Score=61.73  Aligned_cols=75  Identities=16%  Similarity=0.232  Sum_probs=57.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|+|++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+.+
T Consensus        38 l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~---glv~r~~~~~d~R~~~~-~LT~~G~~~~~~~~~  113 (147)
T 1z91_A           38 ITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQ---GLITRKRSEEDERSVLI-SLTEDGALLKEKAVD  113 (147)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHH---TSEECCBCSSCTTSBEE-EECHHHHSGGGGTTT
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHC---CCEEeccCCCCCCeeEE-EECHhHHHHHHHHHH
Confidence            3567788888888754 256677999999999999999999998   3455532       225 799999999998877


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       114 ~~~~~~~  120 (147)
T 1z91_A          114 IPGTILG  120 (147)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7665544

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=98.05  E-value=1.9e-05  Score=60.90  Aligned_cols=71  Identities=18%  Similarity=0.278  Sum_probs=53.3

Q ss_pred             HHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus         7 ~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      +++..+.+.|.+.  +.-|+.+++|+|++|+.|++||+.   -|+.|.. +++ .||+.|+.++..+.+....++...
T Consensus        13 ~~i~~l~~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~---GlV~r~~~~~v-~LT~~G~~~~~~~~~~~~~~e~~l   86 (226)
T 2qq9_A           13 RTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERD---GLVVVASDRSL-QMTPTGRTLATAVMRKHRLAERLL   86 (226)
T ss_dssp             HHHHHHHHHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEECTTSBE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCccHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEeCCCCe-EECHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333254  899999999999999999999998   4566655 456 899999999998887766555544

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

Probab=98.05  E-value=7.7e-06  Score=58.16  Aligned_cols=77  Identities=16%  Similarity=0.191  Sum_probs=57.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHH-HHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAIL-RSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~-~~a~~i   73 (306)
                      |+..++.++..+.+.+ .|.+..|+.+++|++++|+.|++||+. |.--..+.     ...+ .||+.|+.++ ..+...
T Consensus        29 l~~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~-gli~~~~~~~d~r~~~~-~lT~~G~~~~~~~~~~~  106 (142)
T 3bdd_A           29 ISLTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEES-GYIIRKRNPDNQREVLV-WPTEQAREALITNPSAH  106 (142)
T ss_dssp             SCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSSTTCEEE-EECHHHHHHHTTSCCHH
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCCCeeEE-EECHHHHHHHHHHHHHH
Confidence            4567888888887643 378888999999999999999999997 43333322     2234 7999999999 777666


Q ss_pred             HHHHHH
Q psy3760          74 MQEIEG   79 (306)
Q Consensus        74 l~~~~~   79 (306)
                      ...+..
T Consensus       107 ~~~~~~  112 (142)
T 3bdd_A          107 HQAIKT  112 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            655443

>2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB; SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A {Bacillus subtilis}

Probab=98.05  E-value=0.00011  Score=58.42  Aligned_cols=197  Identities=13%  Similarity=0.030  Sum_probs=120.6

Q ss_pred             CCcEEEEecccch--------------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CC
Q psy3760          92 TGNLTIATTHTQA--------------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PS  155 (306)
Q Consensus        92 ~~~l~I~~~~~~~--------------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~  155 (306)
                      .+.|+||+.....              ..+...++..+.++. ++++++...+...++..+.+|++|+++......  ..
T Consensus        20 ~~~l~v~~~~~~pP~~~~~~~~~~g~~~G~~~dl~~~i~~~~-g~~v~~~~~~~~~~~~~l~~G~~D~~~~~~~~t~~r~   98 (271)
T 2iee_A           20 KGKIVVATSGTLYPTSYHDTDSGSDKLTGYEVEVVREAAKRL-GLKVEFKEMGIDGMLTAVNSGQVDAAANDIDVTKDRE   98 (271)
T ss_dssp             HTEEEEEECSCBTTTBEEETTTTCCEEECHHHHHHHHHHHHT-TCEEEEEECCSTTHHHHHHHTSSSEECSSCBCCHHHH
T ss_pred             CCeEEEEECCCCCCeeEeCCCCCCCCceeeHHHHHHHHHHHc-CCeEEEEECCHHHHHHHHHCCCcCEEEeCCcCChhhc
Confidence            3579999862111              246667888888775 789999988999999999999999998532111  11


Q ss_pred             CCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHH--HH
Q psy3760         156 DKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDII--KT  232 (306)
Q Consensus       156 ~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~  232 (306)
                      ..+. +.++.....+++++++.+.   ..-+++||.+..+.... +..    ....++..+.   ....+++...+  +.
T Consensus        99 ~~~~fs~p~~~~~~~l~~~~~~~~---~i~~~~dL~g~~i~v~~-g~~----~~~~l~~~~~---~~~~~~~~~~~~l~~  167 (271)
T 2iee_A           99 EKFAFSTPYKYSYGTAIVRKDDLS---GIKTLKDLKGKKAAGAA-TTV----YMEVARKYGA---KEVIYDNATNEQYLK  167 (271)
T ss_dssp             TTEEECCCSEEEEEEEEECTTTGG---GCSSGGGGTTCEEESCT-TSH----HHHHHHHTTC---EEEECSSCCHHHHHH
T ss_pred             cceEEeecceeCCeEEEEECCCCC---CCCCHHHhCCCEEEEeC-Ccc----HHHHHHHcCC---ceEEeCChhhHHHHH
Confidence            2222 4577888899999988742   13478999888766543 322    2344555554   34566777777  89


Q ss_pred             HHHhccceeeeecceeccc-----ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         233 YVELRMGIGIIASIAFDSN-----RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       233 ~v~~g~gi~~~p~~~~~~~-----~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ++..|..=+++....+..+     ....+..++ .......+++++.+++.  ......|-+.|.+.-+....+++
T Consensus       168 ~L~~GrvD~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~k~~--~~l~~~ln~al~~l~~~G~~~~i  240 (271)
T 2iee_A          168 DVANGRTDVILNDYYLQTLALAAFPDLNITIHP-DIKYMPNKQALVMKKSN--AALQKKMNEALKEMSKDGSLTKL  240 (271)
T ss_dssp             HHHHTSSCEEEEEHHHHHHHHHHCTTSSCEECS-SCCEEEEEECCEEETTC--HHHHHHHHHHHHHHHHHTHHHHH
T ss_pred             HHHcCCccEEeccHHHHHHHHHhCCCCceEEec-CCCcccceEEEEEcCCC--HHHHHHHHHHHHHHHHCCCHHHH
Confidence            9999844355554333221     122344442 22233457778888763  33445554555444443344444

>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=98.03  E-value=2.8e-05  Score=55.44  Aligned_cols=77  Identities=13%  Similarity=0.129  Sum_probs=58.5

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE-----ecCCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI-----RHGKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~-----R~~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ .|++..|+.+++|+|++|+.|++||+. |.--..     |....+ .||+.|+.++..+....
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~-glv~r~~~~~d~r~~~~-~lT~~G~~~~~~~~~~~  108 (145)
T 2a61_A           31 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEAD-GYLTRTPDPADRRAYFL-VITRKGEEVIEKVIERR  108 (145)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC-CCeeecCCCCCCceEEE-EECHHHHHHHHHHHHHH
Confidence            4567788888887643 388999999999999999999999997 332222     122345 79999999999888776


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      .....
T Consensus       109 ~~~~~  113 (145)
T 2a61_A          109 ENFIE  113 (145)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65443

>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=98.03  E-value=3.7e-05  Score=52.13  Aligned_cols=76  Identities=17%  Similarity=0.188  Sum_probs=54.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +.++..+.+.+.+++.-|+.+ ++|++++|++|++||+. |  |+.|..       ..+ .||+.|+.+++.+..+.+-.
T Consensus        25 ~~IL~~L~~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~-G--lI~r~~~~~d~r~~~~-~LT~~G~~~~~~~~~l~~w~  100 (112)
T 1z7u_A           25 LSLMDELFQGTKRNGELMRALDGITQRVLTDRLREMEKD-G--LVHRESFNELPPRVEY-TLTPEGYALYDALSSLCHWG  100 (112)
T ss_dssp             HHHHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHHHHHHH-T--SEEEEEECCSSCEEEE-EECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhccCCHHHHHHHHHHHHHC-C--CEEEeecCCCCCeEEE-EECHhHHHHHHHHHHHHHHH
Confidence            445555554434899999999 99999999999999986 3  333331       224 89999999999888876655


Q ss_pred             HHHHHHHH
Q psy3760          78 EGLKKIGK   85 (306)
Q Consensus        78 ~~~~~~~~   85 (306)
                      ++......
T Consensus       101 ~~~~~~~~  108 (112)
T 1z7u_A          101 ETFAQKKA  108 (112)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55444433

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

Probab=98.03  E-value=2.2e-05  Score=55.74  Aligned_cols=78  Identities=18%  Similarity=0.212  Sum_probs=58.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE----EecCCCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIF----IRHGKRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf----~R~~~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ++..++.++..+.+.+ -|.+..|+.+++|++++|+.|++||+.==+.-.    +|....+ .||+.|+.++..+.+...
T Consensus        34 lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~~  112 (142)
T 2fbi_A           34 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYV-NLTEKGQQCFVSMSGDME  112 (142)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE-EECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEE-EECHHHHHHHHHHHHHHH
Confidence            4567788888888743 278999999999999999999999987322222    1223345 799999999998887766


Q ss_pred             HHHH
Q psy3760          76 EIEG   79 (306)
Q Consensus        76 ~~~~   79 (306)
                      .+..
T Consensus       113 ~~~~  116 (142)
T 2fbi_A          113 KNYQ  116 (142)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

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

Probab=98.02  E-value=1e-05  Score=57.17  Aligned_cols=77  Identities=18%  Similarity=0.169  Sum_probs=57.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE----EecCCCccccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIF----IRHGKRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf----~R~~~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|+|++|+.|++||+.=-+.-.    +|....+ .||+.|+.++..+.+...
T Consensus        27 l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~~  105 (138)
T 3bpv_A           27 LTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYIL-EVTRRGEEIIPLILKVEE  105 (138)
T ss_dssp             CCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE-EECHHHHHTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCceeEEe-eECHhHHHHHHHHHHHHH
Confidence            3566788888888754 266777999999999999999999987322221    1222345 799999999998887776


Q ss_pred             HHH
Q psy3760          76 EIE   78 (306)
Q Consensus        76 ~~~   78 (306)
                      ...
T Consensus       106 ~~~  108 (138)
T 3bpv_A          106 RWE  108 (138)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP: c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A* 1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A* 1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A 1my0_A ...

Probab=98.02  E-value=7.2e-05  Score=58.98  Aligned_cols=173  Identities=14%  Similarity=0.046  Sum_probs=103.0

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeC-------------ChhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQG-------------NPKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYV  169 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~-------------~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~  169 (306)
                      .+...++..+.++. ++++++...             +...++..|.+|++|+++......  ....+. +.++.....+
T Consensus        34 G~~~dl~~~ia~~l-g~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~fs~p~~~~~~~  112 (263)
T 1mqi_A           34 GYCVDLAAEIAKHC-GFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS  112 (263)
T ss_dssp             SHHHHHHHHHHHHH-TCCEEEEECTTCCCCCBCTTTCCBCHHHHHHHTTSCSEECSSCBCCHHHHTTEEECSCSEEECEE
T ss_pred             eeHHHHHHHHHHHc-CceEEEEEccccccCccCCCCCCcHHHHHHHHcCCcCEEEEeeEecHHHHhhcccccceecccEE
Confidence            35566777777664 678888876             788999999999999998521211  112333 3578888999


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCe---EeecCCCCcHHHHHHHHHhCCCc-----------eeEEEEecCHHHHHHHH-
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPL---ITYDLSFSGRIKLDREFSLQKLT-----------PYIVLETINSDIIKTYV-  234 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~---i~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~v-  234 (306)
                      ++++++.+     .-+++||.+...   .....+ ..    .+.+...++.           ......+++...++.++ 
T Consensus       113 ~~~~~~~~-----i~~~~dL~g~~~~~ig~v~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  182 (263)
T 1mqi_A          113 IMIKKGTP-----IESAEDLSKQTEIAYGTLDSG-ST----KEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVR  182 (263)
T ss_dssp             EEEETTCS-----CCSHHHHHTCSSSEEECBSSS-HH----HHHHHHCCSHHHHHHHHHHHHCSSCCCBSSHHHHHHHHH
T ss_pred             EEEcCccc-----cCCHHHHhcccCeeEEEEecc-HH----HHHHHhccchhHHHHHHHHhhCCCceecCCHHHHHHHHh
Confidence            99998875     237899998873   223222 11    1223333321           11244678899999999 


Q ss_pred             -Hhccceeeeec-ceeccc-ccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         235 -ELRMGIGIIAS-IAFDSN-RDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       235 -~~g~gi~~~p~-~~~~~~-~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                       ..|. .+++-. ..+... ...  .+..++  .......++++.+++......+.+.+..++
T Consensus       183 ~~~g~-da~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~k~~~l~~~in~~l~~l~  242 (263)
T 1mqi_A          183 KSKGK-YAYLLESTMNEYIEQRKPCDTMKVG--GNLDSKGYGIATPKGSSLGNAVNLAVLKLN  242 (263)
T ss_dssp             HTTTS-EEEEEEHHHHHHHTTSTTCCEEEES--CCSCCEEECCEEETTCTTHHHHHHHHHHHH
T ss_pred             hcCCc-EEEEechHHHHHHHhcCCCceEEcC--CcccccceEEEEeCCCccHHHHHHHHHHHH
Confidence             8888 454443 333222 222  333332  223345778888887544444444444443

>3l6g_A Betaine ABC transporter permease and substrate BI protein; glycine betaine binding, substrate binding domain, venus FLY cell membrane; HET: B3P; 1.90A {Lactococcus lactis} PDB: 3l6h_A

Probab=98.01  E-value=0.00065  Score=53.33  Aligned_cols=188  Identities=10%  Similarity=0.077  Sum_probs=125.8

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC--------CCcee-ec-
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS--------DKLIS-IP-  162 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~--------~~~~~-~~-  162 (306)
                      +.|+||....-...++..++..+.+.. ++++++...+...+.+.|.+|++|+......+...        ..+.. -+ 
T Consensus         2 ~~I~ig~~~w~e~~i~~~i~~~~Le~~-G~~Ve~~~~~~~~~~~al~~G~iD~~~e~w~~~~~~~~~~~~~~~l~~l~~~   80 (256)
T 3l6g_A            2 KKVDLVYMNWDSEVASINVLTQAMKEH-GFDVKTTALDNAVAWQTVANGQADGMVSAWLPNTHKTQWQKYGKSVDLLGPN   80 (256)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHHHHT-TEEEEEEECCHHHHHHHHHTTSSSEEEEEEETTTTHHHHHHHGGGEEEEEEE
T ss_pred             CCEEEEecCCcHHHHHHHHHHHHHHHC-CCceEEEECChHHHHHHHHCCCCeEEEcccCCcccHHHHHHhCCceEEcccc
Confidence            579999998888889999999988887 99999999888889999999999998764221110        11221 11 


Q ss_pred             cccceEEEEecCCCCCCCCCCcChhhhcC---CCeEeecCCCCcHHHHHHHHHhC-CCc-eeEEEEecCHHH----HHHH
Q psy3760         163 CYQWEYVIIVPLDHPLLLLNSISLKEISN---YPLITYDLSFSGRIKLDREFSLQ-KLT-PYIVLETINSDI----IKTY  233 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~~~~i~~~dl~~---~~~i~~~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~----~~~~  233 (306)
                      .....+.+++++..     .--+++||.+   ..++..+++..........++.. |+. .+.  ...+...    +.++
T Consensus        81 ~~~~~~~l~Vp~~~-----~i~si~DL~~~~~g~~~g~~~G~~~~~~~~~~l~~y~gL~~~~~--v~~s~~~m~~~l~~A  153 (256)
T 3l6g_A           81 LKGAKVGFVVPSYM-----NVNSIEDLTNQANKTITGIEPGAGVMAASEKTLNSYDNLKDWKL--VPSSSGAMTVALGEA  153 (256)
T ss_dssp             EEEEEEEEEEETTS-----CCCBGGGCSSGGGGEEECCCTTCHHHHHHHHHHTTCGGGTTCEE--ECCCHHHHHHHHHHH
T ss_pred             CCCceEEEEECCcc-----CCCCHHHHHHhcCCeEEecCCCchhhHHHHHHHHhcCCCCCeEE--ecCCHHHHHHHHHHH
Confidence            22346888888876     2346777753   46777777776666667778888 775 332  2234332    3477


Q ss_pred             HHhc---cceeeeecceecccccCCceeeecCCCC--ccceEEEEEeCC-ccccHHHHHHHHHH
Q psy3760         234 VELR---MGIGIIASIAFDSNRDKNLRSISASHLF--GTTISRVIIKQG-TYLRSYVYSFIKLL  291 (306)
Q Consensus       234 v~~g---~gi~~~p~~~~~~~~~~~l~~~~~~~~~--~~~~~~l~~~~~-~~~~~~~~~~~~~l  291 (306)
                      +++|   ...+.-|.+....   .+++.+.-+...  +....+.+.+++ ....|.+.+|++-+
T Consensus       154 ~~~g~~~v~~~w~p~~~~~~---~~l~~LeDpk~~~~~~~~~~~vvr~~~~~~~P~~~~~L~~~  214 (256)
T 3l6g_A          154 IKQHKDIVITGWSPHWMFNK---YDLKYLADPKGTMGTSENINTIVRKGLKKENPEAYKVLDKF  214 (256)
T ss_dssp             HHTTCCCCEEEEESCTHHHH---SCEEECBCTTCTTCCCEEEEEEEETTHHHHCHHHHHHHHHC
T ss_pred             HHCCCCEEEEeecCchhhhh---cCeEEecCCccccCCcceEEEeechhHHHHChHHHHHHHhc
Confidence            7788   3444566666544   378888765532  345666666665 23467788888776

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=98.00  E-value=2.1e-05  Score=50.92  Aligned_cols=67  Identities=13%  Similarity=0.133  Sum_probs=49.8

Q ss_pred             chhhHHHHHHHHHh------c-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe----cCCCccccCHhHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ------N-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR----HGKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         2 ~~~~l~~f~~v~~~------~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R----~~~~~~~lT~~G~~l~~~a   70 (306)
                      +.-++-.+..+.+.      + .++.+-|+.+.+++|++||.++.||+.=   |+.|    ++++.+.||++|+.+++.+
T Consensus        15 ~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~G---LV~r~~~~D~R~~v~LT~~G~~~l~~~   91 (96)
T 2obp_A           15 DPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAG---LADVSVEADGRGHASLTQEGAALAAQL   91 (96)
T ss_dssp             CHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTT---SEEEEECTTSCEEEEECHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHCC---CEEeecCCCCceeEEECHHHHHHHHHh
Confidence            34455555555554      1 2899999999999999999999999852   2222    3555568999999999876


Q ss_pred             H
Q psy3760          71 E   71 (306)
Q Consensus        71 ~   71 (306)
                      .
T Consensus        92 ~   92 (96)
T 2obp_A           92 F   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=98.00  E-value=1.9e-05  Score=58.73  Aligned_cols=78  Identities=22%  Similarity=0.205  Sum_probs=58.6

Q ss_pred             CchhhHHHHHHHHHhc----CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE----EecCCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN----FNLTEAAKALYTSQPGVSKAIIELEEELSIDIF----IRHGKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~----~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf----~R~~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+    -+.+.-|+.+++|+|++|+.|++||+.==+.-.    +|....+ .||+.|+.++..+..
T Consensus        67 lt~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~-~LT~~G~~~~~~~~~  145 (181)
T 2fbk_A           67 LNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASI-RLTPQGRALVTHLLP  145 (181)
T ss_dssp             CCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCB-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEE-EECHHHHHHHHHHHH
Confidence            3567888899998864    389999999999999999999999997322221    2223456 899999999998877


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      .......
T Consensus       146 ~~~~~~~  152 (181)
T 2fbk_A          146 AHLATTQ  152 (181)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7665443

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

Probab=97.98  E-value=2.7e-05  Score=56.70  Aligned_cols=77  Identities=14%  Similarity=0.141  Sum_probs=57.9

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ .+.+..|+.+++|++++|+.|++||+. |.--..+     ....+ .||+.|+.++..+....
T Consensus        50 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~~~  127 (162)
T 3cjn_A           50 LSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQAD-GLVRREVDSDDQRSSRV-YLTPAGRAVYDRLWPHM  127 (162)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEC--CCSSEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEecCCCCCCCeeEE-EECHHHHHHHHHHHHHH
Confidence            3567788888888643 278899999999999999999999997 3322222     22335 79999999999888776


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+..
T Consensus       128 ~~~~~  132 (162)
T 3cjn_A          128 RASHD  132 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65443

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=97.97  E-value=3.4e-05  Score=55.24  Aligned_cols=75  Identities=19%  Similarity=0.229  Sum_probs=52.5

Q ss_pred             CchhhHHHHHHHHHh---cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-------cCCCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ---NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-------HGKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~---~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-------~~~~~~~lT~~G~~l~~~a   70 (306)
                      ++..++.++..+.+.   +.+.+.-|+.+++++|++|+.|++||+.   -|+.|       ....+ .||+.|+.+++.+
T Consensus        39 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~---Glv~r~~~~~DrR~~~~-~LT~~G~~~~~~~  114 (148)
T 3jw4_A           39 LNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKK---GYIERRIPENNARQKNI-YVLPKGAALVEEF  114 (148)
T ss_dssp             CCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHT---TSBCCC--------CCC-CBCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHC---CCEEeeCCCCCchhhee-eECHHHHHHHHHH
Confidence            355678888888875   3478999999999999999999999986   23333       23455 8999999999998


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      ......+.+
T Consensus       115 ~~~~~~~~~  123 (148)
T 3jw4_A          115 NNIFLEVEE  123 (148)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888766554

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

Probab=97.97  E-value=5e-05  Score=53.99  Aligned_cols=75  Identities=15%  Similarity=0.162  Sum_probs=58.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+.+
T Consensus        35 lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~-G--lv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~~  110 (143)
T 3oop_A           35 VTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRK-E--LIVREISTEDRRISLL-SLTDKGRKETTELRD  110 (143)
T ss_dssp             SCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEEC----CCSCEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-C--CeeccCCCccCceeee-eECHHHHHHHHHHHH
Confidence            3556788888888654 267888999999999999999999986 4  44443       2334 799999999998888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       111 ~~~~~~~  117 (143)
T 3oop_A          111 IVEASCE  117 (143)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766544

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=97.96  E-value=1.9e-05  Score=54.93  Aligned_cols=74  Identities=18%  Similarity=0.218  Sum_probs=56.9

Q ss_pred             CchhhHHHHHHHHHh--c-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-------cCCCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ--N-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-------HGKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~--~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-------~~~~~~~lT~~G~~l~~~a   70 (306)
                      ++..++.++..+.+.  + -+.+.-|+.+++++|++|+.|++||+. |  |+.|       ....+ .||+.|+.++..+
T Consensus        35 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-G--lv~r~~~~~D~R~~~i-~LT~~G~~~~~~~  110 (127)
T 2frh_A           35 ISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQE-D--YFDKKRNEHDERTVLI-LVNAQQRKKIESL  110 (127)
T ss_dssp             CCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT-T--SSCCBCCSSSSCCCEE-ECCSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEecCCCCCCCeeEE-EECHHHHHHHHHH
Confidence            355678888888875  2 268899999999999999999999985 3  4444       22334 7999999999988


Q ss_pred             HHHHHHHH
Q psy3760          71 EIIMQEIE   78 (306)
Q Consensus        71 ~~il~~~~   78 (306)
                      .+.+..+-
T Consensus       111 ~~~~~~~~  118 (127)
T 2frh_A          111 LSRVNKRI  118 (127)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77765543

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

Probab=97.96  E-value=3.3e-05  Score=55.07  Aligned_cols=74  Identities=15%  Similarity=0.171  Sum_probs=57.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+.   -|+.|.       ...+ .||+.|+.++..+.+
T Consensus        29 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~---Glv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~~  104 (145)
T 3g3z_A           29 LNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQ---GLIEWQEGEQDRRKRLL-SLTETGKAYAAPLTE  104 (145)
T ss_dssp             CCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEECCCSSCGGGSCE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEeeccCCCCCceeee-eEChhHHHHHHHHHH
Confidence            3556788888887654 267888999999999999999999986   355553       2345 799999999988877


Q ss_pred             HHHHHH
Q psy3760          73 IMQEIE   78 (306)
Q Consensus        73 il~~~~   78 (306)
                      ....+.
T Consensus       105 ~~~~~~  110 (145)
T 3g3z_A          105 SAQEFS  110 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776554

>4h1x_A PBP 2, phosphate-binding protein PSTS 2; periplasmic binding protein, PF12849 family; HET: MSE CIT; 1.77A {Streptococcus pneumoniae}

Probab=97.95  E-value=4.2e-05  Score=60.32  Aligned_cols=136  Identities=18%  Similarity=0.233  Sum_probs=102.4

Q ss_pred             ceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhh----------ccCCCCcEEEEecccchhhhhHHHHHHH
Q psy3760          46 IDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEF----------SAYDTGNLTIATTHTQARYALPKIIKEF  115 (306)
Q Consensus        46 ~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~----------~~~~~~~l~I~~~~~~~~~~l~~~l~~~  115 (306)
                      .+||.-.+ +  .+++..+.|+.++..  ++-+++.....-.          .....|+|+|+.+.++ ..++..+...|
T Consensus       104 Rply~y~~-~--~~~~~vk~Fl~f~lS--~~GQ~iv~~~GyvPl~~~~~~~~~~~~~g~i~i~GSst~-~p~~~~~ae~f  177 (265)
T 4h1x_A          104 RPFNIVWS-S--NLSKLGQDFISFIHS--KQGQQVVTDNKFIEAKTETTEYTSQHLSGKLSVVGSTSV-SSLMEKLAEAY  177 (265)
T ss_dssp             EEEEEEEC-T--TCCHHHHHHHHHHHB--HHHHHHHHHTTCBCCCCCCBCCCCCCCEEEEEEEECHHH-HHHHHHHHHHH
T ss_pred             EEEEEEEC-C--CCCHHHHHHHHHHhh--cccceeeecCCcEEecchhhhhhhccccceeEEecCcch-HHHHHHHHHHH
Confidence            45555543 3  478888888887642  2233343333222          2456789999999885 56899999999


Q ss_pred             HHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCceeeccccceEEEEecCCCCCCCCCCcChhhhc
Q psy3760         116 TIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEIS  190 (306)
Q Consensus       116 ~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~  190 (306)
                      .+.||++++.+...++..-+..+..|.+||+....+..+  ..++...++..+.+++++++++|..   .++.++|.
T Consensus       178 ~~~~p~~~v~~~~~GSg~G~~~~~~g~~di~~ssr~l~~~e~~~~~~~~va~d~iavvvn~~n~~~---~Lt~~ql~  251 (265)
T 4h1x_A          178 KKENPEVTIDITSNGSSAGITAVKEKTADIGMVSRELTPEEGKSLTHDAIALDGIAVVVNNDNKAS---QVSMAELA  251 (265)
T ss_dssp             HHHCTEEEEEEEESCHHHHHHHHHHTSCSEEEESSCCCHHHHTTCEEEEEEEEEEEEEECTTCCCC---EECHHHHH
T ss_pred             HhhCCCceeeEecCCcHHHHHHHHcCCCceeeccccCChHHHcCCeEeeEEEEeEEEEECCCCCcc---ccCHHHHH
Confidence            999999999999999999999999999999999755332  2478889999999999999998843   36666654

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

Probab=97.95  E-value=3.8e-05  Score=55.48  Aligned_cols=75  Identities=19%  Similarity=0.298  Sum_probs=59.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+..|+.++++++++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+..
T Consensus        41 lt~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~-G--lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  116 (155)
T 3cdh_A           41 LRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDAR-G--LVTRVADAKDKRRVRV-RLTDDGRALAESLVA  116 (155)
T ss_dssp             CCHHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-T--SEEECC------CCCE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEeccCCCcCCeeEe-EECHHHHHHHHHHHH
Confidence            3556788888887643 278999999999999999999999987 3  44443       2345 799999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       117 ~~~~~~~  123 (155)
T 3cdh_A          117 SARAHET  123 (155)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8776544

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=97.95  E-value=2.1e-05  Score=52.07  Aligned_cols=61  Identities=20%  Similarity=0.269  Sum_probs=47.1

Q ss_pred             chhhHHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHH
Q psy3760           2 NLHQFRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQA   65 (306)
Q Consensus         2 ~~~~l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~   65 (306)
                      |...++++..+.+.  . +++..|+.+|+|||++|++|+.||+.  .-...|.|+.. +++|+.|..
T Consensus        26 ~~~Rl~IL~~l~~~~~~-~~~ela~~l~is~stvs~hL~~L~~~--lv~~~~~gr~~~y~l~~~~~~   89 (99)
T 2zkz_A           26 HPMRLKIVNELYKHKAL-NVTQIIQILKLPQSTVSQHLCKMRGK--VLKRNRQGLEIYYSINNPKVE   89 (99)
T ss_dssp             SHHHHHHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHHHHBTT--TBEEEEETTEEEEECCCHHHH
T ss_pred             CHHHHHHHHHHHHCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHH--hhhheEeCcEEEEEEChHHHH
Confidence            34567777555533  5 89999999999999999999999998  66667777654 278887753

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

Probab=97.93  E-value=2.6e-05  Score=56.74  Aligned_cols=75  Identities=16%  Similarity=0.250  Sum_probs=57.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.++++++++|+.|++||+. |  |+.|..       ..+ .||+.|+.++..+..
T Consensus        51 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~-G--lv~r~~~~~DrR~~~~-~LT~~G~~~~~~~~~  126 (161)
T 3e6m_A           51 LPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDE-G--LAARSISDADQRKRTV-VLTRKGKKKLAEISP  126 (161)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHT-T--SEEECC---CCCSCEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEeeCCcccCCeeEe-eECHHHHHHHHHHHH
Confidence            3556778888887643 256788999999999999999999985 4  555432       334 899999999998888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       127 ~~~~~~~  133 (161)
T 3e6m_A          127 LINDFHA  133 (161)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7666544

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

Probab=97.92  E-value=4.1e-05  Score=56.15  Aligned_cols=74  Identities=19%  Similarity=0.199  Sum_probs=57.2

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++|++++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+..
T Consensus        43 lt~~~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~-G--lV~r~~~~~DrR~~~~-~LT~~G~~~~~~~~~  118 (168)
T 2nyx_A           43 ITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGA-E--LIDRLPHPTSRRELLA-ALTKRGRDVVRQVTE  118 (168)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHT-T--SEEEEECSSCSSCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-C--CEEeccCCCCCCeeEE-EECHHHHHHHHHHHH
Confidence            3566788888887743 267888999999999999999999986 3  44442       1225 799999999998877


Q ss_pred             HHHHHH
Q psy3760          73 IMQEIE   78 (306)
Q Consensus        73 il~~~~   78 (306)
                      ......
T Consensus       119 ~~~~~~  124 (168)
T 2nyx_A          119 HRRTEI  124 (168)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766544

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=97.90  E-value=2.8e-05  Score=56.47  Aligned_cols=74  Identities=15%  Similarity=0.213  Sum_probs=56.8

Q ss_pred             CchhhHHHHHHHH-Hh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAV-RQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~-~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+. +. +-+.+.-|+.++++++++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+.
T Consensus        45 l~~~~~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~---Gli~r~~~~~d~R~~~~-~lT~~G~~~~~~~~  120 (160)
T 3boq_A           45 LSLAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKD---GMVVKAMSADDRRSFSA-KLTDAGLTTFKQAS  120 (160)
T ss_dssp             CCHHHHHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHH---TSEEEC--------CEE-EECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHC---CCEEeecCCCCCCeEEE-EEChhHHHHHHHHH
Confidence            3566788888884 32 2378999999999999999999999997   4555532       225 79999999999887


Q ss_pred             HHHHHHH
Q psy3760          72 IIMQEIE   78 (306)
Q Consensus        72 ~il~~~~   78 (306)
                      +....+.
T Consensus       121 ~~~~~~~  127 (160)
T 3boq_A          121 EAHNRIL  127 (160)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766543

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=97.90  E-value=3.8e-05  Score=56.20  Aligned_cols=75  Identities=20%  Similarity=0.379  Sum_probs=59.3

Q ss_pred             CchhhHHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.  +.+.+.-|+.++++++++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+.
T Consensus        51 lt~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~---GlV~r~~~~~DrR~~~l-~LT~~G~~~~~~~~  126 (166)
T 3deu_A           51 LTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDK---GLISRQTCASDRRAKRI-KLTEKAEPLIAEME  126 (166)
T ss_dssp             CCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHT---TSEEEC--------CEE-EECGGGHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHC---CCEEeeCCCCCCCeeEE-EECHHHHHHHHHHH
Confidence            356788888888872  2378999999999999999999999985   4555542       344 79999999999988


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      +....+..
T Consensus       127 ~~~~~~~~  134 (166)
T 3deu_A          127 EVIHKTRG  134 (166)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            87776544

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

Probab=97.90  E-value=9.3e-06  Score=58.58  Aligned_cols=75  Identities=15%  Similarity=0.212  Sum_probs=57.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++|++++|+.|++||+.=   |+.|.       ...+ .||+.|+.++..+..
T Consensus        45 l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~g---lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~~  120 (153)
T 2pex_A           45 LTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAG---LVTRTRAASDERQVII-ALTETGRALRSKAGA  120 (153)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTT---SEEEEC-------CEE-EECHHHHHGGGGSTT
T ss_pred             CCHHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCC---CEeecCCcccCCeeEe-eECHHHHHHHHHHHH
Confidence            3556788888888755 1456669999999999999999999873   33432       2345 799999999988887


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       121 ~~~~~~~  127 (153)
T 2pex_A          121 VPEQVFC  127 (153)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            7766544

>3p7i_A PHND, subunit of alkylphosphonate ABC transporter; phosphonate binding protein, transport protein; 1.71A {Escherichia coli UTI89} PDB: 3qk6_A 3quj_A* 3s4u_A

Probab=97.89  E-value=0.00049  Score=56.04  Aligned_cols=205  Identities=12%  Similarity=0.091  Sum_probs=119.0

Q ss_pred             cCCCCcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcc-ccCC---CCCce
Q psy3760          89 AYDTGNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTE-ILSP---SDKLI  159 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~-~~~~---~~~~~  159 (306)
                      .....+|+||+.+.....-+    .+++..+.++. ++.+++.. .+...+++.|.+|++|+++... ....   ..+..
T Consensus        10 ~~~~~~l~~Gv~p~~~~~~~~~~~~~l~~~L~k~l-G~~ve~~~~~~~~~~i~aL~~G~vDia~~~~~~~~~~~~~~~~~   88 (321)
T 3p7i_A           10 EEQEKALNFGIISTESQQNLKPQWTPFLQDMEKKL-GVKVNAFFAPDYAGIIQGMRFNKVDIAWYGNLSAMEAVDRANGQ   88 (321)
T ss_dssp             ----CCEEEEECCSSCHHHHHHHHHHHHHHHHHHH-TSCEEEECCSSHHHHHHHHHTTSCSEEECCHHHHHHHHHHSCEE
T ss_pred             hhcCCcEEEEEecCCCHHHHHHHHHHHHHHHHHHH-CCCEEEEecCCHHHHHHHHHcCCCcEEEEChHHHHHHHHhcCCE
Confidence            34567899999887655533    44556666654 78888875 6788899999999999998631 1000   11211


Q ss_pred             ee--cc-----ccceEEEEecCCCCCCCCCCcChhhh----cCCCeEeecCCCCcHHHHHHH--HHhCCCcee---EEEE
Q psy3760         160 SI--PC-----YQWEYVIIVPLDHPLLLLNSISLKEI----SNYPLITYDLSFSGRIKLDRE--FSLQKLTPY---IVLE  223 (306)
Q Consensus       160 ~~--~l-----~~~~~~~v~~~~~~l~~~~~i~~~dl----~~~~~i~~~~~~~~~~~~~~~--~~~~~~~~~---~~~~  223 (306)
                      ..  +.     .....+++++++.|     .-+++||    .+..+.....+......+...  +...|+.+.   .+ .
T Consensus        89 ~~a~~~~~~g~~~y~~~lvv~~ds~-----i~sl~DL~~~~kgk~va~~~~gsts~~l~~~~~l~~~~Gi~~~~~~~v-~  162 (321)
T 3p7i_A           89 VFAQTVAADGSPGYWSVLIVNKDSP-----INNLNDLLAKRKDLTFGNGDPNSTSGFLVPGYYVFAKNNISASDFKRT-V  162 (321)
T ss_dssp             EEEEEEETTCCSSBCEEEEEETTCS-----CCSHHHHHHTGGGCEEEECCTTCTTTTHHHHHHTTGGGTCCGGGSSEE-E
T ss_pred             EEEEEeccCCCcceEEEEEEECCCC-----CCCHHHHHhhcCCCEEEeCCCCccHHHHHHHHHHHHHcCCChhHceee-e
Confidence            11  10     11235788888865     2378999    777665444443333333333  367787753   23 4


Q ss_pred             ecCHHHHHHHHHhc-cceeeeecceeccc-c-----cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         224 TINSDIIKTYVELR-MGIGIIASIAFDSN-R-----DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       224 ~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~-----~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      ..+...++..+.+| .-.++.+...+..+ .     .++++.+.-....+  .+.++++++.. ....+++-+.|.+..+
T Consensus       163 ~~~~~~a~~al~~G~vDa~~~~~~~~~~~~~~~p~~~~~lrvl~~s~~~p--~~~i~~~k~~~-~~l~~~l~~aL~~~~~  239 (321)
T 3p7i_A          163 NAGHETNALAVANKQVDVATNNTENLDKLKTSAPEKLKELKVIWKSPLIP--GDPIVWRKNLS-ETTKDKIYDFFMNYGK  239 (321)
T ss_dssp             ECCHHHHHHHHHTTSSSEEEEEHHHHHTHHHHCHHHHTTEEEEEECSCBC--CCEEEEETTSC-HHHHHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHCCCceEEEechHHHHHHHHhCcchhccEEEEEEcCCCC--CCceeeeCCCC-HHHHHHHHHHHHhcCC
Confidence            66777888888888 34444554443333 2     35677664333222  34566777643 4556667777766655


Q ss_pred             HHHHHhh
Q psy3760         297 RKFINKI  303 (306)
Q Consensus       297 ~~~~~~~  303 (306)
                      ....+++
T Consensus       240 d~~~~~~  246 (321)
T 3p7i_A          240 TPEEKAV  246 (321)
T ss_dssp             SHHHHHH
T ss_pred             CHHHHHH
Confidence            4444443

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=97.89  E-value=9.8e-05  Score=48.15  Aligned_cols=74  Identities=18%  Similarity=0.191  Sum_probs=59.1

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKE   86 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~   86 (306)
                      ++..+...- +.+.-|+.+|+|.+++++-+..|++.   -|..+..+++ .+|+.|+.++...+.+...+..+.+.-+.
T Consensus        13 IL~~i~~~~-~~t~La~~~~ls~~~~~~~l~~L~~~---GLI~~~~~~~-~LT~kG~~~l~~l~~~~~~l~~l~~~e~~   86 (95)
T 1r7j_A           13 ILEACKSGS-PKTRIMYGANLSYALTGRYIKMLMDL---EIIRQEGKQY-MLTKKGEELLEDIRKFNEMRKNMDQLKEK   86 (95)
T ss_dssp             HHHHHTTCB-CHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEETTEE-EECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCC-CHHHHHHHhCcCHHHHHHHHHHHHHC---CCeEEECCee-EEChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444335 89999999999999999999999984   5778888888 79999999999988887777766544433

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=97.87  E-value=4.5e-05  Score=58.21  Aligned_cols=60  Identities=22%  Similarity=0.249  Sum_probs=50.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      +.+.-|+.|++|+|++|+.|++||+.   -|+.|.. +++ .||+.|+.+...+.+.-..++...
T Consensus        22 ~~~~lA~~l~vs~~tvs~~l~~Le~~---GlV~r~~~~~i-~LT~~G~~~~~~~~~~h~~~e~~l   82 (214)
T 3hrs_A           22 TNKEIAQLMQVSPPAVTEMMKKLLAE---ELLIKDKKAGY-LLTDLGLKLVSDLYRKHRLIEVFL   82 (214)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEETTTEE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCChhHHHHHHHHHHHC---CCEEEecCCCe-EECHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999987   4677776 556 899999999888887666555544

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

Probab=97.87  E-value=3.3e-05  Score=56.04  Aligned_cols=75  Identities=23%  Similarity=0.309  Sum_probs=57.7

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++++|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+.+
T Consensus        48 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-G--lv~r~~~~~DrR~~~l-~LT~~G~~~~~~~~~  123 (159)
T 3s2w_A           48 IGSGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVDE-G--YVFRQRDEKDRRSYRV-FLTEKGKKLEPDMKK  123 (159)
T ss_dssp             CCTTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEEECC---CCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEecCCCCCCeeEE-EECHHHHHHHHHHHH
Confidence            3456778888887765 256777999999999999999999985 4  44443       2234 799999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       124 ~~~~~~~  130 (159)
T 3s2w_A          124 IASEWGE  130 (159)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8776654

>4ef1_A Pheromone COB1/lipoprotein, YAEC family; periplasmic methionine binding protein, NLPA lipoprotein, ST genomics; 1.90A {Enterococcus faecalis} PDB: 4ef2_A*

Probab=97.87  E-value=0.0004  Score=53.49  Aligned_cols=198  Identities=14%  Similarity=0.084  Sum_probs=115.5

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccCC-----CCCceeecc--
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPC--  163 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l--  163 (306)
                      ..+|+||+++.....++.. +....+.. ++.++++. .+.......|.+|++|+.+..+.+.-     ..+.....+  
T Consensus         3 ~~~i~VG~~~~p~~~i~~~-v~~~l~k~-Gi~veiv~F~dy~~pN~AL~~G~iD~n~fQh~pyl~~~~k~~g~~Lv~v~~   80 (246)
T 4ef1_A            3 DSVLKVGASPVPHAEILEH-VKPLLEKE-GVKLEVTTYTDYVLPNKALESGDIDANYFQHVPFFNEAVKENDYDFVNAGA   80 (246)
T ss_dssp             CEEEEEEECTTTHHHHHHH-HHHHHHHT-TEEEEEEECSSSSHHHHHHHHTSCSEEEEEEHHHHHHHHHHHTCCEEEEEE
T ss_pred             CcEEEEEEeCCChHHHHHH-HHHHHHhc-CCEEEEEEeCCchhHHHHHHCCCCCEEecCCHHHHHHHHHHCCCCEEEEee
Confidence            3579999998755555544 44444443 99999988 45567788999999999997532111     123333333  


Q ss_pred             -ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-------------------e-eEEE
Q psy3760         164 -YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-------------------P-YIVL  222 (306)
Q Consensus       164 -~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-------------------~-~~~~  222 (306)
                       ..+++.++ ++.       --+++||.+-.-|..+.+.....+....|+..|+-                   | +..+
T Consensus        81 ~~~~p~glY-S~k-------iksl~dL~~Ga~IAIpnd~sn~~RaL~lL~~~GLI~Lk~~~~~~~~t~~DI~~Npk~l~~  152 (246)
T 4ef1_A           81 IHLEPVGLY-SKK-------YKSLQEIPDGSTIYVSSSVSDWPRVLTILEDAGLITLKEGVDRTTATFDDIDKNTKKLKF  152 (246)
T ss_dssp             EEECCCEEE-CSS-------CSSGGGSCTTCEEEEESCGGGHHHHHHHHHHTTSEEECTTCCGGGCCGGGEEEETTCCEE
T ss_pred             ccccceEEe-cCC-------CCCHHHcCCCCEEEeecCCchHHHHHHHHHHCCCeeecCCCCcCcCCHhHHhcCCCccEE
Confidence             33455554 222       34889997444444444444445566788888871                   1 1233


Q ss_pred             --EecCHHHHHHHHHhc--cceeeeecceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         223 --ETINSDIIKTYVELR--MGIGIIASIAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       223 --~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                        +++. ..+.+.+..|  ++..+-+.+....--.+  +-..+  ++....+-..++++++...+|.+++|++.+++.--
T Consensus       153 ~~el~a-aql~~al~dg~vDaavin~n~a~~agl~p~~dal~~--E~~~~~y~n~i~vr~~~~~~~~~k~lv~~~~s~~v  229 (246)
T 4ef1_A          153 NHESDP-AIMTTLYDNEEGAAVLINSNFAVDQGLNPKKDAIAL--EKESSPYANIIAVRKEDENNENVKKLVKVLRSKEV  229 (246)
T ss_dssp             EEEECG-GGHHHHHHTTCSSEEEECHHHHHHTTCCHHHHCSEE--CSCCGGGCEEEEEEGGGTTCHHHHHHHHHHHSHHH
T ss_pred             eeecCH-HHHHHHhccccccEEEEechHHHHcCCCCccCceEE--cCCCCCeEEEEEEeccccCCHHHHHHHHHHcCHHH
Confidence              4444 4555556663  44444444444331111  11122  22223445567788888889999999999877655


Q ss_pred             HHHHHh
Q psy3760         297 RKFINK  302 (306)
Q Consensus       297 ~~~~~~  302 (306)
                      +.++++
T Consensus       230 ~~~i~~  235 (246)
T 4ef1_A          230 QDWITK  235 (246)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555544

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

Probab=97.86  E-value=5.4e-05  Score=53.94  Aligned_cols=75  Identities=17%  Similarity=0.255  Sum_probs=56.5

Q ss_pred             CchhhHHHHHHH-HHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREA-VRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v-~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+ .+. +.|.+.-|+.+++|+|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+.
T Consensus        35 l~~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~-g--lv~r~~~~~d~R~~~~-~lT~~G~~~~~~~~  110 (146)
T 2fbh_A           35 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQ-G--LVRRLAVAEDRRAKHI-VLTPKADVLIADIE  110 (146)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEECCBTTBCSCEE-EECTTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-C--CeeecCCCcccCeeee-EECHhHHHHHHHHH
Confidence            345678888888 432 2379999999999999999999999986 3  33332       2335 79999999999887


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      .....+..
T Consensus       111 ~~~~~~~~  118 (146)
T 2fbh_A          111 AIAASVRN  118 (146)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77665543

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=97.84  E-value=0.00011  Score=53.38  Aligned_cols=75  Identities=15%  Similarity=0.212  Sum_probs=58.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.| -+.+.-|+.++++++++|+.|++||+. |  |+.|..       ..+ .||+.|+.++..+.+
T Consensus        44 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-G--lv~r~~~~~DrR~~~l-~LT~~G~~~~~~~~~  119 (162)
T 3k0l_A           44 ISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLAN-G--WIEKAPDPTHGRRILV-TVTPSGLDKLNQCNQ  119 (162)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHT-T--SEEEEECCSSSCCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-c--CeEecCCCCcCCeeEe-EECHhHHHHHHHHHH
Confidence            3556788888888744 378899999999999999999999985 3  444431       234 899999999998888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       120 ~~~~~~~  126 (162)
T 3k0l_A          120 VVQQLEA  126 (162)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7665544

>3n5l_A Binding protein component of ABC phosphonate TRAN; structural genomics, joint center for structural genomics; HET: UNL; 1.97A {Pseudomonas aeruginosa}

Probab=97.84  E-value=0.00057  Score=55.41  Aligned_cols=203  Identities=12%  Similarity=0.076  Sum_probs=119.2

Q ss_pred             CCcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC----CCCCceee-
Q psy3760          92 TGNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS----PSDKLISI-  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~----~~~~~~~~-  161 (306)
                      ..+|+||+.+......+    .+++..+.++. ++.+++.. .+...+++.|.+|++|+++......    ...+.... 
T Consensus         3 ~~~l~iG~~p~~~p~~~~~~~~~l~~~l~k~l-G~~ve~~~~~~~~~~i~al~~G~vDi~~~~~~~~~~~~~~~~~~~~a   81 (310)
T 3n5l_A            3 QPVINFGIISTESSQNLKSIWEPFLKDMSQQT-GYQVKAFFAPDYAGIIQGMRFDKVDIAWYGNKAAMEAVDRAHGEIFA   81 (310)
T ss_dssp             CCEEEEEECCSSCHHHHHHHHHHHHHHHHHHH-SSEEEEECCSSHHHHHHHHHTTSCSEEECCHHHHHHHHHHSCEEEEE
T ss_pred             CcEEEEEEecCCCHHHHHHHHHHHHHHHHHHh-CCCEEEEeCCCHHHHHHHHHcCCCCEEEECcHHHHHHHHhcCCeEEE
Confidence            45799999987765433    34556666654 78999885 5778899999999999998641100    01112111 


Q ss_pred             -cc-----ccceEEEEecCCCCCCCCCCcChhhh----cCCCeEeecCCCCcHHHHHHH--HHhCCCce----eEEEEec
Q psy3760         162 -PC-----YQWEYVIIVPLDHPLLLLNSISLKEI----SNYPLITYDLSFSGRIKLDRE--FSLQKLTP----YIVLETI  225 (306)
Q Consensus       162 -~l-----~~~~~~~v~~~~~~l~~~~~i~~~dl----~~~~~i~~~~~~~~~~~~~~~--~~~~~~~~----~~~~~~~  225 (306)
                       +.     .....+++++++.|     .-+++||    .+..+.....+......+...  +...|+.+    ..+ ...
T Consensus        82 ~~~~~~g~~~~~~~lvv~~ds~-----i~sl~DL~~~~kgk~ia~~~~gs~~~~l~~~~~l~~~~Gi~~~~~~~~v-~~g  155 (310)
T 3n5l_A           82 QTVAASGAPGYWSLLIANKDSK-----IDSLEDMLANAKSLTFGNGDPNSTSGYLVPGYYVFAKNNVDPVKAFKRT-LNS  155 (310)
T ss_dssp             EEEETTCCSEEEEEEEEETTCS-----CCSHHHHHHTGGGCEEEECCTTCTTTTHHHHHHTTTTTTCCHHHHSSEE-EEC
T ss_pred             EEeccCCCcceEEEEEEECCCC-----CCCHHHHhhhcCCCEEEecCCCccHhHHHHHHHHHHHcCCChHHhcccc-ccC
Confidence             10     11235788888875     2378999    777665544444333333332  36778764    334 467


Q ss_pred             CHHHHHHHHHhc-cceeeeecceeccc-cc-----CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         226 NSDIIKTYVELR-MGIGIIASIAFDSN-RD-----KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       226 ~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~-----~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      +...++..+.+| .-.++++...+..+ ..     +.++.+......+  .+.++++++.. ....+++-+.+.+..+..
T Consensus       156 ~~~~~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~~lrvl~~s~~~p--~~~i~~~~~~~-~~l~~~l~~al~~~~~d~  232 (310)
T 3n5l_A          156 SHEVNALAVANKQVDVATFNTEGMERLELTQPEKARQLKVIWKSPLIP--GDPLVWRNNLS-DEQKNKLRDFFFKYGANA  232 (310)
T ss_dssp             CHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCHHHHTTEEEEEEEEEEE--CCEEEEETTSC-HHHHHHHHHHHHHCCCSH
T ss_pred             CHHHHHHHHHcCCccEEEecchhHHHHHHhCccchhCEEEEEECCCCC--CCcEEEECCCC-HHHHHHHHHHHHhcCCCh
Confidence            777788888888 44444554444333 22     4666654332222  33566777643 445666666666665544


Q ss_pred             HHHhhh
Q psy3760         299 FINKIL  304 (306)
Q Consensus       299 ~~~~~~  304 (306)
                      ..++++
T Consensus       233 ~~~~~l  238 (310)
T 3n5l_A          233 EQKKVL  238 (310)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            444443

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

Probab=97.82  E-value=5.3e-05  Score=54.59  Aligned_cols=68  Identities=10%  Similarity=0.213  Sum_probs=54.4

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe------c-C--CCccccCHhHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR------H-G--KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R------~-~--~~~~~lT~~G~~l~~~a~   71 (306)
                      +..++.++..+.+.+ -+.+.-|+.+++|+|++|+.|++||+.   -|+.|      . +  ..+ .||+.|+.++..+.
T Consensus        40 t~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~---Glv~r~~~~~~~d~R~~~~-~LT~~G~~~~~~~~  115 (154)
T 2qww_A           40 TIQQLAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISL---GLVVKLNKTIPNDSMDLTL-KLSKKGEDLSKRST  115 (154)
T ss_dssp             CHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEESCC--CTTCTTCEE-EECHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCcCCCCCCceeEe-EECHHHHHHHHHHH
Confidence            456788888888754 268999999999999999999999995   45555      1 1  234 79999999999888


Q ss_pred             HH
Q psy3760          72 II   73 (306)
Q Consensus        72 ~i   73 (306)
                      ..
T Consensus       116 ~~  117 (154)
T 2qww_A          116 AN  117 (154)
T ss_dssp             SC
T ss_pred             hh
Confidence            77

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

Probab=97.80  E-value=0.00012  Score=52.56  Aligned_cols=74  Identities=23%  Similarity=0.344  Sum_probs=56.8

Q ss_pred             chhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      +..++.++..+.+.+  .+.+.-|+.+++++|++|+.|++||+. |  |+.|..       ..+ .||+.|+.++..+.+
T Consensus        30 t~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~-G--lV~R~~~~~DrR~~~l-~LT~~G~~~~~~~~~  105 (151)
T 4aik_A           30 TQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK-G--LITRHTSANDRRAKRI-KLTEQSSPIIEQVDG  105 (151)
T ss_dssp             CHHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHHT-T--SEEEEECSSCTTCEEE-EECGGGHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHhC-C--CeEeecCCCCCcchhh-hcCHHHHHHHHHHHH
Confidence            456788888887643  134678999999999999999999983 4  455432       234 899999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+..
T Consensus       106 ~~~~~~~  112 (151)
T 4aik_A          106 VISSTRK  112 (151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8776654

>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell junction, cell membrane, glycoprotein, ION transport, ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A* 3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A* 2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A* 2i0c_A* ...

Probab=97.77  E-value=0.00021  Score=56.20  Aligned_cols=196  Identities=11%  Similarity=0.053  Sum_probs=116.8

Q ss_pred             CCcEEEEecccch-----------------hhhhHHHHHHHHHhCCCcEEEEEe-------------CChhHHHHHHHcC
Q psy3760          92 TGNLTIATTHTQA-----------------RYALPKIIKEFTIQFPKVKLSLLQ-------------GNPKQITEMIRND  141 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------------~~~l~~~l~~~~~~~p~~~i~~~~-------------~~~~~~~~~l~~~  141 (306)
                      .++|+||+....+                 ..+...++..+.++. ++.+++..             .+...++..|.+|
T Consensus         3 ~~~l~v~~~~~~P~~~~~~~~~~~~~~g~~~G~~vdl~~~ia~~l-g~~~~~~~~p~~~~g~~~~~~~~~~~~~~~l~~g   81 (259)
T 3g3k_A            3 NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTHL-GFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDH   81 (259)
T ss_dssp             CCCEEEEECCBTTTBEECCCSSCCCGGGGEESHHHHHHHHHHHHH-TCCEEEEECTTCCCCCBCTTTCCBCHHHHHHHTT
T ss_pred             CcEEEEEEecCCCeEEEeecccccCCCceeeeEHHHHHHHHHHHc-CCeEEEEECCCCCcCcccCCCCcchHHHHHHhcC
Confidence            4578888854311                 345667777776664 66777764             4678899999999


Q ss_pred             CeeEEEEccccC--CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCe--EeecCCCCcHHHHHHHHHhCCC
Q psy3760         142 QADIAIVTEILS--PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL--ITYDLSFSGRIKLDREFSLQKL  216 (306)
Q Consensus       142 ~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~--i~~~~~~~~~~~~~~~~~~~~~  216 (306)
                      ++|+++......  ....+. +.+++....+++++++.+     .-+++||.+..-  +....+..    ....+...+.
T Consensus        82 ~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~-----i~~~~dL~g~~~~~ig~~~~~~----~~~~~~~~~~  152 (259)
T 3g3k_A           82 KADLAVAPLAITYVREEVIDFSKPFMTLGISILYRKGTP-----IDSADDLAKQTKIEYGAVEDGA----TMTFFKRSKI  152 (259)
T ss_dssp             SCSEECSSCBCCHHHHTTEEECSCSEEECEEEEEESSSS-----CCSHHHHHTCSSSEEEEETTSH----HHHHHHHCCS
T ss_pred             cccEEEeeeEecccccceEeeeeeeeeCCEEEEEeCCcc-----ccCHHHhccCCCceEEEecCcH----HHHHHhhccc
Confidence            999998632211  122333 468888999999998875     237999988762  22222222    2334444333


Q ss_pred             ce-----------eEEEEecCHHHHHHHHHhccceeeeecceeccc---ccCCceeeecCCCCccceEEEEEeCCccccH
Q psy3760         217 TP-----------YIVLETINSDIIKTYVELRMGIGIIASIAFDSN---RDKNLRSISASHLFGTTISRVIIKQGTYLRS  282 (306)
Q Consensus       217 ~~-----------~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~---~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~  282 (306)
                      ..           .....+++...++.++.+|. .+++.+.....+   ...++..++..  .....+++..+++.+   
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~i~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~a~~k~~~---  226 (259)
T 3g3k_A          153 STYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD-YAFLMESTTIEFVTQRNCNLTQIGGL--IDSKGYGVGTPMGSP---  226 (259)
T ss_dssp             HHHHHHHHHHHHTHHHHEESSHHHHHHHHHHSS-EEEEEEHHHHHHHHHHCTTEEEESSC--SSCEEECCEEETTCT---
T ss_pred             hhHHHHHHHHHhcCCCcccCCHHHHHHHHHhCC-eEEEechHHHHHHhcCCceEEEeccc--ceeeeEEEEECCCCc---
Confidence            21           12346789999999999998 666555333222   24556555433  234577888888753   


Q ss_pred             HHHHHHHHHhHHhhHHHHHhh
Q psy3760         283 YVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       283 ~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ....|=+.|.+.-+....+++
T Consensus       227 l~~~in~~l~~l~~~G~~~~i  247 (259)
T 3g3k_A          227 YRDKITLAILKLQEQGKLHMM  247 (259)
T ss_dssp             HHHHHHHHHHHHHHTC-CHHH
T ss_pred             cHHHHHHHHHHHHhcChHHHH
Confidence            444444444444333333433

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=97.77  E-value=7.2e-05  Score=52.15  Aligned_cols=76  Identities=12%  Similarity=0.105  Sum_probs=54.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----CC-ccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----KR-IRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~-~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      .++..+.+.+.+++.-|+.+ ++|++++|++|++||+.   -|+.|..     +. .+.||+.|+.+++....+.+-.++
T Consensus        39 ~IL~~L~~g~~~~~eLa~~l~gis~~tls~~L~~Le~~---GlV~r~~~~~d~r~~~y~LT~~G~~l~~~l~~l~~w~~~  115 (131)
T 1yyv_A           39 LILVALRDGTHRFSDLRRXMGGVSEXMLAQSLQALEQD---GFLNRVSYPVVPPHVEYSLTPLGEQVSDXVAALADWIEL  115 (131)
T ss_dssp             HHHHHGGGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHH---TCEEEEEECSSSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHhccCCHHHHHHHHHHHHHC---CcEEEEecCCCCCeEEEEECccHHHHHHHHHHHHHHHHH
Confidence            34444443323899999999 79999999999999985   3444432     21 238999999999999888666665


Q ss_pred             HHHHHH
Q psy3760          80 LKKIGK   85 (306)
Q Consensus        80 ~~~~~~   85 (306)
                      ....+.
T Consensus       116 ~~~~~~  121 (131)
T 1yyv_A          116 NLPQVL  121 (131)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555443

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=97.76  E-value=6.9e-05  Score=54.89  Aligned_cols=75  Identities=17%  Similarity=0.345  Sum_probs=56.0

Q ss_pred             CchhhHHHHHHHHHh---cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ---NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~---~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a   70 (306)
                      ++..++.++..+.+.   +-+.+.-|+.++++++++|+.|++||+. |  |+.|..       ..+ .||+.|+.++..+
T Consensus        44 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-G--lv~r~~~~~DrR~~~l-~LT~~G~~~~~~~  119 (168)
T 3u2r_A           44 LSAQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDR-G--LVLRTRKPENRRVVEV-ALTDAGLKLLKDL  119 (168)
T ss_dssp             CCHHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHT-T--SEEEEEETTEEEEEEE-EECHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-C--CEeecCCCCCCCeeEe-EECHHHHHHHHHH
Confidence            355678888888874   3389999999999999999999999985 4  444432       245 8999999999998


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      ......+..
T Consensus       120 ~~~~~~~~~  128 (168)
T 3u2r_A          120 EEPVRQCHE  128 (168)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            887666543

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=97.73  E-value=7.7e-05  Score=53.31  Aligned_cols=71  Identities=7%  Similarity=0.159  Sum_probs=52.8

Q ss_pred             chhhHHHHHHHHH--hc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR--QN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         2 ~~~~l~~f~~v~~--~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      +..++.++..+..  .| -+.+.-|+.+++++|++|+.|++||+.   -|+.|..       ..+ .||+.|+.+++.+.
T Consensus        34 t~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~---Glv~r~~~~~DrR~~~l-~LT~~G~~~~~~~~  109 (147)
T 4b8x_A           34 TFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRS---GLVAKRPNPNDGRGTLA-TITDKGREVVEAAT  109 (147)
T ss_dssp             CHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEEECC----CEEE-EECHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhC---CCEEEeecCCcCceeEE-EECHHHHHHHHHHH
Confidence            4567777777653  32 267899999999999999999999984   3455432       224 79999999998877


Q ss_pred             HHHHH
Q psy3760          72 IIMQE   76 (306)
Q Consensus        72 ~il~~   76 (306)
                      +....
T Consensus       110 ~~~~~  114 (147)
T 4b8x_A          110 RDLMA  114 (147)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=97.73  E-value=7.4e-05  Score=52.89  Aligned_cols=75  Identities=16%  Similarity=0.308  Sum_probs=57.0

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+.   -|+.|.       ...+ .||+.|+.++..+.+
T Consensus        34 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~---Glv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~~  109 (140)
T 3hsr_A           34 LTYTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKK---DYVVRTREEKDERNLQI-SLTEQGKAIKSPLAE  109 (140)
T ss_dssp             CCHHHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEEC-------CEE-EECHHHHHTHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC---CCeEecCCCCCcceeee-eEChHHHHHHHHHHH
Confidence            3556777888877544 257888999999999999999999985   455543       2344 899999999999887


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      ....+.+
T Consensus       110 ~~~~~~~  116 (140)
T 3hsr_A          110 ISVKVFN  116 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7665543

>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=97.72  E-value=0.00011  Score=52.37  Aligned_cols=69  Identities=22%  Similarity=0.206  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC------CCccccCHhHHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG------KRIRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~------~~~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      +.++..+.+...+++.-|+.+++|++++|++|++||+.   -|+.|..      ..+ .||+.|+.+++....+.+-.+
T Consensus        27 l~IL~~L~~g~~~~~eLa~~lgis~~tls~~L~~Le~~---GlI~r~~~~~d~~~~y-~LT~~G~~l~~~l~~l~~w~~  101 (146)
T 2f2e_A           27 MLIVRDAFEGLTRFGEFQKSLGLAKNILAARLRNLVEH---GVMVAVPAESGSHQEY-RLTDKGRALFPLLVAIRQWGE  101 (146)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHCCCHHHHHHHHHHHHHT---TSEEEEECSSSSCEEE-EECHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHC---CCEEEEecCCCCeEEE-EECchHHHHHHHHHHHHHHHH
Confidence            33444444433499999999999999999999999974   3445442      244 899999999988777644433

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

Probab=97.70  E-value=0.00016  Score=51.55  Aligned_cols=66  Identities=23%  Similarity=0.161  Sum_probs=53.6

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~   71 (306)
                      +..++.++..+.+.+.|.+.-|+.+++|+|++|+.|++||+. |  |+.|.       ...+ .||+.|..++..+.
T Consensus        37 t~~~~~iL~~l~~~~~t~~eLa~~l~~s~~tvs~~l~~L~~~-G--lv~r~~~~~d~R~~~~-~lT~~g~~~~~~~~  109 (146)
T 3tgn_A           37 TNTQEHILMLLSEESLTNSELARRLNVSQAAVTKAIKSLVKE-G--MLETSKDSKDARVIFY-QLTDLARPIAEEHH  109 (146)
T ss_dssp             CHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEC----------CC-EECGGGHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CeEeccCCCCCceeEE-EECHhHHHHHHHHH
Confidence            556788888888776799999999999999999999999984 4  44442       2445 89999999999997

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

Probab=97.70  E-value=0.00015  Score=47.80  Aligned_cols=67  Identities=12%  Similarity=0.129  Sum_probs=49.5

Q ss_pred             hhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHH-HHHHHHH
Q psy3760           4 HQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQ-AILRSIE   71 (306)
Q Consensus         4 ~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~-~l~~~a~   71 (306)
                      .+++++..+.+. +.|++.-|+.+++|+|++|++|+.|| +.|.--..+.++.. +.+|+.|. .++....
T Consensus        25 ~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~-~~glv~~~~~~r~~~y~l~~~~~~~l~~~l~   94 (99)
T 3cuo_A           25 KRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMR-DEGLIDSQRDAQRILYSIKNEAVNAIIATLK   94 (99)
T ss_dssp             HHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHH-HTTSEEEEECSSCEEEEECCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHH-HCCCEEEEecCCEEEEEEChHHHHHHHHHHH
Confidence            456667677665 23889999999999999999999998 57877777765543 27899874 4444433

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=97.70  E-value=0.00028  Score=52.73  Aligned_cols=76  Identities=13%  Similarity=0.193  Sum_probs=57.7

Q ss_pred             CchhhHHHHHHHHH---hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---C--CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVR---QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---G--KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~---~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~--~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+   .+-+.+.-|+.+++|+|++|+.|++||+. |.---.++   +  ..+ .||+.|+.++..+..
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~-GlV~r~~~~~DrR~~~l-~LT~~G~~~~~~~~~  116 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKN-GYVDVIPSPHDKRAINV-KVTDLGKKVMVTCSR  116 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCSSCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCCCCCCeeEE-EECHHHHHHHHHHHH
Confidence            35677888888885   23489999999999999999999999974 43333222   1  234 899999999998888


Q ss_pred             HHHHHH
Q psy3760          73 IMQEIE   78 (306)
Q Consensus        73 il~~~~   78 (306)
                      ....+.
T Consensus       117 ~~~~~~  122 (189)
T 3nqo_A          117 TGINFM  122 (189)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=97.68  E-value=0.00025  Score=45.60  Aligned_cols=68  Identities=13%  Similarity=0.082  Sum_probs=55.4

Q ss_pred             chhhHHHHHHHHH--hcCCHHHHHH-HhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVR--QNFNLTEAAK-ALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         2 ~~~~l~~f~~v~~--~~~s~~~aA~-~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      +..++-.+..+++  .- |.+.-|+ .+++..+++||.++.||.. |.-  +.++..+ .+|+.|+.+++.+.++-
T Consensus        15 ~~~QfsiL~~L~~~~~~-t~~~Lae~~l~~drstvsrnl~~L~r~-GlV--e~~~~Dl-~LT~~G~~~l~~a~~~W   85 (95)
T 1bja_A           15 NEKTATILITIAKKDFI-TAAEVREVHPDLGNAVVNSNIGVLIKK-GLV--EKSGDGL-IITGEAQDIISNAATLY   85 (95)
T ss_dssp             CHHHHHHHHHHHHSTTB-CHHHHHHTCTTSCHHHHHHHHHHHHTT-TSE--EEETTEE-EECHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCC-CHHHHHHHHhcccHHHHHHHHHHHHHC-CCe--ecCCCCe-eeCHhHHHHHHHHHHHH
Confidence            4556667777766  45 8888999 9999999999999999988 532  2556667 79999999999998887

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=97.68  E-value=8.8e-05  Score=51.46  Aligned_cols=77  Identities=14%  Similarity=0.097  Sum_probs=56.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----CC-ccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----KR-IRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~-~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      .++..+.....+|+.=++.+ +||++++|++|++||+.   -|+.|..     +. .++||+.|+.+++....+.+=.++
T Consensus        30 ~IL~~L~~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~---GLV~R~~~~~d~r~v~y~LT~~G~~l~~~l~~l~~W~~~  106 (131)
T 4a5n_A           30 ILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEAD---GIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGES  106 (131)
T ss_dssp             HHHHHHTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHT---TSEEEEEECSSSCEEEEEECTTGGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCcCHHHHHHHhcccCHHHHHHHHHHHHHC---CCEEEEecCCCCCeEEEEECHhHHHHHHHHHHHHHHHHH
Confidence            34444443333899999999 99999999999999986   4566652     12 238999999999999888765555


Q ss_pred             HHHHHHh
Q psy3760          80 LKKIGKE   86 (306)
Q Consensus        80 ~~~~~~~   86 (306)
                      -...+..
T Consensus       107 ~~~~~~~  113 (131)
T 4a5n_A          107 NRDVLES  113 (131)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5544444

>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane, ionotropic glutamate receptors, transmembrane, membrane protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A

Probab=97.65  E-value=0.00012  Score=57.65  Aligned_cols=184  Identities=9%  Similarity=0.085  Sum_probs=105.8

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEe------------CChhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQ------------GNPKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYVI  170 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~------------~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~~  170 (306)
                      .+...++..+.+.. ++++++..            .+...++..|.+|++|+++......  ....+. +.++.....++
T Consensus        31 G~~~dl~~~i~~~l-g~~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~fs~p~~~~~~~~  109 (265)
T 2v3u_A           31 GFSIDVLDALSNYL-GFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGV  109 (265)
T ss_dssp             SHHHHHHHHHHHHH-TCEEEEEECTTCCCCCBCTTSCBCHHHHHHHTTSCSEECSSCBCCHHHHTTEEECSCSEEECEEE
T ss_pred             EEEHHHHHHHHHHc-CCcEEEEEccCCcccccCCCCCcchHHHHHHcCCcCeEEeeeEeehhhhccccccceeeeccEEE
Confidence            45667777777664 78888874            4677899999999999998421111  112232 45777888999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee------------------EEEEecCHHHHHH
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY------------------IVLETINSDIIKT  232 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~  232 (306)
                      +++++.+     .-+++||. .. +....+......+..++...+..+.                  ....+++...++.
T Consensus       110 ~~~~~~~-----i~~~~dL~-~~-v~v~~g~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  182 (265)
T 2v3u_A          110 LLRRGTS-----IQSLQDLS-KQ-TDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQ  182 (265)
T ss_dssp             EEETTCC-----CCSHHHHH-TC-SSSCEECBTTSHHHHHHHHHHTCTTCSCTHHHHHHHHHCC-----CCBSSHHHHHH
T ss_pred             EEECCCC-----ccchhhhh-hh-hcEEEEEeccHHHHHHHHhcCCCcccccHHHHHHHHHHHhhcCcccccCCHHHHHH
Confidence            9988765     34788888 33 2222222222344555555444321                  1346789999999


Q ss_pred             HHHhccceeeeec-ceeccc--ccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         233 YVELRMGIGIIAS-IAFDSN--RDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       233 ~v~~g~gi~~~p~-~~~~~~--~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ++.+|.. +++-. ..+...  ..+  .+..++.  ......++++.+++..   ....|-+.|.+..+....+++
T Consensus       183 ~l~~G~~-a~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~~~---l~~~in~~l~~l~~~g~~~~i  252 (265)
T 2v3u_A          183 KVKYGNY-AFVWDAAVLEYVAINDPDCSFYTVGN--TVADRGYGIALQHGSP---YRDVFSQRILELQQSGDMDIL  252 (265)
T ss_dssp             HHHHSSC-EEEEEHHHHHHHHHHCTTCCEEEEC-----CCEEECCEEETTCT---THHHHHHHHHHHHHHTHHHHH
T ss_pred             HHHcCCE-EEEEcchHHHHHHhcCCCccEEEecc--ccCCcceEEEEeCCCc---cHHHHHHHHHHHhhCChHHHH
Confidence            9999987 55443 222222  122  3444432  2234577788888753   444444444443333334443

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=97.65  E-value=7.4e-05  Score=50.13  Aligned_cols=70  Identities=11%  Similarity=0.138  Sum_probs=50.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +.++..+.+.+.+++.-|+.+ ++|++++|++|++||+.   -|+.|..       ..+ .||+.|+.+++....+.+-.
T Consensus        17 ~~IL~~L~~~~~~~~eLa~~l~~is~~tls~~L~~Le~~---GlI~r~~~~~d~r~~~y-~LT~~G~~l~~~~~~l~~w~   92 (107)
T 2hzt_A           17 XVILXHLTHGKKRTSELKRLMPNITQKMLTQQLRELEAD---GVINRIVYNQVPPKVEY-ELSEYGRSLEGILDMLXAWG   92 (107)
T ss_dssp             HHHHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHT---TSEEEEEECSSSCEEEE-EECTTGGGGHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC---CCEEEeecCCCCCeEEE-EECccHHHHHHHHHHHHHHH
Confidence            344555544334899999999 99999999999999985   3444432       234 89999999998877775544


Q ss_pred             HH
Q psy3760          78 EG   79 (306)
Q Consensus        78 ~~   79 (306)
                      ++
T Consensus        93 ~~   94 (107)
T 2hzt_A           93 AN   94 (107)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=97.64  E-value=0.00026  Score=54.71  Aligned_cols=72  Identities=21%  Similarity=0.300  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLK   81 (306)
Q Consensus         6 l~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~   81 (306)
                      |+++..+.+.|.+.  +.-|+.+++|+|++|+.|++||+.   -|..|.. +++ .||+.|+.++..+.+....++...
T Consensus        12 L~~L~~l~~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~---GlV~r~~~~~v-~LT~~G~~~~~~~~~~~~~~e~~l   86 (230)
T 1fx7_A           12 LRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERD---GLLRVAGDRHL-ELTEKGRALAIAVMRKHRLAERLL   86 (230)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEECTTSCE-EECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEeCCccE-EECHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444333255  899999999999999999999986   4666664 455 899999999988887766665544

>3k2d_A ABC-type metal ION transport system, periplasmic; alpha/beta domain, immune system; 2.60A {Vibrio vulnificus}

Probab=97.62  E-value=0.0023  Score=48.84  Aligned_cols=201  Identities=9%  Similarity=-0.010  Sum_probs=116.3

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeecc-
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPC-  163 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l-  163 (306)
                      ...+|+||+++.....++..+-..+.++ -++.++++.. +.......|.+|++|+.+..+.+.-     ..++....+ 
T Consensus         4 ~~~~ikVG~~~~p~~~il~~~~~~l~~k-~Gi~veiv~F~Dy~~pN~AL~~G~IDaN~fQh~pyL~~~nk~~g~~lv~v~   82 (237)
T 3k2d_A            4 DTSKVKVGVMAGAEAQVAEVAAKVAKEK-YGLDVELVTFTDYVTPNAALDDGSIDMNAFQHKPYLDRQVEDRDYKLTIAG   82 (237)
T ss_dssp             CCCCEEEEEETTHHHHHHHHHHHHHHHH-HCCCEEEEEESCTTSHHHHHHHTSCSEEEEEEHHHHHHHHHHHCCCEEEEE
T ss_pred             CCceEEEEEeCCChHHHHHHHHHHHHHh-cCCEEEEEEeCChHhHHHHHHcCCCCeeccCCHHHHHHHHHHCCCCEEEEe
Confidence            3468999998875555555454555533 2788888773 5567889999999999988533111     112222222 


Q ss_pred             --ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEE
Q psy3760         164 --YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVL  222 (306)
Q Consensus       164 --~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~  222 (306)
                        ..+++.++ +++       --+++||.+-.-|..+.+.....+....|+..|+-                  | +..+
T Consensus        83 ~~~~~p~glY-S~k-------~ksl~dL~~Ga~IaipnD~tN~~RaL~lL~~aGLIkLk~~~~~~~t~~DI~~Npk~lk~  154 (237)
T 3k2d_A           83 NTFVYPIAGY-SKQ-------VKSVAALADGVRIAVPNDPTNLGRSLLLLEQQGLIKLRPEVGLLATVRDIVENPKNITI  154 (237)
T ss_dssp             ECCCCCCEEE-CSS-------CSCSTTCCTTCEEEEECSHHHHHHHHHHHHHTTSCEECTTCCSSCCGGGEEECTTCCEE
T ss_pred             eecccceEEe-cCC-------CCCHHHhcCCCEEEecCCccHHHHHHHHHHHCCCEEecCCCCCCCCHHHHhCCCCCCEE
Confidence              23444444 222       34788887555566665555555667788888871                  1 1123


Q ss_pred             EecCHHHHHHHHHhccceeeeecceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         223 ETINSDIIKTYVELRMGIGIIASIAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      .--+...+.+.+...++..+-+.+....--.+  +-..+  ++....+-..++++++...+|.+++|++.+++.--+.++
T Consensus       155 ~e~~aaql~r~l~dvD~avin~nya~~agl~p~~dal~~--E~~~~~y~nviavr~~~~d~~~~k~lv~~~~s~~vk~~i  232 (237)
T 3k2d_A          155 MELDAAQLPRSLDDVALSIINTTYASSINLTPEKDGVFV--EDKESPYVNLIVARQDNVQNENVQNFVKAYQTEEVYTAA  232 (237)
T ss_dssp             EEECGGGHHHHTTTSSEEEECHHHHGGGTCCHHHHCSEE--CCSSSSCCEEEEEETTTTTSHHHHHHHHHHTSHHHHHHH
T ss_pred             EEcCHHHHhhhccCccEEEecccHHHHcCCCcccceeEE--cCCCCCcEEEEEEeccccCCHHHHHHHHHHCCHHHHHHH
Confidence            32333444454555554444444544332111  11122  222223455677888888999999999999776555555


Q ss_pred             Hh
Q psy3760         301 NK  302 (306)
Q Consensus       301 ~~  302 (306)
                      ++
T Consensus       233 ~~  234 (237)
T 3k2d_A          233 KE  234 (237)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>1sw5_A Osmoprotection protein (PROX); binding-protein, compatible solutes, cation-PI interactions, classical hydrogen bonds, protein binding; 1.80A {Archaeoglobus fulgidus} SCOP: c.94.1.1 PDB: 1sw4_A 1sw1_A 1sw2_A 3mam_A*

Probab=97.57  E-value=0.0011  Score=52.78  Aligned_cols=203  Identities=12%  Similarity=0.131  Sum_probs=118.4

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe-C-ChhHHHHHHHcCCeeEEEEc-c------ccCCCC------
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ-G-NPKQITEMIRNDQADIAIVT-E------ILSPSD------  156 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~-~-~~~~~~~~l~~~~~Di~i~~-~------~~~~~~------  156 (306)
                      ...|+||....-....+..++..+.+.. ++++++.. . ++....+.|.+|++|++..+ +      ....++      
T Consensus         5 ~~~i~ig~~~~~~~~~~~~~~~~~le~~-G~~Ve~~~~~g~~~~~~~al~~G~iD~~~eytGt~~~~~~~~~~~~~~~~~   83 (275)
T 1sw5_A            5 SERVVIGSKPFNEQYILANMIAILLEEN-GYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQ   83 (275)
T ss_dssp             -CCEEECCCSSHHHHHHHHHHHHHHHHT-TCCEEECTTCCSHHHHHHHHHHTSSSEEEEEHHHHHHTTSCCCCCSSCCHH
T ss_pred             CCCEEEEcCCCcHHHHHHHHHHHHHHHc-CCcEEEEeCCCchHHHHHHHHcCCCcEEEeehhhHHHHhcCCCCccCCCHH
Confidence            3479999988766667778887777766 89999987 4 46788999999999999842 1      101000      


Q ss_pred             --------------Cceeecc--ccceEEEEecCCCCCCCCCCcChhhhcCCC--eEe-ecCCCCcH-HHHHHHHHhCCC
Q psy3760         157 --------------KLISIPC--YQWEYVIIVPLDHPLLLLNSISLKEISNYP--LIT-YDLSFSGR-IKLDREFSLQKL  216 (306)
Q Consensus       157 --------------~~~~~~l--~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~--~i~-~~~~~~~~-~~~~~~~~~~~~  216 (306)
                                    ++....-  ....+.++++++.... ..--+++||.+..  +.. .......+ ..+..+++..|+
T Consensus        84 ~~~~~~~~~~~~~~~l~~l~~~~~~~~~~l~V~~~~a~~-~~i~si~DL~g~~~~~~~g~~~~~~~~~~g~~~~~~~yGl  162 (275)
T 1sw5_A           84 YIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEE-NGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGF  162 (275)
T ss_dssp             HHHHHHHHHHHHHHCCEEEEEEEEECCEEEEEEHHHHHH-HTCCBGGGGTTTGGGCEEEECHHHHHSTTSHHHHHHHHTC
T ss_pred             HHHHHHHHHhhhcCCeEEeccCCCCCeeEEEEeHHHHHH-cCCCcHHHHHhhhcceEeccCcccccccchHHHHHHhcCC
Confidence                          2222111  2345677777654100 0234789998872  221 11110000 123346667788


Q ss_pred             ceeEEEEecCHHHHHHHHHhccceee---eecceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         217 TPYIVLETINSDIIKTYVELRMGIGI---IASIAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       217 ~~~~~~~~~~~~~~~~~v~~g~gi~~---~p~~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      .+..+... +...+..++.+|.-.++   -|.....   ..+++.+.-+.. .+..+++.+.+++....|.+..|++.+.
T Consensus       163 ~~~~~~~~-~~~~~~~Al~~g~vd~~~~~~p~~~~~---~~~l~~L~d~~~~~~~~~~~~v~~~~~~~~P~~~~~l~~l~  238 (275)
T 1sw5_A          163 EFKEVKQM-EPTLMYEAIKNKQVDVIPAYTTDSRVD---LFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLE  238 (275)
T ss_dssp             CCSEEEEC-CGGGHHHHHHTTSCSEEEEETTCHHHH---HTTEEECBCTTCCSCCCEEEEEECTTGGGCHHHHHHHHTTT
T ss_pred             CcccccCC-CHHHHHHHHHcCCCeEEEEeCCCcchh---cCCeEEccCCcccCCccceeeeeehhhccChHHHHHHHHHH
Confidence            76544344 56678889998854443   3444432   246776665542 2345666666766432277778887776


Q ss_pred             HHhhHHHH
Q psy3760         293 PKLNRKFI  300 (306)
Q Consensus       293 ~~~~~~~~  300 (306)
                      ..+.....
T Consensus       239 ~~l~~~~~  246 (275)
T 1sw5_A          239 DRIDTDTM  246 (275)
T ss_dssp             TCCCHHHH
T ss_pred             ccCCHHHH
Confidence            55544444

>3qsl_A Putative exported protein; unknown, structural genomics, PSI-biology, midwest center FO structural genomics, MCSG, unknown function; HET: MSE CIT; 2.00A {Bordetella bronchiseptica}

Probab=97.57  E-value=0.0075  Score=49.33  Aligned_cols=199  Identities=9%  Similarity=-0.034  Sum_probs=111.9

Q ss_pred             CCcEEEEecccchhhhhHHHHHH----HHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC-----CCCCceee
Q psy3760          92 TGNLTIATTHTQARYALPKIIKE----FTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-----PSDKLISI  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~----~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~  161 (306)
                      ...++|++.........+..+..    |.+  .++++++.. .+...+.+.|.+|++|+++......     ....+...
T Consensus        32 ~~~~~i~~~~~~~~~~~~~~~a~~~g~~~~--~g~~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~  109 (346)
T 3qsl_A           32 KAKVQIAVGGKPLIYYLPLTIAEVKGFFKD--EGLDVSIADFAGGSKALQAVVGGSADVVSGAFEHTLSLQAKGQFYRAF  109 (346)
T ss_dssp             CSEEEEEESCTTSGGGHHHHHHHHTTHHHH--TTCEEEEEECSSHHHHHHHHHTTSCSEEEEETHHHHHHHHTTCCEEEE
T ss_pred             CCceEEEecCccchhhhHHHHHHHCCchHh--hCCeEEEEecCChHHHHHHHHCCCCCEEccchHHHHHHHhCCCCeEEE
Confidence            45677766544322233322222    333  378888884 4677889999999999998752211     11222222


Q ss_pred             c--cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-E-EEEecCHHHHHHHHHhc
Q psy3760         162 P--CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-I-VLETINSDIIKTYVELR  237 (306)
Q Consensus       162 ~--l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~v~~g  237 (306)
                      .  .......++++++..   ...-+++||.+.++.....+......+..+++..|+.+. + ....++...+..++.+|
T Consensus       110 ~~~~~~~~~~~~v~~~~~---~~i~s~~DL~Gk~i~~~~~gs~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~~al~~G  186 (346)
T 3qsl_A          110 ALQGRAPMIGVGVSKKNL---PGYKGPADLKGRKIGVTAPGSSTNMVVNFFLAKHGLKASDVSFIGVGAGAGAVTALRSG  186 (346)
T ss_dssp             EESBSSCCEEEEEETTTC---TTCCSGGGGTTCEEEESSTTSHHHHHHHHHHHHTTCCGGGSEEEECCSSHHHHHHHHHT
T ss_pred             EecccCCCcEEEEecCcc---cCCCChHHcCCCEEEECCCCcHHHHHHHHHHHHcCCCHHHeEEEecCCcHHHHHHHHcC
Confidence            1  222356777777651   123478999988776665565555667788899998763 2 34455556778888887


Q ss_pred             -cceeeeecceeccc-ccCCceeeecCCC---------CccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         238 -MGIGIIASIAFDSN-RDKNLRSISASHL---------FGTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       238 -~gi~~~p~~~~~~~-~~~~l~~~~~~~~---------~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                       .-.++++....... ..+..+.+.....         .......++.+++.  ..+..+++|++.+.+..
T Consensus       187 ~vDa~~~~~p~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a~  257 (346)
T 3qsl_A          187 QIDAISNTDPVVSMLETSGDIQIIVDTRTLKDTKEIFGGNMPAGCLYAPQAFVDANPNTAQALTNAIVRAD  257 (346)
T ss_dssp             SCSEEEEETTHHHHHHHTTCEEEEEECSSHHHHHHHHSSCCCCEEEEEEHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             CccEEEecchhHHHHHhCCCeEEEEecccccchhhhcCCCCceEEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence             33334454444333 3444444422110         01113344445441  24567888888776554

>4edp_A ABC transporter, substrate-binding protein; clostridium PERF ATCC 13124, center for structural genomics of infectious DI csgid; 1.85A {Clostridium perfringens}

Probab=97.54  E-value=0.013  Score=47.99  Aligned_cols=199  Identities=13%  Similarity=0.125  Sum_probs=120.9

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC---eeEEEEccc----------cCCCC--
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ---ADIAIVTEI----------LSPSD--  156 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~---~Di~i~~~~----------~~~~~--  156 (306)
                      .++|+|.........+...++..|.+++ +++|++...+..+..+.+..+.   .|+.+....          ..+-+  
T Consensus        34 ~~~l~v~~~~~~~~~~~~~~~~~f~~~~-gi~V~~~~~~~~~~~~kl~a~~~~~pDv~~~~~~~~~~~~~~g~l~~l~~~  112 (351)
T 4edp_A           34 GKKLVVSTWGLNEDVLKETVFEPFAKEH-GVEIVLDIGNNSERLTKMKNNPNSQIDITYLAESFAEQGVEAGIFDKLDYS  112 (351)
T ss_dssp             --CEEEEECCTTHHHHHHHTHHHHHHHH-TCCEEEEECCHHHHHHHHHHCTTCCCCEEEEEHHHHHHHHHHTCBCCCCGG
T ss_pred             CCeEEEEEccCcHHHHHHHHHHHHHHHH-CCEEEEEeCCcHHHHHHHHhcCCCCCCEEEECcHHHHHHHHCCCcccCCch
Confidence            3679998755445667889999999999 9999999999889999998776   999986421          00000  


Q ss_pred             -----------------CceeeccccceEEEEecCCCCCCCCCCcChhhhcC----CCeEeecCCCCcHHHH-HHHHHhC
Q psy3760         157 -----------------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN----YPLITYDLSFSGRIKL-DREFSLQ  214 (306)
Q Consensus       157 -----------------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~----~~~i~~~~~~~~~~~~-~~~~~~~  214 (306)
                                       .+-..|+.....+++.+++.   ...+-+++||.+    -..............+ .......
T Consensus       113 ~~~~~~~~~~~~~~~~g~~y~~P~~~~~~~l~ynkd~---~~~p~tw~el~~~~~~g~~~~~~~~~~~g~~~~~~~~~~~  189 (351)
T 4edp_A          113 KIPNASEMNEKAKSTVEAGYGPAYTLNSIGIVVDPSA---GIEINSWEDLWKPELKNKIAIPDITTTNGPAMVEIAAEKA  189 (351)
T ss_dssp             GCGGGGGBCTTTHHHHHHTSSCEEEEEEEEEEECGGG---CCCCCSGGGGGCGGGTTCEEEECTTSTTHHHHHHHHHHHH
T ss_pred             hCCChHHhhHHhhccCCCeeEEEEEeeEEEEEEcCCC---CCCCCCHHHHhChHhcCCeeecCcccccchHHHHHHHHhc
Confidence                             11234666677888888885   345679999954    2233333332221111 1111211


Q ss_pred             CC-----------------ceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc--ccCCceeeecCCCCccceEEEEE
Q psy3760         215 KL-----------------TPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVII  274 (306)
Q Consensus       215 ~~-----------------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~  274 (306)
                      |.                 .++......+.....+++.+| .++++...+.+...  ....+...............+..
T Consensus       190 G~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~f~~G~~a~~~~~~~~~~~~~~~~~~~~~~~P~~g~~~~~~~~~i  269 (351)
T 4edp_A          190 GVDVKTDNGEAAFKELEALKPNVVKTYSKSSDLANMFSNGEIVAAVASDFAFGTISKAKPEVINVIPESGTYLNFNTINI  269 (351)
T ss_dssp             TCCHHHHTTHHHHHHHHHHGGGEEEEECCHHHHHHHHHTTSCSEEEEEHHHHHHHHHHCTTCEEECCTTCCBEEEEEEEE
T ss_pred             CCCCChhhHHHHHHHHHHHHHhhhcccCChHHHHHHHHcCCEEEEecCcHHHHHHHhcCCCeeeeCCCCCcccceeeEEE
Confidence            21                 233443456777888888888 44555555544433  23444443222222333445666


Q ss_pred             eCCccccHHHHHHHHHHhHH
Q psy3760         275 KQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       275 ~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .++.....++.+|++++.+.
T Consensus       270 ~~~s~~~~~A~~fi~~l~s~  289 (351)
T 4edp_A          270 NKNSKNKDLAYEFINYALSK  289 (351)
T ss_dssp             BTTCSCHHHHHHHHHHHTSH
T ss_pred             ECCCCCHHHHHHHHHHhcCH
Confidence            77777788999999999654

>3uif_A Sulfonate ABC transporter, periplasmic sulfonate- protein SSUA; structural genomics; 2.60A {Methylobacillus flagellatus}

Probab=97.53  E-value=0.0026  Score=52.35  Aligned_cols=196  Identities=11%  Similarity=0.005  Sum_probs=110.3

Q ss_pred             CCcEEEEeccc--------chhhhhHH---HHHHHHHhCCCcEEEE--EeCC--hhHHHHHHHcCCeeEEEEccccC---
Q psy3760          92 TGNLTIATTHT--------QARYALPK---IIKEFTIQFPKVKLSL--LQGN--PKQITEMIRNDQADIAIVTEILS---  153 (306)
Q Consensus        92 ~~~l~I~~~~~--------~~~~~l~~---~l~~~~~~~p~~~i~~--~~~~--~~~~~~~l~~~~~Di~i~~~~~~---  153 (306)
                      .++||||+...        .....+..   +...|.+.  ++++++  ....  ...+.+.|.+|++|+++......   
T Consensus         5 ~~~lrig~~~~~~~~~p~~~~~p~~a~~~gl~~~~~~~--G~~v~~~~~~~~g~~~~~~~al~~G~~D~~~~~~~~~~~~   82 (348)
T 3uif_A            5 LKVVRIASVATNVGGKTVYAGSASLVVNGAFPEELRKQ--GIKVEWVPAAMASVGPVINEGFASGKIDFGIYGDLPPIIL   82 (348)
T ss_dssp             CEEEEEEEEEEEETTEEEECTHHHHHHHSSHHHHHHHT--TEEEEEEEECTTCHHHHHHHHHHTTCCCEEEEESHHHHHH
T ss_pred             CceEEEEeeccCCCCccccCcHHHHHHHccHHHHHHhc--CCeEEEEecccCCCcHHHHHHHHcCCCCEEecCcHHHHHH
Confidence            46899999842        11111222   22244443  888888  5442  45678999999999999642211   


Q ss_pred             --CCCCcee--eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHH
Q psy3760         154 --PSDKLIS--IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSD  228 (306)
Q Consensus       154 --~~~~~~~--~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  228 (306)
                        ....+..  .........++++++.+     .-+++||.+.++... .+......+..++...|+.+. +.+..-+..
T Consensus        83 ~~~g~~~~~v~~~~~~~~~~lvv~~~s~-----i~s~~DLkGk~I~v~-~gs~~~~~~~~~l~~~Gl~~~~v~~v~~~~~  156 (348)
T 3uif_A           83 NASKPTVQLVAPWGTTSNSYLVVPKNST-----AKSIKDLKGKKIALH-RGRPWELAFSNLLQSEGLTFKDFKIVNVNPQ  156 (348)
T ss_dssp             HHHSCCEEEEEECCCCCCCEEEEETTCC-----CCSGGGGTTSEEEEC-TTSTHHHHHHHHHHHTTCCGGGSEEECCCHH
T ss_pred             HhCCCCEEEEEeccCCCceEEEEECCCC-----CCCHHHcCCCEEEec-CCChHHHHHHHHHHHcCCCHHHeEEEECCHH
Confidence              1112222  22334567788887765     347899999877664 555555667788899998753 233333677


Q ss_pred             HHHHHHHhccc-eeeeecceecccccCCceee-ecCCCC--ccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         229 IIKTYVELRMG-IGIIASIAFDSNRDKNLRSI-SASHLF--GTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       229 ~~~~~v~~g~g-i~~~p~~~~~~~~~~~l~~~-~~~~~~--~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                      .+..++.+|.. .++.+.........+..+.+ ...+..  ......++.+++-  ..+..+++|++.+.+..
T Consensus       157 ~~~~al~~G~vDa~~~~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a~  229 (348)
T 3uif_A          157 VGAAALASGTVDGFFSLFDSYILEDRGVGKIIWSTKTAPVDWKLMGGVWARNDFVKQNPEITQAIVTAYLKSV  229 (348)
T ss_dssp             HHHHHHHHTSSSEEEESTTHHHHHHTTSEEEEEEGGGSCGGGSCCEEEEEEHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCEEEechHHHHHHhcCCcEEEEeccccCCCCcceeEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence            88888888832 23444433322133332322 222211  1123344555432  24567788887776654

>3un6_A Hypothetical protein saouhsc_00137; structural genomics, center for structural genomics of infec diseases, csgid; 2.01A {Staphylococcus aureus subsp}

Probab=97.49  E-value=0.0032  Score=51.73  Aligned_cols=198  Identities=10%  Similarity=0.036  Sum_probs=106.4

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHH-HH--hCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEcccc-----CCCCCceee
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEF-TI--QFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEIL-----SPSDKLISI  161 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~-~~--~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~  161 (306)
                      ...+|+||..+...  ..+-.+..- ..  ..-++.+++.... ...+.+.|.+|++|+++.....     .....+...
T Consensus        50 ~~~~l~vg~~~~~~--~~p~~~a~~l~g~~~~~G~~Ve~~~~~~~~~~~~al~~G~~D~~~~~~~~~~~~~~~g~~~~~v  127 (341)
T 3un6_A           50 NQQVIKIGYLPITH--SANLMMTKKLLSQYNHPKYKLELVKFNNWPDLMDALNSGRIDGASTLIELAMKSKQKGSNIKAV  127 (341)
T ss_dssp             -CCEEEEEECSSGG--GHHHHHHHHHHHTSSSCSSEEEEEECSSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTCCCEEE
T ss_pred             CCceEEEEEEeccc--cHHHHHHHHhhChHHHcCCcEEEEEcCCHHHHHHHHHcCCCCEEecchHHHHHHHHCCCCeEEE
Confidence            35689999976422  222222221 12  1247888888764 7789999999999999875211     111222222


Q ss_pred             cc-ccceEEEEecCCCCCCCCCCcChhhh-cCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHHhcc
Q psy3760         162 PC-YQWEYVIIVPLDHPLLLLNSISLKEI-SNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRM  238 (306)
Q Consensus       162 ~l-~~~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~  238 (306)
                      -. ......++++++.+.     -+++|| .+..+.....+......+..+++..|+.+. +.+..-+...+..++.+|.
T Consensus       128 ~~~~~~~~~ivv~~~s~I-----~s~~DL~kGk~i~v~~~~s~~~~~~~~~l~~~Gl~~~dv~~~~~~~~~~~~al~~G~  202 (341)
T 3un6_A          128 ALGHHEGNVIMGQKGMHL-----NEFNNNGDDYHFGIPHRYSTHYLLLEELRKQLKIKPGHFSYHEMSPAEMPAALSEHR  202 (341)
T ss_dssp             EESCEECEEEEESTTCCG-----GGCCSSSSCEEEEESCSSSHHHHHHHHHHHHTTCCTTSEEEEECCGGGHHHHHHTTS
T ss_pred             eecCCCceEEEEcCCCCC-----CCHHHhCCCCEEEECCCCCHHHHHHHHHHHHcCCCHHHeEEEEcChHHHHHHHHcCC
Confidence            11 235567778877642     367788 666655544333333344568888998763 3333334556777788873


Q ss_pred             -ceeeeecceeccc-ccCCceeee-cCCCCccc-eEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         239 -GIGIIASIAFDSN-RDKNLRSIS-ASHLFGTT-ISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       239 -gi~~~p~~~~~~~-~~~~l~~~~-~~~~~~~~-~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                       -..+++....... ..+..+.+. ..+..+.. ...++.+++.  ..+..+++|++.+.+..
T Consensus       203 vDa~~~~~p~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~~~a~~~a~  265 (341)
T 3un6_A          203 ITGYSVAEPFGALGEKLGKGKTLKHGDDVIPDAYCCVLVLRGELLDQHKDVAQAFVQDYKKSG  265 (341)
T ss_dssp             CSEEEEETTHHHHHHHSSCCEEEEEGGGTSTTCCCEEEEECHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             CCEEEecCCHHHHHHhcCCeEEEEeccccCCCCceEEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence             3334444433222 223223322 22211222 2445555432  24566778887776543

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=97.46  E-value=0.00045  Score=47.17  Aligned_cols=64  Identities=17%  Similarity=0.110  Sum_probs=48.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQAILR   68 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~l~~   68 (306)
                      ..++++..+.+...+++.-|+.+++|+|++|++|+.|| +.|.--..|.|+.. +++|+.|...+.
T Consensus        19 ~R~~Il~~L~~~~~~~~eLa~~l~is~~tvs~hL~~L~-~~GlV~~~~~gr~~~y~l~~~~~~~l~   83 (118)
T 3f6o_A           19 TRRAVLGRLSRGPATVSELAKPFDMALPSFMKHIHFLE-DSGWIRTHKQGRVRTCAIEKEPFTAVE   83 (118)
T ss_dssp             HHHHHHHHHHTCCEEHHHHHTTCCSCHHHHHHHHHHHH-HTTSEEEEEETTEEEEEECSHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCcCHHHHHHHHHHHH-HCCCeEEEecCCEEEEEECHHHHHHHH
Confidence            34566666665444899999999999999999999997 56777777776543 389998876553

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=97.45  E-value=0.00018  Score=48.25  Aligned_cols=64  Identities=17%  Similarity=0.185  Sum_probs=46.9

Q ss_pred             HHHHHHHhcCCHHHHHHHhC-CCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALY-TSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~il~   75 (306)
                      ++..+.+.+.+++.-|+.++ +|++++|++|++||+.   -|+.|..       ..+ .||+.|+.+++....+.+
T Consensus        30 IL~~L~~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~---GlV~r~~~~~d~r~~~y-~LT~~G~~l~~~l~~l~~  101 (107)
T 2fsw_A           30 IIFQINRRIIRYGELKRAIPGISEKMLIDELKFLCGK---GLIKKKQYPEVPPRVEY-SLTPLGEKVLPIIDEIAK  101 (107)
T ss_dssp             HHHHHTTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHT---TSEEEEEECSSSCEEEE-EECHHHHTTHHHHHHHHH
T ss_pred             HHHHHHhCCcCHHHHHHHcccCCHHHHHHHHHHHHHC---CCEEEeecCCCCCeeEE-EECccHHHHHHHHHHHHH
Confidence            44444433238999999995 9999999999999984   2444432       224 899999999988776644

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

Probab=97.45  E-value=0.00058  Score=48.76  Aligned_cols=71  Identities=18%  Similarity=0.178  Sum_probs=53.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+.   -|+.|.       ...+ .||+.|+.++..+..
T Consensus        39 lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~---Glv~r~~~~~D~R~~~~-~LT~~G~~~~~~~~~  114 (149)
T 4hbl_A           39 ITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQS---GWVKRERQQSDKRQLII-TLTDNGQQQQEAVFE  114 (149)
T ss_dssp             CCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHH---TSEEC---------CEE-EECSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEeeCCCCCCcceeee-eECHHHHHHHHHHHH
Confidence            3556788888887655 156788999999999999999999985   355543       2334 799999999877665


Q ss_pred             HHH
Q psy3760          73 IMQ   75 (306)
Q Consensus        73 il~   75 (306)
                      ...
T Consensus       115 ~~~  117 (149)
T 4hbl_A          115 AIS  117 (149)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor, membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus norvegicus} SCOP: c.94.1.1

Probab=97.44  E-value=0.00088  Score=54.29  Aligned_cols=193  Identities=12%  Similarity=0.060  Sum_probs=110.8

Q ss_pred             CCCcEEEEecccc-----------------hhhhhHHHHHHHHHhCCCcEEEEE-------------eCChhHHHHHHHc
Q psy3760          91 DTGNLTIATTHTQ-----------------ARYALPKIIKEFTIQFPKVKLSLL-------------QGNPKQITEMIRN  140 (306)
Q Consensus        91 ~~~~l~I~~~~~~-----------------~~~~l~~~l~~~~~~~p~~~i~~~-------------~~~~~~~~~~l~~  140 (306)
                      ..+.|+||+....                 ...+...++..+.++. ++++++.             ..+...++..|.+
T Consensus        11 ~~~~l~V~~~~~~P~~~~~~~~~~~~~~g~~~G~~vdl~~~ia~~l-g~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~   89 (312)
T 1yae_A           11 SNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTIL-GFTYEIRLVEDGKYGAQDDVNGQWNGMVRELID   89 (312)
T ss_dssp             CSCEEEEEECCBTTTBEECCCSSCCCGGGGEESHHHHHHHHHHHHH-CCEEEEEECSSCCCCCBCTTTCCBCSHHHHHHT
T ss_pred             cCceEEEEEeccCCeeEEeccccccCCCceEEEEEHHHHHHHHHHc-CCeEEEEecCCCccceeccCCCcchHHHHHHhC
Confidence            3568999985421                 1235566787777764 6777777             3567789999999


Q ss_pred             CCeeEEEEccccCC--CCCce-eeccccceEEEEecCCCCCC--------------------CCCCcChhhhcCCC---e
Q psy3760         141 DQADIAIVTEILSP--SDKLI-SIPCYQWEYVIIVPLDHPLL--------------------LLNSISLKEISNYP---L  194 (306)
Q Consensus       141 ~~~Di~i~~~~~~~--~~~~~-~~~l~~~~~~~v~~~~~~l~--------------------~~~~i~~~dl~~~~---~  194 (306)
                      |++|+++.......  ...+. +.+++....+++++++.+..                    ....-+++||.+..   +
T Consensus        90 g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~~~~~~~~~~pf~~~p~tv~~~~~~i~~~~dL~g~~~~~v  169 (312)
T 1yae_A           90 HKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNGGSLVPRGSERMESPIDSADDLAKQTKIEY  169 (312)
T ss_dssp             TSCSEECSSCBCCHHHHHHEEEEEEEEEECEEEEEEC----------------------------CCSHHHHHTCSSSEE
T ss_pred             CCcCEEeecceechhhcceEEecceeeecceEEEEeCCccccccceeeecccccCCcccccccCCCCCHHHHhhccCceE
Confidence            99999985322111  12222 45788888899998875310                    12234789998873   3


Q ss_pred             EeecCCCCcHHHHHHHHHhCCCce-----------eEEEEecCHHHHHHHHHhccceeeeecce-eccc--ccCCceeee
Q psy3760         195 ITYDLSFSGRIKLDREFSLQKLTP-----------YIVLETINSDIIKTYVELRMGIGIIASIA-FDSN--RDKNLRSIS  260 (306)
Q Consensus       195 i~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~~--~~~~l~~~~  260 (306)
                      .....+ ..    ...+...+...           .....+++...++.++.+|. -+++-... +..+  ...++..++
T Consensus       170 g~v~~~-~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~-Da~i~~~~~~~~~~~~~~~l~~~~  243 (312)
T 1yae_A          170 GAVEDG-AT----MTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD-YAFLMESTTIEFVTQRNCNLTQIG  243 (312)
T ss_dssp             ECBTTS-HH----HHHHHHCCBHHHHHHHHHHHHTHHHHCBSSHHHHHHHHHHSS-EEEEEEHHHHHHHHTTCTTEEEES
T ss_pred             EEEeCC-hH----HHHHHhccCchHHHHHHHHHhcCCCcccCCHHHHHHHHHcCC-cEEEeccHHHHHHHhcCCCEEEec
Confidence            323322 22    23333332210           12345789999999999998 66655432 2222  224555554


Q ss_pred             cCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         261 ASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       261 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      .  ......++++.+++......+.+.+..++
T Consensus       244 ~--~~~~~~~~~a~~k~~~l~~~in~~l~~l~  273 (312)
T 1yae_A          244 G--LIDSKGYGVGTPMGSPYRDKITIAILQLQ  273 (312)
T ss_dssp             S--CSSCEEEEEEEETTCSSHHHHHHHHHHHH
T ss_pred             c--cccccceEEEEeCCCCcHHHHHHHHHHHH
Confidence            2  23345788888887544444444444443

>2g29_A Nitrate transport protein NRTA; solute-binding protein, alpha-beta protein; 1.50A {Synechocystis SP}

Probab=97.42  E-value=0.0039  Score=52.79  Aligned_cols=201  Identities=5%  Similarity=-0.019  Sum_probs=108.6

Q ss_pred             CCCcEEEEecccchh--hhhHHHHHHHHHhCCCc-EEEEEeC-ChhHHHHHHHcCC----eeEEEEccccC---------
Q psy3760          91 DTGNLTIATTHTQAR--YALPKIIKEFTIQFPKV-KLSLLQG-NPKQITEMIRNDQ----ADIAIVTEILS---------  153 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~--~~l~~~l~~~~~~~p~~-~i~~~~~-~~~~~~~~l~~~~----~Di~i~~~~~~---------  153 (306)
                      ....|+||..+....  .++.. -..|.+++ ++ .+++... +...+.+.|.+|+    +|+++...+..         
T Consensus        31 e~~~l~ig~~~~~~~~p~~vA~-~~G~~~~~-Gl~~Ve~~~~~~~~~~~~al~~G~~~~giD~a~~~~~~~~~~~~~~~~  108 (417)
T 2g29_A           31 EVTTAKLGFIALTDAAPLIIAK-EKGFYAKY-GMPDVEVLKQASWGTTRDNLVLGSASGGIDGAHILTPMPYLITMGTVT  108 (417)
T ss_dssp             SCSCCEEEECSSGGGHHHHHHH-HTTHHHHT-TCTTCEEEECSCHHHHHHHHHHCGGGTSCSEEEEETHHHHHHHHCTTS
T ss_pred             CCceEEEEeeccHhHHHHHHHH-HCCchHHc-CCCeeEEEecCCHHHHHHHHHCCCCcCCcCeEeecchHHHHHHhCccc
Confidence            356799999775321  11111 12244444 67 7777774 6778999999999    99998731100         


Q ss_pred             CCCCceeecc---ccceEEEEecCCCCCCCC-CCcC-----hhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee--EEE
Q psy3760         154 PSDKLISIPC---YQWEYVIIVPLDHPLLLL-NSIS-----LKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY--IVL  222 (306)
Q Consensus       154 ~~~~~~~~~l---~~~~~~~v~~~~~~l~~~-~~i~-----~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~  222 (306)
                      ...+.....+   ......++++++.+...- ..+.     ++||.+..+.....+......+..+++..|+.|.  +.+
T Consensus       109 ~~~~~~~~~~~~~~~~g~~i~v~~~~~~~~i~~s~~~l~~~~~dLkGk~iav~~~gs~~~~~l~~~L~~~Gl~~~~dv~~  188 (417)
T 2g29_A          109 DGKPTPMYILARLNVNGQGIQLGNNYKDLKVGTDAAPLKEAFAKVTDPKVAMTFPGGTHDMWIRYWLAAGGMEPGKDFST  188 (417)
T ss_dssp             SSCCCCEEEEEECCBSCEEEEECGGGGGGCCCSCCTTHHHHHHTSSSCEEEESSTTSHHHHHHHHHHHHTTCCBTTTBEE
T ss_pred             CCCCCCEEEEEEeccCCeEEEEecchhhccccCCHHHHHHHHHhcCCCEEEEeCCCCHHHHHHHHHHHHcCCCCCCceEE
Confidence            1112222222   334466777776532111 1111     3788877777665554444566678999999873  443


Q ss_pred             EecCHHHHHHHHHhc--cceeeeecceeccc-ccC-CceeeecCCCCccc-eEEEEEeCC--ccccHHHHHHHHHHhHH
Q psy3760         223 ETINSDIIKTYVELR--MGIGIIASIAFDSN-RDK-NLRSISASHLFGTT-ISRVIIKQG--TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~-~~~-~l~~~~~~~~~~~~-~~~l~~~~~--~~~~~~~~~~~~~l~~~  294 (306)
                      ..-....+..++.+|  ++++ +++...... ..+ ..+.....+..... ...++.+++  ...+..+++|++.+.+.
T Consensus       189 v~~~~~~~~~aL~~G~vDa~~-~~eP~~~~~~~~g~~~~~~~~~~~~~~~p~~~l~~~~~~~~~~p~~~~~~~~A~~~A  266 (417)
T 2g29_A          189 IVVPPAQMVANVKVNAMESFC-VGEPWPLQTVNQGVGYQALTTGQLWKDHPEKAFGMRADWVDQNPKAAKALLMAVMEA  266 (417)
T ss_dssp             EECCGGGHHHHHHTTSCSEEE-EETTHHHHHHHHTSCEEEEEGGGTBTTCBCEEEEEEHHHHHHCHHHHHHHHHHHHHH
T ss_pred             EECCHHHHHHHHHcCCCCEEE-eCCCHHHHHHHcCCCEEEEechhhcCCCceEEEEECHHHHHHCHHHHHHHHHHHHHH
Confidence            333456778888888  4443 343332222 222 22233332211212 245555554  22356778888777554

>1xs5_A 29 kDa protein, membrane lipoprotein TPN32; periplasmic binding protein, methionine, membrane protein; 1.85A {Treponema pallidum} SCOP: c.94.1.1

Probab=97.42  E-value=0.0044  Score=48.01  Aligned_cols=188  Identities=10%  Similarity=0.048  Sum_probs=104.2

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccc--
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCY--  164 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~--  164 (306)
                      ..|+||+.++....++ ..+..+.+.. ++.+++... +.....+.|.+|++|+.+..+.+.-     ..+.....+.  
T Consensus         3 ~~i~vG~~~~~~~~~~-~~~~~~~~~~-Gl~ve~~~f~d~~~~n~AL~~G~iD~n~fq~~~~l~~~~~~~g~~l~~v~~~   80 (241)
T 1xs5_A            3 ETVGVGVLSEPHARLL-EIAKEEVKKQ-HIELRIVEFTNYVALNEAVMRGDILMNFFQHVPHMQQFNQEHNGDLVSVGNV   80 (241)
T ss_dssp             EEEEEEECSTTHHHHH-HHHHHHHHTT-TEEEEEEECSCHHHHHHHHHHTSSSEEEEEEHHHHHHHHHHHTCCEEEEEEE
T ss_pred             ceEEEEecCCCcHHHH-HHHHHHHHHc-CCeEEEEEcCChHHHHHHHHcCCCCEeccCCHHHHHHHHHHCCCCEEEEEee
Confidence            3699999987654333 3344444444 899999884 5678899999999999975422110     1122222222  


Q ss_pred             -cceEEEEecCCCCCCCCCCcChhhh-cCCCeEeecCCCCcHHHHHHHHHhCCC------------------ce-eEEEE
Q psy3760         165 -QWEYVIIVPLDHPLLLLNSISLKEI-SNYPLITYDLSFSGRIKLDREFSLQKL------------------TP-YIVLE  223 (306)
Q Consensus       165 -~~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~~~~~~~~~~~~~~~~~~~~------------------~~-~~~~~  223 (306)
                       ..++.++        ..+--+++|| .+.....+ .+.....+...+++..|+                  .| +..+.
T Consensus        81 ~~~p~g~y--------s~kiksl~dL~~G~~Iaip-~d~sn~~ral~lL~~aGli~l~~~~~~~~t~~dI~~np~~v~~~  151 (241)
T 1xs5_A           81 HVEPLALY--------SRTYRHVSDFPAGAVIAIP-NDSSNEARALRLLEAAGFIRMRAGSGLFATVEDVQQNVRNVVLQ  151 (241)
T ss_dssp             EECCCEEE--------CSSCCSGGGCCTTCEEEEE-CSHHHHHHHHHHHHHTTSCEECTTCCTTCCGGGEEECTTCCEEE
T ss_pred             ccccceee--------cCCCCChHHcCCCCEEEEe-CCCchHHHHHHHHHHCCCEEecCCCCCccChhhhhcCCCceEEE
Confidence             1222222        1234579999 66665554 444445566778988887                  12 22232


Q ss_pred             ecCHHHHHHHHHhccceeeeecceeccc-ccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         224 TINSDIIKTYVELRMGIGIIASIAFDSN-RDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       224 ~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      --+...+...+..-++ ++++...+... ..+  .-....  +........++.+++...++.+++|++.+++.
T Consensus       152 ~l~~~~~~~al~~VDa-a~i~~~~a~~agl~~~~~~l~~e--~~~~~~~nviv~r~~~~~~~~vk~l~~a~~s~  222 (241)
T 1xs5_A          152 EVESALLPRVFDQVDG-AVINGNYAIMAGLSARRDGLAVE--PDASAYANVLVVKRGNEADARVQAVLRALCGG  222 (241)
T ss_dssp             EECGGGHHHHGGGSSE-EEECHHHHHHTTCCTTTTCSEEC--SCGGGGCEEEEEETTCTTCHHHHHHHHHHTSH
T ss_pred             EeCHHHHHHhhhccCE-EEECcHHHHHcCCCcccceEEEc--CCCCceEEEEEEECCccChHHHHHHHHHHCCH
Confidence            2233444444443344 44554333221 111  112222  21123445677777777899999999988643

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=97.41  E-value=0.00035  Score=54.22  Aligned_cols=80  Identities=16%  Similarity=0.159  Sum_probs=51.4

Q ss_pred             chhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         2 ~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      +..++.++..+.+. +.|.+.-|+.+++++||+++.++.||+. |.---.+..+.+ .||+.|+.+++....+ -.|+++
T Consensus       151 ~~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~-GlV~r~~r~~~~-~LT~~G~~l~~~~~~~-~~w~~a  227 (244)
T 2wte_A          151 SREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF-GILTQKGKDRKV-ELNELGLNVIKLNKSV-IESSKS  227 (244)
T ss_dssp             CHHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEETTTTEE-EECHHHHHHHHHTC---------
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeCCccEE-EECHHHHHHHHHHhcc-cccHHH
Confidence            44566777666543 2388999999999999999999999986 544333334566 8999999998774443 344444


Q ss_pred             HHHH
Q psy3760          81 KKIG   84 (306)
Q Consensus        81 ~~~~   84 (306)
                      ...+
T Consensus       228 q~~~  231 (244)
T 2wte_A          228 SEEL  231 (244)
T ss_dssp             ----
T ss_pred             HHHH
Confidence            4443

>3ix1_A N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine protein; periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidin protein; HET: NFM; 2.40A {Bacillus halodurans c-125}

Probab=97.40  E-value=0.0023  Score=51.51  Aligned_cols=195  Identities=5%  Similarity=-0.084  Sum_probs=102.5

Q ss_pred             cEEEEecccchh-hhhHHHHHHHHHhCCCcEEEEEeCChh-HHHHHHHcCCeeEEEEccccC---CCCCceee----ccc
Q psy3760          94 NLTIATTHTQAR-YALPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIRNDQADIAIVTEILS---PSDKLISI----PCY  164 (306)
Q Consensus        94 ~l~I~~~~~~~~-~~l~~~l~~~~~~~p~~~i~~~~~~~~-~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~----~l~  164 (306)
                      +|++|..+.... .+....-..+.++. ++++++...... ...+.|.+|++|++++.....   ...+....    ...
T Consensus         6 ~l~l~~~p~~~~~~~~va~~~g~~~~~-Gl~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~~~~~~~   84 (302)
T 3ix1_A            6 EVMLDWYPNAVHTFLYVAIENGYFAEE-GLDVDIVFPTNPTDPIQLTASGAIPLALSYQPDVILARSKDLPVVSVASVVR   84 (302)
T ss_dssp             EEECSSSCCGGGHHHHHHHHTTHHHHT-TEEEEEECCSSTTHHHHHHHHTSCSEEEECHHHHHHHHHTTCCEEEEEEEEC
T ss_pred             EEEecceeCcccHHHHHHHHcChHHHc-CCcEEEecCCCCchHHHHHHCCCCCEEecCHHHHHHHHHCCCCEEEEEEEec
Confidence            455665543221 12222223333433 788888865554 899999999999999851100   11222222    222


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc--ccee-
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR--MGIG-  241 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~-  241 (306)
                      .....++++++.+     .-+++||.+.++..... ......+..++...|+.+..+-.++.......++.+|  +++. 
T Consensus        85 ~~~~~l~~~~~s~-----i~s~~DL~Gk~i~~~~~-~~~~~~~~~~l~~~Gl~~~~v~~~~~~~~~~~al~~G~vDa~~~  158 (302)
T 3ix1_A           85 SPLNHVMFLAEQD-----FDSPADLVGLTVGYPGI-PVNEPILKTMVEAAGGDYEQVHLMDVGFELGASIVSGRADAVVG  158 (302)
T ss_dssp             SCCEEEEEEGGGC-----CSSGGGGTTSEEEECSC-TTHHHHHHHHHHHTTCCGGGCEEEECTTCHHHHHHHSSSSEEEE
T ss_pred             cCCEEEEEECCCC-----CCChHHcCCCEEEeCCC-cchHHHHHHHHHHcCCCHHHeEEEecCccHHHHHhCCCCCEEEE
Confidence            3467777777653     34789999988766544 3345567788899998764222222122345666677  3432 


Q ss_pred             -eeecc-eecccccCCceeeecCCC-C-ccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         242 -IIASI-AFDSNRDKNLRSISASHL-F-GTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       242 -~~p~~-~~~~~~~~~l~~~~~~~~-~-~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                       +.+.. .........+..+...+. . ......++.+++.  ..+..+++|++.+.+..
T Consensus       159 ~~~~~~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~p~~v~~~~~a~~~a~  218 (302)
T 3ix1_A          159 TYINHEYPVLKHEGHDISYFNPVDYGVPEYDELVLISNEAYVEESGEVLAAFWRAALKGY  218 (302)
T ss_dssp             EETTTHHHHHHHTTCCEEEECGGGTTCCCCCSEEEEEEHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             eeecchHHHHHhcCCCceEeCHHHcCCCCCcccEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence             22221 111111223344443321 1 1223345555442  23567888888876654

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

Probab=97.39  E-value=0.0027  Score=42.87  Aligned_cols=81  Identities=16%  Similarity=0.116  Sum_probs=51.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHHHHHHH-HHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQAILRSI-EIIMQEIEGLKK   82 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~l~~~a-~~il~~~~~~~~   82 (306)
                      .++++..+.+.+.|++.-|+.+++|+|++|++|+.||+ .|.--..+.++.. +.+|+.|...+... ..+...++....
T Consensus        23 r~~IL~~L~~~~~~~~ela~~l~is~~tv~~~l~~L~~-~gli~~~~~gr~~~y~l~~~~~~~~~~~~~~~~~~~~~~l~  101 (114)
T 2oqg_A           23 RWEILTELGRADQSASSLATRLPVSRQAIAKHLNALQA-CGLVESVKVGREIRYRALGAELNKTARTLERIGAEWDRRLA  101 (114)
T ss_dssp             HHHHHHHHHHSCBCHHHHHHHSSSCHHHHHHHHHHHHH-TTSEEEEEETTEEEEEECSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCeeEEecCCEEEEEechHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555333338999999999999999999999985 4544444444432 27999997654433 333333444444


Q ss_pred             HHHh
Q psy3760          83 IGKE   86 (306)
Q Consensus        83 ~~~~   86 (306)
                      .+..
T Consensus       102 ~l~~  105 (114)
T 2oqg_A          102 AIKQ  105 (114)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>3tqw_A Methionine-binding protein; transport and binding proteins, transport protein; HET: MSE; 2.00A {Coxiella burnetii}

Probab=97.39  E-value=0.0021  Score=49.21  Aligned_cols=199  Identities=7%  Similarity=0.007  Sum_probs=113.4

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccc--
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCY--  164 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~--  164 (306)
                      .+|+||+++.....++..+-..+.++ -++.++++. .+.......|.+|++|+.+..+.+.     ...++....++  
T Consensus         3 ~~ikVG~~~~p~~~i~~~~~~~l~~~-~Gi~veiv~F~Dy~~pN~AL~~G~iDaN~fQh~pyl~~~~k~~g~~lv~v~~~   81 (240)
T 3tqw_A            3 AMVRVGTIAGPETQLMEVAKQVALNR-YGLHVNIITFSDYNTPNEALADGSVDANMFQHLPYLKAQIEMRGYKIVSIGKT   81 (240)
T ss_dssp             -CEEEEEETTHHHHHHHHHHHHHHHH-HCCCEEEEEESCTTSHHHHHHTTSCSEEEEEEHHHHHHHHHHHCCCEEEEEEE
T ss_pred             ceEEEEEeCCChHHHHHHHHHHHHHh-cCCeEEEEEeCChHhHHHHHHcCCcCeeccCCHHHHHHHHHHCCCCEEEEeec
Confidence            47999999865555555444555533 277887776 3556788999999999998753211     11233333332  


Q ss_pred             -cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC-----------ce--------eEEEEe
Q psy3760         165 -QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-----------TP--------YIVLET  224 (306)
Q Consensus       165 -~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~-----------~~--------~~~~~~  224 (306)
                       .+++.++ +       ++--+++||.+-.-|..+.+.....+....|+..|+           ++        +..+.-
T Consensus        82 ~~~p~glY-S-------~k~ksl~dL~~Ga~Iaipnd~tn~~RaL~lL~~aGLI~Lk~~~~~~~T~~DI~~Npk~l~~~e  153 (240)
T 3tqw_A           82 FVYPMGLY-S-------KKITALTQLKTGAKIAVPSDPSNEARALLLLEKAQLIQLKTHVTINATPMDIASNPKKLKIVE  153 (240)
T ss_dssp             EECCCEEE-C-------SSCSSGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSCEECCC--CCCCGGGEEECTTCCEEEE
T ss_pred             cccceEEe-c-------CCCCCHHHhcCCCEEEEecCccHHHHHHHHHHHCCCEEecCCCCCcCChhhhccCCCCcEEEE
Confidence             2344443 2       223588999855556666555555666788999988           11        112222


Q ss_pred             cCHHHHHHHHHhccceeeeecceeccccc--CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         225 INSDIIKTYVELRMGIGIIASIAFDSNRD--KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       225 ~~~~~~~~~v~~g~gi~~~p~~~~~~~~~--~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      -+...+.+.+...++..+-+.+....--.  .+-..+.  +....+-..++++++...++.+++|++.+++.--+.++++
T Consensus       154 ~~aaql~r~l~dvD~avin~n~a~~agl~p~~dal~~E--~~~~~y~nviavr~~~~d~~~~k~lv~a~~s~evk~~i~~  231 (240)
T 3tqw_A          154 LDAAQLSRSLGDVDLAAINTNYAIPAGLSPSRDALLTE--GPNSPYANVVAVREDDKNDPRLKQLVSALHSPAVLSAAKK  231 (240)
T ss_dssp             ECGGGGGGCTTTCSEEEECHHHHGGGTCCTTTTCSEEC--CSSSSCEEEEEEEGGGTTCHHHHHHHHHHTSHHHHHHHHH
T ss_pred             cCHHHHHHhccCccEEEEcchHHHHcCCCcccCeeEEc--CCCCCeeEEEEEeccccCCHHHHHHHHHHCCHHHHHHHHH
Confidence            22233333344444444444444433211  1222222  2222345567788888899999999999876654555544

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=97.36  E-value=0.0011  Score=44.23  Aligned_cols=76  Identities=12%  Similarity=-0.005  Sum_probs=55.2

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec----CCCccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH----GKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~----~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +..++.++..+.+.+ .|.+.-|+.+++|++++++.|+.||+. |.--..+.    .+.+ .+|+.|+.++..+.+.+..
T Consensus        19 ~~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~-glv~~~~~~~~r~~~~-~~t~~g~~~~~~~~~~~~~   96 (109)
T 1sfx_A           19 KPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKR-GFVRREIVEKGWVGYI-YSAEKPEKVLKEFKSSILG   96 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEEESSSEEEE-EEECCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEeecCCceEEE-EecCcHHHHHHHHHHHHHH
Confidence            345666777776532 378999999999999999999999875 43322222    2233 6999999999988887766


Q ss_pred             HHH
Q psy3760          77 IEG   79 (306)
Q Consensus        77 ~~~   79 (306)
                      ..+
T Consensus        97 ~~~   99 (109)
T 1sfx_A           97 EIE   99 (109)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>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=97.33  E-value=0.0011  Score=51.73  Aligned_cols=75  Identities=15%  Similarity=0.205  Sum_probs=56.5

Q ss_pred             CchhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      ++..++.++..+.+.+   -+.+.-|+.+++++|++|+.|++||+. |.--=.++   +|.+ +.||+.|+.++..+.+.
T Consensus       156 Lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~-GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~  234 (250)
T 1p4x_A          156 LSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQ-GYLIKERSTEDERKILIHMDDAQQDHAEQLLAQ  234 (250)
T ss_dssp             SCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHH-TSSEEEECSSSTTCEEEECCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeeCCCCCCCeEEEEECHHHHHHHHHHHHH
Confidence            3567888888888764   268999999999999999999999997 43333222   2322 38999999998877666


Q ss_pred             HHH
Q psy3760          74 MQE   76 (306)
Q Consensus        74 l~~   76 (306)
                      .+.
T Consensus       235 ~~~  237 (250)
T 1p4x_A          235 VNQ  237 (250)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>3gxa_A Outer membrane lipoprotein GNA1946; periplasmic, L-methionine bingding, protein binding; 2.25A {Neisseria meningitidis}

Probab=97.32  E-value=0.01  Score=46.40  Aligned_cols=199  Identities=9%  Similarity=-0.034  Sum_probs=115.0

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeec--
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIP--  162 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~--  162 (306)
                      ...+|+||+++.....++..++....+. .++.++++.. +.......|.+|++|+.+..+.+.-     ..++....  
T Consensus        21 ~~~tIkVG~~~~p~~~il~~~~k~~l~k-~Gi~veiv~F~Dy~~pN~AL~~G~IDaN~fQh~pyL~~~nk~~g~~Lv~v~   99 (275)
T 3gxa_A           21 AKKEIVFGTTVGDFGDMVKEQIQPELEK-KGYTVKLVEFTDYVRPNLALAEGELDINVFQHKPYLDDFKKEHNLDITEVF   99 (275)
T ss_dssp             --CEEEEEEETTHHHHHHHHTHHHHHHT-TTCEEEEEEESSSSHHHHHHHHTSCSEEEEECHHHHHHHHHHHTCCEEEEE
T ss_pred             CCCeEEEEEeCCChHHHHHHHHHHHHHH-cCCeEEEEEeCCcHhHHHHHHcCCCCeeecCCHHHHHHHHHHcCCCEEEEe
Confidence            3468999998865555554445555544 3899999884 6678899999999999987533111     11222222  


Q ss_pred             -cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-------------------e-eEE
Q psy3760         163 -CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-------------------P-YIV  221 (306)
Q Consensus       163 -l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-------------------~-~~~  221 (306)
                       ...+++.++. +       +--+++||.+-.-|..+.+.....+....|+..|+-                   | +..
T Consensus       100 ~~~~~p~glYS-~-------kiksl~dL~~Ga~IAIPnDptN~~RaL~lL~~aGLIkLk~~~~~~~~T~~DI~eNpk~lk  171 (275)
T 3gxa_A          100 QVPTAPLGLYP-G-------KLKSLEEVKDGSTVSAPNDPSNFARVLVMLDELGWIKLKDGINPLTASKADIAENLKNIK  171 (275)
T ss_dssp             ECCBCCCEEEE-S-------SCCCGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSSEECTTCCGGGCCGGGEEECTTCCE
T ss_pred             eccccceEEec-C-------CCCCHHHcCCCCEEEecCCccHHHHHHHHHHHCCCEEecCCCCCCcCCHHHHhcCCCCCE
Confidence             2334555543 2       234789998555555555555555666788888761                   1 112


Q ss_pred             EEecCHHHHHHHHHhccceeeeecceeccc-c-cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         222 LETINSDIIKTYVELRMGIGIIASIAFDSN-R-DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       222 ~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      +.--+...+.+.+...++..+-+.+....- . ...|.  .-.  ...+-..++++++...++.+++|++.+++.--+.+
T Consensus       172 ~~eldaaql~r~l~dvD~avIn~nya~~agl~~~dal~--E~~--~~~y~Nvivvr~~d~d~~~ik~lv~a~~S~evk~~  247 (275)
T 3gxa_A          172 IVELEAAQLPRSRADVDFAVVNGNYAISSGMKLTEALF--QEP--SFAYVNWSAVKTADKDSQWLKDVTEAYNSDAFKAY  247 (275)
T ss_dssp             EEEECGGGHHHHTTTSSEEEECHHHHHHTTCCGGGCSE--ECC--CCTTCCEEEEEGGGTTCHHHHHHHHHTTSHHHHHH
T ss_pred             EEEeCHHHHhhhccccCEEEEchhHHHHcCCCccccee--cCC--CCCcEEEEEEeccccCCHHHHHHHHHHcCHHHHHH
Confidence            322233344454555555444444544332 2 12222  211  22334467788888899999999999876655555


Q ss_pred             HHh
Q psy3760         300 INK  302 (306)
Q Consensus       300 ~~~  302 (306)
                      +++
T Consensus       248 i~~  250 (275)
T 3gxa_A          248 AHK  250 (275)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>2rin_A Putative glycine betaine-binding ABC transporter protein; type II binding protein, aromatic BOX, acetylcholine, protein binding; HET: ACH; 1.80A {Rhizobium meliloti} PDB: 2rej_A 2rf1_A 2reg_A* 3hcq_A

Probab=97.31  E-value=0.014  Score=46.80  Aligned_cols=193  Identities=10%  Similarity=0.019  Sum_probs=115.0

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCceee-
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLISI-  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~~-  161 (306)
                      ...|+||....-....+..++..+.+.+ ++++++...+...+.+.|.+|++|++.....+..         ...+... 
T Consensus         6 ~~~I~ig~~~~~~~~~~~~i~~~~Le~~-G~~Ve~~~~~~~~~~~Al~~G~iD~~~~~w~~~~~~~~~~~~~~~~l~~l~   84 (298)
T 2rin_A            6 CGTVRFSDVGWTDITATTATATTILEAL-GYETDVKVLSVPVTYTSLKNKDIDVFLGNWMPTMEADIAPYREDKSVETVR   84 (298)
T ss_dssp             TTEEEEECCSCHHHHHHHHHHHHHHHHH-TCEEEEECCCHHHHHHHHHHTSCCEEEEEEETTTHHHHHHHHTTTSEEEEE
T ss_pred             CCCEEEecCCCcHHHHHHHHHHHHHHHc-CCceEEEECCcHHHHHHHHcCCcEEEhhhccCchHHHHHHHhhCCCEEEec
Confidence            4579999988766667777777776664 8899998888788899999999999975311110         1233322 


Q ss_pred             c-cccceEEEEecCCCCCCCCCCcChhhhc------CCCeEeecCCCCcHHHHHHHHH--hCCCc-eeEEEEecCHHH--
Q psy3760         162 P-CYQWEYVIIVPLDHPLLLLNSISLKEIS------NYPLITYDLSFSGRIKLDREFS--LQKLT-PYIVLETINSDI--  229 (306)
Q Consensus       162 ~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~------~~~~i~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~--  229 (306)
                      + .......++++++...  +.--+++||.      +-.++..+++......+...++  ..|+. .+.+  ..+...  
T Consensus        85 ~~~~~~~~~l~V~~~~ae--~~I~si~DLk~~~~~~~gk~~g~~~G~~~~~~~~~~l~~~~yGL~d~~~v--~~~~~~~~  160 (298)
T 2rin_A           85 ENLAGAKYTLATNAKGAE--LGIKDFKDIAAHKDELDGKIYGIEPGNDGNRLIIDMVEKGTFDLKGFEVV--ESSEQGML  160 (298)
T ss_dssp             EEEEEEEEEEEEEHHHHH--HTCCBGGGSGGGHHHHTSEEECCSTTCHHHHHHHHHHHHTGGGCTTCEEE--CCCHHHHH
T ss_pred             cCCCCCeEEEEEchhHHh--cCCCCHHHHHHHHHHcCCeEECCCCChHHHHHHHHHhhhhcCCCCCceec--cCCHHHHH
Confidence            1 1234577888775410  0224677776      3457777776666666777786  67873 3322  234333  


Q ss_pred             --HHHHHHhccc---eeeeecceecccccCCceeeecCCCC-c----cceEEEEEeCCc-cccHHHHHHHHHHh
Q psy3760         230 --IKTYVELRMG---IGIIASIAFDSNRDKNLRSISASHLF-G----TTISRVIIKQGT-YLRSYVYSFIKLLS  292 (306)
Q Consensus       230 --~~~~v~~g~g---i~~~p~~~~~~~~~~~l~~~~~~~~~-~----~~~~~l~~~~~~-~~~~~~~~~~~~l~  292 (306)
                        +.+.+.+|.-   .+.-|.+....   .+++.+.-+... .    ....+.+.+++- ...|.+.+|++.+.
T Consensus       161 a~~~~A~~~g~~~v~~~w~p~~~~~~---~~l~~L~d~k~~~~~~~~~~~~~~v~~~~~~~~~P~v~~~L~~~~  231 (298)
T 2rin_A          161 AQVARAEKSGDPIVFLGWEPHPMNAN---FKLTYLSGGDDVFGPNYGGATVHTNVRAGYTTECPNVDKLLQNLS  231 (298)
T ss_dssp             HHHHHHHHTTCCCEEEEEESSTHHHH---SCEEECBSCTTTTCHHHHEEEEEEEEETTHHHHSHHHHHHHHHCC
T ss_pred             HHHHHHHHCCCCEEEEEeccCchhhc---CCeeECCCCccccCCCCCcceEeeeechHHHHHChHHHHHHHHcC
Confidence              3455667743   33345544333   245555433211 1    245555666653 23677888887554

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=97.28  E-value=0.00052  Score=44.91  Aligned_cols=56  Identities=16%  Similarity=0.094  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQA   65 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~   65 (306)
                      .++++..+ +...+++.-|+.+++|++|++++|+.||+. |.--..+  +.+ ++|+.|+.
T Consensus        33 r~~Il~~L-~~~~~~~eLa~~l~is~~tv~~~L~~L~~~-Glv~~~~--g~y-~l~~~g~~   88 (96)
T 1y0u_A           33 RRKILRML-DKGRSEEEIMQTLSLSKKQLDYHLKVLEAG-FCIERVG--ERW-VVTDAGKI   88 (96)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET--TEE-EECTTTCC
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEC--CEE-EECCCchH
Confidence            34555555 433489999999999999999999999876 6544444  355 89998754

>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=97.24  E-value=0.00094  Score=50.60  Aligned_cols=73  Identities=18%  Similarity=0.148  Sum_probs=56.5

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ .+.+.-|+.+++++|++|+.|++||+.   -|+.|..       ..+ .||+.|+.++..+..
T Consensus        46 Lt~~q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~~Le~~---GlV~r~~~~~DrR~~~l-~LT~~G~~~~~~~~~  121 (207)
T 2fxa_A           46 LNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEER---GYLRFSKRLNDKRNTYV-QLTEEGTEVFWSLLE  121 (207)
T ss_dssp             CCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHH---TSEEEECC------CEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEecCCCCCceEEE-EECHHHHHHHHHHHH
Confidence            3456777888887643 278899999999999999999999986   3455543       245 899999999999887


Q ss_pred             HHHHH
Q psy3760          73 IMQEI   77 (306)
Q Consensus        73 il~~~   77 (306)
                      ....+
T Consensus       122 ~~~~~  126 (207)
T 2fxa_A          122 EFDPT  126 (207)
T ss_dssp             HCCGG
T ss_pred             HHHHH
Confidence            65443

>3up9_A Putative uncharacterized protein; membrane lipoprotein, L-methionine binding protein, NLPA LIP structural genomics; HET: PG4 PE4; 2.35A {Actinomyces odontolyticus} SCOP: c.94.1.0

Probab=97.20  E-value=0.013  Score=45.08  Aligned_cols=202  Identities=12%  Similarity=0.047  Sum_probs=115.6

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccc
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCY  164 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~  164 (306)
                      ...+|+||+++.....++..+-..+.+++ ++.++++.. +.......|.+|++|+.+..+.+.     ...++....++
T Consensus         5 ~~~~ikVG~~~~p~~~il~~v~~~l~k~~-Gi~veiv~F~Dy~~pN~AL~~G~IDaN~fQH~pyL~~~nk~~g~~lv~v~   83 (245)
T 3up9_A            5 DVVTLTVGATPSPHAKILTYINDNLAADA-GIKLDIVEYTDYVQPNTALNDGDLDANFYQTVPYLENAEKQFGYNFEAGE   83 (245)
T ss_dssp             CCEEEEEEECTTTHHHHHHHHHHHTHHHH-TEEEEEEECSSSHHHHHHHHTTSCSEEEEEEHHHHHHHHHHHCCCEEECC
T ss_pred             CCceEEEEEeCCChHHHHHHHHHHHHHHc-CCeEEEEEecCcccHHHHHHcCCCceeccCCHHHHHHHHHHCCCCEEEEe
Confidence            34589999988755555544444444433 799999885 566788899999999999853311     11233333333


Q ss_pred             ---cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc---e--------------eEEEEe
Q psy3760         165 ---QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT---P--------------YIVLET  224 (306)
Q Consensus       165 ---~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~---~--------------~~~~~~  224 (306)
                         .+++.++ +++       --+++||.+---|..+.+.....+....|+..|+-   +              +..+.-
T Consensus        84 ~~~~~p~giY-S~k-------~ksl~dL~~Ga~IaIPnD~tN~~RaL~lL~~aGLIkLk~~~~~~~~~T~~DIk~lk~~e  155 (245)
T 3up9_A           84 GIHLEPLGVF-SNK-------HKSLDELPDGGTIGIISDTANQSRALELLATQGLVSIPEGDGDVNINTVTKLKNFDFRE  155 (245)
T ss_dssp             CCEECCCEEE-CSS-------CSCGGGCCTTEEEEEECSHHHHHHHHHHHHHTTSEECCCCC--CSTTTSEESSSEEEEE
T ss_pred             eecccceEEE-eCC-------CCCHHHcCcCCEEEEecCcchHHHHHHHHHHCCCEEecCCCCCcCcCChhhccccEEEE
Confidence               2445554 222       34788998555555555545445556688888762   1              222332


Q ss_pred             cCHHHHHHHHHhccceeeeecceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         225 INSDIIKTYVELRMGIGIIASIAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       225 ~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      -+...+.+.+...++..+-+.+....--.+  +-..+.-.. ...+-..++++++...++.+++|++.+++.--+.++++
T Consensus       156 ~daaqlpr~l~dvd~avin~nya~~agl~p~~dal~~E~~~-~~py~nviavr~~~~d~~~~k~lv~a~~s~evk~~i~~  234 (245)
T 3up9_A          156 VEGPQLVRSLDDFDYAVINGNFAQEGGKTISGDALVVESPV-DNPAVNVLVWKGDSKKVDAIAKLEKLLHSDEVKQYIEK  234 (245)
T ss_dssp             ECGGGHHHHTTTSSEEEECHHHHHHTTCCHHHHCSEECCCT-TCCCEEEEEEETTCTTHHHHHHHHHHHTSHHHHHHHHH
T ss_pred             eCHHHHhhhcccCCEEEEchhHHHHcCcCcccCeeEECCCC-CCCcEEEEEEeccccCCHHHHHHHHHHCCHHHHHHHHH
Confidence            333445555555454444334444331111  111222111 22334567778888899999999999876654555544

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

Probab=97.15  E-value=0.001  Score=43.64  Aligned_cols=60  Identities=13%  Similarity=0.125  Sum_probs=44.0

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQ   64 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~   64 (306)
                      ..++++..+.+.+.+++.-|+.+++|+|++|++|+.||+ .|.---.|.|+.. +++|+.+.
T Consensus        24 ~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~-~Glv~~~~~g~~~~y~l~~~~~   84 (98)
T 3jth_A           24 RRLQILCMLHNQELSVGELCAKLQLSQSALSQHLAWLRR-DGLVTTRKEAQTVYYTLKSEEV   84 (98)
T ss_dssp             HHHHHHHHTTTSCEEHHHHHHHHTCCHHHHHHHHHHHHH-TTSEEEECCTTCCEEEECCHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCeEEEEeCCEEEEEECHHHH
Confidence            345566666653337999999999999999999999986 6766556665543 27888753

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

Probab=97.10  E-value=0.0017  Score=43.45  Aligned_cols=58  Identities=12%  Similarity=0.059  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPG   63 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G   63 (306)
                      .++++..+.+.+.|++.-|+.+++|+|++|++|+.||+ .|.--..|.|+.. +++|+.|
T Consensus        27 r~~IL~~L~~~~~s~~eLa~~lgis~stvs~~L~~L~~-~GlV~~~~~gr~~~y~l~~~~   85 (108)
T 2kko_A           27 RLQILDLLAQGERAVEAIATATGMNLTTASANLQALKS-GGLVEARREGTRQYYRIAGED   85 (108)
T ss_dssp             THHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHH-HTSEEEEEETTEEEEEESCHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCCeEEEEeCCEEEEEEChHH
Confidence            35556666553347899999999999999999999986 5766666666543 2789877

>3o66_A Glycine betaine/carnitine/choline ABC transporter; structural genomics, PSI-2, protein structure initiative; HET: PGE; 1.86A {Staphylococcus aureus subsp} SCOP: c.94.1.0

Probab=97.09  E-value=0.0028  Score=50.34  Aligned_cols=204  Identities=10%  Similarity=0.082  Sum_probs=121.7

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCC--cEEEEEe--CChhHHHHHHHcCCeeEEE-Ec-----cccCC-----
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPK--VKLSLLQ--GNPKQITEMIRNDQADIAI-VT-----EILSP-----  154 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~--~~i~~~~--~~~~~~~~~l~~~~~Di~i-~~-----~~~~~-----  154 (306)
                      ...+.|+||....-...++..++..+.+...+  +.+++..  +++..+.+.|.+|++|+.. -+     .+..+     
T Consensus         6 ~~~~~I~ig~~~~te~~il~~i~~~~Le~~~G~~~~V~~~~~lg~~~~~~~al~~G~iDv~~~eytGt~w~~~l~~~~~~   85 (282)
T 3o66_A            6 STKNDVKITALSTSESQIISHMLRLLIEHDTHGKIKPTLVNNLGSSTIQHNALINGDANISGVRYNGTDLTGALKEAPIK   85 (282)
T ss_dssp             -CCCCCEEEEESSHHHHHHHHHHHHHHHHHTTTSCCCEEEEEESSHHHHHHHHHHTSCSEEEEEEHHHHHHTTTCCCCCC
T ss_pred             CCCCCEEEEcCCCcHHHHHHHHHHHHHHhccCCceeEEEEecCCCcHHHHHHHHcCCCCEeehhccchhhHhhcCCCCCC
Confidence            45678999999998899999999998887656  7777775  5666789999999999998 21     11111     


Q ss_pred             CC---------------Cceee--ccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecCCCCcHH--HHHHHHH
Q psy3760         155 SD---------------KLISI--PCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDLSFSGRI--KLDREFS  212 (306)
Q Consensus       155 ~~---------------~~~~~--~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~~~~~~~--~~~~~~~  212 (306)
                      .+               ++...  -.+...+.+++++..... ..--+++||..++   .+..+.++..+.  -+....+
T Consensus        86 ~~~~~~~~~~~~~~~~~~l~~l~~~~~~n~~~laV~~~~a~~-~~l~sisDL~~~~~~~~~g~~~ef~~r~gdG~~~l~~  164 (282)
T 3o66_A           86 DPKKAMIATQQGFKKKFDQTFFDSYGFANTYAFMVTKETAKK-YHLETVSDLAKHSKDLRLGMDSSWMNRKGDGYEGFKK  164 (282)
T ss_dssp             SHHHHHHHHHHHHHHHHSEEECCCCSCBCCEEEEECHHHHHH-HTCSBSGGGTTTGGGCEEEEEGGGCC--CCSHHHHHH
T ss_pred             CHHHHHHHHHHHhhhccCeEEeccCCcCCeEEEEEeHHHHhH-cCCCCHHHHHhcccceEEecCcccccCchhHHHHHHH
Confidence            00               11111  012346777777753111 1234788888764   333443222111  2344455


Q ss_pred             hCCCceeEEEEecCHHHHHHHHHhccce---eeeecceecccccCCceeeecCC-CCccceEEEEEeCCc-cccHHHHHH
Q psy3760         213 LQKLTPYIVLETINSDIIKTYVELRMGI---GIIASIAFDSNRDKNLRSISASH-LFGTTISRVIIKQGT-YLRSYVYSF  287 (306)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~v~~g~gi---~~~p~~~~~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~~-~~~~~~~~~  287 (306)
                      ..|+..... ...+...+.+++++|..+   +..|+++..   ..+|+.+.-+. ..+......+.+++- ...|.+.++
T Consensus       165 ~Ygl~~~~~-~~~d~g~~~~A~~~~~~~v~~~wsp~~~~~---~~dL~~LeD~k~~fp~~~~~~vvr~~~~~~~P~~~~~  240 (282)
T 3o66_A          165 EYGFDFGTV-RPMQIGLVYDALNTEKLDVALGYSTDGRIA---AYDLKVLKDDKQFFPPYAASAVATNELLRQHPELKTT  240 (282)
T ss_dssp             HHCCCCSEE-EEECGGGHHHHHHTTSCSEEEEETTCHHHH---HTTCEECBCTTCCSCCCBEEEEEEHHHHHHCTHHHHH
T ss_pred             HcCCCCccc-cccCHHHHHHHHHcCCCeEEEEeCCCchhh---hcCceEcCCCcccccccceeEEEcHHHHhHCHHHHHH
Confidence            567765433 333445788899998544   345555544   34688876554 233445666666653 235778888


Q ss_pred             HHHHhHHhhHH
Q psy3760         288 IKLLSPKLNRK  298 (306)
Q Consensus       288 ~~~l~~~~~~~  298 (306)
                      ++-+...+...
T Consensus       241 L~~l~~~lt~~  251 (282)
T 3o66_A          241 INKLTGKISTS  251 (282)
T ss_dssp             HHTTTTCCCHH
T ss_pred             HHHHhccCCHH
Confidence            87775444333

>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor, NR1, ligand binding protein; 1.35A {Rattus norvegicus} SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A* 1pb8_A 1pb9_A

Probab=97.07  E-value=0.00049  Score=55.26  Aligned_cols=188  Identities=11%  Similarity=-0.011  Sum_probs=105.0

Q ss_pred             CCcEEEEecccc-----------hhhhhHHHHHHHHHhCCCcEEEEEeC-----------------ChhHHHHHHHcCCe
Q psy3760          92 TGNLTIATTHTQ-----------ARYALPKIIKEFTIQFPKVKLSLLQG-----------------NPKQITEMIRNDQA  143 (306)
Q Consensus        92 ~~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~p~~~i~~~~~-----------------~~~~~~~~l~~~~~  143 (306)
                      .+.+++|+....           ...+...++..+.+.. +++++++..                 +...++..|.+|++
T Consensus        40 ~~~l~vg~~~~~~P~~~~~~~g~~~G~~vDll~~ia~~l-g~~~~~~~~~d~~~g~~~~~~~~~~~~w~~~~~~l~~g~~  118 (292)
T 1pb7_A           40 KKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTM-NFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQA  118 (292)
T ss_dssp             CCEEEEEEC--------CEEEEEEESHHHHHHHHHHHHH-TCCEEEEECTTCCCCCEEECTTSSCEEECHHHHHHHHTSC
T ss_pred             cceeecccCCCCCCccccccccCcceeHHHHHHHHHHHc-CceEEEEEecCCcccccccccccccCcHHHHHHHHHcCCc
Confidence            478999887643           3456777777777654 667777663                 56789999999999


Q ss_pred             eEEEEccccC--CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhc--CC---CeEeecCCCCcHHHHHHHHHhC-
Q psy3760         144 DIAIVTEILS--PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEIS--NY---PLITYDLSFSGRIKLDREFSLQ-  214 (306)
Q Consensus       144 Di~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~--~~---~~i~~~~~~~~~~~~~~~~~~~-  214 (306)
                      |+++......  ....+. +.|+......++++++.++.     +++|+.  +.   ..+....+....    .++... 
T Consensus       119 D~~~~~~~~t~~R~~~~~fs~Py~~~~~~i~~~~~~~i~-----~~~dl~~~g~~~~~~~~~~~~~~~~----~~~~~~~  189 (292)
T 1pb7_A          119 DMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRIT-----GINDPRLRNPSDKFIYATVKQSSVD----IYFRRQV  189 (292)
T ss_dssp             SEECSSCBCCHHHHTTEEECSCSEEEEEEEEEETTCCCC-----STTCHHHHSCBTTBCEECBTTSHHH----HHHHTCG
T ss_pred             CEEEeeeEecHHHhcceEechhhHhcCeEEEEECCcCCC-----CCcCccccCcccceEEEEEcCchHH----HHhhhcc
Confidence            9998532211  112333 45777888899999887532     455664  32   222222222211    122111 


Q ss_pred             CC---ce-eEEEEecCHHHHHHHHHhccceeeeec-ceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHH
Q psy3760         215 KL---TP-YIVLETINSDIIKTYVELRMGIGIIAS-IAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSF  287 (306)
Q Consensus       215 ~~---~~-~~~~~~~~~~~~~~~v~~g~gi~~~p~-~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  287 (306)
                      ..   .+ .....+++...++.++.+|..-+++-+ ..+...  ...++..+.  .......++++.+++......+...
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~~G~vDa~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~k~~~l~~~in~a  267 (292)
T 1pb7_A          190 ELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTG--ELFFRSGFGIGMRKDSPWKQNVSLS  267 (292)
T ss_dssp             GGHHHHHHHTTTCBSSHHHHHHHHHTTSCSEEEEEHHHHHHHHHHCTTEEECS--SCSEEEEECCEEETTCSSHHHHHHH
T ss_pred             cHHHHHHHHHhhcCCCHHHHHHHHHcCCceEEEEcHHHHHHHHhcCCCEEEcC--ccccCCceEEEEeCCCHHHHHHHHH
Confidence            00   00 012246789999999999975555443 333222  234554443  2233457778888875444444444


Q ss_pred             HHHH
Q psy3760         288 IKLL  291 (306)
Q Consensus       288 ~~~l  291 (306)
                      +..+
T Consensus       268 l~~l  271 (292)
T 1pb7_A          268 ILKS  271 (292)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=97.04  E-value=0.00066  Score=50.31  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=38.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI   70 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a   70 (306)
                      +-..-|+.|++|+|++|..+++|+++ |  |..+.++|+ +||+.|+.+....
T Consensus        32 ~~~~LA~~LgvS~~SV~~~lkkL~e~-G--LV~~~~~Gv-~LTe~G~~~A~~i   80 (200)
T 2p8t_A           32 GRKQISERLELGEGSVRTLLRKLSHL-D--IIRSKQRGH-FLTLKGKEIRDKL   80 (200)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-T--SEEEC--CE-EECHHHHHHHHHH
T ss_pred             cHHHHHHHhCCCHHHHHHHHHHHHHC-C--CEEEeCCCe-EECHHHHHHHHHH
Confidence            56778999999999999999999974 3  455555787 8999999975543

>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=97.00  E-value=0.0045  Score=40.86  Aligned_cols=59  Identities=25%  Similarity=0.236  Sum_probs=43.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPG   63 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G   63 (306)
                      ..++++..+.+...+++.-|+.+++|+|++|++|+.||+ .|.---.|.++.. +++|+.+
T Consensus        24 ~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~-~Glv~~~~~g~~~~y~l~~~~   83 (102)
T 3pqk_A           24 VRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRE-SGIVETRRNIKQIFYRLTEAK   83 (102)
T ss_dssp             HHHHHHHHHHTCCBCHHHHHHHHTCCTTHHHHHHHHHHH-TTSEEEECSSSCCEEEECSST
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCeEEEEeCCEEEEEECcHH
Confidence            345566666554348999999999999999999999974 5665555555543 3788863

>4ib2_A Putative lipoprotein; putative methionine-bindning, NLPA lipoprotein, PF03180 FAMI structural genomics, joint center for structural genomics; 1.76A {Ruminococcus gnavus}

Probab=96.99  E-value=0.0051  Score=47.55  Aligned_cols=200  Identities=13%  Similarity=0.081  Sum_probs=113.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeecc---
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPC---  163 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l---  163 (306)
                      .+|+||+++.....++.. +..+.+.. ++.++++.. +.......|.+|++|+.+..+.+.     ...++....+   
T Consensus        11 ~~ikVG~~~~p~~~il~~-v~~~~~k~-Gi~veiv~F~Dy~~pN~AL~~G~iDaN~fQh~pyL~~~~k~~g~~lv~v~~~   88 (252)
T 4ib2_A           11 KTIKVAASATPHAEILEQ-AKSILKKE-GYQLEVTVFDDYVQPNEVVESGEFDANYFQHVPYLESFNEEKGTHLVDAGDI   88 (252)
T ss_dssp             HEEEEEECTTTHHHHHHH-HHHHHHHT-TCEEEEEECSSSSHHHHHHHTTSSSEEEEEEHHHHHHHHHHHCCCEEEEEEE
T ss_pred             ceEEEEEcCCChHHHHHH-HHHHHHhc-CCeEEEEEecChhhHHHHHHcCCcCeeecCCHHHHHHHHHHCCCCEEEEeec
Confidence            469999998755555544 44444443 899999885 556788999999999998753311     1122333333   


Q ss_pred             ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEEEe
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVLET  224 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~~~  224 (306)
                      ..+++.++. +       +--+++||.+-.-|..+.+.....+....|+..|+-                  | +..+.-
T Consensus        89 ~~~p~glyS-~-------kiksl~dLk~Ga~IAipnd~sN~~RaL~lL~~aGLIkLk~~~~~~~t~~DI~~Npk~lk~~e  160 (252)
T 4ib2_A           89 HYEPFGIYP-G-------TKKSLDEISEGDKIAVPNDTTNEARALLLLQDNGIITLKDGAGLNATVNDIEENPYNVEIVE  160 (252)
T ss_dssp             EECCCEEEE-S-------SCSCGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSCEECTTCGGGCCGGGEEECTTCCEEEE
T ss_pred             cccceEeec-C-------CcCCHHHcCCCCEEEeeCCCCHHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCcEEEE
Confidence            233444432 2       234889998555555555545555666788888851                  1 112322


Q ss_pred             cCHHHHHHHHHhccceeeeecceecccccC--CceeeecCCCC--ccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760         225 INSDIIKTYVELRMGIGIIASIAFDSNRDK--NLRSISASHLF--GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       225 ~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~~~~~~--~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  300 (306)
                      -+...+.+.+...++..+-+.+....--.+  +-..+.-....  ..+--.++++++...++.+++|++.+++.--+.++
T Consensus       161 l~aaql~r~l~dvD~avin~n~a~~agl~p~~dal~~E~~~~~~~~~y~Niiavr~~~~d~~~~k~lv~a~~s~evk~~i  240 (252)
T 4ib2_A          161 LEAAQVARVTGETAYVVLNGNYALEAGYSVAKDALAYEKSDSEAAKTYVNIIAVKEGNEKEEKIQALVKALKSDEIKEYI  240 (252)
T ss_dssp             ECGGGGGGGTTTSSEEEECHHHHHHTTCCHHHHCSEECCTTBHHHHHSEEEEEEETTCTTCHHHHHHHHHHTSHHHHHHH
T ss_pred             cCHHHHHhhhccCCEEEEchhHHHHcCCCCccceeEecCCCcccCCCeeEEEEEecCccCCHHHHHHHHHHCCHHHHHHH
Confidence            233344444445454444444544331111  12222211110  23445677788888999999999998776555555


Q ss_pred             Hh
Q psy3760         301 NK  302 (306)
Q Consensus       301 ~~  302 (306)
                      ++
T Consensus       241 ~~  242 (252)
T 4ib2_A          241 EK  242 (252)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=96.94  E-value=0.0016  Score=46.52  Aligned_cols=65  Identities=20%  Similarity=0.209  Sum_probs=49.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQAILRSI   70 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~l~~~a   70 (306)
                      .++++..+.+...+++.-|+.+++|+|++|++|+.||+ .|.--..|.|+.. +++|+.|...+...
T Consensus        60 R~~IL~~L~~~~~t~~eLa~~lgls~stvs~hL~~L~~-aGlV~~~~~Gr~~~y~lt~~~~~~l~~~  125 (151)
T 3f6v_A           60 RRRLVQLLTSGEQTVNNLAAHFPASRSAISQHLRVLTE-AGLVTPRKDGRFRYYRLDPQGLAQLRAL  125 (151)
T ss_dssp             HHHHHHHGGGCCEEHHHHHTTSSSCHHHHHHHHHHHHH-TTSEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCEEEEecCCEEEEEEChHHHHHHHHH
Confidence            45666666554348999999999999999999999975 4666666666543 38999997766543

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

Probab=96.91  E-value=0.0017  Score=40.01  Aligned_cols=45  Identities=18%  Similarity=0.227  Sum_probs=38.8

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++.++|..+.+.. |....|+.+|+|++|++++++++.+.||..
T Consensus        13 ~~~e~~il~~~~~g~-s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   57 (74)
T 1fse_A           13 TKREREVFELLVQDK-TTKEIASELFISEKTVRNHISNAMQKLGVK   57 (74)
T ss_dssp             CHHHHHHHHHHTTTC-CHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            446677787776666 999999999999999999999999999863

>1r9l_A Glycine betaine-binding periplasmic protein; periplasmic binding protein, cation-PI interactions, tryptophan BOX, protein binding; 1.59A {Escherichia coli} SCOP: c.94.1.1 PDB: 1r9q_A*

Probab=96.90  E-value=0.021  Score=46.04  Aligned_cols=199  Identities=5%  Similarity=-0.045  Sum_probs=116.4

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccCC---------CCCcee
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILSP---------SDKLIS  160 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~  160 (306)
                      ....|+||....-...++..++..+.+.. ++.+++.. .+...+.+.|.+|++|+......+..         ...+..
T Consensus         6 ~~~~I~ig~~~~~e~~~~~~i~~~~Le~~-Gy~Ve~~~~~~~~~~~~Al~~G~iDi~~e~w~~~~~~~~~~~~~~~~l~~   84 (309)
T 1r9l_A            6 KGITVNPVQSTITEETFQTLLVSRALEKL-GYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYR   84 (309)
T ss_dssp             TTCEECEEECSCGGGHHHHHHHHHHHHHT-TCEECCCEECCHHHHHHHHHHTSSCEEEEEEETTTHHHHHHTTGGGTEEE
T ss_pred             CCceEEEeecCccHHHHHHHHHHHHHHHc-CCCeEEeecCchHHHHHHHhcCCceEEeccccCccHHHHHHhhcCCcEEE
Confidence            45679999988766667777777777765 78888653 57778899999999999974321110         012222


Q ss_pred             ecc--ccceEEEEecCCCCCCCCCCcChhhhcC--------------CCeEeecCCCCcHHHHHHHHHhCCCceeEEEEe
Q psy3760         161 IPC--YQWEYVIIVPLDHPLLLLNSISLKEISN--------------YPLITYDLSFSGRIKLDREFSLQKLTPYIVLET  224 (306)
Q Consensus       161 ~~l--~~~~~~~v~~~~~~l~~~~~i~~~dl~~--------------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (306)
                      ..-  ......++++++.... ..--+++||.+              -.++..+++...+..+...++..|+...+....
T Consensus        85 l~~~~~~~~~~l~V~~~~a~~-~~i~si~DL~~~~~~~~f~~~~~gkg~~~~~~~G~~~~~~~~~~l~~yGL~~~~~~~~  163 (309)
T 1r9l_A           85 EGVFVNGAAQGYLIDKKTADQ-YKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQ  163 (309)
T ss_dssp             CSCSEEEEEEEEEEEHHHHHH-HTCCBGGGGGSHHHHGGGCSSSSSSEEEECCCTTSHHHHHHHHHHHHTTCTTTEEEEC
T ss_pred             ecccCCCceEEEEEchhhhhh-cCCCCHHHHcCchHHHHcCCCCCCCceEEecCCCcchhHHHHHHHHhcCCCCceEEcC
Confidence            111  2345778887752100 01236777762              146777777666667788889999875344333


Q ss_pred             cCH----HHHHHHHHhcccee---eeecceeccc-ccCCceeeecC---------------C---C-CccceEEEEEeCC
Q psy3760         225 INS----DIIKTYVELRMGIG---IIASIAFDSN-RDKNLRSISAS---------------H---L-FGTTISRVIIKQG  277 (306)
Q Consensus       225 ~~~----~~~~~~v~~g~gi~---~~p~~~~~~~-~~~~l~~~~~~---------------~---~-~~~~~~~l~~~~~  277 (306)
                      .+.    ..+..++.+|..+.   .-|.+....+ ...+++.+..+               +   . .+...+..+.+++
T Consensus       164 ~s~~~~~~~~~~A~~~g~~~v~~~w~P~~~~~~~~~g~dl~~Le~~~~~~~~~~~~~~~L~d~k~~~~p~~~~~~v~~~~  243 (309)
T 1r9l_A          164 GNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKA  243 (309)
T ss_dssp             SCHHHHHHHHHHHHHTTCCCEEEEEESSSHHHHSCBTTTEEECBCSSCCCTTCTTCCCBCTTSCBCSSCSEEEEEEEEHH
T ss_pred             CCHHHHHHHHHHHHHCCCCEEEEeecCchHhhhccccCCceEeccCcccccccccccccCCCccccCCCcceEEEEechh
Confidence            443    24556777885433   3455544432 01155553322               1   1 2344555555554


Q ss_pred             c-cccHHHHHHHHHH
Q psy3760         278 T-YLRSYVYSFIKLL  291 (306)
Q Consensus       278 ~-~~~~~~~~~~~~l  291 (306)
                      - ...|.+..|++-+
T Consensus       244 ~~~~~P~~~~~L~~~  258 (309)
T 1r9l_A          244 WAEKNPAAAKLFAIM  258 (309)
T ss_dssp             HHHHCHHHHHHHHHC
T ss_pred             HHHHChHHHHHHHhC
Confidence            2 2367778887655

>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=96.85  E-value=0.0067  Score=41.49  Aligned_cols=75  Identities=7%  Similarity=0.050  Sum_probs=54.9

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhC----CCchHHHHHHHHHHHHcCceeEEecCCCc--cccCHhHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALY----TSQPGVSKAIIELEEELSIDIFIRHGKRI--RGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~----isq~~~s~~i~~LE~~lg~~Lf~R~~~~~--~~lT~~G~~l~~~a~~il   74 (306)
                      +..++.++..+.+.+ .|.+.-|+.++    +|+||+++.|++||+. |.---.++++..  +.+|+.|+.++..+.++.
T Consensus         9 t~~~~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~-Glv~r~~~~rr~~~~~lT~~g~~~~~~~~~~~   87 (123)
T 1okr_A            9 SSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKK-GFIDRKKDNKIFQYYSLVEESDIKYKTSKNFI   87 (123)
T ss_dssp             CHHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-TSEEEEEETTEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHC-CCeEEEecCCeEEEEEecCHHHHHHHHHHHHH
Confidence            345666776666543 26788899999    8999999999999986 433333333322  269999999999998888


Q ss_pred             HHH
Q psy3760          75 QEI   77 (306)
Q Consensus        75 ~~~   77 (306)
                      +.+
T Consensus        88 ~~~   90 (123)
T 1okr_A           88 NKV   90 (123)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            776

>3ir1_A Outer membrane lipoprotein GNA1946; D-methionine cultured, protein binding; 2.15A {Neisseria meningitidis}

Probab=96.85  E-value=0.028  Score=43.10  Aligned_cols=196  Identities=9%  Similarity=-0.037  Sum_probs=113.7

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeecc---c
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPC---Y  164 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l---~  164 (306)
                      +|+||+++.....++........+. .++.++++.. +.......|.+|++|+.+..+.+.-     ..++....+   .
T Consensus         2 ~ikVG~~~~p~~~il~~~~k~~l~k-~Gi~leiv~F~Dy~~pN~AL~~G~iDaN~fQh~pyL~~~nk~~g~~Lv~v~~~~   80 (245)
T 3ir1_A            2 EIVFGTTVGDFGDMVKEQIQPELEK-KGYTVKLVEFTDYVRPNLALAEGELDINVFQHKPYLDDFKKEHNLDITEVFQVP   80 (245)
T ss_dssp             EEEEEEETTHHHHHHHHTHHHHHHT-TTCEEEEEEESSSSHHHHHHHHTSCSEEEEECHHHHHHHHHHHTCCEEEEEECC
T ss_pred             eEEEEEcCCChHHHHHHHHHHHHHH-cCceEEEEEeCCcHhHHHHHHCCCcCeeccCCHHHHHHHHHHcCCCEEEEeeec
Confidence            6899998875555555445555444 3899988874 5567889999999999987533111     112222222   3


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-------------------e-eEEEEe
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-------------------P-YIVLET  224 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-------------------~-~~~~~~  224 (306)
                      -+++.++. +.       --+++||.+---|..+.+.....+....|+..|+-                   | +..+.-
T Consensus        81 ~~p~glYS-~k-------~ksl~dl~~Ga~IaIPnDptN~~RaL~lL~~aGLIkLk~~~~~~~~T~~DI~~Npk~lk~~e  152 (245)
T 3ir1_A           81 TAPLGLYP-GK-------LKSLEEVKDGSTVSAPNDPSNFARVLVMLDELGWIKLKDGINPLTASKADIAENLKNIKIVE  152 (245)
T ss_dssp             BCCCEEEE-SS-------CCCGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSSEECTTCCGGGCCGGGEEECTTCCEEEE
T ss_pred             ccceEEec-CC-------CCCHHHcCCCCEEEecCCccHHHHHHHHHHHCCCEEecCCCCCCcCCHHHHhcCCCCCEEEE
Confidence            34555542 22       34788998655666666555555666788888761                   1 112222


Q ss_pred             cCHHHHHHHHHhccceeeeecceeccc-c-cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         225 INSDIIKTYVELRMGIGIIASIAFDSN-R-DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       225 ~~~~~~~~~v~~g~gi~~~p~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      -+...+.+.+...++..+-+.+....- . ...|.  .  +....+-..++++++...++.+++|++.+++.--+.++++
T Consensus       153 ~daaql~r~l~dvD~avin~nya~~agl~~~dal~--E--~~~~~y~Nvivvr~~~~d~~~ik~lv~a~~S~evk~~i~~  228 (245)
T 3ir1_A          153 LEAAQLPRSRADVDFAVVNGNYAISSGMKLTEALF--Q--EPSFAYVNWSAVKTADKDSQWLKDVTEAYNSDAFKAYAHK  228 (245)
T ss_dssp             ECGGGSGGGGGTSSEEEECHHHHHHTTCCGGGCSE--E--CCCCTTCCEEEEEGGGTTCHHHHHHHHHTTSHHHHHHHHH
T ss_pred             eCHHHHhhhccccCEEEEchhHHHHcCCCccccee--c--CCCCCcEEEEEEeccccCCHHHHHHHHHHCCHHHHHHHHH
Confidence            223333444445454444444444332 2 11222  2  2122334457778888889999999999876654555543

>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=96.83  E-value=0.0057  Score=47.63  Aligned_cols=77  Identities=13%  Similarity=0.178  Sum_probs=57.3

Q ss_pred             CchhhHHHHHHHHHh---cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ---NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~---~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      ++..|+.++..+.+.   |-+.+.-|+.++++++++|+.|++||+. |.--=.|+   .|.+ +.||+.|+.++..+.+.
T Consensus        32 lt~~q~~vL~~L~~~~~~~~~~~el~~~l~~~~~t~t~~l~rLe~~-G~i~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~  110 (250)
T 1p4x_A           32 MTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKH-SYISKVRSKIDERNTYISISEEQREKIAERVTL  110 (250)
T ss_dssp             SCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHT-TSCEEEECSSSTTSEEEECCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeEEEEECHHHHHHHHHHHHH
Confidence            356788888888873   2279999999999999999999999997 53332322   1222 37999999987777666


Q ss_pred             HHHHH
Q psy3760          74 MQEIE   78 (306)
Q Consensus        74 l~~~~   78 (306)
                      .+...
T Consensus       111 ~~~~~  115 (250)
T 1p4x_A          111 FDQII  115 (250)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=96.81  E-value=0.0015  Score=38.55  Aligned_cols=31  Identities=10%  Similarity=0.020  Sum_probs=26.7

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      -.++.++| +.++||+.||||++|+.+.|+++
T Consensus        27 ~~aL~~~g-n~~~aA~~LGIsr~tL~rklkk~   57 (61)
T 1g2h_A           27 KLFYAEYP-STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             HHHHHHSC-SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             HHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHh
Confidence            34566678 99999999999999999999874

>4got_A Methionine-binding lipoprotein METQ; NLPA lipoprotein, PF03180 family, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.95A {Bacillus subtilis subsp}

Probab=96.79  E-value=0.09  Score=40.52  Aligned_cols=201  Identities=11%  Similarity=0.118  Sum_probs=118.5

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC------CCCCceeecc
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS------PSDKLISIPC  163 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~------~~~~~~~~~l  163 (306)
                      ...+|+||+++.....++-. +....+. .++.++++.. +....-..|.+|++|+-+..+.+.      ...++....+
T Consensus         4 ~~k~i~vgat~~P~aeil~~-vk~~l~k-~Gi~leiv~F~Dy~~pN~AL~~G~iDaN~fQH~pyL~~~~k~~~g~~lv~v   81 (249)
T 4got_A            4 GKKEIVVAATKTPHAEILKE-AEPLLKE-KGYTLKVKVLSDYKMYNKALADKEVDANYFQHIPYLEQEMKENTDYKLVNA   81 (249)
T ss_dssp             CTTEEEEEECTTTHHHHHHH-HHHHHHT-TTCEEEEECCSSTHHHHHHHHTTSCSEEEEEEHHHHHHHHHHCTTCCEEEE
T ss_pred             CCceEEEEeCCCCHHHHHHH-HHHHHHh-cCCeEEEEEeCCccchhHHHHcCCcceeeccCHHHHHHHHHhCCCCceEEe
Confidence            34689999999876666654 4444444 3899999885 566678889999999999753321      1223333333


Q ss_pred             cc---ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc----------e----------eE
Q psy3760         164 YQ---WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT----------P----------YI  220 (306)
Q Consensus       164 ~~---~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~----------~----------~~  220 (306)
                      +.   +++.++.        ++--+++||.+---|..+.+.....+-...|+..|+-          +          +.
T Consensus        82 ~~~~~~P~glYS--------~k~ksl~dl~~Ga~IaIPnDptN~~RaL~lL~~aGLIkLk~~~~~~~~t~~DI~~Npk~l  153 (249)
T 4got_A           82 GAVHLEPFGIYS--------KTYKSLKDLPDGATIILTNNVAEQGRMLAMLENAGLITLDSKVETVDATLKDIKKNPKNL  153 (249)
T ss_dssp             EEEEECCCEEEC--------SSCSSGGGCCTTCEEEEECCGGGHHHHHHHHHHTTSCEECTTSCGGGCCGGGEEECTTCC
T ss_pred             eeeeeccccccc--------cCcCchhhcCCCCEEEEecCccchHHHHHHHHHCCCEEECCCCCccccCcchhhhCCccc
Confidence            32   3344442        2234888997777777777666666777788888651          0          11


Q ss_pred             EEEecCHHHHHHHHHhc-cceeeeec-ceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         221 VLETINSDIIKTYVELR-MGIGIIAS-IAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       221 ~~~~~~~~~~~~~v~~g-~gi~~~p~-~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                      .+.--+...+.+.+..+ ...++++. +....--.+  +...+.-.. ...+-..++++++...+|.+++|++.+++.--
T Consensus       154 ~~~e~~aaql~r~l~d~~vD~avin~n~a~~agl~p~~dal~~E~~~-~~py~Nvivvr~~d~d~~~ik~lv~a~~s~ev  232 (249)
T 4got_A          154 EFKKVAPELTAKAYENKEGDAVFINVNYAIQNKLNPKKDAIEVESTK-NNPYANIIAVRKGEEDSAKIKALMEVLHSKKI  232 (249)
T ss_dssp             EEEEECTTTHHHHHHTTCSSEEEECHHHHHHTTCCHHHHCSEECCST-TCCCCEEEEEETTCTTSHHHHHHHHHHTSHHH
T ss_pred             cceecCHhHhhhhcccccccEEEechhHHHHcCCChhhhhhcccCCC-CCceEEEEEEcccccCCHHHHHHHHHHCCHHH
Confidence            22222334455555553 34555554 433321111  122222111 12234567788888899999999999876544


Q ss_pred             HHHHHh
Q psy3760         297 RKFINK  302 (306)
Q Consensus       297 ~~~~~~  302 (306)
                      +.++++
T Consensus       233 k~~I~~  238 (249)
T 4got_A          233 KDFIEK  238 (249)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            445543

>3r6u_A Choline-binding protein; substrate binding protein, ABC-transporter, extracellular, transport protein; 1.61A {Bacillus subtilis} SCOP: c.94.1.0 PDB: 3ppq_A 3ppo_A* 3ppp_A 3ppn_A 3ppr_A*

Probab=96.75  E-value=0.0073  Score=48.03  Aligned_cols=204  Identities=9%  Similarity=0.056  Sum_probs=124.6

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC--ChhHHHHHHHcCCeeEEE-Ec--------cccCC--CC---
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG--NPKQITEMIRNDQADIAI-VT--------EILSP--SD---  156 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~--~~~~~~~~l~~~~~Di~i-~~--------~~~~~--~~---  156 (306)
                      +.|+||....-...++..++..+.+...++++++...  +...+.+.|.+|++|+.. -+        .+...  .+   
T Consensus        12 ~~I~ig~~~~te~~il~~i~~~~Le~~~G~~V~~~~~lg~~~~~~~al~~G~iDv~~~eytGt~~~~~l~~~~~~~~~~~   91 (284)
T 3r6u_A           12 QTIKIGAQSMSESEIIASMLGQLIEHHTDLKTTTIKNLGSNAVQQQALMNGEIDIAATRYTGDALTGTLRMEPEKDPDKA   91 (284)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHSSCCEEEEEEECSHHHHHHHHHTTSCSEEEEEEHHHHHHHTTCCCCCCSHHHH
T ss_pred             CCEEEEeCCCcHHHHHHHHHHHHHHhcCCCCeEEEecCCchHHHHHHHHcCCCCEEehhccchhHHHhcCCCCCCCHHHH
Confidence            6899999999889999999999888877888888853  666789999999999999 31        11110  00   


Q ss_pred             ------------Cceee--ccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecCCCCcH--HHHHHHHHhCCCc
Q psy3760         157 ------------KLISI--PCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDLSFSGR--IKLDREFSLQKLT  217 (306)
Q Consensus       157 ------------~~~~~--~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~~~~~~--~~~~~~~~~~~~~  217 (306)
                                  ++...  -.+...+.+++++...-. ..--+++||..++   .+..+..+..+  +-+..+.+..|+.
T Consensus        92 ~~~~~~~~~~~~~l~~l~~~~~~~~~~laV~~~~a~~-~~l~sisDL~~~~~~~~~g~~~ef~~r~G~G~~~l~~~YGl~  170 (284)
T 3r6u_A           92 LALTQREFKKRYDLKWYDSYGFDNTYAFTVSKELADQ-YHLETVSDVKKWAPQLKLGVDNYWMKLKGNGYQDFTKTYGMT  170 (284)
T ss_dssp             HHHHHHHHHHHHCEEECCCCSCBCCEEEEEEHHHHHH-HTCCBSGGGGGGGGGCEEEECTTGGGCSSSSHHHHHHHHCCC
T ss_pred             HHHHHHHhHhhcCeEEeccCCcCCeEEEEEeHHHHhH-cCCCCHHHHHhhhhceeeccCcccccCchhHHHHHHHHcCCC
Confidence                        11111  112346778888763111 1234778887763   23333321111  1233445566776


Q ss_pred             eeEEEEecCHHHHHHHHHhccce---eeeecceecccccCCceeeecCC-CCccceEEEEEeCCc-cccHHHHHHHHHHh
Q psy3760         218 PYIVLETINSDIIKTYVELRMGI---GIIASIAFDSNRDKNLRSISASH-LFGTTISRVIIKQGT-YLRSYVYSFIKLLS  292 (306)
Q Consensus       218 ~~~~~~~~~~~~~~~~v~~g~gi---~~~p~~~~~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~~-~~~~~~~~~~~~l~  292 (306)
                      ... +...+...+.+++.+|..+   +..|+++..   ..+|+.+.-+. ..+......+.+++- ...|.+.++++-+.
T Consensus       171 ~~~-~~~~~~g~~~~A~~~~~~~v~~~wsp~~~~~---~~dL~~LeD~k~~fp~~~v~~vvr~~~~~~~P~~~~~L~~l~  246 (284)
T 3r6u_A          171 FGG-TYPMQIGLVYDAVKSGKMDIVLAYSTDGRIK---SYGLKMLKDDKQFFPPYDCSPVVPEKVLKEHPELEGIIKKML  246 (284)
T ss_dssp             CSE-EEECCGGGHHHHHHHTSCSEEEEETTCHHHH---HTTEEECBCTTCCSCCCBEEEEEEHHHHHHSTTHHHHHHTTT
T ss_pred             ccc-ccccCHHHHHHHHHcCCCeEEEEeCCCchhh---cCCceEcCCCcccCCccceeEEEcHHhhhHCHHHHHHHHHHH
Confidence            543 3334555778889888544   345555544   34688776554 234456677777653 23578888888887


Q ss_pred             HHhhHHHHH
Q psy3760         293 PKLNRKFIN  301 (306)
Q Consensus       293 ~~~~~~~~~  301 (306)
                      ..+......
T Consensus       247 ~~lt~~~m~  255 (284)
T 3r6u_A          247 GKIDTATMQ  255 (284)
T ss_dssp             TCCCHHHHH
T ss_pred             ccCCHHHHH
Confidence            555444433

>1zbm_A Hypothetical protein AF1704; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.30A {Archaeoglobus fulgidus} SCOP: c.94.1.1

Probab=96.74  E-value=0.082  Score=41.76  Aligned_cols=185  Identities=9%  Similarity=-0.032  Sum_probs=93.7

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHh-C-CCcEEEEEeCChhHHHHHHHcCCeeEEEEccc-cC-CCCCceeeccc
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQ-F-PKVKLSLLQGNPKQITEMIRNDQADIAIVTEI-LS-PSDKLISIPCY  164 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~-~-p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~-~~-~~~~~~~~~l~  164 (306)
                      ...+.+|+||..+....  .+-.+. ..+. + .++++++...+...+.+.|.+|++|++++... .. ...++....+.
T Consensus         6 ~~~~~~l~l~~~p~~~~--~p~~~a-~~~G~f~~Gl~ve~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~   82 (280)
T 1zbm_A            6 HHHSHKIRVAHTPDADD--AFMFYA-MTHGKVDTWLEIEHVIEDIETLNRKAFNAEYEVTAISAHAYALLDDKYRILSAG   82 (280)
T ss_dssp             -CTTCEEEEEECSSHHH--HHHHHH-HHTTCSCCSCEEEEEECCHHHHHHHGGGTCCSEEEEEHHHHTTSTTTEEECSSC
T ss_pred             ccccceEEEeecCCchH--HHHHHH-HHcCCcCCCceEEEEeCCHHHHHHHHHcCCCCEEEECHHHHHHhcCCCcEEeec
Confidence            34567899999876443  222222 2221 1 16788887788888899999999999986411 11 12233332211


Q ss_pred             ---c-ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHH-HHHHHHhCCCceeEEEEecCHHHHHHHHHhc--
Q psy3760         165 ---Q-WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK-LDREFSLQKLTPYIVLETINSDIIKTYVELR--  237 (306)
Q Consensus       165 ---~-~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--  237 (306)
                         . ....++++++.          +||.+.++.....+ ..... +..++...    ++  ...+...+..++.+|  
T Consensus        83 ~~~~~~~~~vlv~~~~----------~DLkGK~Iav~~~~-s~~~~ll~~~l~~~----~~--~~~~~~~~~~al~~G~v  145 (280)
T 1zbm_A           83 ASVGDGYGPVVVAKSE----------ISLDGKRIAVPGRY-TTANLLLKLAVEDF----EP--VEMPFDRIIQAVLDEEV  145 (280)
T ss_dssp             CEEESSCCCEEEESSC----------CCCTTCEEEESCTT-SHHHHHHHHHCSSC----EE--EECCGGGHHHHHHTTSS
T ss_pred             cccCCCeeEEEEEcCc----------hhcCCCEEEecCCC-cHHHHHHHHHhccC----ce--EecCHHHHHHHHHcCCC
Confidence               1 11223444331          77888776664333 23233 33333321    22  223455677778887  


Q ss_pred             cceeeeecceecccccCCceee-ecC-----CCCccceE-EEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         238 MGIGIIASIAFDSNRDKNLRSI-SAS-----HLFGTTIS-RVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       238 ~gi~~~p~~~~~~~~~~~l~~~-~~~-----~~~~~~~~-~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      +++.+....... ....++..+ .+.     ........ .++.+++- .+..+++|.+.+.+..
T Consensus       146 Da~~~~~~~~~~-~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~p~~v~~~~~a~~~a~  208 (280)
T 1zbm_A          146 DAGLLIHEGQIT-YADYGLKCVLDLWDWWSEQVKLPLPLGLNAIRRDL-SVEVQEEFLRAMRESI  208 (280)
T ss_dssp             SEEEECSGGGGT-GGGGTCEEEEEHHHHHHTTCSSCEEEEEEEEETTS-CHHHHHHHHHHHHHHH
T ss_pred             CEEEEechHHhH-HHhcCCeEeccHHHHHHHhhCCCCCeeEEEEcccC-CHHHHHHHHHHHHHHH
Confidence            443322222222 222334322 211     10111223 34556654 4677888888776553

>1p99_A Hypothetical protein PG110; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.70A {Staphylococcus aureus subsp} SCOP: c.94.1.1

Probab=96.68  E-value=0.017  Score=46.28  Aligned_cols=189  Identities=9%  Similarity=0.042  Sum_probs=99.9

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEccccCC-----CC-Cceeecccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEILSP-----SD-KLISIPCYQ  165 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~~~-----~~-~~~~~~l~~  165 (306)
                      ..|+||+. +.....+ ..+..+.+.. ++.+++...+ .....+.|.+|++|+++..+.+.-     .. +.....+..
T Consensus        39 ~~i~IG~~-~~~~~~~-~~~~~~~~~~-G~~Ve~~~f~~~~~~~~AL~~G~iD~~~~~~~~~l~~~~~~~~g~~l~~v~~  115 (295)
T 1p99_A           39 KKVTIGVA-SNDTKAW-EKVKELAKKD-DIDVEIKHFSDYNLPNKALNDGDIDMNAFQHFAFLDQYKKAHKGTKISALST  115 (295)
T ss_dssp             -CEEEEES-SSCCHHH-HHHHHHHGGG-TCCEEEEECSSTTSHHHHHHTTSSSEEEEEEHHHHHHHHHHCTTCCEEEEEE
T ss_pred             CeEEEEEe-CCcHHHH-HHHHHHHHHc-CCeEEEEEeCChHHHHHHHHcCCCCEEccCCHHHHHHHHHhcCCCCEEEEEe
Confidence            47999998 4333333 3333444443 7888888754 367899999999999985322110     11 222222221


Q ss_pred             ---ceEEEEecCCCCCCCCCCcChhhh-cCCCeEeecCCCCcHHHHHHHHHhCCC------------------ce-eEEE
Q psy3760         166 ---WEYVIIVPLDHPLLLLNSISLKEI-SNYPLITYDLSFSGRIKLDREFSLQKL------------------TP-YIVL  222 (306)
Q Consensus       166 ---~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~~~~~~~~~~~~~~~~~~~~------------------~~-~~~~  222 (306)
                         .++.++        ..+--+++|| .+...... .+.........+++..|+                  .| ++.+
T Consensus       116 ~~~~p~g~y--------s~~iksl~DL~~Gk~IAip-~~~s~~~~~l~lL~~~Gli~l~~~~~~~~t~~dI~~np~~v~~  186 (295)
T 1p99_A          116 TVLAPLGIY--------SDKIKDVKKVKDGAKVVIP-NDVSNQARALKLLEAAGLIKLKKDFGLAGTVKDITSNPKHLKI  186 (295)
T ss_dssp             EEECCCEEE--------CSSCSCGGGCCTTCEEEEE-CSHHHHHHHHHHHHHTTSCEECTTCCTTCCGGGEEECTTCCEE
T ss_pred             eccccceee--------cCCCCChHHcCCCCEEEec-CCCcHHHHHHHHHHHCCCccccCCCCCcCChhhhhcCCCceEE
Confidence               122222        1234579999 66665554 444445566678888886                  11 2233


Q ss_pred             EecCHHHHHHHHHhccceeeeecceecccccC--Cceeee-cCCC-CccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         223 ETINSDIIKTYVELRMGIGIIASIAFDSNRDK--NLRSIS-ASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~-~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      .--+...+..+...-+++.+-+.+....-..+  ....+. -... .......++.+++...++.+++|++.+.+
T Consensus       187 v~~~~~~~~~al~~VDaa~i~~~~a~~ag~~~~~~~i~~e~~~~~~~~~~~n~ivvr~~~~~~~~vk~l~~a~~s  261 (295)
T 1p99_A          187 TAVDAQQTARALSDVDIAVINNGVATKAGKDPKNDPIFLEKSNSDAVKPYINIVAVNDKDLDNKTYAKIVELYHS  261 (295)
T ss_dssp             EEECGGGTTGGGGTSSEEEECHHHHHHTTCCTTTSCSEECCCSSGGGGGGEEEEEEEGGGTTCHHHHHHHHHHHS
T ss_pred             EEcCHHHHHHHhhcCCEEEECcHHHHHcCCCcccceEEecCCcccCCCceeEEEEEeCCccChHHHHHHHHHHCC
Confidence            32233334444444455554443433221111  222222 1110 11334456677776778999999998873

>2x7q_A Ca3427, possible thiamine biosynthesis enzyme; unknown function; 2.00A {Candida albicans} PDB: 2x7p_A

Probab=96.65  E-value=0.13  Score=41.58  Aligned_cols=196  Identities=9%  Similarity=0.053  Sum_probs=100.5

Q ss_pred             CCCCcEEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEe--CChhHHHHHHHcCCeeEEEEccccC---CCCC---cee
Q psy3760          90 YDTGNLTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQ--GNPKQITEMIRNDQADIAIVTEILS---PSDK---LIS  160 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~--~~~~~~~~~l~~~~~Di~i~~~~~~---~~~~---~~~  160 (306)
                      ....+|+||..+..... +....-..+.+.. ++++++..  .++..+.+.|.+|++|++++.....   ...+   +..
T Consensus        12 ~~~~~l~ig~~~~~~~~p~~~A~~~G~~~~~-Gl~V~~~~~~~g~~~~~~al~~G~~D~~~~~~~~~~~~~~~g~~~~~~   90 (321)
T 2x7q_A           12 HQLPTLKVAYIPEHFSTPLFFAQQQGYYKAH-DLSIEFVKVPEGSGRLINLLNSNEVDIAIGLTEAFIADIAKGNENIHV   90 (321)
T ss_dssp             --CCCEEEEECCSGGGHHHHHHHHTTHHHHT-TCCEEEEECTTCHHHHHHHHHTTSCSEEEEEHHHHHHHHHTTCTTEEE
T ss_pred             cCCceEEEEeeCCccchHHHHHHHCCcHHHC-CceEEEEECCCCHHHHHHHHHcCCccEEecCcHHHHHHHHCCCCcEEE
Confidence            34568999998765432 2211112233332 67777765  3344578999999999999752100   0112   322


Q ss_pred             e-ccccce--EEEEecCCC-CCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHH-HhCCCceeE-EEEecCHHHHHHHH
Q psy3760         161 I-PCYQWE--YVIIVPLDH-PLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF-SLQKLTPYI-VLETINSDIIKTYV  234 (306)
Q Consensus       161 ~-~l~~~~--~~~v~~~~~-~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~v  234 (306)
                      . .+...+  +.++++++. +     .-+++||   .-|...........+...+ +..|+.+.+ ...+++...+..++
T Consensus        91 v~~~~~~~~~~~i~v~~ds~~-----i~s~~DL---K~i~~~~~gs~~~~~~~~l~~~~Gl~~dv~~v~~~~~~~~~~al  162 (321)
T 2x7q_A           91 LDTYVKSPLLWAVSTGSNRDD-----VTDAKQL---KRIGVSRIGSGSYVMSFVLAHQLGVPSFDQFQVLSNFKNLRDSV  162 (321)
T ss_dssp             EEEEECSCCEEEEEEESSCTT-----CSSGGGC---CEEEESSTTSHHHHHHHHHHHHHTSCCCCEEEECCSHHHHHHHH
T ss_pred             EEEecCCCcceEEEECCCCCC-----CCChHHc---ceEEeeCCCcHHHHHHHHHHHhcCCCcceEEEEcCChHHHHHHH
Confidence            1 122223  356677664 3     2368888   3444443223333444444 567876522 23455777888888


Q ss_pred             Hhc----cceeeeeccee-ccc-ccCCceeeecCCCCccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760         235 ELR----MGIGIIASIAF-DSN-RDKNLRSISASHLFGTTISRVIIKQGT--YLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       235 ~~g----~gi~~~p~~~~-~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~  295 (306)
                      .+|    ..=+++.+... ... ..+.+..+.-.. .+.....++.+++.  ..+..+++|++.+.+..
T Consensus       163 ~~G~~~~~vDa~~~ep~~~~~~~~~g~~~~~~d~~-~~~~~~~l~~~~~~~~~~p~~v~~~~~a~~~a~  230 (321)
T 2x7q_A          163 NLKDGVEGSDAFMWEYFTSKKYYDNHEIKQIDQIY-TPWSSWVVATSSDSLQAKSDVIKNFIDAVNQGI  230 (321)
T ss_dssp             TTCTTSCCCSEEEEEHHHHHHHHHTTSEEEEEEEE-CSSCSEEEEEEHHHHHHSHHHHHHHHHHHHHHH
T ss_pred             HcCCCccceEEEEecCccchhhccCCceEEccccC-CCCceEEEEEcHHHHhhCHHHHHHHHHHHHHHH
Confidence            888    44444543322 112 334455432111 11112345555442  13566778877776543

>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, cell junction, glycoprotein, ION transport channel, magnesium; 1.45A {Rattus norvegicus} PDB: 2rc7_A 2rc9_A 2rca_A 2rcb_A

Probab=96.55  E-value=0.0055  Score=49.07  Aligned_cols=187  Identities=11%  Similarity=0.096  Sum_probs=103.8

Q ss_pred             hhhhHHHHHHHHHhCCCcEEEEE-----------eCChhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEEE
Q psy3760         105 RYALPKIIKEFTIQFPKVKLSLL-----------QGNPKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYVI  170 (306)
Q Consensus       105 ~~~l~~~l~~~~~~~p~~~i~~~-----------~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~~  170 (306)
                      ..+...++..+.+.. +++++++           ..+...++..|.+|++|+++......  ....+. +.++.....++
T Consensus        69 ~G~~vdll~~ia~~l-g~~~~~~~~~~~~~g~~~~~~w~~~~~~l~~g~~D~~~~~~~~t~eR~~~~~fs~P~~~~~~~i  147 (294)
T 2rc8_A           69 YGYCIDLLEQLAEDM-NFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGI  147 (294)
T ss_dssp             ESHHHHHHHHHHHHH-TEEEEEEECTTCCCCCEETTEECHHHHHHHHTSCSEECSSCBCCHHHHTTSEECSCSEEEEEEE
T ss_pred             eEEhHHHHHHHHHHc-CCcEEEEECCCCcccccCCCCHHHHHHHHHCCCcCEEEeccccCHhHhceEEEccchHhcceEE
Confidence            345566666666553 6777763           34567899999999999998532111  112233 46788888999


Q ss_pred             EecCCCCCCCCCCcChhhhc------CCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh--ccceee
Q psy3760         171 IVPLDHPLLLLNSISLKEIS------NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL--RMGIGI  242 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~------~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~--g~gi~~  242 (306)
                      +++++.+    ..-+++||.      +..+.... +......+.+.+...+.... .+.+++...++.++.+  |..=++
T Consensus       148 ~~~~~~~----~i~~~~dL~~~~~~~g~~vg~~~-gs~~~~~l~~~~~~~~~~i~-~~~~~~~~~~~~~l~~~~GrvDa~  221 (294)
T 2rc8_A          148 LVRTRGT----ELSGIHDPKLHHPSQGFRFGTVR-ESSAEDYVRQSFPEMHEYMR-RYNVPATPDGVQYLKNDPEKLDAF  221 (294)
T ss_dssp             EEETTSC----CCCSTTCHHHHSCCTTCCEECBT-TSHHHHHHHHHCHHHHHHHG-GGCBSSHHHHHHHHHSSSCCCSEE
T ss_pred             EEECCCC----CcCChhhhhhcCcccCeEEEEEc-CChHHHHHHHHHHHHHHHHH-HhcCCCHHHHHHHHHhccCceeEE
Confidence            9988753    123677887      66666544 33333333332211110000 1246788999999999  754444


Q ss_pred             e-ecceeccc--ccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         243 I-ASIAFDSN--RDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       243 ~-p~~~~~~~--~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      + ....+...  ..+  .+..+.  .......++++.+++.   +....|-+.|.+..+....+++
T Consensus       222 i~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~ia~~k~~---~l~~~in~al~~l~~~G~~~~l  282 (294)
T 2rc8_A          222 IMDKALLDYEVSIDADCKLLTVG--KPFAIEGYGIGLPPNS---PLTSNISELISQYKSHGFMDVL  282 (294)
T ss_dssp             EEEHHHHHHHHHTCSSSCEEECS--CCEEEEEECCEECTTC---THHHHHHHHHHHHHHTTHHHHH
T ss_pred             EecHHHHHHHHhhCCCCCEEEcC--CcccccceEEEecCCC---HHHHHHHHHHHHHHhCCCHHHH
Confidence            3 33333222  222  233332  2233456777788774   4555555555544444444444

>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=96.52  E-value=0.0031  Score=54.55  Aligned_cols=73  Identities=16%  Similarity=0.230  Sum_probs=57.4

Q ss_pred             CchhhHHHHHHHHHh--c-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCc-cccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ--N-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRI-RGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~--~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~-~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.  + .+.+.-|+.+++++|++|+.|++||+. |  |+.|.     +|.+ +.||+.|+.+++.+.
T Consensus       402 lt~~q~~vl~~l~~~~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~-g--~v~r~~~~~D~R~~~i~lT~~g~~~~~~~~  478 (487)
T 1hsj_A          402 LNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDL-K--LLSKKRSLQDERTVIVYVTDTQKANIQKLI  478 (487)
T ss_dssp             CCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTT-T--TSCCEECCSSSSCCEEECCSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEeecCCCCCCCeEEEEECHHHHHHHHHHH
Confidence            456788899999887  3 278999999999999999999999986 4  44442     2332 389999999988887


Q ss_pred             HHHHH
Q psy3760          72 IIMQE   76 (306)
Q Consensus        72 ~il~~   76 (306)
                      +..+.
T Consensus       479 ~~~~~  483 (487)
T 1hsj_A          479 SELEE  483 (487)
T ss_dssp             HHHGG
T ss_pred             HHHHH
Confidence            76554

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=96.48  E-value=0.0042  Score=36.86  Aligned_cols=31  Identities=13%  Similarity=0.238  Sum_probs=25.5

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      ++.+++.+.++||+.||||++++.+.|+++.
T Consensus        27 aL~~~~gn~~~aA~~LGisr~tL~rklkk~g   57 (63)
T 3e7l_A           27 KLREYDYDLKRTAEEIGIDLSNLYRKIKSLN   57 (63)
T ss_dssp             HHHHTTTCHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             HHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            3444444999999999999999999998763

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

Probab=96.46  E-value=0.0046  Score=38.31  Aligned_cols=52  Identities=19%  Similarity=0.119  Sum_probs=42.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCc
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRI   56 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~   56 (306)
                      |.++++.-++.-...- |++.-|+.+++|.+||.+-|..||+.=   +..|.  .+|.
T Consensus         2 m~L~~Il~~L~~~g~v-sv~eLa~~l~VS~~TIRrdL~~Le~~G---~l~R~~~~Gga   55 (78)
T 1xn7_A            2 ASLIQVRDLLALRGRM-EAAQISQTLNTPQPMINAMLQQLESMG---KAVRIQEEPDG   55 (78)
T ss_dssp             CCHHHHHHHHHHSCSB-CHHHHHHHTTCCHHHHHHHHHHHHHHT---SEEEECCCCCC
T ss_pred             chHHHHHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEecCcCCC
Confidence            6677777777777777 899999999999999999999999874   45666  4443

>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor nmdar2A; protein-ligand complex, metal transport,membrane protein; HET: GLU; 1.70A {Rattus norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A* 3oem_A* 3oek_A*

Probab=96.43  E-value=0.0061  Score=48.54  Aligned_cols=183  Identities=13%  Similarity=0.126  Sum_probs=96.5

Q ss_pred             hhhhHHHHHHHHHhCCCcEEEEE-----------eCChhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEEE
Q psy3760         105 RYALPKIIKEFTIQFPKVKLSLL-----------QGNPKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYVI  170 (306)
Q Consensus       105 ~~~l~~~l~~~~~~~p~~~i~~~-----------~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~~  170 (306)
                      ..+...++..+.+.. ++++++.           ..+...++..|.+|++|+++......  ....+. +.|+.....++
T Consensus        58 ~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~fs~p~~~~~~~~  136 (284)
T 2a5s_A           58 KGFCIDILKKLSRTV-KFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISV  136 (284)
T ss_dssp             ESHHHHHHHHHHHHH-TCCEEEEECCSSSSCCEETTEECHHHHHHHTTSCSEECSSCBCCHHHHTTEEECCCCEEECEEE
T ss_pred             eEEhHHHHHHHHHHC-CCCEEEEEccCCccCcccCCCHHHHHHHHhcCCcCEEEEEEEEeccccceEEeccCchhcCEEE
Confidence            456666777776654 4566664           34567899999999999998531111  112333 46788888999


Q ss_pred             EecCCCCCCCCCCc---Chhhhc-CCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHhccc-eeeee
Q psy3760         171 IVPLDHPLLLLNSI---SLKEIS-NYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVELRMG-IGIIA  244 (306)
Q Consensus       171 v~~~~~~l~~~~~i---~~~dl~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g~g-i~~~p  244 (306)
                      +++++.++......   ++++|. +..+.....+. ....+.+.+...+  .... +..++...++.++.+|.. ..+..
T Consensus       137 ~~~~~~~~~~~~dl~~~~~~~l~~~~~vg~v~~~s-~~~~l~~~~~~~~--~~i~~~~~~~~~~~l~~l~~G~vDa~i~d  213 (284)
T 2a5s_A          137 MVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGS-TERNIRNNYPYMH--QYMTRFNQRGVEDALVSLKTGKLDAFIYD  213 (284)
T ss_dssp             EEETTCCCCSTTSHHHHSGGGSSSCCCEECCTTSH-HHHHHHTTCHHHH--HHHGGGCCSSHHHHHHHHHTTSCSEEEEE
T ss_pred             EEECCcccccccccccCChhHcCCCceEEEEeCCc-hHHHHHHHHHHHH--HHHHhccCCCHHHHHHHHHcCCeeEEEEc
Confidence            99988764432211   234444 34454443332 2222211111000  0011 113688999999999965 44444


Q ss_pred             cceeccc--ccCC--ceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         245 SIAFDSN--RDKN--LRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       245 ~~~~~~~--~~~~--l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ...+..+  ..+.  +..+..........++++.+++......+.+.+..+
T Consensus       214 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~a~~k~~~l~~~ln~~l~~l  264 (284)
T 2a5s_A          214 AAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQF  264 (284)
T ss_dssp             HHHHHHHHHTCTTSCEEEEECCCGGGCEEECCEEETTCTTHHHHHHHHHHH
T ss_pred             hHHHHHHHhcCCCCCEEEeCCccccccCceEEEecCCCHHHHHHHHHHHHH
Confidence            4433322  2222  333321122334577888888754333333333333

>2i49_A Bicarbonate transporter; alpha-beta protein, C-clamp, ABC transporter, periplasmic SO binding protein, bicarbonate-binding protein; 1.35A {Synechocystis SP} PDB: 2i48_A 2i4b_A 2i4c_A

Probab=96.42  E-value=0.16  Score=43.04  Aligned_cols=202  Identities=9%  Similarity=-0.039  Sum_probs=106.8

Q ss_pred             CCCcEEEEecccchhh-hhHHHHHHHHHhCCCc-EEEEEeC-ChhHHHHHHHcCC----eeEEEEccccC---------C
Q psy3760          91 DTGNLTIATTHTQARY-ALPKIIKEFTIQFPKV-KLSLLQG-NPKQITEMIRNDQ----ADIAIVTEILS---------P  154 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~-~l~~~l~~~~~~~p~~-~i~~~~~-~~~~~~~~l~~~~----~Di~i~~~~~~---------~  154 (306)
                      ....|+||..+..... +....-..|.+++ ++ .+++... +...+.+.|.+|+    +|++++..+..         .
T Consensus        34 e~~~lriG~~~~~~~apl~vA~~~G~f~~~-Gl~~Vel~~~~s~~~~~~al~~G~~~~~~D~a~~~~~~~~~~~~g~~~~  112 (429)
T 2i49_A           34 ETANIKLGYIPIVEAAPLIIAQEKGFFAKY-GMTGVEVSKQANWASARDNVTIGSQGGGIDGGQWQMPMPHLITEGIITN  112 (429)
T ss_dssp             SCSEEEEEECSSGGGHHHHHHHHTTHHHHT-TCCEEEEEECSSHHHHHHHHHHTGGGTSCSEEEECTTHHHHHHTTTTTT
T ss_pred             CCceEEEEeccchhhHHHHHHHHCChHHHc-CCCeeEEEEcCCHHHHHHHHHcCCCCCceeEEEeccHHHHHHHcCcccc
Confidence            3457999997753221 1111112244444 78 8888775 4678999999999    99999731100         0


Q ss_pred             CCCceee---ccccceEEEEecCCCCCCCCCC----c-C-hhhh-c--CC--CeEeecCCCCcHHHHHHHHHhCCCcee-
Q psy3760         155 SDKLISI---PCYQWEYVIIVPLDHPLLLLNS----I-S-LKEI-S--NY--PLITYDLSFSGRIKLDREFSLQKLTPY-  219 (306)
Q Consensus       155 ~~~~~~~---~l~~~~~~~v~~~~~~l~~~~~----i-~-~~dl-~--~~--~~i~~~~~~~~~~~~~~~~~~~~~~~~-  219 (306)
                      ..+....   .+......++++++..-..-..    + + ++|| .  +.  .+.....+......+..++...|+.|. 
T Consensus       113 ~~g~~~~~v~~~~~~g~~i~v~~~~~~s~i~~~~~~lk~~i~dL~k~~GK~~~Iav~~~gs~~~~~l~~~L~~~Gl~p~~  192 (429)
T 2i49_A          113 GNKVPMYVLAQLITQGNGIAVAPMHEGKGVNLDITKAADYIKGFNKTNGRKFKAAHTFPNVNQDFWIRYWFAAGGVDPDT  192 (429)
T ss_dssp             TCCCCEEEEEECCBCCEEEEECGGGTTTTCSSCCGGGHHHHHTHHHHHSSCCEEEESSTTSHHHHHHHHHHHHTTCCTTT
T ss_pred             CCCCCEEEEEEeccCCcEEEEecchhhcccccchHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHhcCCCCCC
Confidence            1111211   1223345566665532111000    1 1 5888 6  65  444433454444566788999999873 


Q ss_pred             -EEEEecCHHHHHHHHHhc--cceeeeecceeccc-ccC-CceeeecCCCCc-cceEEEEEeCCc--cccHHHHHHHHHH
Q psy3760         220 -IVLETINSDIIKTYVELR--MGIGIIASIAFDSN-RDK-NLRSISASHLFG-TTISRVIIKQGT--YLRSYVYSFIKLL  291 (306)
Q Consensus       220 -~~~~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~-~~~-~l~~~~~~~~~~-~~~~~l~~~~~~--~~~~~~~~~~~~l  291 (306)
                       +.+..-....+..++.+|  +++++ .+...... ..+ ..+.+...+..+ .....++.+++.  .....+++|++.+
T Consensus       193 DV~~v~~~~~~~~~aL~~G~iDa~~~-~eP~~~~a~~~g~g~~~~~~~~~~~~~~~~vl~~~~~~~~~~Pe~v~~~~~A~  271 (429)
T 2i49_A          193 DIDLLAVPPAETVQGMRNGTMDAFST-GDPWPYRIVTENIGYMAGLTAQIWPYHPEEYLAIRADWVDKNPKATKALLKGI  271 (429)
T ss_dssp             TSEEEECCHHHHHHHHHHTCCCEEEE-ETTHHHHHHHTTSCEEEEEHHHHSTTCCCCEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred             cEEEEECChHHHHHHHHcCCccEEEe-ccchHHHHHHCCCCEEEEechHhcCCCceEEEEECHHHHHHCHHHHHHHHHHH
Confidence             555545677888888888  66544 33332222 222 223333222111 112334445432  2356778888777


Q ss_pred             hHH
Q psy3760         292 SPK  294 (306)
Q Consensus       292 ~~~  294 (306)
                      .+.
T Consensus       272 ~~A  274 (429)
T 2i49_A          272 MEA  274 (429)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

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

Probab=96.37  E-value=0.0056  Score=35.92  Aligned_cols=41  Identities=10%  Similarity=0.059  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +.++|..+.+-. |....|+.||+|.+|+..+++++.+.||+
T Consensus         3 e~~vl~l~~~g~-s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A            3 ERQVLKLIDEGY-TNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             HHHHHHHHHTSC-CSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            456666666655 99999999999999999999999999987

>3onq_A Regulator of polyketide synthase expression; structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Bifidobacterium adolescentis}

Probab=96.29  E-value=0.0055  Score=48.10  Aligned_cols=45  Identities=18%  Similarity=0.135  Sum_probs=39.4

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      +.++++.+-.++++|+++||++|+|...|+.++|+++|+.+|..|
T Consensus       197 ~ll~TL~~yl~~~~~~~~tA~~L~iHrNTl~yRL~ri~~l~g~dl  241 (262)
T 3onq_A          197 PTYLTVSTFLKYGSSLENTAKELNVHPNTVRYRLKRAAETTGWDA  241 (262)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHHHHHHSCCT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCcCC
Confidence            346777777787559999999999999999999999999999865

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

Probab=96.27  E-value=0.034  Score=37.98  Aligned_cols=80  Identities=14%  Similarity=0.064  Sum_probs=56.8

Q ss_pred             chhhHHHHHHHHHhcC---CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCC--ccccCHhHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQNF---NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKR--IRGLTKPGQAILRSIEII   73 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~---s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~--~~~lT~~G~~l~~~a~~i   73 (306)
                      +-.+.+++..+.+.+.   |...-|+.+++|+||+++.|+.||+ .|.---.+.   +++  .+-.+..+..+++..++.
T Consensus        25 t~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~-~GlV~r~~~~~d~~~~~~~y~~~~~~~~~~~i~~~  103 (123)
T 3r0a_A           25 TKADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHE-KEILQRSQQNLDGGGYVYIYKIYSKNQIRNIIQKI  103 (123)
T ss_dssp             CHHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHH-TTSEEEEEEECTTSCEEEEEEECCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCCEEeeCCccCCCcceEEEecCCHHHHHHHHHHH
Confidence            3456778888887652   6899999999999999999999995 454332211   222  112344688999999888


Q ss_pred             HHHHHHHHH
Q psy3760          74 MQEIEGLKK   82 (306)
Q Consensus        74 l~~~~~~~~   82 (306)
                      ++.+.+...
T Consensus       104 ~~~~~~~~~  112 (123)
T 3r0a_A          104 VQSWADRLG  112 (123)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888776554

>3hn0_A Nitrate transport protein; ABC transporter, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; 1.75A {Parabacteroides distasonis}

Probab=96.25  E-value=0.12  Score=40.95  Aligned_cols=141  Identities=11%  Similarity=0.124  Sum_probs=78.9

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeecc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPC  163 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l  163 (306)
                      ..+||||.........+..+   +.+..  -++++++.. .+.+++.+.+.+|++|++++....     .....+.....
T Consensus         4 ~~~irvg~~~~~~~~~~~~~---~~~~~~~~g~~v~~~~~~~~~~~~~al~~G~~D~~~~~~~~~~~~~~~g~~~~i~~~   80 (283)
T 3hn0_A            4 DTVIKVSVLRGPSVIAFADW---LENPPIIDNKKVQVKVVDSPDLAQALLIKQETDIAVLPMINAANLYNKGIKIKLAGC   80 (283)
T ss_dssp             CCEEEEEEESSTHHHHTHHH---HHSCCEETTEEEEEEEESCHHHHHHHHHTTCCSEEEEEHHHHHHHHHTTCSCEEEEE
T ss_pred             cceEEEEecCCCcHHHHHHH---HhccccccCccEEEEEeCCHHHHHHHHHCCCCCEEEEcHHHHHHHHHCCCCeEEEEE
Confidence            45899999887543333333   22222  256666654 467789999999999999974210     01112222211


Q ss_pred             ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEec-CHHHHHHHHHhc-ccee
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI-NSDIIKTYVELR-MGIG  241 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~v~~g-~gi~  241 (306)
                      .......+++++.            |.+.+......+......+..++++.|+..+++ ... +...+..++.+| .-.+
T Consensus        81 ~~~g~~~lv~~~~------------LkGK~Iav~~~gs~~~~ll~~~L~~~Gldv~~~-~~~~~~~~~~~al~~G~vDa~  147 (283)
T 3hn0_A           81 PIWGTLYLVEKTP------------LKEPALYVFGNGTTPDILTRYYLGRQRLDYPLN-YAFNTAGEITQGILAGKVNRA  147 (283)
T ss_dssp             EECCCCEEEECSS------------CCSCCEECSSTTSHHHHHHHHHHHHHTCCCCEE-CSCCSHHHHHHHHHHTSCSEE
T ss_pred             ecccEEEEEecCC------------CCCCEEEecCCCCcHHHHHHHHHHHcCCceEEE-EccCCHHHHHHHHHcCCCCEE
Confidence            1111112222221            667777766555545556677788888833222 233 577888888887 3344


Q ss_pred             eeeccee
Q psy3760         242 IIASIAF  248 (306)
Q Consensus       242 ~~p~~~~  248 (306)
                      ++++...
T Consensus       148 ~~~eP~~  154 (283)
T 3hn0_A          148 VLGEPFL  154 (283)
T ss_dssp             EECTTHH
T ss_pred             EecccHH
Confidence            4555443

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

Probab=96.25  E-value=0.011  Score=35.52  Aligned_cols=40  Identities=8%  Similarity=0.144  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           6 FRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         6 l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      .+++..+.+.+  .|.+.-|+.+++|++++++.|+.||++ |.
T Consensus        13 ~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~-G~   54 (67)
T 2heo_A           13 QKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKE-DR   54 (67)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHT-TS
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-Cc
Confidence            34444444432  279999999999999999999999985 44

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=96.23  E-value=0.0056  Score=39.41  Aligned_cols=32  Identities=19%  Similarity=0.081  Sum_probs=26.5

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      .++.+++++.++||+.||||++|+.+.|+++.
T Consensus        58 ~aL~~~~gn~~~aA~~LGIsr~tL~rklkk~~   89 (91)
T 1ntc_A           58 TALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            34455544999999999999999999999874

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=96.21  E-value=0.00076  Score=55.47  Aligned_cols=71  Identities=11%  Similarity=0.237  Sum_probs=0.0

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      ++..++..+.+.+ -+...-|+.|++|++|++|-|++||++   -|..|..+++ .||+.|+.+++.+.++...+.
T Consensus        21 r~~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~---Glv~~~~~gi-~LT~~G~~~~~~~~~~~~~~~   92 (345)
T 2o0m_A           21 ERFQILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQL---NLIEPSKSGM-TLTERGLEVYQGLELVMNQLL   92 (345)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEEecce-EEcHHHHHHHHHHHHHHHHhh
Confidence            4455555555544 245667999999999999999999875   3455566788 799999999999988888763

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=96.20  E-value=0.0051  Score=34.27  Aligned_cols=34  Identities=12%  Similarity=0.052  Sum_probs=27.5

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      .++.....|.|....|+.+++|.+||.+.+++.+
T Consensus        13 ~i~~~~~~g~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           13 QLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            3444455566999999999999999999998765

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=96.20  E-value=0.01  Score=37.32  Aligned_cols=45  Identities=7%  Similarity=0.065  Sum_probs=37.8

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++.++|..+++.. |..+.|+.||+|.+||.++++++.+.|+..
T Consensus        23 t~~e~~vl~l~~~g~-s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   67 (82)
T 1je8_A           23 TPRERDILKLIAQGL-PNKMIARRLDITESTVKVHVKHMLKKMKLK   67 (82)
T ss_dssp             CHHHHHHHHHHTTTC-CHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            345566777766555 999999999999999999999999999874

>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=96.18  E-value=0.047  Score=42.51  Aligned_cols=59  Identities=20%  Similarity=0.204  Sum_probs=43.5

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHH
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAI   66 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l   66 (306)
                      +.++++..+.+.+  .|++.-|+.+++++||+++.++.|++ .|.  ..|. +++. +|++....+
T Consensus         9 r~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~-~G~--v~~~~~~~Y-~lg~~~~~l   70 (249)
T 1mkm_A            9 KAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEE-KGF--VLRKKDKRY-VPGYKLIEY   70 (249)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHH-TTS--EEECTTSCE-EECTHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCc--EEECCCCcE-EECHHHHHH
Confidence            3456666666532  38999999999999999999999998 344  3443 5566 798876443

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

Probab=96.16  E-value=0.013  Score=38.27  Aligned_cols=45  Identities=22%  Similarity=0.121  Sum_probs=39.2

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..++|..+++-. |....|+.|++|.+||...++++.+.||+.
T Consensus        36 t~re~~Vl~l~~~G~-s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~   80 (99)
T 1p4w_A           36 SPKESEVLRLFAEGF-LVTEIAKKLNRSIKTISSQKKSAMMKLGVD   80 (99)
T ss_dssp             CHHHHHHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            446677787777665 999999999999999999999999999983

>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=96.11  E-value=0.0075  Score=42.94  Aligned_cols=43  Identities=21%  Similarity=0.335  Sum_probs=35.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+++++..+.+.+ .|++.-|+.+|+|+++++++|++||+.
T Consensus         1 ld~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~   44 (150)
T 2pn6_A            1 MDEIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKD   44 (150)
T ss_dssp             CCHHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CChHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            5666777777776543 389999999999999999999999875

>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=96.09  E-value=0.012  Score=41.96  Aligned_cols=43  Identities=14%  Similarity=0.159  Sum_probs=34.5

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ .|++.-|+.+|+|++|++++|++||+.
T Consensus         5 ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   48 (151)
T 2cyy_A            5 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES   48 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3445667777676532 289999999999999999999999876

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=96.08  E-value=0.0066  Score=36.78  Aligned_cols=27  Identities=11%  Similarity=0.046  Sum_probs=23.6

Q ss_pred             HHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760          12 AVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        12 v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      +...| |..+.|+.||||++|||+.+..
T Consensus         7 i~~~G-~~~~lA~~lGVs~~aVs~W~~g   33 (71)
T 2hin_A            7 VRHFG-DVEKAAVGVGVTPGAVYQWLQA   33 (71)
T ss_dssp             HHHHS-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHC-CHHHHHHHHCCCHHHHHHHHhC
Confidence            44568 9999999999999999999864

>2f5x_A BUGD; periplasmic binding protein, transport protein; 1.72A {Bordetella pertussis tohama I}

Probab=95.98  E-value=0.48  Score=38.15  Aligned_cols=207  Identities=10%  Similarity=0.048  Sum_probs=111.2

Q ss_pred             CCCcEEEEeccc--chhhhhHHHHHHHHHhCCCcEEEEEe--CChh-HHHHHHHcCCee---EEEEccc-----cC-CC-
Q psy3760          91 DTGNLTIATTHT--QARYALPKIIKEFTIQFPKVKLSLLQ--GNPK-QITEMIRNDQAD---IAIVTEI-----LS-PS-  155 (306)
Q Consensus        91 ~~~~l~I~~~~~--~~~~~l~~~l~~~~~~~p~~~i~~~~--~~~~-~~~~~l~~~~~D---i~i~~~~-----~~-~~-  155 (306)
                      ..+.|+|-++..  =....+.+.+.+...+.-+..+.+..  +... ...+.+.++..|   +++....     .. .. 
T Consensus        15 P~kpi~liVp~~~GG~~D~~aR~la~~l~~~lg~~vvV~N~pGa~g~ig~~~v~~a~~DGytl~~~~~~~~~~~~~~~~~   94 (312)
T 2f5x_A           15 PERPVNMVVPFAAGGPTDNVARSLAESMRPTLGETVVVENKGGAGGTIGTTQVARAQPDGYSILLMHAGFSTAPSLYKNP   94 (312)
T ss_dssp             CSSCEEEEESSCTTSHHHHHHHHHHHHHHHHHSSCEEEEECCCGGGHHHHHHHHTSCSSSSEEEEEETHHHHGGGTCSCC
T ss_pred             CCCCEEEEEeeCCccHHHHHHHHHHHHHHHHhCCCEEEEecCChHHHHHHHHHHhCCCCCcEEEEecCHHHHHHHHcCCC
Confidence            445666666543  33445566665554443345555544  3222 234667877777   8775321     00 11 


Q ss_pred             -----CCceee-ccccceEEEEecCCCCCCCCCCcChhhhcC--------CCeEeecCCCCcHHHHHHHHHhCCCceeEE
Q psy3760         156 -----DKLISI-PCYQWEYVIIVPLDHPLLLLNSISLKEISN--------YPLITYDLSFSGRIKLDREFSLQKLTPYIV  221 (306)
Q Consensus       156 -----~~~~~~-~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~--------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (306)
                           .++... .+...+.+++++++.|.     -+++||..        ..+-....+....-....+++..|+....+
T Consensus        95 ~yd~~~df~pv~~~~~~~~~lvv~~ds~~-----~sl~dL~~~ak~~p~~~~~g~~g~Gs~~hl~~~~l~~~~Gi~~~~V  169 (312)
T 2f5x_A           95 GYEPYTSFEPIGLVVDVPMTIIARGDFPP-----NNIKELAEYVKKNADKISLANAGIGAASHLCGTMLVEALGVNLLTI  169 (312)
T ss_dssp             SSCTTTSEEEEEEEEEEEEEEEECTTCSC-----CSHHHHHHHHHHHGGGCEEEESSTTSHHHHHHHHHHHHHTCCCEEE
T ss_pred             CCCcccccceeeecccCcEEEEEeCCCCC-----CCHHHHHHHHHhCCCceEEeCCCCCcHHHHHHHHHHHHHCCCeEEe
Confidence                 233322 25677889999988763     37888853        233332223222223334456678876544


Q ss_pred             EEecCHHHHHHHHHhc-cceeeeecceeccc-ccCCceeeecCCC--------C----------ccc--eEEEEEeCCcc
Q psy3760         222 LETINSDIIKTYVELR-MGIGIIASIAFDSN-RDKNLRSISASHL--------F----------GTT--ISRVIIKQGTY  279 (306)
Q Consensus       222 ~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~--------~----------~~~--~~~l~~~~~~~  279 (306)
                       .......+...+..| .-+++.....+..+ +.++++.+.+...        .          ...  -..++.+++.+
T Consensus       170 -py~G~~~a~~aL~~G~VD~~~~~~~~~~~~i~~g~lr~Lav~~~~r~~~~pdvPt~~E~G~~~~~~~~w~gl~ap~g~p  248 (312)
T 2f5x_A          170 -PYKGTAPAMNDLLGKQVDLMCDQTTNTTQQITSGKVKAYAVTSLKRVPTLPDLPTMDESGYKGFEVGIWHGMWAPKGTP  248 (312)
T ss_dssp             -ECSSHHHHHHHHHTTSSCEEEEEHHHHHHHHHTTSSEEEEECSSSCCTTSTTSCBTTTTTCTTCCCEEEEEEEEETTCC
T ss_pred             -ccCChHHHHHHHHcCCccEEEechHHHHHHHHcCCeEEEEEcCccchhhcCCCCCHhhcCCCCeeEEEEEEEEEcCCCC
Confidence             345556677777777 33334433333333 5677777654210        0          011  23456677754


Q ss_pred             ccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         280 LRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       280 ~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                       ...+.++-+.+.+.++....++.+
T Consensus       249 -~~vv~~l~~al~~~~~~p~~~~~~  272 (312)
T 2f5x_A          249 -KPVVDKLVKSLQAGLADPKFQERM  272 (312)
T ss_dssp             -HHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHHcCHHHHHHH
Confidence             667888888888877666655543

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

Probab=95.96  E-value=0.0063  Score=38.47  Aligned_cols=43  Identities=16%  Similarity=0.114  Sum_probs=36.5

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      |.++++.-++.-...- |++.-|+.+++|.+||.+-|..||+.=
T Consensus         2 m~L~~Il~~L~~~g~v-sv~eLA~~l~VS~~TIRrDL~~Le~~G   44 (87)
T 2k02_A            2 ASLMEVRDMLALQGRM-EAKQLSARLQTPQPLIDAMLERMEAMG   44 (87)
T ss_dssp             CCTHHHHHHHHHSCSE-EHHHHHHHTTCCHHHHHHHHHHHHTTC
T ss_pred             chHHHHHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            6677777777666666 889999999999999999999999863

>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=95.94  E-value=0.014  Score=41.54  Aligned_cols=42  Identities=24%  Similarity=0.162  Sum_probs=34.1

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.| .|++.-|+.+|+|+++++++|++||+.
T Consensus         6 d~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   48 (150)
T 2w25_A            6 DDIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESR   48 (150)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            455667777776542 389999999999999999999999874

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=95.89  E-value=0.022  Score=36.48  Aligned_cols=44  Identities=16%  Similarity=0.193  Sum_probs=38.9

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..++|..+++-. |....|+.|++|..||..+++++-+.||+
T Consensus        31 t~rE~~Vl~l~~~G~-s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           31 TPRECLILQEVEKGF-TNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            446778888888554 99999999999999999999999999997

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=95.89  E-value=0.056  Score=44.62  Aligned_cols=114  Identities=14%  Similarity=0.175  Sum_probs=65.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH-HH-HHHhhccCCCCcE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL-KK-IGKEFSAYDTGNL   95 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~-~~-~~~~~~~~~~~~l   95 (306)
                      |+...|+..|+|++||||.|..             ..++   .++=+   +.+.+..+++.-. -+ ..+.+..+.++.|
T Consensus        11 Ti~diA~~aGVS~~TVSrvLn~-------------~~~V---s~~tr---~rV~~~a~~lgY~~pn~~a~~l~~~~s~~I   71 (366)
T 3h5t_A           11 TLASIAAKLGISRTTVSNAYNR-------------PEQL---SAELR---QRILDTAEDMGYLGPDPVARSLRTRRAGAI   71 (366)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHC-------------GGGS---CHHHH---HHHHHHHHHTTC--------------CCEE
T ss_pred             CHHHHHHHhCCCHHHHHHHHCC-------------CCCC---CHHHH---HHHHHHHHHhCCCCCCHHHHHhhcCCCCEE
Confidence            6788999999999999999952             1122   22221   2222222222211 11 1122223333444


Q ss_pred             EEEeccc----chhhhhHHHHHHHHHhCCCcEEEEEeCC------hhHHHHHHHcCCeeEEEEcc
Q psy3760          96 TIATTHT----QARYALPKIIKEFTIQFPKVKLSLLQGN------PKQITEMIRNDQADIAIVTE  150 (306)
Q Consensus        96 ~I~~~~~----~~~~~l~~~l~~~~~~~p~~~i~~~~~~------~~~~~~~l~~~~~Di~i~~~  150 (306)
                      -+-++..    +...++..++..+.+...+..+.+...+      ..+.++.+.+..+|-.|+..
T Consensus        72 gvi~~~~~~~~~~~~~~~~~~~gi~~~a~g~~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~  136 (366)
T 3h5t_A           72 GVLLTEDLTYAFEDMASVDFLAGVAQAAGDTQLTLIPASPASSVDHVSAQQLVNNAAVDGVVIYS  136 (366)
T ss_dssp             EEEESSCTTHHHHSHHHHHHHHHHHHHSSSCEEEEEECCCCTTCCHHHHHHHHHTCCCSCEEEES
T ss_pred             EEEecCCccccccCHHHHHHHHHHHHHHhhCCEEEEEcCCCccHHHHHHHHHHHhCCCCEEEEec
Confidence            4444442    4556788888888888778888876643      23478888999999988853

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=95.83  E-value=0.072  Score=35.37  Aligned_cols=75  Identities=9%  Similarity=0.011  Sum_probs=48.5

Q ss_pred             HHHHHHHhcCCHHHHHHH----hCCCchHHHHHHHHHHHHcCceeEEe-----cC--CCccccCHhHHHHHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKA----LYTSQPGVSKAIIELEEELSIDIFIR-----HG--KRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~----l~isq~~~s~~i~~LE~~lg~~Lf~R-----~~--~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      ++..+.+...+...-++.    +++|++++++.|++||+.=   |+.|     ++  +..+++|+.|+..+.........
T Consensus        14 IL~~L~~~~~~gyel~~~l~~~~~i~~~tly~~L~~Le~~G---lI~~~~~~~~~r~r~~y~LT~~G~~~l~~~~~~~~~   90 (108)
T 3l7w_A           14 ILAIVSKHDSYGYDISQTIKLIASIKESTLYPILKKLEKAG---YLSTYTQEHQGRRRKYYHLTDSGEKHLVYLTKEWSV   90 (108)
T ss_dssp             HHHHHHHSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTT---SEEEEEEEETTEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHhCCCcChHHHHHHHHHHCC---CeEEEeecCCCCcceEEEECHHHHHHHHHHHHHHHH
Confidence            344444422133444455    5899999999999999862   2222     11  22338999999999888777777


Q ss_pred             HHHHHHHHH
Q psy3760          77 IEGLKKIGK   85 (306)
Q Consensus        77 ~~~~~~~~~   85 (306)
                      +....+.+-
T Consensus        91 ~~~~i~~~l   99 (108)
T 3l7w_A           91 YKMTIDGIV   99 (108)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            766655443

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=95.77  E-value=0.023  Score=36.86  Aligned_cols=45  Identities=9%  Similarity=0.110  Sum_probs=38.1

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-++.++|..+.+-. |....|+.||+|.+||.++++++.+.|+..
T Consensus        29 t~~e~~vl~l~~~g~-s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   73 (95)
T 3c57_A           29 TDQERTLLGLLSEGL-TNKQIADRMFLAEKTVKNYVSRLLAKLGME   73 (95)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            345666777776655 999999999999999999999999999874

>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=95.72  E-value=0.02  Score=40.43  Aligned_cols=42  Identities=17%  Similarity=0.344  Sum_probs=33.4

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.+ .|++.-|+.+|+|+++++++|++||+.
T Consensus         4 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   46 (144)
T 2cfx_A            4 DQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESF   46 (144)
T ss_dssp             CHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            445556666666532 389999999999999999999999875

>3pu5_A Extracellular solute-binding protein; structural genomics, PSI-2, protein structure initiative; 2.05A {Bordetella parapertussis}

Probab=95.70  E-value=0.65  Score=37.51  Aligned_cols=198  Identities=12%  Similarity=-0.005  Sum_probs=113.2

Q ss_pred             CCCcEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc----CCeeEEEEccc----------c--C
Q psy3760          91 DTGNLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN----DQADIAIVTEI----------L--S  153 (306)
Q Consensus        91 ~~~~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~----~~~Di~i~~~~----------~--~  153 (306)
                      ..++|+|.+-.+ ....+...++..|.+++ +++|++...+..++...|..    ...|+.+....          .  .
T Consensus         4 ~~~~l~v~~~~g~~~~~~~~~~~~~F~~~~-gi~V~~~~~~~~~~~~kl~~~~~~~~~Dv~~~~~~~~~~~~~~g~l~~l   82 (333)
T 3pu5_A            4 ADDHIYVTSSGGSFLENVRKHMAEPFEKQS-GVKVTLVPGTNPAHALKILSSRGTPPYDVAAFGGNDMYRLIRAKKLAQV   82 (333)
T ss_dssp             TTCEEEEEECCHHHHHHHHHHTHHHHHHHH-CCEEEEEECCHHHHHHHHHHCCSSCSCSEEEECHHHHHHHHHTTCBCCC
T ss_pred             cCCeEEEEeCCCcHHHHHHHHHHHHHHHHH-CCEEEEecCCCHHHHHHHHhCcCCCCCCEEEEChHHHHHHHHCcCcccC
Confidence            356889888664 33445568999999998 99999988888888888887    35899986411          0  0


Q ss_pred             CC----------C------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCC----Ce----EeecCCCC-c-HHHH
Q psy3760         154 PS----------D------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PL----ITYDLSFS-G-RIKL  207 (306)
Q Consensus       154 ~~----------~------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~----i~~~~~~~-~-~~~~  207 (306)
                      +.          +      ..-..++.....+++.+++..  ...+-+++||.+.    ..    ....+... . ...+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~y~vP~~~~~~~l~ynkd~~--~~~P~tw~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~  160 (333)
T 3pu5_A           83 DEKSVPSLADVPEKFKADWEGCGSLYDYSSVGIAYRPDKI--QGGVKSWKEFVERTVAGEFGKQVFFNNLSSNVRGAEVL  160 (333)
T ss_dssp             CTTTCGGGGGSCGGGTGGGTTSCEECCBEEEEEEECTTTS--TTCCSSHHHHHHHHHHTTTTTCEEEECGGGTSSHHHHH
T ss_pred             ChhhCCChhhCCHHHHhccCCccceeEeeeeEEEEchhhc--CCCCCCHHHHhChhhCCCccccccccCCcchhhHHHHH
Confidence            00          0      112355666778888888853  2456799998531    12    33332211 1 1111


Q ss_pred             H-----------------HHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc--c-cCCceeeecCCCCc
Q psy3760         208 D-----------------REFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN--R-DKNLRSISASHLFG  266 (306)
Q Consensus       208 ~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~--~-~~~l~~~~~~~~~~  266 (306)
                      .                 ++++.  +.++.....++.....+++.+|. ++++.....+...  . .+.+......+...
T Consensus       161 ~~~~~~~g~~~~~~~~a~~~l~~--l~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~g~~~~~~~~P~~g~~  238 (333)
T 3pu5_A          161 SMFGKIYGSGYGDIEASIATLER--MKPHIFKFFTAFNDPVVLLTSGEGAIGPGWDGRTFIAEDSTKGMVKWVDPTEGAV  238 (333)
T ss_dssp             HHHHHHHSSSTTCHHHHHHHHHH--HGGGEEEEECSTTHHHHHHHHTSCSEEEEEHHHHHHHHHHTTTSSEEECCTTCCE
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHH--hCcccccccCChHHHHHHHHcCCEEEEecccHHHHHHHhCCCCceeEEcCCCcee
Confidence            1                 12222  23555344455556678888884 3444333322222  1 22244443222222


Q ss_pred             cceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         267 TTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       267 ~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ....++...++. ...++++|++++.+.
T Consensus       239 ~~~~~~~i~k~s-~~~~A~~Fi~~l~s~  265 (333)
T 3pu5_A          239 SSGPVMAVVKGG-KEDLAKAFMNYALGE  265 (333)
T ss_dssp             EECCEEEEBTTS-CHHHHHHHHHHHTSH
T ss_pred             eccceEEEeCCC-CHHHHHHHHHHHcCH
Confidence            223345556777 788999999999654

>2ozz_A Hypothetical protein YHFZ; alpha-beta structure, structural genomics, PSI-2, protein structure initiative; 2.30A {Shigella flexneri 2A} SCOP: c.94.1.1

Probab=95.66  E-value=0.51  Score=35.99  Aligned_cols=176  Identities=11%  Similarity=0.061  Sum_probs=99.2

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCCC-----CCceee----
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSPS-----DKLISI----  161 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~~-----~~~~~~----  161 (306)
                      .+.+.=.++-+ -+...-.+.+.+.+.+-++.+.+... +++..+..|.+|++|++|++....+.     +.-...    
T Consensus        15 ~~~~~~~mPlp-ys~~yeGlatgl~~~f~gi~~~i~~mrg~~~RI~aL~~gk~D~aI~S~~aa~e~~~~~~r~~~vdFg~   93 (231)
T 2ozz_A           15 INNVVCAMPLP-YTRLYEGLASGLKAQFDGIPFYYAHMRGADIRVECLLNGVYDMAVVSRLAAESYLSQNNLCIALELGP   93 (231)
T ss_dssp             CSSEEEEECCC-CSHHHHHHHHHHHHTTTTSCEEEEECSCHHHHHHHHHTTSCSEEEEEHHHHHHHHHHSCEEEEEECCT
T ss_pred             cCcEEEEcccc-hhhhhhHHHHHHHHHhcCCcEEEEEccChHHHHHHHHcCCCCEEEEecccchhhhcccCeEEEEEcCC
Confidence            44554444444 45566777788888888999999999 99999999999999999997221111     011111    


Q ss_pred             ccc-cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760         162 PCY-QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI  240 (306)
Q Consensus       162 ~l~-~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi  240 (306)
                      +.+ ..+ .++++++..    ..+        .-|..+.++.-...+.+... .+..  +.+.=.+...++..+.+|.-=
T Consensus        94 ~yYv~~h-~li~~~~~~----~~i--------krVGvd~gS~dq~~lt~~~~-~g~~--Ve~ve~~y~~~i~~L~~G~ID  157 (231)
T 2ozz_A           94 HTYVGEH-QLICRKGES----GNV--------KRVGLDSRSADQKIMTDVFF-GDSD--VERVDLSYHESLQRIVKGDVD  157 (231)
T ss_dssp             TSSSCCE-EEEEETTCG----GGC--------CEEEECTTCHHHHHHHHHHH-TTSC--CEEEECCHHHHHHHHHHTSCC
T ss_pred             CccccCe-EEEEeCCCc----ccc--------EEEEecCCChhHHHHHhhhc-CCCe--EEEEECCHHHHHHHHHcCCcc
Confidence            222 223 344444421    111        56666666443333343332 4432  232326777778888888443


Q ss_pred             eeee---cceecccccCCceeeecCC---CCccceEEEEEeCCccccHHHHHHHH
Q psy3760         241 GIIA---SIAFDSNRDKNLRSISASH---LFGTTISRVIIKQGTYLRSYVYSFIK  289 (306)
Q Consensus       241 ~~~p---~~~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~  289 (306)
                      +.+-   .....  ..+++...++..   ........++.++++   +.+++.++
T Consensus       158 A~Iwn~d~~~a~--~~~~l~~~~l~~~~~~~~~~eavI~v~k~n---~~L~~~ln  207 (231)
T 2ozz_A          158 AVIWNVVAENEL--TMLGLEATPLTDDPRFLQATEAVVLTRVDD---YPMQQLLR  207 (231)
T ss_dssp             EEEEEC-CHHHH--HHTTEEEEECCSCHHHHHTTCEEEEEETTC---HHHHHHHH
T ss_pred             EEEEcCcchhhh--cCCCcceeccccccccccCCceEEEEECCC---HHHHHHHH
Confidence            4433   22222  356677777766   222335557778874   34444444

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=95.64  E-value=0.016  Score=37.72  Aligned_cols=30  Identities=17%  Similarity=-0.029  Sum_probs=25.1

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ++.+++++.++||+.||||++++.+.|++.
T Consensus        66 aL~~~~gn~~~AA~~LGIsR~TL~rkLkk~   95 (98)
T 1eto_A           66 VMQYTLGNQTRAALMMGINRGTLRKKLKKY   95 (98)
T ss_dssp             HHHHTTTCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            344544499999999999999999999875

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=95.64  E-value=0.054  Score=38.16  Aligned_cols=73  Identities=10%  Similarity=-0.023  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHh--------CCCchHHHHHHHHHHHHcCceeEEe------cCCCccccCHhHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKAL--------YTSQPGVSKAIIELEEELSIDIFIR------HGKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l--------~isq~~~s~~i~~LE~~lg~~Lf~R------~~~~~~~lT~~G~~l~~~a~   71 (306)
                      +.++..+.+...+...-++.+        .+|+++|+..|++||+. |.---.+      .++..++||+.|+.+++...
T Consensus        44 ~~IL~~L~~~~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~-GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~  122 (145)
T 1xma_A           44 TIILSLLIEGDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKN-GYIKSYYGEETQGKRRTYYRITPEGIKYYKQKC  122 (145)
T ss_dssp             HHHHHHHHHCCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHT-TSEEEEEEEEC--CEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHC-CCEEEEEeccCCCCCeEEEEECHHHHHHHHHHH
Confidence            444555554221456666666        69999999999999985 2211111      11233489999999988765


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      +....+.+
T Consensus       123 ~~~~~~~~  130 (145)
T 1xma_A          123 EEWELTKK  130 (145)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            54444433

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=95.62  E-value=0.098  Score=35.36  Aligned_cols=73  Identities=16%  Similarity=0.163  Sum_probs=46.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHh------C--CCc-hHHHHHHHHHHHHcCceeEEe---c--CCCccccCHhHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKAL------Y--TSQ-PGVSKAIIELEEELSIDIFIR---H--GKRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l------~--isq-~~~s~~i~~LE~~lg~~Lf~R---~--~~~~~~lT~~G~~l~~~a~   71 (306)
                      +.++..+.+...+...-++.+      .  +|+ ++++..|++||+. |.-=...   .  ++..+++|+.|+..++...
T Consensus        16 ~~IL~~L~~~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~-GlI~~~~~~~~~~~r~~Y~LT~~G~~~l~~~~   94 (118)
T 2esh_A           16 STILLLVAEKPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEES-GFLSTEWDTTVSPPRKIYRITPQGKLYLREIL   94 (118)
T ss_dssp             HHHHHHHHHSCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHT-TSEEEEEECSSSSCEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHC-CCeEEEeecCCCCCceEEEEChHHHHHHHHHH
Confidence            344445554222666777777      3  999 9999999999985 3222221   1  1223389999999988776


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      .....+.+
T Consensus        95 ~~~~~~~~  102 (118)
T 2esh_A           95 RSLEDMKR  102 (118)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55544433

>2dvz_A BUGE, putative exported protein; periplamsic binding proteins, carboxylate binding, glutamate, transport protein; HET: GLU; 2.30A {Bordetella pertussis}

Probab=95.58  E-value=0.35  Score=38.98  Aligned_cols=207  Identities=10%  Similarity=-0.007  Sum_probs=109.0

Q ss_pred             CCCcEEEEecccc--hhhhhHHHHHHHHHhCCCcEEEEEe--CChhH-HHHHHHcCCee---EEEEccc-c------C-C
Q psy3760          91 DTGNLTIATTHTQ--ARYALPKIIKEFTIQFPKVKLSLLQ--GNPKQ-ITEMIRNDQAD---IAIVTEI-L------S-P  154 (306)
Q Consensus        91 ~~~~l~I~~~~~~--~~~~l~~~l~~~~~~~p~~~i~~~~--~~~~~-~~~~l~~~~~D---i~i~~~~-~------~-~  154 (306)
                      +.+.|+|-++...  ....+.+.+.+...+.-+..+.+..  +.... ..+.+.++..|   ++++... .      . .
T Consensus        17 P~~pi~iivp~~~GG~~D~~aR~la~~l~~~lg~~vvV~N~pGa~g~ig~~~v~~a~~DGytl~~~~~~~~~~~~~~~~~   96 (314)
T 2dvz_A           17 PSKAIRVIVPFAPGGSTDIIARLVTQRMSQELGQPMVVENKGGAGGAIGASEAARAEPDGYTLSIATVSTMAVNPACRPK   96 (314)
T ss_dssp             CSSCEEEEESSCTTSHHHHHHHHHHHHHHHHHTSCEEEEECCCGGGHHHHHHHHHSCTTSSEEEEECHHHHTHHHHHSTT
T ss_pred             CCCCEEEEEccCCccHHHHHHHHHHHHHHHHhCCCEEEEECCCchHHHHHHHHHhCCCCCcEEEEecCcHHHHHHHHhCC
Confidence            4556777665432  3345555665554443344455543  32222 24667776666   8775311 0      0 1


Q ss_pred             C------CCceee-ccccceEEEEecCCCCCCCCCCcChhhhcC----CC--eEeecC--CCCcHHHHHHHHHhCCCcee
Q psy3760         155 S------DKLISI-PCYQWEYVIIVPLDHPLLLLNSISLKEISN----YP--LITYDL--SFSGRIKLDREFSLQKLTPY  219 (306)
Q Consensus       155 ~------~~~~~~-~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~----~~--~i~~~~--~~~~~~~~~~~~~~~~~~~~  219 (306)
                      .      .++... .+...+.+++++++.|.     -+++||..    .|  +-.-..  +....-....+++..|+...
T Consensus        97 ~~~yd~~~df~pv~~~~~~~~~lvv~~ds~~-----~tl~dL~~~ak~~p~~~~~g~~g~Gs~~hl~~~~l~~~~Gi~~~  171 (314)
T 2dvz_A           97 DLPYDPIKDFQPVTNFANTANVVAVNPKFPA-----KDFKGFLEELKKNPGKYSYGSSGTCGVLHLMGESFKMATGTDIV  171 (314)
T ss_dssp             TCSCCTTTSEEEEEEEEEECEEEEECTTSSC-----SSHHHHHHHHHTSTTTCEEEESCTTSHHHHHHHHHHHHHTCCCE
T ss_pred             CCCCCchhccceeeEcccCCEEEEEeCCCCC-----CCHHHHHHHHHhCCCcEEEeCCCCCcHHHHHHHHHHHHhCCCeE
Confidence            1      223222 25677889999998763     36788854    12  222222  32222233344566788765


Q ss_pred             EEEEecCHHHHHHHHHhc-cceeeeecceeccc-ccCCceeeecC---------C-------CC--c--cceEEEEEeCC
Q psy3760         220 IVLETINSDIIKTYVELR-MGIGIIASIAFDSN-RDKNLRSISAS---------H-------LF--G--TTISRVIIKQG  277 (306)
Q Consensus       220 ~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~~~l~~~~~~---------~-------~~--~--~~~~~l~~~~~  277 (306)
                      .+ .......+...+..| .-+++.....+..+ +.+.++.+.+.         +       ..  .  ..-..++.+++
T Consensus       172 ~V-py~G~~~a~~al~~G~vD~~~~~~~~~~~~i~~g~lr~Lav~~~~r~~~~pdvPt~~e~G~~~~~~~~w~gl~ap~g  250 (314)
T 2dvz_A          172 HV-PYKGSGPAVADAVGGQIELIFDNLPSSMPQIQAGKLRAMAIAWPTRIDAIKDVPTFADAGFPVLNQPVWYGLLAPKG  250 (314)
T ss_dssp             EE-ECSSHHHHHHHHHHTSSSEEEEEHHHHHHHHHTTSSEEEEEESSSCCGGGTTSCBTTTTTCGGGCCCEEEEEEEETT
T ss_pred             Ec-ccCCHHHHHHHHHcCCceEEEEcHHHHHHHHHcCCEEEEEecCccccccCCCCCCHHhcCCCceEEeEEEEEEEcCC
Confidence            44 344555666666666 33444433333333 66777766432         1       00  0  11234566777


Q ss_pred             ccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         278 TYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      .+ .+.+.++.+.+.+.++....++.+
T Consensus       251 ~p-~~vv~~l~~al~~~~~~p~~~~~~  276 (314)
T 2dvz_A          251 TP-MDVVNKLRDAAVVALKDPKVIKAL  276 (314)
T ss_dssp             CC-HHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CC-HHHHHHHHHHHHHHHcCHHHHHHH
Confidence            64 677888888888877666655543

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

Probab=95.46  E-value=0.026  Score=36.24  Aligned_cols=44  Identities=11%  Similarity=0.094  Sum_probs=37.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      -+..++|..+++-. |....|+.||+|.+||.++++++.+.|+..
T Consensus        32 ~~e~~vl~l~~~g~-s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           32 EREMEILLLIAKGY-SNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             SHHHHHHHHHHTTC-CTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            35566676666655 999999999999999999999999999863

>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=95.43  E-value=0.031  Score=39.80  Aligned_cols=42  Identities=10%  Similarity=0.075  Sum_probs=33.3

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.+ .|++.-|+.+|+|+++++++|++||+.
T Consensus         7 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   49 (152)
T 2cg4_A            7 DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQA   49 (152)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            444556666666532 289999999999999999999999875

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

Probab=95.42  E-value=0.028  Score=40.97  Aligned_cols=42  Identities=14%  Similarity=0.207  Sum_probs=33.0

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.+ .|++.-|+.+|+|++|++++|++||+.
T Consensus        16 d~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~   58 (171)
T 2ia0_A           16 DDLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQER   58 (171)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            344556666665542 289999999999999999999999875

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=95.38  E-value=0.0089  Score=33.52  Aligned_cols=36  Identities=3%  Similarity=-0.069  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      +.+..+.+.+.|.|....|+.+|+|.+|+.+.+++.
T Consensus        10 ~~~~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           10 EQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            344444555556699999999999999999988754

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

Probab=95.38  E-value=0.023  Score=32.38  Aligned_cols=32  Identities=19%  Similarity=0.260  Sum_probs=25.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      +....+...|.|..+.|+.+|+|++|+++.++
T Consensus        22 ~~i~~l~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           22 SVAHELAKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33334445566999999999999999999875

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=95.37  E-value=0.1  Score=36.75  Aligned_cols=65  Identities=14%  Similarity=0.133  Sum_probs=45.4

Q ss_pred             hhHHHHHHHHHh----cCCHHHHHHHhC-CCchHHHHHHHHHHHHcCceeEEe----cCCC----ccccCHhHHHHHHH
Q psy3760           4 HQFRFVREAVRQ----NFNLTEAAKALY-TSQPGVSKAIIELEEELSIDIFIR----HGKR----IRGLTKPGQAILRS   69 (306)
Q Consensus         4 ~~l~~f~~v~~~----~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~~Lf~R----~~~~----~~~lT~~G~~l~~~   69 (306)
                      ..+.++..+...    - |...-++.++ +|++||+++|+.|++.==++-...    .++|    ...||+.|+.++..
T Consensus        30 tR~~IL~~Ll~~p~~~~-ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l~~  107 (151)
T 3u1d_A           30 TRLDVLHQILAQPDGVL-SVEELLYRNPDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALLRA  107 (151)
T ss_dssp             HHHHHHHHHHHSTTSCB-CHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCC-CHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHHHH
Confidence            456667777664    3 6777788888 999999999999997532222211    1111    23799999999977

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=95.37  E-value=0.17  Score=33.99  Aligned_cols=58  Identities=12%  Similarity=0.082  Sum_probs=39.8

Q ss_pred             CCCchHHHHHHHHHHHHcCceeEE----e-cCCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760          27 YTSQPGVSKAIIELEEELSIDIFI----R-HGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG   84 (306)
Q Consensus        27 ~isq~~~s~~i~~LE~~lg~~Lf~----R-~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~   84 (306)
                      ++++++++..|++||++==+.--.    . .++...++|+.|+..+....+..+.+.+..+.+
T Consensus        44 ~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~~~~~~~i~~i  106 (116)
T 3f8b_A           44 ELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENMRLAFESWSRVDKIIENL  106 (116)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEECHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999862111111    0 112233899999999988877777666655433

>2czl_A Hypothetical protein TTHA1568; conserved hypothetical protein, extremely thermoph bacteria, structural genomics, NPPSFA; HET: CME TLA XPE; 1.55A {Thermus thermophilus} SCOP: c.94.1.1 PDB: 2dbp_A* 3a3u_A*

Probab=95.35  E-value=0.25  Score=38.72  Aligned_cols=181  Identities=9%  Similarity=0.040  Sum_probs=88.4

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCCceeecc----c-
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDKLISIPC----Y-  164 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~~~~~~l----~-  164 (306)
                      +||||..+....  . +++-.+.+.+  .++++++...+...+.+.+.+|++|++++....  .....+.....    . 
T Consensus         3 ~l~ig~~~~~~~--~-p~~~a~~~g~~~~g~~v~~~~~~~~~~~~al~~G~~D~~~~~~~~~~~~~~~~~i~~~~~~~~~   79 (272)
T 2czl_A            3 ALRLGFSPCPND--T-FIFYALVHGRVESPVPLEPVLEDVETLNRWALEGRLPLTKLSYAAYAQVRDRYVALRSGGALGR   79 (272)
T ss_dssp             CEEEEECSSHHH--H-HHHHHHHTTSSCCSSCEEEEECCHHHHHHHHHTTCCSEEEEEHHHHTTCTTTEEECSSSCEEES
T ss_pred             eEEEeecCCCcH--H-HHHHHHHhCccCCCceeEEecCCHHHHHHHHHcCCCCEEEecHHHHHhhhCceEEeecccccCC
Confidence            589999887533  2 2222222221  156667766777788899999999999875211  11122332221    1 


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc--cceee
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR--MGIGI  242 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~~  242 (306)
                      ....+ +++++         +++||.+.++..... ......+.+.+....   +++ .. ....+..++.+|  +++.+
T Consensus        80 ~~~~~-lv~~~---------~~~dLkGk~Ia~~~~-~~~~~~ll~~ll~~~---~~~-~~-~~~~~~~al~~G~vDa~~~  143 (272)
T 2czl_A           80 GVGPL-VVARG---------PLQALEGLRVAVPGR-HTTAYFLLSLYAQGF---VPV-EV-RYDRILPMVAQGEVEAGLI  143 (272)
T ss_dssp             SCCCE-EEESS---------CCSCCTTCEEEESCT-TSHHHHHHHHHCSSC---EEE-EC-CGGGHHHHHHTTSSSEEEE
T ss_pred             CCceE-EEECC---------ChHHhCCCEEEeCCC-CchHHHHHHHHhccC---cee-ec-ChHHHHHHHHCCCCCEEEE
Confidence            11112 22222         167888877666543 333344444443322   222 22 334677777777  44443


Q ss_pred             eecceecccccCCceee-ecCC------CCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760         243 IASIAFDSNRDKNLRSI-SASH------LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL  295 (306)
Q Consensus       243 ~p~~~~~~~~~~~l~~~-~~~~------~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  295 (306)
                      ..+.... ....+++.+ .+..      ..+.....++.+++- ....+++|++.+.+..
T Consensus       144 ~~ep~~~-~~~~g~~~~~d~~~~w~~~~g~~~~~~~~~~~~~~-~p~~v~~~~~a~~~a~  201 (272)
T 2czl_A          144 IHESRFT-YPRYGLVQVVDLGAWWEERTGLPLPLGAILARRDL-GEGLIRALDEAVRRSV  201 (272)
T ss_dssp             CTTHHHH-GGGGTCEEEEEHHHHHHHHHSSCEEEEEEEEEGGG-CHHHHHHHHHHHHHHH
T ss_pred             ecchhhh-hhhcCCccHHHHHHHHHHhcCCCCCcchhhccccc-CHHHHHHHHHHHHHHH
Confidence            2143322 212233322 2211      011112233445544 4667888888776543

>2qpq_A Protein BUG27; alpha/beta domain, venus flytrap, transport protein; HET: CIT; 1.92A {Bordetella pertussis}

Probab=95.32  E-value=0.86  Score=36.44  Aligned_cols=206  Identities=11%  Similarity=0.043  Sum_probs=111.1

Q ss_pred             CCcEEEEec--ccchhhhhHHHHHHHHHhCCCcEEEEEeC--Chh-HHHHHHHcCCee---EEEEccc-c-----CC---
Q psy3760          92 TGNLTIATT--HTQARYALPKIIKEFTIQFPKVKLSLLQG--NPK-QITEMIRNDQAD---IAIVTEI-L-----SP---  154 (306)
Q Consensus        92 ~~~l~I~~~--~~~~~~~l~~~l~~~~~~~p~~~i~~~~~--~~~-~~~~~l~~~~~D---i~i~~~~-~-----~~---  154 (306)
                      .+.|+|-++  ++=....+.+.+.+...+.-+..+.+...  ... ...+.+.++..|   +++.... .     ..   
T Consensus         7 ~~pi~~ivp~~~GG~~D~~aR~la~~l~~~lg~~vvV~n~~Ga~g~ig~~~v~~a~~DGytl~~~~~~~~~~~~~~~~~~   86 (301)
T 2qpq_A            7 NKPLDIIVTFPPGGGTDMLARLIGNYLTESLGQTAVVENRPGASGNVGARLVADRAPDGYSLLMVNSSFAVNPGVFRNLP   86 (301)
T ss_dssp             CSCEEEEESSCTTSHHHHHHHHHHHHHHHGGGSCEEEEECCTGGGHHHHHHHHTSCSSSSEEEEEETHHHHHHHHCTTCS
T ss_pred             CCCEEEEEccCCCcHHHHHHHHHHHHHHHHhCCCEEEEECCChhHHHHHHHHHhCCCCCcEEEEeCCHHHHHHHhccCCC
Confidence            345776554  33345566667766655544555555543  222 223678877777   7775311 0     01   


Q ss_pred             ---CCCcee-eccccceEEEEecCCCCCCCCCCcChhhhcC----CC--eEeecC--CCCcHHHHHHHHHhCCCceeEEE
Q psy3760         155 ---SDKLIS-IPCYQWEYVIIVPLDHPLLLLNSISLKEISN----YP--LITYDL--SFSGRIKLDREFSLQKLTPYIVL  222 (306)
Q Consensus       155 ---~~~~~~-~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~----~~--~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~  222 (306)
                         ..++.. -.+...+.+++++++.|.     -+++||..    .|  +-.-..  +...+-....+.+..|+....+ 
T Consensus        87 yd~~~d~~pv~~~~~~~~~lvv~~~s~~-----~sl~dL~~~ak~~p~~~~~g~~g~Gs~~hl~~~~l~~~~G~~~~~V-  160 (301)
T 2qpq_A           87 FDPKKDFAAVINVAYVPSVFVVPAGSKY-----KTLGELMAAAKQTNTQVTYGSCGNGTPQHLAGELLNVSAKTHMVHV-  160 (301)
T ss_dssp             SCTTTTEEEEEEEEEEEEEEEEETTCSC-----CSHHHHHHHTCSSSCCCEEEESSTTSHHHHHHHHHHHHHTCCCEEE-
T ss_pred             CCchhcchhhhehhcCCeEEEEeCCCCC-----CCHHHHHHHHHhCCCceEEecCCCCcHHHHHHHHHHHHhCCCeEEe-
Confidence               123332 235678889999998763     36788853    22  222222  2222223334455678876544 


Q ss_pred             EecCHHHHHHHHHhc-cceeeeecceeccc-ccCCceeeecCCC--------------------CccceEEEEEeCCccc
Q psy3760         223 ETINSDIIKTYVELR-MGIGIIASIAFDSN-RDKNLRSISASHL--------------------FGTTISRVIIKQGTYL  280 (306)
Q Consensus       223 ~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~--------------------~~~~~~~l~~~~~~~~  280 (306)
                      .......+...+..| .-+++.....+..+ +.+.++.+.+...                    ....-+.++.+++.+ 
T Consensus       161 py~g~~~a~~al~~G~vD~~~~~~~~~~~~i~~g~lr~Lav~~~~r~~~~pdvPt~~e~G~~~~~~~~w~gl~ap~g~p-  239 (301)
T 2qpq_A          161 PYKGCGPALNDVLGSQIGLAVVTASSAIPFIKAGKLQALAVTSKERSALLPEVPTVAEQGVAGYELNQWHGLLVPGATP-  239 (301)
T ss_dssp             ECSSHHHHHHHHHTTSSSCEEEEHHHHHHHHHTTSEEEEEECSSSCCTTCTTSCBSGGGTCTTCCCEEEEEEEEETTCC-
T ss_pred             ccCChHHHHHHHHCCCccEEEEcHHHHHHHHhcCCeEEEEEcCCccccccCCCCChHHhCCCceEEEeEEEEEecCCCC-
Confidence            345556677777777 33334433333333 6677777654310                    001123456677754 


Q ss_pred             cHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         281 RSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       281 ~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ...+.++-+.+.+.++....++.+
T Consensus       240 ~~vv~~l~~al~~~~~~~~~~~~~  263 (301)
T 2qpq_A          240 MAVRQKLYDGIAKVMQRDDVQKKL  263 (301)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCHHHHHHH
Confidence            667888888888877666555443

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=95.31  E-value=0.12  Score=34.71  Aligned_cols=66  Identities=11%  Similarity=0.057  Sum_probs=45.1

Q ss_pred             CHHHHHHHh------CCCchHHHHHHHHHHHHcCceeEEe---c---CCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKAL------YTSQPGVSKAIIELEEELSIDIFIR---H---GKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG   84 (306)
Q Consensus        18 s~~~aA~~l------~isq~~~s~~i~~LE~~lg~~Lf~R---~---~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~   84 (306)
                      +...-++.+      .+|+++|...|++||+. |.-=-..   .   ++.+.++|+.|+..+....+....+.+..+.+
T Consensus        24 ~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~-GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~~~~~~~~~~~~i~~i  101 (115)
T 4esb_A           24 YGYELSTKLNKHGFTFVSEGSIYPLLLRMQKE-KLIEGTLKASSLGPKRKYYHITDKGLEQLEEFKQSWGMVSTTVNNL  101 (115)
T ss_dssp             EHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHT-TSEEEEEEECTTSCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCCcChHHHHHHHHHHC-CCeEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666      49999999999999997 3221111   1   12223899999999988877766666655433

>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=95.30  E-value=0.036  Score=38.84  Aligned_cols=43  Identities=26%  Similarity=0.241  Sum_probs=34.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ .|++.-|+.+|+|++++++++++||+.
T Consensus         2 ld~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~   45 (141)
T 1i1g_A            2 IDERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEK   45 (141)
T ss_dssp             CCSHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4555666776665432 389999999999999999999999975

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

Probab=95.25  E-value=0.03  Score=34.72  Aligned_cols=42  Identities=12%  Similarity=-0.003  Sum_probs=35.6

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      ++.++|....+.. |....|+.+|+|.++|.++++++-+.|+.
T Consensus        20 ~e~~vl~l~~~g~-s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A           20 RERQVLSAVVAGL-PNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HHHHHHHHHTTTC-CHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            4556666665555 99999999999999999999999999986

>1xvx_A YFUA; periplasmic iron binding protein, iron binding protein; 1.53A {Yersinia enterocolitica} SCOP: c.94.1.1 PDB: 1xvy_A*

Probab=95.19  E-value=0.93  Score=36.15  Aligned_cols=199  Identities=11%  Similarity=0.032  Sum_probs=110.7

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc----CCeeEEEEccccC----CCCC----c-
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN----DQADIAIVTEILS----PSDK----L-  158 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~----~~~Di~i~~~~~~----~~~~----~-  158 (306)
                      .++|+|.....  ...+..++..|.++ |+++|++...++.++.+.+..    +..|+.+......    ...+    + 
T Consensus         4 ~~~L~v~~~~~--~~~~~~~~~~F~~~-~gi~V~~~~~~~~~~~~kl~~~~~~~~pDv~~~~~~~~~~~~~~~g~l~~l~   80 (312)
T 1xvx_A            4 DSGIVVYNAQH--ENLVKSWVDGFTKD-TGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLD   80 (312)
T ss_dssp             CSCEEEEECSC--HHHHHHHHHHHHHH-HCCCEEEEECCHHHHHHHHHHHGGGCCCSEEEESSSHHHHHHHHTTCBCCCC
T ss_pred             CceEEEEecCc--HHHHHHHHHHHHHh-hCCEEEEEECChHHHHHHHHHhhCCCCCCEEEecchHHHHHHHhCCCcccCC
Confidence            56789877543  56788999999999 999999998888888877752    5689998742100    0001    1 


Q ss_pred             ----------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecCCCCcHHHHHH-HHHhCC---
Q psy3760         159 ----------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDLSFSGRIKLDR-EFSLQK---  215 (306)
Q Consensus       159 ----------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~~~~~~~~~~~-~~~~~~---  215 (306)
                                      ...++.....+++.+++..-....+-+|+||.+..   -+...+.......+.. .....|   
T Consensus        81 ~~~~~~~~~~~~~~~gy~~P~~~~~~~l~ynk~~~~~~~~P~tw~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~~G~~~  160 (312)
T 1xvx_A           81 AVTQAQVAQEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKA  160 (312)
T ss_dssp             HHHHHHBCGGGSCSSSSCEEEEEEEEEEEECTTTSCGGGSCSSGGGGGSGGGTTSEEECTTSHHHHHHHHHHHHHHCHHH
T ss_pred             hHHHhhCCHHHCCCCCeEEEEeccceEEEEEhhhccccCCCCCHHHHhCHHhcCCEeeCCCCccHHHHHHHHHHHhCcHH
Confidence                            13455566788888888632223456899987532   1222222111111111 111111   


Q ss_pred             -------CceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc------ccCCcee-eecCC--CCccceEEEEEeCCc
Q psy3760         216 -------LTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN------RDKNLRS-ISASH--LFGTTISRVIIKQGT  278 (306)
Q Consensus       216 -------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~------~~~~l~~-~~~~~--~~~~~~~~l~~~~~~  278 (306)
                             +..+. ....+.....+++.+|. ++++.....+...      ....+.. +|.+.  ........+...++.
T Consensus       161 a~~~~~~l~~~~-~~~~~~~~~~~~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~g~~~~~~~~~i~~~s  239 (312)
T 1xvx_A          161 TLEWLKAMKTNF-TAYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASS  239 (312)
T ss_dssp             HHHHHHHHHHHE-EECSSHHHHHHHHHTTSSSEEEEETHHHHHHHTTTCTTTTTCEEECCCTTCGGGCEEEEEEEEBTTC
T ss_pred             HHHHHHHHHHhC-cccCCchHHHHHHHcCceEEEEecchhHHHHHhhcccCCCceEEEccCCCCCcceeeeeeEEEecCC
Confidence                   11222 23346667788888884 4445443322210      1123333 23221  111223345556666


Q ss_pred             cccHHHHHHHHHHhHH
Q psy3760         279 YLRSYVYSFIKLLSPK  294 (306)
Q Consensus       279 ~~~~~~~~~~~~l~~~  294 (306)
                      ....++++|++++.+.
T Consensus       240 ~~~~~A~~fi~fl~s~  255 (312)
T 1xvx_A          240 KHPKEAQEFVKWITGK  255 (312)
T ss_dssp             SSHHHHHHHHHHHHSH
T ss_pred             CCHHHHHHHHHHHhCH
Confidence            6778899999999653

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=95.14  E-value=0.27  Score=33.09  Aligned_cols=78  Identities=14%  Similarity=0.093  Sum_probs=50.2

Q ss_pred             HHHHHHHhcCCHHHHHHHh------CCCchHHHHHHHHHHHHcCceeEE-----ecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKAL------YTSQPGVSKAIIELEEELSIDIFI-----RHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l------~isq~~~s~~i~~LE~~lg~~Lf~-----R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      ++..+.+...+...-++.+      ++|+++|+..|++||+.==+.--.     +.++...++|+.|+..+.....-...
T Consensus        16 IL~lL~~~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~~~~~~~~   95 (117)
T 4esf_A           16 VLEIISRRETYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQELELFWKKWDF   95 (117)
T ss_dssp             HHHHHHHSCBCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHHHHHHHHHHH
Confidence            3334444222566777777      799999999999999972111111     11223348999999999888777666


Q ss_pred             HHHHHHHHH
Q psy3760          77 IEGLKKIGK   85 (306)
Q Consensus        77 ~~~~~~~~~   85 (306)
                      +.+..+.+-
T Consensus        96 ~~~~i~~il  104 (117)
T 4esf_A           96 VSSKINVLK  104 (117)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666555443

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

Probab=95.13  E-value=0.041  Score=33.07  Aligned_cols=46  Identities=11%  Similarity=0.018  Sum_probs=35.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      -++-.+|....-.|.|....|+.+|+|.+++.+++++..+.|...|
T Consensus        18 ~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           18 TDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            3455566665445569999999999999999999999888886554

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

Probab=95.09  E-value=0.11  Score=36.77  Aligned_cols=35  Identities=23%  Similarity=0.168  Sum_probs=29.5

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      .+++.|.|..++|+.+|+|.+||++.+++.++. |.
T Consensus        43 ~~~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~-G~   77 (149)
T 1k78_A           43 ELAHQGVRPCDISRQLRVSHGCVSKILGRYYET-GS   77 (149)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHH-SC
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHc-CC
Confidence            334456699999999999999999999999877 54

>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=95.09  E-value=0.032  Score=36.94  Aligned_cols=73  Identities=15%  Similarity=0.150  Sum_probs=44.5

Q ss_pred             hhhHHHHHHHHH--hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCc--cccCHhHHHHHHHHHHH
Q psy3760           3 LHQFRFVREAVR--QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRI--RGLTKPGQAILRSIEII   73 (306)
Q Consensus         3 ~~~l~~f~~v~~--~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~--~~lT~~G~~l~~~a~~i   73 (306)
                      ..++..+..+.+  .+.|.+.-|+.+++|++|+++.|+.||+. |.---.+.     |+..  +.+|+   .+.+.+.+.
T Consensus        21 ~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~-g~v~~~~~~~~~~gr~~~~~~l~~---~~~~~~~~~   96 (109)
T 2d1h_A           21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL-GLVVRTKTEGKKIGRPKYYYSISS---NILEKIRND   96 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEC-------CCEEEEECT---THHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEeeccccCCCCCCCeeeecCH---HHHHHHHHH
Confidence            345555655554  22378999999999999999999999764 43333322     1211  25666   445555555


Q ss_pred             HHHHHH
Q psy3760          74 MQEIEG   79 (306)
Q Consensus        74 l~~~~~   79 (306)
                      ++.+.+
T Consensus        97 ~~~~~~  102 (109)
T 2d1h_A           97 LLNCAK  102 (109)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            544443

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=95.05  E-value=0.042  Score=39.59  Aligned_cols=44  Identities=11%  Similarity=0.194  Sum_probs=34.7

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      |-.+.+++..+.+.+ .|++.-|+.+|+|++|++++|++||+. |.
T Consensus         9 d~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~   53 (162)
T 2p5v_A            9 DKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDA-GI   53 (162)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT-TS
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC
Confidence            445666666666542 289999999999999999999999876 44

>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=94.97  E-value=0.13  Score=36.08  Aligned_cols=43  Identities=16%  Similarity=0.111  Sum_probs=32.3

Q ss_pred             hhhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      ..+.+++..+.  +.+.|.+.-|+.+++|+||+|+.++.||+. |.
T Consensus        26 ~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~~-G~   70 (152)
T 1ku9_A           26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEEL-GF   70 (152)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TS
T ss_pred             hhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC
Confidence            34455555553  222379999999999999999999999984 44

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=94.97  E-value=0.034  Score=40.07  Aligned_cols=43  Identities=19%  Similarity=0.234  Sum_probs=34.7

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ .|++.-|+.+|+|++|++++|++||+.
T Consensus         1 lD~~d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~   44 (162)
T 3i4p_A            1 MDRLDRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEED   44 (162)
T ss_dssp             CCHHHHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4555667776666542 389999999999999999999999985

>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=94.94  E-value=0.022  Score=42.31  Aligned_cols=45  Identities=9%  Similarity=0.161  Sum_probs=33.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIF   49 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf   49 (306)
                      .+.+++..+.+.+.|++.-|+.+|+|++|++++|++||+. |.---
T Consensus        21 ~~~~IL~~L~~~~~s~~eLA~~lglS~stv~~~l~~Le~~-GlI~~   65 (192)
T 1uly_A           21 TRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEA-GLVEV   65 (192)
T ss_dssp             HHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence            4455555555434488999999999999999999999875 55433

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

Probab=94.88  E-value=0.037  Score=34.54  Aligned_cols=29  Identities=21%  Similarity=0.188  Sum_probs=26.2

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      |.+.-|+.+++|++++++.|+.||+. |.-
T Consensus        16 s~~eLa~~lgvs~~tv~r~L~~L~~~-GlI   44 (81)
T 2htj_A           16 KTAEIAEALAVTDYQARYYLLLLEKA-GMV   44 (81)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHH-TSE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-CCE
Confidence            78899999999999999999999986 553

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

Probab=94.83  E-value=0.059  Score=38.25  Aligned_cols=42  Identities=17%  Similarity=0.257  Sum_probs=33.2

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-.+.+++..+.+.+ .|++.-|+.+|+|++++++++++||+.
T Consensus         8 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   50 (151)
T 2dbb_A            8 DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKL   50 (151)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            344556666666532 288999999999999999999999976

>1nh8_A ATP phosphoribosyltransferase; prtase, de novo His biosynthesis, PRPP, structural genomics, PSI, protei structure initiative; HET: AMP HIS; 1.80A {Mycobacterium tuberculosis H37RV} SCOP: c.94.1.1 d.58.5.3 PDB: 1nh7_A*

Probab=94.77  E-value=0.42  Score=37.86  Aligned_cols=160  Identities=10%  Similarity=0.095  Sum_probs=98.4

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++.-....++..-+..|.+|+||+..+..     +-..+.-..++.-++++.+|++ +.     -+++++.+.+..+  
T Consensus        63 i~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~elldLgfG~crl~vAvp~~-~~-----~~~~~l~~~RIAT--  134 (304)
T 1nh8_A           63 VEFFFLRPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAG-RN-----WTTADLAGMRIAT--  134 (304)
T ss_dssp             EEEEEECGGGHHHHHHHSSCSEEEEEHHHHHHHTCCEEEEEECSCCCEEEEEEEETT-SC-----CCGGGGTTCEEEE--
T ss_pred             EEEEEEChhhHHHHHhCCCccEEEeeeeeeeecCCCceEEecCCcccEEEEEEEECC-Cc-----CChHHhCCCEEEe--
Confidence            455555677999999999999999852211     1122334445677899999887 32     2577776644443  


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCC
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                         .+.+...++|.+.|+...++....+.+..   ...|.+=+++.--.. ..++..+|+.+  .+.....+..|+.++.
T Consensus       135 ---kYp~l~r~yf~~~gi~~~Ii~l~GsvE~a---P~~GlADaIvDiVsTG~TLraNgL~~i--~e~I~~SsA~LI~n~~  206 (304)
T 1nh8_A          135 ---AYPNLVRKDLATKGIEATVIRLDGAVEIS---VQLGVADAIADVVGSGRTLSQHDLVAF--GEPLCDSEAVLIERAG  206 (304)
T ss_dssp             ---SCHHHHHHHHHHHTCCCEEEECSSCCTHH---HHTTSCSEEEEEESSSHHHHHTTEEEE--EEEEEEECEEEEEEC-
T ss_pred             ---CcHHHHHHHHHHCCCeEEEEECCCceeec---cCCCcccEEEEEeCChHHHHHCcCEEc--ccEEEEEEEEEEEccc
Confidence               34467788999999987766666666654   344544444433211 12245678877  3334455778888776


Q ss_pred             ccc---cHHHHHHHHHHhHHhhHHH
Q psy3760         278 TYL---RSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       278 ~~~---~~~~~~~~~~l~~~~~~~~  299 (306)
                      ...   ...++.+++.++..+.++.
T Consensus       207 s~~~~k~~~i~~l~~rl~~vl~A~~  231 (304)
T 1nh8_A          207 TDGQDQTEARDQLVARVQGVVFGQQ  231 (304)
T ss_dssp             -------CHHHHHHHHHHHHHHHTT
T ss_pred             cchhhhHHHHHHHHHHHHHHHHhcc
Confidence            433   3567788888877765543

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=94.72  E-value=0.062  Score=43.52  Aligned_cols=57  Identities=12%  Similarity=0.024  Sum_probs=46.4

Q ss_pred             HHHHHHHHh--cCC---HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHH
Q psy3760           7 RFVREAVRQ--NFN---LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL   67 (306)
Q Consensus         7 ~~f~~v~~~--~~s---~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~   67 (306)
                      .++..+.+.  | +   .++||+.||++.+++.+.+++.-..-|  |+.+.++|. .+|+.|..++
T Consensus       251 ~~i~~~~~~~~g-~~~~~~~~a~~lgi~~~tl~~~l~~~~i~~~--li~~~~~g~-~~~~~~~~~~  312 (324)
T 1hqc_A          251 EILEVLILRFGG-GPVGLATLATALSEDPGTLEEVHEPYLIRQG--LLKRTPRGR-VPTELAYRHL  312 (324)
T ss_dssp             HHHHHHHHHSCS-SCCCHHHHHHHTTSCHHHHHHHTHHHHHHTT--SEEEETTEE-EECHHHHHHT
T ss_pred             HHHHHHHHHhcC-CCchHHHHHHHhCCCHHHHHHHHhHHHHHhc--chhcCCccc-eecHHHHHHH
Confidence            566666654  6 7   999999999999999999998555544  667888888 6999999876

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=94.68  E-value=0.068  Score=43.30  Aligned_cols=43  Identities=23%  Similarity=0.074  Sum_probs=37.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |-..-|+.|++|+++|+|+|+.|++ .|..+....++|. +|.+.
T Consensus        21 Sg~eLa~~lgvSr~aV~k~i~~L~~-~G~~i~~~~~~GY-~L~~~   63 (323)
T 3rkx_A           21 SGQSIAESLNISRTAVKKVIDQLKL-EGCKIDSVNHKGH-LLQQL   63 (323)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHH-TTCEEEEETTTEE-EEEEC
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHh-cCCeEEEeCCCeE-EEecC
Confidence            8889999999999999999999986 8998888788887 56543

>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=94.67  E-value=0.048  Score=34.89  Aligned_cols=47  Identities=6%  Similarity=-0.009  Sum_probs=37.5

Q ss_pred             chhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe
Q psy3760           2 NLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR   51 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R   51 (306)
                      +-.++.++..+.+.|   -+...-|++++++++++++.|++||+.   .|+.|
T Consensus        19 t~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~k---glIkr   68 (91)
T 2dk5_A           19 DNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESK---KLIKA   68 (91)
T ss_dssp             CSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHT---TSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEE
Confidence            456778888888633   467789999999999999999999983   55653

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

Probab=94.66  E-value=0.027  Score=35.00  Aligned_cols=31  Identities=16%  Similarity=0.246  Sum_probs=27.2

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +.|.|...-|++||+|.+++.++|.+||++=
T Consensus        28 ~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG   58 (82)
T 1oyi_A           28 IEGATAAQLTRQLNMEKREVNKALYDLQRSA   58 (82)
T ss_dssp             SSTEEHHHHHHHSSSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            4445899999999999999999999999863

>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=94.64  E-value=0.059  Score=35.88  Aligned_cols=41  Identities=22%  Similarity=0.217  Sum_probs=32.0

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      .++++..+.+.|  .|...-|+.+|+|+++++++|+.|+++ |.
T Consensus        20 ~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~-Gl   62 (110)
T 1q1h_A           20 VIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQ-GF   62 (110)
T ss_dssp             THHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHH-TS
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC
Confidence            455555554332  389999999999999999999999976 54

>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=94.54  E-value=0.22  Score=38.51  Aligned_cols=60  Identities=18%  Similarity=0.176  Sum_probs=43.7

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHHHH
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQAIL   67 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~l~   67 (306)
                      +-+.++..+.+.+  .|++.-|+.+++++||+++.++.||+. |.  +.|.+  ++. +|++....+-
T Consensus         7 r~l~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~-G~--v~~~~~~~~Y-~lg~~~~~lg   70 (241)
T 2xrn_A            7 RAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEE-FL--VEALGPAGGF-RLGPALGQLI   70 (241)
T ss_dssp             HHHHHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTT-TS--EEECGGGCEE-EECSHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC--EEEeCCCCeE-EECHHHHHHH
Confidence            3456666666542  379999999999999999999999974 43  44443  566 7988765544

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=94.52  E-value=0.076  Score=39.27  Aligned_cols=56  Identities=20%  Similarity=0.141  Sum_probs=41.4

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      +..+++..+.+.+  .|...-|+.+++|.+|+.+.|+.||+ .|.++-. .++|. .+++.
T Consensus        22 R~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~-~G~~I~~-~~~Gy-~l~~~   79 (187)
T 1j5y_A           22 RLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRS-LGYNIVA-TPRGY-VLAGG   79 (187)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHH-HTCCCEE-ETTEE-ECCTT
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCCeEEE-ECCEE-EECCc
Confidence            3455555555432  38999999999999999999999998 6887644 55676 56643

>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=94.44  E-value=0.058  Score=35.40  Aligned_cols=48  Identities=13%  Similarity=0.011  Sum_probs=34.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAIL   67 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~   67 (306)
                      |...-|+.+++|+++|.++|+.||++ |.--..+. ++|. .+++.+..-+
T Consensus        45 s~~eLa~~lgVSr~tVr~al~~L~~~-GlI~~~~gG~~G~-~V~~~~~~~~   93 (102)
T 2b0l_A           45 VASKIADRVGITRSVIVNALRKLESA-GVIESRSLGMKGT-YIKVLNNKFL   93 (102)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSSCE-EEEECCHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEeCCCCcE-EEecCCHHHH
Confidence            67889999999999999999999987 54322332 3676 4666554433

>1sbp_A Sulfate-binding protein; 1.70A {Salmonella typhimurium} SCOP: c.94.1.1

Probab=94.42  E-value=0.69  Score=36.88  Aligned_cols=186  Identities=14%  Similarity=0.077  Sum_probs=95.9

Q ss_pred             hhhhhHHHHHHHHHhC---CCcEEEEEe--CChhHHHHHHHcC-CeeEEEEccccC----CCCCce-----------eec
Q psy3760         104 ARYALPKIIKEFTIQF---PKVKLSLLQ--GNPKQITEMIRND-QADIAIVTEILS----PSDKLI-----------SIP  162 (306)
Q Consensus       104 ~~~~l~~~l~~~~~~~---p~~~i~~~~--~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~~~-----------~~~  162 (306)
                      ....+..++..|.+.|   |++.+++..  .++.++...+..| ..|+++......    ...++.           ..+
T Consensus        13 ~~~~~~~~~~~F~~~~~~~~gi~V~v~~~~~~s~~l~~~~~~g~~~Dv~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~p   92 (310)
T 1sbp_A           13 TRELYEQYNKAFSAHWKQETGDNVVIDQSHGGSGKQATSVINGIEADTVTLALAYDVNAIAERGRIDKNWIKRLPDDSAP   92 (310)
T ss_dssp             THHHHHHHHHHHHHHHHHHHSCEEEEEEEESCHHHHHHHHHTTCCCSEEEESSHHHHHHHHHTTSSCTTGGGGSHHHHCS
T ss_pred             CHHHHHHHHHHHHHHhhhCCCceEEEEeecCChHHHHHHHhcCCCCCEEEeCcHHHHHHHHhCCCcCcchhhcCCccCCc
Confidence            3557788999998765   898887754  7777888888877 799998642100    011110           011


Q ss_pred             cccceEEEEecCCCCCCCCCCcChhhhcC--CCeEeecCCCC-cH--HHHHHHH---HhCCC------------ceeEEE
Q psy3760         163 CYQWEYVIIVPLDHPLLLLNSISLKEISN--YPLITYDLSFS-GR--IKLDREF---SLQKL------------TPYIVL  222 (306)
Q Consensus       163 l~~~~~~~v~~~~~~l~~~~~i~~~dl~~--~~~i~~~~~~~-~~--~~~~~~~---~~~~~------------~~~~~~  222 (306)
                      . ...++++.+++.+   ..+-+|+||.+  ..+....+... ..  ..+..+.   ...|.            .++...
T Consensus        93 ~-~~~~~l~yn~~~~---~~p~tw~dL~~~~~ki~~~~p~~~~~~~~~~~~~~~~~~~~~gg~~~~a~~~l~~l~~~~~~  168 (310)
T 1sbp_A           93 Y-TSTIVFLVRKGNP---KQIHDWNDLIKPGVSVITPNPKSSGGARWNYLAAWGYALHHNNNDQAKAEDFVKALFKNVEV  168 (310)
T ss_dssp             E-EBCEEEEEETTCT---TCCCSGGGGGSTTCCEECCCTTTCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTEEE
T ss_pred             e-eEEEEEEEeCCCC---CCCCCHHHHcCccceEecCCCcccchhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcc
Confidence            1 2347888888874   23568999975  34444333211 11  1111111   12221            123332


Q ss_pred             EecCHH-HHHHHHHhc-cceeeeecceeccc--c-c-CCceeeecCCCCccceEEEEEeCCc----cccHHHHHHHHHHh
Q psy3760         223 ETINSD-IIKTYVELR-MGIGIIASIAFDSN--R-D-KNLRSISASHLFGTTISRVIIKQGT----YLRSYVYSFIKLLS  292 (306)
Q Consensus       223 ~~~~~~-~~~~~v~~g-~gi~~~p~~~~~~~--~-~-~~l~~~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~~~~l~  292 (306)
                      ...+.. ....++.+| ..+++.........  . . ..+..+ ++.........+...++.    ....++++|++++.
T Consensus       169 ~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~g~~~~~~v-~P~~g~~~~~~~~i~~~~~~~s~~~~~A~~fi~fl~  247 (310)
T 1sbp_A          169 LDSGARGSTNTFVERGIGDVLIAWENEALLATNELGKDKFEIV-TPSESILAEPTVSVVDKVVEKKDTKAVAEAYLKYLY  247 (310)
T ss_dssp             CCSSHHHHHHHHHTSCCCSEEEEEHHHHHHHHHTTTTTTEEEE-CCSEEECBCCEEEECHHHHHHHTCHHHHHHHHHGGG
T ss_pred             cCCccHHHHHHHHhCCCccEEEeechHHHHHHHhcCCCceEEE-ccCCceeccCCeEEeccccccccCHHHHHHHHHHHc
Confidence            233443 367778777 44444433222111  1 1 345444 332111111233333332    45678999999986


Q ss_pred             HH
Q psy3760         293 PK  294 (306)
Q Consensus       293 ~~  294 (306)
                      +.
T Consensus       248 s~  249 (310)
T 1sbp_A          248 SP  249 (310)
T ss_dssp             SH
T ss_pred             Ch
Confidence            54

>4esw_A Pyrimidine biosynthesis enzyme THI13; thiamin pyrimidine biosynthesis, transferase; HET: CIT; 1.60A {Candida albicans} PDB: 4esx_A*

Probab=94.39  E-value=0.78  Score=37.34  Aligned_cols=138  Identities=14%  Similarity=0.172  Sum_probs=78.6

Q ss_pred             CCcEEEEecccchhhhhH----HHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC---CCCCceeec-
Q psy3760          92 TGNLTIATTHTQARYALP----KIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS---PSDKLISIP-  162 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~----~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~-  162 (306)
                      ...|++...-.......|    .-..-|.+.  ++++++.. .+.....+.|.+|++|+++......   ...+..... 
T Consensus         6 ~~kvt~~LdW~p~~~~ap~~vA~~kG~f~e~--GLdVei~~~~~~~~~~~al~sG~~D~g~~~~~~~~~a~~~G~~v~~v   83 (342)
T 4esw_A            6 TNKITFLLNWEAAPYHIPVYLANIKGYFKDE--NLDIAILEPSNPSDVTELVGSGKVDMGLKAMVGTLAAKARGFPVTSI   83 (342)
T ss_dssp             CCEEEEECSSSSCGGGHHHHHHHHTTHHHHT--TCEEEEEEESSGGGHHHHHHHTSSSEEEEEHHHHHHHHHTTCCEEEE
T ss_pred             CCcEEEEECCEeCcChHHHHHHHHCCchHHc--CCeEEEEeCCChHHHHHHHHcCCcCEEEecHHHHHHHHHCCCCeEEE
Confidence            456888865433333333    333334444  77787766 4556789999999999999752111   112222211 


Q ss_pred             ---cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760         163 ---CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR  237 (306)
Q Consensus       163 ---l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g  237 (306)
                         .......+++.++.+.    .-+++||.+......  +......+..+++..|+.+..+..++.......++.+|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~----~~~~~dLkGK~ig~~--~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~al~~G  155 (342)
T 4esw_A           84 GSLLDEPFTGICYLEGSGI----TSDFQSLKGKRIGYV--GEFGKIQVDELTKHYGMTPDDYVAVRCGMNVAKYILEG  155 (342)
T ss_dssp             EEEECSCCEEEEEETTSSC----CSSGGGGTTCEEEES--SSHHHHHHHHHHGGGTCCGGGSEEEECGGGHHHHHHHT
T ss_pred             EEeccCCcccccccccccc----cCCHHHhCCCEEEec--CCchHHHHHHHHHHcCCChhheEEecCCHHHHHHHHcC
Confidence               1223344555554431    125899998877653  23345577888999999875443333333445666677

>1o63_A ATP phosphoribosyltransferase; structural genomics; 2.00A {Thermotoga maritima} SCOP: c.94.1.1 PDB: 1o64_A 1usy_E* 1usy_H*

Probab=94.32  E-value=0.86  Score=34.21  Aligned_cols=155  Identities=14%  Similarity=0.085  Sum_probs=94.9

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++.-....++..-+..|.+|++|+..+.     .+-..+.-..++.-++++.+|++.+.        +++ +....   
T Consensus        40 i~~~~~R~~DIp~yV~~G~aDlGItG~D~l~E~~~~v~elldLgfG~crl~vAvp~~~~~--------~~~-~~RIA---  107 (219)
T 1o63_A           40 IVCFMVRPFDVPTYLVHGVADIGFCGTDVLLEKETSLIQPFFIPTNISRMVLAGPKGRGI--------PEG-EKRIA---  107 (219)
T ss_dssp             EEEEEECGGGHHHHHHTTSCSEEEEEHHHHHHSCCCCBCCSEEEEEEEEEEEEEETTTCC--------CSS-CEEEE---
T ss_pred             eEEEEECchhHHHHHhCCCccEEEeeeEeeeecCCCeeEEeccccccEEEEEEEECCCcc--------ccC-CcEEE---
Confidence            34444557789999999999999985221     12223344556678899999988653        333 22222   


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCC
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                        ..+.+...++|++.|+...++....+.+.+   ..-|.+=+++.--.. ..++..+|+.+.   .....+..|+.++.
T Consensus       108 --Tkyp~l~r~yf~~~Gi~~~Ii~l~GsvE~a---P~~GlADaIvDivsTG~TLraNgL~~ie---~I~~SsA~LI~n~~  179 (219)
T 1o63_A          108 --TKFPNVTQRYCESKGWHCRIIPLKGSVELA---PIAGLSDLIVDITETGRTLKENNLEILD---EIFVIRTHVVVNPV  179 (219)
T ss_dssp             --ESCHHHHHHHHHHHTCCEEEEECSSCTTHH---HHHTSCSEEEEEESSSHHHHHTTEEEEE---EEEEEEEEEEECHH
T ss_pred             --ECcHHHHHHHHHHCCCceEEEECCCceeec---cCCCCcceeEEeeccHHHHHHCCCEEee---EEeeeEEEEEECch
Confidence              234567788999999987666556666554   334544444433211 122456787773   34455778887765


Q ss_pred             cc--ccHHHHHHHHHHhHHhhHH
Q psy3760         278 TY--LRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       278 ~~--~~~~~~~~~~~l~~~~~~~  298 (306)
                      ..  ....++.+++.|+..+.++
T Consensus       180 s~~~k~~~i~~l~~rl~~vl~~~  202 (219)
T 1o63_A          180 SYRTKREEVVSFLEKLQEVIEHD  202 (219)
T ss_dssp             HHHHTHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhc
Confidence            32  2356777888887776443

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=94.29  E-value=0.072  Score=32.85  Aligned_cols=26  Identities=12%  Similarity=0.240  Sum_probs=24.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |...-|+.|++|.++|.++|.+||++
T Consensus        33 t~~eLA~~Lgvs~~tV~~~L~~L~~~   58 (77)
T 1qgp_A           33 TAHDLSGKLGTPKKEINRVLYSLAKK   58 (77)
T ss_dssp             EHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            78999999999999999999999975

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

Probab=94.28  E-value=0.067  Score=30.97  Aligned_cols=34  Identities=12%  Similarity=0.054  Sum_probs=26.7

Q ss_pred             HHHHHhcCC----HHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          10 REAVRQNFN----LTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        10 ~~v~~~~~s----~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..+.+.|.|    +..+|+.+||+.++|.+.+++.++.
T Consensus        15 ~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~   52 (59)
T 2glo_A           15 LESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNL   52 (59)
T ss_dssp             HHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHH
T ss_pred             HHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            444444447    9999999999999999999876653

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=94.27  E-value=0.5  Score=31.70  Aligned_cols=77  Identities=17%  Similarity=0.038  Sum_probs=50.1

Q ss_pred             HHHHHHhcCCHHHHHHHh------CCCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKAL------YTSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l------~isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +..+.+.-.+...-++.+      .++++++...|++||+.==+.--..     .++...++|+.|+..+.....-...+
T Consensus        19 L~lL~~~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l~~~~~~~~~~   98 (116)
T 3hhh_A           19 LAIIQRKETYGYEITKILNDQGFTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAELADFWQRWTLL   98 (116)
T ss_dssp             HHHHHHSCBCHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHHH
Confidence            334444322556777777      7999999999999998621111110     11223389999999998887777776


Q ss_pred             HHHHHHHH
Q psy3760          78 EGLKKIGK   85 (306)
Q Consensus        78 ~~~~~~~~   85 (306)
                      .+..+.+-
T Consensus        99 ~~~i~~il  106 (116)
T 3hhh_A           99 SKQVNKMK  106 (116)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66555443

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=94.17  E-value=0.12  Score=32.23  Aligned_cols=27  Identities=11%  Similarity=0.204  Sum_probs=25.1

Q ss_pred             CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          17 FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        17 ~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .+...-|++|++|.++|.++|.+||++
T Consensus        28 ~t~~eLA~~Lgvsr~tV~~~L~~Le~~   54 (81)
T 1qbj_A           28 TTAHDLSGKLGTPKKEINRVLYSLAKK   54 (81)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            388999999999999999999999975

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=94.14  E-value=0.089  Score=31.44  Aligned_cols=44  Identities=11%  Similarity=0.126  Sum_probs=35.6

Q ss_pred             hhHHHHHHHH-----HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           4 HQFRFVREAV-----RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         4 ~~l~~f~~v~-----~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      ++-++|....     +.. |+...|+.+|+|.++|.+.+.+.-+.|...+
T Consensus         9 ~er~il~l~~~l~~~~g~-s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~   57 (68)
T 2p7v_B            9 REAKVLRMRFGIDMNTDY-TLEEVGKQFDVTRERIRQIEAKALRKLRHPS   57 (68)
T ss_dssp             HHHHHHHHHTTTTSSSCC-CHHHHHHHHTCCHHHHHHHHHHHHHGGGSCC
T ss_pred             HHHHHHHHHHccCCCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4455666665     444 9999999999999999999999998887654

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=94.09  E-value=0.15  Score=34.30  Aligned_cols=65  Identities=12%  Similarity=0.071  Sum_probs=41.9

Q ss_pred             CHHHHHHHhC------CCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALY------TSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQAILRSIEIIMQEIEGLKK   82 (306)
Q Consensus        18 s~~~aA~~l~------isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~   82 (306)
                      +...-++.+.      +++++++..|++||+.==+.--..     .++...++|++|+..+....+....+.+..+
T Consensus        29 ~gyel~~~l~~~~~~~i~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l~~~~~~~~~~~~~i~  104 (117)
T 3elk_A           29 HGYELQKSMFETTGQALPQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFLCDHSQALQLARKIID  104 (117)
T ss_dssp             EHHHHHHHHHHHHSCCCCTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHHHHTSTTHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455556664      999999999999998731221111     1122348999999999886555555444443

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=94.07  E-value=0.055  Score=31.62  Aligned_cols=23  Identities=30%  Similarity=0.134  Sum_probs=20.0

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      ...+ |-.+.|+.+|+||++||+.
T Consensus         8 ~~~~-tq~~lA~~lGvs~~~Vs~w   30 (61)
T 1rzs_A            8 DHFG-TQRAVAKALGISDAAVSQW   30 (61)
T ss_dssp             HHHS-SHHHHHHHHTCCHHHHHHC
T ss_pred             HHcC-CHHHHHHHhCCCHHHHHHH
Confidence            3446 8899999999999999985

>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=94.02  E-value=0.088  Score=32.53  Aligned_cols=48  Identities=15%  Similarity=0.109  Sum_probs=35.3

Q ss_pred             CHHHHHHHhCCCch-HHHHHHHHHHHHcCceeEEecCCCccccCHhHHHH
Q psy3760          18 NLTEAAKALYTSQP-GVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI   66 (306)
Q Consensus        18 s~~~aA~~l~isq~-~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l   66 (306)
                      +...-|+.|+||.. +|.+++..||++==+.=.. .++.++.||+.|+..
T Consensus        27 ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~~-~gRP~w~LT~~g~~~   75 (79)
T 1xmk_A           27 SALNLAKNIGLTKARDINAVLIDMERQGDVYRQG-TTPPIWHLTDKKRER   75 (79)
T ss_dssp             EHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEEC-SSSCEEEECHHHHTT
T ss_pred             CHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEecC-CCCCCeEeCHhHHhH
Confidence            56778999999999 9999999999962222111 234455899999863

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=93.93  E-value=0.14  Score=34.29  Aligned_cols=46  Identities=20%  Similarity=0.200  Sum_probs=36.7

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      -++-++|....-.|.|....|+.+|+|.+||.+++++....|...|
T Consensus        25 ~~~r~vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   70 (113)
T 1s7o_A           25 DKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYE   70 (113)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            3455667766455569999999999999999999999988886543

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=93.92  E-value=0.072  Score=41.66  Aligned_cols=57  Identities=26%  Similarity=0.274  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHH
Q psy3760           5 QFRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQA   65 (306)
Q Consensus         5 ~l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~   65 (306)
                      .++++..+.+.  +.|++.-|+.+++++||+++.++.|++ .|.  ..|.+++. +|++....
T Consensus        16 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~-~G~--v~~~~~~Y-~Lg~~~~~   74 (257)
T 2g7u_A           16 GFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQK-LGY--VAGSGGRW-SLTPRVLS   74 (257)
T ss_dssp             HHHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHH-TTS--EEEETTEE-EECGGGHH
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCC--EEeCCCEE-EEcHHHHH
Confidence            34555555432  238999999999999999999999998 343  45556776 79987644

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=93.91  E-value=0.29  Score=33.17  Aligned_cols=34  Identities=21%  Similarity=0.166  Sum_probs=28.9

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.+.+.|.|...+|+.+++|.+||++.+++.++.
T Consensus        27 ~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~   60 (128)
T 1pdn_C           27 VEMAADGIRPCVISRQLRVSHGCVSKILNRYQET   60 (128)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            3344556699999999999999999999999876

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=93.90  E-value=0.16  Score=30.13  Aligned_cols=44  Identities=9%  Similarity=0.009  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      ++|..-+..++.| -|+.+||+..||.++|+..+++..-..++.+
T Consensus        17 ~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~~~~~~~~~   61 (70)
T 2cob_A           17 EILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKNP   61 (70)
T ss_dssp             HHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHHTTTTSSC
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHhhcccccCC
Confidence            4555566666666 4999999999999999999999987777643

>4i1d_A ABC transporter substrate-binding protein; structural genomics, PSI-biology; 2.20A {Bradyrhizobium japonicum}

Probab=93.84  E-value=2.1  Score=34.31  Aligned_cols=197  Identities=6%  Similarity=-0.058  Sum_probs=112.2

Q ss_pred             CCcEEEEecccc-hhhhhHHHHHHHHHhCCCcEEEEEeC--ChhHHHHHHHcCC--eeEEEEccc----------cCC--
Q psy3760          92 TGNLTIATTHTQ-ARYALPKIIKEFTIQFPKVKLSLLQG--NPKQITEMIRNDQ--ADIAIVTEI----------LSP--  154 (306)
Q Consensus        92 ~~~l~I~~~~~~-~~~~l~~~l~~~~~~~p~~~i~~~~~--~~~~~~~~l~~~~--~Di~i~~~~----------~~~--  154 (306)
                      .++|+|....+. ...+...++..|.+++ +++|++...  ....+...+..|.  .|+.+....          ..+  
T Consensus         2 ~~~L~v~~~~g~~~~~~~~~~~~~F~~~~-gi~V~~~~~~~~~~~l~~~~~~g~~~~Dv~~~~~~~~~~~~~~g~l~~l~   80 (324)
T 4i1d_A            2 NAQITFVSQGGAYQAAQTVAILDPSAKKL-GITINQDSIPDAWPAIKTQVGSGKPIWDVVDTPTGYCLRGGEQGLIEKLD   80 (324)
T ss_dssp             CCEEEEEECCHHHHHHHHHHTHHHHHHHH-TCEEEEEECSCCHHHHHHHHHTTCCSCCEEEEEHHHHHHHHHTTCBCCCC
T ss_pred             CCeEEEEeCCCcHHHHHHHHHHHHHHHHH-CCEEEEecCCCcHHHHHHHHHhCCCCeEEEECCHHHHHHHHHCCCcccCC
Confidence            357888887653 3445677899999998 999998874  3456777776664  899987411          000  


Q ss_pred             CC-------------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCC-C----eEeecCCCCcH------------
Q psy3760         155 SD-------------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY-P----LITYDLSFSGR------------  204 (306)
Q Consensus       155 ~~-------------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~-~----~i~~~~~~~~~------------  204 (306)
                      ..             .....++.....+++.+++.. ....+-+++||.+. .    +..........            
T Consensus        81 ~~~~~~~~~~~~~~~~~y~vp~~~~~~~l~yn~~~~-~~~~P~tw~dl~~~~~~~g~~~~~~~~~~~~~~~~~~~g~~~~  159 (324)
T 4i1d_A           81 FSKIPNAAAMPEAYRSPYSVSYEFYSSVLAYSQKTF-PKDAPNSWVDFWDVKKFPGRRALRNHPIATLEAALMADGVAPD  159 (324)
T ss_dssp             GGGCHHHHTSCGGGBCSSCEEEEEEEEEEEEETTTC-SSCCCCSHHHHHCTTTSCSCEEEESSSTTHHHHHHHHTTCCGG
T ss_pred             hhhCcChhhCCcccccCceeeeecceEEEEEehhhc-CCCCCCCHHHHhChhhcCCceeccCCchhHHHHHHHhcCCChh
Confidence            00             112355666777888888753 22346799999664 1    33333221110            


Q ss_pred             -------HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc--ccCCceeeecCCCCccceEEEEE
Q psy3760         205 -------IKLDREFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVII  274 (306)
Q Consensus       205 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~  274 (306)
                             ....+.+..  +.++......+.....+++.+|. .+++.....+...  ....+.... +. .....-++..
T Consensus       160 ~~~~~~~~~a~~~l~~--l~~~~~~~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~~~~~~~~~~~~-~g-~~~~~~~~~i  235 (324)
T 4i1d_A          160 KLYPLDVDRAFKKLEE--IKPHITVWWTSGAQSAQLLNDGEVDMEMAWNGRVSAVAKEGAKVSFTY-NQ-GILQSTSLCI  235 (324)
T ss_dssp             GCCSCCHHHHHHHHHH--HGGGCSEEECSHHHHHHHHHHTSCSEEEEEHHHHHHHHHTTCSEEEEE-EE-EEEEEEEEEE
T ss_pred             hcCHHHHHHHHHHHHH--HhhhhhhhccCcchHHHHHhCCCEEEEecccHHHHHHHhcCCCeEEEe-cC-eeeeccEEEE
Confidence                   011112222  12343233446667778888884 4444444333222  223444443 22 2222335556


Q ss_pred             eCCccccHHHHHHHHHHhHH
Q psy3760         275 KQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       275 ~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .++.....++++|++++.+.
T Consensus       236 ~k~s~~~~~A~~fi~fl~s~  255 (324)
T 4i1d_A          236 LKGAPNLETAVKFLNEAVDP  255 (324)
T ss_dssp             BTTCTTHHHHHHHHHHHTCH
T ss_pred             ECCCCCHHHHHHHHHHHhCH
Confidence            77777788999999998654

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=93.81  E-value=0.041  Score=40.53  Aligned_cols=40  Identities=13%  Similarity=0.163  Sum_probs=32.4

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhC-CCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALY-TSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~   43 (306)
                      .-++++..+.+...+.+.-|+.|+ +|||++|++|+.|++.
T Consensus        24 ~Rl~il~~L~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~a   64 (182)
T 4g6q_A           24 LRWRITQLLIGRSLTTRELAELLPDVATTTLYRQVGILVKA   64 (182)
T ss_dssp             HHHHHHHHTTTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence            446677777664448889999996 9999999999999874

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

Probab=93.77  E-value=0.14  Score=32.69  Aligned_cols=43  Identities=9%  Similarity=0.112  Sum_probs=33.0

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      ++-++|....-.|+|+...|+.||+|.+||.+++.+.-+.|..
T Consensus        41 ~~r~vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~   83 (92)
T 3hug_A           41 EHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRL   83 (92)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            4455666644555699999999999999999888877766643

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=93.73  E-value=0.1  Score=42.23  Aligned_cols=56  Identities=18%  Similarity=0.296  Sum_probs=43.0

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      ++.+++..+.+.+ -|...-|+++++|++|+.|.|+.||+ .|..+..+.++|. ++.+
T Consensus         6 r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~-~G~~i~~~~g~GY-~l~~   62 (321)
T 1bia_A            6 VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRD-WGVDVFTVPGKGY-SLPE   62 (321)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHH-TTCCCEEETTTEE-ECSS
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHh-CCCcEEEecCCCc-EEee
Confidence            4444555554432 27888999999999999999999997 8998887778887 5654

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=93.72  E-value=0.077  Score=39.72  Aligned_cols=39  Identities=21%  Similarity=0.233  Sum_probs=31.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .+.++..+.+...+++.-|+.+++|++++|++|+.||+.
T Consensus        17 rl~IL~~L~~~~~s~~eLa~~l~is~stvs~hLk~Le~~   55 (202)
T 2p4w_A           17 RRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEA   55 (202)
T ss_dssp             HHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            455555555444488999999999999999999999974

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=93.71  E-value=0.18  Score=31.83  Aligned_cols=30  Identities=3%  Similarity=-0.046  Sum_probs=25.7

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.|.|+..+|+.+|||.++|.+.+++.+..
T Consensus        36 ~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~   65 (87)
T 2elh_A           36 HDGESKASVARDIGVPESTLRGWCKNEDKL   65 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            444499999999999999999999887753

>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=93.60  E-value=0.12  Score=38.43  Aligned_cols=42  Identities=17%  Similarity=0.215  Sum_probs=31.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-cCCCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-HGKRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-~~~~~~~lT~   61 (306)
                      |++.-|+.+|+|++|++++|++||+. |.--..+ ..+++ ++++
T Consensus        26 s~~eia~~lgl~~~tv~~~l~~Le~~-G~i~~~~~~~r~i-~~~~   68 (196)
T 3k2z_A           26 SVREIARRFRITPRGALLHLIALEKK-GYIERKNGKPRAL-RISK   68 (196)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHT-TSEECC---TTCC-EESS
T ss_pred             CHHHHHHHcCCCcHHHHHHHHHHHHC-CCEEecCCCcceE-EecC
Confidence            99999999999999999999999985 3332222 23455 5664

>2vd2_A ATP phosphoribosyltransferase; HISG, glycosyltransferase, histidine biosynthes amino-acid biosynthesis; 2.85A {Bacillus subtilis}

Probab=93.52  E-value=0.74  Score=34.50  Aligned_cols=154  Identities=12%  Similarity=0.105  Sum_probs=91.8

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++.-....++..-+..|.+|+||+..+..     +-..+.-..++.-++++.+|++.        +++++ +....+  
T Consensus        49 v~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~el~dLgfG~crl~vAvp~~~--------~~~~~-~~RIAT--  117 (214)
T 2vd2_A           49 LRFILAKPMDVTTYVEHGVADVGIAGKDVMLEEERDVYEVLDLNISKCHLAVAGLPNT--------DWSGV-APRIAT--  117 (214)
T ss_dssp             EEEEEECTTHHHHHHHHTSSSEEECCTHHHHSCSCSSEEEEECTTSCCEEEEEECTTC--------CCCSS-SCEEEE--
T ss_pred             EEEEEECchhHHHHHhCCCccEEEeeeeeeeecCCCeEEeeccccCCEEEEEEEECCC--------ChhhC-CcEEEE--
Confidence            344445566899999999999999852211     11122334456778999998874        13334 222222  


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce-ecccccCCceeeecCCCCccceEEEEEeCC
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA-FDSNRDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                         .+.+...++|.+.|+...++....+.+..   ..-|.+=+++.--. -..++..+|+.+.   .....+..|+.++.
T Consensus       118 ---kyp~l~~~yf~~~gi~~~ii~l~GsvE~a---P~~GlADaIvDivsTG~TLraNgL~~ie---~I~~ssA~LI~n~~  188 (214)
T 2vd2_A          118 ---KYPNVASSYFREQGEQVEIIKLNGSIELA---PLIGLADRIVDIVSTGQTLKENGLVETE---HICDITSRFIVNPV  188 (214)
T ss_dssp             ---SCHHHHHHHHHHHCCCCEEEECCSCTTHH---HHTTSCSEEEEEECCSSSSCTTSCEEEE---EEEECCCEEEECHH
T ss_pred             ---CcHHHHHHHHHHcCCcEEEEECCCceeec---cCCCCceEEEEEeCCHHHHHHCCCEEeE---EEEeeEEEEEEcch
Confidence               34567788999999987666656666554   34454444544321 1223567788774   23345677887665


Q ss_pred             cc--ccHHHHHHHHHHhHHhhH
Q psy3760         278 TY--LRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       278 ~~--~~~~~~~~~~~l~~~~~~  297 (306)
                      ..  ....++.+++.++..+.+
T Consensus       189 s~~~k~~~i~~l~~rl~~vl~a  210 (214)
T 2vd2_A          189 SYRMKDDVIDEMASRLSLVVEG  210 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHHHh
Confidence            32  234566677776665543

>1h3d_A ATP-phosphoribosyltransferase; hisitidine biosynthesis, glycosyltransferase; HET: AMP TLA; 2.7A {Escherichia coli} SCOP: c.94.1.1 d.58.5.3 PDB: 1q1k_A*

Probab=93.44  E-value=2.3  Score=33.68  Aligned_cols=161  Identities=11%  Similarity=0.143  Sum_probs=99.8

Q ss_pred             EEEEEeCChhHHHHHHHcCCeeEEEEccccC-----------CCCC---ceeeccccceEEEEecCCCCCCCCCCcChhh
Q psy3760         123 KLSLLQGNPKQITEMIRNDQADIAIVTEILS-----------PSDK---LISIPCYQWEYVIIVPLDHPLLLLNSISLKE  188 (306)
Q Consensus       123 ~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-----------~~~~---~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~d  188 (306)
                      .+++.-....++..-+..|.+|+||+..+..           ...+   +.-..++.-++++.+|++.+.     .+.++
T Consensus        47 ~v~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~~~~~~~~~~v~el~dLgfG~crl~vAvp~~~~~-----~~~~~  121 (299)
T 1h3d_A           47 PIDILRVRDDDIPGLVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAW-----DGPLS  121 (299)
T ss_dssp             SEEEEEECGGGHHHHHHTTSSSEEEEEHHHHHHHHHHHHHHTCCCCEEEEEECSCCCEEEEEEEETTSCC-----CCGGG
T ss_pred             CEEEEEeChhHHHHHHhCCCCcEEEeeeeeeeccccccccccCCCcEEEEeccCcCCEEEEEEEECCCCC-----CChHH
Confidence            3566666778999999999999999852210           0111   223355678899999987642     23566


Q ss_pred             hcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCcc
Q psy3760         189 ISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGT  267 (306)
Q Consensus       189 l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~  267 (306)
                      +.+.+..+     .+.+...++|.+.|+...++....+.+..   ..-|.+=+++---.. ..++..+|+.+.   ....
T Consensus       122 l~g~RIAT-----kyp~l~~~yf~~~gi~~~ii~l~GsvE~a---P~~GlADaIvDivsTG~TLraNgL~~ie---~I~~  190 (299)
T 1h3d_A          122 LNGKRIAT-----SYPHLLKRYLDQKGISFKSCLLNGSVEVA---PRAGLADAICDLVSTGATLEANGLREVE---VIYR  190 (299)
T ss_dssp             GTTCEEEE-----SCHHHHHHHHHHHTCCCEEEECSSCTTHH---HHTTSCSEEEEEESSCHHHHHTTEEEEE---EEEE
T ss_pred             hCCCEEEe-----CcHHHHHHHHHHcCCcEEEEECCCceeec---cCCCccceEEecccCHHHHHHCCCEEeE---EEEe
Confidence            65544332     34567788899999987766555666554   445544444433211 123456787762   3445


Q ss_pred             ceEEEEEeCCccc---cHHHHHHHHHHhHHhhHHH
Q psy3760         268 TISRVIIKQGTYL---RSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       268 ~~~~l~~~~~~~~---~~~~~~~~~~l~~~~~~~~  299 (306)
                      .+..|+.++....   ...++.+++.++..+.++.
T Consensus       191 SsA~LI~n~~s~~~~k~~~i~~l~~rl~~v~~A~~  225 (299)
T 1h3d_A          191 SKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARE  225 (299)
T ss_dssp             ECEEEEEESSCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeccccChhHHHHHHHHHHHHHHHHHhhc
Confidence            5778888877532   2457777777777665544

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=93.17  E-value=0.68  Score=30.03  Aligned_cols=56  Identities=14%  Similarity=0.057  Sum_probs=37.0

Q ss_pred             HHHHHh--CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760          21 EAAKAL--YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus        21 ~aA~~l--~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~   76 (306)
                      .-++..  .++.+++...+++||++==+.-..+.++.+.++|++|+..+....+....
T Consensus        33 ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~~~   90 (99)
T 2co5_A           33 EILKRFDIDISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFFKK   90 (99)
T ss_dssp             HHHHHHCCBCCHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhHHh
Confidence            334444  69999999999999985211111122344449999999988876654443

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=93.15  E-value=0.2  Score=39.19  Aligned_cols=56  Identities=9%  Similarity=0.039  Sum_probs=39.4

Q ss_pred             HHHHHHHHH--hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-CccccCHhHHH
Q psy3760           6 FRFVREAVR--QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-RIRGLTKPGQA   65 (306)
Q Consensus         6 l~~f~~v~~--~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-~~~~lT~~G~~   65 (306)
                      ++++..+.+  .+.+++.-|+.+++++||+++.++.|++ .|.  ..|..+ +. +|++....
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~-~G~--v~~~~~~~Y-~lg~~~~~   84 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCA-RSV--LTSRADGSY-SLGPEMLR   84 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHH-TTS--EEECTTSCE-EECHHHHH
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCC--EEECCCCeE-EecHHHHH
Confidence            444444432  2338999999999999999999999998 344  344433 55 78887444

>2vd3_A ATP phosphoribosyltransferase; metal-binding, glycosyltransferase, HISG, histidine, magnesi transferase; HET: HIS; 2.45A {Methanobacterium thermoautotrophicum}

Probab=93.01  E-value=0.6  Score=36.78  Aligned_cols=159  Identities=14%  Similarity=0.124  Sum_probs=96.0

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeeccccceEEEEecCCCCCCCCCCcChhhh-cCCCeEee
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI-SNYPLITY  197 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~  197 (306)
                      +++.-....++..-+..|.+|+||+..+.     .+-..+.-..++.-++++.+|++.+.     -+++++ .+.+..+ 
T Consensus        47 i~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~el~dLgfG~crl~vAvp~~~~~-----~~~~~l~~~~RIAT-  120 (289)
T 2vd3_A           47 IEVMFSRAADIPEFVADGAADLGITGYDLIVERGSDVEILEDLKYGRASLVLAAPEDSTI-----RGPEDIPRGAVIAT-  120 (289)
T ss_dssp             EEEEEECTTTHHHHHHHTSSSEEEEEHHHHHHHTCCCEEEEECSCSCEEEEEEEETTSSC-----CSGGGCCTTCEEEE-
T ss_pred             EEEEEEChhhHHHHHhCCCccEEEeeeeeeeecCCCceEEecCCCCCEEEEEEEECCCCC-----CCHHHhcCCCEEEe-
Confidence            44444556689999999999999985221     11222334456678899999988642     156677 4433322 


Q ss_pred             cCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeC
Q psy3760         198 DLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQ  276 (306)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~  276 (306)
                          .+.+...++|.+.|+...++....+.+..   ...|.+=+++---.. ..++..+|+.+   +.....+..|+.++
T Consensus       121 ----kyp~l~~~yf~~~gi~~~ii~l~GsvE~a---p~~GlADaIvDivsTG~TLraNgL~~i---e~I~~ssA~LI~n~  190 (289)
T 2vd3_A          121 ----EFPGITENYLREHGIDAEVVELTGSTEIA---PFIGVADLITDLSSTGTTLRMNHLRVI---DTILESSVKLIANR  190 (289)
T ss_dssp             ----SCHHHHHHHHHHTTCCCEEEECSSCGGGT---TTTTSCSEEEEEESSTHHHHHTTEEEE---EEEEEECEEEEECH
T ss_pred             ----CcHHHHHHHHHHcCCcEEEEECCCceeec---cCCCcccEEEEEeCChHHHHHCCCEEe---EEEEeeEEEEEEcc
Confidence                34567788999999977666555665544   334444344332111 11245677777   22445577788776


Q ss_pred             Ccc--ccHHHHHHHHHHhHHhhHH
Q psy3760         277 GTY--LRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       277 ~~~--~~~~~~~~~~~l~~~~~~~  298 (306)
                      ...  ....++.+++.++..+.++
T Consensus       191 ~s~~~k~~~i~~l~~rl~~v~~A~  214 (289)
T 2vd3_A          191 ESYATKSGIIEELRTGIRGVIDAE  214 (289)
T ss_dssp             HHHHHSHHHHHHHHHHHHHHHHTT
T ss_pred             chhhhHHHHHHHHHHHHHHHHHhc
Confidence            532  2356777777777765443

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=92.90  E-value=0.2  Score=38.63  Aligned_cols=44  Identities=14%  Similarity=0.089  Sum_probs=39.6

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |..+.|+.|++|..||..+++++-+.||+
T Consensus       177 t~re~~vl~~~~~G~-s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (237)
T 3szt_A          177 TARETEMLKWTAVGK-TYGEIGLILSIDQRTVKFHIVNAMRKLNS  220 (237)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            456778888888766 99999999999999999999999999997

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=92.88  E-value=0.23  Score=33.24  Aligned_cols=46  Identities=15%  Similarity=0.124  Sum_probs=36.6

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      -++-++|....-.|.|+...|+.+|+|.+||.+++.+..+.|...|
T Consensus        28 ~~~r~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   73 (113)
T 1xsv_A           28 NKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   73 (113)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            3455666666555669999999999999999999999888885544

>4euo_A ABC transporter, substrate binding protein (polya; class D of PBP, GABA-binding, transport protein; 1.28A {Agrobacterium tumefaciens} PDB: 4eq7_A

Probab=92.84  E-value=3  Score=33.31  Aligned_cols=193  Identities=10%  Similarity=0.072  Sum_probs=107.7

Q ss_pred             cEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcC--CeeEEEEcccc----------C--CCC-
Q psy3760          94 NLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRND--QADIAIVTEIL----------S--PSD-  156 (306)
Q Consensus        94 ~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~--~~Di~i~~~~~----------~--~~~-  156 (306)
                      +|+|..-.+.. ..+...++..|.+++ +++|++.. .....+...+..|  ..|+++.....          .  +.. 
T Consensus         2 ~l~v~~wgg~~~~~~~~~~~~~Fe~~~-gi~V~~~~~~~~~kl~a~~~~g~~~~Dv~~~~~~~~~~~~~~g~l~~l~~~~   80 (320)
T 4euo_A            2 DLVFSSWGGTTQDAQKAAWAEKFMVET-GINVLQDGPTDYGKLKAMVEANGVTWDVVDVEGDYAAQAGPKGLLEKLDFSV   80 (320)
T ss_dssp             CEEEECCCHHHHHHHHHHHHHHHHHHH-SCCEEEECCCCHHHHHHHHHTTCCCCSEEEEEHHHHHHHTTTTCBCCCCTTT
T ss_pred             eEEEEeCCCcHHHHHHHHHHHHHHHHH-CCEEEEeCCCCHHHHHHHHHcCCCCceEEEcCHHHHHHHHHCCCcccCChhh
Confidence            46776655433 334456889999988 89998875 3345566666665  48999864110          0  011 


Q ss_pred             -----------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCC-----CeEeec-CCCCcHH--------------
Q psy3760         157 -----------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY-----PLITYD-LSFSGRI--------------  205 (306)
Q Consensus       157 -----------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~-----~~i~~~-~~~~~~~--------------  205 (306)
                                 .....++.....+++.+++..  ...+-+++||.+.     .+.... +......              
T Consensus        81 ~~~~~~~~~~~~~y~~p~~~~~~~l~yn~~~~--~~~P~tw~dl~~~~~~~g~i~~~~~~~~~~~~~al~~~G~~~~~~~  158 (320)
T 4euo_A           81 IDKTKLDPRFVTDYSVGSFYYSFVIGCNVDSV--SACPKSWADLFDTAKFPGKRTFYKWSAPGVIEAALLADGVTADKLY  158 (320)
T ss_dssp             SCGGGBCGGGCBTTBEEEEEEEEEEEECGGGS--SCCCCSHHHHTCTTTSCSCEEEECSSSTTHHHHHHHHTTCCGGGCC
T ss_pred             CChhhCChhhcccceeeeeeeeEEEEEEhhhh--CCCCCCHHHHhChhhCCCcEEEeCCCchHHHHHHHHHcCCChhhcC
Confidence                       012345555677888887752  2256799999763     233433 2211110              


Q ss_pred             -----HHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc-eeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCC
Q psy3760         206 -----KLDREFSLQKLTPYIVLETINSDIIKTYVELRMG-IGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       206 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                           ...+++.  .+.+++ ...++.....+++.+|.. +++.....+...  ....+.... +. .....-+++..++
T Consensus       159 ~~~~~~a~~~l~--~l~~~~-~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~-~g-~~~~~~~~~i~k~  233 (320)
T 4euo_A          159 PLDLDRAFKKLD--TIKSDI-IWWSGGAQSQQLIASAEAPFGSVWNGRMTALEQSGVKVETSW-AQ-NITAADSLVVPKG  233 (320)
T ss_dssp             SCCHHHHHHHHH--TTGGGE-EEECSHHHHHHHHHTTSSCEEEEEHHHHHHHHHTTCCCEEEE-EE-EEEEEEEEECBTT
T ss_pred             HHHHHHHHHHHH--Hhhhce-eEeCCCchHHHHHHcCCEEEEEeecHHHHHHHhCCCCeEEEe-cC-ceeecceEEEECC
Confidence                 1112222  234555 344566778888888843 444333222222  233455444 22 2222334566777


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .....++++|++++.+.
T Consensus       234 s~~~e~A~~fi~fl~s~  250 (320)
T 4euo_A          234 TKNKDAAMKFIALATSA  250 (320)
T ss_dssp             CSCHHHHHHHHHHHTSH
T ss_pred             CCCHHHHHHHHHHHhCH
Confidence            77788999999999654

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=92.84  E-value=0.18  Score=38.79  Aligned_cols=44  Identities=9%  Similarity=-0.001  Sum_probs=38.8

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |....|+.|++|..||..+++++-+.||+
T Consensus       177 t~~e~~vl~~~~~g~-s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          177 SPREMLCLVWASKGK-TASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            446677787777766 99999999999999999999999999997

>3e13_X Putative iron-uptake ABC transport system, periplasmic iron-binding protein; beta sheet surrounded by alpha helices; 1.60A {Campylobacter jejuni} SCOP: c.94.1.1 PDB: 1y4t_A

Probab=92.75  E-value=3.1  Score=33.13  Aligned_cols=199  Identities=12%  Similarity=0.085  Sum_probs=108.5

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc-C---CeeEEEEcccc--C-----------CC
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN-D---QADIAIVTEIL--S-----------PS  155 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~-~---~~Di~i~~~~~--~-----------~~  155 (306)
                      ++|+|.....  ...+..++..|.+++ +++|++...++.++.+.|.. +   ..|+.+.....  .           ..
T Consensus         2 ~~l~v~~~~~--~~~~~~~~~~F~~~~-gi~V~~~~~~~~~~~~kl~a~~~~~~~Dv~~~~~~~~~~~~~~~g~l~~l~~   78 (322)
T 3e13_X            2 SELNIYSARH--YNADFEIIKKFEEKT-GIKVNHTQAKASELIKRLSLEGSNSPADIFITADISNLTEAKNLGLLSPVSS   78 (322)
T ss_dssp             CEEEEEECCC--CTHHHHHHHHHHHHH-CCEEEEEECCHHHHHHHHHHHGGGCCCCEEEESCHHHHHHHHHTTCEECCCC
T ss_pred             CEEEEEeCCC--HHHHHHHHHHHHHhh-CcEEEEEECCcHHHHHHHHHhccCCCCCEEEecCcHHHHHHHHCCCcccCCh
Confidence            4678877665  357888999999985 99999999888898888873 3   69999874211  0           00


Q ss_pred             CCc-------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCCCc-HHHHHHHHHhCC--
Q psy3760         156 DKL-------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSFSG-RIKLDREFSLQK--  215 (306)
Q Consensus       156 ~~~-------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~~~-~~~~~~~~~~~~--  215 (306)
                      ..+             ...++.....+++.+++.++....+-+|+||.+.    .+........+ ...+...+...|  
T Consensus        79 ~~~~~~~~~~~~~~~g~~~~~~~~~~~l~yn~~~~~~~~~p~tw~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~G~~  158 (322)
T 3e13_X           79 KYLEEFIPAHLRDKDKEWFAITKRARIIAYNKNTNIDISKMKNYEDLAKAEFKGEIVMRSATAPYSKTLLASIIANDGNK  158 (322)
T ss_dssp             HHHHHHSCGGGBCTTSSCEEEEEEEEEEEEETTSCCCCTTCCSGGGGGSGGGTTCEECCCTTSHHHHHHHHHHHHHHCHH
T ss_pred             hHhhhhchhhhCCCCCcEEEeeceeEEEEECCccccCCCCCCCHHHHhhhhhcCeEeecCCCCchhHHHHHHHHHhcCHH
Confidence            000             0123333467888888862333356799999763    23333332221 111111111111  


Q ss_pred             --------CceeEE-EEecCHHHHHHHHHhcc-ceeeeecceeccc----------ccCCceee-ecC--CCCccceEEE
Q psy3760         216 --------LTPYIV-LETINSDIIKTYVELRM-GIGIIASIAFDSN----------RDKNLRSI-SAS--HLFGTTISRV  272 (306)
Q Consensus       216 --------~~~~~~-~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~----------~~~~l~~~-~~~--~~~~~~~~~l  272 (306)
                              +..+.. ....+.....+++.+|. ++++...+.....          ....+..+ |-.  .........+
T Consensus       159 ~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~g~~~~~~~~  238 (322)
T 3e13_X          159 EAKAWAKGVLENLATNPKGGDRDQARQVFAGEAKFAVMNTYYIGLLKNSKNPKDVEVGNSLGIIFPNQDNRGTHINISGI  238 (322)
T ss_dssp             HHHHHHHHHHHHBSSSCCSSHHHHHHHHHHTSCSEEEEEHHHHHHHHTCSSHHHHHHHHTEEEECTTTTTTCBCEEEEEE
T ss_pred             HHHHHHHHHHHhcCcCCCCCcHHHHHHHHCCCCcEEeechHHHHHHHhccccchhccccceeEecCCCCCCCceeeeeee
Confidence                    001111 11234455567778884 4555433321111          01344444 221  1222233355


Q ss_pred             EEeCCccccHHHHHHHHHHhHH
Q psy3760         273 IIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       273 ~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ...++.....++++|++++.+.
T Consensus       239 ~i~~~s~~~~~A~~fi~fl~s~  260 (322)
T 3e13_X          239 AMTKSSKNQDAAKKFMEFMLSP  260 (322)
T ss_dssp             EEETTCSCHHHHHHHHHHHTSH
T ss_pred             EEecCCCCHHHHHHHHHHHhCH
Confidence            5667777788999999999654

>1gtk_A Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} SCOP: c.94.1.1 d.50.2.1 PDB: 1ah5_A* 2ypn_A* 1ypn_A* 1pda_A*

Probab=92.75  E-value=3.1  Score=33.15  Aligned_cols=184  Identities=15%  Similarity=0.050  Sum_probs=101.7

Q ss_pred             CcEEEEecccchhhhhHHHH-HHHHHhCCCcEEEEEeCC--------------------hhHHHHHHHcCCeeEEEEccc
Q psy3760          93 GNLTIATTHTQARYALPKII-KEFTIQFPKVKLSLLQGN--------------------PKQITEMIRNDQADIAIVTEI  151 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l-~~~~~~~p~~~i~~~~~~--------------------~~~~~~~l~~~~~Di~i~~~~  151 (306)
                      ..|+||+-.|-...+=...+ ..+.+.||++.++++...                    ..++.+.|.+|++|+++.+..
T Consensus         4 ~~irIgTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~i~d~pL~~iGgkGlFtkELe~aLl~g~iDiAVHSlK   83 (313)
T 1gtk_A            4 NVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMK   83 (313)
T ss_dssp             CEEEEEECCSHHHHHHHHHHHHHHHHHCTTCEEEEEECC-----------------CTTHHHHHHHHHTTSCSEEEEEGG
T ss_pred             ceEEEEeCCCHHHHHHHHHHHHHHHHhCCCCcEEEEeeecCCcccccccHHHcCCccchHHHHHHHHHcCCCcEEEecCC
Confidence            45999998775554444444 566677999999886532                    226779999999999998743


Q ss_pred             cC---CCCCcee--eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecC
Q psy3760         152 LS---PSDKLIS--IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN  226 (306)
Q Consensus       152 ~~---~~~~~~~--~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (306)
                      .-   .++++..  ++--.++.-++++++       ..++++|..--.|..+   +.|.. .++ .......+++-.-.|
T Consensus        84 DvPt~lp~gl~l~av~~RedprDalV~~~-------~~~l~~LP~Ga~VGTS---SlRR~-aQL-~~~rPdl~i~~lRGN  151 (313)
T 1gtk_A           84 DVPVEFPQGLGLVTICEREDPRDAFVSNN-------YDSLDALPAGSIVGTS---SLRRQ-CQL-AERRPDLIIRSLRGN  151 (313)
T ss_dssp             GSCSCCCTTEEEEEECCCCCCCEEEECSS-------CSSGGGCCTTCEEECC---CHHHH-HHH-HHHCTTSEEECCCSC
T ss_pred             CCCCCCCCCcEEEEEecCCCcceEEEECC-------CCChhhCCCCCEEecC---CHHHH-HHH-HHHCCCCEEEeCCCC
Confidence            22   2334332  222223333333322       2367777655555543   34332 222 333334455556689


Q ss_pred             HHHHHHHHHhccceeee-ecceeccc-ccCCce-eeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         227 SDIIKTYVELRMGIGII-ASIAFDSN-RDKNLR-SISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       227 ~~~~~~~v~~g~gi~~~-p~~~~~~~-~~~~l~-~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      +++=+.-+..|..=+++ ..--.... ....+. .++.+.   .+-+.-+.+-++.+   +..+..+++.+
T Consensus       152 V~TRL~KL~~g~~DaiiLA~AGL~RLgl~~~i~~~l~~~~~lPA~gQGalaIe~r~~---d~~~~~ll~~l  219 (313)
T 1gtk_A          152 VGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLD---DSRTRELLAAL  219 (313)
T ss_dssp             HHHHHHHHHTTSCSEEEEEHHHHHHTTCGGGCSEECCTTTSCCCTTTTCEEEEEETT---CHHHHHHHGGG
T ss_pred             HHHHHHHhhCCCCCEEEHhhhHHHHcCCccccceeeChhhcCCCcCCceEEEEEccC---cHHHHHHHHHC
Confidence            99999999998544443 22212222 122222 345443   12256777777765   34455555444

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=92.70  E-value=0.69  Score=36.43  Aligned_cols=60  Identities=8%  Similarity=0.101  Sum_probs=41.1

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHH
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAIL   67 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~   67 (306)
                      +-|.++-.+++.+  .|++.-|+.++++.||+.|.++.|++. |.  ..|++ ++. +|++.-..+-
T Consensus        31 Ral~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~tL~~~-G~--v~~~~~~~Y-~LG~~~~~lg   93 (275)
T 3mq0_A           31 RAVRILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLAVMTEL-DL--LARSADGTL-RIGPHSLRWA   93 (275)
T ss_dssp             HHHHHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHHHHHHT-TS--EEECTTSEE-EECTHHHHHH
T ss_pred             HHHHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC--EEECCCCcE-EehHHHHHHH
Confidence            3455666666643  379999999999999999999999974 44  45554 345 7887654443

>2b4l_A Glycine betaine-binding protein; substrate-binding protein, closed liganded, ABC-transporter, compatible solutes, transport protein; 2.00A {Bacillus subtilis} PDB: 2b4m_A* 3chg_D

Probab=92.69  E-value=0.73  Score=36.15  Aligned_cols=108  Identities=13%  Similarity=0.114  Sum_probs=70.8

Q ss_pred             HHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcEEEEecc
Q psy3760          22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTH  101 (306)
Q Consensus        22 aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~l~I~~~~  101 (306)
                      .=+.+.+|...++..+.+++ + |.           .+-+.++.++..=..+++.+-.      .........|+||...
T Consensus       113 ~L~~~~lt~~~~~~l~~~v~-~-~~-----------~~~~vA~~wl~~~~~~~~~W~~------~~~~~~~~~I~ig~~~  173 (268)
T 2b4l_A          113 LLSQFKWTQDEMGEIMIKVE-E-GE-----------KPAKVAAEYVNKHKDQIAEWTK------GVQKVKGDKINLAYVA  173 (268)
T ss_dssp             HHHTCCCCHHHHHHHHHHHH-T-TC-----------CHHHHHHHHHHHCHHHHHHHTT------TCCCCSSCEEEEEECC
T ss_pred             HHHhcCCCHHHHHHHHHHHH-c-CC-----------CHHHHHHHHHHHCHHHHHHHhC------ccccccCcceEEEccC
Confidence            33445577777766666655 2 21           2444555555444444444332      3334455689999998


Q ss_pred             cchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEc
Q psy3760         102 TQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT  149 (306)
Q Consensus       102 ~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~  149 (306)
                      .-....+..++..+.+.. ++++++...++....+.|.+|++|+....
T Consensus       174 w~e~~~~~~v~~~~Le~~-Gy~Ve~~~~~~~~~~~al~~G~iD~~~e~  220 (268)
T 2b4l_A          174 WDSEIASTNVIGKVLEDL-GYEVTLTQVEAGPMWTAIATGSADASLSA  220 (268)
T ss_dssp             CHHHHHHHHHHHHHHHHH-TCEEEEEECCTTHHHHHHHHTSSSEEEEE
T ss_pred             ccHHHHHHHHHHHHHHHc-CCceEEEECChHHHHHHHHCCCCeEEehh
Confidence            777677777776666654 88888877777778999999999998654

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=92.62  E-value=0.45  Score=32.95  Aligned_cols=53  Identities=13%  Similarity=0.073  Sum_probs=37.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      ...+.+.+.|.|.+++|+.+|+|.+||.+.+++.++. |..  .+.++.- .+|+.-
T Consensus        13 ~~i~~~~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~-g~~--~~~gr~~-~l~~~~   65 (141)
T 1u78_A           13 AQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSY-GTS--KRAPRRK-ALSVRD   65 (141)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSGGGT-TCC--CCCCCCC-SSCHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHccccc-CCc--CCCCCCC-cCCHHH
Confidence            3344455666699999999999999999999987653 432  2345555 577643

>4h1x_A PBP 2, phosphate-binding protein PSTS 2; periplasmic binding protein, PF12849 family; HET: MSE CIT; 1.77A {Streptococcus pneumoniae}

Probab=92.57  E-value=1.2  Score=34.91  Aligned_cols=103  Identities=13%  Similarity=0.124  Sum_probs=66.7

Q ss_pred             eEeecCCCCcHHHHHHHHHhCCC--------ceeEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCC-
Q psy3760         194 LITYDLSFSGRIKLDREFSLQKL--------TPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASH-  263 (306)
Q Consensus       194 ~i~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~-  263 (306)
                      .+..+.+++.+..|.+.+...+.        ........++...+.+.|.+. .+|+++....+.    ..+..++++. 
T Consensus        13 vv~R~~~SGT~~~F~e~v~~~~~~~~~~~~~~~~~~~~~~~~~~vv~~Va~~~~AIGY~~~~y~~----~~vk~l~idgV   88 (265)
T 4h1x_A           13 VISRENGSGTRGAFTEITGILKKDGDKKIDNTAKTAVIQNSTEGVLSAVQGNANAIGYISLGSLT----KSVKALEIDGV   88 (265)
T ss_dssp             EEEECTTCHHHHHHHHHHTCEEESSSCEEECCCTTCEEESSHHHHHHHHHHCTTEEEEEEGGGCC----TTSEECEETTB
T ss_pred             EEeCCCCCcHHHHHHHHHhhhCccccccccccCccceeeCCcHHHHHHHHcCCCcEEEeehHHhh----cccccceeccc
Confidence            44555666778888877642210        112234567777888888776 789998876553    3466666543 


Q ss_pred             -----------CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         264 -----------LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       264 -----------~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                                 .+..+++|++.+.+  .++.++.|++++.+.-.+..+++
T Consensus        89 ~Pt~e~i~~g~YPlsRply~y~~~~--~~~~vk~Fl~f~lS~~GQ~iv~~  136 (265)
T 4h1x_A           89 KASRDTVLDGEYPLQRPFNIVWSSN--LSKLGQDFISFIHSKQGQQVVTD  136 (265)
T ss_dssp             CCSHHHHHTTCSCSEEEEEEEECTT--CCHHHHHHHHHHHBHHHHHHHHH
T ss_pred             CcchhhhhcCCCCeEEEEEEEECCC--CCHHHHHHHHHHhhcccceeeec
Confidence                       13467888887654  48999999999986555555544

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=92.52  E-value=0.33  Score=31.57  Aligned_cols=39  Identities=15%  Similarity=0.126  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +++.-..+..|.+-...|++||+|.++||+.|++-.+.+
T Consensus        24 ~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~   62 (101)
T 2w7n_A           24 IEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAF   62 (101)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            344445566667999999999999999999999998886

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=92.45  E-value=0.64  Score=32.18  Aligned_cols=73  Identities=11%  Similarity=0.029  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGK   85 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~   85 (306)
                      |+|+.  .=+. |.++-|+.||+|.+++-..|..||.+==++=+.|++..++.+.+.  .   +..++.+-.+++...+.
T Consensus        17 LE~Lk--~G~~-~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~ayw~L~~s--~---y~~kV~dilrel~~~l~   88 (165)
T 2vxz_A           17 LALLA--DGCK-TTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVALVCLSMD--Q---YRQLVDGMIREVERLVT   88 (165)
T ss_dssp             HHHHT--TCCE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEEEEESCHH--H---HHHHHHHHHHHHHHHHH
T ss_pred             HHHHH--hCCc-cHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEEEEEecHH--H---HHHHHHHHHHHHHHHHH
Confidence            44444  4455 889999999999999999999999998888888888777777655  2   22344444444444444


Q ss_pred             h
Q psy3760          86 E   86 (306)
Q Consensus        86 ~   86 (306)
                      .
T Consensus        89 s   89 (165)
T 2vxz_A           89 T   89 (165)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=92.07  E-value=0.37  Score=35.25  Aligned_cols=52  Identities=15%  Similarity=0.296  Sum_probs=37.0

Q ss_pred             HhcCCHHHHHHHh--------CCCchHHHHHHHHHHHHcCceeEEe--------cCCCccccCHhHHHHHHH
Q psy3760          14 RQNFNLTEAAKAL--------YTSQPGVSKAIIELEEELSIDIFIR--------HGKRIRGLTKPGQAILRS   69 (306)
Q Consensus        14 ~~~~s~~~aA~~l--------~isq~~~s~~i~~LE~~lg~~Lf~R--------~~~~~~~lT~~G~~l~~~   69 (306)
                      +-. +...-++.+        ++|+++|++.+++||+. |  |+.+        .++.+.++|+.|+..+..
T Consensus        14 ~~~-~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~-G--lI~~~~~~~~~~~~r~~Y~lT~~G~~~l~~   81 (179)
T 1yg2_A           14 RDA-TGYDITKEFSASIGYFWKASHQQVYRELNKMGEQ-G--LVTCVLEPQEGKPDRKVYSITQAGRSALGE   81 (179)
T ss_dssp             CCB-CHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHT-T--SEEECCC---------CEEECHHHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHC-C--CeEEEeecCCCCCCceEEEeChHHHHHHHH
Confidence            344 777888888        79999999999999985 2  2221        123334899999997765

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=92.00  E-value=0.47  Score=31.79  Aligned_cols=51  Identities=16%  Similarity=0.032  Sum_probs=34.1

Q ss_pred             hCCCchHHHHHHHHHHHHcCceeEEe-c------CCCccccCHhHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEELSIDIFIR-H------GKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~Lf~R-~------~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +++|+++|+..|++||++ |.-=-.. .      ++...++|+.|+..++...+-...+
T Consensus        52 ~~is~gtLY~~L~rLe~~-GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~~~~  109 (115)
T 2dql_A           52 YRLSDTVLYSAIKFLEDN-RAITGYWKKLEGRGRPRRMYQVSPEWQHQAEDLARLWQNY  109 (115)
T ss_dssp             EECCHHHHHHHHHHHHHT-TSEEEEEECCTTCSSCEEEEEECGGGHHHHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHC-CCEEEEeeecCCCCCCcEEEEECHHHHHHHHHHHHHHHHH
Confidence            479999999999999985 2211111 1      1223489999999888765444433

>1z7m_E ATP phosphoribosyltransferase; ATP-PRT, histidine biosynthesis, hiszg, alloste evolution; 2.90A {Lactococcus lactis} SCOP: c.94.1.1 PDB: 1z7n_E*

Probab=91.99  E-value=0.56  Score=35.03  Aligned_cols=153  Identities=11%  Similarity=0.147  Sum_probs=89.5

Q ss_pred             EEEEEeCChhHHHHHHHcCCeeEEEEcccc---C---CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEe
Q psy3760         123 KLSLLQGNPKQITEMIRNDQADIAIVTEIL---S---PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT  196 (306)
Q Consensus       123 ~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~---~---~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~  196 (306)
                      .+++.-....++..-+..|.+|+||+....   .   +-..+.-..++.-++++.+|++.+.       ++++.+....+
T Consensus        43 ~i~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~~v~el~dLgfG~crl~vAvp~~~~~-------~~~~~~~RIAT  115 (208)
T 1z7m_E           43 DLQIIFGKPNDVITFLEHGIVDIGFVGKDTLDENDFDDYYELLYLKIGQCIFALASYPDFSN-------KNFQRHKRIAS  115 (208)
T ss_dssp             SCCEEEECHHHHHHHHHTTSCSEEEEEHHHHHHSSCCCEEEEEEETTCCCEEEEEECGGGGG-------CCCSSCEEEEE
T ss_pred             CEEEEEECchhHHHHHhCCCccEEEeeeeeeeecCCCCeEEeeccccCCEEEEEEEECCCcc-------chhcCCCEEEE
Confidence            455666667899999999999999985221   1   1122233445677899999887643       22332222221


Q ss_pred             ecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEe
Q psy3760         197 YDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIK  275 (306)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~  275 (306)
                           .+.+...++|.+.|+...++....+.+..   ..-|.+=+++---.. ..++..+|+.+.   .....+..|+.+
T Consensus       116 -----kyp~l~~~yf~~~gi~~~ii~l~GsvE~a---p~~GlAD~IvDivsTG~TLr~NgL~~ie---~I~~ssA~LI~n  184 (208)
T 1z7m_E          116 -----KYPRVTKKYFAQKQEDIEIIKLEGSVELG---PVVGLADAIVDIVETGNTLSANGLEVIE---KISDISTRMIVN  184 (208)
T ss_dssp             -----SCHHHHHHHHHHTTCCEEEEECSSCTTHH---HHTTSCSEEEEEESSSHHHHTTTCEEEE---EEEECCEEEEEE
T ss_pred             -----CchHHHHHHHHHcCCceEEEECCCceeec---cCCCcccEEEEEeCChHHHHHCCCEEeE---EEEeeEEEEEEc
Confidence                 34567788999999987666555666554   444544444433211 223567788774   234557788877


Q ss_pred             CCccc--cHHHHHHHHHHhH
Q psy3760         276 QGTYL--RSYVYSFIKLLSP  293 (306)
Q Consensus       276 ~~~~~--~~~~~~~~~~l~~  293 (306)
                      +....  ...++.+++.++.
T Consensus       185 ~~s~~~k~~~i~~l~~rl~~  204 (208)
T 1z7m_E          185 KSSFKFKKDKIIEMVERLED  204 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHCC
T ss_pred             chHhHHHHHHHHHHHHHHHH
Confidence            65421  2334444444443

>2nxo_A Hypothetical protein SCO4506; PFAM, DUF178, NYSGXRC, 10093F, PSI-2, structural genomics, protein structure initiative; 2.04A {Streptomyces coelicolor} SCOP: c.94.1.1

Probab=91.97  E-value=0.59  Score=37.12  Aligned_cols=117  Identities=14%  Similarity=0.120  Sum_probs=61.7

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeec---cccc
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIP---CYQW  166 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~---l~~~  166 (306)
                      ...||||..+.....   +++..+.+.+-...+++...+..++.+.|.+|++|++.++....  ....+...+   +...
T Consensus         6 ~~~lriG~~~~~~~~---pl~~a~~~g~~~~~~~~~~~~~~~l~~al~~G~iDia~~~~~~~~~~~~~~~il~~~~~~~~   82 (291)
T 2nxo_A            6 RTRPRVGHIQFLNCL---PLYWGLARTGTLLDFELTKDTPEKLSEQLVRGDLDIGPVTLVEFLKNADDLVAFPDIAVGCD   82 (291)
T ss_dssp             -CCCEEEEECSGGGH---HHHHHHHHTSGGGGCEEEEECHHHHHHHHHTTSCSEEEEEHHHHHHTGGGEEEEEEEEEEES
T ss_pred             cCCeEEEEecCCCch---hhHHHHHhCCCCCCeEEEECCHHHHHHHHHcCCCCEeehhHHHHHhCcccEEEcCCcccccc
Confidence            347999998874432   22223333331234444566778899999999999998752110  011121111   1111


Q ss_pred             eE---EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHH-HHHHHHhC-CCceeEE
Q psy3760         167 EY---VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK-LDREFSLQ-KLTPYIV  221 (306)
Q Consensus       167 ~~---~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~-~~~~~~~~-~~~~~~~  221 (306)
                      ..   ++++++       .  +++||.+.+......+ ..... +..++++. |+.++.+
T Consensus        83 g~~~sv~lv~~-------~--~i~DLkGKkIav~~~s-~t~~~ll~~ll~~~~Gl~~~~v  132 (291)
T 2nxo_A           83 GPVMSCVIVSQ-------V--PLDRLDGARVALGSTS-RTSVRLAQLLLSERFGVQPDYY  132 (291)
T ss_dssp             SCCSSEEEEES-------S--CTTSCSSSEEEEETTC-SHHHHHHHHHHHHTSCCCCEEE
T ss_pred             CCceEEEEEeC-------C--CHHHhCCCEEEeCCCC-hHHHHHHHHHHHHhhCCCCeEE
Confidence            00   122222       1  2378988877766544 44344 44566665 8877544

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

Probab=91.83  E-value=0.13  Score=31.65  Aligned_cols=26  Identities=19%  Similarity=0.029  Sum_probs=24.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |+..-|+.+++|.+|+-+.|+.||+.
T Consensus        26 sv~EIa~~lgvS~~TVrr~L~~Le~k   51 (77)
T 2jt1_A           26 KTRDIADAAGLSIYQVRLYLEQLHDV   51 (77)
T ss_dssp             EHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            58999999999999999999999986

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=91.79  E-value=0.13  Score=30.41  Aligned_cols=21  Identities=29%  Similarity=0.169  Sum_probs=18.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++...|+.+|+|++|||+.|.
T Consensus         2 T~~diA~~aGVS~sTVSrvLn   22 (65)
T 1uxc_A            2 KLDEIARLAGVSRTTASYVIN   22 (65)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHc
Confidence            578899999999999999873

>1ve4_A ATP phosphoribosyltransferase; riken structural genomics/proteomics initiative structural genomics; 1.20A {Thermus thermophilus} SCOP: c.94.1.1

Probab=91.77  E-value=2.9  Score=31.07  Aligned_cols=148  Identities=12%  Similarity=0.105  Sum_probs=87.5

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEcccc---C--CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEIL---S--PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD  198 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~---~--~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~  198 (306)
                      +++.-....++..-+..|.+|+||+..+.   .  +-..+.-..++.-++++.+|++.          +++ +....+  
T Consensus        47 i~~~~~R~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~el~dLgfG~crl~vAvp~~~----------~~~-~~RIAT--  113 (206)
T 1ve4_A           47 VALLELRNKDVPIYVDLGIAEIGVVGKDVLLDSGRDLFEPVDLGFGACRLSLIRRPGD----------TGP-IRRVAT--  113 (206)
T ss_dssp             EEEEEECGGGHHHHHHTTSSSEEEEEHHHHHHCCSCCEEEEECCCSCEEEEEEECTTC----------CSC-CCEEEE--
T ss_pred             eEEEEECchhHHHHHhCCCccEEEeeeeeeeecCCCeEEeeccccCcEEEEEEEECCc----------ccC-CCEEEE--
Confidence            45555567799999999999999985221   1  11223334455778888888764          233 222222  


Q ss_pred             CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCC
Q psy3760         199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                         .+.+...++|.+.|+...++....+.+..   ..-|.+=+++---.. ..++..+|+.+.   .....+..|+.++.
T Consensus       114 ---kyp~l~~~yf~~~gi~~~ii~l~GsvE~a---p~~GlAD~IvDivsTG~TLraNgL~~ie---~I~~ssA~LI~n~~  184 (206)
T 1ve4_A          114 ---KYPNFTARLLKERGWAADVVELSGNIELA---AVTGLADAVVDVVQTGATLRAAGLVEVE---VLAHSTARLVVNRQ  184 (206)
T ss_dssp             ---SCHHHHHHHHHHTTCCCEEEECSSCTHHH---HHTTSSSEEEEEESSSHHHHHTTCEEEE---EEEEECEEEEECHH
T ss_pred             ---CchHHHHHHHHHCCCcEEEEECCCceeec---cCCCCceEEEEeccCHHHHHHCCCEEeE---EEEeeEEEEEEcch
Confidence               34567788999999987766666666654   444544444433211 122456787773   23455777887665


Q ss_pred             cc--ccHHHHHHHHHHhH
Q psy3760         278 TY--LRSYVYSFIKLLSP  293 (306)
Q Consensus       278 ~~--~~~~~~~~~~~l~~  293 (306)
                      ..  ....++.+++.++.
T Consensus       185 s~~~k~~~i~~l~~rl~~  202 (206)
T 1ve4_A          185 ALKLKRAVLKPLIQRLRE  202 (206)
T ss_dssp             HHHHTHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHH
Confidence            32  12345555555544

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=91.74  E-value=0.24  Score=38.03  Aligned_cols=44  Identities=11%  Similarity=0.103  Sum_probs=38.4

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |....|+.|++|..||..+++++-+.||+
T Consensus       175 t~~e~~vl~~~~~g~-s~~eIa~~l~is~~tV~~~~~~~~~kl~~  218 (234)
T 1l3l_A          175 DPKEATYLRWIAVGK-TMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_dssp             CHHHHHHHHHHTTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            345677777777665 99999999999999999999999999997

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=91.34  E-value=0.38  Score=37.74  Aligned_cols=45  Identities=16%  Similarity=0.140  Sum_probs=40.1

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |..+.|+.|++|..||..+++++-+.||+.
T Consensus       199 t~re~~vl~~~~~G~-s~~eIA~~l~is~~TV~~~~~~~~~kl~~~  243 (265)
T 3qp6_A          199 SQREYDIFHWMSRGK-TNWEIATILNISERTVKFHVANVIRKLNAN  243 (265)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            456788888888766 999999999999999999999999999873

>4gl0_A LMO0810 protein; structural genomics, IDP05673, spermidine, putrescine, ABC transporter, niaid; HET: MSE PGE PG4; 1.92A {Listeria monocytogenes}

Probab=91.33  E-value=1.7  Score=35.05  Aligned_cols=197  Identities=16%  Similarity=0.147  Sum_probs=103.9

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcC--CeeEEEEccc----------c--CCC
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRND--QADIAIVTEI----------L--SPS  155 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~--~~Di~i~~~~----------~--~~~  155 (306)
                      ..++|+|..=.   .++-+.++..|.+++ +++|++...+ .+++...|..|  ..|+++....          .  .+.
T Consensus         9 ~~~~L~vy~W~---~y~~~~~i~~Fek~t-GIkV~~~~~~s~e~~~~kl~ag~~~~DVv~~~~~~~~~~~~~gll~~ld~   84 (333)
T 4gl0_A            9 GSNTLTIYNWG---DYIDPSLITKFEKET-GIKVIYQTFDSNEAMMTKIEQGGTTFDIAVPSDYAISKMKEENLLIPLDH   84 (333)
T ss_dssp             -CCEEEEEEET---TCSCHHHHHHHHHHH-CCEEEEEEESCHHHHHHHHHTCSSCCSEECCBHHHHHHHHHTTCBCCCCG
T ss_pred             CCCEEEEEeCC---ccCCHHHHHHHHHHH-CCEEEEEeCCCHHHHHHHHHcCCCCCeEEEeCHHHHHHHHHcCCcccccc
Confidence            35689998632   233467899999998 8999987754 44577788776  5799874310          0  000


Q ss_pred             --------------------CCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCCC---------
Q psy3760         156 --------------------DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSFS---------  202 (306)
Q Consensus       156 --------------------~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~~---------  202 (306)
                                          .+....+..-...+++..++. +....+-+++||.+-.    ....+....         
T Consensus        85 ~~~~n~~~~~~~~~~~~~~~~~~y~vp~~~~~~~i~yn~~~-~~~~~~~sw~dl~dp~~kg~~~~~~~~~~~~~~a~~~~  163 (333)
T 4gl0_A           85 SKLPNEKYLDPRFMDLSFDDDNKYSMPYFWGTLGIIYNKEM-FPDKNFDTWNALFDPELKNQILLIDGAREVMGLGLNSL  163 (333)
T ss_dssp             GGCGGGGGBCGGGSSCGGGGGGSSEEEEEEEEEEEEEETTT-CTTCCTTSGGGGGCGGGTTCEEEESCHHHHHHHHHHHT
T ss_pred             ccccccccCCHHHhhhccCCCCceEeceeeeeeeeeechhh-cccCCcccHHhhcCHHhhhccccCCcHHHHHHHHHHHH
Confidence                                012234455556677777765 2333455788886522    333222110         


Q ss_pred             -------cHHHHHHHHHh-CCCceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc--ccCCceeeecCCCCccceEE
Q psy3760         203 -------GRIKLDREFSL-QKLTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN--RDKNLRSISASHLFGTTISR  271 (306)
Q Consensus       203 -------~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~  271 (306)
                             ....+...... ....++.....+  .....++..| ..+++.........  ....+..+-..+......-+
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~Ge~~~~~~~~~~~~~~~~~~~~~~~~~p~eG~~~~~~~  241 (333)
T 4gl0_A          164 GYSLNDTNKAHLQAARDKLETMTPNVKAIVG--DEIKLLMADNEAGVAVTFSGEAAEMLSENEDLEYVIPKDGSNLWFDN  241 (333)
T ss_dssp             TCCTTCCCHHHHHHHHHHHHHHGGGEEEEES--TTHHHHTSCC-CCEEEEEHHHHHHHHHHCTTEEEECCSSCEEEEEEE
T ss_pred             hhcccCCCHHHHHHHHHHHHhhccccceecc--hhhhhhhhccchheehhhhHHHHHHHhhccccccccCCCCCccccce
Confidence                   00111111110 011223322222  2334555666 44444444332222  33445544433333333445


Q ss_pred             EEEeCCccccHHHHHHHHHHhHH
Q psy3760         272 VIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       272 l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ++..++.+...++++|++++.+-
T Consensus       242 ~~I~k~a~n~e~A~~fi~fllsp  264 (333)
T 4gl0_A          242 MVIPKTAKNVDGAHKFINFMLKP  264 (333)
T ss_dssp             EECBTTCSCHHHHHHHHHHHHSH
T ss_pred             EEEEcCCCCHHHHHHHHHHhcCH
Confidence            66688888899999999998653

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=91.27  E-value=0.38  Score=29.05  Aligned_cols=42  Identities=7%  Similarity=0.053  Sum_probs=31.2

Q ss_pred             hhHHHHHHHHH----hcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760           4 HQFRFVREAVR----QNFNLTEAAKALYTSQPGVSKAIIELEEELS   45 (306)
Q Consensus         4 ~~l~~f~~v~~----~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg   45 (306)
                      ++-++|....-    .|.|+...|+.+|+|.++|.+.+.+.-+.|.
T Consensus        14 ~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A           14 REAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             HHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            34455555552    3449999999999999999997777666664

>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane, glycoprotein, transport, membrane, postsynaptic cell membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus norvegicus}

Probab=91.21  E-value=1.8  Score=39.91  Aligned_cols=70  Identities=16%  Similarity=0.095  Sum_probs=47.4

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCC-------------hhHHHHHHHcCCeeEEEEccccCC--CCCce-eeccccceEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGN-------------PKQITEMIRNDQADIAIVTEILSP--SDKLI-SIPCYQWEYV  169 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~-------------~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~-~~~l~~~~~~  169 (306)
                      .+...++..+.+.. +.++++....             .+.++..|.+|++|+++.......  ...+. +.|.....++
T Consensus       414 G~~~dl~~~~a~~l-~~~~~~~~~~~~~~g~~~~~~g~~~~~~~~l~~~~~D~~~~~~~~t~~R~~~~dfs~py~~~~~~  492 (823)
T 3kg2_A          414 GYCVDLAAEIAKHC-GFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS  492 (823)
T ss_dssp             SHHHHHHHHHHHHH-TCCEEEEECSSCCCCCBCTTTCCBCHHHHHHHTTSCSEECSCCBCCHHHHTTEEECSCSEEECEE
T ss_pred             EEHHHHHHHHHHHc-CCcEEEEEccCCcccccCCCCCchhhHHHhhccccCcEEecceecchhheeeEEeccchhhCCEE
Confidence            35567788887765 5566666643             678999999999999987422111  12233 4577788888


Q ss_pred             EEecCCC
Q psy3760         170 IIVPLDH  176 (306)
Q Consensus       170 ~v~~~~~  176 (306)
                      +++++..
T Consensus       493 ~~v~~~~  499 (823)
T 3kg2_A          493 IMIKKPQ  499 (823)
T ss_dssp             EEEECCC
T ss_pred             EEEECCC
Confidence            8887754

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=91.12  E-value=0.43  Score=32.68  Aligned_cols=39  Identities=10%  Similarity=0.065  Sum_probs=31.7

Q ss_pred             hhHHHHHHHHHh-------cCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQ-------NFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~-------~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .++.+++.+...       - |.+.-|+.+++|.+++++.|+.||+.
T Consensus        33 ~e~~vll~L~~~~~~~~~~p-s~~~LA~~l~~s~~~V~~~l~~Le~k   78 (128)
T 2vn2_A           33 GELVLLLHMQSFFEEGVLFP-TPAELAERMTVSAAECMEMVRRLLQK   78 (128)
T ss_dssp             HHHHHHHHHHHHHTTTCSSC-CHHHHHHTSSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            445555566543       4 89999999999999999999999985

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=91.05  E-value=1.4  Score=30.19  Aligned_cols=44  Identities=14%  Similarity=0.164  Sum_probs=34.4

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ   64 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~   64 (306)
                      |...-|+.+++|+++|.++++.|+++ |. +-.+.++|. ..++...
T Consensus        30 se~~La~~~gvSr~tVr~Al~~L~~~-Gl-i~~~~g~G~-~V~~~~~   73 (129)
T 2ek5_A           30 STNELAAFHRINPATARNGLTLLVEA-GI-LYKKRGIGM-FVSAQAP   73 (129)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHTT-TS-EEEETTTEE-EECTTHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-Cc-EEEecCCEE-EEecCch
Confidence            67789999999999999999999976 65 444556776 4666543

>3rpw_A ABC transporter; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; HET: MSE; 1.65A {Rhodopseudomonas palustris}

Probab=90.95  E-value=5.6  Score=32.39  Aligned_cols=199  Identities=6%  Similarity=-0.088  Sum_probs=111.7

Q ss_pred             CCCcEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeC--ChhHHHHHHHcC--CeeEEEEcccc-----------CC
Q psy3760          91 DTGNLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQG--NPKQITEMIRND--QADIAIVTEIL-----------SP  154 (306)
Q Consensus        91 ~~~~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~--~~~~~~~~l~~~--~~Di~i~~~~~-----------~~  154 (306)
                      ..++|+|....+ ....+...++..|.++ ++++|++...  ....+...+..|  ..|+.+.....           .+
T Consensus        31 ~~~~l~v~~~~~~~~~~~~~~~~~~Fe~~-~gi~V~~~~~~~~~~kl~~~~~~g~~~~Dv~~~~~~~~~~~~~g~l~~l~  109 (365)
T 3rpw_A           31 QSNVVIMQDPGGGYGDALRKVMYDPFEKE-TGIKVVTVQEARSGPRIKAQAEAGKAQWDLTFIFDQETKLLGDCCLADID  109 (365)
T ss_dssp             CCSEEEEEECCHHHHHHHHHHTHHHHHHH-HSCEEEEEECSCCHHHHHHHHHHTCCCCSBEEECHHHHHHTHHHHBCCCC
T ss_pred             cCCeEEEEecCCchhHHHHHHHHHHHHHh-hCCEEEEecCCCcHHHHHHHHHcCCCCceEEEcCHHHHHHHhCCCcccCC
Confidence            456899988764 3345677899999998 6999999876  344555566566  37999874210           00


Q ss_pred             CC-----------C-------ceeeccccceEEEEecCCCCCCCCCCcChhhhcCC-----CeEeecCCCCcH-------
Q psy3760         155 SD-----------K-------LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY-----PLITYDLSFSGR-------  204 (306)
Q Consensus       155 ~~-----------~-------~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~-----~~i~~~~~~~~~-------  204 (306)
                      ..           +       ....+......+++.+++..-....+-+|+||.+.     ......+.....       
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~l~ynk~~~~~~~~P~tw~dl~~~~~~~g~~~~~~~~~~~~~~~~~~~  189 (365)
T 3rpw_A          110 YSKLSESAHKTLAAMPDNLKRKKGVALQVIGVGLVYNKDKFKGDKAPQTWADFWDVKKFPGRRCMPAWPRFTFEAALMAD  189 (365)
T ss_dssp             GGGSCHHHHHHHHTSCGGGEETTEEEEEEEEEEEEEETTTSCTTSSCCSHHHHHCTTTSCSCEEEESSSTTHHHHHHHHT
T ss_pred             hhhcCchhhhhhhhcCccccCCeEEeeeeeeEEEEEEhhhcCCCCCCCCHHHHhChhhCCCceeCCcCchHHHHHHHHHc
Confidence            00           1       11345555677888888864222356799999664     233333221110       


Q ss_pred             ------------HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc--ccCCceeeecCCCCccce
Q psy3760         205 ------------IKLDREFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN--RDKNLRSISASHLFGTTI  269 (306)
Q Consensus       205 ------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~  269 (306)
                                  ....++++.  +.++......+.....+++.+|. .+++.....+...  ....+.... +. .....
T Consensus       190 g~~~~~~~~~~~~~a~~~l~~--l~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~-pg-~~~~~  265 (365)
T 3rpw_A          190 GVTKDKLYPIDMDRALKKLKE--IKPHVVKWWTTAAQPPQLILDGEADMCLAYTGSMSKLALEGAPIDLTF-NQ-GFVYY  265 (365)
T ss_dssp             TCCTTSCCSCCHHHHHHHHHH--HGGGEEEEECSTTHHHHHHHTTSCSEEEEEHHHHHHHHHHTCSEEEEE-EE-EEEEE
T ss_pred             CCChhhcCchhHHHHHHHHHH--HhhhcccccCCccHHHHHHHcCCeEEEEehhHHHHHHHhCCCCeEEee-CC-eeeec
Confidence                        111122222  23444334455556778888884 3444433332222  223344333 22 22223


Q ss_pred             EEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         270 SRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       270 ~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      -++...++.....++++|++++.+.
T Consensus       266 ~~~~i~k~s~~~~~A~~fi~~l~s~  290 (365)
T 3rpw_A          266 DFFSIPKGAPNYDNALKLLSWRLDP  290 (365)
T ss_dssp             EEEECBTTCTTHHHHHHHHHHHTCH
T ss_pred             eEEEEECCCCCHHHHHHHHHHHcCH
Confidence            3455577777788999999998653

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

Probab=90.94  E-value=0.52  Score=29.63  Aligned_cols=44  Identities=9%  Similarity=0.069  Sum_probs=33.3

Q ss_pred             hHHHHHHHHH----hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760           5 QFRFVREAVR----QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI   48 (306)
Q Consensus         5 ~l~~f~~v~~----~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L   48 (306)
                      +-++|....-    .|.|+...|+.||+|.++|.+.+.+.-..|...+
T Consensus        23 er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l   70 (87)
T 1tty_A           23 EAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPS   70 (87)
T ss_dssp             HHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTB
T ss_pred             HHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3445555442    3449999999999999999999998888885543

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=90.70  E-value=0.36  Score=29.37  Aligned_cols=26  Identities=8%  Similarity=0.184  Sum_probs=21.6

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      .+.+.|.|..+-|+.+|+|+++||+.
T Consensus        17 ~l~~~glT~~~LA~~~Gvs~stls~~   42 (74)
T 1neq_A           17 GLKKRKLSLSALSRQFGYAPTTLANA   42 (74)
T ss_dssp             HHHTTSCCHHHHHHHHSSCHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence            34466679999999999999999954

>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=90.34  E-value=0.86  Score=29.20  Aligned_cols=47  Identities=9%  Similarity=0.022  Sum_probs=37.3

Q ss_pred             chhhHHHHHHHHHhcCC----HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec
Q psy3760           2 NLHQFRFVREAVRQNFN----LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH   52 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s----~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~   52 (306)
                      +-.+..++..+.+.| +    ...-+.++++.|.++++.|+.||..   .|+.|-
T Consensus        36 t~~E~lVy~~I~~aG-n~GIw~kdL~~~tnL~~~~vtkiLK~LE~k---~lIK~V   86 (95)
T 2yu3_A           36 DNQEKLVYQIIEDAG-NKGIWSRDVRYKSNLPLTEINKILKNLESK---KLIKAV   86 (95)
T ss_dssp             SHHHHHHHHHHHHHT-TSCEEHHHHHHHHTCCHHHHHHHHHHHHHH---TSEEEE
T ss_pred             CHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhC---CCEEEe
Confidence            345677788888877 5    4578899999999999999999984   565554

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=90.32  E-value=0.07  Score=40.86  Aligned_cols=40  Identities=13%  Similarity=0.109  Sum_probs=30.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..++++..+.+...|++.-|+.+++|+||+|++|+.||+.
T Consensus        13 ~R~~IL~~L~~g~~s~~ELa~~lglS~stVs~hL~~Le~a   52 (232)
T 2qlz_A           13 VRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMERE   52 (232)
T ss_dssp             HHHHHHHHHTTTTTCSSSSCTTCCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3445555555433477888999999999999999999874

>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=90.29  E-value=0.61  Score=36.41  Aligned_cols=57  Identities=11%  Similarity=0.110  Sum_probs=39.7

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHHH
Q psy3760           6 FRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQAI   66 (306)
Q Consensus         6 l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~l   66 (306)
                      +.++-.+.+.  +.|++.-|+.+++++||++|.++.|++. |.  ..|.+  ++. +|++.-..+
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~-G~--v~~~~~~~~Y-~lG~~~~~l   69 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEA-GF--VEQVEGARSY-RLGPQVLRL   69 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHT-TS--EEECSSSSEE-EECTTHHHH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CC--EEEcCCCCcE-EcCHHHHHH
Confidence            4444444432  2379999999999999999999999974 44  34443  565 687664443

>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=90.18  E-value=2.1  Score=28.81  Aligned_cols=76  Identities=8%  Similarity=0.090  Sum_probs=52.3

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhC----CCchHHHHHHHHHHHHcCceeEEecCCCcc-c-cCHhHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALY----TSQPGVSKAIIELEEELSIDIFIRHGKRIR-G-LTKPGQAILRSIEIIM   74 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~----isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~-lT~~G~~l~~~a~~il   74 (306)
                      +..++.++..+.+.| -|.+.-|+.++    +++||+++.|++||+. |.---.++++..+ . +|+.|..+...+++++
T Consensus         9 t~~q~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~k-Glv~R~~~~r~~~~~~~~~~~~~~~~~~~~~~   87 (126)
T 1sd4_A            9 SMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKK-EIIKRYKSENIYFYSSNIKEDDIKMKTAKTFL   87 (126)
T ss_dssp             CHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHC-CceEEEeCCCeEEEEEecCHHHHHHHHHHHHH
Confidence            345677778887654 26788899997    5999999999999984 4444444444431 2 4667777777777777


Q ss_pred             HHHH
Q psy3760          75 QEIE   78 (306)
Q Consensus        75 ~~~~   78 (306)
                      +.+.
T Consensus        88 ~~~~   91 (126)
T 1sd4_A           88 NKLY   91 (126)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

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

Probab=90.10  E-value=0.76  Score=29.44  Aligned_cols=41  Identities=20%  Similarity=0.147  Sum_probs=35.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~l   44 (306)
                      +++-.+++-..++.|+.+-++.+ |...+||+.+++++|+.+
T Consensus        34 RqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~ki~~~~   75 (94)
T 1j1v_A           34 RQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLR   75 (94)
T ss_dssp             HHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence            55666667777778999999999 899999999999999976

>2pfz_A Putative exported protein; extracytoplasmic solute receptor, tripartite ATP independent periplasmic transport, pyroglutamic acid; 1.80A {Bordetella pertussis tohama I}

Probab=90.06  E-value=6.1  Score=31.40  Aligned_cols=185  Identities=10%  Similarity=0.093  Sum_probs=93.3

Q ss_pred             cEEEEecccch---hhhhHHHHHHHHHh-CCCcEEEEEeC----ChhHHHHHHHcCCeeEEEEccccCC--CCCce--ee
Q psy3760          94 NLTIATTHTQA---RYALPKIIKEFTIQ-FPKVKLSLLQG----NPKQITEMIRNDQADIAIVTEILSP--SDKLI--SI  161 (306)
Q Consensus        94 ~l~I~~~~~~~---~~~l~~~l~~~~~~-~p~~~i~~~~~----~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~--~~  161 (306)
                      ++|++...+-.   ...+..+...+.+. .-.+++++...    +..+.++.+..|.+|++++......  .+.+.  ..
T Consensus         2 ~lk~~~~~~~~~~~~~~~~~fa~~v~~~s~G~i~i~~~~~g~Lg~~~~~~~~v~~G~id~~~~~~~~~~~~~p~~~~~~l   81 (301)
T 2pfz_A            2 KWDLPTAYPASNLHVENLTQFVKDVDSLSGGKLKITLHNNASLYKAPEIKRAVQGNQAQIGEILLTNFANEDPVYELDGL   81 (301)
T ss_dssp             EEEEECSSCTTSHHHHHHHHHHHHHHHHHTTSCEEEEECTTSSSCGGGHHHHHHTTSSSEEEEEGGGGTTTCGGGTGGGS
T ss_pred             eeEecccCCCCchhhHHHHHHHHHHHHHcCCeEEEEEccCcccCChHHHHHHHHCCceeeEechhhhccccCchhhhhcC
Confidence            46777643322   12223333334333 34688888774    3478999999999999987522110  00000  00


Q ss_pred             c-----------------------cccceEEEEec----CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhC
Q psy3760         162 P-----------------------CYQWEYVIIVP----LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ  214 (306)
Q Consensus       162 ~-----------------------l~~~~~~~v~~----~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~  214 (306)
                      |                       +....+.++..    ..+-..+++.-+++||.+.++-..  + .   .....++..
T Consensus        82 Pf~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~~~~~~~~~~pI~s~~DlkG~KiR~~--~-~---~~~~~~~~l  155 (301)
T 2pfz_A           82 PFLATGYDASFKLYQAQKPFLEKKLASQGMMLLYSVAWPPQGIFANRDIKQVSDMKGLKWRAY--S-P---VTAKIAELV  155 (301)
T ss_dssp             TTSCCSHHHHHHHHHHHHHHHHHHHHTTTEEEEEEEECCCCEEEESSCCSSGGGGTTCEEEES--S-H---HHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEecccCCcceeeCCCCCChHHhcCCEEecC--C-h---hHHHHHHHc
Confidence            0                       00112222221    122223344458999999988764  2 1   235677777


Q ss_pred             CCceeEEEEecCHHHHHHHHHhc--cceeeeecceeccccc-CCceeeecCCCCccceEEEEEeCCc--cccHHHHHHHH
Q psy3760         215 KLTPYIVLETINSDIIKTYVELR--MGIGIIASIAFDSNRD-KNLRSISASHLFGTTISRVIIKQGT--YLRSYVYSFIK  289 (306)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~  289 (306)
                      |..|..    -....+..++++|  +|. ..|......... .-...+-....... ...++.+++.  .+++..|+.+.
T Consensus       156 Ga~pv~----~~~~E~y~ALq~G~vDg~-~~~~~~~~~~~~~ev~ky~~~~~~~~~-~~~~~~n~~~~~~L~~~~q~~i~  229 (301)
T 2pfz_A          156 GAQPVT----VQQAELAQAMATGVIDSY-MSSGSTGFDTKTYEYIKKFYDTEAWLP-KNAVLVNKKAFDALDPATQQALK  229 (301)
T ss_dssp             TCEEEE----CCGGGHHHHHHTTSCSEE-EECHHHHHHTTGGGTCCEEECCCCCCC-EEEEEEEHHHHHTSCHHHHHHHH
T ss_pred             CCccee----cCHHHHHHHHhcCeeeEE-ecCccccccccHHHHhhhheecccccc-eeEEEEcHHHHhcCCHHHHHHHH
Confidence            876633    2566677778888  565 444433322211 22233333332222 3345555442  34666666554


Q ss_pred             H
Q psy3760         290 L  290 (306)
Q Consensus       290 ~  290 (306)
                      .
T Consensus       230 ~  230 (301)
T 2pfz_A          230 K  230 (301)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2hzl_A Trap-T family sorbitol/mannitol transporter, periplasmic binding protein, SMOM; trap transporter, periplasmic subunit, ligand binding; 1.40A {Rhodobacter sphaeroides 2} PDB: 2hzk_A

Probab=89.96  E-value=7.1  Score=32.01  Aligned_cols=187  Identities=7%  Similarity=-0.041  Sum_probs=96.4

Q ss_pred             CcEEEEecccch----hhhhHHHHHHHHHhCC-CcEEEEEeC----ChhHHHHHHHcCCeeEEEEccccCC--CCCce--
Q psy3760          93 GNLTIATTHTQA----RYALPKIIKEFTIQFP-KVKLSLLQG----NPKQITEMIRNDQADIAIVTEILSP--SDKLI--  159 (306)
Q Consensus        93 ~~l~I~~~~~~~----~~~l~~~l~~~~~~~p-~~~i~~~~~----~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~--  159 (306)
                      .++|++....-.    ......+...+.+.-. .+++++...    +..+.++.+..|.+|++++......  .+.+.  
T Consensus        32 ~~l~~~~~~~~~~~~~~~~~~~fa~~v~e~s~G~v~i~~~~~g~Lg~~~~~~eav~~G~iD~~~~~~~~~~~~~p~~~~~  111 (365)
T 2hzl_A           32 VTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVPGLQAADAVTEGTVECCHTVGYYYWGKDPTFALA  111 (365)
T ss_dssp             CEEEEEESSCTTCTTTTHHHHHHHHHHHHHTTTSSEEEEECTTTSSCGGGHHHHHHTTSSSEEEECGGGGTTTCTHHHHT
T ss_pred             eEEEEeccCCCCCCchhHHHHHHHHHHHHhcCCeEEEEEecCCcccCHHHHHHHHHcCccceeecchhhhcccChhHhhh
Confidence            479999854322    1233344444554433 488888875    4678999999999999998632110  01000  


Q ss_pred             -eecc------------------------ccceEEEE--ecCC--CCC-CCCCCcChhhhcCCCeEeecCCCCcHHHHHH
Q psy3760         160 -SIPC------------------------YQWEYVII--VPLD--HPL-LLLNSISLKEISNYPLITYDLSFSGRIKLDR  209 (306)
Q Consensus       160 -~~~l------------------------~~~~~~~v--~~~~--~~l-~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~  209 (306)
                       ..|+                        ....+.++  ...+  +.. .+++.-+++||.+..+-..  +     ....
T Consensus       112 ~~lPf~~~~~~~~~~~~~~~g~~~~~~~~~~~g~~~l~~~~~g~~~~~~~~~pI~s~~DLkG~KiR~~--~-----~~~~  184 (365)
T 2hzl_A          112 AAVPFSLSARGINAWHYHGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRVG--G-----FAGK  184 (365)
T ss_dssp             TCCTTCCCHHHHHHHHHHSSHHHHHHHHHGGGTEEEEEEEECCSBCCCEESSCCCSTGGGTTCEEECC--T-----THHH
T ss_pred             hcCCCCCCHHHHHHHHHcCChHHHHHHHHHHCCCEEEeccCCCcccceeecCCCCChHHhCCCEEecC--C-----cHHH
Confidence             0111                        11122222  2222  211 2344458999999987665  2     3356


Q ss_pred             HHHhCCCceeEEEEecCHHHHHHHHHhc--cceee-eeccee-cccccCCceeeecCC-CCccceEEEEEeCCc--cccH
Q psy3760         210 EFSLQKLTPYIVLETINSDIIKTYVELR--MGIGI-IASIAF-DSNRDKNLRSISASH-LFGTTISRVIIKQGT--YLRS  282 (306)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~~-~p~~~~-~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~~--~~~~  282 (306)
                      .++..|..|..    -.+..+...+++|  +|... .|.... ..+ ..-...+-... ........++.+++.  ..++
T Consensus       185 ~~~~lGa~pv~----~~~~e~y~ALq~G~VDg~~~~~p~~~~~~~~-~ev~k~~~~~~~~~~~~~~~~v~n~~~~~~L~~  259 (365)
T 2hzl_A          185 VMERLGVVPQQ----IAGGDIYPALEKGTIDATEWVGPYDDEKLGF-FKVAPYYYYPGWWEGGPTVHFMFNKSAYEGLTP  259 (365)
T ss_dssp             HHHTTTCEEEC----CCTTSHHHHHHHTSCSEECCSCHHHHHHHTG-GGTCCEEEECBTTCSSCEEEEEEEHHHHHHSCH
T ss_pred             HHHHcCCccee----cCHHHHHHHHhCCCcceeeccCccchhhcCh-HHhhheeeccCccccccceEEEEcHHHHhcCCH
Confidence            77888876643    2444566777788  56543 233221 111 11122222232 222123455555542  3466


Q ss_pred             HHHHHHHHH
Q psy3760         283 YVYSFIKLL  291 (306)
Q Consensus       283 ~~~~~~~~l  291 (306)
                      ..++++...
T Consensus       260 ~~q~~l~~a  268 (365)
T 2hzl_A          260 TYQSLLRTA  268 (365)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666665543

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=89.93  E-value=1.1  Score=29.87  Aligned_cols=45  Identities=18%  Similarity=0.195  Sum_probs=36.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQA   65 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~   65 (306)
                      |...-|+.+++|.+++.++++.|+++ |. +-.+.++|. ..++....
T Consensus        35 s~~~La~~~~vSr~tvr~al~~L~~~-Gl-i~~~~~~G~-~V~~~~~~   79 (113)
T 3tqn_A           35 SIRKISTEYQINPLTVSKAYQSLLDD-NV-IEKRRGLGM-LVKAGARQ   79 (113)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-TS-EEEETTTEE-EECTTHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-CC-EEEecCCeE-EEeCCchH
Confidence            67789999999999999999999986 65 556667787 46665543

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=89.85  E-value=0.16  Score=39.84  Aligned_cols=55  Identities=18%  Similarity=0.161  Sum_probs=39.7

Q ss_pred             hHHHHHHHHH--hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760           5 QFRFVREAVR--QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus         5 ~l~~f~~v~~--~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      -++++..+.+  .+.|++.-|+.+++++||++|.++.|++. |  +..|.+++. +|++..
T Consensus        23 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~-G--~v~~~~~~Y-~Lg~~~   79 (265)
T 2ia2_A           23 GLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVEL-G--YVATDGSAF-WLTPRV   79 (265)
T ss_dssp             HHHHHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHH-T--SEEESSSEE-EECGGG
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-C--CEEecCCEE-EEcHHH
Confidence            3445555543  22379999999999999999999999983 3  345556666 787764

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=89.84  E-value=0.44  Score=35.06  Aligned_cols=68  Identities=16%  Similarity=0.107  Sum_probs=46.4

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHHHHHH--HHHcCceeEEecCCCccccCHhHHHHHHHHHHH---HHHHHHHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKAIIEL--EEELSIDIFIRHGKRIRGLTKPGQAILRSIEII---MQEIEGLKKIG   84 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~i~~L--E~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i---l~~~~~~~~~~   84 (306)
                      .+.|.|=...|+.||||+++|||.|+.-  +..+ +.||-= .+++  -.|.+..|...+..+   -..++++...+
T Consensus        21 y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~l-v~lfp~-~~~l--s~p~~~~L~k~~~~l~~~~~~l~eLi~~~   93 (192)
T 1zx4_A           21 KNDGMSQKDIAAKEGLSQAKVTRALQAASAPEEL-VALFPV-QSEL--TFSDYKTLCAVGDEMGNKNLEFDQLIQNI   93 (192)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHHH-HTTCSC-GGGC--CHHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCcCHHHHHHHHHHhccchhh-HHHcCC-cccC--ccchHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            4566699999999999999999998763  3444 555543 3443  347788888777766   44445555443

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

Probab=89.77  E-value=0.58  Score=33.33  Aligned_cols=33  Identities=21%  Similarity=0.183  Sum_probs=27.6

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .+.+.|.|..++|+.+++|.+||++.+++.++.
T Consensus        36 ~l~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~   68 (159)
T 2k27_A           36 DLAHQGVRPCDISRQLRVSHGCVSKILGRYYET   68 (159)
T ss_dssp             HHHHHTCCHHHHHHHHTCCSHHHHHHHCCSSTT
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            333455599999999999999999999988765

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

Probab=89.70  E-value=0.62  Score=28.89  Aligned_cols=40  Identities=8%  Similarity=0.159  Sum_probs=31.7

Q ss_pred             hhHHHHHHHHHh---cCCHHHHHHHh-----CCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQ---NFNLTEAAKAL-----YTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~---~~s~~~aA~~l-----~isq~~~s~~i~~LE~~   43 (306)
                      +.+.++-.+.+.   ..|...-++.+     ++|.+||.|.|+.||+.
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~   65 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDA   65 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHC
Confidence            455566666543   23888999999     99999999999999985

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

Probab=89.66  E-value=0.42  Score=30.79  Aligned_cols=27  Identities=19%  Similarity=0.167  Sum_probs=24.4

Q ss_pred             cCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760          16 NFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus        16 ~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      |.|+..+|+.+|||.++|.+.+++.+.
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~~~~~   49 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWIIKYGS   49 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHHHHCC
T ss_pred             CChHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            449999999999999999999998765

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=89.15  E-value=0.1  Score=34.21  Aligned_cols=41  Identities=17%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      |...-|+.+++|+++++++++.||++ |.- -.+.++|. ..++
T Consensus        37 s~~eLa~~~~vSr~tvr~al~~L~~~-Gli-~~~~g~G~-~v~~   77 (102)
T 1v4r_A           37 SVADIRAQFGVAAKTVSRALAVLKSE-GLV-SSRGALGT-VVEK   77 (102)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTS-SCC-EEETTTEE-ESCS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-CCE-EEeCCCeE-EEcc
Confidence            78899999999999999999999854 542 33444565 3443

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

Probab=89.11  E-value=0.39  Score=39.12  Aligned_cols=109  Identities=9%  Similarity=0.133  Sum_probs=59.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHH----hhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGK----EFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~----~~~~~~~~   93 (306)
                      |+...|+..|+|++||||.|.              +++.  ..++=      -+++++..+++-..-.    .+..+.  
T Consensus        12 ti~diA~~agVS~~TVSr~Ln--------------~~~~--vs~~t------r~rV~~~~~~lgY~pn~~a~~l~~~~--   67 (344)
T 3kjx_A           12 TLRDVSEASGVSEMTVSRVLR--------------NRGD--VSDAT------RARVLAAAKELGYVPNKIAGALASNR--   67 (344)
T ss_dssp             CHHHHHHHHCCCSHHHHHHHT--------------TCSC--CCHHH------HHHHHHHHHHHTCCCCCCCSCSTTSC--
T ss_pred             CHHHHHHHHCCCHHHHHHHHc--------------CCCC--CCHHH------HHHHHHHHHHhCCCCCHHHHHhhcCC--
Confidence            789999999999999999884              2222  22221      1223333333221111    111222  


Q ss_pred             cEEEEec-ccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEcc
Q psy3760          94 NLTIATT-HTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVTE  150 (306)
Q Consensus        94 ~l~I~~~-~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~~  150 (306)
                      .-+||+- +.+...++..++..+.+...  ++.+.+....  .   .+.++.+.+.++|-.|+..
T Consensus        68 ~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdGiIi~~  132 (344)
T 3kjx_A           68 VNLVAVIIPSLSNMVFPEVLTGINQVLEDTELQPVVGVTDYLPEKEEKVLYEMLSWRPSGVIIAG  132 (344)
T ss_dssp             CSEEEEEESCSSSSSHHHHHHHHHHHHTSSSSEEEEEECTTCHHHHHHHHHHHHTTCCSEEEEEC
T ss_pred             CCEEEEEeCCCCcHHHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEEC
Confidence            3345542 23345566677766665533  5566554432  2   2356677888999988853

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

Probab=88.71  E-value=0.63  Score=31.06  Aligned_cols=36  Identities=8%  Similarity=0.038  Sum_probs=31.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      ++++..+++-. |...-|+.+|+|..||||.-+.|..
T Consensus        66 ~eV~klL~~G~-syreIA~~~g~S~aTIsRv~r~L~~  101 (119)
T 3kor_A           66 LQVAKMIKQGY-TYATIEQESGASTATISRVKRSLQW  101 (119)
T ss_dssp             HHHHHHHHHTC-CHHHHHHHHCCCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            77788888876 9999999999999999998887753

>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=88.56  E-value=0.63  Score=28.80  Aligned_cols=51  Identities=14%  Similarity=0.182  Sum_probs=35.2

Q ss_pred             hhhHHHHHHHHHhc-CCHHHHHHHhC----CCchHHHHHHHHHHHHcCceeEEecCC
Q psy3760           3 LHQFRFVREAVRQN-FNLTEAAKALY----TSQPGVSKAIIELEEELSIDIFIRHGK   54 (306)
Q Consensus         3 ~~~l~~f~~v~~~~-~s~~~aA~~l~----isq~~~s~~i~~LE~~lg~~Lf~R~~~   54 (306)
                      ..++.++..+.+.+ .|...-|+.++    ++++|+++.|++||+. |.---.+.++
T Consensus         9 ~~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~k-Glv~r~~~gr   64 (82)
T 1p6r_A            9 DAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKK-GALNHHKEGR   64 (82)
T ss_dssp             HHHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHT-TSEEEEEETT
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHC-CCeEEEecCC
Confidence            34566666666532 27788899987    7999999999999974 4433334343

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=88.55  E-value=0.26  Score=34.31  Aligned_cols=51  Identities=18%  Similarity=0.111  Sum_probs=34.4

Q ss_pred             hCCCchHHHHHHHHHHHHcCceeEEe--c-----CCCccccCHhHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEELSIDIFIR--H-----GKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~Lf~R--~-----~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      +++|.++|...|++||++ |.-=...  .     ++...++|+.|+..+....+-.+.+
T Consensus        64 ~~is~gtLYp~L~rLe~~-GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~~~l  121 (138)
T 2e1n_A           64 YRLSDTVLYTALKFLEDE-QIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWERY  121 (138)
T ss_dssp             EECCHHHHHHHHHHHHHT-TSEEEEEECCTTCSSCEEEEEESCSCCHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHC-CCEEEEeecccCCCCCcEEEEECHHHHHHHHHHHHHHHHH
Confidence            479999999999999985 2211111  1     1222489999999888776544443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=88.16  E-value=0.94  Score=36.72  Aligned_cols=60  Identities=15%  Similarity=0.101  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhcCC---HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760           6 FRFVREAVRQNFN---LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR   68 (306)
Q Consensus         6 l~~f~~v~~~~~s---~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~   68 (306)
                      .+++.++++.+.+   .+.+|+.|+++.+++.+.+++.-.+.  -|..+.++|. ..|+.|..++.
T Consensus       266 ~~~l~~l~~~~~~~~~~~~~a~~lg~~~~tl~~~l~~~l~~~--gli~~~~~g~-~~t~~~~~~~~  328 (338)
T 3pfi_A          266 LRYLELLTAAKQKPIGLASIAAALSEDENTIEDVIEPYLLAN--GYIERTAKGR-IASAKSYSALK  328 (338)
T ss_dssp             HHHHHHHHHSCSCCBCHHHHHHHTTCCHHHHHHTTHHHHHHT--TSEEEETTEE-EECHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHHhHHHHHc--CceecCCCcc-cccHHHHHHhc
Confidence            3466666663313   89999999999999999998443343  4567888888 59999988764

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=87.99  E-value=0.91  Score=33.92  Aligned_cols=43  Identities=7%  Similarity=0.060  Sum_probs=38.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+..+++..+++.. |-..-|+.+++|..||..++++|-+.||+
T Consensus       157 ~rE~~vl~~l~~g~-s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~  199 (215)
T 1a04_A          157 PRERDILKLIAQGL-PNKMIARRLDITESTVKVHVKHMLKKMKL  199 (215)
T ss_dssp             HHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            35667788888877 99999999999999999999999999986

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

Probab=87.78  E-value=0.74  Score=29.55  Aligned_cols=40  Identities=10%  Similarity=0.013  Sum_probs=33.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ..+.+..++.+-+.|++.||++.+||++.+.+..+..++.
T Consensus        37 ~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~~~   76 (95)
T 2jrt_A           37 RKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVAAH   76 (95)
T ss_dssp             HHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            4567777777777799999999999999999999887543

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=87.39  E-value=0.47  Score=38.85  Aligned_cols=113  Identities=14%  Similarity=0.209  Sum_probs=31.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      |+...|+..|+|.+||||.|..-.      -+.-..+.         +..+.++    ++.-.-+ ..+.+..+.++.|-
T Consensus        14 ti~diA~~agVS~~TVSr~Ln~~~------~vs~~tr~---------rV~~~a~----~lgY~pn~~a~~l~~~~~~~Ig   74 (355)
T 3e3m_A           14 TMRDVAKAAGVSRMTVSRALKKDS------PISSETRE---------RILKVVK----DMNYVPDQVAGSLTTKRSGFVG   74 (355)
T ss_dssp             ----------------------------------------------------------------------------CEEE
T ss_pred             cHHHHHHHhCCCHHHHHHHHCCCC------CCCHHHHH---------HHHHHHH----HhCCCcCHHHHhhhcCCCCEEE
Confidence            678899999999999999997432      11111111         1111111    1111110 01111222233344


Q ss_pred             EEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--hh---HHHHHHHcCCeeEEEEcc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--PK---QITEMIRNDQADIAIVTE  150 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~~---~~~~~l~~~~~Di~i~~~  150 (306)
                      +-++. +...++..++..+.+..  -++.+.+....  ..   +.++.+.+..+|-.|+..
T Consensus        75 vi~~~-~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiI~~~  134 (355)
T 3e3m_A           75 LLLPS-LNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSY  134 (355)
T ss_dssp             EEESC-SBCHHHHHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHTCCSEEEEEC
T ss_pred             EEeCC-CCchHHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEeC
Confidence            43332 34455555665554432  25666665432  21   456677788999988853

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=87.35  E-value=1  Score=31.84  Aligned_cols=42  Identities=10%  Similarity=0.158  Sum_probs=32.8

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      ++-++|. ..-.|.|+...|+.||+|.++|.+++.+.-+.|-.
T Consensus       113 ~~r~v~~-~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~  154 (164)
T 3mzy_A          113 FEKEVLT-YLIRGYSYREIATILSKNLKSIDNTIQRIRKKSEE  154 (164)
T ss_dssp             HHHHHHH-HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            3445666 44456699999999999999999999888777643

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=87.13  E-value=1.3  Score=35.66  Aligned_cols=109  Identities=12%  Similarity=0.140  Sum_probs=56.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~   93 (306)
                      ++...|+..|+|.+||||.|..-             .++   .+.=      -+++++..+++-.    ..+.+..+.  
T Consensus         4 ti~dvA~~agVS~~TVSrvln~~-------------~~v---s~~t------r~rV~~aa~~lgY~pn~~ar~l~~~~--   59 (332)
T 2hsg_A            4 TIYDVAREASVSMATVSRVVNGN-------------PNV---KPST------RKKVLETIERLGYRPNAVARGLASKK--   59 (332)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHTTC-------------TTS---CHHH------HHHHHHHHHHHTCCSCHHHHHHTTC---
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCC-------------CCC---CHHH------HHHHHHHHHHHCCCcCHHHHHHHhCC--
Confidence            78899999999999999999751             222   1111      1122222222211    112223323  


Q ss_pred             cEEEEecc-cchhhhhHHHHHHHHHhC--CCcEEEEEeCChh-----HHHHHHHcCCeeEEEEcc
Q psy3760          94 NLTIATTH-TQARYALPKIIKEFTIQF--PKVKLSLLQGNPK-----QITEMIRNDQADIAIVTE  150 (306)
Q Consensus        94 ~l~I~~~~-~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~~~-----~~~~~l~~~~~Di~i~~~  150 (306)
                      .-+||+-. .+...++..++..+.+..  -+..+.+.....+     +.++.+.+.++|-.|+..
T Consensus        60 ~~~Ig~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiI~~~  124 (332)
T 2hsg_A           60 TTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMS  124 (332)
T ss_dssp             CCEEEEEEC--CCSHHHHHHHHHHHHHHHHTCEEEEEECCSHHHHHHHHHHHTSCCSSCCEEECC
T ss_pred             CCEEEEEeCCCCCcHHHHHHHHHHHHHHHcCCEEEEEeCCCChHHHHHHHHHHHhCCCcEEEEec
Confidence            34455432 233445555555544332  1556665543321     346667778899888753

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=86.96  E-value=3.5  Score=27.92  Aligned_cols=42  Identities=29%  Similarity=0.211  Sum_probs=32.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |...-|+.+|+|+++|.++++.|+++ |. +-.+.++|. ..++.
T Consensus        37 se~~La~~~~vSr~tvr~Al~~L~~~-Gl-i~~~~g~G~-~V~~~   78 (126)
T 3by6_A           37 SVRETALQEKINPNTVAKAYKELEAQ-KV-IRTIPGKGT-FITGN   78 (126)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-TS-EEEETTTEE-EECSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-CC-EEEecCCeE-EEccC
Confidence            77899999999999999999999875 44 334456676 46653

>3c9h_A ABC transporter, substrate binding protein; structural genom MCSG, PSI-2, protein structure initiative; HET: CIT; 1.90A {Agrobacterium tumefaciens str}

Probab=86.95  E-value=2.4  Score=34.54  Aligned_cols=199  Identities=11%  Similarity=0.010  Sum_probs=106.5

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc------CCeeEEEEcccc-C-----------
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN------DQADIAIVTEIL-S-----------  153 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~------~~~Di~i~~~~~-~-----------  153 (306)
                      .++|+|......  ..+..++..|.++||+++|++...++.+....+..      ...|+.+..... .           
T Consensus        33 ~~~L~v~~~~~~--~~~~~~~~~Fe~~~Pgi~V~~~~~~~~~~~~kl~~~~~ag~~~~DV~~~~~~~~~~~~~~~g~l~~  110 (355)
T 3c9h_A           33 AQTLVVYSSLDE--PLATPMIEGFQKANPDIAVHYEDMLTGEIYDRIVKETDAGKKTADFAFSSAMDLQVKLSNDGYAQR  110 (355)
T ss_dssp             -CEEEEEECSCH--HHHHHHHHHHHHHCTTCEEEEEECCHHHHHHHHHHHHHTTCCBCSEEEESCHHHHHHHHHTTCEEC
T ss_pred             CCEEEEEeCCCH--HHHHHHHHHHHHHCcCeEEEEEeCChHHHHHHHHHHHhcCCCCCCEEEecchHHHHHHHhCCCccc
Confidence            567888776543  46789999999999999999999888776666632      358999864211 0           


Q ss_pred             -CC---CCc--------eeeccccceEEEEecCCCCCCCCCCcChhhhcC--------C--CeEeecCCCC-c-HHHH--
Q psy3760         154 -PS---DKL--------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN--------Y--PLITYDLSFS-G-RIKL--  207 (306)
Q Consensus       154 -~~---~~~--------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~--------~--~~i~~~~~~~-~-~~~~--  207 (306)
                       ..   ..+        ...++.....+++.+++..-....+-+|+||.+        +  .+....+... . ...+  
T Consensus       111 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~YNk~~~~~~~~P~tw~dL~~~~~~~~~~~~g~i~~~~~~~~~~~~~~~~~  190 (355)
T 3c9h_A          111 SDLAMSARWPAWANWRNTAYALTFEPAVFVYHKPSFTTEKPPATRAEFVDYLERHAKEVHGRIATYDIERSGVGFLFMSR  190 (355)
T ss_dssp             CCCTTTTTSCGGGEETTTEEECBCEEEEEEEEGGGCSSSCCCCSHHHHHHHHHHTHHHHTTCEEEECTTC-CHHHHHHHH
T ss_pred             CCChhhhhCcchheeCCeEEEEecCcEEEEEEHHhcCCCCCCCCHHHHHHHHHhcchhhCCceeecCccccchHHHHHhc
Confidence             00   001        013455566788888775322234679999864        1  3343333211 1 1110  


Q ss_pred             --------HHHHHhCCCceeEEEEecCHHHHHHHHHhccc-eeeee-cceecc-c-ccCCceeeecCCCCccceEEEEEe
Q psy3760         208 --------DREFSLQKLTPYIVLETINSDIIKTYVELRMG-IGIIA-SIAFDS-N-RDKNLRSISASHLFGTTISRVIIK  275 (306)
Q Consensus       208 --------~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g-i~~~p-~~~~~~-~-~~~~l~~~~~~~~~~~~~~~l~~~  275 (306)
                              .++++..  .++......+.....+++.+|.. +++.. ...... . ....+......+.......++...
T Consensus       191 ~~~~~~~a~~~l~~l--~~~~~~~~~~~~~~~~~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~P~~g~~~~~~~~~I~  268 (355)
T 3c9h_A          191 DQEQFGDIWSVIKAM--GAAGVKVYSTSSAILERVSDGRFVLGYNILGSYAADWASRHPDVGIVLPKDYTVVMSRIGLVP  268 (355)
T ss_dssp             HHHHCTTHHHHHHHH--HHTTCEEESCHHHHHHHHHTTSCSEEEEEEHHHHHHHHHHCTTEEEECCSSCEEEECCEEEEE
T ss_pred             chhccHHHHHHHHHH--HhcCCeecCCcHHHHHHHHCCCeEEEEecchhHHHHHHhcCCCeeEEecCCCceeeeeEEEEE
Confidence                    1111111  01111123455677788888843 33321 111111 1 123444432112122222234456


Q ss_pred             CCccccHHHHHHHHHHhHH
Q psy3760         276 QGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       276 ~~~~~~~~~~~~~~~l~~~  294 (306)
                      ++.....++++|++++.+.
T Consensus       269 k~s~~~eaA~~Fi~fl~s~  287 (355)
T 3c9h_A          269 EAAANPELGRRYLEFFMSK  287 (355)
T ss_dssp             TTBSCHHHHHHHHHHHHSH
T ss_pred             CCCCCHHHHHHHHHHHcCH
Confidence            6666788899999999653

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=86.92  E-value=0.28  Score=29.22  Aligned_cols=20  Identities=25%  Similarity=0.297  Sum_probs=18.5

Q ss_pred             CHHHHHHHhCCCchHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i   37 (306)
                      ++...|+.+|+|++|||+.+
T Consensus        11 t~~diA~~aGVS~sTVSr~l   30 (67)
T 2l8n_A           11 TMKDVALKAKVSTATVSRAL   30 (67)
T ss_dssp             CHHHHHHHTTCCHHHHHHTT
T ss_pred             CHHHHHHHHCCCHHHHHHHH
Confidence            78899999999999999976

>2pfy_A Putative exported protein; extracytoplasmic solute receptor, tripartite ATP independent periplasmic transport, pyroglutamic acid; 1.95A {Bordetella pertussis tohama I}

Probab=86.87  E-value=10  Score=30.07  Aligned_cols=186  Identities=11%  Similarity=0.068  Sum_probs=92.9

Q ss_pred             cEEEEecccchh---hhhHHHHHHHHHh-CCCcEEEEEeC----ChhHHHHHHHcCCeeEEEEccccC--CCCCce--ee
Q psy3760          94 NLTIATTHTQAR---YALPKIIKEFTIQ-FPKVKLSLLQG----NPKQITEMIRNDQADIAIVTEILS--PSDKLI--SI  161 (306)
Q Consensus        94 ~l~I~~~~~~~~---~~l~~~l~~~~~~-~p~~~i~~~~~----~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~--~~  161 (306)
                      ++|++...+-..   ..+..+...+.+. .-.+++++...    +..+.++.+..|.+|++++.....  ..+.+.  ..
T Consensus         3 ~lk~~~~~~~~~~~~~~~~~fa~~v~e~s~G~i~i~~~~~g~Lg~~~~~~e~v~~G~id~~~~~~~~~~~~~p~~~~~~l   82 (301)
T 2pfy_A            3 SWTMTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSV   82 (301)
T ss_dssp             EEEEECSSCTTSHHHHHHHHHHHHHHHHTTTSEEEEEECTTSSSCGGGHHHHHHHTSSSEEEEEGGGGTTTCGGGGGGGS
T ss_pred             EEEecccCCCCcchhHHHHHHHHHHHHHcCCeEEEEEccchhhCChHHHHHHHHCCCeeeehhhhhhhhccCcccccccC
Confidence            577777543221   1223333334333 34577777664    346899999999999998752211  001000  00


Q ss_pred             cc-----------------------ccceEEEEec----CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhC
Q psy3760         162 PC-----------------------YQWEYVIIVP----LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQ  214 (306)
Q Consensus       162 ~l-----------------------~~~~~~~v~~----~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~  214 (306)
                      |.                       ....+.++..    ..+-..+++.-+++||.+.++-..  + .   .....++..
T Consensus        83 Pfl~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~~~~~~~~~~pI~s~~DlkG~KiR~~--~-~---~~~~~~~~l  156 (301)
T 2pfy_A           83 PFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAY--S-A---STSHMAALM  156 (301)
T ss_dssp             TTTSCSHHHHHHHHHHHHHHHHHHHHTTTEEEEEEEECCCCEEEESSCCSSGGGGTTCEEEEC--S-H---HHHHHHHHT
T ss_pred             CcccCCHHHHHHHHHHhhHHHHHHHHHCCCEEEEeecCCCcceecCCCCCCHHHhCCCEEeec--C-h---hHHHHHHHc
Confidence            00                       0112222221    122223344458999999988664  2 1   235677888


Q ss_pred             CCceeEEEEecCHHHHHHHHHhc--cceeeeecceeccccc-CCceeeecCCCCccceEEEEEeCCc--cccHHHHHHHH
Q psy3760         215 KLTPYIVLETINSDIIKTYVELR--MGIGIIASIAFDSNRD-KNLRSISASHLFGTTISRVIIKQGT--YLRSYVYSFIK  289 (306)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~~~-~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~  289 (306)
                      |..|...    ....+..++++|  +|. ..|......... .-...+-....... ...++.+++.  .+++..|+.+.
T Consensus       157 Ga~pv~~----~~~E~y~ALq~G~vDg~-~~~~~~~~~~~~~ev~k~~~~~~~~~~-~~~~~~n~~~~~~L~~~~q~~i~  230 (301)
T 2pfy_A          157 GAVPTTV----QTPEVPQAFSTGVIDAM-LTSPATGVDSQAWDYVKYYYDAQAFIP-QSFVIANKRAFQRLPAEVRQAVL  230 (301)
T ss_dssp             TSEEEEC----CGGGHHHHHHTTSCSBE-EECHHHHHHTTGGGTCCEEEECCCCCC-EEEEEEEHHHHHHSCHHHHHHHH
T ss_pred             CCcceec----cHHHHHHHHhcceeeeE-ecCccccccccHHHHhhhhcccccccc-eeeEEEcHHHHhcCCHHHHHHHH
Confidence            9766432    556677777888  565 444433222111 11223322332222 3345555542  34666666554


Q ss_pred             HH
Q psy3760         290 LL  291 (306)
Q Consensus       290 ~l  291 (306)
                      ..
T Consensus       231 ~a  232 (301)
T 2pfy_A          231 DA  232 (301)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=86.83  E-value=4.9  Score=27.61  Aligned_cols=72  Identities=8%  Similarity=0.014  Sum_probs=46.5

Q ss_pred             chhhHHHHHHHHHh--cCCHHHHHHHhC----CCchHHHHHHHHHHHHcCceeEEecCCCc-c--ccCHhHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ--NFNLTEAAKALY----TSQPGVSKAIIELEEELSIDIFIRHGKRI-R--GLTKPGQAILRSIEI   72 (306)
Q Consensus         2 ~~~~l~~f~~v~~~--~~s~~~aA~~l~----isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~--~lT~~G~~l~~~a~~   72 (306)
                      +..++.++..+.+.  +.+.+.-|+.++    ++++|+++.|++||+. |.---.++++.. +  .+|+.|. +...++.
T Consensus         8 t~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~k-Glv~r~~~~r~~~~~~~lt~~~~-~~~~~~~   85 (138)
T 2g9w_A            8 GDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKK-NLVLQIRDDRAHRYAPVHGRDEL-VAGLMVD   85 (138)
T ss_dssp             CHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHT-TSEEEEC---CCEEEESSCHHHH-HHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHC-CCEEEEecCCeEEEEeCCCHHHH-HHHHHHH
Confidence            34577788888763  237888899998    8999999999999984 443333333332 1  3677765 3444444


Q ss_pred             HHH
Q psy3760          73 IMQ   75 (306)
Q Consensus        73 il~   75 (306)
                      +++
T Consensus        86 ~~~   88 (138)
T 2g9w_A           86 ALA   88 (138)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            443

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=86.75  E-value=1.2  Score=36.06  Aligned_cols=22  Identities=27%  Similarity=0.259  Sum_probs=0.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      |+...|+..|+|.+||||.|..
T Consensus         6 ti~diA~~agVS~~TVSr~Ln~   27 (339)
T 3h5o_A            6 TMHDVAKAAGVSAITVSRVLNQ   27 (339)
T ss_dssp             ----------------------
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC
Confidence            7788999999999999999975

>4eqb_A Spermidine/putrescine ABC superfamily ATP binding transporter, binding protein; structural genomics, niaid; HET: EPE; 1.50A {Streptococcus pneumoniae TCH8431}

Probab=86.63  E-value=11  Score=30.14  Aligned_cols=194  Identities=19%  Similarity=0.231  Sum_probs=106.9

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcC--CeeEEEEcccc------------CC
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRND--QADIAIVTEIL------------SP  154 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~--~~Di~i~~~~~------------~~  154 (306)
                      ...++|+|..-..   ..-..++..|.+++ +++|++...++ +++...|..|  ..|+++.....            .+
T Consensus         6 ~~~~~l~v~~w~~---~~~~~~~~~Fe~~~-gi~V~~~~~~~~~~~~~kl~a~~~~~Dv~~~~~~~~~~~~~~g~l~~l~   81 (330)
T 4eqb_A            6 RDSQKLVIYNWGD---YIDPELLTQFTEET-GIQVQYETFDSNEAMYTKIKQGGTTYDIAIPSEYMINKMKDEDLLVPLD   81 (330)
T ss_dssp             --CCEEEEEEETT---CSCHHHHHHHHHHH-CCEEEEEEESSHHHHHHHHHHCCSCCSEECCBHHHHHHHHHTTCBCCCC
T ss_pred             CCCCeEEEEeccc---cCCHHHHHHHHHHH-CCEEEEEeCCCHHHHHHHHhcCCCCCCEEEECHHHHHHHHHCCCccCCC
Confidence            3456888887543   34468999999999 99999987654 4577777765  49999853100            00


Q ss_pred             C--------------------CCceeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCCCcHHHHHHH
Q psy3760         155 S--------------------DKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSFSGRIKLDRE  210 (306)
Q Consensus       155 ~--------------------~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~~~~~~~~~~  210 (306)
                      .                    ...-..|......+++.+++..  ...+-+++||.+.    .+.....   ....+...
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~g~~y~vP~~~~~~~l~Ynkd~~--~~~p~tw~el~~~~~~g~~~~~~~---~~~~~~~~  156 (330)
T 4eqb_A           82 YSKIEGIENIGPEFLNQSFDPGNKFSIPYFWGTLGIVYNETMV--DEAPEHWDDLWKLEYKNSIMLFDG---AREVLGLG  156 (330)
T ss_dssp             GGGCCCGGGBCGGGSSCTTSGGGSSCEEEEEEEEEEEEEGGGC--SSCCCSGGGGGCGGGTTCEEEESC---HHHHHHHH
T ss_pred             hhhCcChhhCCHHHHccCcCCCCeEEEEEecccEEEEEEHHHc--CCCCCCHHHHhChHhcCCeEEecC---HHHHHHHH
Confidence            0                    0122355556677788888753  3456799999762    1222221   11122222


Q ss_pred             HHhCC--------------------CceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc--ccCCceeeecCCCCcc
Q psy3760         211 FSLQK--------------------LTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN--RDKNLRSISASHLFGT  267 (306)
Q Consensus       211 ~~~~~--------------------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~  267 (306)
                      +...|                    +.++.... + .....+...+|. ++++.....+...  ....+...-.......
T Consensus       157 l~~~G~~~~~~~~~~~~~a~~~l~~l~~~~~~~-~-~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~P~~g~~~  234 (330)
T 4eqb_A          157 LNSLGYSLNSKDPQQLEETVDKLYKLTPNIKAI-V-ADEMKGYMIQNNVAIGVTFSGEASQMLEKNENLRYVVPTEASNL  234 (330)
T ss_dssp             HHHTTCCTTCCCHHHHHHHHHHHHTTGGGEEEE-E-STTHHHHHHTTCCSEEEEEHHHHHHHHHHCTTEEEECCTTCEEE
T ss_pred             HHHcCCCCCCCCHHHHHHHHHHHHHHhhHhhee-C-cHHHHHHHhcCCEEEEEechHHHHHHHhhCCCeEEEeCCCccce
Confidence            22222                    22333322 2 234567777774 4444444333322  2344444322222222


Q ss_pred             ceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         268 TISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       268 ~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      ..-.++..++.....++.+|++++.+.
T Consensus       235 ~~~~~~i~~~s~~~~~A~~fi~~l~s~  261 (330)
T 4eqb_A          235 WFDNMVIPKTVKNQDSAYAFINFMLKP  261 (330)
T ss_dssp             EEEEEBCBTTCSCHHHHHHHHHHHHSH
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHhcCH
Confidence            233455577777788999999998643

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=86.37  E-value=0.23  Score=35.02  Aligned_cols=49  Identities=18%  Similarity=0.210  Sum_probs=34.5

Q ss_pred             hCCCchHHHHHHHHHHHHcCceeEEe---------cCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEELSIDIFIR---------HGKRIRGLTKPGQAILRSIEIIMQEI   77 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~Lf~R---------~~~~~~~lT~~G~~l~~~a~~il~~~   77 (306)
                      ++++.++|...|++||++ |  |+.+         .++...++|+.|+..+....+-.+.+
T Consensus        74 ~~is~gtLYp~L~rLE~~-G--lI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~~~l  131 (148)
T 2zfw_A           74 YRLSDTVLYTALKFLEDE-Q--IISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWERY  131 (148)
T ss_dssp             EECCSHHHHHHHHHHHHT-S--SEEEECCCCTTSSCCCCEEEESSSSCSTTHHHHHHHHHH
T ss_pred             CCCChhHHHHHHHHHHHC-C--CEEEEeeccCCCCCCcEEEEECHHHHHHHHHHHHHHHHH
Confidence            469999999999999985 2  2221         12333489999999888776544443

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=86.35  E-value=1.6  Score=28.29  Aligned_cols=28  Identities=14%  Similarity=0.118  Sum_probs=22.1

Q ss_pred             HHHh-cCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          12 AVRQ-NFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        12 v~~~-~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      +.+. . |...-|+.+|+|+++|||-=+.|
T Consensus        54 L~~ge~-TQREIA~~lGiS~stISRi~r~L   82 (101)
T 1jhg_A           54 LLRGEM-SQRELKNELGAGIATITRGSNSL   82 (101)
T ss_dssp             HHHCCS-CHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHcCCc-CHHHHHHHHCCChhhhhHHHHHH
Confidence            3344 5 99999999999999999873333

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=85.87  E-value=3.2  Score=33.48  Aligned_cols=109  Identities=16%  Similarity=0.181  Sum_probs=57.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG   93 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~   93 (306)
                      ++...|+..|+|.+||||.|..             ..++   +++      .-+++++..+++-.    ..+.+..+...
T Consensus         2 ti~diA~~agVS~~TVSrvLn~-------------~~~v---s~~------tr~rV~~~a~~lgY~pn~~ar~l~~~~~~   59 (340)
T 1qpz_A            2 TIKDVAKRANVSTTTVSHVINK-------------TRFV---AEE------TRNAVWAAIKELHYSPSAVARSLKVNHTK   59 (340)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT-------------CSCC---CHH------HHHHHHHHHHHHTCCCCHHHHHHHHTCCS
T ss_pred             CHHHHHHHHCCCHHHHHHHHcC-------------cCCC---CHH------HHHHHHHHHHHhCCCCCHHHHhhccCCCC
Confidence            6788999999999999999982             1222   221      11222222222210    11122222333


Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--hh---HHHHHHHcCCeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--PK---QITEMIRNDQADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~~---~~~~~l~~~~~Di~i~~  149 (306)
                      .|-+-++. +...++..++..+.+..  -+..+.+....  ..   +.++.+.++++|-.|+.
T Consensus        60 ~Igvi~~~-~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiI~~  121 (340)
T 1qpz_A           60 SIGLLATS-SEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVM  121 (340)
T ss_dssp             EEEEEESC-SCSHHHHHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHTTCSEEEEC
T ss_pred             EEEEEeCC-CCChHHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEe
Confidence            34333333 34456666665554432  25666654432  22   24667778889988875

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=85.19  E-value=1.7  Score=32.72  Aligned_cols=44  Identities=9%  Similarity=0.108  Sum_probs=38.4

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      -+..+++..+++.- |-..-|+.|++|..||..+++++-+.||+.
T Consensus       152 ~rE~~vL~~l~~g~-s~~eIa~~l~is~~TV~~hi~~l~~KL~~~  195 (225)
T 3c3w_A          152 DQERTLLGLLSEGL-TNKQIADRMFLAEKTVKNYVSRLLAKLGME  195 (225)
T ss_dssp             HHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            35567777778776 999999999999999999999999999873

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=85.15  E-value=6.4  Score=26.54  Aligned_cols=43  Identities=26%  Similarity=0.274  Sum_probs=33.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG   63 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G   63 (306)
                      |...-|+.+++|.++|.++++.|+++ |. +-.+.|+|. ..++..
T Consensus        39 s~~~La~~~~vSr~tvr~Al~~L~~~-G~-i~~~~g~G~-~V~~~~   81 (125)
T 3neu_A           39 SVREMGVKLAVNPNTVSRAYQELERA-GY-IYAKRGMGS-FVTSDK   81 (125)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-TS-EEEETTTEE-EECCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC-Ce-EEEecCCEE-EEecCc
Confidence            67899999999999999999999986 43 344556776 355543

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=85.15  E-value=1.6  Score=35.34  Aligned_cols=112  Identities=11%  Similarity=0.110  Sum_probs=31.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      |+...|+..|+|++||||.|..=      +.+....+         ++..+.++    ++.-.-+ ..+.+..+.++.|-
T Consensus         8 ti~diA~~agVS~~TVSr~Ln~~------~~vs~~tr---------~rV~~~a~----~lgY~pn~~a~~l~~~~~~~Ig   68 (333)
T 3jvd_A            8 SLKEVAELAGVGYATASRALSGK------GYVSPQTR---------EKVQAAAK----ELNYVPNQLAKALREHRSALVG   68 (333)
T ss_dssp             ---------------------------------------------------------------------------CCEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCC------CCCCHHHH---------HHHHHHHH----HHCCCcCHHHHHhhcCCCCEEE
Confidence            77889999999999999999731      11111111         11111111    1111111 11112222333444


Q ss_pred             EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCCh----hHHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGNP----KQITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~~----~~~~~~l~~~~~Di~i~~  149 (306)
                      +-++. +...++..++..+.+...  +..+.+...+.    .+.++.+.+.++|-.|+.
T Consensus        69 vi~~~-~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~  126 (333)
T 3jvd_A           69 VIVPD-LSNEYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHV  126 (333)
T ss_dssp             EEESC-SSSHHHHHHHHHHHHHHHHHTCEEEEEECCSHHHHHHHHHHHHHHTCSEEEEC
T ss_pred             EEeCC-CcChHHHHHHHHHHHHHHHCCCEEEEECCCChHHHHHHHHHHHhCCCCEEEEc
Confidence            43433 344555555555543322  56666655432    235667778889999885

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=85.03  E-value=1.7  Score=33.77  Aligned_cols=43  Identities=23%  Similarity=0.258  Sum_probs=36.0

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+.-++|...++. .|....|+.||+|.+||..++.+.-+.|+.
T Consensus       200 ~~erevl~L~~~G-~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~  242 (258)
T 3clo_A          200 EREKEILRCIRKG-LSSKEIAATLYISVNTVNRHRQNILEKLSV  242 (258)
T ss_dssp             HHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            3455666666655 599999999999999999999999999976

>1nnf_A Iron-utilization periplasmic protein; iron-binding protein, EDTA-Fe-protein complex, metal binding protein; HET: EDT; 1.10A {Haemophilus influenzae} SCOP: c.94.1.1 PDB: 1mrp_A 1d9v_A 3od7_A 3odb_A 1qvs_A 2o6a_A 2o68_A 3kn8_A 3kn7_A 2o69_A 1qw0_A 1o7t_A* 1xc1_A* 1r1n_A* 1d9y_A

Probab=84.83  E-value=13  Score=29.30  Aligned_cols=194  Identities=13%  Similarity=0.063  Sum_probs=102.4

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH--c--CCeeEEEEccccC-----------CC----
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR--N--DQADIAIVTEILS-----------PS----  155 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~--~--~~~Di~i~~~~~~-----------~~----  155 (306)
                      |++-....  ...+..++..|.+ +|+++|++...++.++...|.  .  +..|+.+......           +-    
T Consensus         2 l~v~~~~~--~~~~~~~~~~F~~-~~gi~V~~~~~~~~~~~~kl~~~~~~~~pDv~~~~~~~~~~~~~~~g~l~~l~~~~   78 (309)
T 1nnf_A            2 ITVYNGQQ--KEAATAVAKAFEQ-ETGIKVTLNSGKSEQLAGQLKEEGDKTPADVFYTEQTATFADLSEAGLLAPISEQT   78 (309)
T ss_dssp             EEEEECSC--HHHHHHHHHHHHH-HSCCCEEEEECCHHHHHHHHHHHGGGCCCSEEEESCGGGHHHHHHTTCBCCCCHHH
T ss_pred             eEEEeCCC--HHHHHHHHHHHHh-CCCcEEEEEeCChHHHHHHHHHhcCCCCCCEEEecchhHHHHHHHCCCcccCCHHH
Confidence            45544433  2477889999985 699999998888888888884  2  4689987642100           00    


Q ss_pred             -----CCc-------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCe---EeecCCCCcHHHHH------------
Q psy3760         156 -----DKL-------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL---ITYDLSFSGRIKLD------------  208 (306)
Q Consensus       156 -----~~~-------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~---i~~~~~~~~~~~~~------------  208 (306)
                           +.+       ...++.....+++.+++..-....+-+++||.+..+   +...........+.            
T Consensus        79 ~~~~~~~~~~~~~~g~~~P~~~~~~~l~YNk~~~~~~~~P~tw~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~~G~~~a  158 (309)
T 1nnf_A           79 IQQTAQKGVPLAPKKDWIALSGRSRVVVYDHTKLSEKDMEKSVLDYATPKWKGKIGYVSTSGAFLEQVVALSKMKGDKVA  158 (309)
T ss_dssp             HHTTCCTTCCCCTTSCCEEEEEEEEEEEEETTTCCGGGSCSSGGGGGSGGGTTTEEECTTSHHHHHHHHHHHHHHCHHHH
T ss_pred             hhhcchhhcccCCCCeEEEeeeeEEEEEEehhhccccCCCCCHHHHhchhhcCeEeecCCCchHHHHHHHHHHhcChHHH
Confidence                 001       123445556678888775322234568998876221   22222211111111            


Q ss_pred             -HHHHhCCCceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc-c-----cCCceee-ecCC--CCccceEEEEEeCC
Q psy3760         209 -REFSLQKLTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN-R-----DKNLRSI-SASH--LFGTTISRVIIKQG  277 (306)
Q Consensus       209 -~~~~~~~~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~-----~~~l~~~-~~~~--~~~~~~~~l~~~~~  277 (306)
                       +++...  ..+.. ...+.....+++.+| .++++...+..... .     ...+... |.+.  ........+...++
T Consensus       159 ~~~l~~l--~~~~~-~~~~~~~~~~~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~g~~~~~~~~~i~~~  235 (309)
T 1nnf_A          159 LNWLKGL--KENGK-LYAKNSVALQAVENGEVPAALINNYYWYNLAKEKGVENLKSRLYFVRHQDPGALVSYSGAAVLKA  235 (309)
T ss_dssp             HHHHHHH--HHHEE-ECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHHHHCGGGCSEEEECCCTTCGGGCEEEEEEEEBTT
T ss_pred             HHHHHHH--HHhCC-CCCCCchHHHHHhcCCccEEEccHHHHHHHHhcccCCCCceEEeCCCCCCCceeeccccEEEEcC
Confidence             111111  11222 224556777888888 44445444333221 1     1234432 2221  11222334555666


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .....++++|++++.+.
T Consensus       236 s~~~~aA~~fi~~l~s~  252 (309)
T 1nnf_A          236 SKNQAEAQKFVDFLASK  252 (309)
T ss_dssp             CSCHHHHHHHHHHHHSH
T ss_pred             CCCHHHHHHHHHHHhCH
Confidence            66678899999999653

>3o6p_A Peptide ABC transporter, peptide-binding protein; structural genomics, PSI-2, protein structure initiative; 1.65A {Enterococcus faecalis}

Probab=84.75  E-value=7.8  Score=29.15  Aligned_cols=56  Identities=9%  Similarity=0.044  Sum_probs=43.3

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHh-CCCcEEEEEeCChhHHHHHHHcCCeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQ-FPKVKLSLLQGNPKQITEMIRNDQADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~-~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~  149 (306)
                      .++|.++..-...-+..++.+-.++ .|++++++...+.....+.+.+|+.|+++..
T Consensus       100 ~l~l~~~~~~~~~~~a~~i~~~l~~~i~GI~v~i~~~~~~~~~~~~~~g~~d~~~~~  156 (229)
T 3o6p_A          100 TMDILSSDADSSKKTVEFVQGSIQDALDGVKVTVSPVPFSVRLDRSNKGDFDAVIGG  156 (229)
T ss_dssp             EEEEEEECSHHHHHHHHHHHHHHHHHSTTEEEEEEEECHHHHHHHHHHTCCSEEEEE
T ss_pred             EEEEEeCCChHHHHHHHHHHHHHHHhCCCcEEEEEecCHHHHHHHhhcCCceEEEec
Confidence            6777775443344566677766666 6899999999998899999999999999864

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=83.96  E-value=1.6  Score=26.59  Aligned_cols=25  Identities=16%  Similarity=0.110  Sum_probs=21.3

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .+.| |-...|+.+|+|+++||+..+
T Consensus         9 ~~~g-sq~~lA~~lgvs~~~is~~e~   33 (79)
T 3bd1_A            9 NKLG-SVSALAASLGVRQSAISNWRA   33 (79)
T ss_dssp             HHHS-SHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHhC-CHHHHHHHHCCCHHHHHHHHH
Confidence            4567 899999999999999998643

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=83.85  E-value=1.3  Score=25.59  Aligned_cols=23  Identities=35%  Similarity=0.349  Sum_probs=20.5

Q ss_pred             CHHHHHHHh-----CCCchHHHHHHHHH
Q psy3760          18 NLTEAAKAL-----YTSQPGVSKAIIEL   40 (306)
Q Consensus        18 s~~~aA~~l-----~isq~~~s~~i~~L   40 (306)
                      |...-++.|     ++|++||.|.|+++
T Consensus        21 t~~el~~~l~~~~~~vs~~Tv~R~L~~l   48 (64)
T 2p5k_A           21 TQDELVDMLKQDGYKVTQATVSRDIKEL   48 (64)
T ss_dssp             SHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCCcCHHHHHHHHHHc
Confidence            677889999     99999999999944

>4eq9_A ABC transporter substrate-binding protein-amino A transport; structural genomics, niaid; HET: GSH; 1.40A {Streptococcus pneumoniae}

Probab=83.72  E-value=3.5  Score=31.10  Aligned_cols=52  Identities=13%  Similarity=0.157  Sum_probs=37.9

Q ss_pred             EEEEecccchhhhhHHHHHHHHHhCCCcEEEEE--eCChhHHHHHHHcCCeeEEEEc
Q psy3760          95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLL--QGNPKQITEMIRNDQADIAIVT  149 (306)
Q Consensus        95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~--~~~~~~~~~~l~~~~~Di~i~~  149 (306)
                      .+||+..+.   .....+..+...+|...+.+.  ..+..+.++.|.+|++|.++..
T Consensus       116 ~~i~~~~g~---~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~g~vDa~~~~  169 (246)
T 4eq9_A          116 KSTEVVQAT---TSAKQLEAYNAEHTDNPTILNYTKADFQQIMVRLSDGQFDYKIFD  169 (246)
T ss_dssp             CEEEECTTC---HHHHHHHHHHHHCTTSCCEEEECCCCHHHHHHHHHTTSSSEEEEE
T ss_pred             CEEEEecCc---cHHHHHHHHHhhCCCcceEEEecCCCHHHHHHHHHcCCceEEEec
Confidence            477876543   235566677778886555554  3477899999999999999985

>1iej_A Ovotransferrin; iron, metal binding protein; 1.65A {Gallus gallus} SCOP: c.94.1.2 PDB: 1tfa_A 1nft_A 1nnt_A 1ovb_A 1gv8_A 1gvc_A*

Probab=83.71  E-value=12  Score=30.26  Aligned_cols=116  Identities=12%  Similarity=0.033  Sum_probs=65.1

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEcccc----C-CCCCce---eecc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEIL----S-PSDKLI---SIPC  163 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~----~-~~~~~~---~~~l  163 (306)
                      ..+|+++.......-...+...+..  -+..+++... +..+.++.|.+|++|+++.....    . ...++.   ....
T Consensus         5 ~~vrwCv~s~~E~~KC~~l~~~~~~--~~~~veCv~~~s~~~Ci~aI~~g~aD~~~ld~~~~~~A~~~~~~l~pi~~e~~   82 (332)
T 1iej_A            5 SVIRWCTISSPEEKKCNNLRDLTQQ--ERISLTCVQKATYLDCIKAIANNEADAITLDGGQVFEAGLAPYKLKPIAAEVY   82 (332)
T ss_dssp             EEEEEEESSHHHHHHHHHHHHHTTT--SSEEEEEEECSSHHHHHHHHHTTSCCBEEECHHHHHHHTSTTTCCEEEEEEEE
T ss_pred             CcEEEEECCHHHHHHHHHHHHHHHh--cCCceEEEEcCCHHHHHHHHHcCCCcEEEeCccceeEecccccCCEEEEEEEe
Confidence            3589998875444333433333311  2445665553 67789999999999999984110    0 111221   1111


Q ss_pred             c-------cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCC-cHHHHHHHHHhCCC
Q psy3760         164 Y-------QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFS-GRIKLDREFSLQKL  216 (306)
Q Consensus       164 ~-------~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~-~~~~~~~~~~~~~~  216 (306)
                      .       ...-++|+.++.+      ++++||.+...-....+.. -+..-...+.+.|+
T Consensus        83 ~~~~~~~~~Y~aVaVVkkdS~------isl~dLkGKksChtg~~stsGw~~Pi~~L~~~g~  137 (332)
T 1iej_A           83 EHTEGSTTSYYAVAVVKKGTE------FTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGA  137 (332)
T ss_dssp             ECSSSEESEEEEEEEEETTCC------CCGGGCTTCEEEESCTTCTTTTHHHHHHHHHTTS
T ss_pred             cCCCCCCCceEEEEEEeCCCC------CCHHHHCCCceEcCCCCCccchHHHHHHHHHcCC
Confidence            1       1123677777753      5899999988777666543 12233344445554

>1h45_A Lactoferrin; metal transport, iron transport, metal binding; 1.95A {Homo sapiens} SCOP: c.94.1.2 PDB: 1eh3_A 2pms_A* 1h43_A 1h44_A 1dsn_A 1lct_A 1hse_A 1vfe_A 1l5t_A 1vfd_A 1lgb_C* 1z6v_A 1z6w_A

Probab=83.64  E-value=4.5  Score=32.76  Aligned_cols=101  Identities=14%  Similarity=0.126  Sum_probs=60.4

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCcee--eccc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLIS--IPCY  164 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~--~~l~  164 (306)
                      ..+|+++.......-...+...+.. .++..+++... +..+.++.|.+|++|+++......     ...++..  .+.+
T Consensus         5 ~~vrwCv~s~~e~~KC~~l~~~~~~-~~~~~vecv~~~~~~~ci~aI~~g~AD~~~ld~~~~~~A~~~~~~l~pi~~e~~   83 (334)
T 1h45_A            5 RSVQWCAVSQPEATKCFQWQRNMRR-VRGPPVSCIKRDSPIQCIQAIAENRADAVTLDGGFIYEAGLAPYKLRPVAAEVY   83 (334)
T ss_dssp             TSEEEEESSHHHHHHHHHHHHHHHH-TTCCCEEEEECSSHHHHHHHHHTTSCCBEEECHHHHHHHHSTTTCEEEEEEEEE
T ss_pred             CcEEEEECCHHHHHHHHHHHHHHhh-cCCCceEEEEcCCHHHHHHHHHcCCCCEEEeCccceEEeecCccCCEEEEEEee
Confidence            5699999876554455555555533 33445555543 667899999999999999841100     1122221  1111


Q ss_pred             c--------ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCC
Q psy3760         165 Q--------WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLS  200 (306)
Q Consensus       165 ~--------~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~  200 (306)
                      .        ..-++|+.++.+      ++++||.+...-....+
T Consensus        84 ~~~~~~~~~Y~avaVVkk~s~------isl~dLkGKksch~~~~  121 (334)
T 1h45_A           84 GTERQPRTHYYAVAVVKKGGS------FQLNELQGLKSCHTGLR  121 (334)
T ss_dssp             ECSSSEESEEEEEEEEETTCC------CCGGGCTTCEEEESCTT
T ss_pred             cCCCCCCCceEEEEEEeCCCC------CCHHHHCCCceecCCCC
Confidence            1        122667777763      58999998776665544

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=83.53  E-value=1.2  Score=29.25  Aligned_cols=29  Identities=7%  Similarity=0.047  Sum_probs=25.9

Q ss_pred             cCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760          16 NFNLTEAAKALYTSQPGVSKAIIELEEELS   45 (306)
Q Consensus        16 ~~s~~~aA~~l~isq~~~s~~i~~LE~~lg   45 (306)
                      . |+..+|+.+|||+++|.+.+++.+..-+
T Consensus        31 ~-s~~~va~~~gIs~~tl~~W~~~~~~~~~   59 (108)
T 2rn7_A           31 A-TICSIAPKIGCTPETLRVWVRQHERDTG   59 (108)
T ss_dssp             H-HHHHHHHHHTSCHHHHHHHHHHHHTTSC
T ss_pred             c-cHHHHHHHHCcCHHHHHHHHHHHHhccc
Confidence            5 8999999999999999999999877543

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

Probab=83.53  E-value=2.2  Score=27.57  Aligned_cols=38  Identities=21%  Similarity=0.207  Sum_probs=32.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE   42 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~   42 (306)
                      .+.+...+.+.+.|+.+||+..+||.++|.+..+..++
T Consensus        39 K~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~   76 (101)
T 2oa4_A           39 KIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAE   76 (101)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            45677778877778999999999999999999888764

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=83.52  E-value=1.3  Score=33.40  Aligned_cols=43  Identities=12%  Similarity=0.143  Sum_probs=37.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      -+..+++..+++.. |-..-|+.|++|..|+..++++|-+.||+
T Consensus       162 ~rE~~vL~~l~~g~-s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~  204 (225)
T 3klo_A          162 KREQQIIKLLGSGA-SNIEIADKLFVSENTVKTHLHNVFKKINA  204 (225)
T ss_dssp             HHHHHHHHHHTTTC-CHHHHHHHTTCCHHHHHHHHHHHTTTSCC
T ss_pred             HHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            35566777777765 99999999999999999999999999986

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=83.20  E-value=3.7  Score=31.40  Aligned_cols=44  Identities=20%  Similarity=0.092  Sum_probs=32.8

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ   64 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~   64 (306)
                      |...-|+.+|+|.++|...|+.||.+ |.-- .+.++|. ..++...
T Consensus        51 ~e~~La~~lgVSr~~VReAL~~L~~~-Glv~-~~~~~G~-~V~~~~~   94 (237)
T 3c7j_A           51 RQQELATLFGVSRMPVREALRQLEAQ-SLLR-VETHKGA-VVAPLIT   94 (237)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHT-TSEE-EETTTEE-EECCCHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CCEE-EeCCCce-EEecCCH
Confidence            56778999999999999999999876 5422 3336676 4666554

>2ozz_A Hypothetical protein YHFZ; alpha-beta structure, structural genomics, PSI-2, protein structure initiative; 2.30A {Shigella flexneri 2A} SCOP: c.94.1.1

Probab=83.11  E-value=2.2  Score=32.44  Aligned_cols=49  Identities=10%  Similarity=0.077  Sum_probs=37.4

Q ss_pred             EEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEc
Q psy3760          95 LTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT  149 (306)
Q Consensus        95 l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~  149 (306)
                      -|||+..+.... ++..    ..  +++..++..+.+..+++..|.+|++|.++..
T Consensus       113 krVGvd~gS~dq~~lt~----~~--~~g~~Ve~ve~~y~~~i~~L~~G~IDA~Iwn  162 (231)
T 2ozz_A          113 KRVGLDSRSADQKIMTD----VF--FGDSDVERVDLSYHESLQRIVKGDVDAVIWN  162 (231)
T ss_dssp             CEEEECTTCHHHHHHHH----HH--HTTSCCEEEECCHHHHHHHHHHTSCCEEEEE
T ss_pred             EEEEecCCChhHHHHHh----hh--cCCCeEEEEECCHHHHHHHHHcCCccEEEEc
Confidence            599998764333 3333    22  2688888998899999999999999999993

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=83.06  E-value=0.75  Score=37.26  Aligned_cols=113  Identities=17%  Similarity=0.191  Sum_probs=33.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT   96 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~   96 (306)
                      |+...|+..|+|.+||||.|..-             .++ . -+.-++..+.++    ++.-.-+ ..+.+..+.++.|-
T Consensus         5 ti~diA~~agVS~~TVSrvln~~-------------~~v-s-~~tr~rV~~~a~----~lgY~pn~~a~~l~~~~~~~Ig   65 (338)
T 3dbi_A            5 TMLEVAKRAGVSKATVSRVLSGN-------------GYV-S-QETKDRVFQAVE----ESGYRPNLLARNLSAKSTQTLG   65 (338)
T ss_dssp             --------------------------------------------------------------------------CCSEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCC-------------CCC-C-HHHHHHHHHHHH----HHCCCcCHHHHHhhhCCCCEEE
Confidence            67889999999999999999631             111 1 011111111111    1111111 11222233344444


Q ss_pred             EEeccc-chhhhhHHHHHHHHHhC--CCcEEEEEeCCh--h---HHHHHHHcCCeeEEEEc
Q psy3760          97 IATTHT-QARYALPKIIKEFTIQF--PKVKLSLLQGNP--K---QITEMIRNDQADIAIVT  149 (306)
Q Consensus        97 I~~~~~-~~~~~l~~~l~~~~~~~--p~~~i~~~~~~~--~---~~~~~l~~~~~Di~i~~  149 (306)
                      +-++.. +...++..++..+.+..  -++.+.+.....  .   +.++.+.+.++|-.|+.
T Consensus        66 vi~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~  126 (338)
T 3dbi_A           66 LVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIY  126 (338)
T ss_dssp             EEECTTTTSTTHHHHHHHHHHHHHHHTTCEEEEEECTTSHHHHHHHHHHHHHTTCSEEEEC
T ss_pred             EEecCCcccChhHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEe
Confidence            444431 34456666665554332  256666655322  1   25677888899999885

>1i3j_A I-TEVI, intron-associated endonuclease 1; protein-DNA complex, extended structure, Zn-finger, minor groove helix, helix-turn-helix; 2.20A {Enterobacteria phage T4} SCOP: d.285.1.1 PDB: 1t2t_A

Probab=83.03  E-value=0.92  Score=30.26  Aligned_cols=24  Identities=17%  Similarity=0.081  Sum_probs=21.8

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      -+ |...||+.|+++.++|+++++.
T Consensus        83 f~-S~~eAar~lg~s~~ti~~~~~~  106 (116)
T 1i3j_A           83 FD-CAADAARHFKISSGLVTYRVKS  106 (116)
T ss_dssp             ES-SHHHHHHHHTCCHHHHHHHHHC
T ss_pred             Ec-CHHHHHHHHCCCchhHHHHHhc
Confidence            56 9999999999999999999964

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

Probab=82.71  E-value=2.4  Score=27.03  Aligned_cols=28  Identities=21%  Similarity=0.146  Sum_probs=22.6

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .+.+.+-++...|+.+|+|.+|||+.+.
T Consensus        15 ~l~~~~~ti~dlA~~~gVS~~TVsR~L~   42 (93)
T 2l0k_A           15 YIVETKKTVRVIAKEFGVSKSTVHKDLT   42 (93)
T ss_dssp             HHHHHCCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            3334444899999999999999999884

>2qry_A Thiamine-binding periplasmic protein; thiamin binding protein, ABC transporter, transport protein; HET: TPS; 2.25A {Escherichia coli}

Probab=82.51  E-value=17  Score=29.00  Aligned_cols=199  Identities=14%  Similarity=0.029  Sum_probs=107.8

Q ss_pred             CCCcEEEEecccchhh--hhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHc----CCeeEEEEcc-c----------c
Q psy3760          91 DTGNLTIATTHTQARY--ALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRN----DQADIAIVTE-I----------L  152 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~--~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~----~~~Di~i~~~-~----------~  152 (306)
                      ..++|+|....+....  .+..++..|.+++ +++|++...+ ..++.+.|..    +..|+.+... .          .
T Consensus        21 ~~~~L~v~~~~~~~~~~~~~~~~~~~Fe~~~-gi~V~~~~~~~~~~~~~kl~~~~~~~~pDv~~~~~~~~~~~~~~~g~l   99 (330)
T 2qry_A           21 MKPVLTVYTYDSFAADWGPGPVVKKAFEADC-NCELKLVALEDGVSLLNRLRMEGKNSKADVVLGLDNNLLDAASKTGLF   99 (330)
T ss_dssp             -CCEEEEEECHHHHSTTSSHHHHHHHHHTTS-CSEEEEEECSCHHHHHHHHHHHGGGCCCSEEEEEEGGGHHHHHHHTCB
T ss_pred             CCCeEEEEeccccccchhhhHHHHHHHHHHH-CCEEEEEeCCCHHHHHHHHHhccCCCCCCEEEEcChHHHHHHHHCCce
Confidence            4568999886543333  3688999999998 9999998865 6677666643    3689988321 1          0


Q ss_pred             CCC--C-----------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCCC-cH-HHH------
Q psy3760         153 SPS--D-----------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSFS-GR-IKL------  207 (306)
Q Consensus       153 ~~~--~-----------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~~-~~-~~~------  207 (306)
                      .+-  .           +....|+.....+++.+++-.  ...+-+++||.+..    +....+... .. ..+      
T Consensus       100 ~~l~~~~~~~~~~~~~~~~y~vP~~~~~~~l~YNkd~~--~~~P~Tw~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  177 (330)
T 2qry_A          100 AKSGVAADAVNVPGGWNNDTFVPFDYGYFAFVYDKNKL--KNPPQSLKELVESDQNWRVIYQDPRTSTPGLGLLLWMQKV  177 (330)
T ss_dssp             CCCCCCGGGCCCTTCCCCSSCEEEEEEEEEEEEETTTC--SSCCSSHHHHHHCSSCCCEEEECTTTCHHHHHHHHHHHHH
T ss_pred             eccccccccccCCHHHhcCeEEEEeccceEEEEehhhc--cCCCCCHHHHHhHHhcCeeEeeCCCCCchHHHHHHHHHHh
Confidence            010  0           011345556677888888753  23567999986532    233222211 11 111      


Q ss_pred             -----HHHHHhCCCceeEEEEecCHHHHHHHHHhccce-eeeeccee--ccc--ccCCceeeecCCCCccceEEEEEeCC
Q psy3760         208 -----DREFSLQKLTPYIVLETINSDIIKTYVELRMGI-GIIASIAF--DSN--RDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       208 -----~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi-~~~p~~~~--~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                           .+++...  ..+......+.....+++.+|... ++......  ...  ...++...++++.......++...++
T Consensus       178 ~g~~a~~~~~~l--~~~~~~~~~~~~~~~~~f~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~p~~g~~~~~~~~~i~~~  255 (330)
T 2qry_A          178 YGDDAPQAWQKL--AKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAA  255 (330)
T ss_dssp             HGGGHHHHHHHH--HTTEEEEESSHHHHHHHHHTTSCSEEEEETTHHHHHHHHHCCCCEEECCCTTCEEEEEEEEEEBTT
T ss_pred             hChHHHHHHHHH--HhcCceeccChHHHHHHHhCCCEEEEEecccHHHHHhhhccCCceeEEeCCCCCeeeeeEEEEECC
Confidence                 1111111  123332344566677788888443 33322211  111  12344444333222222334555677


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .....++.+|++++.+.
T Consensus       256 s~~~~~A~~fi~fl~s~  272 (330)
T 2qry_A          256 SKQPELAQKFLQFMVSP  272 (330)
T ss_dssp             CSCHHHHHHHHHHHTSH
T ss_pred             CCCHHHHHHHHHHHcCH
Confidence            77778899999999653

>3u5c_T 40S ribosomal protein S19-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_S 3o30_M 3o2z_M 3u5g_T 3jyv_T*

Probab=82.41  E-value=1.8  Score=29.89  Aligned_cols=37  Identities=24%  Similarity=0.167  Sum_probs=28.7

Q ss_pred             chHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHH
Q psy3760          30 QPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSI   70 (306)
Q Consensus        30 q~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a   70 (306)
                      -+-+-+.+++||+   ..|+++.. +|- .+|+.|+.++..+
T Consensus        98 g~iiR~~LQqLE~---~g~vek~~~~GR-~lT~~G~~~LD~i  135 (144)
T 3u5c_T           98 GSINRKVLQALEK---IGIVEISPKGGR-RISENGQRDLDRI  135 (144)
T ss_dssp             HHHHHHHHHHHHH---TTSEECCSSSSC-EECHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHH---CCCeeecCCCCc-EECHhHHHHHHHH
Confidence            3567788999997   46778774 577 6999999988764

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=82.04  E-value=1.1  Score=36.13  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=0.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      |+...|+..|+|++||||.|...
T Consensus         7 ti~diA~~agVS~~TVSrvln~~   29 (332)
T 2o20_A            7 TIYDVARVAGVSMATVSRVVNGN   29 (332)
T ss_dssp             -----------------------
T ss_pred             cHHHHHHHHCCCHHHHHHHHcCC
Confidence            67889999999999999999864

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=81.31  E-value=1.3  Score=30.42  Aligned_cols=37  Identities=32%  Similarity=0.367  Sum_probs=29.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |...-|+.+++|.++|.++++.||.+ |. +..+.++|.
T Consensus        40 ser~La~~~gVSr~tVReAl~~L~~e-Gl-v~~~~g~G~   76 (134)
T 4ham_A           40 SIREFASRIGVNPNTVSKAYQELERQ-EV-IITVKGKGT   76 (134)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT-TS-EEEETTTEE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHC-Cc-EEEEcCcEE
Confidence            56788999999999999999999876 33 334455665

>3iz6_S 40S ribosomal protein S19 (S19E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=81.27  E-value=1.6  Score=30.25  Aligned_cols=38  Identities=16%  Similarity=0.115  Sum_probs=28.8

Q ss_pred             CchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHH
Q psy3760          29 SQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSI   70 (306)
Q Consensus        29 sq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a   70 (306)
                      |-+-+-+.+++||+   ..|+++.. +|- .+|+.|+.++..+
T Consensus        99 sg~iiR~~LQqLE~---~g~Vek~~~gGR-~lT~~G~~~LD~i  137 (146)
T 3iz6_S           99 SGAISRNILQQLQK---MGIIDVDPKGGR-LITSQGRRDLDQV  137 (146)
T ss_dssp             CHHHHHHHHHHHHH---HTSEEEETTTEE-EECHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHH---CCCeEecCCCCc-EECHhHHHHHHHH
Confidence            34567788999997   46777775 576 6999999988764

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

Probab=81.21  E-value=4  Score=26.47  Aligned_cols=42  Identities=14%  Similarity=0.111  Sum_probs=34.8

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS   45 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg   45 (306)
                      +|+-.+++---++.|+.+-++.+|...+||..+++++|+.+.
T Consensus        38 RqiAmYL~r~~t~~Sl~~IG~~fgRDHsTV~ha~~ki~~~~~   79 (101)
T 3pvv_A           38 RQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMA   79 (101)
T ss_dssp             HHHHHHHHHHHCCCCHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            455555555556679999999999999999999999999874

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

Probab=80.64  E-value=1.9  Score=29.32  Aligned_cols=38  Identities=16%  Similarity=0.125  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCHH-HHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           7 RFVREAVRQNFNLT-EAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         7 ~~f~~v~~~~~s~~-~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      ++...+.+.|.+.. .+|+.+||++++|++.++.-+...
T Consensus        15 ~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~   53 (131)
T 1hlv_A           15 RIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAIL   53 (131)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHH
T ss_pred             HHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhhc
Confidence            33333335552333 799999999999999999877643

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=80.62  E-value=1.3  Score=31.08  Aligned_cols=32  Identities=22%  Similarity=0.166  Sum_probs=25.0

Q ss_pred             HHHHHhcCCHHHHHHHh-----CCCchHHHHHHHHHHH
Q psy3760          10 REAVRQNFNLTEAAKAL-----YTSQPGVSKAIIELEE   42 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l-----~isq~~~s~~i~~LE~   42 (306)
                      +.-..-. |...=++.|     ++||+|+||-|++|+.
T Consensus        14 i~~~~~~-tq~eL~~~L~~~G~~VtqaTisRDL~eL~~   50 (149)
T 1b4a_A           14 IMSNDIE-TQDELVDRLREAGFNVTQATVSRDIKEMQL   50 (149)
T ss_dssp             HHHSCCC-SHHHHHHHHHHTTCCCCHHHHHHHHHHTTC
T ss_pred             HHHCCCc-cHHHHHHHHHHcCCCcCHHHHHHHHHHcCC
Confidence            3333445 777888999     9999999999999854

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=80.61  E-value=2.7  Score=30.98  Aligned_cols=43  Identities=12%  Similarity=0.090  Sum_probs=36.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +..+++..+++.. |-..-|+.|++|..|+..+++++-+.||..
T Consensus       146 rE~~vl~~l~~g~-s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~~  188 (208)
T 1yio_A          146 REQQVLQLTIRGL-MNKQIAGELGIAEVTVKVHRHNIMQKLNVR  188 (208)
T ss_dssp             HHHHHHHHHTTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHcCC-cHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence            4456666677666 999999999999999999999999999863

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

Probab=80.45  E-value=1.2  Score=33.91  Aligned_cols=38  Identities=13%  Similarity=0.099  Sum_probs=30.0

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      -..-|..+|+|+.++||.+++|+++ |  + ..+++.+ .+.+
T Consensus       181 ~~~iA~~lg~sr~tvsR~l~~L~~~-g--i-~~~~~~i-~I~d  218 (237)
T 3fx3_A          181 KMLIAGRLGMKPESLSRAFSRLKAA-G--V-TVKRNHA-EIED  218 (237)
T ss_dssp             THHHHHHTTCCHHHHHHHHHHHGGG-T--E-ECCTTEE-EESC
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHC-C--e-EeeCCEE-EEcC
Confidence            4578999999999999999999987 6  3 4556666 4543

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=80.35  E-value=2.2  Score=30.63  Aligned_cols=24  Identities=46%  Similarity=0.347  Sum_probs=20.1

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      .+.|.|-.++|+.||+|++++|+-
T Consensus       100 ~~~glTQ~elA~~LGvsr~tis~y  123 (170)
T 2auw_A          100 HRNNLSLTTAAEALGISRRMVSYY  123 (170)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHH
Confidence            445668899999999999999863

---

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	306
d1al3a_	237	c.94.1.1 (A:) Cofactor-binding fragment of LysR-ty	5e-34
d2fyia1	220	c.94.1.1 (A:88-307) LysR-type regulatory protein C	4e-24
d1i6aa_	212	c.94.1.1 (A:) Hydrogen peroxide-inducible genes Ly	1e-15
d2esna1	89	a.4.5.37 (A:3-91) Probable LysR-type transcription	4e-11
d2esna2	212	c.94.1.1 (A:92-303) Probable LysR-type transcripti	1e-10
d1utha_	219	c.94.1.1 (A:) LysR-type regulatory protein DntR {B	4e-10
d1ixca1	89	a.4.5.37 (A:1-89) LysR-type regulatory protein Cbn	7e-09
d1ixca2	205	c.94.1.1 (A:90-294) LysR-type regulatory protein C	2e-06
d1b9ma1	127	a.4.5.8 (A:-1-126) N-terminal domain of molybdate-	5e-05

>d1al3a_ c.94.1.1 (A:) Cofactor-binding fragment of LysR-type protein CysB {Klebsiella aerogenes [TaxId: 28451]} Length = 237

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Cofactor-binding fragment of LysR-type protein CysB
species: Klebsiella aerogenes [TaxId: 28451]

 Score =  122 bits (306), Expect = 5e-34
 Identities = 93/214 (43%), Positives = 139/214 (64%)

Query: 91  DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
           D G+L +ATTHTQARYALP +IK F  ++P+V L + QG+P QI E +    AD AI TE
Sbjct: 4   DKGSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATE 63

Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
            L   D L+ +PCY W   I+V  +HPL    S+S++E++ YPL+TY   F+GR +LD  
Sbjct: 64  ALHLYDDLVMLPCYHWNRSIVVTPEHPLATKGSVSIEELAQYPLVTYTFGFTGRSELDTA 123

Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTIS 270
           F+   LTP IV    ++D+IKTYV L +G+G+IAS+A D   D +L  + A+ +F  + +
Sbjct: 124 FNRAGLTPRIVFTATDADVIKTYVRLGLGVGVIASMAVDPVSDPDLVKLDANGIFSHSTT 183

Query: 271 RVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304
           ++  ++ T+LRSY+Y FI+  +P L R  ++  +
Sbjct: 184 KIGFRRSTFLRSYMYDFIQRFAPHLTRDVVDTAV 217

>d2fyia1 c.94.1.1 (A:88-307) LysR-type regulatory protein Cbl {Escherichia coli [TaxId: 562]} Length = 220

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein Cbl
species: Escherichia coli [TaxId: 562]

 Score = 95.6 bits (236), Expect = 4e-24
 Identities = 85/211 (40%), Positives = 139/211 (65%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
           +G LTIATTHTQARY+LP++IK F   FP+V+L L+QG P++I  +++N +ADI I +E 
Sbjct: 5   SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASER 64

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
           LS   +L++ P ++W + ++VP DHPL  ++ ++L+ I+ +PLITY    +GR ++D  F
Sbjct: 65  LSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDAF 124

Query: 212 SLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISR 271
           + + L   IVL   +SD+IKTYV L +GIG++A  +     ++NL  +   HLF      
Sbjct: 125 ARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEEENLIRLDTRHLFDANTVW 184

Query: 272 VIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302
           + +K+G   R+YV+ F++L +  L+ + I +
Sbjct: 185 LGLKRGQLQRNYVWRFLELCNAGLSVEDIKR 215

>d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]} Length = 212

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain
species: Escherichia coli [TaxId: 562]

 Score = 72.1 bits (175), Expect = 1e-15
 Identities = 33/211 (15%), Positives = 74/211 (35%), Gaps = 6/211 (2%)

Query: 92  TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
           +G L I    T   Y LP II      FPK+++ L +           +     A++  +
Sbjct: 4   SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQT-HQLLAQLDSGKLDAVILAL 62

Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREF 211
           +  S+  I +P +    ++ +  DHP     ++ + +++   L+  +     R +     
Sbjct: 63  VKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFC 122

Query: 212 SLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISR 271
                         + + ++  V    G GI    A     ++    +           R
Sbjct: 123 FEAGADEDTHFRATSLETLRNMV--AAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRR 180

Query: 272 ---VIIKQGTYLRSYVYSFIKLLSPKLNRKF 299
              ++ + G+ LRS      + +  +++  F
Sbjct: 181 TIGLVYRPGSPLRSRYEQLAEAIRARMDGHF 211

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]} Length = 89

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 56.4 bits (136), Expect = 4e-11
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 1  MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
          ++L+         R   N+  AA  L  S    S A+  L + L  ++F+R G R++  T
Sbjct: 6  LDLNLLLVFDALYRHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQ-PT 63

Query: 61 KPGQAILRSIEIIMQEIE 78
          +  + +  ++   ++ + 
Sbjct: 64 QRAEHLAAAVAAALRALG 81

>d2esna2 c.94.1.1 (A:92-303) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]} Length = 212

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 57.8 bits (138), Expect = 1e-10
 Identities = 23/173 (13%), Positives = 45/173 (26%), Gaps = 2/173 (1%)

Query: 89  AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI- 147
                    A T   A   LP ++       P V+L L+    K   E + + + D A+ 
Sbjct: 4   GQSQRTFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALG 63

Query: 148 VTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKL 207
             E      + I    +  +  ++V       L  + +L+                   +
Sbjct: 64  YDEEHERLPEGIQAHDWFADRYVVVARRDHPRLAGAPTLEGYLAERHAVVTPWNEDSGVI 123

Query: 208 DREFSLQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSI 259
           DR  +   L   + ++                +       A        L   
Sbjct: 124 DRLLARSGLRREVAVQLPTVLAALFLAGSTDFLLTAPRHAARALAEAAGLALY 176

>d1utha_ c.94.1.1 (A:) LysR-type regulatory protein DntR {Burkholderia sp. [TaxId: 36773]} Length = 219

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein DntR
species: Burkholderia sp. [TaxId: 36773]

 Score = 56.7 bits (135), Expect = 4e-10
 Identities = 24/172 (13%), Positives = 55/172 (31%), Gaps = 3/172 (1%)

Query: 89  AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIV 148
              T    +A T     Y +P +++    + P +++S L+ N   + E + +   D+A+ 
Sbjct: 8   FASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLAL- 66

Query: 149 TEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLD 208
             +L                 + +         + +SLK+ S    +      +G  ++D
Sbjct: 67  -GLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVD 125

Query: 209 REFSLQKLTPYIVLETINSDIIKTYVELRMGIGII-ASIAFDSNRDKNLRSI 259
                  +   + L   +   I   +     I  +    A        L + 
Sbjct: 126 GLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTS 177

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]} Length = 89

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

 Score = 50.0 bits (119), Expect = 7e-09
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 1  MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
          M   Q ++         N+  AAK L+ SQP +++ +  LE +L + +  R  + I  LT
Sbjct: 1  MEFRQLKYFIAVAEAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIE-LT 58

Query: 61 KPGQAILRSIEIIMQEIE 78
            G A L     I++   
Sbjct: 59 AAGHAFLEDARRILELAG 76

>d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]} Length = 205

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

 Score = 45.6 bits (106), Expect = 2e-06
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 93  GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ 142
           G L++A   T    +LP +++ F    P   +SL      +  E +    
Sbjct: 2   GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGT 51

>d1b9ma1 a.4.5.8 (A:-1-126) N-terminal domain of molybdate-dependent transcriptional regulator ModE {Escherichia coli [TaxId: 562]} Length = 127

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: N-terminal domain of molybdate-dependent transcriptional regulator ModE
domain: N-terminal domain of molybdate-dependent transcriptional regulator ModE
species: Escherichia coli [TaxId: 562]

 Score = 40.2 bits (93), Expect = 5e-05
 Identities = 14/109 (12%), Positives = 39/109 (35%), Gaps = 5/109 (4%)

Query: 1   MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
            +  +   ++  +  + ++++ AK    S      AI E+ +     +  R      G  
Sbjct: 18  ADPRRISLLK-HIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGG 76

Query: 61  KP----GQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQAR 105
                 GQ +++  +++ Q  +    +  +  A    +L  A +    +
Sbjct: 77  AVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQ 125

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	306
d2fyia1	220	LysR-type regulatory protein Cbl {Escherichia coli	100.0
d1al3a_	237	Cofactor-binding fragment of LysR-type protein Cys	100.0
d1i6aa_	212	Hydrogen peroxide-inducible genes LysR-type activa	100.0
d1utha_	219	LysR-type regulatory protein DntR {Burkholderia sp	99.97
d1ixca2	205	LysR-type regulatory protein CbnR {Ralstonia eutro	99.97
d2esna2	212	Probable LysR-type transcriptional regulator PA047	99.97
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	99.96
d2esna1	89	Probable LysR-type transcriptional regulator PA047	99.95
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	99.91
d1twya_	249	ABC transporter, periplasmic substrate-binding pro	99.49
d1ii5a_	226	Glutamate receptor ligand binding core {Synechocys	98.29
d1atga_	231	Molybdate-binding protein, ModA {Azotobacter vinel	98.08
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	98.05
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	98.04
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	98.03
d1wdna_	223	Glutamine-binding protein {Escherichia coli [TaxId	97.99
d1xt8a1	248	Putative amino-acid transporter CjaA {Campylobacte	97.94
d1ixha_	321	Phosphate-binding protein {Escherichia coli [TaxId	97.93
d1xs5a_	240	Putative lipoprotein (NlpA family) {Treponema pall	97.89
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.87
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.86
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	97.85
d1pc3a_	333	Phosphate-binding protein {Mycobacterium tuberculo	97.83
d1amfa_	231	Molybdate-binding protein, ModA {Escherichia coli	97.82
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	97.8
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	97.79
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	97.79
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.75
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.73
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.73
d1us5a_	298	Putative GluR0 ligand binding core {Thermus thermo	97.67
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.67
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	97.67
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	97.59
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.55
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	97.52
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.48
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	97.39
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	97.38
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	97.32
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	97.3
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	97.26
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	97.21
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	97.2
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	97.18
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	97.18
d1lsta_	238	Lysine-,arginine-,ornithine-binding (LAO) protein	97.15
d1pb7a_	289	N-methyl-D-aspartate receptor subunit 1 {Rat (Ratt	97.12
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	97.11
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	97.05
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	97.02
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.92
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.82
d1d1la_	61	cro lambda repressor {Bacteriophage lambda [TaxId:	96.8
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	96.71
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	96.62
d1mqia_	260	Glutamate receptor ligand binding core {Rat (Rattu	96.61
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	96.57
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	96.54
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.51
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	96.51
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.5
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	96.47
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.43
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	96.4
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	96.4
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	96.38
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	96.26
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	96.23
d2ozza1	228	Hypothetical protein YhfZ {Shigella flexneri [TaxI	96.23
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.17
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	96.17
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	96.14
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.13
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	96.13
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	96.01
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	95.98
d2a5sa1	277	N-methyl-D-aspartate receptor subunit 1 {Rat (Ratt	95.86
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.84
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	95.83
d1p99a_	255	Putative lipoprotein (NlpA family) {Staphylococcus	95.82
d1sbpa_	309	Sulphate-binding protein {Salmonella typhimurium [	95.28
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	94.87
d1xvxa_	311	Ferric-binding protein FbpA {Yersinia enterocoliti	94.57
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	94.23
d1sw5a_	270	Osmoprotection protein ProX {Archaeoglobus fulgidu	94.1
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	94.01
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	93.7
d1h3da1	220	ATP phosphoribosyltransferase (ATP-PRTase, HisG),	93.69
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	93.63
d1pdaa1	217	Porphobilinogen deaminase (hydroxymethylbilane syn	93.62
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.5
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	93.47
d1u3em2	69	Intron-encoded homing endonuclease I-HmuI {Bacteri	92.75
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.72
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	92.7
d2nxoa1	277	Hypothetical protein SCo4506 {Streptomyces coelico	92.39
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	92.32
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	91.61
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	91.55
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	91.06
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	90.93
d1zyba1	73	Probable transcription regulator BT4300, C-termina	90.9
d1i3ja_	96	DNA-binding domain of intron endonuclease I-TevI {	90.81
d1o63a_	203	ATP phosphoribosyltransferase (ATP-PRTase, HisG),	90.79
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	90.7
d2f34a1	246	Glutamate receptor ligand binding core {Rat (Rattu	90.42
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	89.59
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	89.59
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	89.56
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	89.09
d2onsa1	311	Molybdate-binding protein, ModA {Archaeoglobus ful	88.93
d1nh8a1	210	ATP phosphoribosyltransferase (ATP-PRTase, HisG),	88.65
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	88.35
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	88.21
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	88.01
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	86.87
d1y0ua_	89	Putative arsenical resistance operon repressor AF0	86.45
d2qmwa1	184	Prephenate dehydratase {Staphylococcus aureus [Tax	86.33
d1r9la_	309	Glycine betaine-binding periplasmic protein ProX {	86.31
d1q35a_	318	Ferric-binding protein FbpA {Mannheimia haemolytic	85.27
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	85.22
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	85.19
d1hlva1	66	DNA-binding domain of centromere binding protein B	85.0
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	84.87
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	83.52
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	82.95
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	82.81
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	82.67
d2p5ka1	63	Arginine repressor (ArgR), N-terminal DNA-binding	82.45
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	81.39
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	81.31
d2b0la1	91	GTP-sensing transcriptional pleiotropic repressor	81.28
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	80.47
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	80.24
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	80.03

>d2fyia1 c.94.1.1 (A:88-307) LysR-type regulatory protein Cbl {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein Cbl
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.5e-35  Score=229.96  Aligned_cols=213  Identities=40%  Similarity=0.729  Sum_probs=199.3

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV  169 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~  169 (306)
                      ..+|+||||++++++..++|+++..|.++||++++++...++.++.+.|.+|++|++|+..+....+++...++.+++++
T Consensus         3 ~~sG~l~i~~~~~~~~~~Lp~~l~~f~~~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~~~~~~~l~~~~~~   82 (220)
T d2fyia1           3 DTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHS   82 (220)
T ss_dssp             TCCEEEEEEECHHHHHHTHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEESSSSTTCTTEEEEEEEEECEE
T ss_pred             CCCEEEEEEEEHHHHHHHHHHHHHHHHHHCCCcEEEEEECCcHHHHHHHHhhhhhhhhhcccccccccccccccccccce
Confidence            46899999999999999999999999999999999999999999999999999999999766555678999999999999


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++++++||++.++.++++||.++||+.+..++..+..+..++...++.|++.+++++...+..++.+|.|++++|.+.+.
T Consensus        83 ~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~ilp~~~~~  162 (220)
T d2fyia1          83 LLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSG  162 (220)
T ss_dssp             EEEETTCGGGTSSSCCHHHHTTSCEEEECTTSTTHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTSCEEEEEGGGGS
T ss_pred             eeccccccccccCcchhhhhccccccccccccchHHHHHHHHhhcccCCceeEEEccHHHHHHHHhhcceEEeCcHHHHH
Confidence            99999999999999999999999999999988889999999999999999999999999999999999999999998887


Q ss_pred             ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760         250 SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK  302 (306)
Q Consensus       250 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  302 (306)
                      ....++++.+++.+......+|++|++++..+|.++.|++++++.+....+++
T Consensus       163 ~~~~~~l~~l~~~~~~~~~~~~l~~~~~~~~~~~~~~Fi~~~~~~~~~~~~~~  215 (220)
T d2fyia1         163 EQEEENLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKR  215 (220)
T ss_dssp             TTCCTTEEEECCTTTSCCEEEEEEEETTCCBCHHHHHHHHHHCSSSCHHHHHH
T ss_pred             HHhcCCEEEEeCCCCCCceEEEEEEECCCcCCHHHHHHHHHHHHcCCHHHHHH
Confidence            76667799999988777889999999999999999999999999998777743

>d1al3a_ c.94.1.1 (A:) Cofactor-binding fragment of LysR-type protein CysB {Klebsiella aerogenes [TaxId: 28451]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Cofactor-binding fragment of LysR-type protein CysB
species: Klebsiella aerogenes [TaxId: 28451]

Probab=100.00  E-value=2e-34  Score=225.89  Aligned_cols=213  Identities=44%  Similarity=0.814  Sum_probs=198.5

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~  170 (306)
                      .+|+||||++++++..++|+++.+|.++||++++++...+++++.+.|.+|++|++|+..+....+++...+++++++++
T Consensus         4 ~~G~LrIg~~~~~~~~~LP~~l~~f~~~~P~v~v~l~~~~~~~l~~~l~~g~~D~ai~~~~~~~~~~l~~~~l~~~~~~~   83 (237)
T d1al3a_           4 DKGSLYVATTHTQARYALPGVIKGFIERYPRVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSI   83 (237)
T ss_dssp             CEEEEEEEECHHHHHHTSHHHHHHHHHHCTEEEEEEEECCHHHHHHHHHTTCCSEEEESSCCCTTSCEEEEEEEEECEEE
T ss_pred             CcEEEEEEeEHHHHHHHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHhccCCcEEEEeecccccccccccccccceEEE
Confidence            47899999999999999999999999999999999999999999999999999999997554556889999999999999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++++||++.+..++++||.++|+|.+..+...+..+..++...|+.+++.+++++..++++++.+|.|++++|.+.+..
T Consensus        84 v~~~~h~la~~~~~~~~dL~~~p~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~s~~~~~~~v~~g~Gi~~~p~~~v~~  163 (237)
T d1al3a_          84 VVTPEHPLATKGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGVGVIASMAVDP  163 (237)
T ss_dssp             EECTTSTTTTTSCCCHHHHHTSEEEEECTTSTTHHHHHHHHHHHTCCCEEEEEESSHHHHHHHHHHTSCEEEEEGGGCCT
T ss_pred             EEecCccccccccccchhhccCCcccccccchHHHHHHHHHHHcCCCCcceeecCCHHHHHHHhcCCCEEEechHHhhhh
Confidence            99999999999999999999999999999988999999999999999999999999999999999999999999988876


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ...+.++.+++++......+|++|++++..+++++.|++.+.+.+.+...+..
T Consensus       164 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~Fie~~~~~l~r~~~~~~  216 (237)
T d1al3a_         164 VSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVVDTA  216 (237)
T ss_dssp             TTCTTSEEEECBTTBCCEEEEEEEETTCCCCHHHHHHHHHHCTTCCHHHHHHH
T ss_pred             hhCCCEEEEECCCCCcceEEEEEEeCCCccCHHHHHHHHHHHHHhCHHHHHHH
Confidence            68899999999998888899999999999999999999999887766555543

>d1i6aa_ c.94.1.1 (A:) Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.6e-33  Score=215.86  Aligned_cols=207  Identities=16%  Similarity=0.254  Sum_probs=192.9

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVI  170 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~  170 (306)
                      .+|+||||++++++..++++++..|+++||++++++...++.++.+.+.+|++|++++..+ ...+++...++..+++++
T Consensus         3 l~G~lrig~~~~~~~~~lp~~l~~f~~~~P~v~l~i~~~~~~~~~~~l~~~~~d~~~~~~~-~~~~~~~~~~l~~~~~~~   81 (212)
T d1i6aa_           3 MSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV-KESEAFIEVPLFDEPMLL   81 (212)
T ss_dssp             TCEEEEEEECTTTHHHHHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEEECC-GGGTTSEEEEEEEEEEEE
T ss_pred             CeEEEEEEeEHHHHHHHHHHHHHHHHHHCCCcEEEEEECCCccccccccccchhhhheecc-cccccccceeccccceEE
Confidence            4689999999999999999999999999999999999999999999999999999999654 667889999999999999


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      +++++||++.++.++++|+.++|++.+..+...+..+.+++...+..+++.+++++.+++.+++++|.|++++|.+.+..
T Consensus        82 ~~~~~hpla~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~lp~~~~~~  161 (212)
T d1i6aa_          82 AIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPP  161 (212)
T ss_dssp             EEETTSGGGGCSCEEGGGGTTSEEECCTTTTCSSCTTSSCSSCTTSEEECTTTTSCHHHHHHHHHTTSCBEEEEGGGSCS
T ss_pred             EeecCChhhcCCcccchhhcceeEEEecCCCccchhhhhhhhcccccccceeecCCHHHHHHHHHcCCccccchHHHHHh
Confidence            99999999999999999999999999998888878888888888999999999999999999999999999999999887


Q ss_pred             c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760         251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK  298 (306)
Q Consensus       251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~  298 (306)
                      . ..++++.+|+.++.+.++++++|++++..++++++|++++++.++..
T Consensus       162 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~lr~~~~~~  210 (212)
T d1i6aa_         162 ERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGH  210 (212)
T ss_dssp             SSEETTEEEECEESSCCEEEEEEEECTTCTTHHHHHHHHHHHHHHHTTT
T ss_pred             hhccceEEEEecCCCCceeEEEEEEECcCccCHHHHHHHHHHHHHHHhc
Confidence            6 78899999998877788999999999999999999999999988654

>d1utha_ c.94.1.1 (A:) LysR-type regulatory protein DntR {Burkholderia sp. [TaxId: 36773]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein DntR
species: Burkholderia sp. [TaxId: 36773]

Probab=99.97  E-value=1.2e-29  Score=196.27  Aligned_cols=206  Identities=14%  Similarity=0.117  Sum_probs=191.0

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV  169 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~  169 (306)
                      ...+++|||++++++..++|+++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++...++..+.++
T Consensus         9 ~~~~~~rI~~~~~~~~~~lp~ll~~f~~~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~   87 (219)
T d1utha_           9 ASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLP-ELQTGFFQRRLFRHRYV   87 (219)
T ss_dssp             TCCCEEEEECCHHHHHHHHHHHHHHHHHHCTTCEEEEECTTSSCHHHHHHHTSCCEEEECCT-TCCTTEEEEEEEEECEE
T ss_pred             ccCCEEEEEEcHHHHHHHHHHHHHHHHHHCCCCEEEEEeccHHHHHHHHhcCCceeeeeecc-cccccchhhhccccccc
Confidence            45789999999999999999999999999999999999999999999999999999999655 67788999999999999


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD  249 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~  249 (306)
                      ++++++||+.. ..++.+++.+++++....+...+..+..++...++.+++.+++++..++..++.+|.|++++|.+++.
T Consensus        88 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~gi~i~p~~~~~  166 (219)
T d1utha_          88 CMFRKDHPSAK-SPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAV  166 (219)
T ss_dssp             EEEETTCSSCC-SSCCHHHHHHSEEEEECCTTSGGGGHHHHHHHTTCCCEEEEEESSSTTHHHHHHTSSCBEEEEHHHHH
T ss_pred             ccccccchhhh-ccccHHHHhcCCcEEecCCcchhHHHHHHHHhcCCcccccccCCCHHHHHHHHhCCCcceechHHHHH
Confidence            99999998875 46899999999999999888888899999999999999999999999999999999999999999887


Q ss_pred             cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760         250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR  297 (306)
Q Consensus       250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~  297 (306)
                      .. ..++++.+|++.+.+..+++++|++....+|+.++|.+.|.+.+++
T Consensus       167 ~~~~~~~l~~~~lp~~~~~~~i~l~w~~~~~~~pa~~~lr~~i~~~~~e  215 (219)
T d1utha_         167 RCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE  215 (219)
T ss_dssp             HHTTTTTEEEEECSSCCCCEEEEEEEEGGGTTCHHHHHHHHHHHHHHCC
T ss_pred             HhhhcCCEEEEcCCCCCCcEEEEEEEcCCCCCCHHHHHHHHHHHHHHHH
Confidence            66 7788999999887778899999999999999999999999998864

>d1ixca2 c.94.1.1 (A:90-294) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=99.97  E-value=7.7e-29  Score=189.07  Aligned_cols=201  Identities=11%  Similarity=0.066  Sum_probs=183.1

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV  172 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~  172 (306)
                      |+||||+.++++..++|+++.+|.++||++++++...+++++.+.+.+|++|++++... ....+.....+..+.+++++
T Consensus         2 G~lrIg~~~~~~~~~Lp~~l~~f~~~~P~v~l~i~~~~~~~l~~~l~~g~~D~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (205)
T d1ixca2           2 GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFF-PRHPGIEIVNIAQEDLYLAV   80 (205)
T ss_dssp             EEEEEEECSGGGGTHHHHHHHHHHHHCTTEEEEEEECCHHHHHHHHHHTSCSEEEESCC-CCCTTEEEEEEEEEEEEEEE
T ss_pred             eEEEEEEEhHHHHHHHHHHHHHHHHHCCCcEEEEEECCCccchhhhhhhhccccccccc-cccchheeeecccccccccc
Confidence            78999999999999999999999999999999999999999999999999999999654 66678899999999999999


Q ss_pred             cCCCCCCCCCCcChhhhcCCCeEeecCC--CCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760         173 PLDHPLLLLNSISLKEISNYPLITYDLS--FSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS  250 (306)
Q Consensus       173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~  250 (306)
                      .++|++.....++..|+..++++.+...  ..+++.+...+...+..++..+++++..+++.++++|.|++++|.+++..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~  160 (205)
T d1ixca2          81 HRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAI  160 (205)
T ss_dssp             EGGGGGGTCSEECGGGGTTCEEEECCCSSSSCHHHHHHHHHHHTTCCCEEEEECSSHHHHHHHHHTTSCBEEEEHHHHTS
T ss_pred             cccccccccccccccccccCcccccccccccchhhhhhhhhhhccccccccccccchhhhhhhccccceEEEccHHHHhc
Confidence            9999999999999999999999987654  34678888999999999999999999999999999999999999987754


Q ss_pred             cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760         251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  296 (306)
                       ..++++.+|+++.....+++++|++++ .+|++++|++++++..+
T Consensus       161 -~~~~l~~~~l~~~~~~~~~~l~~~~~~-~~p~~~~fi~~l~~~~~  204 (205)
T d1ixca2         161 -RWPDIAFARIVGTRVKVPISCIFRKEK-QPPILARFVEHVRRSAK  204 (205)
T ss_dssp             -CCTTEEEEEECCTTCEEEEEEEEESSS-CCHHHHHHHHHHHHHHC
T ss_pred             -ccCCEEEEECCCCCceeEEEEEEECCC-CCHHHHHHHHHHHHHcC
Confidence             567899999988777889999999986 58999999999998764

>d2esna2 c.94.1.1 (A:92-303) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.97  E-value=2.3e-29  Score=193.57  Aligned_cols=204  Identities=15%  Similarity=0.059  Sum_probs=183.2

Q ss_pred             cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeeccccc
Q psy3760          89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQW  166 (306)
Q Consensus        89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~~  166 (306)
                      ...+|++|||++++++..++|+++..|.++||++++++...+++.+.+.|.+|++|++|+.....  .........+..+
T Consensus         4 ~~~~~~~rI~~~~~~~~~~lp~ll~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~~~~~~   83 (212)
T d2esna2           4 GQSQRTFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVEALASGRIDFALGYDEEHERLPEGIQAHDWFAD   83 (212)
T ss_dssp             TTCCCEEEEECCHHHHHHHHHHHHHHHHHHSTTCEEEEECCSSSCCHHHHHHTSSSEEEECCSTTCCCCTTEEEEEEEEE
T ss_pred             CcCCcEEEEEEcHHHHHHHHHHHHHHHHHHCCCcEEEEEecCcHHHHHHHHHhccccccccccccccccccccccccchh
Confidence            45679999999999999999999999999999999999999999999999999999999864322  2455677888888


Q ss_pred             eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecc
Q psy3760         167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASI  246 (306)
Q Consensus       167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~  246 (306)
                      .++++++++||+... +.+++++.+++++....+...+..+++++...+..+++.+++++..++..+|.+|.|++++|.+
T Consensus        84 ~~~~~~~~~~~~~~~-~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~ilp~~  162 (212)
T d2esna2          84 RYVVVARRDHPRLAG-APTLEGYLAERHAVVTPWNEDSGVIDRLLARSGLRREVAVQLPTVLAALFLAGSTDFLLTAPRH  162 (212)
T ss_dssp             CEEEEEESSCTTCSS-SCCHHHHHTSEEEEECTTCCSSCHHHHHHHHTTCCCEEEEEESCHHHHHHHHHTSSCEEEEEHH
T ss_pred             hhcccccccchhhcc-ccCHHHHhcCccccccCCCCcchhHHHHHHHhCcccccccccccHHHHHHHHhcCCEEEEcchh
Confidence            999999999998765 5799999999999999988888899999999999999999999999999999999999999999


Q ss_pred             eeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         247 AFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       247 ~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ++..+ ..++++.++++...+.++++++|++++..+|+.++|++.||+
T Consensus       163 ~~~~~~~~~~l~~~~l~~~~~~~~i~l~wh~~~~~~pa~~wl~~~ir~  210 (212)
T d2esna2         163 AARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQLKG  210 (212)
T ss_dssp             HHHHHHHHHTEEEECCSSCCCCEEEEEEEECC--CCHHHHHHHHHSCC
T ss_pred             hHhhhhhcCCEEEEeCCCCCCcEEEEEEECCCCCCCHHHHHHHHHHHh
Confidence            88776 788999999988777889999999999999999999999875

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=99.96  E-value=4.9e-30  Score=165.84  Aligned_cols=86  Identities=24%  Similarity=0.383  Sum_probs=77.6

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++++| ||++||+.||+|||+||++|++||+++|++||+|+++++ .||++|+.++++++++++.++.+
T Consensus         1 Mdl~~L~~f~~v~e~g-s~~~AA~~L~isq~avs~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~il~~~~~~   78 (89)
T d1ixca1           1 MEFRQLKYFIAVAEAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGI-ELTAAGHAFLEDARRILELAGRS   78 (89)
T ss_dssp             CCHHHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC-----C-CBCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHhcCCceeeEecCCcc-CccHhHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999 999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHhhc
Q psy3760          81 KKIGKEFS   88 (306)
Q Consensus        81 ~~~~~~~~   88 (306)
                      .+..+...
T Consensus        79 ~~~~~~~~   86 (89)
T d1ixca1          79 GDRSRAAA   86 (89)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHc
Confidence            88776643

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.95  E-value=3.7e-28  Score=157.09  Aligned_cols=80  Identities=20%  Similarity=0.320  Sum_probs=77.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL   80 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~   80 (306)
                      ||+++|++|++++++| ||++||+.||+|||++|++|++||+.+|++||+|+++++ .||++|+.++++++++++.+++.
T Consensus         6 ldl~~L~~f~~v~~~g-s~t~AA~~l~isq~avs~~l~~lE~~~g~~Lf~R~~~~~-~lT~~g~~l~~~~~~~l~~l~~~   83 (89)
T d2esna1           6 LDLNLLLVFDALYRHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRM-QPTQRAEHLAAAVAAALRALGEG   83 (89)
T ss_dssp             SCTTHHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEEETTEE-EECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC-CHHHHHHHHCCCCcHhhHHHHHHHhcCCceeEEECCCce-eECHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999 999999999999999999999999999999999999999 79999999999999999998886


Q ss_pred             HH
Q psy3760          81 KK   82 (306)
Q Consensus        81 ~~   82 (306)
                      .+
T Consensus        84 ~~   85 (89)
T d2esna1          84 LE   85 (89)
T ss_dssp             TG
T ss_pred             HH
Confidence            54

>d1twya_ c.94.1.1 (A:) ABC transporter, periplasmic substrate-binding protein VCA0807 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: ABC transporter, periplasmic substrate-binding protein VCA0807
species: Vibrio cholerae [TaxId: 666]

Probab=99.49  E-value=4.1e-12  Score=98.53  Aligned_cols=202  Identities=17%  Similarity=0.234  Sum_probs=144.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC---CCCCceeeccccceEEE
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS---PSDKLISIPCYQWEYVI  170 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~l~~~~~~~  170 (306)
                      .|+|+.+.++ ..++..+...|.+.||++++.+...++...+++|.+|++|++++..+..   ....+...++..+.+++
T Consensus         2 ~i~i~GS~s~-~~~~~~l~~~f~~~~p~~~v~v~~~gS~~~~~~l~~g~~di~~~s~~~~~~e~~~~~~~~~ia~d~lvi   80 (249)
T d1twya_           2 EITISGSTSV-ARIMDVLAEKYNQQHPETYVAVQGVGSTAGISLLKKGVADIAMTSRYLTESEAQNTLHTFTLAFDGLAI   80 (249)
T ss_dssp             EEEEEECHHH-HHHHHHHHHHHHHHCTTCEEEEEESCHHHHHHHHHTTSCSEEEESSCCCTTTCCTTCEEEEEEEEEEEE
T ss_pred             eEEEEecccH-HHHHHHHHHHHHHHCCCcEEEEEeCCcHHHHHHHHcCCCeeeecccchhhhhhhcceeeEEEEeecccc
Confidence            5889998886 4599999999999999999999999999999999999999999975433   24578889999999999


Q ss_pred             EecCCCCCCC-----------CCCcChhhhcC----CCeEeecCCCCcHHHHHHHHHhCCC---------ceeEEEEecC
Q psy3760         171 IVPLDHPLLL-----------LNSISLKEISN----YPLITYDLSFSGRIKLDREFSLQKL---------TPYIVLETIN  226 (306)
Q Consensus       171 v~~~~~~l~~-----------~~~i~~~dl~~----~~~i~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~  226 (306)
                      ++++++|...           ++..+|+|+..    ..++....+++.+..+.+.+.....         .+. ....++
T Consensus        81 iv~~~np~~~lt~~ql~~I~~g~i~~W~~~~~~~~~i~~~~r~~~Sgt~~~f~~~~~~~~~~~~~~~~~~~~~-~~~~~~  159 (249)
T d1twya_          81 VVNQANPVTNLTREQLYGIYKGQITNWKQVGGNDQKIAVVTREASSGTRYSFESLMGLTKTVKDREVSDVAPT-ALVVNS  159 (249)
T ss_dssp             EECTTCCCCEECHHHHHHHHHTSCCBGGGGTSCSCBCEEEEECTTCHHHHHHHHHHTCEEEETTEEEECSCTT-SEEESS
T ss_pred             ccccccccccccHHHHHhhhhhhccchhhhcccccccceecCCCCchHHHHHHHHHcccccccccccccccce-eEEecC
Confidence            9999999643           12223444422    2356666666667667666532211         112 245677


Q ss_pred             HHHHHHHHHhc-cceeeeecceecccccCCceeeecCCC------------CccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760         227 SDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHL------------FGTTISRVIIKQGTYLRSYVYSFIKLLSP  293 (306)
Q Consensus       227 ~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~------------~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  293 (306)
                      ...+...+..+ .+++++....+.    .++..++++..            +..+++|+++++++ .++.++.|++++.+
T Consensus       160 ~~~v~~~v~~~~~aig~~~~~~~~----~~~k~l~i~~~~ps~~~i~~g~YPl~r~~~~~~~~~~-~~~~a~~Fi~f~~S  234 (249)
T d1twya_         160 NSMMKTLVNHNTQAVGFISIGSVD----KSVKAIQFEKADPTSDNIAKHTYQLSRPFLILHYSDN-ADEQTKEFIAFLKS  234 (249)
T ss_dssp             HHHHHHHHHHCTTEEEEEEGGGCC----TTSEECEETTBCCCHHHHHTTCSCCEEEEEEEECTTT-CCHHHHHHHHHHHS
T ss_pred             cHHHHHHHhcCCCceEEEEeeccc----ccchhhhccccccchhhhccCCCCceeEEEEEEECCC-CCHHHHHHHHHHhC
Confidence            88888888765 679988865543    35666666431            23467788877665 47889999999987


Q ss_pred             HhhHHHHHh
Q psy3760         294 KLNRKFINK  302 (306)
Q Consensus       294 ~~~~~~~~~  302 (306)
                      .-.+..+++
T Consensus       235 ~~gq~ii~~  243 (249)
T d1twya_         235 ESAKKLIVE  243 (249)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            555555443

>d1ii5a_ c.94.1.1 (A:) Glutamate receptor ligand binding core {Synechocystis sp., GluR0 [TaxId: 1143]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Glutamate receptor ligand binding core
species: Synechocystis sp., GluR0 [TaxId: 1143]

Probab=98.29  E-value=3.4e-05  Score=57.58  Aligned_cols=199  Identities=11%  Similarity=0.032  Sum_probs=118.2

Q ss_pred             CCCcEEEEecccch------------hhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccCC---
Q psy3760          91 DTGNLTIATTHTQA------------RYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILSP---  154 (306)
Q Consensus        91 ~~~~l~I~~~~~~~------------~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~~---  154 (306)
                      ....||||+....+            ..+...++..+.++ -++.+++.. .+...+++.+.+|++|+++......+   
T Consensus         2 ~a~~lrVg~~~~pP~~~~~~~~~g~~~G~~~dl~~~ia~~-~g~~~~~v~~~~~~~~~~~l~~G~~D~~~~~~~~t~~r~   80 (226)
T d1ii5a_           2 SAMALKVGVVGNPPFVFYGEGKNAAFTGISLDVWRAVAES-QKWNSEYVRQNSISAGITAVAEGELDILIGPISVTPERA   80 (226)
T ss_dssp             CSCCEEEEECCCTTTCEEC-----CEESHHHHHHHHHHHH-HTCCEEEEECSCHHHHHHHHHTTSCSEEEEEEECCHHHH
T ss_pred             CCCCEEEEEeCCCCCeEeecCCCCcEEEHHHHHHHHHHHH-hCCCeEEEEcCCHHHHHHHHhcCCcccccccccchhhhh
Confidence            35689999865321            24566788887665 378888654 57789999999999999874311111   


Q ss_pred             -CCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHH
Q psy3760         155 -SDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKT  232 (306)
Q Consensus       155 -~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (306)
                       ...+. +.+++.....++++++...   ..-+++||.+..+...... .    ...++...+.   ....+++...++.
T Consensus        81 ~~~~~~fs~p~~~~~~~~~~~~~~~~---~~~~~~dl~~~~i~~~~g~-~----~~~~~~~~~~---~i~~~~~~~~~~~  149 (226)
T d1ii5a_          81 AIEGITFTQPYFSSGIGLLIPGTATP---LFRSVGDLKNKEVAVVRDT-T----AVDWANFYQA---DVRETNNLTAAIT  149 (226)
T ss_dssp             TSTTEEECCCCEEEEEEEEEEGGGTT---TCSSGGGGTTCEEEEETTS-H----HHHHHHHTTC---EEEEESSHHHHHH
T ss_pred             hhhcccccccccccCcceEEEecccc---cchhhhhhhhhccccccCc-h----hhhccccccc---eeeccchHHHHHH
Confidence             12333 4678888888888776542   1237899988877765432 2    2344554443   2456789999999


Q ss_pred             HHHhcccee-eeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         233 YVELRMGIG-IIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       233 ~v~~g~gi~-~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ++.+|..=+ +........+  ..+.......+.......++++.+++..   ....|-+.|++.-+....+++.
T Consensus       150 ~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~~~in~~i~~l~~~g~l~~i~  221 (226)
T d1ii5a_         150 LLQKKQVEAVMFDRPALIYYTRQNPNLNLEVTEIRVSLEPYGFVLKENSP---LQKTINVEMLNLLYSRVIAEFT  221 (226)
T ss_dssp             HHHTTSCSEEEEEHHHHHHHHHHCGGGCEEECSCCSEEEEEEEEEETTCT---THHHHHHHHHHHHHTTHHHHHH
T ss_pred             HHhCCCeeeEeccchhHHHHHhhcccccccccCcCCCCceEEEEECCCHH---HHHHHHHHHHHHHhCcHHHHHH
Confidence            999995533 4444444333  2233222222222334466666676644   3444444444433344455543

>d1atga_ c.94.1.1 (A:) Molybdate-binding protein, ModA {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Molybdate-binding protein, ModA
species: Azotobacter vinelandii [TaxId: 354]

Probab=98.08  E-value=0.00052  Score=50.78  Aligned_cols=202  Identities=10%  Similarity=0.067  Sum_probs=120.6

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccCC--------CCCceeeccc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILSP--------SDKLISIPCY  164 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~~--------~~~~~~~~l~  164 (306)
                      .|||.+..++. ..+..+...|.++ .++++++...++.++..++.+| ..|+.+.......        ..........
T Consensus         1 el~v~~~~~~~-~~~~~l~~~Fe~~-tGi~V~~~~g~s~~l~~~i~~g~~~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (231)
T d1atga_           1 ELKVVTATNFL-GTLEQLAGQFAKQ-TGHAVVISSGSSGPVYAQIVNGAPYNVFFSADEKSPEKLDNQGFALPGSRFTYA   78 (231)
T ss_dssp             CEEEEEEGGGH-HHHHHHHHHHHHH-HCCCEEEEEECHHHHHHHHHTTCCCSEEECSSSHHHHHHHHTTCBCTTCCEEEE
T ss_pred             CEEEEEecchH-HHHHHHHHHHHHh-hCCEEEEEECChHHHHHHHHcCCCCceEEecchhhhhhhhhhccccccccceec
Confidence            47899988864 4588899999887 5799999999999999999887 6888877422110        1111222233


Q ss_pred             cceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecCCCC-cHHHHHHHHHhCCCc-----eeEEEEecCHHHHHHHHH
Q psy3760         165 QWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDLSFS-GRIKLDREFSLQKLT-----PYIVLETINSDIIKTYVE  235 (306)
Q Consensus       165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~~~~-~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~v~  235 (306)
                      ...+....+.+.+    .+.++++|..-.   +...++... ........+...+..     .+......+.......+.
T Consensus        79 ~~~~~~~~~~~~~----~~~~~~~l~~~~~~~i~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (231)
T d1atga_          79 IGKLVLWSAKPGL----VDNQGKVLAGNGWRHIAISNPQIAPYGLAGTQVLTHLGLLDKLTAQERIVEANSVGQAHSQTA  154 (231)
T ss_dssp             ECCEEEEESSTTT----SCTTSGGGGSSSCSCEEEECTTTCHHHHHHHHHHHHTTCHHHHHHTTCEEEESSHHHHHHHHH
T ss_pred             ccceeeecccCCC----CCCcHHHhcCcccCEEEEecCccchhhHHHHHhhhhhhhhhhhcccceeeeccccchhhHHhh
Confidence            3334444444332    345777776543   333344333 233333344444332     233456677778777788


Q ss_pred             hc-cceeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760         236 LR-MGIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN  301 (306)
Q Consensus       236 ~g-~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  301 (306)
                      .| ..+++.....+...  ....+.....++......+.+...++......+++|+++|.+.=.+..+.
T Consensus       155 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~~A~~Fidfl~S~e~Q~i~~  223 (231)
T d1atga_         155 SGAADLGFVALAQIIQAAAKIPGSHWFPPANYYEPIVQQAVITKSTAEKANAEQFMSWMKGPKAVAIIK  223 (231)
T ss_dssp             TTSSSEEEEEGGGTCCTTSCCSSEEECCCGGGSCCCEEEEEEBTTCSCHHHHHHHHHHTTSHHHHHHHH
T ss_pred             ccchhhhhhHHHHHHHhhccccceeeeecCCCceeeeeeEEEECCCCCHHHHHHHHHHHCCHHHHHHHH
Confidence            77 55666555444333  23333333333333344566666778888899999999997654444443

>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=98.05  E-value=1e-05  Score=50.03  Aligned_cols=57  Identities=21%  Similarity=0.157  Sum_probs=42.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc-cccCHhHHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI-RGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~-~~lT~~G~~l~~~a~~il~   75 (306)
                      |.+.-|+.+++|+|++|+.|++||+. |.---.++++.. +.||+.|+.+++.+..-+.
T Consensus        23 t~~eLa~~l~i~~~~vs~~l~~Le~~-GlV~r~~D~R~~~i~LT~~G~~~l~~~~~~~~   80 (85)
T d3ctaa1          23 TSSKLADMLGISQQSASRIIIDLEKN-GYITRTVTKRGQILNITEKGLDVLYTEFADLS   80 (85)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeecccccccceECHHHHHHHHHHHHHHH
Confidence            57899999999999999999999986 222223334333 2799999988777664443

>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=98.04  E-value=6e-06  Score=54.62  Aligned_cols=70  Identities=19%  Similarity=0.203  Sum_probs=53.5

Q ss_pred             CchhhHHHHHHHHHhcC---CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNF---NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~---s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a   70 (306)
                      |+..++.++..+.+...   +.+.-|+.+++++|++|+.|++||+. |  |+.|.       ...+ .||+.|+.++..+
T Consensus        31 Ls~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~-g--li~r~~~~~D~R~~~i-~LT~~G~~~~~~~  106 (115)
T d2frha1          31 ISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQE-D--YFDKKRNEHDERTVLI-LVNAQQRKKIESL  106 (115)
T ss_dssp             CCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT-T--SSCCBCCSSSSCCCEE-ECCSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhh-h--hheeeecccCCceEEE-EECHHHHHHHHHH
Confidence            46778888888877641   57789999999999999999999976 4  44443       2333 8999999988765


Q ss_pred             HHHH
Q psy3760          71 EIIM   74 (306)
Q Consensus        71 ~~il   74 (306)
                      ..-+
T Consensus       107 ~~~~  110 (115)
T d2frha1         107 LSRV  110 (115)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>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=98.03  E-value=1.3e-05  Score=54.84  Aligned_cols=75  Identities=19%  Similarity=0.261  Sum_probs=58.8

Q ss_pred             CchhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE   71 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~   71 (306)
                      ++..++.++..+.+.+  -+.+.-|+.+++++|++|+.|++||+   ..|..|..       ..+ .||+.|+.++..+.
T Consensus        26 lt~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~---~gli~r~~~~~D~R~~~i-~lT~~G~~~~~~~~  101 (137)
T d2fbha1          26 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLES---QGLVRRLAVAEDRRAKHI-VLTPKADVLIADIE  101 (137)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHH---TTSEEEECCBTTBCSCEE-EECTTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH---cCCccccCCCCCCCchhh-hcCHHHHHHHHHHH
Confidence            3556788888887643  25789999999999999999999998   34555542       244 89999999999988


Q ss_pred             HHHHHHHH
Q psy3760          72 IIMQEIEG   79 (306)
Q Consensus        72 ~il~~~~~   79 (306)
                      +......+
T Consensus       102 ~~~~~~~~  109 (137)
T d2fbha1         102 AIAASVRN  109 (137)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            87776654

>d1wdna_ c.94.1.1 (A:) Glutamine-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Glutamine-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.99  E-value=0.0002  Score=53.13  Aligned_cols=159  Identities=9%  Similarity=0.019  Sum_probs=98.8

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc-eeeccccceEEEEecCCCCCCCCC
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL-ISIPCYQWEYVIIVPLDHPLLLLN  182 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~~~l~~~~  182 (306)
                      .+...++..+.+.. ++++++...+.......|.+|++|+++......  ....+ -+.++.....+++++++.+.    
T Consensus        23 G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~----   97 (223)
T d1wdna_          23 GFDVDLWAAIAKEL-KLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNND----   97 (223)
T ss_dssp             SHHHHHHHHHHHHH-TCCEEEEEECGGGHHHHHHTTSSSEEEEEEECCHHHHTTSEECSCCEEEEEEEEEETTCCS----
T ss_pred             EHHHHHHHHHHHHh-CCcEEEEecCHHHHHhhhhhccceeeecccccchhhhcceEecccEEEeeeEEEEECCCCC----
Confidence            46677777777765 788888888889999999999999987531111  12223 35788888888998877642    


Q ss_pred             CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce-eeeecceeccc----ccCCce
Q psy3760         183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI-GIIASIAFDSN----RDKNLR  257 (306)
Q Consensus       183 ~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi-~~~p~~~~~~~----~~~~l~  257 (306)
                      .-+++||.+....... +...    ..++...... ......++...+..++..|..= .+........+    ....+.
T Consensus        98 i~~~~dl~~~~v~v~~-g~~~----~~~~~~~~~~-~~~~~~~~~~~~~~~l~~g~vD~~~~~~~~~~~~~~~~~~~~~~  171 (223)
T d1wdna_          98 VKSVKDLDGKVVAVKS-GTGS----VDYAKANIKT-KDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFK  171 (223)
T ss_dssp             CSSSTTTTTCEEEEET-TSHH----HHHHHHHCCC-SEEEEESSHHHHHHHHHTTSCSEEEEEHHHHHHHHHTTTTTTEE
T ss_pred             CCCHHHHCCCEEEEEe-ecch----hhhhhhhccc-cceeeeCCHHHHHHHHhcCCccccccccHHhhhhhhhcCCCcce
Confidence            2367888887655543 3322    2333333322 2355678899999999999443 33443332222    223444


Q ss_pred             eeecCCCCccceEEEEEeCC
Q psy3760         258 SISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       258 ~~~~~~~~~~~~~~l~~~~~  277 (306)
                      .++.  +.....++++.+++
T Consensus       172 ~~~~--~~~~~~~~~~~~k~  189 (223)
T d1wdna_         172 AVGD--SLEAQQYGIAFPKG  189 (223)
T ss_dssp             EEEE--EEEEEEEEEEECTT
T ss_pred             ecCC--CCCcceEEEEEECC
Confidence            4332  23345777777765

>d1xt8a1 c.94.1.1 (A:10-257) Putative amino-acid transporter CjaA {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Putative amino-acid transporter CjaA
species: Campylobacter jejuni [TaxId: 197]

Probab=97.94  E-value=0.00013  Score=55.35  Aligned_cols=174  Identities=12%  Similarity=0.118  Sum_probs=106.9

Q ss_pred             CCcEEEEecccch-----------hhhhHHHHHHHHHh--CCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CC
Q psy3760          92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQ--FPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SD  156 (306)
Q Consensus        92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~--~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~  156 (306)
                      +|.||||+.....           ..+...++..+.++  ..++.+++...+.......+.+|++|+++.......  ..
T Consensus        10 ~g~l~v~v~~~~pP~~~~~~~g~~~G~~~Dl~~~ia~~l~~~~~~i~~~~~~~~~~~~~l~~g~~d~~~~~~~~t~~R~~   89 (248)
T d1xt8a1          10 NGVVRIGVFGDKPPFGYVDEKGNNQGYDIALAKRIAKELFGDENKVQFVLVEAANRVEFLKSNKVDIILANFTQTPQRAE   89 (248)
T ss_dssp             HSSEEEEECSEETTTEEECTTSCEESHHHHHHHHHHHHHHSCTTCEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHT
T ss_pred             CCEEEEEEcCCCCCceEECCCCCEeEHHHHHHHHHHHHhcCCCceeeeeeecccccccccccCcccccccccccchhhhc
Confidence            4789999865322           13455567776554  357889998888889999999999999985322111  22


Q ss_pred             Cce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760         157 KLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE  235 (306)
Q Consensus       157 ~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  235 (306)
                      .+. +.|+.....+++++++.++     -+++||.+........ ..    ..++++...... .....++...++.++.
T Consensus        90 ~~~fs~p~~~~~~~~~~~~~~~i-----~~~~dl~g~~i~v~~g-s~----~~~~l~~~~~~~-~i~~~~s~~~~~~~l~  158 (248)
T d1xt8a1          90 QVDFCSPYMKVALGVAVPKDSNI-----TSVEDLKDKTLLLNKG-TT----ADAYFTQNYPNI-KTLKYDQNTETFAALM  158 (248)
T ss_dssp             TEEECCCCEEEEEEEEEETTCCC-----CSSGGGTTSEEEEETT-SH----HHHHHHHHCTTS-EEEEESSHHHHHHHHH
T ss_pred             ceeecccccccceeEEEecCccc-----chhhhhccceeeecCC-Ch----HHHhhhcccccc-ccccccchhhHHHhhc
Confidence            333 4578888899999987642     3678998887655443 22    245555543333 3446788999999999


Q ss_pred             hccceee-eecceeccc--ccCCceeeecCCCCccceEEEEEeCC
Q psy3760         236 LRMGIGI-IASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQG  277 (306)
Q Consensus       236 ~g~gi~~-~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~  277 (306)
                      +|..=++ .+.......  ..++.... ++.......++++.+++
T Consensus       159 ~g~vD~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~k~  202 (248)
T d1xt8a1         159 DKRGDALSHDNTLLFAWVKDHPDFKMG-IKELGNKDVIAPAVKKG  202 (248)
T ss_dssp             TTSSSEEEEEHHHHHHHHHHCTTEEEE-EEEEEEEEEECCEEETT
T ss_pred             ccccccccccHHHHHHHHHhCCcceEe-cccCCCCceEEEEEECC
Confidence            9944333 333333222  33444332 22222233555666665

>d1ixha_ c.94.1.1 (A:) Phosphate-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Phosphate-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.93  E-value=0.00071  Score=53.13  Aligned_cols=154  Identities=13%  Similarity=-0.005  Sum_probs=103.0

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC----CCceeeccccceE
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS----DKLISIPCYQWEY  168 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~----~~~~~~~l~~~~~  168 (306)
                      +.|+++.+.+ ...++..+...|.+.+| ..+.+...++..-+..+.+|.+||+....+..+.    .++...++..+.+
T Consensus         2 ~si~~~GSst-v~p~~~~~a~~~~~~~~-~~v~~~~~GSg~G~~~~~~g~~di~~ssr~~~~~e~~~~~~~~~~v~~~~i   79 (321)
T d1ixha_           2 ASLTGAGATF-PAPVYAKWADTYQKETG-NKVNYQGIGSSGGVKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGV   79 (321)
T ss_dssp             CEEEEEECST-THHHHHHHHHHHHHHHC-CEEEEEECCHHHHHHHHHTTCSSEEEESSCCCHHHHHHHTEEEEEEEEEEE
T ss_pred             ceEEEEchhh-HHHHHHHHHHHHHHhCC-CeEEEEccCcHHHHHHHHcCCCeEEEeChhhCHHHHhhcCCeeeEEEEEEE
Confidence            5688887766 46688889999988876 4999999999999999999999999987553322    2577888888899


Q ss_pred             EEEecCCCCCCC--------------CCCcChhhh-----------cCCC--eEeecCCCCcHHHHHHHHHhC-------
Q psy3760         169 VIIVPLDHPLLL--------------LNSISLKEI-----------SNYP--LITYDLSFSGRIKLDREFSLQ-------  214 (306)
Q Consensus       169 ~~v~~~~~~l~~--------------~~~i~~~dl-----------~~~~--~i~~~~~~~~~~~~~~~~~~~-------  214 (306)
                      .+++...++...              .+..+|+|.           .+.|  .+....+++.+..+.+++...       
T Consensus        80 ~~~v~~~n~~~~~l~Lt~~~l~~If~g~It~W~~~~~~~~n~~~~lPd~~I~v~~R~~~SGT~~~f~~~l~~~~~~~~~~  159 (321)
T d1ixha_          80 VLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWDDEAIAKLNPGLKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKNN  159 (321)
T ss_dssp             EEEECCTTCCTTCCEECHHHHHHHHTTCCCBTTCHHHHHHCTTCCCCCCBCEEEEESSCCHHHHHHHHHHHHHCHHHHHH
T ss_pred             EEEeccCCCCcccccccHHHHhhhhcCccccccCccccccCcCCCCCCcceEEecCCCCCchhHHHHHHHHhcChhhhhc
Confidence            999977665432              222345543           2344  334444555666777666431       


Q ss_pred             -CCc----eeEEEEecCHHHHHHHHHhc-cceeeeeccee
Q psy3760         215 -KLT----PYIVLETINSDIIKTYVELR-MGIGIIASIAF  248 (306)
Q Consensus       215 -~~~----~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~  248 (306)
                       +..    ........+...+.+.|... .+|+++.-..+
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~v~~~V~~~~~aIGy~~~~~~  199 (321)
T d1ixha_         160 VGTGSTVKWPIGLGGKGNDGIAAFVQRLPGAIGYVEYAYA  199 (321)
T ss_dssp             TCCCSSCCCSSCEEESHHHHHHHHHHHSTTEEEEEEHHHH
T ss_pred             cCcCccccccccccccccchhhheeeccCCceeeeeeeee
Confidence             111    11223445566677777664 88998887543

>d1xs5a_ c.94.1.1 (A:) Putative lipoprotein (NlpA family) {Treponema pallidum [TaxId: 160]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Putative lipoprotein (NlpA family)
species: Treponema pallidum [TaxId: 160]

Probab=97.89  E-value=0.00015  Score=54.58  Aligned_cols=189  Identities=10%  Similarity=0.059  Sum_probs=106.8

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC-----CCCCceee---cc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-----PSDKLISI---PC  163 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~---~l  163 (306)
                      .+||||+.+......+ ..+..+.+++ ++++++.. .+...+.+.|.+|++|+++....+.     ...++...   ..
T Consensus         3 ~ti~ig~~~~~~~~~l-~~~k~~~k~~-Gi~Ve~v~f~~g~~~~~Al~~G~iD~~~~~~~~~l~~~~~~~~~~i~~v~~~   80 (240)
T d1xs5a_           3 ETVGVGVLSEPHARLL-EIAKEEVKKQ-HIELRIVEFTNYVALNEAVMRGDILMNFFQHVPHMQQFNQEHNGDLVSVGNV   80 (240)
T ss_dssp             EEEEEEECSTTHHHHH-HHHHHHHHTT-TEEEEEEECSCHHHHHHHHHHTSSSEEEEEEHHHHHHHHHHHTCCEEEEEEE
T ss_pred             ceEEEEecCCCcHHHH-HHHHHHHHHc-CCEEEEEEeCChhhHHHHHHcCCcceeccCCHHHHHHHHHhCCCcEEEeecc
Confidence            5899999887555444 4556666665 88999877 4777899999999999988642111     00111111   12


Q ss_pred             ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC-ce------------------eEE-EE
Q psy3760         164 YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TP------------------YIV-LE  223 (306)
Q Consensus       164 ~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~------------------~~~-~~  223 (306)
                      ....++++.+        ...++.|+.+-.-|..+.+......+...+...+. ..                  +.. ..
T Consensus        81 ~~~~~~l~~~--------~~~s~~d~~~gkkia~p~~~s~~~~~l~~l~~~g~~~~~~~~~~~~~~~di~~~~~~~~~~~  152 (240)
T d1xs5a_          81 HVEPLALYSR--------TYRHVSDFPAGAVIAIPNDSSNEARALRLLEAAGFIRMRAGSGLFATVEDVQQNVRNVVLQE  152 (240)
T ss_dssp             EECCCEEECS--------SCCSGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSCEECTTCCTTCCGGGEEECTTCCEEEE
T ss_pred             ccCceEEEec--------CCCChhhccCCCEEEecCCCcHHHHHHHHHHHcCCcccccCcccccccchhhhccccccccc
Confidence            2233333322        23466676555566666665566677777777753 11                  111 22


Q ss_pred             ecCHHHHHHHHHhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         224 TINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       224 ~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      .+...+ ......-++..+-+.+.......+.-..+...+........++.++....++.+++|++.++
T Consensus       153 ~~~~~~-a~~~~~vdaa~~~~p~~~~a~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~i~~~~~a~~  220 (240)
T d1xs5a_         153 VESALL-PRVFDQVDGAVINGNYAIMAGLSARRDGLAVEPDASAYANVLVVKRGNEADARVQAVLRALC  220 (240)
T ss_dssp             ECGGGH-HHHGGGSSEEEECHHHHHHTTCCTTTTCSEECSCGGGGCEEEEEETTCTTCHHHHHHHHHHT
T ss_pred             CCHHHH-HHhhccccEEEEcchHHHHhcCCcccceeeecCCCCCeEEEEEEeccccCCHHHHHHHHHHC
Confidence            222222 22233345555555554443322222222233323344566777888888999999998874

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.87  E-value=4.8e-05  Score=48.76  Aligned_cols=70  Identities=13%  Similarity=0.119  Sum_probs=48.1

Q ss_pred             hhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCC-ccccCHhHHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKR-IRGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         4 ~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~-~~~lT~~G~~l~~~a~~il~   75 (306)
                      .++.++..+.  ..- +++.-|+.+++|+|++|+++++||+. |.--..+.   ++. .++||+.|+..++.....++
T Consensus        17 ~r~~IL~~L~~~~~~-~~~eLa~~l~is~~~vs~~l~~L~~~-glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~~~~~   92 (100)
T d1ub9a_          17 VRLGIMIFLLPRRKA-PFSQIQKVLDLTPGNLDSHIRVLERN-GLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLK   92 (100)
T ss_dssp             HHHHHHHHHHHHSEE-EHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCe-eHHHHHHHHhhccccccHHHHHHhhh-ceeEEEEcCcCCccccccCCHHHHHHHHHHHHHHH
Confidence            3556666664  345 89999999999999999999999975 33222222   221 23899999987766544333

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.86  E-value=4.7e-05  Score=52.49  Aligned_cols=77  Identities=18%  Similarity=0.177  Sum_probs=60.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.+ -+.+.-|+.++++.|++|+.|++||+. |.---.+++     ..+ .||+.|+.++..+.+..
T Consensus        27 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~-glI~r~~~~~D~R~~~l-~LT~~G~~~~~~~~~~~  104 (144)
T d1lj9a_          27 LTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ-GFIYRQEDASNKKIKRI-YATEKGKNVYPIIVREN  104 (144)
T ss_dssp             CTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHHHHHhh-hcccccCCCCCCCcccc-ccCHHHHHHHHHHHHHH
Confidence            3557888888898876 244689999999999999999999997 554444432     244 89999999999999888


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ..+..
T Consensus       105 ~~~~~  109 (144)
T d1lj9a_         105 QHSNQ  109 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77655

>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=97.85  E-value=5.1e-05  Score=52.38  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=55.9

Q ss_pred             chhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      +..++.++..+.+.+  .|.+.-|+.+++++|++|+.|++||+.   .|+.|..       ..+ .||+.|+.++..+..
T Consensus        33 t~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~~---glv~r~~~~~DrR~~~i-~LT~~G~~~~~~~~~  108 (145)
T d2hr3a1          33 QFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERG---GLIVRHADPQDGRRTRV-SLSSEGRRNLYGNRA  108 (145)
T ss_dssp             HHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT---TSEEEEC------CCEE-EECHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHc---CCeEeeeCccchhHHHh-ccCHHHHHHHHHHHH
Confidence            456788888887664  268999999999999999999999984   4555543       235 899999999988765


Q ss_pred             HHHH
Q psy3760          73 IMQE   76 (306)
Q Consensus        73 il~~   76 (306)
                      ....
T Consensus       109 ~~~~  112 (145)
T d2hr3a1         109 KREE  112 (145)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

>d1pc3a_ c.94.1.1 (A:) Phosphate-binding protein {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Phosphate-binding protein
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.83  E-value=0.00096  Score=52.69  Aligned_cols=155  Identities=10%  Similarity=-0.046  Sum_probs=100.3

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccce
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQWE  167 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~~  167 (306)
                      .+|+++.+.++ ..++..+...|.+.||++++.+...++..-+..+.+|.+||+.+..+...     ..++...++..+.
T Consensus        10 ~~l~~~GSst~-~p~~~~~a~~y~~~~~~~~v~~~~~GSg~G~~~~~~g~~di~~ssr~l~~~E~~~~~~~~~~~v~~~~   88 (333)
T d1pc3a_          10 VTLAETGSTLL-YPLFNLWGPAFHERYPNVTITAQGTGSGAGIAQAAAGTVNIGASDAYLSEGDMAAHKGLMNIALAISA   88 (333)
T ss_dssp             EEEEEEECTTT-HHHHHHHHHHHHHHSTTEEEECCBCCHHHHHHHHHTTSCSEEEESSCCCHHHHHHSTTEEEEEEEEEE
T ss_pred             ceEEEEccchH-HHHHHHHHHHHHHHCCCeeEEEeccCcHHHHHHHHcCCCcEEEeCHHHhhHHHhhhcceeeeeEEEee
Confidence            36888888764 56888999999999999999999999999999999999999999754332     2356677788888


Q ss_pred             EEEEecCCCCCCC-------------CCCcChhh-----------hcCCCe--EeecCCCCcHHHHHHHHHhCCC-----
Q psy3760         168 YVIIVPLDHPLLL-------------LNSISLKE-----------ISNYPL--ITYDLSFSGRIKLDREFSLQKL-----  216 (306)
Q Consensus       168 ~~~v~~~~~~l~~-------------~~~i~~~d-----------l~~~~~--i~~~~~~~~~~~~~~~~~~~~~-----  216 (306)
                      +++++........             .+..+|.|           +.+.|.  +....+.+.+..+.+++....-     
T Consensus        89 i~v~v~~~~~~~~~~Lt~~~l~~i~~G~itnW~~~~~~~~n~~~~~p~~~I~v~~r~~~SGT~~~f~~~l~~~~~~~~~~  168 (333)
T d1pc3a_          89 QQVNYNLPGVSEHLKLNGKVLAAMYQGTIKTWDDPQIAALNPGVNLPGTAVVPLHRSDGSGDTFLFTQYLSKQDPEGWGK  168 (333)
T ss_dssp             EEEEECCTTCCSCCEECHHHHHHHHHTSCCBTTCHHHHHHSTTCCCCCCBCEECEESSCCHHHHHHHHHHHHHCTTTTTT
T ss_pred             eeeeeeecccccccccHHHHHhHhhCCCccccccccccccccCCCCCCcceEEecCCCCccchhhhHHHhhhcCccchhh
Confidence            8888765533211             11223444           122333  3334455566677776643210     


Q ss_pred             -----------ceeEEEEecCHHHHHHHHHhc-cceeeeeccee
Q psy3760         217 -----------TPYIVLETINSDIIKTYVELR-MGIGIIASIAF  248 (306)
Q Consensus       217 -----------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~  248 (306)
                                 ........++...+.+.|... .+++++....+
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~aIGy~~~~~~  212 (333)
T d1pc3a_         169 SPGFGTTVDFPAVPGALGENGNGGMVTGCAETPGCVAYIGISFL  212 (333)
T ss_dssp             TTCCSSSCCCCCCTTCCEECHHHHHHHHHHHSTTEEEEEEGGGH
T ss_pred             ccCccccccccccccceeccCcHHHHHHHhcCcccccccceeeh
Confidence                       001123444555566666554 78888776543

>d1amfa_ c.94.1.1 (A:) Molybdate-binding protein, ModA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Molybdate-binding protein, ModA
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=0.0022  Score=47.30  Aligned_cols=203  Identities=12%  Similarity=0.078  Sum_probs=113.4

Q ss_pred             CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC--------CCCCceeecc
Q psy3760          93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS--------PSDKLISIPC  163 (306)
Q Consensus        93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~--------~~~~~~~~~l  163 (306)
                      |.|+|.+..++ ...+.+++..|.++ ++++|++...++.+++..|..| ..|+.+......        ..........
T Consensus         1 Gel~vy~a~s~-~~~~~~l~~~Fek~-~gi~V~~~~~~sg~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (231)
T d1amfa_           1 GKITVFAAASL-TNAMQDIATQFKKE-KGVDVVSSFASSSTLARQIEAGAPADLFISADQKWMDYAVDKKAIDTATRQTL   78 (231)
T ss_dssp             CEEEEEEEGGG-HHHHHHHHHHHHHH-HCCEEEEEEECHHHHHHHHHHTCCCSEEECSSHHHHHHHHHTTCBCGGGCEEE
T ss_pred             CEEEEEEEcCh-HHHHHHHHHHHHHh-hCCEEEEEECChHHHHHHHHhCCCceEEEecchhhhHHHHhccccCcccceee
Confidence            67899998775 45678899999875 7899999999999999999887 455544421000        0011111112


Q ss_pred             ccceEEEEecCCCC---CCCCCCcChhhhcCCCeEee-cCCCC-cHHHHHHHHHhCCCc---eeEEEEecCHHHHHHHHH
Q psy3760         164 YQWEYVIIVPLDHP---LLLLNSISLKEISNYPLITY-DLSFS-GRIKLDREFSLQKLT---PYIVLETINSDIIKTYVE  235 (306)
Q Consensus       164 ~~~~~~~v~~~~~~---l~~~~~i~~~dl~~~~~i~~-~~~~~-~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~  235 (306)
                      ......++......   ......-++.|+.....+.. ++... ............+..   ........+...+...+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (231)
T d1amfa_          79 LGNSLVVVAPKASVQKDFTIDSKTNWTSLLNGGRLAVGDPEHVPAGIYAKEALQKLGAWDTLSPKLAPAEDVRGALALVE  158 (231)
T ss_dssp             EEECEEEEEETTCCCCCCCCSTTCCHHHHHTTCCEEEECTTTCHHHHHHHHHHHHTTCHHHHGGGEEEESSHHHHHHHHH
T ss_pred             ecccceeeecccccccccccccHHHHHhhcCCCcEEEECCCCchHHHHHHHHHHHhCCccccccccccccchhHHHHHHH
Confidence            22333333333332   22244567888866544433 33322 333444455555543   234556778888889998


Q ss_pred             hccc-eeeeecceecccccCCceeeecC-CCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760         236 LRMG-IGIIASIAFDSNRDKNLRSISAS-HLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       236 ~g~g-i~~~p~~~~~~~~~~~l~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      .|.+ +++......... .+.-....++ +......+.+...++.. ++.+++|+++|.+.=.+..
T Consensus       159 ~g~~~~~i~~~~~~~~~-~~~~~~~~~p~~~~~~~~~~~~i~~~~~-~~~A~~Fi~fl~S~e~Q~i  222 (231)
T d1amfa_         159 RNEAPLGIVYGSDAVAS-KGVKVVATFPEDSHKKVEYPVAVVEGHN-NATVKAFYDYLKGPQAAEI  222 (231)
T ss_dssp             TTSSSEEEEEHHHHHHC-SSEEEEEECCGGGSCCEEEEEEEBTTCC-SHHHHHHHHHHTSHHHHHH
T ss_pred             cCCceEEEeehhhhhhc-cCCCceEEeCCCCceEeEEEEEEECCCC-CHHHHHHHHHHCCHHHHHH
Confidence            8843 333333222221 2222222333 22334444555556655 5789999999976533333

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.80  E-value=4.7e-05  Score=52.23  Aligned_cols=74  Identities=20%  Similarity=0.342  Sum_probs=57.5

Q ss_pred             chhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      +..++.++..+.+.+  -+.+.-|+.+++++|++|+.|+.||+   ..|..|..       ..+ .||+.|+.++..+..
T Consensus        30 t~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~~---~glI~~~~~~~D~R~~~l-~lT~~G~~~~~~~~~  105 (140)
T d3deua1          30 TQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLED---KGLISRQTCASDRRAKRI-KLTEKAEPLIAEMEE  105 (140)
T ss_dssp             CHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHH---TTSEEEC--------CEE-EECGGGHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHHh---CCCEEecccCCCCCceee-EECHHHHHHHHHHHH
Confidence            456777888887632  26678999999999999999999998   34555443       345 899999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      .......
T Consensus       106 ~~~~~~~  112 (140)
T d3deua1         106 VIHKTRG  112 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8766544

>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=97.79  E-value=0.00012  Score=49.00  Aligned_cols=76  Identities=13%  Similarity=0.182  Sum_probs=57.4

Q ss_pred             CchhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC---CCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG---KRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~---~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      |+..++.++..+.+.+   -|.+.-|+.+++++|++|+.|++||+ -|.--..|+.   |.+ +.||+.|+..+..+...
T Consensus        32 Lt~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~-~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~  110 (125)
T d1p4xa1          32 MTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVK-HSYISKVRSKIDERNTYISISEEQREKIAERVTL  110 (125)
T ss_dssp             SCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHH-TTSCEEEECSSSTTSEEEECCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHH-CCCceeecccCCCCeEEEEECHHHHHHHHHHHHH
Confidence            4667888888887752   26789999999999999999999987 5666666542   222 38999999988766555


Q ss_pred             HHHH
Q psy3760          74 MQEI   77 (306)
Q Consensus        74 l~~~   77 (306)
                      ++++
T Consensus       111 ~~~~  114 (125)
T d1p4xa1         111 FDQI  114 (125)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.79  E-value=4.4e-05  Score=54.36  Aligned_cols=74  Identities=22%  Similarity=0.244  Sum_probs=58.6

Q ss_pred             chhhHHHHHHHHHhc----CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN----FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSI   70 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~----~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a   70 (306)
                      +..++.++..+.+.|    .|.+.-|+.++++++++|+.|++||+.   -|+.|..       ..+ +||+.|+.++..+
T Consensus        61 t~~q~~vL~~L~~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~---GlV~r~~~~~DrR~~~i-~LT~~G~~l~~~~  136 (172)
T d2fbka1          61 NAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEK---GLIERREDERDRRSASI-RLTPQGRALVTHL  136 (172)
T ss_dssp             CHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHH---TSEECCC-------CCB-EECHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhCCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhC---CCeeeeccccchhhHHh-hcCHHHHHHHHHH
Confidence            456778888887664    278999999999999999999999997   3444442       334 8999999999998


Q ss_pred             HHHHHHHHH
Q psy3760          71 EIIMQEIEG   79 (306)
Q Consensus        71 ~~il~~~~~   79 (306)
                      ........+
T Consensus       137 ~~~~~~~~~  145 (172)
T d2fbka1         137 LPAHLATTQ  145 (172)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            877776554

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.75  E-value=0.00014  Score=49.84  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=59.1

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCc-cccCHhHHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRI-RGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~-~~lT~~G~~l~~~a~~il~   75 (306)
                      |+..++.++..+.+.+ -+.+.-|+.+++|+|++|+.|++||+ -|.---.++   +|.. +.||+.|+.++..+.+...
T Consensus        34 lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~-~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~~  112 (141)
T d1lnwa_          34 LTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEG-RNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMS  112 (141)
T ss_dssp             CCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHH-TTSEEEEECSSSSSSEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHH-hhceeeeccCCCCcchhhccCHHHHHHHHHHHHHHH
Confidence            4566788888887765 37889999999999999999999988 444333332   2221 2799999999998888777


Q ss_pred             HHHH
Q psy3760          76 EIEG   79 (306)
Q Consensus        76 ~~~~   79 (306)
                      .+.+
T Consensus       113 ~~~~  116 (141)
T d1lnwa_         113 RVHD  116 (141)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6654

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=97.73  E-value=6.6e-05  Score=51.64  Aligned_cols=77  Identities=13%  Similarity=0.144  Sum_probs=58.2

Q ss_pred             CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+. |-+.+.-|+.+++++|++|+.+++||+. |.--..+++     ..+ .||+.|+.++..+.+..
T Consensus        33 lt~~q~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l~~L~~~-glv~r~~~~~D~R~~~v-~lT~~G~~~~~~~~~~~  110 (143)
T d1s3ja_          33 VTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQK-NLIARTHNTKDRRVIDL-SLTDEGDIKFEEVLAGR  110 (143)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHh-hhheeeeecCCCCceEE-EECHHHHHHHHHHHHHH
Confidence            355677888888776 3488999999999999999999999974 333322222     125 89999999999988887


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      .....
T Consensus       111 ~~~~~  115 (143)
T d1s3ja_         111 KAIMA  115 (143)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77443

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=97.73  E-value=9.6e-05  Score=50.52  Aligned_cols=77  Identities=12%  Similarity=0.104  Sum_probs=58.4

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il   74 (306)
                      ++..++.++..+.+.| -|.+.-|+.+++++|++|+.|++||+. |.--..++     ..-+ .||+.|+.+++.+....
T Consensus        28 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~-gli~r~~~~~D~R~~~i-~LT~~G~~~~~~~~~~~  105 (139)
T d2a61a1          28 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEAD-GYLTRTPDPADRRAYFL-VITRKGEEVIEKVIERR  105 (139)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEE-EECHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHhc-CeeeeeeccCCCCeEEE-EECHHHHHHHHHHHHHH
Confidence            3556777888887773 367899999999999999999999974 43333322     3444 89999999999888877


Q ss_pred             HHHHH
Q psy3760          75 QEIEG   79 (306)
Q Consensus        75 ~~~~~   79 (306)
                      ....+
T Consensus       106 ~~~~~  110 (139)
T d2a61a1         106 ENFIE  110 (139)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>d1us5a_ c.94.1.1 (A:) Putative GluR0 ligand binding core {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Putative GluR0 ligand binding core
species: Thermus thermophilus [TaxId: 274]

Probab=97.67  E-value=0.0013  Score=51.01  Aligned_cols=139  Identities=9%  Similarity=0.062  Sum_probs=100.3

Q ss_pred             cEEEEecccch-hhhhHHHHHHH-HHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc---------------CCC
Q psy3760          94 NLTIATTHTQA-RYALPKIIKEF-TIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL---------------SPS  155 (306)
Q Consensus        94 ~l~I~~~~~~~-~~~l~~~l~~~-~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~---------------~~~  155 (306)
                      .|+||+.+.=+ .+.+...+.++ .+..|++++.+.. .++.+-+..|.+|++|++++....               ...
T Consensus         4 ~l~i~tg~~gg~y~~~~~~la~~l~~~~~~i~~~~~~t~Gs~~Nl~~l~~g~~d~a~~~~~~~~~a~~g~~~~~~~~~~~   83 (298)
T d1us5a_           4 FITIGSGSTTGVYFPVATGIAKLVNDANVGIRANARSTGGSVANINAINAGEFEMALAQNDIAYYAYQGCCIPAFEGKPV   83 (298)
T ss_dssp             EEEEECCCTTSSHHHHHHHHHHHHHHHTSSEEEEEECCSCHHHHHHHHHTTSCSEEEEEHHHHHHHHHTCSSTTTTTCCC
T ss_pred             eEEEEeCCCCChHHHHHHHHHHHHhhcCCCeEEEEEeCCCHHHHHHHHHCCCceEEEeccHHHHHHhcCccccccccccc
Confidence            58999965322 23455555554 4558999999887 566678899999999999985210               123


Q ss_pred             CCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEecCHHHHHH
Q psy3760         156 DKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLETINSDIIKT  232 (306)
Q Consensus       156 ~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  232 (306)
                      +++. ...++.+.+.++++++..     .-+++||.+.+.-....++..+......|+..|+.+..  .....+......
T Consensus        84 ~~lr~l~~l~~~~~~~~v~~~s~-----i~s~~DL~gk~v~~g~~gsg~~~~~~~~l~~~g~~~dd~~~~~~~~~~~~~~  158 (298)
T d1us5a_          84 KTIRALAALYPEVVHVVARKDAG-----IRTVADLKGKRVVVGDVGSGTEQNARQILEAYGLTFDDLGQAIRVSASQGIQ  158 (298)
T ss_dssp             TTEEEEEEEEEEEEEEEEETTSS-----CSSGGGGTTSEEECCCTTCHHHHHHHHHHHHTTCCGGGSSEEECCCHHHHHH
T ss_pred             cceeEEEEechhhheeeccccCC-----cCchhhccCccccccCCCchHHHHHHHHHHHhCCCcccccceeccchhHHHH
Confidence            4553 566778889999988754     34799999988888888877777888899999987632  345567777777


Q ss_pred             HHHhc
Q psy3760         233 YVELR  237 (306)
Q Consensus       233 ~v~~g  237 (306)
                      ++.+|
T Consensus       159 al~~g  163 (298)
T d1us5a_         159 LMQDK  163 (298)
T ss_dssp             HHHTT
T ss_pred             HhcCC
Confidence            78777

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.67  E-value=6.8e-05  Score=51.10  Aligned_cols=76  Identities=21%  Similarity=0.250  Sum_probs=58.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      |+..++.++..+.+.| -+.+.-|+.+++++|++|+.|++||+.   -|..|.       ...+ .||+.|+.++..+..
T Consensus        28 lt~~q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~~L~~~---gli~r~~~~~D~R~~~l-~lT~~G~~~~~~~~~  103 (136)
T d2fbia1          28 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERD---GIVRRWKAPKDQRRVYV-NLTEKGQQCFVSMSG  103 (136)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHT---TSEEEEEETTEEEEEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEeecCccCchhhh-ccCHHHHHHHHHHHH
Confidence            4566778888888775 245677999999999999999999986   344433       2345 899999999999988


Q ss_pred             HHHHHHHH
Q psy3760          73 IMQEIEGL   80 (306)
Q Consensus        73 il~~~~~~   80 (306)
                      .......-
T Consensus       104 ~~~~~~~~  111 (136)
T d2fbia1         104 DMEKNYQR  111 (136)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77765553

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=97.67  E-value=0.00014  Score=49.42  Aligned_cols=77  Identities=13%  Similarity=0.085  Sum_probs=59.9

Q ss_pred             CchhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~   72 (306)
                      |+..++.++..+.+.+   -|.+.-|+.+++++|++|+.+++||+. |.--..+..     ..+ .+|+.|+.+++.+.+
T Consensus        27 lt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~-g~v~r~~~~~D~R~~~i-~lT~~G~~~~~~~~~  104 (135)
T d3broa1          27 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIK-KLLYRKVSGKDSRQKCL-KLTKKANKLETIILS  104 (135)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEE-EECHHHHTTHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHH-HHHHHHhhhhhhhhhhh-cccHHHHHHHHHHHH
Confidence            4567888888888763   156789999999999999999999974 444444432     234 899999999999888


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      .......
T Consensus       105 ~~~~~~~  111 (135)
T d3broa1         105 YMDSDQS  111 (135)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776654

>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=97.59  E-value=0.00025  Score=47.27  Aligned_cols=73  Identities=15%  Similarity=0.200  Sum_probs=51.2

Q ss_pred             CchhhHHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      ++..++.++..+.+.+   -+++.-|+.+++++|++|+.|++||+. |.-=-.++   +|.+ +.||+.|+.++....+-
T Consensus        31 Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~-glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~~~  109 (125)
T d1p4xa2          31 LSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQ-GYLIKERSTEDERKILIHMDDAQQDHAEQLLAQ  109 (125)
T ss_dssp             SCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHH-TSSEEEECSSSTTCEEEECCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhc-cCEeeeecCCCCCeEEEEECHHHHHHHHHHHHH
Confidence            4567788888886532   257899999999999999999999975 32222222   2222 38999999877655444


Q ss_pred             H
Q psy3760          74 M   74 (306)
Q Consensus        74 l   74 (306)
                      +
T Consensus       110 ~  110 (125)
T d1p4xa2         110 V  110 (125)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=97.55  E-value=0.00011  Score=50.22  Aligned_cols=75  Identities=20%  Similarity=0.239  Sum_probs=58.9

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.| -+.+.-|+.+++|+|++|+.+++||+.   -|..|.       ...+ .||+.|+.++..+..
T Consensus        30 lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~~---gli~r~~~~~D~R~~~l-~lT~~G~~~~~~~~~  105 (140)
T d2etha1          30 MKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKR---GLVVREMDPVDRRTYRV-VLTEKGKEIFGEILS  105 (140)
T ss_dssp             SBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHT---TSEEEEECTTTSSCEEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC---CCeeeeecccccchhhh-hcCHHHHHHHHHHHH
Confidence            4567888888888887 267888999999999999999999985   344433       2344 899999999988877


Q ss_pred             HHHHHHH
Q psy3760          73 IMQEIEG   79 (306)
Q Consensus        73 il~~~~~   79 (306)
                      .......
T Consensus       106 ~~~~~~~  112 (140)
T d2etha1         106 NFESLLK  112 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7666544

>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=97.52  E-value=5.8e-05  Score=43.48  Aligned_cols=42  Identities=24%  Similarity=0.369  Sum_probs=37.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      |...-|+.||+|.+||.+.|++||+ .|.++....|+|. +|++
T Consensus        21 s~~eLa~~l~vS~~ti~r~i~~L~~-~G~~I~~~~g~GY-~L~~   62 (63)
T d1biaa1          21 SGEQLGETLGMSRAAINKHIQTLRD-WGVDVFTVPGKGY-SLPE   62 (63)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHH-TTCCCEEETTTEE-ECSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHH-CCCcEEEeCCCeE-EeCC
Confidence            6778899999999999999999997 7999988888887 6764

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=97.48  E-value=0.00026  Score=48.21  Aligned_cols=73  Identities=18%  Similarity=0.166  Sum_probs=54.9

Q ss_pred             chhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----C--CCccccCHhHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----G--KRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus         2 ~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~--~~~~~lT~~G~~l~~~a~~i   73 (306)
                      +..++.++..+.+. +-|.+.-|+.++++++++|+.|++||+.   -+..|.     +  ..+ .+|+.|+.+++.+.+.
T Consensus        33 t~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~---glv~r~~~~~D~R~~~i-~lT~~G~~~~~~~~~~  108 (138)
T d1jgsa_          33 TAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLV-KLTTGGAAICEQCHQL  108 (138)
T ss_dssp             CHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEEECTTCSSCEEE-EECHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhC---CCEEEeeccCCCCeeEE-EECHHHHHHHHHHHHH
Confidence            45667777777664 3478889999999999999999999985   344433     1  244 8999999999988776


Q ss_pred             H-HHHH
Q psy3760          74 M-QEIE   78 (306)
Q Consensus        74 l-~~~~   78 (306)
                      . +.++
T Consensus       109 ~~~~~~  114 (138)
T d1jgsa_         109 VGQDLH  114 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            5 3444

>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=97.39  E-value=0.00017  Score=48.96  Aligned_cols=76  Identities=16%  Similarity=0.224  Sum_probs=55.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      |+..++.++..+.+.+ .|.+.-|+.+++++|++|+.+++||+.   -|..|.     +|.. +.||+.|+.++..+...
T Consensus        32 lt~~q~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l~~L~~~---Gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~  108 (136)
T d2bv6a1          32 LTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQV---DLIKRERSEVDQREVFIHLTDKSETIRPELSNA  108 (136)
T ss_dssp             CCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHT---TSEEEEECSSSTTCEEEEECHHHHHHHHHHTTH
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHHHHHHHC---CCEEEeecCCcccchhhccCHHHHHHHHHHHHH
Confidence            3456677777775533 367889999999999999999999984   344443     2222 37999999999888877


Q ss_pred             HHHHHH
Q psy3760          74 MQEIEG   79 (306)
Q Consensus        74 l~~~~~   79 (306)
                      .+.+.+
T Consensus       109 ~~~~~~  114 (136)
T d2bv6a1         109 SDKVAS  114 (136)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666543

>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=97.38  E-value=0.00029  Score=49.28  Aligned_cols=73  Identities=18%  Similarity=0.148  Sum_probs=55.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI   72 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~   72 (306)
                      ++..++.++..+.+.+ -|.+.-|+.+++++|++|+.|++||+.   -|..|..       ..+ +||+.|+.++..+.+
T Consensus        39 Lt~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~~---gli~r~~~~~D~R~~~l-~lT~~G~~~~~~~~~  114 (162)
T d2fxaa1          39 LNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEER---GYLRFSKRLNDKRNTYV-QLTEEGTEVFWSLLE  114 (162)
T ss_dssp             CCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHH---TSEEEECC------CEE-EECHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHHC---CCceeecccccCeeeee-ccCHhHHHHHHHHHH
Confidence            3556777777777655 268899999999999999999999985   3444432       244 899999999988877


Q ss_pred             HHHHH
Q psy3760          73 IMQEI   77 (306)
Q Consensus        73 il~~~   77 (306)
                      ..+..
T Consensus       115 ~~~~~  119 (162)
T d2fxaa1         115 EFDPT  119 (162)
T ss_dssp             HCCGG
T ss_pred             HHHHH
Confidence            65443

>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=97.32  E-value=0.00019  Score=47.05  Aligned_cols=73  Identities=15%  Similarity=0.147  Sum_probs=52.4

Q ss_pred             CchhhHHHHHHHHH--h-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCc-cccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVR--Q-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRI-RGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~--~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~-~~lT~~G~~l~~~a~~i   73 (306)
                      ++..++.++..++.  . +-|.+.-|+.+++++|++|+.|++||+. |.---.++   +|.+ +.||+.|+.+++.+...
T Consensus        30 Lt~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~-gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~  108 (115)
T d1hsja1          30 LNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDL-KLLSKKRSLQDERTVIVYVTDTQKANIQKLISE  108 (115)
T ss_dssp             CCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTT-TTSCCEECCSSSSCCEEECCSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHc-CCeEEEeecCCCceEEEEECHHHHHHHHHHHHH
Confidence            45677788877773  2 2378899999999999999999999953 43333332   2222 38999999998776544


Q ss_pred             H
Q psy3760          74 M   74 (306)
Q Consensus        74 l   74 (306)
                      +
T Consensus       109 ~  109 (115)
T d1hsja1         109 L  109 (115)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.30  E-value=0.00035  Score=39.64  Aligned_cols=43  Identities=26%  Similarity=0.234  Sum_probs=36.0

Q ss_pred             CchhhHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+-+.++ |+++-|+.+|+|.+++.++|++||++
T Consensus         1 lD~~D~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~   44 (60)
T d1i1ga1           1 IDERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEK   44 (60)
T ss_dssp             CCSHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            55666777777776643 89999999999999999999999986

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=97.26  E-value=0.00014  Score=49.51  Aligned_cols=77  Identities=14%  Similarity=0.182  Sum_probs=55.5

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCC-ccccCHhHHHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKR-IRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~-~~~lT~~G~~l~~~a~~il~~   76 (306)
                      +..++.++..+.+.+ .+.+.-|+.++++++++|+.|++||+. |.--..++   +|. .+.||+.|+.+++.+.++.+.
T Consensus        32 t~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~-glv~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~~  110 (137)
T d1z91a1          32 TYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQ-GLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGT  110 (137)
T ss_dssp             CHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHH-TSEECCBCSSCTTSBEEEECHHHHSGGGGTTTHHHH
T ss_pred             CHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhc-cceEEeecCCCCCeEEEEECHHHHHHHHHHHHHHHH
Confidence            456677777776533 367888999999999999999999985 33222322   221 138999999999988887666


Q ss_pred             HHH
Q psy3760          77 IEG   79 (306)
Q Consensus        77 ~~~   79 (306)
                      +..
T Consensus       111 ~~~  113 (137)
T d1z91a1         111 ILG  113 (137)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=97.21  E-value=0.00025  Score=44.92  Aligned_cols=58  Identities=17%  Similarity=0.314  Sum_probs=45.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHh
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKP   62 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~   62 (306)
                      ..++++..+.+...+++.-|+.+++|||++|++++.|++. |.-=..|.|+.+. ++++.
T Consensus        24 ~Rl~Il~~L~~~~~~v~ela~~l~is~stvS~HL~~L~~a-glV~~~r~G~~~~Y~l~~~   82 (98)
T d1r1ta_          24 NRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNL-RLVSYRKQGRHVYYQLQDH   82 (98)
T ss_dssp             HHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEESSH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEEECCEEEEEEChH
Confidence            3456666666655599999999999999999999999864 7777778887753 56654

>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=97.20  E-value=0.00059  Score=42.67  Aligned_cols=58  Identities=17%  Similarity=0.194  Sum_probs=45.8

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHh
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKP   62 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~   62 (306)
                      ..++++..+.+...+++.-|+.+++|||++|++++.|++ .|.--..|.|+.++ ++++.
T Consensus        19 ~Rl~Il~~L~~~~~~v~el~~~l~~s~~~vS~HL~~L~~-~glv~~~r~G~~~~Y~l~~~   77 (94)
T d1r1ua_          19 NRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKS-VHLVKAKRQGQSMIYSLDDI   77 (94)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHH-TTSEEEEEETTEEEEEESSH
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH-CCceEEEEECCEEEEEECcH
Confidence            345666666665559999999999999999999999985 67878888888753 66653

>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=97.18  E-value=0.00055  Score=38.81  Aligned_cols=43  Identities=14%  Similarity=0.159  Sum_probs=35.6

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||--+.+.+..+.+.+ .|+.+-|+++|+|.+++.++|++||++
T Consensus         1 lD~~D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~   44 (60)
T d2cyya1           1 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES   44 (60)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            5556667777777643 289999999999999999999999986

>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=97.18  E-value=0.00046  Score=39.56  Aligned_cols=43  Identities=16%  Similarity=0.358  Sum_probs=34.8

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||-.+.+++..+.+.+ .|+++-|+.+|+|.++++++|++||++
T Consensus         3 lD~~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~   46 (63)
T d2cfxa1           3 LDQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESF   46 (63)
T ss_dssp             CCHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4555666777776552 389999999999999999999999985

>d1lsta_ c.94.1.1 (A:) Lysine-,arginine-,ornithine-binding (LAO) protein {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Lysine-,arginine-,ornithine-binding (LAO) protein
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.15  E-value=0.017  Score=42.53  Aligned_cols=202  Identities=13%  Similarity=0.089  Sum_probs=117.4

Q ss_pred             CcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCc-
Q psy3760          93 GNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKL-  158 (306)
Q Consensus        93 ~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~-  158 (306)
                      .+||||+....+           ..+...++.++.++. ++++++...+....+..+.+|++|+++......+  ...+ 
T Consensus         4 ~tl~v~~~~~~pP~~~~d~~G~~~G~~~dl~~~ia~~l-g~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~r~~~~~   82 (238)
T d1lsta_           4 QTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRM-QVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIA   82 (238)
T ss_dssp             SEEEEEECSCBTTTBEECTTCCEESHHHHHHHHHHHHH-TCEEEEEECCGGGHHHHHHTTSCSEECSSCBCCHHHHHHCE
T ss_pred             CEEEEEECCCCCCeeEECCCCCEEEhHHHHHHHHHHHh-CCceEEeechHHHHHHHHHhcccceeecccchhhhhhhhcc
Confidence            579999843211           234577887777764 7899999999999999999999998875422121  1122 


Q ss_pred             eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760         159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      -+.++......++++++.+.    .-+++|+.+..+..... ......+.+.....+   .......+...+..++.+|.
T Consensus        83 ~s~p~~~~~~~l~~~~~~~~----~~~~~dl~~~~i~v~~g-~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~l~~gr  154 (238)
T d1lsta_          83 FSDKLYAADSRLIAAKGSPI----QPTLESLKGKHVGVLQG-STQEAYANDNWRTKG---VDVVAYANQDLIYSDLTAGR  154 (238)
T ss_dssp             ECSCSBCCCEEEEEETTCCC----CSSHHHHTTCEEEEETT-SHHHHHHHHHTGGGT---CEEEEESSHHHHHHHHHTTS
T ss_pred             cCCCccccCceEEEEecCcc----cCCccccCCCEEEEEec-chHHHHHHHhhhccc---cceeeeCCHHHHHHHHhhhc
Confidence            34577788889999888653    24789999888766543 222222223222222   23457889999999999996


Q ss_pred             ceeeee-cceec----cccc-CCceeeecCC---CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760         239 GIGIIA-SIAFD----SNRD-KNLRSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN  305 (306)
Q Consensus       239 gi~~~p-~~~~~----~~~~-~~l~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  305 (306)
                      .=+++- .....    .... ..........   ......++++.+++.  +.....|=+.|++.-+...++++.+
T Consensus       155 ~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~~--~~l~~~in~~l~~~~~~G~~~~I~~  228 (238)
T d1lsta_         155 LDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDD--TELKAAFDKALTELRQDGTYDKMAK  228 (238)
T ss_dssp             CSEEEEEHHHHHHHTTTSGGGTTEEECSSCBCCHHHHCSSBCCEECTTC--HHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred             ccEEEecHHHHHHHHHhCccCCceEEEeecccccccccccEEEEEeCCC--HHHHHHHHHHHHHHHHCcHHHHHHH
Confidence            544433 22111    1111 1222221111   111224556666663  3444445455555544555555543

>d1pb7a_ c.94.1.1 (A:) N-methyl-D-aspartate receptor subunit 1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: N-methyl-D-aspartate receptor subunit 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.12  E-value=0.00035  Score=54.09  Aligned_cols=195  Identities=11%  Similarity=-0.011  Sum_probs=109.3

Q ss_pred             CCCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeC-----------------ChhHHHHHHHcCC
Q psy3760          91 DTGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQG-----------------NPKQITEMIRNDQ  142 (306)
Q Consensus        91 ~~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~-----------------~~~~~~~~l~~~~  142 (306)
                      ..+.+++|+.....           ..+-..++..+.+.. ++++++...                 ..+.++..|.+|+
T Consensus        36 ~~~~~~~~~~~~~pp~~~~~~~~~~~G~~vDl~~~ia~~l-g~~~e~~~v~~~~~g~~~~~~~~~~~~w~~~~~~l~~g~  114 (289)
T d1pb7a_          36 VKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTM-NFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQ  114 (289)
T ss_dssp             CCCEEEEEEC--------CEEEEEEESHHHHHHHHHHHHH-TCCEEEEECTTCCCCCEEECTTSSCEEECHHHHHHHHTS
T ss_pred             cCceEEeeccCCCCCccccCCCCceEEEhHHHHHHHHHHh-CCcEEEEEccccccccccccccccccChhHhhhhhhhhh
Confidence            35678888765322           345667777776653 667777643                 3678999999999


Q ss_pred             eeEEEEccccC--CCCCc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc--
Q psy3760         143 ADIAIVTEILS--PSDKL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT--  217 (306)
Q Consensus       143 ~Di~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~--  217 (306)
                      +|+++......  ....+ -+.|+.....+++++++.+..........++...-.+....+.    ..+.+++.....  
T Consensus       115 ~Di~~~~~s~t~eR~~~~~Fs~Py~~~~~~l~vrk~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~  190 (289)
T d1pb7a_         115 ADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQS----SVDIYFRRQVELST  190 (289)
T ss_dssp             CSEECSSCBCCHHHHTTEEECSCSEEEEEEEEEETTCCCCSTTCHHHHSCBTTBCEECBTTS----HHHHHHHTCGGGHH
T ss_pred             eeEEeeccccCHHHHHhcccccccceeeeEEEEECCCCcccccchhhcCCceeEEEEEeccH----HHHHHHHhhhhhhh
Confidence            99998742211  11223 3567888999999999886544332222222222223322222    223333322110  


Q ss_pred             --ee-EEEEecCHHHHHHHHHhccceeeeeccee-ccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         218 --PY-IVLETINSDIIKTYVELRMGIGIIASIAF-DSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       218 --~~-~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                        +. .....++...++.++.+|..-+++.+... ..+  ..+++..++  ......++++..+++.+....+...++.+
T Consensus       191 ~~~~~~~~~~~~~~~~~~~l~~g~~da~i~d~~~~~~~~~~~~~l~~~~--~~~~~~~~~~a~~k~~~l~~~in~al~~l  268 (289)
T d1pb7a_         191 MYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTG--ELFFRSGFGIGMRKDSPWKQNVSLSILKS  268 (289)
T ss_dssp             HHHHHTTTCBSSHHHHHHHHHTTSCSEEEEEHHHHHHHHHHCTTEEECS--SCSEEEEECCEEETTCSSHHHHHHHHHHH
T ss_pred             ccccceEEEcCCHHHHHHHHhCCCeEEEEehhhHHHHHHhhCCCEEEec--cccCceeEEEEEcCChHHHHHHHHHHHHH
Confidence              11 12346889999999999977666554332 222  345555543  22334567788888765444444444444


Q ss_pred             h
Q psy3760         292 S  292 (306)
Q Consensus       292 ~  292 (306)
                      +
T Consensus       269 ~  269 (289)
T d1pb7a_         269 H  269 (289)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.11  E-value=0.00018  Score=40.97  Aligned_cols=32  Identities=9%  Similarity=0.040  Sum_probs=28.0

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      +-.++.++| +.++||+.||||++|+.+.|+++
T Consensus        26 I~~aL~~~g-n~~~aA~~Lgisr~tL~rKlkk~   57 (61)
T d1g2ha_          26 LKLFYAEYP-STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             HHHHHHHSC-SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             HHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHh
Confidence            445677889 99999999999999999999864

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.05  E-value=0.0027  Score=40.67  Aligned_cols=70  Identities=19%  Similarity=0.196  Sum_probs=51.8

Q ss_pred             HHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecCCC-------ccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHGKR-------IRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~~~-------~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      ++..+..-...|+.=.+.+ +||+..+|+++++||+.   -|+.|....       . .||+.|+.|.+-...+.+=.++
T Consensus        24 Il~~L~~g~~RF~el~~~l~gIS~~~Ls~rLk~L~~~---glv~R~~~~~~p~~veY-~LT~~G~~L~pil~~l~~W~~~   99 (108)
T d1z7ua1          24 LMDELFQGTKRNGELMRALDGITQRVLTDRLREMEKD---GLVHRESFNELPPRVEY-TLTPEGYALYDALSSLCHWGET   99 (108)
T ss_dssp             HHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHHHHHHH---TSEEEEEECCSSCEEEE-EECHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHCcCCChhHHHHHHHHHHHC---CcceeeccCCCcceehh-hhchhHHHHHHHHHHHHHHHHH
Confidence            3344444323899999999 89999999999999986   356665222       4 7999999999988877665544


Q ss_pred             HH
Q psy3760          80 LK   81 (306)
Q Consensus        80 ~~   81 (306)
                      -.
T Consensus       100 ~~  101 (108)
T d1z7ua1         100 FA  101 (108)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=97.02  E-value=0.00044  Score=39.14  Aligned_cols=33  Identities=15%  Similarity=0.175  Sum_probs=28.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      .+..++.+++++.++||+.||||.+|+.+.|++
T Consensus        24 ~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmkk   56 (60)
T d1umqa_          24 HIQRIYEMCDRNVSETARRLNMHRRTLQRILAK   56 (60)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHHH
Confidence            355667777779999999999999999999986

>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=96.92  E-value=0.0014  Score=42.37  Aligned_cols=76  Identities=16%  Similarity=0.138  Sum_probs=53.5

Q ss_pred             CchhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEII   73 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~i   73 (306)
                      ++..++.+|..+.+.+  .|.+.-|+.+++++|++|+.|++||+ -|.---.+.     ++.+ .+|..|..+.+.+..-
T Consensus        19 Ls~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~-~GlV~r~~~~~d~rg~~~-~~~~~~~~~~~~i~~~   96 (109)
T d2d1ha1          19 ITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIE-LGLVVRTKTEGKKIGRPK-YYYSISSNILEKIRND   96 (109)
T ss_dssp             CCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHH-TTSEEEEEC-------CC-EEEEECTTHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHH-CCCEEEeecCCCCCceeE-EEeeCCHHHHHHHHHH
Confidence            3456788888887643  26788999999999999999999997 454433222     3445 5899998888776554


Q ss_pred             HHHHH
Q psy3760          74 MQEIE   78 (306)
Q Consensus        74 l~~~~   78 (306)
                      +....
T Consensus        97 ~~~~~  101 (109)
T d2d1ha1          97 LLNCA  101 (109)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.82  E-value=0.0074  Score=36.90  Aligned_cols=68  Identities=22%  Similarity=0.199  Sum_probs=51.4

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHH---HHHHHHHHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII---MQEIEGLKKIGK   85 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i---l~~~~~~~~~~~   85 (306)
                      -+.. +.|+-....|+|...+++-|..|++.   -|....++.. .+|+.|..|++..+++   ++.++++...+.
T Consensus        16 ~~g~-~kT~i~~~aNLs~~~~~kyl~~L~~~---GLI~~~~~~Y-~iT~kG~~~L~~~~~~~~~~~~l~~l~~~i~   86 (90)
T d1r7ja_          16 KSGS-PKTRIMYGANLSYALTGRYIKMLMDL---EIIRQEGKQY-MLTKKGEELLEDIRKFNEMRKNMDQLKEKIN   86 (90)
T ss_dssp             TTCB-CHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEETTEE-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCC-CccHHHHHcCCCHHHHHHHHHHHHHC---CCeeecCCEE-EECccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445 89999999999999999999999874   4556677777 7999999997775554   445555544443

>d1d1la_ a.35.1.2 (A:) cro lambda repressor {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro lambda repressor
species: Bacteriophage lambda [TaxId: 10710]

Probab=96.80  E-value=0.00044  Score=37.85  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=19.7

Q ss_pred             CHHHHHHHhCCCchHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      .=++||+.||++|++|||+|+.
T Consensus        15 GQaKaA~~LGv~Q~AIsKAira   36 (61)
T d1d1la_          15 GQTKTAKDLGVYQSAINKAIHA   36 (61)
T ss_dssp             CHHHHHHHHTCCTHHHHHHHHT
T ss_pred             ChHHHHHHcCccHHHHHHHHhc
Confidence            3589999999999999999974

>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=96.71  E-value=0.0046  Score=39.57  Aligned_cols=58  Identities=14%  Similarity=0.158  Sum_probs=42.4

Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHh
Q psy3760           4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKP   62 (306)
Q Consensus         4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~   62 (306)
                      ..++++..+++.| .+.+.-|+.+++|||++|++|+.|++ .|.--..|.|+.+. ++++.
T Consensus        32 ~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~-aGlv~~~r~G~~~~Y~l~~~   91 (108)
T d1u2wa1          32 NRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYK-QGVVNFRKEGKLALYSLGDE   91 (108)
T ss_dssp             HHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHH-TTSEEEC----CCEEEESCH
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHH-CCeeEEEEECCEEEEEECHH
Confidence            4577887777544 26888999999999999999999985 57777778877653 67665

>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=96.62  E-value=0.002  Score=36.43  Aligned_cols=26  Identities=23%  Similarity=0.438  Sum_probs=23.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.+.-|+.||+|+|++|.+|++|++.
T Consensus        23 ~~~~iA~~L~vs~~SVs~mikrL~~~   48 (61)
T d2ev0a1          23 RVSDIAEALAVHPSSVTKMVQKLDKD   48 (61)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            57889999999999999999999874

>d1mqia_ c.94.1.1 (A:) Glutamate receptor ligand binding core {Rat (Rattus norvegicus), GluR2 [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Glutamate receptor ligand binding core
species: Rat (Rattus norvegicus), GluR2 [TaxId: 10116]

Probab=96.61  E-value=0.011  Score=44.36  Aligned_cols=187  Identities=13%  Similarity=0.046  Sum_probs=99.0

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCC-------------hhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGN-------------PKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYV  169 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~-------------~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~  169 (306)
                      .+-..++..+.+.. +++++++...             .+.+...+.+|++|+++......  ....+. +.|++.....
T Consensus        32 G~~idl~~~ia~~l-g~~~~~~~~~~~~~~~~~~~~~~w~~~~~~l~~G~~D~~~~~~t~T~eR~~~~~FS~Py~~~~~~  110 (260)
T d1mqia_          32 GYCVDLAAEIAKHC-GFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGIS  110 (260)
T ss_dssp             SHHHHHHHHHHHHH-TCCEEEEECTTCCCCCBCTTTCCBCHHHHHHHTTSCSEECSSCBCCHHHHTTEEECSCSEEECEE
T ss_pred             EEHHHHHHHHHHHh-CCCeEEEecCCCccceeccccccHHHHHHhhhcCcHHHHHhhhcCcHHHHhhCcCCCCeEcccce
Confidence            45567777776654 7888887754             67899999999999998642211  123333 4677888889


Q ss_pred             EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-----------eeEEEEecCHHHHHHHHHhcc
Q psy3760         170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-----------PYIVLETINSDIIKTYVELRM  238 (306)
Q Consensus       170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~v~~g~  238 (306)
                      ++++++.+     ..++++|.+...+....-..  ......+......           ......+.+.......+..+.
T Consensus       111 ~~~~~~~~-----~~~~~dl~~~~~~~~g~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  183 (260)
T d1mqia_         111 IMIKKGTP-----IESAEDLSKQTEIAYGTLDS--GSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSK  183 (260)
T ss_dssp             EEEETTCS-----CCSHHHHHTCSSSEEECBSS--SHHHHHHHHCCSHHHHHHHHHHHHCSSCCCBSSHHHHHHHHHHTT
T ss_pred             eeeccccc-----hhhhhhhcccccceeeEEcc--hHHHHHHHhccchHHHHHHHHhhccccceeecChHHHHHHHHcCC
Confidence            99988775     34677887765433321111  1112222211110           111223445555555555554


Q ss_pred             ce-eeeecc-eeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         239 GI-GIIASI-AFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       239 gi-~~~p~~-~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      +. +++-.. ..... ....+....+........++++.+++..   ....|=+.|.+.-+....+++
T Consensus       184 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~k~s~---l~~~in~aL~~l~~~G~~~~l  248 (260)
T d1mqia_         184 GKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSS---LGNAVNLAVLKLNEQGLLDKL  248 (260)
T ss_dssp             TSEEEEEEHHHHHHHTTSTTCCEEEESCCSCCEEECCEEETTCT---THHHHHHHHHHHHHTTHHHHH
T ss_pred             CCEEEEecHHHHHHHHhcCCCceEEecccCCcceEEEEEcCChH---HHHHHHHHHHHHHHCCHHHHH
Confidence            33 333222 22211 3333444444443445567777788764   444444444444333344443

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=96.57  E-value=0.0015  Score=40.86  Aligned_cols=65  Identities=12%  Similarity=0.186  Sum_probs=47.9

Q ss_pred             HHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecCC-----C--ccccCHhHHHHHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHGK-----R--IRGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~~-----~--~~~lT~~G~~l~~~a~~il~~   76 (306)
                      ++..+......|+.=.+.+ ++|+..+|+++++||+.   -|++|...     .  . +||+.|+.|.+-...+.+=
T Consensus        16 Il~~L~~g~~rF~el~~~l~gis~~~Ls~rLk~Le~~---glv~r~~~~~~p~~veY-~LT~~G~~L~pil~~l~~W   88 (95)
T d2hzta1          16 ILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEAD---GVINRIVYNQVPPKVEY-ELSEYGRSLEGILDMLCAW   88 (95)
T ss_dssp             HHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHT---TSEEEEEECSSSCEEEE-EECTTGGGGHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHhhcCChhHHHHHHHHHHHh---HHHhheeccccccchhh-hhhhhHHHHHHHHHHHHHH
Confidence            3334433223899999998 99999999999999874   45665521     1  4 7999999999888777543

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.0044  Score=34.91  Aligned_cols=35  Identities=23%  Similarity=0.191  Sum_probs=30.1

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++++++.|.|-.+||+.++||.++++|.+++.+++
T Consensus        23 iv~~~~~G~s~r~aA~rf~VS~s~v~k~l~r~reT   57 (63)
T d1k78a1          23 IVELAHQGVRPCDISRQLRVSHGCVSKILGRYYET   57 (63)
T ss_dssp             HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence            44556667799999999999999999999998775

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.51  E-value=0.0039  Score=35.50  Aligned_cols=43  Identities=9%  Similarity=0.093  Sum_probs=34.2

Q ss_pred             CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ||--+.+++..+.+.+ .|+++-|+.+|+|.+++.++|++||+.
T Consensus         3 lD~~D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~   46 (63)
T d2cg4a1           3 IDNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQA   46 (63)
T ss_dssp             CCHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4445566666666542 388999999999999999999999986

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=96.51  E-value=0.0033  Score=36.36  Aligned_cols=44  Identities=7%  Similarity=0.063  Sum_probs=40.5

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI   46 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~   46 (306)
                      +-+..+++..+++-. |....|+.|++|..||..+++++=+.||+
T Consensus         8 T~rE~~vl~ll~~G~-s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1           8 TPRERDILKLIAQGL-PNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             CHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHhCC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            457788999999876 99999999999999999999999999987

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

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

Probab=96.50  E-value=0.0021  Score=33.93  Aligned_cols=37  Identities=8%  Similarity=0.066  Sum_probs=33.1

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAI   37 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i   37 (306)
                      |+-++++....+.+.|.|..+.|+.+|||.+||.|.+
T Consensus         6 lt~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           6 INKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             SCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            4567888888999999999999999999999999875

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.47  E-value=0.0063  Score=39.28  Aligned_cols=71  Identities=13%  Similarity=0.158  Sum_probs=51.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----CC--ccccCHhHHHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----KR--IRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~--~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      .++..+..-...|+.=.+.+ +||+..+|+++++||+.   -|+.|.-     ..  . .||+.|+.|.+-...+.+=.+
T Consensus        28 ~Il~~L~~g~~RF~el~~~l~gis~~~Ls~rL~~Le~~---glv~R~~~~~~p~~veY-~LT~~G~~L~~il~~l~~W~~  103 (114)
T d1yyva1          28 LILVALRDGTHRFSDLRRKMGGVSEKMLAQSLQALEQD---GFLNRVSYPVVPPHVEY-SLTPLGEQVSDKVAALADWIE  103 (114)
T ss_dssp             HHHHHGGGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHH---TCEEEEEECSSSCEEEE-EECHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCHHHHHHHccccchhHHHHHHHHHHHH---HHHhhcccCCCCchhHh-HhhHhHHHHHHHHHHHHHHHH
Confidence            33444443222589999999 89999999999999985   4566652     11  4 899999999998888876544


Q ss_pred             HHH
Q psy3760          79 GLK   81 (306)
Q Consensus        79 ~~~   81 (306)
                      +=.
T Consensus       104 ~~~  106 (114)
T d1yyva1         104 LNL  106 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>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=96.43  E-value=0.0093  Score=38.22  Aligned_cols=78  Identities=22%  Similarity=0.242  Sum_probs=53.6

Q ss_pred             chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec----C-CC-ccccCHhHHHHHHHHHHHH
Q psy3760           2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH----G-KR-IRGLTKPGQAILRSIEIIM   74 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~----~-~~-~~~lT~~G~~l~~~a~~il   74 (306)
                      +..+.+++.++.+.| -|...-|+.++++++++++.|++||+. |.  ..|.    + +. .+.+|+.++.+-..-..+.
T Consensus        19 t~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~-Gl--V~r~~~~~~~r~~~~~a~~~~e~l~~~~~~~~   95 (109)
T d1sfxa_          19 KPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKR-GF--VRREIVEKGWVGYIYSAEKPEKVLKEFKSSIL   95 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TS--EEEEEEESSSEEEEEEECCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHHhC-CC--EEEEeccCCCccccccCCCHHHHHHHHHHHHH
Confidence            446778888888765 366788999999999999999999975 43  3332    1 21 1268888765555545566


Q ss_pred             HHHHHHHH
Q psy3760          75 QEIEGLKK   82 (306)
Q Consensus        75 ~~~~~~~~   82 (306)
                      +.++++..
T Consensus        96 ~~l~eLe~  103 (109)
T d1sfxa_          96 GEIERIEK  103 (109)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHH
Confidence            66666554

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=96.40  E-value=0.0023  Score=40.50  Aligned_cols=66  Identities=18%  Similarity=0.201  Sum_probs=47.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----CCc-cccCHhHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----KRI-RGLTKPGQAILRSIEIIMQ   75 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~-~~lT~~G~~l~~~a~~il~   75 (306)
                      .++..+......|+.=.+.+ |||+..+|+++++||+.   -|+.|.-     ..+ .+||+.|+.|.+-...+.+
T Consensus        24 ~Il~~L~~g~~rF~el~~~l~gIs~~~Ls~rLkeL~~~---glv~r~~~~~~p~~veY~LT~~G~~L~pil~~l~~   96 (102)
T d2fswa1          24 LIIFQINRRIIRYGELKRAIPGISEKMLIDELKFLCGK---GLIKKKQYPEVPPRVEYSLTPLGEKVLPIIDEIAK   96 (102)
T ss_dssp             HHHHHHTTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHT---TSEEEEEECSSSCEEEEEECHHHHTTHHHHHHHHH
T ss_pred             HHHHHHccCCCCHHHHHhhCcccchhHHHHHHHHHHHC---CceeecccCCCCCeehhhhhHhHHHHHHHHHHHHH
Confidence            33444444323799999998 99999999999999985   3556542     111 2799999999997776654

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.40  E-value=0.002  Score=39.98  Aligned_cols=34  Identities=18%  Similarity=0.096  Sum_probs=28.2

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      +-.++.+++++.++||+.|||+..|+.+.|+++-
T Consensus        56 I~~aL~~~~Gn~~~AA~~LGI~R~TL~~Klk~~g   89 (91)
T d1ntca_          56 LTTALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHHHHCCCHHHHHHHHHHHC
Confidence            3445555666999999999999999999999874

>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=96.38  E-value=0.0015  Score=37.14  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=23.7

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.+.-|+.|++|+||+|+.|++|++.
T Consensus        25 ~~~~iA~~L~vs~~SVt~mvkrL~~~   50 (63)
T d2isya1          25 LRARIAERLDQSGPTVSQTVSRMERD   50 (63)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            56788999999999999999999974

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.26  E-value=0.0089  Score=40.20  Aligned_cols=67  Identities=22%  Similarity=0.239  Sum_probs=48.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe----cCCCc-cccCHhHHHHHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR----HGKRI-RGLTKPGQAILRSIEIIMQE   76 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R----~~~~~-~~lT~~G~~l~~~a~~il~~   76 (306)
                      .++..+.+-...|+.=.+.+++|+..+|++|+.||+. |  |++|    .+.++ .+||+.|+.|++-...+.+=
T Consensus        24 ~Il~~l~~G~~rf~el~~~lgis~~vLs~rL~~L~~~-g--Lv~r~~~~~p~r~~Y~LT~~G~~L~pil~~l~~W   95 (142)
T d2f2ea1          24 LIVRDAFEGLTRFGEFQKSLGLAKNILAARLRNLVEH-G--VMVAVPAESGSHQEYRLTDKGRALFPLLVAIRQW   95 (142)
T ss_dssp             HHHHHHHTTCCSHHHHHHHHCCCHHHHHHHHHHHHHT-T--SEEEEECSSSSCEEEEECHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHhhccHHHHHHHHHHHHHh-c--ceeeecCCCCCeeEEecCcCcchHHHHHHHHHHH
Confidence            3344444443379999999999999999999999975 3  4555    22221 27999999999877666554

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.23  E-value=0.0046  Score=35.47  Aligned_cols=46  Identities=11%  Similarity=0.117  Sum_probs=41.2

Q ss_pred             CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      ++-+..+++..+++-. |..+-|+.|++|..|+..+++++=..||+.
T Consensus         5 Lt~rE~~vl~l~~~G~-s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   50 (65)
T d1l3la1           5 LDPKEATYLRWIAVGK-TMEEIADVEGVKYNSVRVKLREAMKRFDVR   50 (65)
T ss_dssp             CCHHHHHHHHHHTTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             cCHHHHHHHHHHHhcC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            3557889999999877 999999999999999999999999999863

>d2ozza1 c.94.1.1 (A:1-228) Hypothetical protein YhfZ {Shigella flexneri [TaxId: 623]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Hypothetical protein YhfZ
species: Shigella flexneri [TaxId: 623]

Probab=96.23  E-value=0.03  Score=41.10  Aligned_cols=188  Identities=8%  Similarity=-0.042  Sum_probs=97.5

Q ss_pred             CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760          91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV  169 (306)
Q Consensus        91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~  169 (306)
                      ...++.-+++-.+. .....+...+.+++-++.+++... +.....+.|.+|++|+++......    .....-+.....
T Consensus        11 ~~~~~v~~mPl~ys-~~y~g~~~gl~~~~~Gl~ve~~~~~g~~~~~~al~~G~~D~~~~~~~~~----~~~~~~g~~~~~   85 (228)
T d2ozza1          11 DINNVVCAMPLPYT-RLYEGLASGLKAQFDGIPFYYAHMRGADIRVECLLNGVYDMAVVSRLAA----ESYLSQNNLCIA   85 (228)
T ss_dssp             SCSSEEEEECCCCS-HHHHHHHHHHHHTTTTSCEEEEECSCHHHHHHHHHTTSCSEEEEEHHHH----HHHHHHSCEEEE
T ss_pred             CcccEEEEecHhHH-HHHHHHHHHHHHHhcCCeEEEEEecCchHHHHHHHcCCCCEEecCcHHH----HHHHhcCCCceE
Confidence            34455555554433 334445566777777899999874 667889999999999998852211    111111111222


Q ss_pred             EEecCCCCCCCCC--CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHHhccce-eeeec
Q psy3760         170 IIVPLDHPLLLLN--SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRMGI-GIIAS  245 (306)
Q Consensus       170 ~v~~~~~~l~~~~--~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~gi-~~~p~  245 (306)
                      +...+........  .-+++||.+....... +...+    .++.+.++.+. +.+.--+...+..++.+|.-= ++.+.
T Consensus        86 ~~~~~~~~v~~~~~~i~~~~dLkGk~vgv~~-~s~~~----~~l~~~~~~~~~v~~v~~~~~~~~~al~~G~vDa~v~~~  160 (228)
T d2ozza1          86 LELGPHTYVGEHQLICRKGESGNVKRVGLDS-RSADQ----KIMTDVFFGDSDVERVDLSYHESLQRIVKGDVDAVIWNV  160 (228)
T ss_dssp             EECCTTSSSCCEEEEEETTCGGGCCEEEECT-TCHHH----HHHHHHHHTTSCCEEEECCHHHHHHHHHHTSCCEEEEEC
T ss_pred             EEEecceeecccCcccCChhhcCCCEEEecC-CChHH----HHHHHcCCCccceEEEeCCHHHHHHHHHcCceeEEEeCc
Confidence            2222222222211  2378899888776643 32222    23444444432 233333577788888888332 33444


Q ss_pred             ceecccccCCceeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760         246 IAFDSNRDKNLRSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL  291 (306)
Q Consensus       246 ~~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l  291 (306)
                      ..................   ........++.+++   ++.++.+++.+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vivir~~---~~~v~~lv~a~  206 (228)
T d2ozza1         161 VAENELTMLGLEATPLTDDPRFLQATEAVVLTRVD---DYPMQQLLRAV  206 (228)
T ss_dssp             -CHHHHHHTTEEEEECCSCHHHHHTTCEEEEEETT---CHHHHHHHHHH
T ss_pred             HHHHHHHhcCcccceeecccccccceeEEEEEcCC---cHHHHHHHHHH
Confidence            443333222322222222   12233445666655   66777777765

>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=96.17  E-value=0.01  Score=33.88  Aligned_cols=53  Identities=21%  Similarity=0.162  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760           5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT   60 (306)
Q Consensus         5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT   60 (306)
                      +.+++..+.+.+  -|...-|+.|++|..||.|-|+.|++ .|.++.. .++|. .|.
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~-~G~~I~~-~~gGY-~L~   63 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRS-LGYNIVA-TPRGY-VLA   63 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHH-HTCCCEE-ETTEE-ECC
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEE-eCCCE-EeC
Confidence            444555555543  26788999999999999999999986 4888765 44576 564

>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=96.17  E-value=0.024  Score=38.54  Aligned_cols=77  Identities=10%  Similarity=-0.019  Sum_probs=49.4

Q ss_pred             hhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHH--HHHHHHHHH
Q psy3760           3 LHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQ--AILRSIEII   73 (306)
Q Consensus         3 ~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~--~l~~~a~~i   73 (306)
                      ....+++..++..+  .|++.-|+.+|+|.+++|+.|++|++. |.---.+     ....+ .+|+.|.  .+.+...+.
T Consensus        26 ~~~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~-GlV~r~~~~~drr~~~~-~~t~~g~~~~~~~~~~~~  103 (151)
T d1ku9a_          26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEEL-GFVRKVWIKGERKNYYE-AVDGFSSIKDIAKRKHDL  103 (151)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCTTCSSCEEE-ECCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHC-CCEEEEEcCCCCceeEE-eCCHHHHHHHHHHHHHhh
Confidence            34556666665442  279999999999999999999999973 3332222     22333 7999995  344445544


Q ss_pred             HHHHHHHH
Q psy3760          74 MQEIEGLK   81 (306)
Q Consensus        74 l~~~~~~~   81 (306)
                      ++.+.+..
T Consensus       104 ~~~~~~~l  111 (151)
T d1ku9a_         104 IAKTYEDL  111 (151)
T ss_dssp             HHHHHHHH
T ss_pred             hHHHHHHH
Confidence            44444433

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=96.14  E-value=0.0069  Score=37.00  Aligned_cols=45  Identities=22%  Similarity=0.121  Sum_probs=40.7

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |...-|+.|++|+.|+..+++.+=..||+.
T Consensus        24 T~rE~~vl~ll~~G~-s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~   68 (87)
T d1p4wa_          24 SPKESEVLRLFAEGF-LVTEIAKKLNRSIKTISSQKKSAMMKLGVD   68 (87)
T ss_dssp             CHHHHHHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence            456788999999887 999999999999999999999999999863

>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=96.13  E-value=0.0025  Score=37.40  Aligned_cols=38  Identities=13%  Similarity=0.091  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         6 l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      -++|..+.+.| .|-+.-|+.+++|++|+++.+++|++.
T Consensus         9 ~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~   47 (71)
T d1z05a1           9 GRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDA   47 (71)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            35555666665 144556999999999999999999975

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=96.13  E-value=0.0041  Score=38.14  Aligned_cols=30  Identities=17%  Similarity=0.012  Sum_probs=25.6

Q ss_pred             HHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          11 EAVRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ++-+++++.++||+.||||.+|+.+.|+++
T Consensus        57 aL~~~~gn~~~aA~~LGisR~tL~~klk~~   86 (89)
T d1etxa_          57 VMQYTRGNATRAALMMGINRGTLRKKLKKY   86 (89)
T ss_dssp             HHHHTTTCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHcCCcHHHHHHHHCCCHHHHHHHHHHh
Confidence            455554499999999999999999999975

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=96.01  E-value=0.0067  Score=34.98  Aligned_cols=45  Identities=18%  Similarity=0.227  Sum_probs=40.3

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |....|+.||+|..||..+++.+=+.||+.
T Consensus         6 T~rE~~vl~l~~~G~-s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~   50 (67)
T d1fsea_           6 TKREREVFELLVQDK-TTKEIASELFISEKTVRNHISNAMQKLGVK   50 (67)
T ss_dssp             CHHHHHHHHHHTTTC-CHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHHHccC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            457788888888876 999999999999999999999999999863

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=95.98  E-value=0.0078  Score=35.01  Aligned_cols=45  Identities=11%  Similarity=0.057  Sum_probs=40.3

Q ss_pred             chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760           2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID   47 (306)
Q Consensus         2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~   47 (306)
                      +-+..+++..+++-. |....|+.||+|..||..+++.+=..||+.
T Consensus        14 T~rE~~vl~~l~~G~-s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   58 (70)
T d1yioa1          14 TGREQQVLQLTIRGL-MNKQIAGELGIAEVTVKVHRHNIMQKLNVR   58 (70)
T ss_dssp             CHHHHHHHHHHTTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            456778888888866 999999999999999999999999999874

>d2a5sa1 c.94.1.1 (A:7-142,A:145-285) N-methyl-D-aspartate receptor subunit 1 {Rat (Rattus norvegicus), subtype 2A [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: N-methyl-D-aspartate receptor subunit 1
species: Rat (Rattus norvegicus), subtype 2A [TaxId: 10116]

Probab=95.86  E-value=0.0078  Score=45.86  Aligned_cols=189  Identities=13%  Similarity=0.051  Sum_probs=98.5

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeCC-----------hhHHHHHHHcCCeeEEEEccccC--CCCCce-eeccccceEEEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQGN-----------PKQITEMIRNDQADIAIVTEILS--PSDKLI-SIPCYQWEYVII  171 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~~-----------~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~-~~~l~~~~~~~v  171 (306)
                      .+-..++..+.++- +++++++...           .+.++..|.+|++|+++......  ....+. +.|.+.....++
T Consensus        55 G~~iDl~~~ia~~l-g~~~e~~~v~~~~~g~~~~~~w~~~l~~l~~g~~Di~i~~~tit~eR~~~v~Fs~Py~~~~~~il  133 (277)
T d2a5sa1          55 GFCIDILKKLSRTV-KFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVM  133 (277)
T ss_dssp             SHHHHHHHHHHHHH-TCCEEEEECCSSSSCCEETTEECHHHHHHHTTSCSEECSSCBCCHHHHTTEEECCCCEEECEEEE
T ss_pred             eeHHHHHHHHHHHh-CCCEEEEEccCCCcCccCCCCHHHHHhhhhcccEEEEEEccEeehhhhhhhcccCCceecceEEE
Confidence            45555666665553 5666665433           67899999999999998642212  122333 346777888888


Q ss_pred             ecCCCCCCC-CCCcChhhhcC-CCeEeecCCCCcHHHHHHHHHhCCCcee---EEEEecCHHHHHHHHHhccceeeeec-
Q psy3760         172 VPLDHPLLL-LNSISLKEISN-YPLITYDLSFSGRIKLDREFSLQKLTPY---IVLETINSDIIKTYVELRMGIGIIAS-  245 (306)
Q Consensus       172 ~~~~~~l~~-~~~i~~~dl~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~g~gi~~~p~-  245 (306)
                      ++++.+... .....+.++.. ....... +.    ...+++.+......   ......+...++.++.+|..=+++-+ 
T Consensus       134 v~k~~~~~~~~~~~~~~~~~~~~~~g~v~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~d~  208 (277)
T d2a5sa1         134 VSRQVTGLSDKKFQRPHDYSPPFRFGTVP-NG----STERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDA  208 (277)
T ss_dssp             EETCCCSTTSHHHHSGGGSSSCCCEECCT-TS----HHHHHHHTTCHHHHHHHGGGCCSSHHHHHHHHHTTSCSEEEEEH
T ss_pred             EecCcccCChhHhcCccccchheeeeccc-hh----hHHHHHHHhhhhhcceEEEecCCCHHHHHHHHHcCCcceecccH
Confidence            888764221 11112222221 2233222 22    22334433321111   11345788889999999976555433 


Q ss_pred             ceeccc--ccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760         246 IAFDSN--RDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI  303 (306)
Q Consensus       246 ~~~~~~--~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  303 (306)
                      ..+...  ..+  ++..+..+.......++++.+++.+.   ...+=..|.+.-+....+++
T Consensus       209 ~~~~y~~~~~~~~~l~~~~~~~~~~~~~ygia~~k~s~l---~~~in~al~~l~~~G~~~~L  267 (277)
T d2a5sa1         209 AVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPW---KRQIDLALLQFVGDGEMEEL  267 (277)
T ss_dssp             HHHHHHHHTCTTSCEEEEECCCGGGCEEECCEEETTCTT---HHHHHHHHHHHHHHTHHHHH
T ss_pred             HHHHHHHhhCCCCcEEEecCCCCcCcceEEEEEeCChHH---HHHHHHHHHHHHHCCHHHHH
Confidence            333222  233  34444433333344666777887544   44444444443334444544

>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=95.84  E-value=0.037  Score=32.48  Aligned_cols=60  Identities=17%  Similarity=0.165  Sum_probs=42.9

Q ss_pred             hhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHH
Q psy3760           4 HQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI   66 (306)
Q Consensus         4 ~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l   66 (306)
                      +-++++-.+++.+  .|++.-|+.++++.|++.|.++.|++.   -+..|+..|.++|++..-.+
T Consensus         6 r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~---g~l~~~~~g~y~lG~~l~~l   67 (75)
T d1mkma1           6 KAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK---GFVLRKKDKRYVPGYKLIEY   67 (75)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT---TSEEECTTSCEEECTHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEECCCCCEeecHHHHHH
Confidence            3455566666543  389999999999999999999999974   34555533333788766544

>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=95.83  E-value=0.0046  Score=36.07  Aligned_cols=39  Identities=10%  Similarity=0.086  Sum_probs=33.3

Q ss_pred             hhHHHHHHHHHhcCCHHHH--HHHhCCCchHHHHHHHHHHHH
Q psy3760           4 HQFRFVREAVRQNFNLTEA--AKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~a--A~~l~isq~~~s~~i~~LE~~   43 (306)
                      +.-.+|..+.+.| .++++  |+.+|+|.+|+|+.+++|++.
T Consensus         6 N~~~Il~~i~~~g-~~sr~eLa~~~gLS~~Tvs~iv~~L~~~   46 (70)
T d1z6ra1           6 NAGAVYRLIDQLG-PVSRIDLSRLAQLAPASITKIVHEMLEA   46 (70)
T ss_dssp             HHHHHHHHHHSSC-SCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4456778888888 88775  899999999999999999886

>d1p99a_ c.94.1.1 (A:) Putative lipoprotein (NlpA family) {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Putative lipoprotein (NlpA family)
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.82  E-value=0.089  Score=39.10  Aligned_cols=186  Identities=8%  Similarity=0.013  Sum_probs=93.0

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC------CCCCceeecccc-
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS------PSDKLISIPCYQ-  165 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~------~~~~~~~~~l~~-  165 (306)
                      .|+||+... .. -+...+..+.+.+ ++++++... +..+..+.|.+|++|+++....+.      ...+.....+.. 
T Consensus         1 ~v~ig~~~~-~~-~~~~~~~~~~~k~-Gl~Ve~~~f~~~~~~~~Al~~G~iD~~~~~~~~~l~~~~~~~~~~~i~~~~~~   77 (255)
T d1p99a_           1 KVTIGVASN-DT-KAWEKVKELAKKD-DIDVEIKHFSDYNLPNKALNDGDIDMNAFQHFAFLDQYKKAHKGTKISALSTT   77 (255)
T ss_dssp             CEEEEESSS-CC-HHHHHHHHHHGGG-TCCEEEEECSSTTSHHHHHHTTSSSEEEEEEHHHHHHHHHHCTTCCEEEEEEE
T ss_pred             CEEEEEcCC-cH-HHHHHHHHHHHHc-CCEEEEEEcCCchhHHHHHHcCCCCEEccCCHHHHHHHHhhCCCceEEEeccc
Confidence            489999975 23 3344445555554 788888774 667899999999999998642211      011222211111 


Q ss_pred             --ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC-Ccee-------------------EEEE
Q psy3760         166 --WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK-LTPY-------------------IVLE  223 (306)
Q Consensus       166 --~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~-------------------~~~~  223 (306)
                        ..+.++        .....+..++.+-.-|..+.+......+...+...+ +.++                   ..+.
T Consensus        78 ~~~~~~~~--------~~~~~~~~d~~~GkkIavp~~~s~~~~~l~~l~~~~~i~l~~~~~~~~~~~Di~~~~~~~~~~~  149 (255)
T d1p99a_          78 VLAPLGIY--------SDKIKDVKKVKDGAKVVIPNDVSNQARALKLLEAAGLIKLKKDFGLAGTVKDITSNPKHLKITA  149 (255)
T ss_dssp             EECCCEEE--------CSSCSCGGGCCTTCEEEEECSHHHHHHHHHHHHHTTSCEECTTCCTTCCGGGEEECTTCCEEEE
T ss_pred             ccccccee--------ccccccccccCCCCeEEecCCCcHHHHHHHHHHhcCceeccCCCCCCCChhhhhhccccccccC
Confidence              111111        233467777764444444444344455555555544 2211                   1122


Q ss_pred             ecCHHHHHHHHHhccceeeeecceeccc-ccCC--ceeeecCC--CCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760         224 TINSDIIKTYVELRMGIGIIASIAFDSN-RDKN--LRSISASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLS  292 (306)
Q Consensus       224 ~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~--l~~~~~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~  292 (306)
                      .....+.  ......-.++++....... ..+.  .....-..  ........++.++....++.+++|++.++
T Consensus       150 ~~~~~~a--~~~g~vDaa~~~~p~~~~a~~~~~~~~l~~~~~~~~~~~~~~~v~~~~~~~~n~e~v~~~~~a~~  221 (255)
T d1p99a_         150 VDAQQTA--RALSDVDIAVINNGVATKAGKDPKNDPIFLEKSNSDAVKPYINIVAVNDKDLDNKTYAKIVELYH  221 (255)
T ss_dssp             ECGGGTT--GGGGTSSEEEECHHHHHHTTCCTTTSCSEECCCSSGGGGGGEEEEEEEGGGTTCHHHHHHHHHHH
T ss_pred             cchhhhh--hhcCCccEEEecccHHHHhCCCCCCCeEEEcCCcccCCCceEEEEEeCchhhCCHHHHHHHHHHc
Confidence            2222211  1122233344444333222 2222  22222121  12234556777877777899999998874

>d1sbpa_ c.94.1.1 (A:) Sulphate-binding protein {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Sulphate-binding protein
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.28  E-value=0.24  Score=37.75  Aligned_cols=201  Identities=15%  Similarity=0.133  Sum_probs=107.8

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhC-----CCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC---------CCCCc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQF-----PKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS---------PSDKL  158 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~-----p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~---------~~~~~  158 (306)
                      .++|.++.+  ..++..+...|.++|     +++.++....++..+...+.+| .+|+.+......         -.+..
T Consensus         5 ~~~~~y~~~--~e~~~ei~~af~~~~~~~tG~~V~v~~~~~gsg~~~~~i~~g~~aDV~~~a~~~~~~~l~~~gll~~~~   82 (309)
T d1sbpa_           5 LLNVSYDPT--RELYEQYNKAFSAHWKQETGDNVVIDQSHGGSGKQATSVINGIEADTVTLALAYDVNAIAERGRIDKNW   82 (309)
T ss_dssp             EEEEECSTT--HHHHHHHHHHHHHHHHHHHSCEEEEEEEESCHHHHHHHHHTTCCCSEEEESSHHHHHHHHHTTSSCTTG
T ss_pred             EEEEeccch--HHHHHHHHHHHHHHHHHhcCCCEEEEecCCchHHHHHHHHcCCCCCEEEeCCHHHHHHHHHCCCccccc
Confidence            466666443  456667777776554     5677776778888888888887 789999842210         01111


Q ss_pred             e-----eeccccceEEEEecCCCCCCCCCCcChhhhcCCC--eEeecCCCCcHH------HHHHHHHhCC----------
Q psy3760         159 I-----SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP--LITYDLSFSGRI------KLDREFSLQK----------  215 (306)
Q Consensus       159 ~-----~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~--~i~~~~~~~~~~------~~~~~~~~~~----------  215 (306)
                      .     ...++...+++++++++|.   .+-+|.||.+-.  .+...+......      .........+          
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~w~dL~~~~~k~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (309)
T d1sbpa_          83 IKRLPDDSAPYTSTIVFLVRKGNPK---QIHDWNDLIKPGVSVITPNPKSSGGARWNYLAAWGYALHHNNNDQAKAEDFV  159 (309)
T ss_dssp             GGGSHHHHCSEEBCEEEEEETTCTT---CCCSGGGGGSTTCCEECCCTTTCHHHHHHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             hhcccccceeeeeeeEEEEcCCCcc---cccchhhhhcccccccccccccccchHHHHHHHHhhhhhcccchHHHHHHHH
Confidence            1     1223455688888888763   356899997643  333333222110      0111111111          


Q ss_pred             --Ccee-EEEEecCHHHHHHHHHhcc-ceeeeecceeccc----ccCCceeeecCCCCccceEEEEE----eCCccccHH
Q psy3760         216 --LTPY-IVLETINSDIIKTYVELRM-GIGIIASIAFDSN----RDKNLRSISASHLFGTTISRVII----KQGTYLRSY  283 (306)
Q Consensus       216 --~~~~-~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~----~~~~l~~~~~~~~~~~~~~~l~~----~~~~~~~~~  283 (306)
                        +..+ ..+..++......++..|. .+++...+.+...    ....+..+..+.... ...++++    .++.....+
T Consensus       160 ~~l~~~~~~~~~~~~~~~~~~v~~Ge~~~~i~~~~~a~~~~~~~~~~~~~~v~p~~~~~-~~~~v~~~~~~~~~~~n~~~  238 (309)
T d1sbpa_         160 KALFKNVEVLDSGARGSTNTFVERGIGDVLIAWENEALLATNELGKDKFEIVTPSESIL-AEPTVSVVDKVVEKKDTKAV  238 (309)
T ss_dssp             HHHHHTEEECCSSHHHHHHHHHTSCCCSEEEEEHHHHHHHHHTTTTTTEEEECCSEEEC-BCCEEEECHHHHHHHTCHHH
T ss_pred             HHHhccCceeccCcHHHHHHHHHcCCeeEEEEeccHHHHHHHhhcCCceEEecCCCccc-ccCCeEEEEeeccCCCCHHH
Confidence              1112 2344455567778888884 4555554432111    223455544433221 1223332    244455778


Q ss_pred             HHHHHHHHhHHhhHHHH
Q psy3760         284 VYSFIKLLSPKLNRKFI  300 (306)
Q Consensus       284 ~~~~~~~l~~~~~~~~~  300 (306)
                      +++|+++|.+.=.+..+
T Consensus       239 A~~FidfllS~egQ~i~  255 (309)
T d1sbpa_         239 AEAYLKYLYSPEGQEIA  255 (309)
T ss_dssp             HHHHHHGGGSHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHH
Confidence            99999999775444433

>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=94.87  E-value=0.015  Score=41.52  Aligned_cols=39  Identities=10%  Similarity=0.207  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      .++++..+.+...|++.-|+.+|+|++++|++|+.||+.
T Consensus        21 R~~Il~~L~~~~~s~~ela~~lg~s~~~v~~hl~~L~~~   59 (190)
T d1ulya_          21 RRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEA   59 (190)
T ss_dssp             HHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            345555555544599999999999999999999999875

>d1xvxa_ c.94.1.1 (A:) Ferric-binding protein FbpA {Yersinia enterocolitica, YfuA [TaxId: 630]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Ferric-binding protein FbpA
species: Yersinia enterocolitica, YfuA [TaxId: 630]

Probab=94.57  E-value=0.67  Score=35.19  Aligned_cols=199  Identities=10%  Similarity=0.016  Sum_probs=114.7

Q ss_pred             CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc----CCeeEEEEcccc---------------
Q psy3760          92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN----DQADIAIVTEIL---------------  152 (306)
Q Consensus        92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~----~~~Di~i~~~~~---------------  152 (306)
                      .+.|.|.++..  ..++.+++..|.++ +++++++...++.++.+.|..    ..+|+.++....               
T Consensus         3 ~~~lvvYs~~~--~~~~~~ii~~Fek~-tGI~V~~~~~~s~~l~~ki~aeg~~~~~Dv~~~~d~~~~~~~~~~~l~~~~~   79 (311)
T d1xvxa_           3 DSGIVVYNAQH--ENLVKSWVDGFTKD-TGIKVTLRNGGDSELGNQLVQEGSASPADVFLTENSPAMVLVDNAKLFAPLD   79 (311)
T ss_dssp             CSCEEEEECSC--HHHHHHHHHHHHHH-HCCCEEEEECCHHHHHHHHHHHGGGCCCSEEEESSSHHHHHHHHTTCBCCCC
T ss_pred             CCeEEEEECCC--HHHHHHHHHHHHHh-hCCEEEEEECChHHHHHHHHHcCCCCCCCEEEECCHHHHHHHHhcCcccccc
Confidence            45788876543  66889999999998 699999999999988887765    357998864110               


Q ss_pred             ----------CCCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCCCcHHHHHHHHHhCCC--
Q psy3760         153 ----------SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSFSGRIKLDREFSLQKL--  216 (306)
Q Consensus       153 ----------~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~~~~~~~~~~~~~~~~--  216 (306)
                                ..+++-.+.+......+++..++..-...-+-+++||.+..    +.....+..........+...|.  
T Consensus        80 ~~~~~~i~~~~~d~~~~~~~~~~~~~~i~yn~~~~~~~~~P~t~~dl~~~~~~g~~~~~~~~~~~~~~~~~~~~~~g~~~  159 (311)
T d1xvxa_          80 AVTQAQVAQEYRPEHGRWTGIAARSTVFVYNPEKISEAELPKSIMDLAKPEWKGRWAASPSGADFQAIVSAMLELKGEKA  159 (311)
T ss_dssp             HHHHHHBCGGGSCSSSSCEEEEEEEEEEEECTTTSCGGGSCSSGGGGGSGGGTTSEEECTTSHHHHHHHHHHHHHHCHHH
T ss_pred             ccccccccccccccCCceeeeeeceEEEEEeccccccccCCccHHhhcchhhhcccccchhhhHHHHHHHHHHHhcCcHH
Confidence                      00122234566666778888877643333356899987643    33333332222222222222221  


Q ss_pred             --------ceeEEEEecCHHHHHHHHHhcc-ceeeeecceecc----c--ccCCceeeecCCC---CccceEEEEEeCCc
Q psy3760         217 --------TPYIVLETINSDIIKTYVELRM-GIGIIASIAFDS----N--RDKNLRSISASHL---FGTTISRVIIKQGT  278 (306)
Q Consensus       217 --------~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~----~--~~~~l~~~~~~~~---~~~~~~~l~~~~~~  278 (306)
                              ..+.. ...+.......+..|. .+++........    .  .........++..   .....-.+...++.
T Consensus       160 ~~~~~~~l~~~~~-~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~I~k~s  238 (311)
T d1xvxa_         160 TLEWLKAMKTNFT-AYKGNSTVMKAVNAGQIDGGVIYHYYRFVDQAKTGENSGKTQLHYFKHQDPGAFVSISGGGVLASS  238 (311)
T ss_dssp             HHHHHHHHHHHEE-ECSSHHHHHHHHHTTSSSEEEEETHHHHHHHTTTCTTTTTCEEECCCTTCGGGCEEEEEEEEBTTC
T ss_pred             HHHHHHHhhcccc-ccccchHhhhhhhCCCcccccchhhHHHHHHHHhhhccccceeeccccCCCCceeeeeeeeeecCC
Confidence                    22333 3455667778888884 355554422111    1  1122222222211   11122245567888


Q ss_pred             cccHHHHHHHHHHhHH
Q psy3760         279 YLRSYVYSFIKLLSPK  294 (306)
Q Consensus       279 ~~~~~~~~~~~~l~~~  294 (306)
                      +....+++|++++.+.
T Consensus       239 ~n~~~A~~Fi~fl~s~  254 (311)
T d1xvxa_         239 KHPKEAQEFVKWITGK  254 (311)
T ss_dssp             SSHHHHHHHHHHHHSH
T ss_pred             CCHHHHHHHHHHHcCH
Confidence            8888999999999754

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.23  E-value=0.12  Score=33.47  Aligned_cols=62  Identities=18%  Similarity=0.017  Sum_probs=45.6

Q ss_pred             HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHH
Q psy3760           8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSI   70 (306)
Q Consensus         8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a   70 (306)
                      -++++++.|-|..++|+.+++|++++++.+++.++.=...-=.+. +++- ..|++-..++...
T Consensus        24 rIv~~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr-~~t~~~~~~I~~~   86 (123)
T d1pdnc_          24 KIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-IATPEIENRIEEY   86 (123)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCC-SSCSTHHHHHHHT
T ss_pred             HHHHHHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCC-CCCHHHHHHHHHH
Confidence            456667788899999999999999999999999996655443443 3444 3777666654433

>d1sw5a_ c.94.1.1 (A:) Osmoprotection protein ProX {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Osmoprotection protein ProX
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.10  E-value=0.094  Score=39.35  Aligned_cols=196  Identities=12%  Similarity=0.146  Sum_probs=112.9

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe--CChhHHHHHHHcCCeeEEEEcc-----c--cCCCCCc------
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ--GNPKQITEMIRNDQADIAIVTE-----I--LSPSDKL------  158 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~--~~~~~~~~~l~~~~~Di~i~~~-----~--~~~~~~~------  158 (306)
                      .|+||........++..++..+.+.. +..+++..  .+...+...|.+|++|+..-.-     .  ......+      
T Consensus         2 ~v~Ig~~~wte~~v~a~i~~~~Le~~-Gy~ve~~~~~~~~~~~~~al~~GdiDv~~e~w~~~~~~~~~~~~~~~~~~~~~   80 (270)
T d1sw5a_           2 RVVIGSKPFNEQYILANMIAILLEEN-GYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYI   80 (270)
T ss_dssp             CEEECCCSSHHHHHHHHHHHHHHHHT-TCCEEECTTCCSHHHHHHHHHHTSSSEEEEEHHHHHHTTSCCCCCSSCCHHHH
T ss_pred             cEEEecCCCcHHHHHHHHHHHHHHHc-CCceEEEecCCccHHHHHHHHcCCCcEEehhhhhhHHHHHhhccccccchHHH
Confidence            68999999999999999999999874 77887766  4677788999999999986320     0  0000000      


Q ss_pred             --------------ee--eccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecCCCCc-HHHHHHHHHhCCCce
Q psy3760         159 --------------IS--IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDLSFSG-RIKLDREFSLQKLTP  218 (306)
Q Consensus       159 --------------~~--~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~~~~~-~~~~~~~~~~~~~~~  218 (306)
                                    ..  -....+.+.+.+++..... ...-++.|+...+   .+....+... ...........++..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~-~~~~~~~dl~~~~~~~~~g~~~~~~~~~~~~~~~~~~~g~~~  159 (270)
T d1sw5a_          81 FDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEE-NGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEF  159 (270)
T ss_dssp             HHHHHHHHHHHHCCEEEEEEEEECCEEEEEEHHHHHH-HTCCBGGGGTTTGGGCEEEECHHHHHSTTSHHHHHHHHTCCC
T ss_pred             HHHHHhhhcccCCeEEecccccccccccccCHHHHhh-cCcccHHHHhhhhhccccccCccccchhhHHHHHHHhcCCCc
Confidence                          00  0011123444444432211 1122566665432   2222222111 112222333345543


Q ss_pred             eEEEEecCHHHHHHHHHhccceee---eecceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760         219 YIVLETINSDIIKTYVELRMGIGI---IASIAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       219 ~~~~~~~~~~~~~~~v~~g~gi~~---~p~~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  294 (306)
                      .. ....+...+.+++++|..+.+   .|+++...   .+++.+.-+.. .+......+++++....|.+.+|++.+...
T Consensus       160 ~~-~~~~~~a~~~~A~~~~~~iv~~~W~P~~~~~~---~dl~~Ledp~~~~~~~~~~~~~~~~~~~~P~~~~~l~~~~~~  235 (270)
T d1sw5a_         160 KE-VKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDL---FNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDR  235 (270)
T ss_dssp             SE-EEECCGGGHHHHHHTTSCSEEEEETTCHHHHH---TTEEECBCTTCCSCCCEEEEEECTTGGGCHHHHHHHHTTTTC
T ss_pred             cc-ccccchHHHHHHHHcCCCeEEEeccCcccccc---CCcEEecCCcccccccceeEEEccccccCHHHHHHHHHHhcc
Confidence            32 355566677788999855544   56655543   46787776652 344566666777776788888888876433


Q ss_pred             h
Q psy3760         295 L  295 (306)
Q Consensus       295 ~  295 (306)
                      +
T Consensus       236 l  236 (270)
T d1sw5a_         236 I  236 (270)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=94.01  E-value=0.024  Score=31.13  Aligned_cols=24  Identities=29%  Similarity=0.117  Sum_probs=20.8

Q ss_pred             HHHhcCCHHHHHHHhCCCchHHHHH
Q psy3760          12 AVRQNFNLTEAAKALYTSQPGVSKA   36 (306)
Q Consensus        12 v~~~~~s~~~aA~~l~isq~~~s~~   36 (306)
                      +.--| |.++.|+.||||++|||+.
T Consensus         7 i~~FG-~~~k~A~algis~~AVsqW   30 (61)
T d1rzsa_           7 IDHFG-TQRAVAKALGISDAAVSQW   30 (61)
T ss_dssp             HHHHS-SHHHHHHHHTCCHHHHHHC
T ss_pred             HHHhC-CHHHHHHHhCCCHHHHHHH
Confidence            33458 9999999999999999985

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=93.70  E-value=0.048  Score=27.59  Aligned_cols=31  Identities=23%  Similarity=0.248  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760           9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus         9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      ...+.+.|.+-++-|++|||+.++|-|.|++
T Consensus        11 V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          11 VLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4456677779999999999999999998863

>d1h3da1 c.94.1.1 (A:5-224) ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain
species: Escherichia coli [TaxId: 562]

Probab=93.69  E-value=0.26  Score=35.49  Aligned_cols=156  Identities=12%  Similarity=0.145  Sum_probs=91.7

Q ss_pred             EEEEeCChhHHHHHHHcCCeeEEEEccccC-----------CCC---CceeeccccceEEEEecCCCCCCCCCCcChhhh
Q psy3760         124 LSLLQGNPKQITEMIRNDQADIAIVTEILS-----------PSD---KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI  189 (306)
Q Consensus       124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-----------~~~---~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl  189 (306)
                      +++....+.++...+..|.+|+||+.....           ..+   .+.-..++.-++++++|++...     .+..++
T Consensus        44 i~~~~~r~~DIp~~V~~G~~DlGItG~D~l~E~~~~~~~~~~~~~v~~l~dL~fG~crLvvA~p~~~~~-----~~~~~~  118 (220)
T d1h3da1          44 IDILRVRDDDIPGLVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAW-----DGPLSL  118 (220)
T ss_dssp             EEEEEECGGGHHHHHHTTSSSEEEEEHHHHHHHHHHHHHHTCCCCEEEEEECSCCCEEEEEEEETTSCC-----CCGGGG
T ss_pred             EEEEEEChHHHHHHHHhccCcccchhHHHHHhhcccchhccCCcceEEEEecccCceeEEEeccccccc-----cChhHc
Confidence            555555778999999999999999852110           111   2334556778899999987642     345566


Q ss_pred             cCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc--cceeeeecceecccccCCceeeecCCCCcc
Q psy3760         190 SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR--MGIGIIASIAFDSNRDKNLRSISASHLFGT  267 (306)
Q Consensus       190 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~  267 (306)
                      .+.+..+     -+.+....+|.+.|+...++....+.+.+   ..-|  +.|.=+.+.- ..++..+|+.+.   ....
T Consensus       119 ~~~RIAT-----kYp~it~~y~~~~gi~~~ii~~~Ga~E~a---p~~g~AD~IvDiv~TG-~TLk~NgLk~id---~Il~  186 (220)
T d1h3da1         119 NGKRIAT-----SYPHLLKRYLDQKGISFKSCLLNGSVEVA---PRAGLADAICDLVSTG-ATLEANGLREVE---VIYR  186 (220)
T ss_dssp             TTCEEEE-----SCHHHHHHHHHHHTCCCEEEECSSCTTHH---HHTTSCSEEEEEESSC-HHHHHTTEEEEE---EEEE
T ss_pred             CCCEEhh-----hhhHHHHHHHHhccccceeeeccccccce---ecCCCeeEEEEeccch-HHHHHCcCEEee---EEEE
Confidence            5544322     34567788999999877666555555433   3344  3333222211 112567788775   2445


Q ss_pred             ceEEEEEeCCcc---ccHHHHHHHHHHhHHhh
Q psy3760         268 TISRVIIKQGTY---LRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       268 ~~~~l~~~~~~~---~~~~~~~~~~~l~~~~~  296 (306)
                      .+.+++.++...   ....+..+++.++..+.
T Consensus       187 SsA~LI~n~~s~~~~~~~~i~~l~~~l~~vl~  218 (220)
T d1h3da1         187 SKACLIQRDGEMEESKQQLIDKLLTRIQGVIQ  218 (220)
T ss_dssp             ECEEEEEESSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEeccccChhHHHHHHHHHHHHHHHHh
Confidence            577888766543   22234455555555543

>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=93.63  E-value=0.035  Score=31.16  Aligned_cols=26  Identities=19%  Similarity=0.105  Sum_probs=23.4

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      |-..-|+.+++|++|+|+.+++|+++
T Consensus        14 sr~eLa~~~gls~~TVs~~v~~L~~~   39 (62)
T d2hoea1          14 SRVELAEELGLTKTTVGEIAKIFLEK   39 (62)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            56677999999999999999999875

>d1pdaa1 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.62  E-value=0.8  Score=32.61  Aligned_cols=179  Identities=16%  Similarity=0.106  Sum_probs=101.1

Q ss_pred             cEEEEecccc-hhhhhHHHHHHHHHhCCCcEEEEEeC--------------------ChhHHHHHHHcCCeeEEEEcccc
Q psy3760          94 NLTIATTHTQ-ARYALPKIIKEFTIQFPKVKLSLLQG--------------------NPKQITEMIRNDQADIAIVTEIL  152 (306)
Q Consensus        94 ~l~I~~~~~~-~~~~l~~~l~~~~~~~p~~~i~~~~~--------------------~~~~~~~~l~~~~~Di~i~~~~~  152 (306)
                      .||||+-.+- +..-...+...+.+.||++.+++...                    ...++.+.|.+|++|+|+-+...
T Consensus         3 ~IrIgtR~S~LAl~Qa~~v~~~L~~~~p~~~~ei~~i~T~GD~~~~~~l~~~ggkg~Ftkele~~Ll~~~iDiAVHS~KD   82 (217)
T d1pdaa1           3 VLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMKD   82 (217)
T ss_dssp             EEEEEECCSHHHHHHHHHHHHHHHHHCTTCEEEEEECCCHHHHC---------CCCTTTHHHHHHHHTTSCSEEEEEGGG
T ss_pred             cEEEEeCCcHHHHHHHHHHHHHHHHhCCCCcEEEEEEeccCCccccccccccchhHHHHHHHHHHHHcCccceehhhhcc
Confidence            6899997664 44445555677888899999887442                    34567899999999999987442


Q ss_pred             CC---CCCceeeccccceEEEEecCCCCC---CCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecC
Q psy3760         153 SP---SDKLISIPCYQWEYVIIVPLDHPL---LLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN  226 (306)
Q Consensus       153 ~~---~~~~~~~~l~~~~~~~v~~~~~~l---~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (306)
                      -+   ++++        .+..+.++..|-   ..+...++++|....-|...   +.|+. .++ .......+++-.-.+
T Consensus        83 lP~~~~~~l--------~i~a~~~R~d~rD~li~~~~~~l~~l~~~~~IGTs---S~RR~-aql-~~~~p~l~~~~iRGN  149 (217)
T d1pdaa1          83 VPVEFPQGL--------GLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTS---SLRRQ-CQL-AERRPDLIIRSLRGN  149 (217)
T ss_dssp             SCSCCCTTE--------EEEEECCCCCCCEEEECSSCSSTTTSCTTCEEECC---CHHHH-HHH-HHHCTTSEEECCCSC
T ss_pred             cccccCCcc--------ccccccccCCcchhccccCcCCHhhCCCCCEeccc---chhHH-HHH-HHhCCCCceeecccc
Confidence            22   2232        233333333331   11223456666665555543   23322 222 222333455556689


Q ss_pred             HHHHHHHHHhccceee-eecceecccc-cCC-ceeeecCCC---CccceEEEEEeCCccccHHHHHHH
Q psy3760         227 SDIIKTYVELRMGIGI-IASIAFDSNR-DKN-LRSISASHL---FGTTISRVIIKQGTYLRSYVYSFI  288 (306)
Q Consensus       227 ~~~~~~~v~~g~gi~~-~p~~~~~~~~-~~~-l~~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~  288 (306)
                      +++=+.-+..|..=++ +..--...+. ... -..++++..   +-+..+.+.++++.   +.+++++
T Consensus       150 v~TRl~Kl~~g~~DaiILA~AGL~RL~l~~~i~~~l~~~~~~PA~gQGaiaIe~r~~d---~~~~~il  214 (217)
T d1pdaa1         150 VGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDD---SRTRELL  214 (217)
T ss_dssp             HHHHHHHHHTTSCSEEEEEHHHHHHTTCGGGCSEECCTTTSCCCTTTTCEEEEEETTC---HHHHHHH
T ss_pred             hhhHHHHhhccCcCEEEeehhHHhhcCcchheeEEcChhhcCChHhhhheEEEEcCCC---HHHHHHH
Confidence            9999999998844443 3333333331 122 234554431   23678888888863   4444443

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=93.50  E-value=0.093  Score=30.19  Aligned_cols=39  Identities=26%  Similarity=0.148  Sum_probs=29.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      =.+|....-.|.|+...|+.+|+|.+++.+++.+--+.|
T Consensus        27 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~ra~~~L   65 (71)
T d1rp3a2          27 KLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERL   65 (71)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            344545454566999999999999999998887765554

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.47  E-value=0.042  Score=39.13  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      ++++..+.+...|.+.-|+.|++|+++++++|+.||+.
T Consensus        18 ~~Il~~L~~~~~~~~ela~~l~~s~~~v~~HL~~L~~~   55 (194)
T d2p4wa1          18 RRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEA   55 (194)
T ss_dssp             HHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34444444433388999999999999999999999973

>d1u3em2 d.285.1.1 (M:106-174) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SP01 [TaxId: 10685]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain of intron-encoded endonucleases
superfamily: DNA-binding domain of intron-encoded endonucleases
family: DNA-binding domain of intron-encoded endonucleases
domain: Intron-encoded homing endonuclease I-HmuI
species: Bacteriophage SP01 [TaxId: 10685]

Probab=92.75  E-value=0.049  Score=29.74  Aligned_cols=23  Identities=13%  Similarity=0.052  Sum_probs=20.9

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      -. |.++||+.||++.++||+.+.
T Consensus        30 f~-s~~kAaelLGL~r~~Vs~CL~   52 (69)
T d1u3em2          30 YP-STKCACEELGLTRGKVTDVLK   52 (69)
T ss_dssp             ES-CHHHHHHHHTCCHHHHHHHHH
T ss_pred             cc-hHHHHHHHhCcchhHHHHHhc
Confidence            36 899999999999999999875

>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=92.72  E-value=0.16  Score=29.18  Aligned_cols=27  Identities=19%  Similarity=0.132  Sum_probs=24.9

Q ss_pred             cCCHHHHHHHhCC-CchHHHHHHHHHHHH
Q psy3760          16 NFNLTEAAKALYT-SQPGVSKAIIELEEE   43 (306)
Q Consensus        16 ~~s~~~aA~~l~i-sq~~~s~~i~~LE~~   43 (306)
                      - |+..-|+.+|+ |++++.+.|+.||+.
T Consensus        25 P-s~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1          25 P-TRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             C-CHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             C-CHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            5 89999999999 899999999999974

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=92.70  E-value=0.14  Score=32.05  Aligned_cols=40  Identities=23%  Similarity=0.307  Sum_probs=31.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      +=.+|..-.-.|.|+...|+.||+|++||+.++++-.+.|
T Consensus        21 qR~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L   60 (106)
T d1s7oa_          21 QMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKIL   60 (106)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3445555555667999999999999999998887766666

>d2nxoa1 c.94.1.1 (A:5-281) Hypothetical protein SCo4506 {Streptomyces coelicolor [TaxId: 1902]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Hypothetical protein SCo4506
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.39  E-value=0.19  Score=37.74  Aligned_cols=117  Identities=9%  Similarity=-0.008  Sum_probs=64.2

Q ss_pred             EEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecCC
Q psy3760          96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLD  175 (306)
Q Consensus        96 ~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~  175 (306)
                      |||.-+.+.   ..+++-.+.+.+.+..+++...+..++.+.|.+|++|++++.........-....+   ..+.....+
T Consensus         4 riG~i~~~~---~~Pl~~~le~~~~~~~~~~~~~~p~~l~~al~~G~iDia~~~~~~~~~~~~~~~~~---~~~~~~~~~   77 (277)
T d2nxoa1           4 RVGHIQFLN---CLPLYWGLARTGTLLDFELTKDTPEKLSEQLVRGDLDIGPVTLVEFLKNADDLVAF---PDIAVGCDG   77 (277)
T ss_dssp             EEEEECSGG---GHHHHHHHHHTSGGGGCEEEEECHHHHHHHHHTTSCSEEEEEHHHHHHTGGGEEEE---EEEEEEESS
T ss_pred             EEEEeccCC---cchHHHHHHhCCCCCceEEEECCHHHHHHHHHcCCCCEEecCHHHHHHhcCCCeeE---EeecccccC
Confidence            788776642   23466678888778888887777788999999999999998521110000001111   111111111


Q ss_pred             CCCC--CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce
Q psy3760         176 HPLL--LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP  218 (306)
Q Consensus       176 ~~l~--~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  218 (306)
                      ....  ....-+++||.+........+....-.+..++.+.+..+
T Consensus        78 ~~~~~~~~~~~~~~dL~Gk~I~~~~~~~~~~~ll~~ll~~~~~~~  122 (277)
T d2nxoa1          78 PVMSCVIVSQVPLDRLDGARVALGSTSRTSVRLAQLLLSERFGVQ  122 (277)
T ss_dssp             CCSSEEEEESSCTTSCSSSEEEEETTCSHHHHHHHHHHHHTSCCC
T ss_pred             CeeEEEeeccCChHHhCCCeEEECCCChHHHHHHHHHHHhcCCCC
Confidence            1000  011235678888777666554333334456666665553

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.32  E-value=0.15  Score=28.97  Aligned_cols=47  Identities=19%  Similarity=0.189  Sum_probs=37.5

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHH
Q psy3760          20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI   70 (306)
Q Consensus        20 ~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a   70 (306)
                      ..=|+.|+++-..+-.-++.|.++   -|++-++.|. .+|+.|+.++...
T Consensus        21 r~La~~L~l~Er~vRte~~~Lk~~---gLI~~~~~Gm-~lTe~G~~~l~~L   67 (69)
T d2p8ta1          21 KQISERLELGEGSVRTLLRKLSHL---DIIRSKQRGH-FLTLKGKEIRDKL   67 (69)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHT---TSEEEC--CE-EECHHHHHHHHHH
T ss_pred             HHHHHHcCCcHHHHHHHHHHHHHC---CCeeeeCCCC-EECHhHHHHHHHH
Confidence            567899999999999888888763   5677777898 7999999998764

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=91.61  E-value=0.098  Score=31.75  Aligned_cols=26  Identities=19%  Similarity=0.171  Sum_probs=23.7

Q ss_pred             cCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760          16 NFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus        16 ~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      |.|+..+|+.+|||.++|.+.+++..
T Consensus        23 g~s~~~vA~~lGIs~~tl~~W~k~~~   48 (89)
T d2jn6a1          23 GASLQQIANDLGINRVTLKNWIIKYG   48 (89)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHh
Confidence            45999999999999999999999863

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=91.55  E-value=0.21  Score=31.26  Aligned_cols=41  Identities=17%  Similarity=0.237  Sum_probs=31.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      ++=.+|..-.-.|.|+...|+.+|+|.+||..+|++-...|
T Consensus        22 ~QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L   62 (106)
T d1xsva_          22 KQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLV   62 (106)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            34456666666677999999999999999988877655554

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=91.06  E-value=0.24  Score=28.27  Aligned_cols=52  Identities=19%  Similarity=0.219  Sum_probs=42.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHH-cCceeEEecCCCccccCHhHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEE-LSIDIFIRHGKRIRGLTKPGQAILRS   69 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~-lg~~Lf~R~~~~~~~lT~~G~~l~~~   69 (306)
                      |+.|-|++-++.=|++-|.+.+|++- +-..-|.-+|+|-.+||+.|+.+...
T Consensus        26 SLaklsKra~~PMS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lca~   78 (81)
T d2obpa1          26 SLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAAQ   78 (81)
T ss_dssp             BHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHHH
T ss_pred             cHHHHHhhcCCcHHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHHHH
Confidence            78999999999999999999999874 33344556677766899999998765

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.93  E-value=0.093  Score=28.68  Aligned_cols=21  Identities=29%  Similarity=0.276  Sum_probs=19.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++...|+..|+|.+|+|+.|.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln   22 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVIN   22 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHC
Confidence            577899999999999999985

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

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

Probab=90.90  E-value=0.074  Score=30.91  Aligned_cols=36  Identities=25%  Similarity=0.391  Sum_probs=28.1

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |-..-|+.+|+|+.++||.+++|+++=   ++...++.+
T Consensus        29 t~~elA~~lg~sr~tvsr~l~~l~~~g---~I~~~~~~i   64 (73)
T d1zyba1          29 KMDDLARCLDDTRLNISKTLNELQDNG---LIELHRKEI   64 (73)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTT---SCEEETTEE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCC---CEEecCCEE
Confidence            456789999999999999999999863   334455554

>d1i3ja_ d.285.1.1 (A:) DNA-binding domain of intron endonuclease I-TevI {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain of intron-encoded endonucleases
superfamily: DNA-binding domain of intron-encoded endonucleases
family: DNA-binding domain of intron-encoded endonucleases
domain: DNA-binding domain of intron endonuclease I-TevI
species: Bacteriophage T4 [TaxId: 10665]

Probab=90.81  E-value=0.087  Score=32.13  Aligned_cols=24  Identities=17%  Similarity=0.081  Sum_probs=21.9

Q ss_pred             hcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760          15 QNFNLTEAAKALYTSQPGVSKAIIE   39 (306)
Q Consensus        15 ~~~s~~~aA~~l~isq~~~s~~i~~   39 (306)
                      .. |+.+||+.||++.++|.++++.
T Consensus        64 y~-S~~EAar~lgi~~~tI~~R~ks   87 (96)
T d1i3ja_          64 FD-CAADAARHFKISSGLVTYRVKS   87 (96)
T ss_dssp             ES-SHHHHHHHHTCCHHHHHHHHHC
T ss_pred             Ec-cHHHHHHHhCCChHHHHHHHcC
Confidence            46 9999999999999999999974

>d1o63a_ c.94.1.1 (A:) ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.79  E-value=1.1  Score=31.53  Aligned_cols=159  Identities=13%  Similarity=0.038  Sum_probs=92.1

Q ss_pred             CCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC
Q psy3760         119 FPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP  193 (306)
Q Consensus       119 ~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~  193 (306)
                      .|++.+-+  .-..++...+..|.+|+||+....     .+-..+....++..++++.+|.+.+.....          .
T Consensus        35 ~~~i~~~~--~r~~DIp~~V~~G~~DlGI~G~D~l~E~~~~v~~~~~L~~g~~~l~vA~p~~~~~~~~~----------~  102 (203)
T d1o63a_          35 GKDIVCFM--VRPFDVPTYLVHGVADIGFCGTDVLLEKETSLIQPFFIPTNISRMVLAGPKGRGIPEGE----------K  102 (203)
T ss_dssp             ETTEEEEE--ECGGGHHHHHHTTSCSEEEEEHHHHHHSCCCCBCCSEEEEEEEEEEEEEETTTCCCSSC----------E
T ss_pred             CCCeEEEE--ecchhhhHHHHhcccccccchHHHHhhhcccceeeeecceeeeEEEEeccccccccccc----------c
Confidence            45655544  457789999999999999985111     111223345667778888888876543211          1


Q ss_pred             eEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEE
Q psy3760         194 LITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRV  272 (306)
Q Consensus       194 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l  272 (306)
                      -|.    ..+.+...++|...|+...++-...+.+.+   ..-|.+=+++.-... ..+...+|+.+.-   ....+..+
T Consensus       103 rIA----TkYpnlt~~f~~~~gi~~~ii~l~GavE~A---p~~G~AD~IvDivsTG~TLk~NgLk~i~~---i~~~sa~l  172 (203)
T d1o63a_         103 RIA----TKFPNVTQRYCESKGWHCRIIPLKGSVELA---PIAGLSDLIVDITETGRTLKENNLEILDE---IFVIRTHV  172 (203)
T ss_dssp             EEE----ESCHHHHHHHHHHHTCCEEEEECSSCTTHH---HHHTSCSEEEEEESSSHHHHHTTEEEEEE---EEEEEEEE
T ss_pred             eee----echhhHHHHHHHHccCceEEEeccCCCCCC---ccccccceeeeeccchHHHHHCCCEEccc---eeeeEHHH
Confidence            121    234567788999999876655555555443   333433233322111 1124567776642   22345566


Q ss_pred             EEeCCc--cccHHHHHHHHHHhHHhhHHH
Q psy3760         273 IIKQGT--YLRSYVYSFIKLLSPKLNRKF  299 (306)
Q Consensus       273 ~~~~~~--~~~~~~~~~~~~l~~~~~~~~  299 (306)
                      +.++..  ...+.+..+++.+++.++...
T Consensus       173 i~n~~s~~~k~~~i~~ll~~l~~vl~~~~  201 (203)
T d1o63a_         173 VVNPVSYRTKREEVVSFLEKLQEVIEHDS  201 (203)
T ss_dssp             EECHHHHHHTHHHHHHHHHHHHHHHHHHH
T ss_pred             hcChhhhhhhHHHHHHHHHHHHHHHHhhc
Confidence            665432  234667788888887776654

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.70  E-value=0.11  Score=28.63  Aligned_cols=21  Identities=29%  Similarity=0.169  Sum_probs=18.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++...|+..|+|.+|+|+.|.
T Consensus         2 Tl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           2 KLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CHHHHHHHHTSCTTHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHc
Confidence            577889999999999999986

>d2f34a1 c.94.1.1 (A:5-116,A:119-252) Glutamate receptor ligand binding core {Rat (Rattus norvegicus), GluR5 [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Glutamate receptor ligand binding core
species: Rat (Rattus norvegicus), GluR5 [TaxId: 10116]

Probab=90.42  E-value=1.1  Score=32.05  Aligned_cols=184  Identities=14%  Similarity=0.004  Sum_probs=93.4

Q ss_pred             hhhHHHHHHHHHhCCCcEEEEEeC------------ChhHHHHHHHcCCeeEEEEccccCC---CCCceeeccccceEEE
Q psy3760         106 YALPKIIKEFTIQFPKVKLSLLQG------------NPKQITEMIRNDQADIAIVTEILSP---SDKLISIPCYQWEYVI  170 (306)
Q Consensus       106 ~~l~~~l~~~~~~~p~~~i~~~~~------------~~~~~~~~l~~~~~Di~i~~~~~~~---~~~~~~~~l~~~~~~~  170 (306)
                      .+-..++.++.++. ++++++...            ..+.++..+.+|++|+++.......   ..-.-+.|.......+
T Consensus        30 G~~iDl~~~ia~~l-g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~D~~i~~~~~t~~R~~~~~fs~P~~~~~~~~  108 (246)
T d2f34a1          30 GYCLDLLKELSNIL-GFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISI  108 (246)
T ss_dssp             SHHHHHHHHHHHHH-TCEEEEEECTTCCCCCBCTTSCBCHHHHHHHTTSCSEECSSCBCCHHHHTTEEECSCSEEECEEE
T ss_pred             EeHHHHHHHHHHHh-CCCeEEEeccccccccccccCchhhhhhhhhhccccEEEeccccchhhhhcccccCCchhhheee
Confidence            45666777776653 577777653            4668999999999999987422121   1223356777788888


Q ss_pred             EecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce-----------eEEEEecCHHHHHHHHHhccc
Q psy3760         171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP-----------YIVLETINSDIIKTYVELRMG  239 (306)
Q Consensus       171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~v~~g~g  239 (306)
                      +++++.+.    ..+..++..........+ ..    ...+.......           ..................+..
T Consensus       109 ~~~~~~~~----~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (246)
T d2f34a1         109 LYRKPIDS----ADDLAKQTKIEYGAVRDG-ST----MTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDY  179 (246)
T ss_dssp             EEETSCCS----HHHHHTCSSSEEECBTTS-HH----HHHHHHCCCHHHHHHHHHHHHTHHHHSBSSHHHHHHHHHHSSE
T ss_pred             eeeccccc----cchhhhcccceeEEEecc-ee----ehhhhhcccchhhhhhhhcchhhHHHHhhhhhHHHHHhhccce
Confidence            88777542    223444445554443322 11    11111111110           011122333344444444444


Q ss_pred             eeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760         240 IGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL  304 (306)
Q Consensus       240 i~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  304 (306)
                      ..+.........  ..+++..++.  ......++++.+++..   ....|-+.|.+.-+....+++.
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~a~~k~s~---l~~~~n~~l~~l~~~G~~~~i~  241 (246)
T d2f34a1         180 ALLMESTSIEYVTQRNCNLTQIGG--LIDSKGYGVGTPIGSP---YRDKITIAILQLQEEGKLHMMK  241 (246)
T ss_dssp             EEEEEHHHHHHHHHHCTTEEEESS--CSSCEEECCEEETTCT---THHHHHHHHHHHHHTTHHHHHH
T ss_pred             EEEechHHHHHHHhcCCCeEEecc--cCCCceEEEEEeCChH---HHHHHHHHHHHHHHCCHHHHHH
Confidence            444332222211  3455555443  2334467777787754   4445544554444444555543

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

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

Probab=89.59  E-value=0.11  Score=29.72  Aligned_cols=36  Identities=25%  Similarity=0.384  Sum_probs=28.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |=..-|.-+|+|..++||.|++|+++   -++..+++.+
T Consensus        31 t~~~lA~~~G~sRetvsr~L~~l~~~---glI~~~~~~I   66 (69)
T d1i5za1          31 TRQEIGQIVGCSRETVGRILKMLEDQ---NLISAHGKTI   66 (69)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT---TSEEEETTEE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEcCCEE
Confidence            44677999999999999999999985   2445555544

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=89.59  E-value=0.15  Score=30.59  Aligned_cols=59  Identities=15%  Similarity=0.116  Sum_probs=46.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHH
Q psy3760           5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI   66 (306)
Q Consensus         5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l   66 (306)
                      +|.+|-.+.+...|+.+-|+++++++..+.+-++-|..   .-+|.+.+.+.+.+|+.|+.|
T Consensus        23 ~L~ifd~l~~gp~s~~eLA~~~g~~~~~l~rlLr~l~a---~gl~~e~~~~~y~lt~~s~~L   81 (85)
T d1tw3a1          23 TLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVA---IGLLEEDAPGEFVPTEVGELL   81 (85)
T ss_dssp             HTTHHHHHHTTCCBHHHHHHHHTCCHHHHHHHHHHHHH---TTSEEEEETTEEEECTTGGGG
T ss_pred             HcCcHHHhccCCCCHHHHHHHhCcChhHHHHHHHHHHH---CCCeEecCCCeEecCHHHHHh
Confidence            45677777777569999999999999998888887765   347877665545899998765

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=89.56  E-value=0.13  Score=28.07  Aligned_cols=21  Identities=19%  Similarity=0.245  Sum_probs=18.9

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++...|+..|+|.+|+|+.|.
T Consensus         3 Ti~dvA~~agvS~~TVSr~Ln   23 (57)
T d2hsga1           3 TIYDVAREASVSMATVSRVVN   23 (57)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHhC
Confidence            577889999999999999876

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

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

Probab=89.09  E-value=0.29  Score=29.76  Aligned_cols=35  Identities=17%  Similarity=0.193  Sum_probs=29.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE   41 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE   41 (306)
                      +.|..+.+.|.|-...|+++|.|+++|+++|+-|+
T Consensus        10 ~a~~~L~e~g~t~~~iA~~~Gks~~~V~~~LrLl~   44 (93)
T d1vz0a1          10 RGYQALLEMGLTQEEVARRVGKARSTVANALRLLQ   44 (93)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHGGG
T ss_pred             HHHHHHHHcCCCHHHHHHHHccchHHHHHHHHHHH
Confidence            45666677777999999999999999999998764

>d2onsa1 c.94.1.1 (A:32-342) Molybdate-binding protein, ModA {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Molybdate-binding protein, ModA
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=88.93  E-value=0.45  Score=35.20  Aligned_cols=55  Identities=11%  Similarity=0.187  Sum_probs=43.2

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC--CeeEEEEc
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND--QADIAIVT  149 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~--~~Di~i~~  149 (306)
                      +|+|....+. ...+..++.+|.++||+++|++...++.+..+.+..+  ..|+.+..
T Consensus         3 ~L~v~~ags~-~~~~~~~~~~Fe~~~P~I~V~~~~~~~~~~~~~~~a~g~~pDv~~~~   59 (311)
T d2onsa1           3 KLKVFHAGSL-TEPMKAFKRAFEEKHPNVEVQTEAAGSAATIRKVTELGRKADVIATA   59 (311)
T ss_dssp             EEEEEEEGGG-HHHHHHHHHHHHHHCTTEEEEEEEECHHHHHHHHHTSCCCCSEEEES
T ss_pred             EEEEEeccCc-HHHHHHHHHHHHHHCcCcEEEEEeCCcHHHHHHHHhCCCCCCEEEEC
Confidence            4677665443 4578899999999999999999999888888888664  36887653

>d1nh8a1 c.94.1.1 (A:1-210) ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.65  E-value=1  Score=31.95  Aligned_cols=160  Identities=11%  Similarity=0.145  Sum_probs=88.1

Q ss_pred             CCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-----CCCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC
Q psy3760         119 FPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-----SPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP  193 (306)
Q Consensus       119 ~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-----~~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~  193 (306)
                      .+++.+-+.  -..++...+..|.+|+||+....     .+-..+.-..++.-++++.++++.+      .+..++.+..
T Consensus        40 ~~~i~v~~~--R~~DIp~~V~~G~~DlGI~G~D~l~E~~~~v~~~~dL~fG~c~l~vA~p~~~~------~~~~~l~~~r  111 (210)
T d1nh8a1          40 VNNVEFFFL--RPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRN------WTTADLAGMR  111 (210)
T ss_dssp             TTTEEEEEE--CGGGHHHHHHHSSCSEEEEEHHHHHHHTCCEEEEEECSCCCEEEEEEEETTSC------CCGGGGTTCE
T ss_pred             CCCeEEEEe--CHHHHHHHHHhccCceeeecHHHHhhcccchhhhhcccccceEEEEEeecCCC------CChhhhcCCE
Confidence            455655444  56799999999999999985211     1112233446677789999988754      3456665544


Q ss_pred             eEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEE
Q psy3760         194 LITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRV  272 (306)
Q Consensus       194 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l  272 (306)
                      ..+     -+.+...++|.+.|+...++....+.+.+   ...|..=+++--... ..+...+|+.+.-.  .......+
T Consensus       112 IAT-----kYpnit~~ff~~~gi~~~ii~~~Ga~E~a---p~~g~AD~IvDiv~TG~TLk~N~L~~i~~~--l~~S~a~i  181 (210)
T d1nh8a1         112 IAT-----AYPNLVRKDLATKGIEATVIRLDGAVEIS---VQLGVADAIADVVGSGRTLSQHDLVAFGEP--LCDSEAVL  181 (210)
T ss_dssp             EEE-----SCHHHHHHHHHHHTCCCEEEECSSCCTHH---HHTTSCSEEEEEESSSHHHHHTTEEEEEEE--EEEECEEE
T ss_pred             Eee-----ehHHHHHHHHHHcCCceeEEEEecCcccc---ccCCcceEEEeeeccHHHHHHCCCEEcchh--hhheehee
Confidence            332     24467788999999876655444555443   444433233322111 11245677776321  12223344


Q ss_pred             EEeCCc---cccHHHHHHHHHHhHHhh
Q psy3760         273 IIKQGT---YLRSYVYSFIKLLSPKLN  296 (306)
Q Consensus       273 ~~~~~~---~~~~~~~~~~~~l~~~~~  296 (306)
                      +-++..   .....+..+++.++..+.
T Consensus       182 i~~~~~~~~~~~~~i~~l~~~l~~vl~  208 (210)
T d1nh8a1         182 IERAGTDGQDQTEARDQLVARVQGVVF  208 (210)
T ss_dssp             EEEC--------CHHHHHHHHHHHHHH
T ss_pred             EeccccCChhHHHHHHHHHHHHHHHHh
Confidence            444332   233446667776666554

>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=88.35  E-value=0.38  Score=28.79  Aligned_cols=63  Identities=14%  Similarity=0.076  Sum_probs=42.0

Q ss_pred             chhhHHHHHHHHHh----c--CCHHHHHHH--hCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHH
Q psy3760           2 NLHQFRFVREAVRQ----N--FNLTEAAKA--LYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILR   68 (306)
Q Consensus         2 ~~~~l~~f~~v~~~----~--~s~~~aA~~--l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~   68 (306)
                      +-++-.+|.++++.    |  =+...-|+.  +++|.+||-..++.||+. |.  ..+.  ..|.+ ||+.|-++|-
T Consensus         3 t~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~-G~--l~~~h~s~Gri-PT~~g~r~yv   75 (87)
T d1stza1           3 NDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYL-GY--IYQPHTSAGRI-PTDKGLRFYY   75 (87)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHT-TS--EECCSSCSCBE-ECHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHC-Cc--ccCCCCCCCCc-ccHHHHHHHH
Confidence            33455555555542    1  044567777  556899999999999975 54  3443  46664 9999988864

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=88.21  E-value=0.7  Score=25.98  Aligned_cols=38  Identities=13%  Similarity=0.080  Sum_probs=28.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      ++|.--.-.|.|+...|+.+|+|.+|+..++.+--..|
T Consensus        25 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L   62 (68)
T d1or7a1          25 MAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREAI   62 (68)
T ss_dssp             HHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            34444444556999999999999999998887765544

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.01  E-value=0.17  Score=27.79  Aligned_cols=21  Identities=24%  Similarity=0.153  Sum_probs=19.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHH
Q psy3760          18 NLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~   38 (306)
                      ++...|+..|+|.+|+|+.|.
T Consensus         4 Ti~diA~~agvS~sTVSr~l~   24 (59)
T d1efaa1           4 TLYDVAEYAGVSYQTVSRVVN   24 (59)
T ss_dssp             CHHHHHHTTTSCHHHHHHHHT
T ss_pred             CHHHHHHHHCCCHHHHHHHHC
Confidence            678899999999999999875

>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=86.87  E-value=0.31  Score=28.51  Aligned_cols=37  Identities=24%  Similarity=0.318  Sum_probs=28.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |...-|+.+++|.+|+.++++.|+++ |. +..+.++|.
T Consensus        24 se~~La~~~~vSr~tvr~Al~~L~~~-Gl-i~~~~g~G~   60 (78)
T d3bwga1          24 VLETLMAQFEVSKSTITKSLELLEQK-GA-IFQVRGSGI   60 (78)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHT-TS-EEEETTTEE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-Cc-EEEEcCcEE
Confidence            67788999999999999999999965 33 333444554

>d1y0ua_ a.4.5.5 (A:) Putative arsenical resistance operon repressor AF0168 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Putative arsenical resistance operon repressor AF0168
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.45  E-value=0.58  Score=26.59  Aligned_cols=50  Identities=22%  Similarity=0.223  Sum_probs=42.6

Q ss_pred             HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760          10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ   64 (306)
Q Consensus        10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~   64 (306)
                      .-+.+.+ |=..--+.|++|.-.+-++++-||.=|   -++|.+.+. ++|.+|+
T Consensus        38 rmi~kgr-sedEIm~~l~LSkkqldYHLk~LE~Gf---ciErvge~w-~~T~~G~   87 (89)
T d1y0ua_          38 RMLDKGR-SEEEIMQTLSLSKKQLDYHLKVLEAGF---CIERVGERW-VVTDAGK   87 (89)
T ss_dssp             HHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHTT---SEEEETTEE-EECTTTC
T ss_pred             HHHHccC-CHHHHHHHhccCHHHHHHHHHHHHccc---eeEecCCce-eeccccc
Confidence            3344666 999999999999999999999999876   358999998 7999986

>d2qmwa1 c.94.1.1 (A:1-184) Prephenate dehydratase {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Prephenate dehydratase
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.33  E-value=3.7  Score=28.26  Aligned_cols=145  Identities=13%  Similarity=0.023  Sum_probs=72.4

Q ss_pred             CCCcEEEEE-eCChhHHHHHHHcCCeeEEEEccccCCCCCce---eeccccceE----EEEecCCCCCCCCCCcChhhhc
Q psy3760         119 FPKVKLSLL-QGNPKQITEMIRNDQADIAIVTEILSPSDKLI---SIPCYQWEY----VIIVPLDHPLLLLNSISLKEIS  190 (306)
Q Consensus       119 ~p~~~i~~~-~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~---~~~l~~~~~----~~v~~~~~~l~~~~~i~~~dl~  190 (306)
                      +++-...+. ..+-.++++.+.+|++|.|++.-.... .|..   ...|.+.++    -++.+-.|-|......+++++ 
T Consensus        21 f~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~-~G~V~~t~D~L~~~~~~I~~E~~l~I~h~Ll~~~~~~l~~I-   98 (184)
T d2qmwa1          21 FSENEATFQPKSNLFEVIKAVADDDTSIGVVPIENSI-EGTINIVADALAQQDVFAHGEIRLDINFALYGNGTDSISDI-   98 (184)
T ss_dssp             CCTTSSEEEEESSHHHHHHHHHHCSSEEEEEEEESCS-SSCSHHHHHHHHTTSSEEEEEEEEECCEEEECCSSCCSTTC-
T ss_pred             cccCCceeeecCCHHHHHHHHHcCCCceeEEEeeccc-ccchHHHHHhhhccCceeEeeecccchhhhccccccccccc-
Confidence            554333333 356678999999999999999622111 1110   111111111    112233343332222233333 


Q ss_pred             CCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccccCCcee--eecCCCCc-c
Q psy3760         191 NYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRS--ISASHLFG-T  267 (306)
Q Consensus       191 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~l~~--~~~~~~~~-~  267 (306)
                        .-|...+  ....+-..|+++++.  +.. .+++.......+..|. .++.|...+..+   +|..  -.+.+... .
T Consensus        99 --~~V~SHp--qal~QC~~~l~~~~~--~~~-~~~sta~aa~~~~~~~-aAIas~~aa~~y---gL~il~~~I~D~~~N~  167 (184)
T d2qmwa1          99 --KKVYSIA--PAISQTTNYIHQHQF--DYD-YVDSTIQSLTKIENGV-AAIAPLGSGEAY---GFTPIDTHIEDYPHNV  167 (184)
T ss_dssp             --CEEEECH--HHHHHSHHHHHHTTC--EEE-ECSSHHHHHHTCBTTE-EEEEETTTSGGG---TCCEEEECCCSCSCCE
T ss_pred             --ceEEEec--chHHHHHHHHHhhcc--chh-hhhhHHHHHhhhhhhh-hccccHhHHHHc---CChhhhhCCCCCCCCe
Confidence              3443332  223456778877753  333 4677666666665553 477777776653   4444  45655333 3


Q ss_pred             ceEEEEEeC
Q psy3760         268 TISRVIIKQ  276 (306)
Q Consensus       268 ~~~~l~~~~  276 (306)
                      ..+.++.++
T Consensus       168 TRF~vi~~~  176 (184)
T d2qmwa1         168 TRFLVIKNQ  176 (184)
T ss_dssp             EEEEEEESC
T ss_pred             EeEEEEecC
Confidence            344444443

>d1r9la_ c.94.1.1 (A:) Glycine betaine-binding periplasmic protein ProX {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Glycine betaine-binding periplasmic protein ProX
species: Escherichia coli [TaxId: 562]

Probab=86.31  E-value=0.67  Score=35.17  Aligned_cols=59  Identities=3%  Similarity=-0.110  Sum_probs=50.0

Q ss_pred             CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEE-EEeCChhHHHHHHHcCCeeEEEEc
Q psy3760          90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLS-LLQGNPKQITEMIRNDQADIAIVT  149 (306)
Q Consensus        90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~-~~~~~~~~~~~~l~~~~~Di~i~~  149 (306)
                      +...+|+||..+.-...++..++.++.+. -+.+++ +...++..+...|.+|++|+..-+
T Consensus         5 ~~~~ti~~~~~~wte~~i~~ei~~q~Le~-~Gy~V~~~~~~~~~~~~~al~~GdiDv~~Ey   64 (309)
T d1r9la_           5 GKGITVNPVQSTITEETFQTLLVSRALEK-LGYTVNKPSEVDYNVGYTSLASGDATFTAVN   64 (309)
T ss_dssp             TTTCEECEEECSCGGGHHHHHHHHHHHHH-TTCEECCCEECCHHHHHHHHHHTSSCEEEEE
T ss_pred             CCCCEEEEecCCccHHHHHHHHHHHHHHH-cCCceeeecCCChHHHHHHHHcCCCeEEEee
Confidence            34568999999988999999999999987 588885 466788888999999999998754

>d1q35a_ c.94.1.1 (A:) Ferric-binding protein FbpA {Mannheimia haemolytica [TaxId: 75985]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Ferric-binding protein FbpA
species: Mannheimia haemolytica [TaxId: 75985]

Probab=85.27  E-value=5.9  Score=29.61  Aligned_cols=198  Identities=11%  Similarity=0.081  Sum_probs=102.1

Q ss_pred             cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC---CeeEEEEcccc-----------CC-----
Q psy3760          94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND---QADIAIVTEIL-----------SP-----  154 (306)
Q Consensus        94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~---~~Di~i~~~~~-----------~~-----  154 (306)
                      .|+|.+..  ...++.+++..|.+++ ++++++...++........+|   .+|+.+.....           ..     
T Consensus         3 ev~vY~~~--~~~~~~~l~~~Fek~t-GIkV~~~~~~~~~~~kl~~e~~~~~~Dvv~~~~~~~~~~~~~~g~~~~~~~~~   79 (318)
T d1q35a_           3 EVNVYSYR--QPYLIEPMLKNFEKDT-GIKVNIIFADKGLVDRVKQEGELSPADVLLTVDISRVMEIVNADLAQKIDSKV   79 (318)
T ss_dssp             EEEEEESS--CGGGTHHHHHHHHHHH-CCEEEEEECC-CCHHHHHHHGGGCCCCEEEESCHHHHHHHHHTTCBCCCCCHH
T ss_pred             eEEEEeCC--CHhHHHHHHHHHHHhh-CCEEEEEECCHHHHHHHHhcCCCCCCCEEEECCHHHHHHHHhcCcccccCchh
Confidence            57777654  4668888999999985 999999877654333333333   59998753110           00     


Q ss_pred             ----------CCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCCCcHH-HHHHHHHhCC----
Q psy3760         155 ----------SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSFSGRI-KLDREFSLQK----  215 (306)
Q Consensus       155 ----------~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~~~~~-~~~~~~~~~~----  215 (306)
                                ..+-...+.....++++..++-.-....+.++.+|.+-.    +...++...... .+.......+    
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~i~yN~~~~~~~~~p~s~~dl~~~~~kg~i~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (318)
T d1q35a_          80 LEKNIPAQFRDSNDQWFGLTTRARVIYTSKDRVGKLPAGFDYLDLAKPEYKGKVCVRSGKNSYNVSLFAAMIEHYGIEKT  159 (318)
T ss_dssp             HHHHSCGGGBCTTSSCEEEEEEEEEEEEETTTTCSCCTTCCGGGGGSGGGTTCEECSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhchhhhhhcccccccccceeEEEEechhhhccccCcchhhhhhhhhccCeEEecCCchhhHHHHHHHHhhccCchhH
Confidence                      112234555556777888876432223466888886532    344443322211 1111111000    


Q ss_pred             ------Cce-eEEEEecCHHHHHHHHHhccceeeee-ccee-------cc-c-ccCCceeeecCC-CCccceEEEEEeCC
Q psy3760         216 ------LTP-YIVLETINSDIIKTYVELRMGIGIIA-SIAF-------DS-N-RDKNLRSISASH-LFGTTISRVIIKQG  277 (306)
Q Consensus       216 ------~~~-~~~~~~~~~~~~~~~v~~g~gi~~~p-~~~~-------~~-~-~~~~l~~~~~~~-~~~~~~~~l~~~~~  277 (306)
                            ... ...............+.+|..-..+. ....       .. . ..+.....+.+. .......++...++
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~i~k~  239 (318)
T d1q35a_         160 KAFLEGLKANLARKPQGGDRDQVKAIKEGICDYSIGNSYYYGKMLDDEKQKSWAEAAIINFPSGEHGTHKNISGVVIAKH  239 (318)
T ss_dssp             HHHHHHHHHTBSSCCCSCHHHHHHHHHHTSCSEEEEETHHHHHHHHSTTTHHHHHTEEEECCCSTTCBEEEEEEEEEBTT
T ss_pred             HHHHHHhhhccceeccccchhhhhhhhcCccceeeehhhhHHHHHhhhhhhhhhcccceeccccccccccccceEEEECC
Confidence                  000 11112344556677777774332222 1110       00 0 112222233332 23333455666788


Q ss_pred             ccccHHHHHHHHHHhHH
Q psy3760         278 TYLRSYVYSFIKLLSPK  294 (306)
Q Consensus       278 ~~~~~~~~~~~~~l~~~  294 (306)
                      .+...++++|++++.+.
T Consensus       240 a~~~~~A~~fi~fllsp  256 (318)
T d1q35a_         240 SPNKANAVKLIEYLSGE  256 (318)
T ss_dssp             CTTHHHHHHHHHHHHSH
T ss_pred             CCCHHHHHHHHHHHcCH
Confidence            88899999999999654

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=85.22  E-value=0.14  Score=28.81  Aligned_cols=32  Identities=13%  Similarity=0.062  Sum_probs=28.5

Q ss_pred             HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        20 ~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      .+.|+.+|+|.+||++.+++     |.|...+.++|.
T Consensus         6 ~~lA~iFGVS~~TI~~W~~~-----G~Pv~~~Gg~G~   37 (68)
T d1j9ia_           6 KQLADIFGASIRTIQNWQEQ-----GMPVLRGGGKGN   37 (68)
T ss_dssp             HHHHHHTTCCHHHHHHHTTT-----TCCCSSCCCSSS
T ss_pred             HHHHHHhCCCHHHHHHHHHC-----CCCeecCCCCCc
Confidence            56899999999999999864     999999998875

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

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

Probab=85.19  E-value=0.61  Score=29.52  Aligned_cols=72  Identities=13%  Similarity=0.086  Sum_probs=44.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG   79 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~   79 (306)
                      -..|..+.+.|.|....|+++|.|.+.||+.++-+.  +...+...-..|.+..+.+...+....+.--...+.
T Consensus        20 A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~L~~--lp~~v~~~~~~g~i~~~~a~~~l~~~~~~~~~~~~~   91 (114)
T d1r71a_          20 ADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLD--LPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEA   91 (114)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGGGS--CCHHHHHHHHTTSCCCHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHHHhC--CCHHHHHHHHcCCCCHHHHHHHHHHhhhcCHHHHHH
Confidence            345666677766999999999999999999998664  333332222233224555555555444443333333

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.00  E-value=0.5  Score=26.46  Aligned_cols=39  Identities=15%  Similarity=0.172  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760           6 FRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEEL   44 (306)
Q Consensus         6 l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~l   44 (306)
                      ++++..+.+.. .+-+..|+.+||+.||||..+++=|+.+
T Consensus        14 ~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK~kil   53 (66)
T d1hlva1          14 SRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAIL   53 (66)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHH
T ss_pred             HHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            44444444433 1345699999999999999998866554

>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=84.87  E-value=0.46  Score=27.42  Aligned_cols=37  Identities=16%  Similarity=0.209  Sum_probs=29.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      |...=|+.+++|.+++.++++.|+++  --|..+.++|.
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~--G~i~~~~g~G~   65 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARD--GWLTIQHGKPT   65 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEETTEEE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHC--CcEEEEeCceE
Confidence            67888999999999999999999986  23334445554

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

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

Probab=83.52  E-value=0.58  Score=27.39  Aligned_cols=40  Identities=18%  Similarity=0.228  Sum_probs=32.0

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK   61 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~   61 (306)
                      |-..-|..+|+|..++||.|++|+++   -++..+++.+ .+.+
T Consensus        31 t~~eLA~~~G~sretvsr~L~~l~~~---glI~~~~~~i-~I~d   70 (81)
T d2gaua1          31 SREELATLSNMTVSNAIRTLSTFVSE---RMLALDGKRI-KIID   70 (81)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHHHHHHT---TSEEEETTEE-EESC
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCCEE-EEcC
Confidence            44568999999999999999999986   3566777777 4554

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

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

Probab=82.95  E-value=0.64  Score=27.17  Aligned_cols=35  Identities=26%  Similarity=0.321  Sum_probs=28.5

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR   55 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~   55 (306)
                      |-..=|..+|+|.+++||.|++|+++   .++.+.+++
T Consensus        32 t~~eiA~~lG~sretvsr~l~~l~~~---g~I~~~~~~   66 (80)
T d1ft9a1          32 TVEEIANLIGSSRQTTSTALNSLIKE---GYISRQGRG   66 (80)
T ss_dssp             CHHHHHHHHCSCHHHHHHHHHHHHHT---TSSEECSTT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCC
Confidence            45678999999999999999999986   456666555

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

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

Probab=82.81  E-value=0.64  Score=27.15  Aligned_cols=41  Identities=15%  Similarity=0.125  Sum_probs=28.6

Q ss_pred             CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760          18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP   62 (306)
Q Consensus        18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~   62 (306)
                      |-..-|..+|+|.+++|+.|++|+++=   ++..+++.+ .+.+.
T Consensus        32 t~~elA~~~g~sretvsr~l~~l~~~g---lI~~~~~~i-~I~d~   72 (80)
T d3e5ua1          32 SQKSIGEITGVHHVTVSRVLASLKREN---ILDKKKNKI-IVYNL   72 (80)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTT---SEEC----C-EESCH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCC---cEEecCCEE-EEcCH
Confidence            345679999999999999999999863   455666666 45553

>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=82.67  E-value=0.75  Score=27.78  Aligned_cols=57  Identities=18%  Similarity=0.195  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC---CccccCHhHHHH
Q psy3760           6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK---RIRGLTKPGQAI   66 (306)
Q Consensus         6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~---~~~~lT~~G~~l   66 (306)
                      |.+|-.+++...|...-|++++++...+.+-++.|..   .-||.+...   .+ ++|+.|+.|
T Consensus        30 L~ifd~L~~gp~t~~eLA~~~g~~~~~l~rLlr~L~a---~gll~~~~d~~~~~-~~t~~g~lL   89 (92)
T d1qzza1          30 LRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTV---VGVLEGGEKQGRPL-RPTRLGMLL   89 (92)
T ss_dssp             TTHHHHHHTTCCSHHHHHHHHTCCHHHHHHHHHHHHH---TTSEECCCC-CCCC-EECTTGGGG
T ss_pred             cCchHHHhCCCCCHHHHHHHHCcCchHHHHHHHHHHH---CCCeeeecCCCcee-cccHHHHhc
Confidence            4566666665569999999999999999999888854   568888632   35 789998765

>d2p5ka1 a.4.5.3 (A:2-64) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=82.45  E-value=0.3  Score=27.18  Aligned_cols=17  Identities=35%  Similarity=0.387  Sum_probs=14.6

Q ss_pred             HhCCCchHHHHHHHHHH
Q psy3760          25 ALYTSQPGVSKAIIELE   41 (306)
Q Consensus        25 ~l~isq~~~s~~i~~LE   41 (306)
                      -..+||+|+||-|++|.
T Consensus        32 G~~vTQaTlSRDL~eLg   48 (63)
T d2p5ka1          32 GYKVTQATVSRDIKELH   48 (63)
T ss_dssp             TCCCCHHHHHHHHHHHT
T ss_pred             CCCeeHHHHHHHHHHhC
Confidence            36799999999999883

>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=81.39  E-value=0.51  Score=26.76  Aligned_cols=36  Identities=19%  Similarity=0.127  Sum_probs=26.6

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI   56 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~   56 (306)
                      -..-|+.+++|..++-++++.|+++ | -+..+.++|.
T Consensus        28 ~~~La~~~~vSr~tvr~Al~~L~~~-G-li~~~~~~G~   63 (69)
T d2hs5a1          28 EPDICAALDVSRNTVREAFQILIED-R-LVAHELNRGV   63 (69)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHT-T-SEEEETTTEE
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHC-C-cEEEEcCCEE
Confidence            4577999999999999999999965 2 2333344454

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=81.31  E-value=2.5  Score=25.94  Aligned_cols=55  Identities=18%  Similarity=0.147  Sum_probs=34.5

Q ss_pred             hCCCchHHHHHHHHHHHHcCceeE-EecC----CCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760          26 LYTSQPGVSKAIIELEEELSIDIF-IRHG----KRIRGLTKPGQAILRSIEIIMQEIEGLKKI   83 (306)
Q Consensus        26 l~isq~~~s~~i~~LE~~lg~~Lf-~R~~----~~~~~lT~~G~~l~~~a~~il~~~~~~~~~   83 (306)
                      ..+|++++-..+++||++==+.-- ..++    +.+.++|++|+..+....   ++++.+...
T Consensus        38 ~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~~~~---~~~~~~~~~   97 (103)
T d1xmaa_          38 YVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKC---EEWELTKKV   97 (103)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHH---HHHHHHHHH
T ss_pred             ecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHHHHH---HHHHHHHHH
Confidence            469999999999999986322211 1111    222389999998776544   344444433

>d2b0la1 a.4.5.66 (A:167-257) GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CodY HTH domain
domain: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=81.28  E-value=0.76  Score=26.42  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=23.0

Q ss_pred             HHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760          19 LTEAAKALYTSQPGVSKAIIELEEE   43 (306)
Q Consensus        19 ~~~aA~~l~isq~~~s~~i~~LE~~   43 (306)
                      -++-|.+.|||.|-+-.+++++|.-
T Consensus        37 ASkiADrvgiTRSVIVNALRK~ESA   61 (91)
T d2b0la1          37 ASKIADRVGITRSVIVNALRKLESA   61 (91)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             ehhhhhhhCchHHHHHHHHHHhhhc
Confidence            4789999999999999999999974

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=80.47  E-value=0.95  Score=26.95  Aligned_cols=26  Identities=23%  Similarity=0.245  Sum_probs=21.6

Q ss_pred             HHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760          13 VRQNFNLTEAAKALYTSQPGVSKAII   38 (306)
Q Consensus        13 ~~~~~s~~~aA~~l~isq~~~s~~i~   38 (306)
                      .+.|.|-...|+.+|+|+++||+-++
T Consensus        11 ~~~glsq~~LA~~lGvs~~~is~ie~   36 (87)
T d2icta1          11 DELNVSLREFARAMEIAPSTASRLLT   36 (87)
T ss_dssp             HHHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHhhcHHHHHHHHH
Confidence            34466889999999999999998654

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein TM0937
species: Thermotoga maritima [TaxId: 2336]

Probab=80.24  E-value=4.2  Score=25.39  Aligned_cols=52  Identities=17%  Similarity=0.246  Sum_probs=33.5

Q ss_pred             CCCchHHHHHHHHHHHHcCceeEEecC----CCccccCHhHHHHHHHHHHHHHHHH
Q psy3760          27 YTSQPGVSKAIIELEEELSIDIFIRHG----KRIRGLTKPGQAILRSIEIIMQEIE   78 (306)
Q Consensus        27 ~isq~~~s~~i~~LE~~lg~~Lf~R~~----~~~~~lT~~G~~l~~~a~~il~~~~   78 (306)
                      .+++++|-..+++||++==+.--...+    +.+.++|++|+..+.....-...+.
T Consensus        43 ~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~~~~~~~~~~~   98 (114)
T d2esha1          43 IGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSLEDMK   98 (114)
T ss_dssp             CCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHH
Confidence            357889999999999863232222222    2333899999998875554444333

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=80.03  E-value=0.61  Score=27.59  Aligned_cols=26  Identities=15%  Similarity=0.158  Sum_probs=22.9

Q ss_pred             HhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760          14 RQNFNLTEAAKALYTSQPGVSKAIIEL   40 (306)
Q Consensus        14 ~~~~s~~~aA~~l~isq~~~s~~i~~L   40 (306)
                      ..- |+..-|+..++|+|||+|-.++|
T Consensus        35 ~~~-si~~lA~~~~vS~sTi~Rf~kkl   60 (83)
T d2o3fa1          35 IES-TVNEISALANSSDAAVIRLCKSL   60 (83)
T ss_dssp             HTC-CHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HHc-cHHHHHHHHCCCHHHHHHHHHHh
Confidence            356 99999999999999999988765