Psyllid ID: psy17626

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180----
Protein Sequence
MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHHcccEEEEccccccHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccccccccEEHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHHcccEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHccccEEEEEEccccc
Coil and Loop (DISEMBL)
mfpgtmhigYNRFRFLLECLADLDRQLkshggqlfivqgspiSIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVShtlwdpevviqtngnvppltYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLkshggqlfivqgspiSIFQKLKRELNFTKLCFEQDCEAY
Flexible Loop (DISEMBL)
mfpgtmhiGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEfvshtlwdpevVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
Low Complexity Region (SEG)
MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
Disordered region (IsUnstruct)
*****MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ*****
Disordered Region (DISOPRED)
MFPG**HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
Disordered Region (DISEMBL)
MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
Disordered Region (DISPRO)
*****MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY
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	184	2.2.26 [Sep-21-2011]
Q7PYI7	545	Cryptochrome-1 OS=Anophel	yes	N/A	0.711	0.240	0.511	3e-35
Q17DK5	545	Cryptochrome-1 OS=Aedes a	N/A	N/A	0.646	0.218	0.537	4e-35
O77059	542	Cryptochrome-1 OS=Drosoph	yes	N/A	0.646	0.219	0.5	7e-33
Q293P8	540	Cryptochrome-1 OS=Drosoph	yes	N/A	0.652	0.222	0.512	1e-31
Q8WP19	586	Cryptochrome-1 OS=Macaca	N/A	N/A	0.679	0.213	0.408	3e-23
Q16526	586	Cryptochrome-1 OS=Homo sa	yes	N/A	0.679	0.213	0.408	3e-23
P97784	606	Cryptochrome-1 OS=Mus mus	yes	N/A	0.641	0.194	0.432	5e-23
Q32Q86	588	Cryptochrome-1 OS=Rattus	yes	N/A	0.641	0.200	0.432	5e-23
Q6ZZY0	620	Cryptochrome-1 OS=Sylvia	N/A	N/A	0.597	0.177	0.415	2e-22
Q5IZC5	620	Cryptochrome-1 OS=Erithac	N/A	N/A	0.597	0.177	0.415	2e-22

>sp|Q7PYI7|CRY1_ANOGA Cryptochrome-1 OS=Anopheles gambiae GN=Cry1 PE=2 SV=4

 Score =  147 bits (372), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 68/133 (51%), Positives = 92/133 (69%), Gaps = 2/133 (1%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR +FLLE LADLDRQ +  GGQL + +G  +++ ++L  ELN  KLC+EQDC
Sbjct: 51  GTRIVGYNRMKFLLESLADLDRQFRDLGGQLLVFRGDSVTVLRRLFEELNIKKLCYEQDC 110

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG- 122
           E +W +RD  V K C   ++   E VSHTLW+P  VIQTNG++PPLTY+M+LHTV+ IG 
Sbjct: 111 EPIWKERDDAVAKLCRTMDVRCVENVSHTLWNPIEVIQTNGDIPPLTYQMFLHTVNIIGD 170

Query: 123 -TMHIGYNRFRFL 134
               +G   F ++
Sbjct: 171 PPRPVGAPNFEYV 183

Blue light-dependent regulator that is the input of the circadian feedback loop. Has no photolyase activity for cyclobutane pyrimidine dimers or 6-4 photoproducts. Regulation of expression by light suggests a role in photoreception for locomotor activity rhythms. Functions, together with per, as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells. Genes directly activated by the transcription factors Clock (Clk) and cycle (cyc) are repressed by cry.
Anopheles gambiae (taxid: 7165)

>sp|Q17DK5|CRY1_AEDAE Cryptochrome-1 OS=Aedes aegypti GN=cry PE=3 SV=1

 Score =  147 bits (371), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 64/119 (53%), Positives = 88/119 (73%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +G+NR +FLLE LADLDRQL+  GGQL++ +G+ +++ ++L  ELN  KLCFEQDC
Sbjct: 49  GTKLVGFNRMKFLLESLADLDRQLREIGGQLYVFKGNAVNVMRRLFEELNIRKLCFEQDC 108

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  ++  C   ++   E VSHTLWDP+ +I+TNG +PPLTY+M+LHTV  IG
Sbjct: 109 EPIWKARDDAIQNLCRMMDVKCVEKVSHTLWDPQQIIRTNGGIPPLTYQMFLHTVDIIG 167

Blue light-dependent regulator that is the input of the circadian feedback loop. Has no photolyase activity for cyclobutane pyrimidine dimers or 6-4 photoproducts. Regulation of expression by light suggests a role in photoreception for locomotor activity rhythms. Functions, together with per, as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells. Genes directly activated by the transcription factors Clock (Clk) and cycle (cyc) are repressed by cry.

Aedes aegypti (taxid: 7159)

>sp|O77059|CRY1_DROME Cryptochrome-1 OS=Drosophila melanogaster GN=cry PE=1 SV=1

 Score =  139 bits (351), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 61/122 (50%), Positives = 88/122 (72%), Gaps = 3/122 (2%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHG---GQLFIVQGSPISIFQKLKRELNFTKLCFE 60
           GT ++GYNR RFLL+ L D+D QL++     G+L + +G P  IF++L  ++   ++C E
Sbjct: 48  GTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIE 107

Query: 61  QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC 120
           QDCE +W++RD+ ++  C E NI   E VSHTLWDP++VI+TNG +PPLTY+M+LHTV  
Sbjct: 108 QDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQI 167

Query: 121 IG 122
           IG
Sbjct: 168 IG 169

Blue light-dependent regulator that is the input of the circadian feedback loop. Has no photolyase activity for cyclobutane pyrimidine dimers or 6-4 photoproducts. Regulation of expression by light suggests a role in photoreception for locomotor activity rhythms. Functions, together with per, as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells. Genes directly activated by the transcription factors Clock (Clk) and cycle (cyc) are repressed by cry. Necessary for light-dependent magnetosensitivity, an intact circadian system is not required for the magnetoreception mechanism to operate. Required for both the naive and trained responses to magnetic field, consistent with the notion that cry is in the input pathway of magnetic sensing.

Drosophila melanogaster (taxid: 7227)

>sp|Q293P8|CRY1_DROPS Cryptochrome-1 OS=Drosophila pseudoobscura pseudoobscura GN=cry PE=3 SV=2

 Score =  135 bits (341), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 63/123 (51%), Positives = 84/123 (68%), Gaps = 3/123 (2%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHG---GQLFIVQGSPISIFQKLKRELNFTKLCFE 60
           GT  +GYNR RFLL+ L DLD QL+S     G+LF+ +G P  IF++L  ++   K+C E
Sbjct: 48  GTKSVGYNRMRFLLDSLQDLDEQLQSATEGRGRLFVFEGEPTLIFRRLHEQVRLHKICAE 107

Query: 61  QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC 120
            DCE +W++RD+  +  C E  I   E VSHTLWDP +VI+TNG +PPLTY+M+LHTV  
Sbjct: 108 LDCEPIWNERDESARLLCRELGIEYVEKVSHTLWDPRLVIETNGGIPPLTYQMFLHTVQI 167

Query: 121 IGT 123
           IG 
Sbjct: 168 IGV 170

Blue light-dependent regulator that is the input of the circadian feedback loop. Has no photolyase activity for cyclobutane pyrimidine dimers or 6-4 photoproducts. Regulation of expression by light suggests a role in photoreception for locomotor activity rhythms. Light induces the degradation of cry, likely due to conformational change in the photoreceptor leading to targeting to the proteasome. Under circadian regulation, expression is influenced by the clock pacemaker genes period, timeless, Clock and cycle. Binding to tim irreversibly commits tim to proteasomal degradation. Functions, together with per, as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells. Genes directly activated by the transcription factors Clock (Clk) and cycle (cyc) are repressed by cry. Necessary for light-dependent magnetosensitivity, an intact circadian system is not required for the magnetoreception mechanism to operate. Required for both the naive and trained responses to magnetic field, consistent with the notion that Cry is in the input pathway of magnetic sensing.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|Q8WP19|CRY1_MACFA Cryptochrome-1 OS=Macaca fascicularis GN=CRY1 PE=2 SV=1

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
           D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct: 101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query: 122 GTMHI 126
             + I
Sbjct: 161 EPLEI 165

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Macaca fascicularis (taxid: 9541)

>sp|Q16526|CRY1_HUMAN Cryptochrome-1 OS=Homo sapiens GN=CRY1 PE=1 SV=1

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
           D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct: 101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query: 122 GTMHI 126
             + I
Sbjct: 161 EPLEI 165

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Homo sapiens (taxid: 9606)

>sp|P97784|CRY1_MOUSE Cryptochrome-1 OS=Mus musculus GN=Cry1 PE=1 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 51/118 (43%), Positives = 73/118 (61%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
           D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   VS
Sbjct: 101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVS 158

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Mus musculus (taxid: 10090)

>sp|Q32Q86|CRY1_RAT Cryptochrome-1 OS=Rattus norvegicus GN=Cry1 PE=2 SV=1

 Score =  107 bits (266), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 51/118 (43%), Positives = 73/118 (61%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
           D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   VS
Sbjct: 101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVS 158

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Rattus norvegicus (taxid: 10116)

>sp|Q6ZZY0|CRY1_SYLBO Cryptochrome-1 OS=Sylvia borin GN=CRY1 PE=2 SV=1

 Score =  105 bits (262), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/118 (41%), Positives = 73/118 (61%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N  KL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNIAKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
           D E    +RD  +KK  +E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S
Sbjct: 101 DSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLIS 158

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Sylvia borin (taxid: 73324)

>sp|Q5IZC5|CRY1_ERIRU Cryptochrome-1 OS=Erithacus rubecula GN=CRY1 PE=2 SV=2

 Score =  105 bits (262), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/118 (41%), Positives = 73/118 (61%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N  KL  E 
Sbjct: 41  FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNIAKLSIEY 100

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
           D E    +RD  +KK  +E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S
Sbjct: 101 DSEPFGKERDAAIKKLASEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLIS 158

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Erithacus rubecula (taxid: 37610)

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	184
307611923	536	cryptochrome 1 [Bombyx mori] gi|30641610	0.646	0.222	0.554	2e-35
62955979	548	antennal cryptochrome [Mamestra brassica	0.646	0.217	0.554	6e-35
148467519	348	antennal cryptochrome 1 [Spodoptera litt	0.646	0.341	0.554	2e-34
404313303	528	cryptochrome 1 [Mythimna separata]	0.646	0.225	0.554	2e-34
324103935	548	cryptochrome [Spodoptera exigua] gi|3241	0.646	0.217	0.554	2e-34
312371404	608	hypothetical protein AND_22153 [Anophele	0.711	0.215	0.526	2e-34
13022111	525	cryptochrome [Antheraea pernyi]	0.646	0.226	0.537	2e-34
124107288	539	cryptochrome precursor [Dianemobius nigr	0.646	0.220	0.554	8e-34
158301399	545	AGAP001958-PA [Anopheles gambiae str. PE	0.711	0.240	0.511	1e-33
386762983	528	cryptochrome 1 [Agrotis ipsilon]	0.646	0.225	0.546	1e-33

>gi|307611923|ref|NP_001182628.1| cryptochrome 1 [Bombyx mori] gi|306416108|gb|ADM86932.1| cryptochrome 1 [Bombyx mori] gi|306416112|gb|ADM86934.1| cryptochrome 1 [Bombyx mori]

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 88/119 (73%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD+Q K +GG+L +V+G P ++F++L  E    KLCFEQDC
Sbjct: 44  GTKVVGYNRMRYLLEALDDLDKQFKKYGGRLLLVKGKPSAVFRRLWEEFGIRKLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD+ VK  C E  +T +E VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRPRDESVKTACREIGVTCREHVSHTLWEPDTVIKANGGIPPLTYQMFLHTVATIG 162

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|62955979|gb|AAY23345.1| antennal cryptochrome [Mamestra brassicae]

 Score =  152 bits (384), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 85/119 (71%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD QLK HGG+L +++G P  +F++L  E    +LCFEQDC
Sbjct: 44  GTKVVGYNRMRYLLEALEDLDNQLKKHGGRLIMIKGKPNVVFRRLWEEFGIRRLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VK  C E  +  KE VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRARDDSVKSACKEIGVVCKEHVSHTLWEPDTVIKANGGIPPLTYQMFLHTVATIG 162

Source: Mamestra brassicae

Species: Mamestra brassicae

Genus: Mamestra

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148467519|gb|ABQ65680.1| antennal cryptochrome 1 [Spodoptera littoralis]

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 84/119 (70%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD Q K HGG+L +++G P  +F++L  E    KLCFEQDC
Sbjct: 44  GTKVVGYNRMRYLLEALDDLDNQFKKHGGRLIMLKGKPNVVFRRLWEEFGIRKLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VK  C E  +  KE VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRARDDSVKNACKEIGVVCKEHVSHTLWEPDTVIKANGGIPPLTYQMFLHTVATIG 162

Source: Spodoptera littoralis

Species: Spodoptera littoralis

Genus: Spodoptera

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|404313303|gb|AFR54426.1| cryptochrome 1 [Mythimna separata]

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 85/119 (71%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD QLK HGG+L +++G P  +F++L  E    +LCFEQDC
Sbjct: 44  GTKLVGYNRMRYLLEALEDLDSQLKKHGGRLIMLKGKPNVVFRRLWEEFGIRRLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VK  C E  +  KE VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRARDDSVKAACKEIGVVCKENVSHTLWEPDTVIKANGGIPPLTYQMFLHTVATIG 162

Source: Mythimna separata

Species: Mythimna separata

Genus: Mythimna

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324103935|gb|ADY17887.1| cryptochrome [Spodoptera exigua] gi|324103937|gb|ADY17888.1| cryptochrome [Spodoptera exigua]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 84/119 (70%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD Q K HGG+L +++G P  +F++L  E    KLCFEQDC
Sbjct: 44  GTKVVGYNRMRYLLEALDDLDSQFKKHGGRLIMLKGKPNVVFRRLWEEFGIRKLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VK  C E  +  KE VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRARDDSVKNACKEIGVVCKEHVSHTLWEPDTVIKANGGIPPLTYQMFLHTVATIG 162

Source: Spodoptera exigua

Species: Spodoptera exigua

Genus: Spodoptera

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312371404|gb|EFR19605.1| hypothetical protein AND_22153 [Anopheles darlingi]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/133 (52%), Positives = 92/133 (69%), Gaps = 2/133 (1%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR +FLLE LADLDRQ +  GGQL + +G   ++ ++L  ELN  KLCFEQDC
Sbjct: 111 GTRVVGYNRMKFLLESLADLDRQFRELGGQLLVFRGDSETVLRRLFEELNIKKLCFEQDC 170

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG- 122
           E +W +RD++V K C   ++   E VSHTLW+P  VIQTNG++PPLTY+M+LHTV  IG 
Sbjct: 171 EPIWRERDERVTKLCETMDVKCVENVSHTLWNPNEVIQTNGDIPPLTYQMFLHTVDIIGE 230

Query: 123 -TMHIGYNRFRFL 134
               +G   F F+
Sbjct: 231 PPRPVGAPDFEFI 243

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|13022111|gb|AAK11644.1|AF333998_1 cryptochrome [Antheraea pernyi]

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 64/119 (53%), Positives = 85/119 (71%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD Q K +GG+L +++G P  +F++L  E    KLCFEQDC
Sbjct: 44  GTKLVGYNRMRYLLEALEDLDNQFKKYGGKLIMLKGKPSDVFRRLWEEFGIRKLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E LW  RD  VK  C E  +  +E+VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ +G
Sbjct: 104 EPLWRARDDGVKSACREIGVACREYVSHTLWEPDTVIRANGGIPPLTYQMFLHTVTIVG 162

Source: Antheraea pernyi

Species: Antheraea pernyi

Genus: Antheraea

Family: Saturniidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|124107288|dbj|BAF45421.1| cryptochrome precursor [Dianemobius nigrofasciatus]

 Score =  148 bits (374), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 87/119 (73%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR +FLLE L D+D QLK +GG L++  G+P+ +FQ + + +   KLCFEQDC
Sbjct: 50  GTKLVGYNRMKFLLESLQDIDSQLKKYGGNLYLFHGTPLCVFQYISQTIGLHKLCFEQDC 109

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VKK+C EN I   E VSHTLW+P  VI+TNG +PPLT++M++HTVS IG
Sbjct: 110 EPIWQHRDDLVKKFCKENGIKCIERVSHTLWNPHDVIKTNGGIPPLTFEMFVHTVSVIG 168

Source: Dianemobius nigrofasciatus

Species: Dianemobius nigrofasciatus

Genus: Dianemobius

Family: Gryllidae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158301399|ref|XP_321104.4| AGAP001958-PA [Anopheles gambiae str. PEST] gi|205696380|sp|Q7PYI7.4|CRY1_ANOGA RecName: Full=Cryptochrome-1; Short=agCRY1 gi|78191295|gb|ABB29886.1| cryptochrome 1 [Anopheles gambiae] gi|157012451|gb|EAA01270.4| AGAP001958-PA [Anopheles gambiae str. PEST]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 68/133 (51%), Positives = 92/133 (69%), Gaps = 2/133 (1%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR +FLLE LADLDRQ +  GGQL + +G  +++ ++L  ELN  KLC+EQDC
Sbjct: 51  GTRIVGYNRMKFLLESLADLDRQFRDLGGQLLVFRGDSVTVLRRLFEELNIKKLCYEQDC 110

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG- 122
           E +W +RD  V K C   ++   E VSHTLW+P  VIQTNG++PPLTY+M+LHTV+ IG 
Sbjct: 111 EPIWKERDDAVAKLCRTMDVRCVENVSHTLWNPIEVIQTNGDIPPLTYQMFLHTVNIIGD 170

Query: 123 -TMHIGYNRFRFL 134
               +G   F ++
Sbjct: 171 PPRPVGAPNFEYV 183

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386762983|gb|AFJ22638.1| cryptochrome 1 [Agrotis ipsilon]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 65/119 (54%), Positives = 84/119 (70%)

Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
           GT  +GYNR R+LLE L DLD Q K +GG+L +++G P  +F++L  E    KLCFEQDC
Sbjct: 44  GTKLVGYNRMRYLLEALDDLDNQFKKYGGRLIMLKGKPNVVFRRLWEEFGIRKLCFEQDC 103

Query: 64  EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
           E +W  RD  VK  C E  +  KE VSHTLW+P+ VI+ NG +PPLTY+M+LHTV+ IG
Sbjct: 104 EPVWRARDDSVKAACKEIGVVCKEHVSHTLWEPDTVIKANGGIPPLTYQMFLHTVTTIG 162

Source: Agrotis ipsilon

Species: Agrotis ipsilon

Genus: Agrotis

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
UNIPROTKB|Q17DK5	545	cry "Cryptochrome-1" [Aedes ae	0.646	0.218	0.537	3.4e-34
UNIPROTKB|Q7PYI7	545	Cry1 "Cryptochrome-1" [Anophel	0.646	0.218	0.554	7.7e-34
FB|FBgn0025680	542	cry "cryptochrome" [Drosophila	0.646	0.219	0.508	7.1e-32
UNIPROTKB|Q293P8	540	cry "Cryptochrome-1" [Drosophi	0.646	0.220	0.524	4.4e-31
UNIPROTKB|Q16526	586	CRY1 "Cryptochrome-1" [Homo sa	0.679	0.213	0.408	2.5e-22
UNIPROTKB|Q8WP19	586	CRY1 "Cryptochrome-1" [Macaca	0.679	0.213	0.408	2.5e-22
UNIPROTKB|F1MXB2	587	CRY1 "Uncharacterized protein"	0.679	0.212	0.408	2.5e-22
UNIPROTKB|E2RMX4	587	CRY1 "Uncharacterized protein"	0.679	0.212	0.408	2.5e-22
RGD|735083	588	Cry1 "cryptochrome 1 (photolya	0.641	0.200	0.432	2.5e-22
UNIPROTKB|Q32Q86	588	Cry1 "Cryptochrome-1" [Rattus	0.641	0.200	0.432	2.5e-22

UNIPROTKB|Q17DK5 cry "Cryptochrome-1" [Aedes aegypti (taxid:7159)]

 Score = 372 (136.0 bits), Expect = 3.4e-34, P = 3.4e-34
 Identities = 64/119 (53%), Positives = 88/119 (73%)

Query:     4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
             GT  +G+NR +FLLE LADLDRQL+  GGQL++ +G+ +++ ++L  ELN  KLCFEQDC
Sbjct:    49 GTKLVGFNRMKFLLESLADLDRQLREIGGQLYVFKGNAVNVMRRLFEELNIRKLCFEQDC 108

Query:    64 EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
             E +W  RD  ++  C   ++   E VSHTLWDP+ +I+TNG +PPLTY+M+LHTV  IG
Sbjct:   109 EPIWKARDDAIQNLCRMMDVKCVEKVSHTLWDPQQIIRTNGGIPPLTYQMFLHTVDIIG 167

GO:0000060 "protein import into nucleus, translocation" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005641 "nuclear envelope lumen" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0009785 "blue light signaling pathway" evidence=ISS

GO:0009882 "blue light photoreceptor activity" evidence=ISS

GO:0042752 "regulation of circadian rhythm" evidence=ISS

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

GO:0050660 "flavin adenine dinucleotide binding" evidence=ISS

UNIPROTKB|Q7PYI7 Cry1 "Cryptochrome-1" [Anopheles gambiae (taxid:7165)]

 Score = 369 (135.0 bits), Expect = 7.7e-34, P = 7.7e-34
 Identities = 66/119 (55%), Positives = 87/119 (73%)

Query:     4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 63
             GT  +GYNR +FLLE LADLDRQ +  GGQL + +G  +++ ++L  ELN  KLC+EQDC
Sbjct:    51 GTRIVGYNRMKFLLESLADLDRQFRDLGGQLLVFRGDSVTVLRRLFEELNIKKLCYEQDC 110

Query:    64 EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG 122
             E +W +RD  V K C   ++   E VSHTLW+P  VIQTNG++PPLTY+M+LHTV+ IG
Sbjct:   111 EPIWKERDDAVAKLCRTMDVRCVENVSHTLWNPIEVIQTNGDIPPLTYQMFLHTVNIIG 169

GO:0000060 "protein import into nucleus, translocation" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005641 "nuclear envelope lumen" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0009785 "blue light signaling pathway" evidence=ISS

GO:0009882 "blue light photoreceptor activity" evidence=ISS

GO:0042752 "regulation of circadian rhythm" evidence=ISS

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

GO:0050660 "flavin adenine dinucleotide binding" evidence=ISS

FB|FBgn0025680 cry "cryptochrome" [Drosophila melanogaster (taxid:7227)]

 Score = 352 (129.0 bits), Expect = 7.1e-32, P = 7.1e-32
 Identities = 62/122 (50%), Positives = 89/122 (72%)

Query:     4 GTMHIGYNRFRFLLECLADLDRQLKS--HG-GQLFIVQGSPISIFQKLKRELNFTKLCFE 60
             GT ++GYNR RFLL+ L D+D QL++   G G+L + +G P  IF++L  ++   ++C E
Sbjct:    48 GTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIE 107

Query:    61 QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC 120
             QDCE +W++RD+ ++  C E NI   E VSHTLWDP++VI+TNG +PPLTY+M+LHTV  
Sbjct:   108 QDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQI 167

Query:   121 IG 122
             IG
Sbjct:   168 IG 169

GO:0007623 "circadian rhythm" evidence=IGI;IEP;IMP;NAS;TAS;IPI

GO:0009882 "blue light photoreceptor activity" evidence=IMP

GO:0003913 "DNA photolyase activity" evidence=ISS;IMP

GO:0009785 "blue light signaling pathway" evidence=IMP

GO:0050660 "flavin adenine dinucleotide binding" evidence=IMP;IDA

GO:0008020 "G-protein coupled photoreceptor activity" evidence=ISS

GO:0009588 "UV-A, blue light phototransduction" evidence=ISS

GO:0009881 "photoreceptor activity" evidence=IMP;NAS;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0043234 "protein complex" evidence=IPI

GO:0005641 "nuclear envelope lumen" evidence=IDA

GO:0000060 "protein import into nucleus, translocation" evidence=IMP

GO:0009416 "response to light stimulus" evidence=IMP;TAS

GO:0009649 "entrainment of circadian clock" evidence=IDA;IMP

GO:0042332 "gravitaxis" evidence=IMP

GO:0009637 "response to blue light" evidence=NAS;TAS

GO:0006281 "DNA repair" evidence=IEA

GO:0043153 "entrainment of circadian clock by photoperiod" evidence=IMP

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

GO:0042752 "regulation of circadian rhythm" evidence=IMP;IDA

GO:0045475 "locomotor rhythm" evidence=IMP

GO:0007602 "phototransduction" evidence=IMP

GO:0050980 "detection of light stimulus involved in magnetoreception" evidence=IMP

GO:0071000 "response to magnetism" evidence=IMP

GO:0050958 "magnetoreception" evidence=IMP

UNIPROTKB|Q293P8 cry "Cryptochrome-1" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 345 (126.5 bits), Expect = 4.4e-31, P = 4.4e-31
 Identities = 64/122 (52%), Positives = 85/122 (69%)

Query:     4 GTMHIGYNRFRFLLECLADLDRQLKS--HG-GQLFIVQGSPISIFQKLKRELNFTKLCFE 60
             GT  +GYNR RFLL+ L DLD QL+S   G G+LF+ +G P  IF++L  ++   K+C E
Sbjct:    48 GTKSVGYNRMRFLLDSLQDLDEQLQSATEGRGRLFVFEGEPTLIFRRLHEQVRLHKICAE 107

Query:    61 QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC 120
              DCE +W++RD+  +  C E  I   E VSHTLWDP +VI+TNG +PPLTY+M+LHTV  
Sbjct:   108 LDCEPIWNERDESARLLCRELGIEYVEKVSHTLWDPRLVIETNGGIPPLTYQMFLHTVQI 167

Query:   121 IG 122
             IG
Sbjct:   168 IG 169

GO:0000060 "protein import into nucleus, translocation" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005641 "nuclear envelope lumen" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0009785 "blue light signaling pathway" evidence=ISS

GO:0009882 "blue light photoreceptor activity" evidence=ISS

GO:0042752 "regulation of circadian rhythm" evidence=ISS

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

GO:0050660 "flavin adenine dinucleotide binding" evidence=ISS

UNIPROTKB|Q16526 CRY1 "Cryptochrome-1" [Homo sapiens (taxid:9606)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query:   122 GTMHI 126
               + I
Sbjct:   161 EPLEI 165

GO:0006281 "DNA repair" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0042752 "regulation of circadian rhythm" evidence=ISS

GO:0003904 "deoxyribodipyrimidine photo-lyase activity" evidence=IDA

GO:0003914 "DNA (6-4) photolyase activity" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=NAS

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0009785 "blue light signaling pathway" evidence=NAS

GO:0019902 "phosphatase binding" evidence=IPI

GO:0003677 "DNA binding" evidence=TAS

GO:0000988 "protein binding transcription factor activity" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

UNIPROTKB|Q8WP19 CRY1 "Cryptochrome-1" [Macaca fascicularis (taxid:9541)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query:   122 GTMHI 126
               + I
Sbjct:   161 EPLEI 165

GO:0042752 "regulation of circadian rhythm" evidence=ISS

UNIPROTKB|F1MXB2 CRY1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query:   122 GTMHI 126
               + I
Sbjct:   161 EPLEI 165

GO:0042752 "regulation of circadian rhythm" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0003913 "DNA photolyase activity" evidence=IEA

UNIPROTKB|E2RMX4 CRY1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/125 (40%), Positives = 76/125 (60%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   +S +
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLISKM 160

Query:   122 GTMHI 126
               + I
Sbjct:   161 EPLEI 165

GO:0042752 "regulation of circadian rhythm" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0003913 "DNA photolyase activity" evidence=IEA

RGD|735083 Cry1 "cryptochrome 1 (photolyase-like)" [Rattus norvegicus (taxid:10116)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/118 (43%), Positives = 73/118 (61%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   VS
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVS 158

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA;ISO

GO:0003690 "double-stranded DNA binding" evidence=IEA;ISO

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006281 "DNA repair" evidence=IEA

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

GO:0007623 "circadian rhythm" evidence=IEA;ISO

GO:0009881 "photoreceptor activity" evidence=IEA

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA;ISO

GO:0019902 "phosphatase binding" evidence=ISO

GO:0042752 "regulation of circadian rhythm" evidence=ISO;ISS

GO:0003904 "deoxyribodipyrimidine photo-lyase activity" evidence=ISO

GO:0003914 "DNA (6-4) photolyase activity" evidence=ISO

UNIPROTKB|Q32Q86 Cry1 "Cryptochrome-1" [Rattus norvegicus (taxid:10116)]

 Score = 267 (99.0 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 51/118 (43%), Positives = 73/118 (61%)

Query:     2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
             F G+ ++G NR+RFLL+CL DLD  L+    +LF+++G P  +F +L +E N TKL  E 
Sbjct:    41 FAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEY 100

Query:    62 DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
             D E    +RD  +KK   E  + V   +SHTL+D + +I+ NG  PPLTYK +   VS
Sbjct:   101 DSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVS 158

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" 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)
Q293P8	CRY1_DROPS	No assigned EC number	0.5121	0.6521	0.2222	yes	N/A
Q7PYI7	CRY1_ANOGA	No assigned EC number	0.5112	0.7119	0.2403	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	184
pfam00875	164	pfam00875, DNA_photolyase, DNA photolyase	3e-27
pfam00875	164	pfam00875, DNA_photolyase, DNA photolyase	1e-11
COG0415	461	COG0415, PhrB, Deoxyribodipyrimidine photolyase [D	1e-09
TIGR02765	429	TIGR02765, crypto_DASH, cryptochrome, DASH family	6e-09
TIGR03556	471	TIGR03556, photolyase_8HDF, deoxyribodipyrimidine	5e-08
TIGR02765	429	TIGR02765, crypto_DASH, cryptochrome, DASH family	2e-05
TIGR03556	471	TIGR03556, photolyase_8HDF, deoxyribodipyrimidine	0.001
COG0415	461	COG0415, PhrB, Deoxyribodipyrimidine photolyase [D	0.002

>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase

 Score =  100 bits (251), Expect = 3e-27
 Identities = 36/118 (30%), Positives = 52/118 (44%), Gaps = 1/118 (0%)

Query: 1   MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFE 60
              G+  +G  R  FLLE LADLD  L   G +L + +G P  +  +L +EL  + + + 
Sbjct: 36  AQLGSHKLGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWN 95

Query: 61  QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
           +D E    +RD  VK+   E  I V  F  H L  P  V  T    P   +  +    
Sbjct: 96  RDYEPYERQRDAAVKEALREAGIEVHSFDDHLLVPPGEV-LTKKGKPYKVFTPFWKAW 152

This domain binds a light harvesting cofactor. Length = 164

>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 23/63 (36%), Positives = 35/63 (55%)

Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 181
           G+  +G  R  FLLE LADLD  L   G +L + +G P  +  +L +EL  + + + +D 
Sbjct: 39  GSHKLGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWNRDY 98

Query: 182 EAY 184
           E Y
Sbjct: 99  EPY 101

This domain binds a light harvesting cofactor. Length = 164

>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

 Score = 56.2 bits (136), Expect = 1e-09
 Identities = 26/98 (26%), Positives = 42/98 (42%)

Query: 7   HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAL 66
           H       FLL+ L  L + L   G  L + +G P  +  +L ++L  T + + +D E  
Sbjct: 44  HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEW 103

Query: 67  WHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNG 104
             +RD  + +   E  I V  F    L +P  V   +G
Sbjct: 104 ERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSG 141

Length = 461

>gnl|CDD|234002 TIGR02765, crypto_DASH, cryptochrome, DASH family

 Score = 53.9 bits (130), Expect = 6e-09
 Identities = 23/88 (26%), Positives = 40/88 (45%)

Query: 9   GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWH 68
           G  R +FLLE L DL   L+  G  L +  G P  +  +L +EL    +   Q+  +   
Sbjct: 52  GPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEK 111

Query: 69  KRDKKVKKWCAENNITVKEFVSHTLWDP 96
             ++ +++  A   I V++    TL+  
Sbjct: 112 SVERLLQQALARLGIHVEQHWGSTLYHE 139

Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes [Cellular processes, Adaptations to atypical conditions, Regulatory functions, DNA interactions]. Length = 429

>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase, 8-HDF type

 Score = 51.4 bits (123), Expect = 5e-08
 Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 4/103 (3%)

Query: 12  RFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRD 71
           R  +L+ CL +L ++ +  G QL I+QG P+ +  +L ++L    + +  D E    KRD
Sbjct: 49  RVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRD 108

Query: 72  KKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
           + V     E  I V       L  P+  I T    P   Y +Y
Sbjct: 109 RAVAAALKEAGIAVVTLWDQLLHSPD-EILTGSGNP---YTVY 147

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420 [DNA metabolism, DNA replication, recombination, and repair]. Length = 471

>gnl|CDD|234002 TIGR02765, crypto_DASH, cryptochrome, DASH family

 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 18/53 (33%), Positives = 25/53 (47%)

Query: 127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 179
           G  R +FLLE L DL   L+  G  L +  G P  +  +L +EL    +   Q
Sbjct: 52  GPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQ 104

Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes [Cellular processes, Adaptations to atypical conditions, Regulatory functions, DNA interactions]. Length = 429

>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase, 8-HDF type

 Score = 38.7 bits (90), Expect = 0.001
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 130 RFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
           R  +L+ CL +L ++ +  G QL I+QG P+ +  +L ++L    + +  D E Y
Sbjct: 49  RVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPY 103

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420 [DNA metabolism, DNA replication, recombination, and repair]. Length = 471

>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 16/60 (26%), Positives = 28/60 (46%)

Query: 125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
           H       FLL+ L  L + L   G  L + +G P  +  +L ++L  T + + +D E +
Sbjct: 44  HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEW 103

Length = 461

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
PF00875	165	DNA_photolyase: DNA photolyase from Prosite.; Inte	99.95
TIGR02765	429	crypto_DASH cryptochrome, DASH family. Photolyases	99.89
TIGR03556	471	photolyase_8HDF deoxyribodipyrimidine photo-lyase,	99.89
TIGR02766	475	crypt_chrom_pln cryptochrome, plant family. At lea	99.88
COG0415	461	PhrB Deoxyribodipyrimidine photolyase [DNA replica	99.87
PRK10674	472	deoxyribodipyrimidine photolyase; Provisional	99.85
TIGR00591	454	phr2 photolyase PhrII. All proteins in this family	99.8
KOG0133|consensus	531		99.56
PF00875	165	DNA_photolyase: DNA photolyase from Prosite.; Inte	99.26
TIGR02765	429	crypto_DASH cryptochrome, DASH family. Photolyases	99.09
TIGR03556	471	photolyase_8HDF deoxyribodipyrimidine photo-lyase,	99.06
TIGR02766	475	crypt_chrom_pln cryptochrome, plant family. At lea	99.01
COG0415	461	PhrB Deoxyribodipyrimidine photolyase [DNA replica	98.98
PRK10674	472	deoxyribodipyrimidine photolyase; Provisional	98.96
TIGR00591	454	phr2 photolyase PhrII. All proteins in this family	98.88
KOG0133|consensus	531		98.45
PF04244	224	DPRP: Deoxyribodipyrimidine photo-lyase-related pr	97.41
COG3046	505	Uncharacterized protein related to deoxyribodipyri	94.93
PRK12652	357	putative monovalent cation/H+ antiporter subunit E	92.17
PRK09982	142	universal stress protein UspD; Provisional	91.72
COG1609	333	PurR Transcriptional regulators [Transcription]	91.22
TIGR01490	202	HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrol	90.54
cd06287	269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	89.32
COG0560	212	SerB Phosphoserine phosphatase [Amino acid transpo	88.97
PF00532	279	Peripla_BP_1: Periplasmic binding proteins and sug	88.94
PRK14719	360	bifunctional RNAse/5-amino-6-(5-phosphoribosylamin	88.9
PF10087	97	DUF2325: Uncharacterized protein conserved in bact	87.63
COG2217	713	ZntA Cation transport ATPase [Inorganic ion transp	86.77
PRK15005	144	universal stress protein F; Provisional	86.21
PRK15456	142	universal stress protein UspG; Provisional	86.11
TIGR01088	141	aroQ 3-dehydroquinate dehydratase, type II. This m	85.76
PRK13015	146	3-dehydroquinate dehydratase; Reviewed	85.2
TIGR00289	222	conserved hypothetical protein TIGR00289. Homologo	85.12
PF01261	213	AP_endonuc_2: Xylose isomerase-like TIM barrel; In	83.44
TIGR00290	223	MJ0570_dom MJ0570-related uncharacterized domain.	83.09
PF00702	215	Hydrolase: haloacid dehalogenase-like hydrolase; I	82.49
TIGR01488	177	HAD-SF-IB Haloacid Dehalogenase superfamily, subfa	82.48
KOG1615|consensus	227		81.97
PRK11175	305	universal stress protein UspE; Provisional	81.91
cd06297	269	PBP1_LacI_like_12 Ligand-binding domain of unchara	81.54
PF06415	223	iPGM_N: BPG-independent PGAM N-terminus (iPGM_N);	81.34
cd01987	124	USP_OKCHK USP domain is located between the N-term	81.01
COG1139	459	Uncharacterized conserved protein containing a fer	80.44
PRK09484	183	3-deoxy-D-manno-octulosonate 8-phosphate phosphata	80.29
PF12710	192	HAD: haloacid dehalogenase-like hydrolase; PDB: 3P	80.28
PF13419	176	HAD_2: Haloacid dehalogenase-like hydrolase; PDB:	80.08

>PF00875 DNA_photolyase: DNA photolyase from Prosite

Probab=99.95  E-value=1.1e-27  Score=175.53  Aligned_cols=116  Identities=29%  Similarity=0.472  Sum_probs=104.3

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..|++|++|+++||.+|+++|+++|++|+|+.|++.++|++|+++++|++||+|++|++++++||+++++.|++.||.++
T Consensus        42 ~~~~~r~~Fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~  121 (165)
T PF00875_consen   42 RIGPRRRRFLLESLADLQESLRKLGIPLLVLRGDPEEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKVH  121 (165)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEEE
T ss_pred             cCcchHHHHHHHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEEE
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHHHhhhccc
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGT  123 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~  123 (184)
                      .+++++|++|++++++.+ ++|++||+|++.+.+...
T Consensus       122 ~~~~~~L~~~~~i~~~~~-~~~~vFtpf~k~~~~~~~  157 (165)
T PF00875_consen  122 TFDDHTLVPPDDIPKKDG-EPYKVFTPFRKKWEKQLL  157 (165)
T ss_dssp             EE--SSSS-HHHCHSTTS-SSHSSHHHHHHHHHCHCS
T ss_pred             EECCcEEEeccccccCCC-CCcccHHHHHHHHHhcCC
Confidence            999999999999988754 899999999999998765

; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....

>TIGR02765 crypto_DASH cryptochrome, DASH family

Probab=99.89  E-value=1.1e-22  Score=169.48  Aligned_cols=114  Identities=22%  Similarity=0.321  Sum_probs=108.9

Q ss_pred             CCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeE
Q psy17626          6 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITV   85 (184)
Q Consensus         6 ~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~   85 (184)
                      +..|++|++|+++||.+|+++|+++|++|+|+.|++.++|++|+++++|++||+|++|++++++||+.|++.|.+.||.+
T Consensus        49 ~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~  128 (429)
T TIGR02765        49 PKTGPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARLGIHV  128 (429)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhcCceE
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCceeecccccccccCCCCchhHHHHHHHhhh
Q psy17626         86 KEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC  120 (184)
Q Consensus        86 ~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~  120 (184)
                      +.+++++|++|++|++..+ ++|++|++|++.+..
T Consensus       129 ~~~~~~~l~~p~~v~~~~~-~~~~~ft~f~~~~~~  162 (429)
T TIGR02765       129 EQHWGSTLYHEDDLPFDLE-DLPDVFTQFRKQVEA  162 (429)
T ss_pred             EEecCCEeECHHhcCCCCC-CCCCCchHHHHHHHh
Confidence            9999999999999998754 799999999998764

Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.

>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type

Probab=99.89  E-value=2e-22  Score=169.49  Aligned_cols=116  Identities=24%  Similarity=0.453  Sum_probs=109.8

Q ss_pred             CCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeE
Q psy17626          6 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITV   85 (184)
Q Consensus         6 ~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~   85 (184)
                      +..|++|++||++||.+|+++|+++|++|+|+.|++.++|++|+++++|++||+|.+|++++++||++|++.|.+.||.+
T Consensus        43 ~~~~~~r~~Fl~esL~~L~~~L~~~G~~L~v~~G~p~~vl~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~  122 (471)
T TIGR03556        43 DDMAPARVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAV  122 (471)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEECCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHCCCEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCceeecccccccccCCCCchhHHHHHHHhhhcc
Q psy17626         86 KEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG  122 (184)
Q Consensus        86 ~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~  122 (184)
                      +.+++++|++|+.+++++ +++|++|++|++.+....
T Consensus       123 ~~~~~~~l~~p~~i~~~~-~~~y~~ft~f~k~~~~~~  158 (471)
T TIGR03556       123 VTLWDQLLHSPDEILTGS-GNPYTVYTPFWKNWSSLP  158 (471)
T ss_pred             EEeCCcEEECccccccCC-CCCCcchhHHHHHHHhcc
Confidence            999999999999998875 479999999999987654

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.

>TIGR02766 crypt_chrom_pln cryptochrome, plant family

Probab=99.88  E-value=9.4e-22  Score=165.83  Aligned_cols=115  Identities=21%  Similarity=0.290  Sum_probs=107.1

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEE-CChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITV   85 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~   85 (184)
                      ..+++|.+||++||.+|+++|+++|++|+|+. |++.++|++|+++++|++||+|++|++++++||++|+++|.+.||.+
T Consensus        40 ~~~~~~~~fl~~sL~~L~~~L~~~G~~L~v~~~g~~~~~l~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~  119 (475)
T TIGR02766        40 YPGRVSRWWLKQSLAHLDQSLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGISV  119 (475)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHcCCceEEEeCCCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCCEE
Confidence            45778888999999999999999999999985 89999999999999999999999999999999999999999999999


Q ss_pred             EEecCceeecccccccccCCCCchhHHHHHHHhhhcc
Q psy17626         86 KEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG  122 (184)
Q Consensus        86 ~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~  122 (184)
                      +.+++++|++|+++.+++ +++|++|++|++.+....
T Consensus       120 ~~~~~~~l~~p~~i~~~~-~~~~~~ft~f~~~~~~~~  155 (475)
T TIGR02766       120 QSFNADLLYEPWEVYDEL-GRPFTMFAAFWERCLSMP  155 (475)
T ss_pred             EEecCCEEEChhhhcccC-CCCCCeecHHHHHHHhcc
Confidence            999999999999999865 479999999999976543

At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.

>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

Probab=99.87  E-value=8.2e-22  Score=162.43  Aligned_cols=116  Identities=23%  Similarity=0.335  Sum_probs=111.0

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ++|+++.+|+.+||++|+++|+++|++|+|..|+|..++++++++.++++||+|.+|+++++.||..++..|.+.||.++
T Consensus        44 ~~~~~~~~Fl~~sL~~L~~~L~~~gi~L~v~~~~~~~~l~~~~~~~~~~~v~~n~~~~~~~~~rD~al~~~l~~~gi~~~  123 (461)
T COG0415          44 HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEWERQRDAALAQPLTEVGIAVH  123 (461)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHcCCceEEEeCCHHHHHHHHHHHhCcceEEeeeeechhHHHHHHHHHHHHHhcCceEE
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHHHhhhccc
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGT  123 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~  123 (184)
                      .|+|++|++|+++.+..+ ++|++||+|++.+.+...
T Consensus       124 ~~~d~~l~~p~~~~t~~~-~~y~vfT~F~k~~~~~~~  159 (461)
T COG0415         124 SFWDALLHEPGEVRTGSG-EPYKVFTPFYKAWRDRLR  159 (461)
T ss_pred             EeccccccCHhhccCCCC-CCccccchHHHHHHHhcc
Confidence            999999999999999764 799999999999987633

>PRK10674 deoxyribodipyrimidine photolyase; Provisional

Probab=99.85  E-value=9e-21  Score=159.53  Aligned_cols=113  Identities=16%  Similarity=0.203  Sum_probs=105.5

Q ss_pred             CCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEEC----ChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHh
Q psy17626          5 TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQG----SPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAE   80 (184)
Q Consensus         5 ~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g----~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~   80 (184)
                      .+..|++|++||++||.+|+++|+++|++|+|++|    +|.++|++|+++++|++||+|++|++++++||++|++.|. 
T Consensus        44 ~~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~-  122 (472)
T PRK10674         44 AHDMAPRQAAFINAQLNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQHQVTHLFYNYQYEVNERQRDAAVERALR-  122 (472)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHcC-
Confidence            34579999999999999999999999999999975    7999999999999999999999999999999999999996 


Q ss_pred             CCCeEEEecCceeecccccccccCCCCchhHHHHHHHhhh
Q psy17626         81 NNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC  120 (184)
Q Consensus        81 ~gi~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~  120 (184)
                       ||.++.+++++|++|+.+.++++ ++|++|++|++.+.+
T Consensus       123 -~i~~~~~~~~~l~~~~~i~~~~~-~~y~~ft~f~~~~~~  160 (472)
T PRK10674        123 -NVVCQGFDDSVLLPPGSVMTGNH-EMYKVFTPFKNAFLK  160 (472)
T ss_pred             -CCEEEEecCceEeCccccccCCC-CCCCcccHHHHHHHH
Confidence             89999999999999999988755 799999999999865

>TIGR00591 phr2 photolyase PhrII

Probab=99.80  E-value=3.4e-19  Score=149.60  Aligned_cols=109  Identities=8%  Similarity=0.050  Sum_probs=101.3

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..|++|++||++||.+|+++|+++|++|+|+.|+|.++|++|+++++|++||+|++|++++++||+.|++.|++ +|.++
T Consensus        67 ~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~i~~V~~~~~~~~~~~~rd~~v~~~l~~-~i~~~  145 (454)
T TIGR00591        67 AATRRHYFFMLGGLDEVANECERLIIPFHLLDGPPKELLPYFVDLHAAAAVVTDFSPLRQPEQWDEAVGKLLPK-DVPFQ  145 (454)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHcCCceEEeecChHHHHHHHHHHcCCCEEEEecccCcHHHHHHHHHHHHhcC-CCcEE
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999965 89999


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHHHhh
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS  119 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~  119 (184)
                      .+++++|++|+.+.++   .+|.+|++|.+...
T Consensus       146 ~~~~~~l~p~~~~~~~---~~y~~ft~~~k~~~  175 (454)
T TIGR00591       146 QVDAHNVVPCWAASKK---LEYAARTIRGKIRK  175 (454)
T ss_pred             EECCceEeeCcccCCc---eeeeeecHHHHHHH
Confidence            9999999999998764   58999998877643

All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0133|consensus

Probab=99.56  E-value=5.9e-15  Score=123.35  Aligned_cols=121  Identities=36%  Similarity=0.649  Sum_probs=114.8

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      |....|..|++||.|+|.+|+++|+++|++|.+++|.|+.+|+++.+.++++.|.++.+++|+.+.||..++..+.+.|+
T Consensus        45 ~~~~~g~~~~~~l~qsL~~ld~sl~~l~~~L~v~~~~p~~vl~~~~~~~~~~~l~~~~~~~p~~~vrD~~~~~~a~~l~i  124 (531)
T KOG0133|consen   45 GSSNVGRNRWRFLLQSLEDLDQSLRELNSRLFVFRGHPIAVLSRLLEQVGVQKLKFEYDMEPDGKVRDATIKSLATELGL  124 (531)
T ss_pred             hccccchhHHHHHHHHHHHHHHHHHHhCCceEEEeCCchHHHhhhhhccceeEEEEEEeccCccccccHHHHHHHHHhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHHhhhcccc
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTM  124 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~~  124 (184)
                      .+.....++++.|+.+..++++++|.+|+.|+..+.++..+
T Consensus       125 ~v~s~~s~~~~~~~~~i~~n~~k~pls~~~~~~~~~~~~~~  165 (531)
T KOG0133|consen  125 SVVSPVSHTLYLPDKIIEANGGKPPLSYKTFRGVCQSMSAP  165 (531)
T ss_pred             hhcccCchhhhcHHHHHHhcCCCCccccccccccccccccc
Confidence            99999999999999999998889999999999988777554

>PF00875 DNA_photolyase: DNA photolyase from Prosite

Probab=99.26  E-value=1.1e-11  Score=90.79  Aligned_cols=60  Identities=37%  Similarity=0.659  Sum_probs=53.5

Q ss_pred             ccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       125 ~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      ..+.++..|+.+||.+|+++|+++|++|+++.|++.++|.+|+++++|++||+|++|+++
T Consensus        42 ~~~~~r~~Fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~  101 (165)
T PF00875_consen   42 RIGPRRRRFLLESLADLQESLRKLGIPLLVLRGDPEEVLPELAKEYGATAVYFNEEYTPY  101 (165)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHHHTESEEEEE---SHH
T ss_pred             cCcchHHHHHHHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHhcCcCeeEeccccCHH
Confidence            568899999999999999999999999999999999999999999999999999999863

; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....

>TIGR02765 crypto_DASH cryptochrome, DASH family

Probab=99.09  E-value=6.7e-11  Score=98.95  Aligned_cols=61  Identities=30%  Similarity=0.498  Sum_probs=58.1

Q ss_pred             cccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        124 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       124 ~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +..++++..|+.+||.+|+++|+++|++|+++.|++.++|.+|+++++|++||+|++|+++
T Consensus        49 ~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~~~~~~~V~~~~~~~~~  109 (429)
T TIGR02765        49 PKTGPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSE  109 (429)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHhCCCEEEEeccCCHH
Confidence            4478899999999999999999999999999999999999999999999999999999874

Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.

>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type

Probab=99.06  E-value=1.3e-10  Score=98.28  Aligned_cols=64  Identities=27%  Similarity=0.615  Sum_probs=59.0

Q ss_pred             ccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        121 IGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       121 ~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +..+..+.++..|+.+||.+|+++|+++|++|+++.|++.++|.+|+++++|++||+|++|+++
T Consensus        40 ~~~~~~~~~r~~Fl~esL~~L~~~L~~~G~~L~v~~G~p~~vl~~l~~~~~~~~V~~~~~~~~~  103 (471)
T TIGR03556        40 LQADDMAPARVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPY  103 (471)
T ss_pred             hccccCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEECCHHHHHHHHHHHcCCCEEEEecccCHH
Confidence            3344577888999999999999999999999999999999999999999999999999999874

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.

>TIGR02766 crypt_chrom_pln cryptochrome, plant family

Probab=99.01  E-value=2.5e-10  Score=96.67  Aligned_cols=71  Identities=21%  Similarity=0.276  Sum_probs=59.6

Q ss_pred             HHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEe-CChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        114 YLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       114 F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      |...+..+.....+.++..|+.+||.+|+++|+++|++|+|+. |++.++|.+|+++++|++||+|++|+++
T Consensus        29 yi~dp~~~~~~~~~~~~~~fl~~sL~~L~~~L~~~G~~L~v~~~g~~~~~l~~l~~~~~i~~v~~~~~~~~~  100 (475)
T TIGR02766        29 FVWAPEEEGQYYPGRVSRWWLKQSLAHLDQSLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPV  100 (475)
T ss_pred             EEechHHhccccccHHHHHHHHHHHHHHHHHHHHcCCceEEEeCCCHHHHHHHHHHHcCCCEEEEecccCHH
Confidence            3334444443335567778999999999999999999999985 8999999999999999999999999874

At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.

>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

Probab=98.98  E-value=4.4e-10  Score=93.42  Aligned_cols=72  Identities=24%  Similarity=0.469  Sum_probs=65.4

Q ss_pred             HHHHHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        111 YKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       111 ~~~F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      .+.|...++++.  .+++++..|+.+||++|+++|+++|++|++..|++.+++++++++.++++||+|++|+++
T Consensus        32 ~~vfi~~~~~~~--~~~~~~~~Fl~~sL~~L~~~L~~~gi~L~v~~~~~~~~l~~~~~~~~~~~v~~n~~~~~~  103 (461)
T COG0415          32 IAVFILDPEQLG--HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEW  103 (461)
T ss_pred             EEEEEechhhcc--ccCHHHHHHHHHHHHHHHHHHHHcCCceEEEeCCHHHHHHHHHHHhCcceEEeeeeechh
Confidence            455666667776  788899999999999999999999999999999999999999999999999999999863

>PRK10674 deoxyribodipyrimidine photolyase; Provisional

Probab=98.96  E-value=5.2e-10  Score=94.61  Aligned_cols=63  Identities=14%  Similarity=0.221  Sum_probs=57.7

Q ss_pred             cccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeC----ChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQG----SPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       122 ~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g----~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      ..+..+.++..|+.+||.+|+++|+++|++|+|+.|    ++.++|++|+++++|++||+|++|+++
T Consensus        43 ~~~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~~~i~~v~~~~~~~~~  109 (472)
T PRK10674         43 AAHDMAPRQAAFINAQLNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQHQVTHLFYNYQYEVN  109 (472)
T ss_pred             ccCCCCHHHHHHHHHHHHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHHcCCCEEEEecccCHH
Confidence            344578899999999999999999999999999975    699999999999999999999999874

>TIGR00591 phr2 photolyase PhrII

Probab=98.88  E-value=4.1e-09  Score=88.83  Aligned_cols=58  Identities=9%  Similarity=0.098  Sum_probs=55.9

Q ss_pred             CcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       127 ~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +.++..|+.+||.+|+++|+++|++|+|+.|++.++|.+|+++++|++||+|++|+++
T Consensus        69 ~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~i~~V~~~~~~~~~  126 (454)
T TIGR00591        69 TRRHYFFMLGGLDEVANECERLIIPFHLLDGPPKELLPYFVDLHAAAAVVTDFSPLRQ  126 (454)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCceEEeecChHHHHHHHHHHcCCCEEEEecccCcH
Confidence            7788999999999999999999999999999999999999999999999999999874

All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0133|consensus

Probab=98.45  E-value=1.8e-07  Score=78.99  Aligned_cols=77  Identities=32%  Similarity=0.607  Sum_probs=72.0

Q ss_pred             chhHHHHHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        108 PLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       108 ~~v~~~F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      ..++.+|+-.++.++....|..+..|+.++|++|+++|+++|++|.+++|.|.++|++..++.+++.+.++.+++|+
T Consensus        31 ~~~~~v~i~d~~~~~~~~~g~~~~~~l~qsL~~ld~sl~~l~~~L~v~~~~p~~vl~~~~~~~~~~~l~~~~~~~p~  107 (531)
T KOG0133|consen   31 EPVRPVFILDPEEAGSSNVGRNRWRFLLQSLEDLDQSLRELNSRLFVFRGHPIAVLSRLLEQVGVQKLKFEYDMEPD  107 (531)
T ss_pred             CCceeEEEeCHhHhhccccchhHHHHHHHHHHHHHHHHHHhCCceEEEeCCchHHHhhhhhccceeEEEEEEeccCc
Confidence            36677788889999999999999999999999999999999999999999999999999999999999999999875

>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases

Probab=97.41  E-value=0.0021  Score=49.36  Aligned_cols=109  Identities=6%  Similarity=0.095  Sum_probs=65.4

Q ss_pred             ChhhHHHHHHHHHHHHHHHHhcCCeEEEEECC-------hHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhC
Q psy17626          9 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGS-------PISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAEN   81 (184)
Q Consensus         9 ~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~-------~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~   81 (184)
                      -..|..+++.|++...+.|++.|.....+.-+       -.+.|.+++++++++.|.+-+   |.+..-.+.+++++++.
T Consensus        40 HkqKl~l~~saMRhfa~~L~~~G~~V~Y~~~~~~~~~~s~~~~L~~~~~~~~~~~~~~~~---P~d~~l~~~l~~~~~~~  116 (224)
T PF04244_consen   40 HKQKLVLFFSAMRHFADELRAKGFRVHYIELDDPENTQSFEDALARALKQHGIDRLHVME---PGDYRLEQRLESLAQQL  116 (224)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHTT--EEEE-TT-TT--SSHHHHHHHHHHHH----EEEE-----S-HHHHHHHHH----S
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCCEEEEEeCCCccccccHHHHHHHHHHHcCCCEEEEEC---CCCHHHHHHHHhhhccc
Confidence            35678899999999999999999998887533       367899999999999998876   77778888899999999


Q ss_pred             CCeEEEecCc-eeecccccccccCCCCchhHHHHHHHhhh
Q psy17626         82 NITVKEFVSH-TLWDPEVVIQTNGNVPPLTYKMYLHTVSC  120 (184)
Q Consensus        82 gi~~~~~~~~-~L~~p~~i~~~~~~~~~~v~~~F~~~~~~  120 (184)
                      ||++..+.+. -|..+.++..=-++........|++...+
T Consensus       117 ~i~~~~~~~~~Fl~s~~~f~~~~~~~k~~~Me~FYR~mRk  156 (224)
T PF04244_consen  117 GIPLEVLEDPHFLTSREEFAEWFEGRKRLRMEYFYREMRK  156 (224)
T ss_dssp             SS-EEEE--TTSSS-HHHHHHHHTT-SS--HHHHHHHHHH
T ss_pred             CCceEEeCCCCccCCHHHHHHHHccCCceeHHHHHHHHHH
Confidence            9999888665 45555544332122233444667766554

; PDB: 3ZXS_A.

>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]

Probab=94.93  E-value=0.58  Score=39.01  Aligned_cols=107  Identities=9%  Similarity=0.141  Sum_probs=80.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHhcCCeEEEEECCh---HHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626         10 YNRFRFLLECLADLDRQLKSHGGQLFIVQGSP---ISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus        10 ~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~---~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..+.-++..+++.+.+.|+..|.......-++   ...|.+.++.+..++|+..+   |.+..-..++++.--..||++.
T Consensus        45 kqKl~lv~aAMR~Fad~LraeG~~V~Y~~~~~~~~~~~l~~~l~~~~~d~~~~~~---p~~~~l~~~m~~L~~~~g~~i~  121 (505)
T COG3046          45 KQKLVLVFAAMRHFADELRAEGLKVRYERADDNSFGGELRRALEAYPGDRVQVQE---PGDHRLEARMKSLSMALGIEIT  121 (505)
T ss_pred             hhhhHHHHHHHHHHHHHHhhCCceeEEEEcCCcccchHHHHHHHhcCCCeEEEec---CcchhHHHHHHhhhhhcCceeE
Confidence            34566889999999999999999876665444   56789999999999999987   4444555556655556799998


Q ss_pred             EecCc-eeecccccccccCCCCchhHHHHHHHhh
Q psy17626         87 EFVSH-TLWDPEVVIQTNGNVPPLTYKMYLHTVS  119 (184)
Q Consensus        87 ~~~~~-~L~~p~~i~~~~~~~~~~v~~~F~~~~~  119 (184)
                      ...+. .|.++.++..-.++..+-....|++...
T Consensus       122 ~~~~~~Fl~s~a~f~~w~~~~k~~lme~FYr~mR  155 (505)
T COG3046         122 EVENPHFLCSRAEFDAWAGDRKPLLMESFYRRMR  155 (505)
T ss_pred             EecCcceecCHHHhhhhhccCcchhhHHHHHHHH
Confidence            88665 8888888876555556666666766654

>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed

Probab=92.17  E-value=0.76  Score=37.85  Aligned_cols=50  Identities=12%  Similarity=0.125  Sum_probs=41.6

Q ss_pred             CChHHHHHHHHHHcCcceEEEeecccchhHH-HHHHHHHHHHhCCCeEEEe
Q psy17626         39 GSPISIFQKLKRELNFTKLCFEQDCEALWHK-RDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        39 g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~-rd~~v~~~l~~~gi~~~~~   88 (184)
                      |+|.++|.+.+++++++.|+...+|.|.... .-+-++..|.+.|+.+..-
T Consensus        99 G~pae~Iv~~Aee~~aDLIVm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (357)
T PRK12652         99 GDYAEVLIAYAEEHGIDRVVLDPEYNPGGTAPMLQPLERELARAGITYEEA  149 (357)
T ss_pred             CCHHHHHHHHHHHcCCCEEEECCCCCCCCCCcccchHHHHHHhcCCceecC
Confidence            8999999999999999999999999987533 3456677788888887654

>PRK09982 universal stress protein UspD; Provisional

Probab=91.72  E-value=3.3  Score=28.93  Aligned_cols=67  Identities=10%  Similarity=0.051  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHH-HHHHHHHHhCCCeEEE
Q psy17626         19 CLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRD-KKVKKWCAENNITVKE   87 (184)
Q Consensus        19 sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd-~~v~~~l~~~gi~~~~   87 (184)
                      .|.++.+.+...+....+..|+|.+.|.+.+++.+++-|++-..  .....+- -.-.+.++...+++..
T Consensus        69 ~l~~~~~~~~~~~~~~~v~~G~p~~~I~~~A~~~~aDLIVmG~~--~~~~~~~~~va~~V~~~s~~pVLv  136 (142)
T PRK09982         69 KLYKLTKNIQWPKTKLRIERGEMPETLLEIMQKEQCDLLVCGHH--HSFINRLMPAYRGMINKMSADLLI  136 (142)
T ss_pred             HHHHHHHhcCCCcceEEEEecCHHHHHHHHHHHcCCCEEEEeCC--hhHHHHHHHHHHHHHhcCCCCEEE
Confidence            34555554444456778889999999999999999999999754  2222221 2334455666777654

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=91.22  E-value=7  Score=31.72  Aligned_cols=161  Identities=15%  Similarity=0.084  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECCh----HHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGSP----ISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~~----~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      -|..+-+..+.+.+++.|-.+.+...+.    .....+.....+++.|+..- ..     .+....+.+.+.++++..++
T Consensus        71 ~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~-~~-----~~~~~~~~l~~~~~P~V~i~  144 (333)
T COG1609          71 PFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLG-ER-----PNDSLLELLAAAGIPVVVID  144 (333)
T ss_pred             chHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEec-CC-----CCHHHHHHHHhcCCCEEEEe
Confidence            5889999999999999999999886543    23455666778899988875 11     11233445566799988877


Q ss_pred             Ccee-ecccccccccCCCCchhHHHHHHH-hhhccccccCcchhHHHHHHHHHHHHHHHhCCCeE---EEEeCC-----h
Q psy17626         90 SHTL-WDPEVVIQTNGNVPPLTYKMYLHT-VSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQL---FIVQGS-----P  159 (184)
Q Consensus        90 ~~~L-~~p~~i~~~~~~~~~~v~~~F~~~-~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L---~v~~g~-----~  159 (184)
                      ...- .....|..++-...+..-..+... ..+...-. ++.......+.++-..+.|++.|++.   .+..|+     .
T Consensus       145 ~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~-~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~~~~~~~g  223 (333)
T COG1609         145 RSPPGLGVPSVGIDNFAGAYLATEHLIELGHRRIAFIG-GPLDSSASRERLEGYRAALREAGLPINPEWIVEGDFSEESG  223 (333)
T ss_pred             CCCccCCCCEEEEChHHHHHHHHHHHHHCCCceEEEEe-CCCccccHhHHHHHHHHHHHHCCCCCCcceEEecCCChHHH
Confidence            6433 112223332110011111111111 01111111 11133344666888889999999873   555433     2


Q ss_pred             hHHHHHHHHHcC--cCeEEEcccc
Q psy17626        160 ISIFQKLKRELN--FTKLCFEQDC  181 (184)
Q Consensus       160 ~~~l~~l~~~~~--~~~v~~n~~~  181 (184)
                      .+.+.++.....  .|+||+..|.
T Consensus       224 ~~~~~~ll~~~~~~ptAif~~nD~  247 (333)
T COG1609         224 YEAAERLLARGEPRPTAIFCANDL  247 (333)
T ss_pred             HHHHHHHHhcCCCCCcEEEEcCcH
Confidence            345556665443  8999987663

>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490

Probab=90.54  E-value=2.3  Score=31.42  Aligned_cols=68  Identities=19%  Similarity=0.117  Sum_probs=48.0

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecc------------cc--hhHHHHHHHHHHHHhCC
Q psy17626         17 LECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC------------EA--LWHKRDKKVKKWCAENN   82 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~------------~~--~~~~rd~~v~~~l~~~g   82 (184)
                      .....++-+.|++.|.++.|..+.+...+..+++..+++.++.++-.            ++  .....-..+++++++.|
T Consensus        89 ~~~~~~~l~~l~~~g~~v~ivS~s~~~~v~~~~~~lg~~~~~~~~l~~~~~g~~~g~~~~~~~~g~~K~~~l~~~~~~~~  168 (202)
T TIGR01490        89 YPEARDLIRWHKAEGHTIVLVSASLTILVKPLARILGIDNAIGTRLEESEDGIYTGNIDGNNCKGEGKVHALAELLAEEQ  168 (202)
T ss_pred             cHHHHHHHHHHHHCCCEEEEEeCCcHHHHHHHHHHcCCcceEecceEEcCCCEEeCCccCCCCCChHHHHHHHHHHHHcC
Confidence            34556666678888999999999999999999999999988766211            01  11222345777777777


Q ss_pred             Ce
Q psy17626         83 IT   84 (184)
Q Consensus        83 i~   84 (184)
                      +.
T Consensus       169 ~~  170 (202)
T TIGR01490       169 ID  170 (202)
T ss_pred             CC
Confidence            63

A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.

>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=89.32  E-value=8.6  Score=29.80  Aligned_cols=163  Identities=17%  Similarity=0.136  Sum_probs=86.1

Q ss_pred             CChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEE
Q psy17626          8 IGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKE   87 (184)
Q Consensus         8 ~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~   87 (184)
                      -|+.|.-|..+-+..+.+.+++.|-.+.+...+..+   ......+++.|+.... ...    +..++ .+.+.++++..
T Consensus        14 ~~~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~---~~l~~~~vdgiIi~~~-~~~----~~~~~-~l~~~~iPvV~   84 (269)
T cd06287          14 GGPSRLGFMMEVAAAAAESALERGLALCLVPPHEAD---SPLDALDIDGAILVEP-MAD----DPQVA-RLRQRGIPVVS   84 (269)
T ss_pred             CCcccCccHHHHHHHHHHHHHHCCCEEEEEeCCCch---hhhhccCcCeEEEecC-CCC----CHHHH-HHHHcCCCEEE
Confidence            367788899999999999999999998887554211   2445778998887531 111    12233 34567899888


Q ss_pred             ecCcee--ecccccccccCCCCchhHHHHHHH-hhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEE--eC--C--
Q psy17626         88 FVSHTL--WDPEVVIQTNGNVPPLTYKMYLHT-VSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIV--QG--S--  158 (184)
Q Consensus        88 ~~~~~L--~~p~~i~~~~~~~~~~v~~~F~~~-~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~--~g--~--  158 (184)
                      ++...-  .....+..++....+.....+... ..+..--. +........+......+.+++.|.+..+.  .+  +  
T Consensus        85 i~~~~~~~~~~~~V~~d~~~~~~~a~~~L~~~G~~~I~~i~-~~~~~~~~~~R~~gf~~a~~~~g~~~~~~~~~~~~~~~  163 (269)
T cd06287          85 IGRPPGDRTDVPYVDLQSAATARMLLEHLRAQGARQIALIV-GSARRNSYLEAEAAYRAFAAEHGMPPVVLRVDEAGGEE  163 (269)
T ss_pred             eCCCCCCCCCCCeEeeCcHHHHHHHHHHHHHcCCCcEEEEe-CCcccccHHHHHHHHHHHHHHcCCCcceeEecCCCChH
Confidence            765321  011122222110011111111111 11111111 11111223345667778888888754322  21  1  


Q ss_pred             -hhHHHHHHHHHc-CcCeEEEccc
Q psy17626        159 -PISIFQKLKREL-NFTKLCFEQD  180 (184)
Q Consensus       159 -~~~~l~~l~~~~-~~~~v~~n~~  180 (184)
                       ..+.+.++.++. ..++|++..|
T Consensus       164 ~~~~~~~~~l~~~~~~~ai~~~~d  187 (269)
T cd06287         164 AGYAACAQLLAQHPDLDALCVPVD  187 (269)
T ss_pred             HHHHHHHHHHhCCCCCCEEEEcCc
Confidence             124555665543 5899998755

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]

Probab=88.97  E-value=2.4  Score=32.23  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccc-----------h--hHHHHHHHHHHHHhCCCe
Q psy17626         20 LADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEA-----------L--WHKRDKKVKKWCAENNIT   84 (184)
Q Consensus        20 L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~-----------~--~~~rd~~v~~~l~~~gi~   84 (184)
                      ..+|-+.|++.|....|+.|.+......+++..+++.++.|.-...           .  ...-...+++++++.|+.
T Consensus        82 a~elv~~lk~~G~~v~iiSgg~~~lv~~ia~~lg~d~~~an~l~~~dG~ltG~v~g~~~~~~~K~~~l~~~~~~~g~~  159 (212)
T COG0560          82 AEELVAALKAAGAKVVIISGGFTFLVEPIAERLGIDYVVANELEIDDGKLTGRVVGPICDGEGKAKALRELAAELGIP  159 (212)
T ss_pred             HHHHHHHHHHCCCEEEEEcCChHHHHHHHHHHhCCchheeeEEEEeCCEEeceeeeeecCcchHHHHHHHHHHHcCCC
Confidence            6788999999999999999999999999999999998888753211           1  123456788888888887

>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators

Probab=88.94  E-value=9.8  Score=29.93  Aligned_cols=155  Identities=15%  Similarity=0.154  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEEC--ChHH-HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         13 FRFLLECLADLDRQLKSHGGQLFIVQG--SPIS-IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        13 ~~fl~~sL~~L~~~L~~~g~~L~v~~g--~~~~-~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      ..|..+-+..+.+.+++.|-.+.+...  ++.. ...+.+.+.+++.|+.. .....    +..+....+. |+++..++
T Consensus        13 npff~~ii~gIe~~a~~~Gy~l~l~~t~~~~~~e~~i~~l~~~~vDGiI~~-s~~~~----~~~l~~~~~~-~iPvV~~~   86 (279)
T PF00532_consen   13 NPFFAEIIRGIEQEAREHGYQLLLCNTGDDEEKEEYIELLLQRRVDGIILA-SSEND----DEELRRLIKS-GIPVVLID   86 (279)
T ss_dssp             SHHHHHHHHHHHHHHHHTTCEEEEEEETTTHHHHHHHHHHHHTTSSEEEEE-SSSCT----CHHHHHHHHT-TSEEEEES
T ss_pred             CcHHHHHHHHHHHHHHHcCCEEEEecCCCchHHHHHHHHHHhcCCCEEEEe-cccCC----hHHHHHHHHc-CCCEEEEE
Confidence            347888999999999999999887652  2221 23345567899999887 22222    3345555555 99998877


Q ss_pred             Cceeec--ccccccccCCCCchhHHHHHHHhhh---ccccc-----cCcchhHHHHHHHHHHHHHHHhCCCe---EEEEe
Q psy17626         90 SHTLWD--PEVVIQTNGNVPPLTYKMYLHTVSC---IGTMH-----IGYNRFRFLLECLADLDRQLKSHGGQ---LFIVQ  156 (184)
Q Consensus        90 ~~~L~~--p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~-----~~~~r~~fl~~~L~~L~~~L~~~g~~---L~v~~  156 (184)
                      ...--+  -..+..+       -+...+...+.   .+-.+     .++.......+.++-..+.|++.|++   ..+..
T Consensus        87 ~~~~~~~~~~~V~~D-------~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~  159 (279)
T PF00532_consen   87 RYIDNPEGVPSVYID-------NYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFE  159 (279)
T ss_dssp             S-SCTTCTSCEEEEE-------HHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEE
T ss_pred             eccCCcccCCEEEEc-------chHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccc
Confidence            642211  1112121       12222222211   12111     12233345667788889999999984   45555


Q ss_pred             CCh-----hHHHHHHHHHc-CcCeEEEccc
Q psy17626        157 GSP-----ISIFQKLKREL-NFTKLCFEQD  180 (184)
Q Consensus       157 g~~-----~~~l~~l~~~~-~~~~v~~n~~  180 (184)
                      ++.     .+.+.++.+.. .+++|++..|
T Consensus       160 ~~~~~~~g~~~~~~ll~~~p~idai~~~nd  189 (279)
T PF00532_consen  160 GDFDYESGYEAARELLESHPDIDAIFCAND  189 (279)
T ss_dssp             SSSSHHHHHHHHHHHHHTSTT-SEEEESSH
T ss_pred             cCCCHHHHHHHHHHHHhhCCCCEEEEEeCH
Confidence            543     24566776666 6779998765

The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....

>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional

Probab=88.90  E-value=1.9  Score=35.55  Aligned_cols=61  Identities=15%  Similarity=0.118  Sum_probs=44.4

Q ss_pred             HHHhcCC--eEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626         26 QLKSHGG--QLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus        26 ~L~~~g~--~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      +|+++|+  ..+++.+.|.....+..-+.++.+|+.--|..|..+.--.++.+.|++.||+|.
T Consensus        37 ~l~~lgi~g~~i~~s~~p~~~cad~ii~~gi~rVVi~~D~d~~G~~~~~~~~~~L~~aGi~V~   99 (360)
T PRK14719         37 SLKNLKINANFITVSNTPVFQIADDLIAENISEVILLTDFDRAGRVYAKNIMEEFQSRGIKVN   99 (360)
T ss_pred             HHHHcCCCCcEEEEeCCchHHHHHHHHHcCCCEEEEEECCCCCCCccchHHHHHHHHCCCEEE
Confidence            6778887  466677888776666666678888888778777544444566778888898874

>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=87.63  E-value=5.2  Score=26.19  Aligned_cols=68  Identities=19%  Similarity=0.097  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCCeEEEE---ECChHHH--HHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEecCc
Q psy17626         20 LADLDRQLKSHGGQLFIV---QGSPISI--FQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSH   91 (184)
Q Consensus        20 L~~L~~~L~~~g~~L~v~---~g~~~~~--l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~~~   91 (184)
                      ...+.+.+++.|..+.+.   .|.....  |+..+++  ++.|++--++......+  .+++.+++.|+++....+.
T Consensus        12 ~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~i~~--aD~VIv~t~~vsH~~~~--~vk~~akk~~ip~~~~~~~   84 (97)
T PF10087_consen   12 ERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSKIKK--ADLVIVFTDYVSHNAMW--KVKKAAKKYGIPIIYSRSR   84 (97)
T ss_pred             HHHHHHHHHHcCCEEEEEecCCCCccchhHHHHhcCC--CCEEEEEeCCcChHHHH--HHHHHHHHcCCcEEEECCC
Confidence            456778888899999888   3333333  7776654  77788888876555444  5677888899998876544

>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]

Probab=86.77  E-value=2.7  Score=37.85  Aligned_cols=63  Identities=14%  Similarity=0.109  Sum_probs=45.8

Q ss_pred             HHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         22 DLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        22 ~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      +.-+.|+++|++++++.||....-.+++++.+|++++.+-  .|..+..  .|++ +++.|-.+-.+.
T Consensus       544 ~aI~~L~~~Gi~~~mLTGDn~~~A~~iA~~lGId~v~Ael--lPedK~~--~V~~-l~~~g~~VamVG  606 (713)
T COG2217         544 EAIAALKALGIKVVMLTGDNRRTAEAIAKELGIDEVRAEL--LPEDKAE--IVRE-LQAEGRKVAMVG  606 (713)
T ss_pred             HHHHHHHHCCCeEEEEcCCCHHHHHHHHHHcChHhheccC--CcHHHHH--HHHH-HHhcCCEEEEEe
Confidence            4446678899999999999999999999999999999864  4554443  3333 345554444443

>PRK15005 universal stress protein F; Provisional

Probab=86.21  E-value=2.7  Score=29.10  Aligned_cols=45  Identities=13%  Similarity=0.247  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhcC--CeEEEEECChHHHHHHHHHHcCcceEEEeec
Q psy17626         18 ECLADLDRQLKSHG--GQLFIVQGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        18 ~sL~~L~~~L~~~g--~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      +.|.++.+.+...|  ...++..|+|.+.|.+.+++.+++-|+.-..
T Consensus        70 ~~l~~~~~~~~~~~~~~~~~v~~G~p~~~I~~~a~~~~~DLIV~Gs~  116 (144)
T PRK15005         70 SQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPADMIIIASH  116 (144)
T ss_pred             HHHHHHHHHhCCCCCceEEEEeCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            34444444444334  3578889999999999999999999998754

>PRK15456 universal stress protein UspG; Provisional

Probab=86.11  E-value=2.3  Score=29.54  Aligned_cols=45  Identities=16%  Similarity=0.137  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHhcCC--eEEEEECChHHHHHHHHHHcCcceEEEeec
Q psy17626         18 ECLADLDRQLKSHGG--QLFIVQGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~--~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      +.|.++.+.+...|.  ..++..|+|.+.|.+++++++++-|++-..
T Consensus        68 ~~l~~~~~~~~~~~~~v~~~v~~G~~~~~I~~~a~~~~~DLIVmG~~  114 (142)
T PRK15456         68 ERLQTMVSHFTIDPSRIKQHVRFGSVRDEVNELAEELGADVVVIGSR  114 (142)
T ss_pred             HHHHHHHHHhCCCCcceEEEEcCCChHHHHHHHHhhcCCCEEEEcCC
Confidence            345555555543333  567788999999999999999999988653

>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II

Probab=85.76  E-value=10  Score=26.87  Aligned_cols=71  Identities=10%  Similarity=0.011  Sum_probs=50.7

Q ss_pred             HhcCCeEEEEECChHHHHHHHHHHc--CcceEEEeec-ccchhHHHHHHHHHHHHhCCCeEEEecCceeecccccccc
Q psy17626         28 KSHGGQLFIVQGSPISIFQKLKREL--NFTKLCFEQD-CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQT  102 (184)
Q Consensus        28 ~~~g~~L~v~~g~~~~~l~~l~~~~--~~~~v~~~~~-~~~~~~~rd~~v~~~l~~~gi~~~~~~~~~L~~p~~i~~~  102 (184)
                      +++|..+.+++.+.+..|-+...+.  +++.|+.|.. |+.+..    .++.++...++++.+++-...+..+.++..
T Consensus        38 ~~~g~~v~~~QSN~EGelId~i~~a~~~~dgiIINpga~THtSi----Al~DAl~~~~~P~vEVHiSNi~aRE~fR~~  111 (141)
T TIGR01088        38 AQLNVELEFFQSNSEGQLIDKIHEAEGQYDGIIINPGALTHTSV----ALRDALAAVSLPVVEVHLSNVHAREEFRHH  111 (141)
T ss_pred             HHcCCEEEEEeeCcHHHHHHHHHhccccCCEEEEcChHHhhhHH----HHHHHHHcCCCCEEEEEcCCcccccccccc
Confidence            3458999999998887777766654  4678888853 333333    445556677899999988888888776553

This model specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093.

>PRK13015 3-dehydroquinate dehydratase; Reviewed

Probab=85.20  E-value=11  Score=26.84  Aligned_cols=71  Identities=10%  Similarity=0.030  Sum_probs=49.9

Q ss_pred             HhcCCeEEEEECChHHHHHHHHHHc--CcceEEEeec-ccchhHHHHHHHHHHHHhCCCeEEEecCceeecccccccc
Q psy17626         28 KSHGGQLFIVQGSPISIFQKLKREL--NFTKLCFEQD-CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQT  102 (184)
Q Consensus        28 ~~~g~~L~v~~g~~~~~l~~l~~~~--~~~~v~~~~~-~~~~~~~rd~~v~~~l~~~gi~~~~~~~~~L~~p~~i~~~  102 (184)
                      +++|..+.+++.+.+..|-+...+.  +++.|..|.. |+.+..    .++.++...++++.+++-...+..+.++..
T Consensus        40 ~~~g~~~~~~QSN~EGelId~i~~a~~~~dgiIINpga~THtSi----Al~DAl~~~~~P~VEVHiSNi~aRE~fR~~  113 (146)
T PRK13015         40 EALGLEVEFRQSNHEGELIDWIHEARGDVAGIVINPGAYTHTSV----AIRDALAALELPVIEVHISNVHAREAFRHH  113 (146)
T ss_pred             HHcCCEEEEEeeCcHHHHHHHHHHhhhcCCEEEEcchHHhhhHH----HHHHHHHcCCCCEEEEEcCCcccccccccc
Confidence            3458999999988887766666553  5678998853 333333    445556677899999988888877776553

>TIGR00289 conserved hypothetical protein TIGR00289

Probab=85.12  E-value=7.2  Score=29.95  Aligned_cols=66  Identities=20%  Similarity=0.199  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHhcCCeEEEEE--CC---hHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626         18 ECLADLDRQLKSHGGQLFIVQ--GS---PISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~L~v~~--g~---~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..+..++.+-+.+|+||+...  |+   -.+.+...+++.+++.|++-.-...+-+.|   +++.|++.|++..
T Consensus        45 ~~~~~~~~qA~algiPl~~~~~~~~~e~~~~~l~~~l~~~gv~~vv~GdI~s~~qr~~---~e~vc~~~gl~~~  115 (222)
T TIGR00289        45 PNLHLTDLVAEAVGIPLIKLYTSGEEEKEVEDLAGQLGELDVEALCIGAIESNYQKSR---IDKVCRELGLKSI  115 (222)
T ss_pred             CCHHHHHHHHHHcCCCeEEEEcCCchhHHHHHHHHHHHHcCCCEEEECccccHHHHHH---HHHHHHHcCCEEe
Confidence            356677777788999998775  32   334455556677999999986555454444   4566677788765

Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.

>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3

Probab=83.44  E-value=15  Score=26.81  Aligned_cols=134  Identities=13%  Similarity=0.143  Sum_probs=78.3

Q ss_pred             HHHHHcCcceEEEeecccchhH---HHHHHHHHHHHhCCCeEEEecCceeecccccccccCCCC------chhHHHHHHH
Q psy17626         47 KLKRELNFTKLCFEQDCEALWH---KRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVP------PLTYKMYLHT  117 (184)
Q Consensus        47 ~l~~~~~~~~v~~~~~~~~~~~---~rd~~v~~~l~~~gi~~~~~~~~~L~~p~~i~~~~~~~~------~~v~~~F~~~  117 (184)
                      +.+++.|.+.|=+.-.......   ..-+.+++.+++.|+.+...+............  +.+.      -..+......
T Consensus         2 ~~~~~~G~~~vE~~~~~~~~~~~~~~~~~~~~~~~~~~gl~i~~~~~~~~~~~~~~~~--~~~~~~r~~~~~~~~~~i~~   79 (213)
T PF01261_consen    2 EAAAEAGFDGVELRFDDGQPWDEKDDEAEELRRLLEDYGLKIASLHPPTNFWSPDEEN--GSANDEREEALEYLKKAIDL   79 (213)
T ss_dssp             HHHHHTTHSEEEEEHHHHSHHTHHHHHHHHHHHHHHHTTCEEEEEEEEESSSCTGTTS--TTSSSHHHHHHHHHHHHHHH
T ss_pred             hHHHHcCCCEEEEecCCCcccccchHHHHHHHHHHHHcCCeEEEEecccccccccccc--cCcchhhHHHHHHHHHHHHH
Confidence            4567777887766544332222   344688889999999977665444333322211  1011      1122222223


Q ss_pred             hhhccccc----cC----------cchhHHHHHHHHHHHHHHHhCCCeEEEEe-----CChh---HHHHHHHHHcCcCeE
Q psy17626        118 VSCIGTMH----IG----------YNRFRFLLECLADLDRQLKSHGGQLFIVQ-----GSPI---SIFQKLKRELNFTKL  175 (184)
Q Consensus       118 ~~~~~~~~----~~----------~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-----g~~~---~~l~~l~~~~~~~~v  175 (184)
                      ...++...    .+          ......+.+.|..|...+++.|+.+.+-.     ....   +.+.+++++.+-+.+
T Consensus        80 a~~lg~~~i~~~~g~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~~gv~i~lE~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (213)
T PF01261_consen   80 AKRLGAKYIVVHSGRYPSGPEDDTEENWERLAENLRELAEIAEEYGVRIALENHPGPFSETPFSVEEIYRLLEEVDSPNV  159 (213)
T ss_dssp             HHHHTBSEEEEECTTESSSTTSSHHHHHHHHHHHHHHHHHHHHHHTSEEEEE-SSSSSSSEESSHHHHHHHHHHHTTTTE
T ss_pred             HHHhCCCceeecCcccccccCCCHHHHHHHHHHHHHHHHhhhhhhcceEEEecccCccccchhhHHHHHHHHhhcCCCcc
Confidence            33333211    11          13456788899999999999999888754     1222   778899999998888


Q ss_pred             EEccccc
Q psy17626        176 CFEQDCE  182 (184)
Q Consensus       176 ~~n~~~~  182 (184)
                      ..+-|..
T Consensus       160 ~i~~D~~  166 (213)
T PF01261_consen  160 GICFDTG  166 (213)
T ss_dssp             EEEEEHH
T ss_pred             eEEEehH
Confidence            7776653

1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....

>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain

Probab=83.09  E-value=7.9  Score=29.76  Aligned_cols=65  Identities=17%  Similarity=0.201  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHhcCCeEEEEE--C---ChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626         19 CLADLDRQLKSHGGQLFIVQ--G---SPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus        19 sL~~L~~~L~~~g~~L~v~~--g---~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      .+.-++.+-+.+|+||+...  |   +-.+.+.+++++.+++.|++-.-...+-+.|   +++.|++.|++..
T Consensus        46 ~~~~~~~qA~algipl~~~~~~~~~e~~~e~l~~~l~~~gv~~vv~GdI~s~~qr~~---~e~v~~~lgl~~~  115 (223)
T TIGR00290        46 NAHLTDLQAESIGIPLIKLYTEGTEEDEVEELKGILHTLDVEAVVFGAIYSEYQKTR---IERVCRELGLKSF  115 (223)
T ss_pred             CHHHHHHHHHHcCCCeEEeecCCCccHHHHHHHHHHHHcCCCEEEECCcccHHHHHH---HHHHHHhcCCEEe
Confidence            44555566677899997643  2   2445566667777999999986555444444   4556677788755

Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.

>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase)

Probab=82.49  E-value=4  Score=30.14  Aligned_cols=40  Identities=18%  Similarity=0.194  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcce
Q psy17626         17 LECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTK   56 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~   56 (184)
                      .....++=++|++.|+++.++.|+.......+++..++..
T Consensus       129 ~~~~~~~l~~L~~~Gi~~~i~TGD~~~~a~~~~~~lgi~~  168 (215)
T PF00702_consen  129 RPGAKEALQELKEAGIKVAILTGDNESTASAIAKQLGIFD  168 (215)
T ss_dssp             HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTSCS
T ss_pred             hhhhhhhhhhhhccCcceeeeecccccccccccccccccc
Confidence            3456677778888999999999999999999999999955

This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....

>TIGR01488 HAD-SF-IB Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like

Probab=82.48  E-value=2.2  Score=30.68  Aligned_cols=42  Identities=19%  Similarity=0.168  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEe
Q psy17626         19 CLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFE   60 (184)
Q Consensus        19 sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~   60 (184)
                      ...++-+.|++.|.++.|+.|.....+..+++.++++.++.|
T Consensus        77 g~~~~l~~l~~~g~~~~ivS~~~~~~i~~~~~~~g~~~~~~~  118 (177)
T TIGR01488        77 GARELISWLKERGIDTVIVSGGFDFFVEPVAEKLGIDDVFAN  118 (177)
T ss_pred             CHHHHHHHHHHCCCEEEEECCCcHHHHHHHHHHcCCchheee
Confidence            344444555556666666666666666666666666555544

Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences.

>KOG1615|consensus

Probab=81.97  E-value=2.6  Score=31.77  Aligned_cols=43  Identities=16%  Similarity=0.416  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcce--EEEee
Q psy17626         19 CLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTK--LCFEQ   61 (184)
Q Consensus        19 sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~--v~~~~   61 (184)
                      .+.+|-+.|+++|..++++.|.-...+.-++.+.++..  +|+|.
T Consensus        92 Gi~eLv~~L~~~~~~v~liSGGF~~~i~~Va~~Lgi~~~n~yAN~  136 (227)
T KOG1615|consen   92 GIRELVSRLHARGTQVYLISGGFRQLIEPVAEQLGIPKSNIYANE  136 (227)
T ss_pred             CHHHHHHHHHHcCCeEEEEcCChHHHHHHHHHHhCCcHhhhhhhe
Confidence            57789999999999999999999888889999999887  88875

>PRK11175 universal stress protein UspE; Provisional

Probab=81.91  E-value=23  Score=27.87  Aligned_cols=160  Identities=6%  Similarity=-0.028  Sum_probs=85.0

Q ss_pred             HHHHHHHHHhcCCeEE--EE-ECChHHHHHHHHHHcCcceEEEeecccch-hHHH-HHHHHHHHHhCCCeEEEecCceee
Q psy17626         20 LADLDRQLKSHGGQLF--IV-QGSPISIFQKLKRELNFTKLCFEQDCEAL-WHKR-DKKVKKWCAENNITVKEFVSHTLW   94 (184)
Q Consensus        20 L~~L~~~L~~~g~~L~--v~-~g~~~~~l~~l~~~~~~~~v~~~~~~~~~-~~~r-d~~v~~~l~~~gi~~~~~~~~~L~   94 (184)
                      |.+..+.++..|++..  +. .|++.+.|.+.+++.+++-|+.-..-... .... -....+.+....+++..+.....-
T Consensus        71 l~~~~~~~~~~~~~~~~~v~~~g~~~~~i~~~a~~~~~DLiV~G~~~~~~~~~~~~gs~~~~l~~~~~~pvlvv~~~~~~  150 (305)
T PRK11175         71 IREQAKPYLDAGIPIEIKVVWHNRPFEAIIQEVIAGGHDLVVKMTHQHDKLESVIFTPTDWHLLRKCPCPVLMVKDQDWP  150 (305)
T ss_pred             HHHHHHHHhhcCCceEEEEecCCCcHHHHHHHHHhcCCCEEEEeCCCCcHHHhhccChhHHHHHhcCCCCEEEecccccC
Confidence            4444445555676543  34 58999999999999999999997542221 1111 112244566678888777654332


Q ss_pred             cccccccccCCCCc---------hhHHHHHHHhhhc-cc-----cccC--c---------chh-HH---HH-HHHHHHHH
Q psy17626         95 DPEVVIQTNGNVPP---------LTYKMYLHTVSCI-GT-----MHIG--Y---------NRF-RF---LL-ECLADLDR  143 (184)
Q Consensus        95 ~p~~i~~~~~~~~~---------~v~~~F~~~~~~~-~~-----~~~~--~---------~r~-~f---l~-~~L~~L~~  143 (184)
                      ++..|.-.-+++..         .....-....... +.     +-..  +         ... .+   +. +....+++
T Consensus       151 ~~~~Ilva~D~s~~~~~~~~~~~~al~~a~~la~~~~~a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  230 (305)
T PRK11175        151 EGGKILVAVNVASEEPYHDALNEKLVEEAIDLAEQLNHAEVHLVNAYPVTPINIAIELPEFDPSVYNDAIRGQHLLAMKA  230 (305)
T ss_pred             CCCeEEEEeCCCCCccchhHHHHHHHHHHHHHHhhCcCCceEEEEEecCcchhccccccccchhhHHHHHHHHHHHHHHH
Confidence            34444432111111         1111111111111 10     0000  0         000 01   11 12333444


Q ss_pred             HHHhCCCe---EEEEeCChhHHHHHHHHHcCcCeEEEcc
Q psy17626        144 QLKSHGGQ---LFIVQGSPISIFQKLKRELNFTKLCFEQ  179 (184)
Q Consensus       144 ~L~~~g~~---L~v~~g~~~~~l~~l~~~~~~~~v~~n~  179 (184)
                      -+++.|++   ..+..|++.+.+.+.+++.+++-|+...
T Consensus       231 ~~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIVmG~  269 (305)
T PRK11175        231 LRQKFGIDEEQTHVEEGLPEEVIPDLAEHLDAELVILGT  269 (305)
T ss_pred             HHHHhCCChhheeeccCCHHHHHHHHHHHhCCCEEEECC
Confidence            44455654   5667899999999999999999988653

>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs

Probab=81.54  E-value=22  Score=27.30  Aligned_cols=158  Identities=9%  Similarity=-0.034  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECCh----HHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGSP----ISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~~----~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .|..+-+..+.+.++++|..+.+...+.    .+.+..+....+++.|.+... .+.    + ...+.+.+.|+++..++
T Consensus        12 ~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~-~~~----~-~~~~~l~~~~iPvv~~~   85 (269)
T cd06297          12 EFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASY-DLT----E-RLAERRLPTERPVVLVD   85 (269)
T ss_pred             hhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecC-ccC----h-HHHHHHhhcCCCEEEEc
Confidence            4777888899999999999998876532    233444556678999988742 111    1 23344567799998886


Q ss_pred             CceeecccccccccCCCCchhHHHHHHHhhhccccc--cCcchhH------HHHHHHHHHHHHHHhCCCeEE---EEeCC
Q psy17626         90 SHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMH--IGYNRFR------FLLECLADLDRQLKSHGGQLF---IVQGS  158 (184)
Q Consensus        90 ~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~~~--~~~~r~~------fl~~~L~~L~~~L~~~g~~L~---v~~g~  158 (184)
                      ... -+...+..++   .-..+..-...........  .+.....      .-.+.++...+.+++.|+++.   +..++
T Consensus        86 ~~~-~~~~~v~~d~---~~~g~~a~~~L~~~~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~~~~~~~~~  161 (269)
T cd06297          86 AEN-PRFDSFYLDN---RLGGRLAGAYLADFPGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFSPDLLAITD  161 (269)
T ss_pred             cCC-CCCCEEEECc---HHHHHHHHHHHHHhCCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCChhhEEeCC
Confidence            531 0111121111   0011111111111111110  0111111      334567778888888887542   33332


Q ss_pred             -----hhHHHHHHHHHc-CcCeEEEcccc
Q psy17626        159 -----PISIFQKLKREL-NFTKLCFEQDC  181 (184)
Q Consensus       159 -----~~~~l~~l~~~~-~~~~v~~n~~~  181 (184)
                           ..+.+.++.+.. .++.|+++.|.
T Consensus       162 ~~~~~~~~~~~~~l~~~~~~~ai~~~~d~  190 (269)
T cd06297         162 HSEEGGRLAMRHLLEKASPPLAVFASADQ  190 (269)
T ss_pred             CChhhHHHHHHHHHcCCCCCcEEEEcCcH
Confidence                 235666776543 58999988763

Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.

>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5

Probab=81.34  E-value=11  Score=28.95  Aligned_cols=76  Identities=18%  Similarity=0.232  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHhcCCeEEEEE----C------ChHHHHHHHHHHcCcceEEEe-----ecccchh-HHHHHHHHHHHHhC
Q psy17626         18 ECLADLDRQLKSHGGQLFIVQ----G------SPISIFQKLKRELNFTKLCFE-----QDCEALW-HKRDKKVKKWCAEN   81 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~L~v~~----g------~~~~~l~~l~~~~~~~~v~~~-----~~~~~~~-~~rd~~v~~~l~~~   81 (184)
                      +.|.++-+.+++.|+.|+++=    |      +-...|.+++++.++..||.|     +|..|.. ..--+.+.+.+++.
T Consensus        14 ~~l~~~~~~~k~~~~~lHl~GLlSdGGVHSh~~Hl~al~~~a~~~gv~~V~vH~f~DGRDt~P~S~~~yl~~l~~~l~~~   93 (223)
T PF06415_consen   14 PVLLEAIEHAKKNGGRLHLMGLLSDGGVHSHIDHLFALIKLAKKQGVKKVYVHAFTDGRDTPPKSALKYLEELEEKLAEI   93 (223)
T ss_dssp             HHHHHHHHHHCCTT--EEEEEEESS-SSS--HHHHHHHHHHHHHTT-SEEEEEEEE-SSSS-TTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEEEEecCCCccccHHHHHHHHHHHHHcCCCEEEEEEecCCCCCCcchHHHHHHHHHHHHHhh
Confidence            567788888888899999871    2      345678888899999988877     5566663 34456778888776


Q ss_pred             CC-eEEEecCcee
Q psy17626         82 NI-TVKEFVSHTL   93 (184)
Q Consensus        82 gi-~~~~~~~~~L   93 (184)
                      |+ ++-++.++..
T Consensus        94 ~~g~IAsv~GRyy  106 (223)
T PF06415_consen   94 GIGRIASVSGRYY  106 (223)
T ss_dssp             TCTEEEEEEECCC
T ss_pred             CCceEEEEeceee
Confidence            55 7776666544

4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.

>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family

Probab=81.01  E-value=9.1  Score=25.64  Aligned_cols=43  Identities=19%  Similarity=0.268  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhcCCeEEEE-ECChHHHHHHHHHHcCcceEEEeec
Q psy17626         20 LADLDRQLKSHGGQLFIV-QGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        20 L~~L~~~L~~~g~~L~v~-~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      |..+.+..++.+.+..++ .|++.+.|.+.+++++++.|+.-..
T Consensus        51 l~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~dllviG~~   94 (124)
T cd01987          51 LAEALRLAEELGAEVVTLPGDDVAEAIVEFAREHNVTQIVVGKS   94 (124)
T ss_pred             HHHHHHHHHHcCCEEEEEeCCcHHHHHHHHHHHcCCCEEEeCCC
Confidence            444555555667665443 4578888888888888888887654

The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.

>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]

Probab=80.44  E-value=15  Score=31.11  Aligned_cols=69  Identities=20%  Similarity=0.265  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEEC--ChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         16 LLECLADLDRQLKSHGGQLFIVQG--SPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        16 l~~sL~~L~~~L~~~g~~L~v~~g--~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      |-+-|..+.+++.++|+..++-..  ++-+.+.+++.+.+++.|+.++....+|..    +.+.|++.|+++...
T Consensus        63 Ld~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv~~k~~k~vVKsKSmvseEIg----ln~~Le~~G~ev~ET  133 (459)
T COG1139          63 LDEYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIVGEKNGKKVVKSKSMVSEEIG----LNHYLEEKGIEVWET  133 (459)
T ss_pred             HHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHHHHhhccCcEEEEecchhHHHhh----hHHHHHHcCCeEEEc
Confidence            334456677788899999998864  566789999999999999999987766664    456677889987654

>PRK09484 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; Provisional

Probab=80.29  E-value=6.9  Score=28.78  Aligned_cols=51  Identities=16%  Similarity=0.156  Sum_probs=39.2

Q ss_pred             HhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCe
Q psy17626         28 KSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNIT   84 (184)
Q Consensus        28 ~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~   84 (184)
                      ++.|+++.|..|.+...+..++++.+++.+|...+  +    .-..+.+++++.|+.
T Consensus        61 ~~~Gi~v~I~T~~~~~~v~~~l~~lgl~~~f~g~~--~----k~~~l~~~~~~~gl~  111 (183)
T PRK09484         61 LTSGIEVAIITGRKSKLVEDRMTTLGITHLYQGQS--N----KLIAFSDLLEKLAIA  111 (183)
T ss_pred             HHCCCEEEEEeCCCcHHHHHHHHHcCCceeecCCC--c----HHHHHHHHHHHhCCC
Confidence            45799999999999999999999999987765321  1    125777888887873

>PF12710 HAD: haloacid dehalogenase-like hydrolase; PDB: 3P96_A 3N28_A 3FVV_A 1RKU_A 1RKV_A 1Y8A_A 2FEA_B 3KD3_B

Probab=80.28  E-value=5.8  Score=28.75  Aligned_cols=41  Identities=29%  Similarity=0.435  Sum_probs=35.5

Q ss_pred             HHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcce--EEEeec
Q psy17626         22 DLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTK--LCFEQD   62 (184)
Q Consensus        22 ~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~--v~~~~~   62 (184)
                      ++=+.|++.|.+.+|+.|++...+..+++..++..  |+.++.
T Consensus        96 e~i~~~~~~~~~v~IvS~~~~~~i~~~~~~~~i~~~~v~~~~~  138 (192)
T PF12710_consen   96 ELIRELKDNGIKVVIVSGSPDEIIEPIAERLGIDDDNVIGNEL  138 (192)
T ss_dssp             HHHHHHHHTTSEEEEEEEEEHHHHHHHHHHTTSSEGGEEEEEE
T ss_pred             HHHHHHHHCCCEEEEECCCcHHHHHHHHHHcCCCceEEEEEee
Confidence            55566778899999999999999999999999987  888876

>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A

Probab=80.08  E-value=14  Score=25.84  Aligned_cols=63  Identities=16%  Similarity=0.205  Sum_probs=38.6

Q ss_pred             HHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcc----eEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626         20 LADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFT----KLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus        20 L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~----~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +.++=+.|++.|.++.++.+.+...+...++..++.    .|+...+++..--. -...+..+++.|+
T Consensus        82 ~~~~L~~l~~~~~~~~i~Sn~~~~~~~~~l~~~~~~~~f~~i~~~~~~~~~Kp~-~~~~~~~~~~~~~  148 (176)
T PF13419_consen   82 VRELLERLKAKGIPLVIVSNGSRERIERVLERLGLDDYFDEIISSDDVGSRKPD-PDAYRRALEKLGI  148 (176)
T ss_dssp             HHHHHHHHHHTTSEEEEEESSEHHHHHHHHHHTTHGGGCSEEEEGGGSSSSTTS-HHHHHHHHHHHTS
T ss_pred             hhhhhhhcccccceeEEeecCCcccccccccccccccccccccccchhhhhhhH-HHHHHHHHHHcCC
Confidence            445556667678888888888878777777777644    67766665532111 1234444444444

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
4gu5_A	539	Structure Of Full-Length Drosophila Cryptochrome Le		7e-34
4gu5_A	539	Structure Of Full-Length Drosophila Cryptochrome Le		4e-11
3fy4_A	537	(6-4) Photolyase Crystal Structure Length = 537		3e-20
3fy4_A	537	(6-4) Photolyase Crystal Structure Length = 537		7e-09
3cvx_A	543	Drosophila Melanogaster (6-4) Photolyase H369m Muta		2e-17
3cvx_A	543	Drosophila Melanogaster (6-4) Photolyase H369m Muta		1e-09
3cvw_A	543	Drosophila Melanogaster (6-4) Photolyase H365n Muta		2e-17
3cvw_A	543	Drosophila Melanogaster (6-4) Photolyase H365n Muta		1e-09
3cvu_A	543	Drosophila Melanogaster (6-4) Photolyase Bound To D		2e-17
3cvu_A	543	Drosophila Melanogaster (6-4) Photolyase Bound To D		1e-09
1owl_A	484	Structure Of Apophotolyase From Anacystis Nidulans		3e-05
1tez_A	474	Complex Between Dna And The Dna Photolyase From Ana		3e-05

>pdb|4GU5|A Chain A, Structure Of Full-Length Drosophila Cryptochrome Length = 539

Iteration: 1
 Score =  139 bits (351), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 61/122 (50%), Positives = 88/122 (72%), Gaps = 3/122 (2%)
Query: 4   GTMHIGYNRFRFLLECLADLDRQLKSHG---GQLFIVQGSPISIFQKLKRELNFTKLCFE 60
           GT ++GYNR RFLL+ L D+D QL++     G+L + +G P  IF++L  ++   ++C E
Sbjct: 48  GTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIE 107
Query: 61  QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC 120
           QDCE +W++RD+ ++  C E NI   E VSHTLWDP++VI+TNG +PPLTY+M+LHTV  
Sbjct: 108 QDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQI 167
Query: 121 IG 122
           IG
Sbjct: 168 IG 169

>pdb|4GU5|A Chain A, Structure Of Full-Length Drosophila Cryptochrome Length = 539

Iteration: 1
 Score = 64.3 bits (155), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 43/64 (67%), Gaps = 3/64 (4%)
Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHG---GQLFIVQGSPISIFQKLKRELNFTKLCFE 178
           GT ++GYNR RFLL+ L D+D QL++     G+L + +G P  IF++L  ++   ++C E
Sbjct: 48  GTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIE 107
Query: 179 QDCE 182
           QDCE
Sbjct: 108 QDCE 111

>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure Length = 537

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 45/116 (38%), Positives = 65/116 (56%)
Query: 3   PGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQD 62
           PG+   G NR RFLLE L DLD  LK  G +L + +G P  +  +  +E    +LCFE D
Sbjct: 53  PGSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYD 112
Query: 63  CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
            +  +   D KVK + +   + V   VSHTL++P  +I+ NG  PPL+Y+ +L   
Sbjct: 113 TDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVA 168

>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure Length = 537

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 35/63 (55%)
Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 181
           G+   G NR RFLLE L DLD  LK  G +L + +G P  +  +  +E    +LCFE D 
Sbjct: 54  GSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYDT 113
Query: 182 EAY 184
           + Y
Sbjct: 114 DPY 116

>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543

Iteration: 1
 Score = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 63/113 (55%)
Query: 6   MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEA 65
           M +G NR+RFL + L DLD QL+    +LF+V+G P  +F ++ +      L FE D E 
Sbjct: 77  MQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEP 136
Query: 66  LWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
               RD  V+K      + V+   SHT+++PE+VI  N    P+TY+ +L  V
Sbjct: 137 YSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIV 189

>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 100 IQTNGNVPPLTY---KMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ 156
           I T  N  P  Y    +++     +  M +G NR+RFL + L DLD QL+    +LF+V+
Sbjct: 50  IFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVR 109
Query: 157 GSPISIFQKLKRELNFTKLCFEQDCEAY 184
           G P  +F ++ +      L FE D E Y
Sbjct: 110 GKPAEVFPRIFKSWRVEMLTFETDIEPY 137

>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant Bound To Ds Dna With A T-T (6-4) Photolesion And Cofactor F0 Length = 543

Iteration: 1
 Score = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 63/113 (55%)
Query: 6   MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEA 65
           M +G NR+RFL + L DLD QL+    +LF+V+G P  +F ++ +      L FE D E 
Sbjct: 77  MQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEP 136
Query: 66  LWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
               RD  V+K      + V+   SHT+++PE+VI  N    P+TY+ +L  V
Sbjct: 137 YSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIV 189

>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant Bound To Ds Dna With A T-T (6-4) Photolesion And Cofactor F0 Length = 543

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 100 IQTNGNVPPLTY---KMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ 156
           I T  N  P  Y    +++     +  M +G NR+RFL + L DLD QL+    +LF+V+
Sbjct: 50  IFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVR 109
Query: 157 GSPISIFQKLKRELNFTKLCFEQDCEAY 184
           G P  +F ++ +      L FE D E Y
Sbjct: 110 GKPAEVFPRIFKSWRVEMLTFETDIEPY 137

>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543

Iteration: 1
 Score = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 63/113 (55%)
Query: 6   MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEA 65
           M +G NR+RFL + L DLD QL+    +LF+V+G P  +F ++ +      L FE D E 
Sbjct: 77  MQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEP 136
Query: 66  LWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
               RD  V+K      + V+   SHT+++PE+VI  N    P+TY+ +L  V
Sbjct: 137 YSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIV 189

>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 100 IQTNGNVPPLTY---KMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ 156
           I T  N  P  Y    +++     +  M +G NR+RFL + L DLD QL+    +LF+V+
Sbjct: 50  IFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVR 109
Query: 157 GSPISIFQKLKRELNFTKLCFEQDCEAY 184
           G P  +F ++ +      L FE D E Y
Sbjct: 110 GKPAEVFPRIFKSWRVEMLTFETDIEPY 137

>pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans Length = 484

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/110 (22%), Positives = 48/110 (43%), Gaps = 4/110 (3%)
Query: 5   TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCE 64
           +  +   R  +L  CL +L ++ +  G +L ++QG P  +  +L ++L    + + QD E
Sbjct: 44  SADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIE 103
Query: 65  ALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
                RD +V        I   +     L  P+ ++  +GN     Y +Y
Sbjct: 104 PYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGN----PYSVY 149

>pdb|1TEZ|A Chain A, Complex Between Dna And The Dna Photolyase From Anacystis Nidulans Length = 474

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/110 (22%), Positives = 48/110 (43%), Gaps = 4/110 (3%)
Query: 5   TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCE 64
           +  +   R  +L  CL +L ++ +  G +L ++QG P  +  +L ++L    + + QD E
Sbjct: 43  SADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIE 102
Query: 65  ALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
                RD +V        I   +     L  P+ ++  +GN     Y +Y
Sbjct: 103 PYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGN----PYSVY 148

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	184
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	4e-38
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	2e-17
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	1e-37
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	2e-17
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	2e-37
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	1e-15
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	2e-26
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	4e-13
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	4e-25
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	7e-14
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	5e-18
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	1e-07
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	1e-15
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	3e-05
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	4e-15
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	1e-06
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	2e-13
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	2e-07
2xry_A	482	Deoxyribodipyrimidine photolyase; DNA damage, DNA	3e-13
2xry_A	482	Deoxyribodipyrimidine photolyase; DNA damage, DNA	3e-06
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	2e-12
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	6e-05
3umv_A	506	Deoxyribodipyrimidine photo-lyase; CPD cyclobutane	9e-11
3umv_A	506	Deoxyribodipyrimidine photo-lyase; CPD cyclobutane	1e-04

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Length = 537

 Score =  135 bits (343), Expect = 4e-38
 Identities = 45/117 (38%), Positives = 65/117 (55%)

Query: 3   PGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQD 62
           PG+   G NR RFLLE L DLD  LK  G +L + +G P  +  +  +E    +LCFE D
Sbjct: 53  PGSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYD 112

Query: 63  CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS 119
            +  +   D KVK + +   + V   VSHTL++P  +I+ NG  PPL+Y+ +L    
Sbjct: 113 TDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVAG 169

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Length = 537

 Score = 78.1 bits (193), Expect = 2e-17
 Identities = 29/91 (31%), Positives = 39/91 (42%), Gaps = 13/91 (14%)

Query: 94  WDPEVVIQTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLF 153
            DP  +        P             G+   G NR RFLLE L DLD  LK  G +L 
Sbjct: 39  IDPHYMESDPSAFSP-------------GSSRAGVNRIRFLLESLKDLDSSLKKLGSRLL 85

Query: 154 IVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
           + +G P  +  +  +E    +LCFE D + Y
Sbjct: 86  VFKGEPGEVLVRCLQEWKVKRLCFEYDTDPY 116

>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Length = 543

 Score =  135 bits (341), Expect = 1e-37
 Identities = 42/121 (34%), Positives = 64/121 (52%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
               M +G NR+RFL + L DLD QL+    +LF+V+G P  +F ++ +      L FE 
Sbjct: 73  ILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFET 132

Query: 62  DCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI 121
           D E     RD  V+K      + V+   SHT+++PE+VI  N    P+TY+ +L  V  +
Sbjct: 133 DIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQL 192

Query: 122 G 122
            
Sbjct: 193 K 193

>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Length = 543

 Score = 77.7 bits (192), Expect = 2e-17
 Identities = 25/63 (39%), Positives = 36/63 (57%)

Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 181
             M +G NR+RFL + L DLD QL+    +LF+V+G P  +F ++ +      L FE D 
Sbjct: 75  DWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDI 134

Query: 182 EAY 184
           E Y
Sbjct: 135 EPY 137

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1 Length = 489

 Score =  103 bits (259), Expect = 2e-26
 Identities = 20/109 (18%), Positives = 43/109 (39%), Gaps = 1/109 (0%)

Query: 3   PGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQD 62
            G    G  R  FL + + +L   L+  G +L +  G P  +  ++ +++N   + + ++
Sbjct: 50  QGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHRE 109

Query: 63  CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTY 111
                   ++ + K      I  K +   TL  PE +   +    P  +
Sbjct: 110 VTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDL-PFSIQDLPDLF 157

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1 Length = 489

 Score = 65.7 bits (161), Expect = 4e-13
 Identities = 12/63 (19%), Positives = 28/63 (44%)

Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 181
           G    G  R  FL + + +L   L+  G +L +  G P  +  ++ +++N   + + ++ 
Sbjct: 51  GFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREV 110

Query: 182 EAY 184
              
Sbjct: 111 TQE 113

>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Length = 525

 Score =  100 bits (250), Expect = 4e-25
 Identities = 23/112 (20%), Positives = 42/112 (37%), Gaps = 3/112 (2%)

Query: 2   FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 61
           F      G  R  FL+ECL DL + L   G  L I  G P  I   L ++     +   +
Sbjct: 84  FFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHK 143

Query: 62  DCEALWHKRDKKVKKWCAE--NNITVKEFVSHTLWDPEVVIQTNGNVPPLTY 111
           +  +     ++ V +      N+  ++     T++  +  +  +    P  Y
Sbjct: 144 ETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKD-DLPFDVFDLPDVY 194

>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Length = 525

 Score = 67.7 bits (166), Expect = 7e-14
 Identities = 19/70 (27%), Positives = 27/70 (38%)

Query: 115 LHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTK 174
            HT         G  R  FL+ECL DL + L   G  L I  G P  I   L ++     
Sbjct: 79  FHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGART 138

Query: 175 LCFEQDCEAY 184
           +   ++  + 
Sbjct: 139 VFAHKETCSE 148

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A* Length = 484

 Score = 79.5 bits (197), Expect = 5e-18
 Identities = 24/108 (22%), Positives = 45/108 (41%), Gaps = 4/108 (3%)

Query: 7   HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAL 66
            +   R  +L  CL +L ++ +  G +L ++QG P  +  +L ++L    + + QD E  
Sbjct: 46  DMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPY 105

Query: 67  WHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
              RD +V        I   +     L  P+ +  +    P   Y +Y
Sbjct: 106 GRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQI-LSGSGNP---YSVY 149

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A* Length = 484

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 101 QTNGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPI 160
             +  +  L    +      + +  +   R  +L  CL +L ++ +  G +L ++QG P 
Sbjct: 26  AQSAQLIGL----FCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQ 81

Query: 161 SIFQKLKRELNFTKLCFEQDCEAY 184
            +  +L ++L    + + QD E Y
Sbjct: 82  HLIPQLAQQLQAEAVYWNQDIEPY 105

>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A* Length = 509

 Score = 73.0 bits (180), Expect = 1e-15
 Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 5/101 (4%)

Query: 15  FLLECLADLDRQLKSHGGQLFIVQGS-PISIFQKLKRELNFTKLCFEQDCEALWHKRDKK 73
           +L   LA LD  L+S G  L   + +  ++    + +    +++ F    + L   RD +
Sbjct: 62  WLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHR 121

Query: 74  VKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
            K       I V+ F +  L++P  V       P   + M+
Sbjct: 122 AKDVLTAQGIAVRSFNADLLYEPWEV-TDELGRP---FSMF 158

>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A* Length = 509

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 103 NGNVPPLTYKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGS-PIS 161
            G V  L    ++      G  H G     +L   LA LD  L+S G  L   + +  ++
Sbjct: 36  AGPVIAL----FVWAPEEEGHYHPGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVA 91

Query: 162 IFQKLKRELNFTKLCFEQDCEAY 184
               + +    +++ F    +  
Sbjct: 92  SLLDVVKSTGASQIFFNHLYDPL 114

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii} Length = 440

 Score = 71.0 bits (175), Expect = 4e-15
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 2/89 (2%)

Query: 11  NRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKR 70
               F++  L +LD +L+  G +L +  G    +  +   +++   +   +D       R
Sbjct: 49  FAVSFMINSLLELDDELRKKGSRLNVFFGEAEKVVSRFFNKVD--AIYVNEDYTPFSISR 106

Query: 71  DKKVKKWCAENNITVKEFVSHTLWDPEVV 99
           D+K++K C EN I  K +  + L    + 
Sbjct: 107 DEKIRKVCEENGIEFKAYEDYLLTPKSLF 135

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii} Length = 440

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 8/43 (18%), Positives = 20/43 (46%)

Query: 129 NRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELN 171
               F++  L +LD +L+  G +L +  G    +  +   +++
Sbjct: 49  FAVSFMINSLLELDDELRKKGSRLNVFFGEAEKVVSRFFNKVD 91

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A* Length = 420

 Score = 66.3 bits (163), Expect = 2e-13
 Identities = 20/112 (17%), Positives = 39/112 (34%), Gaps = 12/112 (10%)

Query: 3   PGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQD 62
           P  +     R  + LE +  L    ++ GG L++++G P     +  R L    +     
Sbjct: 37  PNNLKTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTS 96

Query: 63  CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
                  RD +V++              H L  P ++   +       Y++Y
Sbjct: 97  HTPYGRYRDGRVREALP--------VPLHLLPAPHLL-PPDLPRA---YRVY 136

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A* Length = 420

 Score = 48.6 bits (117), Expect = 2e-07
 Identities = 12/58 (20%), Positives = 22/58 (37%)

Query: 127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
              R  + LE +  L    ++ GG L++++G P     +  R L    +        Y
Sbjct: 43  TPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPY 100

>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A* Length = 482

 Score = 66.2 bits (162), Expect = 3e-13
 Identities = 15/101 (14%), Positives = 37/101 (36%), Gaps = 11/101 (10%)

Query: 3   PGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELN----FTKLC 58
              +  G  ++ F+L+ L +L+  L       F ++G P     +  ++ N     T   
Sbjct: 77  DEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFS 136

Query: 59  FEQDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVV 99
             +        +++ ++K  +  +I   E  +H +      
Sbjct: 137 PLRI-------KNQWIEKVISGISIPFFEVDAHNVVPCWEA 170

>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A* Length = 482

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 10/47 (21%), Positives = 21/47 (44%)

Query: 125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELN 171
             G  ++ F+L+ L +L+  L       F ++G P     +  ++ N
Sbjct: 81  EAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYN 127

>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1 Length = 471

 Score = 63.3 bits (155), Expect = 2e-12
 Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 7   HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQG----SPISIFQKLKRELNFTKLCFEQD 62
           ++   +   +   L  L   L   G  L   +     + + I +++  E + T L +   
Sbjct: 45  NMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQ 104

Query: 63  CEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
            E     RD +V++     N+  + F    +  P  V  T  +     YK++
Sbjct: 105 YEVNERARDVEVERAL--RNVVCEGFDDSVILPPGAV-MTGNHEM---YKVF 150

>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1 Length = 471

 Score = 41.8 bits (99), Expect = 6e-05
 Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 4/75 (5%)

Query: 114 YLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQG----SPISIFQKLKRE 169
           Y+ T     T ++   +   +   L  L   L   G  L   +     + + I +++  E
Sbjct: 34  YIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAE 93

Query: 170 LNFTKLCFEQDCEAY 184
            + T L +    E  
Sbjct: 94  NSVTHLFYNYQYEVN 108

>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine dimers, UV damaged DNA, DNA repai flavoprotein; HET: FAD; 1.71A {Oryza sativa japonica group} Length = 506

 Score = 59.0 bits (143), Expect = 9e-11
 Identities = 15/95 (15%), Positives = 26/95 (27%), Gaps = 3/95 (3%)

Query: 7   HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAL 66
                +  FLL  L  L     +     F+  G P  I   L + L  + L  +      
Sbjct: 84  SARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGPAEI-PALVQRLGASTLVADFSPLRP 142

Query: 67  WHKRDKKVKKWCAEN--NITVKEFVSHTLWDPEVV 99
             +    V          + V +  +H +      
Sbjct: 143 VREALDAVVGDLRREAPGVAVHQVDAHNVVPVWTA 177

>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine dimers, UV damaged DNA, DNA repai flavoprotein; HET: FAD; 1.71A {Oryza sativa japonica group} Length = 506

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 1/47 (2%)

Query: 125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELN 171
                +  FLL  L  L     +     F+  G P  I   L + L 
Sbjct: 84  SARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGPAEI-PALVQRLG 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	99.92
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	99.91
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	99.89
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	99.88
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	99.87
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	99.87
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	99.85
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	99.85
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	99.83
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	99.81
3umv_A	506	Deoxyribodipyrimidine photo-lyase; CPD cyclobutane	99.78
2xry_A	482	Deoxyribodipyrimidine photolyase; DNA damage, DNA	99.74
3zxs_A	522	Cryptochrome B, rscryb; lyase, cryPro, lumazine, i	99.26
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	99.13
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	99.1
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	99.02
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	98.96
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	98.95
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	98.94
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	98.88
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	98.87
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	98.84
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	98.82
2xry_A	482	Deoxyribodipyrimidine photolyase; DNA damage, DNA	98.75
3umv_A	506	Deoxyribodipyrimidine photo-lyase; CPD cyclobutane	98.74
3zxs_A	522	Cryptochrome B, rscryb; lyase, cryPro, lumazine, i	97.19
3olq_A	319	Universal stress protein E; structural genomics, P	93.81
3hcw_A	295	Maltose operon transcriptional repressor; RNA-bind	93.7
3loq_A	294	Universal stress protein; structural genomics, PSI	93.47
3mt0_A	290	Uncharacterized protein PA1789; structural genomic	92.58
1jmv_A	141	USPA, universal stress protein A; chaperone; 1.85A	90.98
3fvv_A	232	Uncharacterized protein; unknown function, structu	90.41
3huu_A	305	Transcription regulator like protein; PSI-II, NYSG	89.97
3s3t_A	146	Nucleotide-binding protein, universal stress PROT	89.73
1tq8_A	163	Hypothetical protein RV1636; MTCY01B2.28, structur	89.64
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	89.63
3gv0_A	288	Transcriptional regulator, LACI family; transcript	89.16
1mjh_A	162	Protein (ATP-binding domain of protein MJ0577); hy	88.91
3e61_A	277	Putative transcriptional repressor of ribose OPER;	88.66
3fdx_A	143	Putative filament protein / universal stress PROT;	88.1
3hgm_A	147	Universal stress protein TEAD; rossman fold, signa	87.62
3n28_A	335	Phosphoserine phosphatase; HAD family hydrolase, s	87.57
3egc_A	291	Putative ribose operon repressor; structural genom	87.48
3k4h_A	292	Putative transcriptional regulator; structural gen	87.19
3h75_A	350	Periplasmic sugar-binding domain protein; protein	86.8
3dlo_A	155	Universal stress protein; unknown function, struct	86.16
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	86.1
3ksm_A	276	ABC-type sugar transport system, periplasmic COMP;	85.54
2gm3_A	175	Unknown protein; AT3G01520, putative ethylene-resp	85.39
3fg9_A	156	Protein of universal stress protein USPA family; A	84.92
2dum_A	170	Hypothetical protein PH0823; conserved hypothetica	84.34
3vni_A	294	Xylose isomerase domain protein TIM barrel; D-psic	83.65
3ij5_A	211	3-deoxy-D-manno-octulosonate 8-phosphate phosphat;	83.15
3n07_A	195	3-deoxy-D-manno-octulosonate 8-phosphate phosphat;	82.73
3jvd_A	333	Transcriptional regulators; structural genomics, P	82.57
3mmz_A	176	Putative HAD family hydrolase; structural genomics	82.48
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	82.34
3mn1_A	189	Probable YRBI family phosphatase; structural genom	82.05
3tnj_A	150	Universal stress protein (USP); structural genomic	82.01
3idf_A	138	USP-like protein; universal, stress, PSI, MCSG, st	81.97
3bbl_A	287	Regulatory protein of LACI family; protein structu	81.89
3fvv_A	232	Uncharacterized protein; unknown function, structu	81.69
3o74_A	272	Fructose transport system repressor FRUR; dual tra	81.02
2p9j_A	162	Hypothetical protein AQ2171; secsg, riken, PSI, st	80.26
3loq_A	294	Universal stress protein; structural genomics, PSI	80.11

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}

Probab=99.92  E-value=3.4e-25  Score=187.16  Aligned_cols=119  Identities=37%  Similarity=0.679  Sum_probs=112.9

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      |....|++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++||+|++|+|++++||+.|+++|++.||
T Consensus        54 g~~~~g~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~G~~~~vl~~L~~~~~~~~V~~n~~~~p~~~~RD~~v~~~l~~~gI  133 (537)
T 3fy4_A           54 GSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYDTDPYYQALDVKVKDYASSTGV  133 (537)
T ss_dssp             BCSSCBHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHTTSCEEEEEECCCCSHHHHHHHHHHHHHHHHTTC
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHcCCCEEEEeccccHHHHHHHHHHHHHHHHcCC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHHhhhcc
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG  122 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~  122 (184)
                      +++.+++++|++|+++.+++++++|.+||+|++.+.+..
T Consensus       134 ~~~~~~~~~L~~p~~v~~~~~~~~y~vftpf~k~~~~~~  172 (537)
T 3fy4_A          134 EVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVAGEPS  172 (537)
T ss_dssp             EEECCCCSSSSCHHHHHHHTSSSCCSSHHHHHHHHCCCT
T ss_pred             eEEEecCCEEEchhhcccCCCCCCCCccCHHHHHHHhhc
Confidence            999999999999999987666679999999999987753

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*

Probab=99.89  E-value=2.1e-22  Score=168.89  Aligned_cols=116  Identities=20%  Similarity=0.390  Sum_probs=110.1

Q ss_pred             CCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCe
Q psy17626          5 TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNIT   84 (184)
Q Consensus         5 ~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~   84 (184)
                      .+..+++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|++++++||++|+++|++.||+
T Consensus        44 ~~~~~~~r~~fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~p~~~~rd~~v~~~l~~~gi~  123 (484)
T 1owl_A           44 SADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIR  123 (484)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHHHHHTSCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHHHHHHHHHHHHHHHHTTCE
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEeccCChhHHHHHHHHHHHHHHcCcE
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCceeecccccccccCCCCchhHHHHHHHhhhc
Q psy17626         85 VKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI  121 (184)
Q Consensus        85 ~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~  121 (184)
                      ++.+++++|++|+++.+++ +++|.+||+|++.+.+.
T Consensus       124 ~~~~~~~~l~~~~~~~~~~-g~~~~vft~f~~~~~~~  159 (484)
T 1owl_A          124 AVQLWDQLLHSPDQILSGS-GNPYSVYGPFWKNWQAQ  159 (484)
T ss_dssp             EEEECCSSSSCTTTCCCTT-SCCCSSHHHHHHHHHHS
T ss_pred             EEEecCCEEEchhhhcccC-CCCchhhHHHHHHHHHh
Confidence            9999999999999998865 47999999999998764

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1

Probab=99.88  E-value=2.6e-22  Score=168.61  Aligned_cols=115  Identities=17%  Similarity=0.295  Sum_probs=109.5

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +.+..+++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|++++++||++|+++|++.||
T Consensus        51 ~~~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~gi  130 (489)
T 1np7_A           51 GFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGI  130 (489)
T ss_dssp             SCBSSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTEEEEEEECCCSHHHHHHHHHHHHHHHHHTC
T ss_pred             ccCCCCHHHHHHHHHHHHHHHHHHHHCCCcEEEEECCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHhcCC
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHHhh
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS  119 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~  119 (184)
                      +++.+++++|++|+++.+.. +++|.+|++|++.+.
T Consensus       131 ~~~~~~~~~l~~~~~~~~~~-g~~~~vft~F~~~~~  165 (489)
T 1np7_A          131 EAKGYWGSTLCHPEDLPFSI-QDLPDLFTKFRKDIE  165 (489)
T ss_dssp             EEEEECCSSSSCGGGSSSCG-GGCCSSHHHHHHHHH
T ss_pred             eEEEecCCeeeCccccccCC-CCCCchHHHHHHHHH
Confidence            99999999999999998854 579999999999987

>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*

Probab=99.87  E-value=1e-21  Score=166.05  Aligned_cols=116  Identities=19%  Similarity=0.251  Sum_probs=110.3

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCC-
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENN-   82 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~g-   82 (184)
                      |....+++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|++++++||++|+++|++.| 
T Consensus        86 ~~~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~p~~~~rd~~v~~~l~~~gv  165 (525)
T 2j4d_A           86 NFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGN  165 (525)
T ss_dssp             CCBSSCHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHHHHTCSEEEEECCCSHHHHHHHHHHHHHHHTTCS
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHHHHcCCCEEEEeccCCHHHHHHHHHHHHHHHhcCC
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             -CeEEEecCceeecccccccccCCCCchhHHHHHHHhhh
Q psy17626         83 -ITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC  120 (184)
Q Consensus        83 -i~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~  120 (184)
                       |+++.+++++|++|+++++.. +++|.+|++|++.+.+
T Consensus       166 ~i~~~~~~~~~L~~p~~v~~~~-g~~~~vft~F~r~~~~  203 (525)
T 2j4d_A          166 STKLELIWGSTMYHKDDLPFDV-FDLPDVYTQFRKSVEA  203 (525)
T ss_dssp             SCEEEEECCSCSSCGGGSSSCG-GGCCSSHHHHHHHHHH
T ss_pred             ceEEEEecCCEEEccccccccC-CCCcccHHHHHHHHHH
Confidence             899999999999999999875 4799999999999887

>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*

Probab=99.87  E-value=7.9e-22  Score=167.35  Aligned_cols=117  Identities=36%  Similarity=0.639  Sum_probs=109.3

Q ss_pred             CCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeE
Q psy17626          6 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITV   85 (184)
Q Consensus         6 ~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~   85 (184)
                      ...+++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|+|+++.||+.|+++|++.||++
T Consensus        77 ~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~p~~~~rd~~v~~~~~~~gi~~  156 (543)
T 2wq7_A           77 MQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRV  156 (543)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHHHTTEEEEEEECCCSHHHHHHHHHHHHHHHHHTCEE
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEecCcCHHHHHHHHHHHHHHHHcCCEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCceeecccccccccCCCCchhHHHHHHHhhhcc
Q psy17626         86 KEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG  122 (184)
Q Consensus        86 ~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~  122 (184)
                      +.+++++|++|+++..+..+++|.+|++|++.+.++.
T Consensus       157 ~~~~~~~l~~p~~v~~~~~g~~~~vft~F~~~~~~~~  193 (543)
T 2wq7_A          157 ETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLK  193 (543)
T ss_dssp             EEECCSSSSCHHHHHHHTTTSCCCSHHHHHHHHTTSC
T ss_pred             EEecCCEEECccccccccCCCCCccHHHHHHHHHHcc
Confidence            9999999999999655445689999999999987653

>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A*

Probab=99.85  E-value=1.6e-20  Score=158.34  Aligned_cols=113  Identities=19%  Similarity=0.284  Sum_probs=105.8

Q ss_pred             CChhhHHHHHHHHHHHHHHHHhcCCeEEEEE-CChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          8 IGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         8 ~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      .+..+.+||++||.+|+++|+++|++|+|++ |++.++|++|+++++|++|++|++|+|++++||.+|+++|++.||+++
T Consensus        55 ~~~~~~~fl~~sL~~L~~~L~~~G~~L~v~~~g~~~~~l~~l~~~~~~~~V~~~~~~~p~~~~rd~~v~~~l~~~gi~~~  134 (509)
T 1u3d_A           55 PGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVLTAQGIAVR  134 (509)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHHHHHHHHHTCCEEEEECCCSHHHHHHHHHHHHHHHTTTCEEE
T ss_pred             cchHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCcEEE
Confidence            4666777999999999999999999999998 699999999999999999999999999999999999999999999999


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHHHhhhc
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI  121 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~  121 (184)
                      .+++++|++|+++.+++ +++|.+|++|++.+.+.
T Consensus       135 ~~~~~~l~~p~~v~~~~-g~~~~vftpf~r~~~~~  168 (509)
T 1u3d_A          135 SFNADLLYEPWEVTDEL-GRPFSMFAAFWERCLSM  168 (509)
T ss_dssp             EECCSCSSCGGGCCCSS-SCCCSSHHHHHHHHHTC
T ss_pred             EECCCEEEcCCcccCCC-CCCchhHHHHHHHHHhc
Confidence            99999999999998875 47999999999998764

>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1

Probab=99.85  E-value=4.3e-21  Score=160.37  Aligned_cols=113  Identities=15%  Similarity=0.166  Sum_probs=106.4

Q ss_pred             CCCChhhHHHHHHHHHHHHHHHHhcCCeEEEE----ECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhC
Q psy17626          6 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIV----QGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAEN   81 (184)
Q Consensus         6 ~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~----~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~   81 (184)
                      +..+++|++||++||.+|+++|+++|++|+|+    .|++.++|++|+++++|++|++|++|+|++++||++|+++|++ 
T Consensus        44 ~~~~~~r~~fl~~sL~~L~~~L~~~G~~L~v~~~~~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~-  122 (471)
T 1dnp_A           44 HNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRN-  122 (471)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHTCCEEEEECCCSHHHHHHHHHHHHHCTT-
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEEccCCCCHHHHHHHHHHHcCCCEEEEecccCchHHHHHHHHHHHhcC-
Confidence            46899999999999999999999999999999    9999999999999999999999999999999999999999875 


Q ss_pred             CCeEEEecCceeecccccccccCCCCchhHHHHHHHhhhc
Q psy17626         82 NITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI  121 (184)
Q Consensus        82 gi~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~  121 (184)
                       |+++.+++++|++|+++.+++ +++|.+||+|++.+.+.
T Consensus       123 -i~~~~~~~~~l~~~~~~~~~~-g~~~~vft~f~~~~~~~  160 (471)
T 1dnp_A          123 -VVCEGFDDSVILPPGAVMTGN-HEMYKVFTPFKNAWLKR  160 (471)
T ss_dssp             -SEEEEECCSSSSCTTSSCCTT-SCCCSSHHHHHHHHHHH
T ss_pred             -cEEEEecCCEEEchhhcccCC-CCCCcchHHHHHHHHHh
Confidence             999999999999999998875 47999999999988653

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}

Probab=99.83  E-value=4.4e-20  Score=152.90  Aligned_cols=105  Identities=20%  Similarity=0.365  Sum_probs=101.3

Q ss_pred             CChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEE
Q psy17626          8 IGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKE   87 (184)
Q Consensus         8 ~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~   87 (184)
                      .+++|++||++||.+|+++|+++|++|+|++|++.++|++|++  +|++|++|++|++++++||++|+++|++.||+++.
T Consensus        46 ~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~--~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~  123 (440)
T 2e0i_A           46 KSEFAVSFMINSLLELDDELRKKGSRLNVFFGEAEKVVSRFFN--KVDAIYVNEDYTPFSISRDEKIRKVCEENGIEFKA  123 (440)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTTCCCEEEESCHHHHHHHHCT--TCSEEEEECCCSHHHHHHHHHHHHHHHTTTCEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHcCCeEEEEECCHHHHHHHHHc--CCCEEEEecccChHHHHHHHHHHHHHHHcCceEEE
Confidence            8999999999999999999999999999999999999999999  99999999999999999999999999999999999


Q ss_pred             ecCceeecccccccccCCCCchhHHHHHHHhhhc
Q psy17626         88 FVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI  121 (184)
Q Consensus        88 ~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~  121 (184)
                      +++++|++|+++       +|++||+|++.+.+.
T Consensus       124 ~~~~~l~~~~~~-------~y~vftpf~~~~~~~  150 (440)
T 2e0i_A          124 YEDYLLTPKSLF-------HHRNFTSFYNEVSKV  150 (440)
T ss_dssp             ECCSCSSCGGGC-------CCSSHHHHHHHHTTS
T ss_pred             ecCCEEEccccc-------CcccCcHHHHHHHHh
Confidence            999999999988       689999999998764

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A*

Probab=99.81  E-value=1.2e-19  Score=149.63  Aligned_cols=102  Identities=17%  Similarity=0.258  Sum_probs=98.3

Q ss_pred             ChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626          9 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus         9 ~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      +++|++|+++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|++++++||++|+++|   ||+++.+
T Consensus        43 ~~~r~~fl~~sL~~l~~~L~~~g~~l~~~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l---~i~~~~~  119 (420)
T 2j07_A           43 TPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREAL---PVPLHLL  119 (420)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHHHHHHHHHHHHHC---SSCEEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEecccChhHHHHHHHHHHHc---CCeEEEe
Confidence            8899999999999999999999999999999999999999999999999999999999999999999988   9999999


Q ss_pred             cCceeecccccccccCCCCchhHHHHHHHhh
Q psy17626         89 VSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS  119 (184)
Q Consensus        89 ~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~  119 (184)
                      ++++|++|++      +++|.+||+|++.+.
T Consensus       120 ~~~~l~~~~~------~~~~~~~t~f~k~~~  144 (420)
T 2j07_A          120 PAPHLLPPDL------PRAYRVYTPFSRLYR  144 (420)
T ss_dssp             CCCCSSCTTC------SSCCSSHHHHHTTCC
T ss_pred             CCCEEEccCC------CCccccccHHHHHHh
Confidence            9999999997      369999999999876

>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine dimers, UV damaged DNA, DNA repai flavoprotein; HET: FAD; 1.71A {Oryza sativa japonica group}

Probab=99.78  E-value=1.3e-18  Score=146.18  Aligned_cols=108  Identities=14%  Similarity=0.083  Sum_probs=95.6

Q ss_pred             CCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHH--hCCC
Q psy17626          6 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCA--ENNI   83 (184)
Q Consensus         6 ~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~--~~gi   83 (184)
                      +..|++|++||++||.+|+++|+++|++|+|++|+|.++ ++|+++++|++||++.++...+++||++|+++|+  +.||
T Consensus        83 ~~~~~~r~~FL~~sL~dL~~~L~~lG~~L~v~~G~p~~v-~~L~~~~~a~~V~~d~ep~~~~r~rD~~V~~~l~~~~~gi  161 (506)
T 3umv_A           83 LSARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGPAEI-PALVQRLGASTLVADFSPLRPVREALDAVVGDLRREAPGV  161 (506)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHHHHHTTCCEEEESSCTTHH-HHHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHCTTS
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHcCCceEEEecChHHH-HHHHHhcCCCEEEeccChhHHHHHHHHHHHHHHhhccCCe
Confidence            467899999999999999999999999999999999999 9999999999999977766666789999999997  6899


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHH
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHT  117 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~  117 (184)
                      +++.+++++|++|+.+.+++   .|.+++.+.+.
T Consensus       162 ~~~~~~~~~l~~p~~v~~~~---~~~~~t~~~~~  192 (506)
T 3umv_A          162 AVHQVDAHNVVPVWTASAKM---EYSAKTFRGKV  192 (506)
T ss_dssp             EEEEECCSCSSCHHHHCSSC---CSSHHHHHHHH
T ss_pred             EEEEeCCcEEECcccccCCC---CCCccCHHHHH
Confidence            99999999999999987653   46666655443

>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A*

Probab=99.74  E-value=1.3e-17  Score=139.91  Aligned_cols=104  Identities=16%  Similarity=0.163  Sum_probs=95.6

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..+++|++||++||.+|+++|+++|++|+|++|++.++|++|+++++|++|++|++|++++++||+++++.+   ||+++
T Consensus        81 ~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~~~~~~~~v~~~l---gi~~~  157 (482)
T 2xry_A           81 EAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGI---SIPFF  157 (482)
T ss_dssp             GSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHHHHHHHHHHHHHC---CSCEE
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHHHcCCCEEEEecccchhHHHHHHHHHHHc---CCEEE
Confidence            368899999999999999999999999999999999999999999999999999999999999999888665   99999


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHH
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLH  116 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~  116 (184)
                      .+++++|++|+++.+++   .|.+|+.|.+
T Consensus       158 ~~~~~~l~~~~~~~~~~---~~~v~tf~~~  184 (482)
T 2xry_A          158 EVDAHNVVPCWEASQKH---EYAAHTFRPK  184 (482)
T ss_dssp             EECCSSSSCHHHHCSSC---CSSHHHHHHH
T ss_pred             EEeCCEEccccccccCC---CCceecchHH
Confidence            99999999999987653   4899986654

>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine, iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter sphaeroides}

Probab=99.26  E-value=2.6e-11  Score=101.39  Aligned_cols=104  Identities=9%  Similarity=0.047  Sum_probs=92.6

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEE-------CChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHH
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-------GSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCA   79 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~-------g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~   79 (184)
                      ...++|..|++.||++|+++|+++|.+|.++.       |++.++|++++++++++.|+++   +|++..+|+.|+++  
T Consensus        56 ~~h~~Ki~~l~saMr~fa~~L~~~G~~v~y~~~~~~~~~g~~~~~L~~l~~~~~~~~v~~~---~P~e~r~~~~l~~~--  130 (522)
T 3zxs_A           56 PHHPQKIALILAAMRKFARRLQERGFRVAYSRLDDPDTGPSIGAELLRRAAETGAREAVAT---RPGDWRLIEALEAM--  130 (522)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHTTCCEEEECTTCTTCCSSHHHHHHHHHHHHTCCCEEEE---CCSCHHHHHHHHHS--
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHhCCCeEEEEeccCccccCCHHHHHHHHHHHcCCCEEEEe---CcchHHHHHHHHHc--
Confidence            45678999999999999999999999999998       9999999999999999999999   68899999988844  


Q ss_pred             hCCCeEEEecCc-eeeccccccc--ccCCCCchhHHHHHHHhh
Q psy17626         80 ENNITVKEFVSH-TLWDPEVVIQ--TNGNVPPLTYKMYLHTVS  119 (184)
Q Consensus        80 ~~gi~~~~~~~~-~L~~p~~i~~--~~~~~~~~v~~~F~~~~~  119 (184)
                        ||++..+++. .|.+|+++.+  + ++++|.++ +|++.+.
T Consensus       131 --gi~v~~~~~~~fL~~~~e~~~~~~-~~k~~~me-~FYR~~R  169 (522)
T 3zxs_A          131 --PLPVRFLPDDRFLCPADEFARWTE-GRKQLRME-WFYREMR  169 (522)
T ss_dssp             --SSCEEEECCCCSSSCHHHHHHHHT-TCSSCCHH-HHHHHHH
T ss_pred             --CCcEEEeCCCCcccCHHHHHHhhc-CCCCeEee-HHHHHHH
Confidence              9999999986 7999999975  4 45789885 7888765

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}

Probab=99.10  E-value=6.9e-11  Score=99.94  Aligned_cols=63  Identities=41%  Similarity=0.777  Sum_probs=59.4

Q ss_pred             cccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       122 ~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +.+..++++..||.+||.+|+++|+++|++|+|+.|++.++|++|+++++|++||+|++|+|+
T Consensus        54 g~~~~g~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~G~~~~vl~~L~~~~~~~~V~~n~~~~p~  116 (537)
T 3fy4_A           54 GSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYDTDPY  116 (537)
T ss_dssp             BCSSCBHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHTTSCEEEEEECCCCSHH
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHcCCCEEEEeccccHH
Confidence            455688999999999999999999999999999999999999999999999999999999874

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*

Probab=99.02  E-value=9.1e-11  Score=98.32  Aligned_cols=71  Identities=23%  Similarity=0.523  Sum_probs=63.5

Q ss_pred             HHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        114 YLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       114 F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      |...+..++.+..+.++..|+.+||.+|+++|+++|++|+++.|++.++|++|+++++|++||+|++|+|+
T Consensus        35 fi~dp~~~~~~~~~~~r~~fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~p~  105 (484)
T 1owl_A           35 FCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPY  105 (484)
T ss_dssp             EEECHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHTSCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHH
T ss_pred             EEEcchhhcCCCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEeccCChh
Confidence            44444455566788999999999999999999999999999999999999999999999999999999874

>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*

Probab=98.96  E-value=1.7e-10  Score=97.89  Aligned_cols=63  Identities=40%  Similarity=0.740  Sum_probs=58.8

Q ss_pred             cccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       122 ~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      ..+..+.++..|+.+||.+|+++|+++|++|+++.|++.++|.+|+++++|++||+|++|+|+
T Consensus        75 ~~~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~p~  137 (543)
T 2wq7_A           75 DWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPY  137 (543)
T ss_dssp             GCTTSCHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHHHTTEEEEEEECCCSHH
T ss_pred             cccCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEecCcCHH
Confidence            345678889999999999999999999999999999999999999999999999999999873

>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1

Probab=98.95  E-value=9.9e-11  Score=97.75  Aligned_cols=74  Identities=18%  Similarity=0.214  Sum_probs=64.9

Q ss_pred             HHHHHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEE----eCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        111 YKMYLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIV----QGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       111 ~~~F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~----~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      ...|...+..++.+..+.++..|+.+||.+|+++|+++|++|+++    .|++.++|.+|+++++|++||+|++|+|+
T Consensus        31 ~~vfi~dp~~~~~~~~~~~r~~fl~~sL~~L~~~L~~~G~~L~v~~~~~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~  108 (471)
T 1dnp_A           31 LALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVN  108 (471)
T ss_dssp             EEEEEECHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHTCCEEEEECCCSHH
T ss_pred             EEEEEECchhhccCCCCHHHHHHHHHHHHHHHHHHHHCCCeEEEEEccCCCCHHHHHHHHHHHcCCCEEEEecccCch
Confidence            333444555556677899999999999999999999999999999    89999999999999999999999999873

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1

Probab=98.94  E-value=2.9e-10  Score=95.38  Aligned_cols=62  Identities=18%  Similarity=0.404  Sum_probs=58.6

Q ss_pred             ccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        123 TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       123 ~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      .+..++++..|+.+||.+|+++|+++|++|+++.|++.++|++|+++++|++||+|++|+|+
T Consensus        52 ~~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~  113 (489)
T 1np7_A           52 FAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQE  113 (489)
T ss_dssp             CBSSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTEEEEEEECCCSHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHCCCcEEEEECCHHHHHHHHHHHcCCCEEEEecccCHH
Confidence            45678899999999999999999999999999999999999999999999999999999874

>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*

Probab=98.88  E-value=2.2e-09  Score=90.75  Aligned_cols=61  Identities=28%  Similarity=0.447  Sum_probs=57.9

Q ss_pred             cccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        124 MHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       124 ~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +..+.++..|+.+||.+|+++|+++|++|+++.|++.++|.+|+++++|++||+|++|+|+
T Consensus        88 ~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~p~  148 (525)
T 2j4d_A           88 PKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSE  148 (525)
T ss_dssp             BSSCHHHHHHHHHHHHHHHHHHHHTTCCCEEEESCHHHHHHHHHHHHTCSEEEEECCCSHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHHHHcCCCEEEEeccCCHH
Confidence            5578889999999999999999999999999999999999999999999999999999874

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}

Probab=98.87  E-value=4.6e-10  Score=92.91  Aligned_cols=65  Identities=14%  Similarity=0.279  Sum_probs=58.2

Q ss_pred             hhhccccc-cCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        118 VSCIGTMH-IGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       118 ~~~~~~~~-~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +..++.+. .+.++..|+.+||.+|+++|+++|++|+++.|++.++|+++++  +|++||+|++|+|+
T Consensus        37 p~~~~~~~~~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~--~~~~v~~~~~~~~~  102 (440)
T 2e0i_A           37 PRQLINNPYKSEFAVSFMINSLLELDDELRKKGSRLNVFFGEAEKVVSRFFN--KVDAIYVNEDYTPF  102 (440)
T ss_dssp             HHHHSSCTTCCHHHHHHHHHHHHHHHHHHHTTTCCCEEEESCHHHHHHHHCT--TCSEEEEECCCSHH
T ss_pred             hhhhccCCcCCHHHHHHHHHHHHHHHHHHHHcCCeEEEEECCHHHHHHHHHc--CCCEEEEecccChH
Confidence            33344445 7889999999999999999999999999999999999999998  99999999999873

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A*

Probab=98.84  E-value=3.9e-09  Score=86.96  Aligned_cols=58  Identities=21%  Similarity=0.366  Sum_probs=55.9

Q ss_pred             CcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       127 ~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +.++..|+.+||.+|+++|+++|++|+++.|++.++|+++++++++++||+|++|+|+
T Consensus        43 ~~~r~~fl~~sL~~l~~~L~~~g~~l~~~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~  100 (420)
T 2j07_A           43 TPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPY  100 (420)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCHHHHHHHHHHHcCCCEEEEecccChh
Confidence            8888999999999999999999999999999999999999999999999999999873

>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A*

Probab=98.82  E-value=1.7e-09  Score=91.16  Aligned_cols=58  Identities=19%  Similarity=0.288  Sum_probs=52.9

Q ss_pred             CcchhHHHHHHHHHHHHHHHhCCCeEEEEe-CChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       127 ~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +..+..|+.+||.+|+++|+++|++|+++. |++.++|.+|+++++|++||+|++|+|+
T Consensus        56 ~~~~~~fl~~sL~~L~~~L~~~G~~L~v~~~g~~~~~l~~l~~~~~~~~V~~~~~~~p~  114 (509)
T 1u3d_A           56 GRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPL  114 (509)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHHHHHHHHHTCCEEEEECCCSHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHCCCeEEEEeCCCHHHHHHHHHHHcCCCEEEEecccCHH
Confidence            444556999999999999999999999998 6999999999999999999999999873

>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A*

Probab=98.75  E-value=1.2e-08  Score=85.52  Aligned_cols=58  Identities=19%  Similarity=0.340  Sum_probs=55.6

Q ss_pred             cCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccC
Q psy17626        126 IGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEA  183 (184)
Q Consensus       126 ~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~  183 (184)
                      .+.++..|+.+||.+|+++|+++|++|+++.|++.++|++|+++++|++||+|++|++
T Consensus        82 ~~~~r~~Fl~~sL~~L~~~L~~~G~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~  139 (482)
T 2xry_A           82 AGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLR  139 (482)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSH
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHHHcCCCEEEEecccch
Confidence            4778899999999999999999999999999999999999999999999999999986

>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine dimers, UV damaged DNA, DNA repai flavoprotein; HET: FAD; 1.71A {Oryza sativa japonica group}

Probab=98.74  E-value=1.5e-08  Score=85.16  Aligned_cols=56  Identities=21%  Similarity=0.299  Sum_probs=52.4

Q ss_pred             ccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccc
Q psy17626        125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC  181 (184)
Q Consensus       125 ~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~  181 (184)
                      ..+.++..||.+||.+|+++|+++|++|+|+.|++.++ ++|+++++|++||+|.++
T Consensus        84 ~~~~~r~~FL~~sL~dL~~~L~~lG~~L~v~~G~p~~v-~~L~~~~~a~~V~~d~ep  139 (506)
T 3umv_A           84 SARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGPAEI-PALVQRLGASTLVADFSP  139 (506)
T ss_dssp             GCCHHHHHHHHHHHHHHHHHHHHTTCCEEEESSCTTHH-HHHHHHTTCSEEEECCCC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHcCCceEEEecChHHH-HHHHHhcCCCEEEeccCh
Confidence            46788999999999999999999999999999999999 999999999999997654

>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine, iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter sphaeroides}

Probab=97.19  E-value=0.00079  Score=56.51  Aligned_cols=55  Identities=11%  Similarity=0.096  Sum_probs=50.7

Q ss_pred             ccCcchhHHHHHHHHHHHHHHHhCCCeEEEEe-------CChhHHHHHHHHHcCcCeEEEcc
Q psy17626        125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-------GSPISIFQKLKRELNFTKLCFEQ  179 (184)
Q Consensus       125 ~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-------g~~~~~l~~l~~~~~~~~v~~n~  179 (184)
                      ...+.|..|+..|+..++++|++.|.+|.++.       |++.+.|+++++++++++|+++.
T Consensus        56 ~~h~~Ki~~l~saMr~fa~~L~~~G~~v~y~~~~~~~~~g~~~~~L~~l~~~~~~~~v~~~~  117 (522)
T 3zxs_A           56 PHHPQKIALILAAMRKFARRLQERGFRVAYSRLDDPDTGPSIGAELLRRAAETGAREAVATR  117 (522)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHTTCCEEEECTTCTTCCSSHHHHHHHHHHHHTCCCEEEEC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHhCCCeEEEEeccCccccCCHHHHHHHHHHHcCCCEEEEeC
Confidence            34567889999999999999999999999998       88999999999999999999993

>3olq_A Universal stress protein E; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: UNL; 1.82A {Proteus mirabilis}

Probab=93.81  E-value=1.7  Score=33.23  Aligned_cols=162  Identities=9%  Similarity=-0.008  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHhcCCeE--EEE-ECChHHHHHHHHHHcCcceEEEeecccchhHH--HHHHHHHHHHhCCCeEEEecCce
Q psy17626         18 ECLADLDRQLKSHGGQL--FIV-QGSPISIFQKLKRELNFTKLCFEQDCEALWHK--RDKKVKKWCAENNITVKEFVSHT   92 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~L--~v~-~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~--rd~~v~~~l~~~gi~~~~~~~~~   92 (184)
                      +.|.++.+.+...|++.  .+. .|++.+.|.+.+++.+++-|+.-..-......  .-....+.+...++++..+....
T Consensus        73 ~~l~~~~~~~~~~~v~~~~~~~~~g~~~~~i~~~a~~~~~DLiV~G~~g~~~~~~~~~Gs~~~~vl~~~~~PVlvv~~~~  152 (319)
T 3olq_A           73 AWIKQQARYYLEAGIQIDIKVIWHNRPYEAIIEEVITDKHDLLIKMAHQHDKLGSLIFTPLDWQLLRKCPAPVWMVKDKE  152 (319)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEECSCHHHHHHHHHHHHTCSEEEEEEBCC--CCSCBCCHHHHHHHHHCSSCEEEEESSC
T ss_pred             HHHHHHHHHHhhcCCeEEEEEEecCChHHHHHHHHHhcCCCEEEEecCcCchhhcccccccHHHHHhcCCCCEEEecCcc
Confidence            44556666666667754  455 79999999999999999999987643221111  12334556677789988776554


Q ss_pred             eecccccccccCCCCc---------hhHHHHHHHhhhc--c----------ccccC-------cchhHH----HHHHHHH
Q psy17626         93 LWDPEVVIQTNGNVPP---------LTYKMYLHTVSCI--G----------TMHIG-------YNRFRF----LLECLAD  140 (184)
Q Consensus        93 L~~p~~i~~~~~~~~~---------~v~~~F~~~~~~~--~----------~~~~~-------~~r~~f----l~~~L~~  140 (184)
                      .-.+..|.-.-+++..         .....-.......  +          .+...       .....+    ..+..+.
T Consensus       153 ~~~~~~Ilva~D~s~~~~~~~~~s~~al~~a~~la~~~~~~a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (319)
T 3olq_A          153 WPEYGTIVVAANLSNEESYHDALNLKLIELTNDLSHRIQKDPDVHLLSAYPVAPINIAIELPDFDPNLYNNALRGQHLIA  232 (319)
T ss_dssp             CCTTCEEEEECCCSCCSTHHHHHHHHHHHHHHHHHHHHCSSCCEEEEEEECCCSCSCCTTCTTCCHHHHHHHHHHHHHHH
T ss_pred             cccCCeEEEEECCCCcchhHHHHHHHHHHHHHHHHHhccCCCeEEEEEeecCcchhhhccCCcccHHHHHHHHHHHHHHH
Confidence            3334444433233342         1111111111111  1          00000       000112    2233444


Q ss_pred             HHHHHHhCCC---eEEEEeCChhHHHHHHHHHcCcCeEEEcc
Q psy17626        141 LDRQLKSHGG---QLFIVQGSPISIFQKLKRELNFTKLCFEQ  179 (184)
Q Consensus       141 L~~~L~~~g~---~L~v~~g~~~~~l~~l~~~~~~~~v~~n~  179 (184)
                      |+.-+++.|+   ...+..|++.+.|.+++++.+++-|+...
T Consensus       233 l~~~~~~~~~~~~~~~v~~g~~~~~I~~~a~~~~~dLiV~G~  274 (319)
T 3olq_A          233 MKELRQKFSIPEEKTHVKEGLPEQVIPQVCEELNAGIVVLGI  274 (319)
T ss_dssp             HHHHHHHTTCCGGGEEEEESCHHHHHHHHHHHTTEEEEEEEC
T ss_pred             HHHHHHHhCCCcccEEEecCCcHHHHHHHHHHhCCCEEEEec
Confidence            5555566776   47778899999999999999999887653

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}

Probab=93.70  E-value=1.7  Score=32.83  Aligned_cols=156  Identities=10%  Similarity=0.034  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEECCh-H---HHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         13 FRFLLECLADLDRQLKSHGGQLFIVQGSP-I---SIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        13 ~~fl~~sL~~L~~~L~~~g~~L~v~~g~~-~---~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      ..|..+-+..+.+.+++.|..+.+...+. .   ..+.+.+...+++.|+..-....     + ...+.+.+.|+++..+
T Consensus        24 ~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiI~~~~~~~-----~-~~~~~l~~~~iPvV~i   97 (295)
T 3hcw_A           24 NPFYINVLLGISETCNQHGYGTQTTVSNNMNDLMDEVYKMIKQRMVDAFILLYSKEN-----D-PIKQMLIDESMPFIVI   97 (295)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCEEEECCCCSHHHHHHHHHHHHHTTCCSEEEESCCCTT-----C-HHHHHHHHTTCCEEEE
T ss_pred             ChHHHHHHHHHHHHHHHCCCEEEEEcCCCChHHHHHHHHHHHhCCcCEEEEcCcccC-----h-HHHHHHHhCCCCEEEE
Confidence            34888889999999999999998875432 2   23445556678999888532111     1 2334456779999887


Q ss_pred             cCceeec---ccccccccCCCCchhHHHHHHHhhh---cccccc----CcchhHHHHHHHHHHHHHHHhCCCeEEEEeCC
Q psy17626         89 VSHTLWD---PEVVIQTNGNVPPLTYKMYLHTVSC---IGTMHI----GYNRFRFLLECLADLDRQLKSHGGQLFIVQGS  158 (184)
Q Consensus        89 ~~~~L~~---p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~  158 (184)
                      +...--.   ...|..+       .+..-+...+.   .+-.+.    ++.......+.+.-..+.|++.|++..+..++
T Consensus        98 ~~~~~~~~~~~~~V~~D-------~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~  170 (295)
T 3hcw_A           98 GKPTSDIDHQFTHIDND-------NILASENLTRHVIEQGVDELIFITEKGNFEVSKDRIQGFETVASQFNLDYQIIETS  170 (295)
T ss_dssp             SCCCSSGGGGSCEEEEC-------HHHHHHHHHHHHHHHCCSEEEEEEESSCCHHHHHHHHHHHHHHHHTTCEEEEEEEC
T ss_pred             CCCCccccCCceEEecC-------cHHHHHHHHHHHHHcCCccEEEEcCCccchhHHHHHHHHHHHHHHcCCCeeEEecc
Confidence            6532111   0111111       11111111111   111111    22222345566778888999999988766542


Q ss_pred             -----hhHHHHHHHHHc----CcCeEEEcccc
Q psy17626        159 -----PISIFQKLKREL----NFTKLCFEQDC  181 (184)
Q Consensus       159 -----~~~~l~~l~~~~----~~~~v~~n~~~  181 (184)
                           ..+.+.++.+..    ..++||+..|.
T Consensus       171 ~~~~~~~~~~~~~l~~~~~~~~~~ai~~~~d~  202 (295)
T 3hcw_A          171 NEREVILNYMQNLHTRLKDPNIKQAIISLDAM  202 (295)
T ss_dssp             SCHHHHHHHHHHHHHHHTCTTSCEEEEESSHH
T ss_pred             CCHHHHHHHHHHHHhhcccCCCCcEEEECChH
Confidence                 234566777766    68999987653

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus}

Probab=93.47  E-value=1.9  Score=32.67  Aligned_cols=159  Identities=13%  Similarity=0.132  Sum_probs=96.2

Q ss_pred             HHHHHHHHHHHHHHhcCCeEEE---E-ECChHHHHHHHHHHcCcceEEEeecccchhHHH--HHHHHHHHHhCCCeEEEe
Q psy17626         15 FLLECLADLDRQLKSHGGQLFI---V-QGSPISIFQKLKRELNFTKLCFEQDCEALWHKR--DKKVKKWCAENNITVKEF   88 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~~L~v---~-~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~r--d~~v~~~l~~~gi~~~~~   88 (184)
                      -..+.|.++.+.+.+.|++...   . .|++.+.|  .+++.+++-|+.-..-.......  -....+.+...++++..+
T Consensus        83 ~~~~~l~~~~~~~~~~g~~~~~~~v~~~g~~~~~I--~a~~~~~DliV~G~~g~~~~~~~~~Gs~~~~vl~~~~~PVlvv  160 (294)
T 3loq_A           83 KAEEVLPEVAQKIEAAGIKAEVIKPFPAGDPVVEI--IKASENYSFIAMGSRGASKFKKILLGSVSEGVLHDSKVPVYIF  160 (294)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEEECSSCCEECHHHHH--HHHHTTSSEEEEECCCCCHHHHHHHCCHHHHHHHHCSSCEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCcceeEeeccCChhHhe--eeccCCCCEEEEcCCCCccccceeeccHHHHHHhcCCCCEEEe
Confidence            4456677788888888988765   5 89999999  89999999999975422221111  123455667778998877


Q ss_pred             cCcee--ecccccccccCCCCchh--HHHHHHHhhhccc-----cccCcchhHHHHHHHHHHHHHHHhCCCe--EEEEeC
Q psy17626         89 VSHTL--WDPEVVIQTNGNVPPLT--YKMYLHTVSCIGT-----MHIGYNRFRFLLECLADLDRQLKSHGGQ--LFIVQG  157 (184)
Q Consensus        89 ~~~~L--~~p~~i~~~~~~~~~~v--~~~F~~~~~~~~~-----~~~~~~r~~fl~~~L~~L~~~L~~~g~~--L~v~~g  157 (184)
                      ....-  ..+..|.-.-+++....  ...........+.     +-.....   -.+.++++.+.|++.|++  ..+..|
T Consensus       161 ~~~~~~~~~~~~Ilv~~d~s~~s~~al~~a~~la~~~~~~l~ll~v~~~~~---~~~~l~~~~~~l~~~~~~~~~~~~~g  237 (294)
T 3loq_A          161 KHDMVVNSLFDRVLVAYDFSKWADRALEYAKFVVKKTGGELHIIHVSEDGD---KTADLRVMEEVIGAEGIEVHVHIESG  237 (294)
T ss_dssp             CCCTTTTCTTSEEEEECCSSHHHHHHHHHHHHHHHHHTCEEEEEEECSSSC---CHHHHHHHHHHHHHTTCCEEEEEECS
T ss_pred             cCccccCccCCEEEEEECCCHHHHHHHHHHHHHhhhcCCEEEEEEEccCch---HHHHHHHHHHHHHHcCCcEEEEEecC
Confidence            65431  23334433222222211  1111111111111     0001111   345677888888888876  445679


Q ss_pred             ChhHHHHHHHHHcCcCeEEEc
Q psy17626        158 SPISIFQKLKRELNFTKLCFE  178 (184)
Q Consensus       158 ~~~~~l~~l~~~~~~~~v~~n  178 (184)
                      ++.+.|.+++++.+++-|+..
T Consensus       238 ~~~~~I~~~a~~~~~dLlV~G  258 (294)
T 3loq_A          238 TPHKAILAKREEINATTIFMG  258 (294)
T ss_dssp             CHHHHHHHHHHHTTCSEEEEE
T ss_pred             CHHHHHHHHHHhcCcCEEEEe
Confidence            999999999999999988764

>3mt0_A Uncharacterized protein PA1789; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MSE; 1.58A {Pseudomonas aeruginosa}

Probab=92.58  E-value=2.6  Score=31.85  Aligned_cols=159  Identities=10%  Similarity=-0.044  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHhcCCeEEE--E-ECChHHHHHHHHHHcCcceEEEeecccchhHH--HHHHHHHHHHhCCCeEEEec-Cce
Q psy17626         19 CLADLDRQLKSHGGQLFI--V-QGSPISIFQKLKRELNFTKLCFEQDCEALWHK--RDKKVKKWCAENNITVKEFV-SHT   92 (184)
Q Consensus        19 sL~~L~~~L~~~g~~L~v--~-~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~--rd~~v~~~l~~~gi~~~~~~-~~~   92 (184)
                      .|.++.+.+...|++...  . .|++.+.|.+.+++.+++-|+.-..-......  ......+.+...++++..+. +..
T Consensus        52 ~l~~~~~~~~~~~~~~~~~~~~~g~~~~~i~~~a~~~~~dliV~G~~~~~~~~~~~~gs~~~~vl~~~~~PVlvv~~~~~  131 (290)
T 3mt0_A           52 ALNDLAQELREEGYSVSTNQAWKDSLHQTIIAEQQAEGCGLIIKQHFPDNPLKKAILTPDDWKLLRFAPCPVLMTKTARP  131 (290)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEECSSSHHHHHHHHHHHHTCSEEEEECCCSCTTSTTSCCHHHHHHHHHCSSCEEEECCCSC
T ss_pred             HHHHHHHHHhhCCCeEEEEEEeCCCHHHHHHHHHHhcCCCEEEEecccCCchhhcccCHHHHHHHhcCCCCEEEecCCCC
Confidence            355666677777877543  4 47899999999999999999987643221111  12344566677789988876 333


Q ss_pred             eecccccccccCCCCch------hHHHHHHH---hhhccc-----cccCcch-----------hHHHHHHHHHHHHHHHh
Q psy17626         93 LWDPEVVIQTNGNVPPL------TYKMYLHT---VSCIGT-----MHIGYNR-----------FRFLLECLADLDRQLKS  147 (184)
Q Consensus        93 L~~p~~i~~~~~~~~~~------v~~~F~~~---~~~~~~-----~~~~~~r-----------~~fl~~~L~~L~~~L~~  147 (184)
                      . ++..|.-.-+++...      ........   ....+.     +-.....           .....+..+.|+.-+++
T Consensus       132 ~-~~~~Ilva~D~s~~~~~~~~~s~~al~~a~~la~~~~a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (290)
T 3mt0_A          132 W-TGGKILAAVDVGNNDGEHRSLHAGIISHAYDIAGLAKATLHVISAHPSPMLSSADPTFQLSETIEARYREACRTFQAE  210 (290)
T ss_dssp             S-TTCEEEEEECTTCCSHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEEC---------CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCCeEEEEECCCCcchhhhHHHHHHHHHHHHHHHHcCCeEEEEEEecCccccccCchhHHHHHHHHHHHHHHHHHHHH
Confidence            3 555554433333431      11111111   111110     0001000           01112223334444445


Q ss_pred             CCC---eEEEEeCChhHHHHHHHHHcCcCeEEEc
Q psy17626        148 HGG---QLFIVQGSPISIFQKLKRELNFTKLCFE  178 (184)
Q Consensus       148 ~g~---~L~v~~g~~~~~l~~l~~~~~~~~v~~n  178 (184)
                      .|+   ...+..|++.+.|.+++++.+++-|+..
T Consensus       211 ~g~~~~~~~v~~g~~~~~I~~~a~~~~~dLiVmG  244 (290)
T 3mt0_A          211 YGFSDEQLHIEEGPADVLIPRTAQKLDAVVTVIG  244 (290)
T ss_dssp             HTCCTTTEEEEESCHHHHHHHHHHHHTCSEEEEE
T ss_pred             cCCCcceEEEeccCHHHHHHHHHHhcCCCEEEEC
Confidence            565   4677889999999999999999998865

>1jmv_A USPA, universal stress protein A; chaperone; 1.85A {Haemophilus influenzae} SCOP: c.26.2.4

Probab=90.98  E-value=2.3  Score=28.08  Aligned_cols=65  Identities=11%  Similarity=0.067  Sum_probs=43.5

Q ss_pred             HHHHHHhcCCe---EEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         23 LDRQLKSHGGQ---LFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        23 L~~~L~~~g~~---L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      |++-+++.|.+   ..+..|++.+.|.+.+++.+++-|++-.. .......-....+.+...++++..+
T Consensus        69 l~~~~~~~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~-~~~~~~lgs~~~~vl~~~~~pVlvv  136 (141)
T 1jmv_A           69 LLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMSSTRQVMNTIKIDMLVV  136 (141)
T ss_dssp             HHHHHHHSSSCCCCEEEEEECHHHHHHHHHHHTTCCEEEEEEC-CCCHHHHHHHHHHHHTTCCSEEEEE
T ss_pred             HHHHHHHcCCCceEEEEecCCHHHHHHHHHHhcCCCEEEEeCC-CchhhhhcchHHHHHhcCCCCEEEe
Confidence            33333445654   57788999999999999999999999876 3322222333344556667877654

>3fvv_A Uncharacterized protein; unknown function, structural genomics, PSI,MCSG, protein STR initiative, midwest center for structural genomics; 2.10A {Bordetella pertussis}

Probab=90.41  E-value=1.9  Score=31.05  Aligned_cols=45  Identities=13%  Similarity=0.096  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEee
Q psy17626         17 LECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ   61 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~   61 (184)
                      .....++-+.|++.|.++.|..+.+...+..+++..+++.++.+.
T Consensus        94 ~~g~~~~l~~l~~~g~~~~ivS~~~~~~~~~~~~~~g~~~~~~~~  138 (232)
T 3fvv_A           94 TVQAVDVVRGHLAAGDLCALVTATNSFVTAPIARAFGVQHLIATD  138 (232)
T ss_dssp             CHHHHHHHHHHHHTTCEEEEEESSCHHHHHHHHHHTTCCEEEECE
T ss_pred             CHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHHHHcCCCEEEEcc
Confidence            456677788888999999999999999999999999998777653

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}

Probab=89.97  E-value=5  Score=30.26  Aligned_cols=156  Identities=8%  Similarity=-0.005  Sum_probs=85.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEECCh-H---HHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         13 FRFLLECLADLDRQLKSHGGQLFIVQGSP-I---SIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        13 ~~fl~~sL~~L~~~L~~~g~~L~v~~g~~-~---~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      ..|..+-+..+.+.++++|..+.+...+. .   ..+.+.+...+++.|++.-....     + ...+.+.+.|+++..+
T Consensus        39 ~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~-----~-~~~~~l~~~~iPvV~i  112 (305)
T 3huu_A           39 NPFNSDVLNGINQACNVRGYSTRMTVSENSGDLYHEVKTMIQSKSVDGFILLYSLKD-----D-PIEHLLNEFKVPYLIV  112 (305)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCEEEECCCSSHHHHHHHHHHHHHTTCCSEEEESSCBTT-----C-HHHHHHHHTTCCEEEE
T ss_pred             CcHHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEeCCcCC-----c-HHHHHHHHcCCCEEEE
Confidence            35788888899999999999998876432 2   23445555678999887532111     1 2334456779999988


Q ss_pred             cCceeecccccccccCCCCchhHHHHHHHhhh---cccccc----CcchhHHHHHHHHHHHHHHHhCCCeEE-EEeCChh
Q psy17626         89 VSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC---IGTMHI----GYNRFRFLLECLADLDRQLKSHGGQLF-IVQGSPI  160 (184)
Q Consensus        89 ~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~-v~~g~~~  160 (184)
                      +...  +...+..=    ....+..-+...+.   .+-.+.    +........+.+.-..+.|++.|++.. +..++..
T Consensus       113 ~~~~--~~~~~~~V----~~D~~~~g~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~  186 (305)
T 3huu_A          113 GKSL--NYENIIHI----DNDNIDAAYQLTQYLYHLGHRHILFLQESGHYAVTEDRSVGFKQYCDDVKISNDCVVIKSMN  186 (305)
T ss_dssp             SCCC--SSTTCCEE----ECCHHHHHHHHHHHHHHTTCCSEEEEEESSCBHHHHHHHHHHHHHHHHTTCCCCEEEECSHH
T ss_pred             CCCC--cccCCcEE----EeCHHHHHHHHHHHHHHCCCCeEEEEcCCcccchhHHHHHHHHHHHHHcCCCcccEEecCcH
Confidence            7654  22111110    01111111111111   111111    222223344667778888998888754 5666543


Q ss_pred             ---HHHHHH-HH-HcCcCeEEEccc
Q psy17626        161 ---SIFQKL-KR-ELNFTKLCFEQD  180 (184)
Q Consensus       161 ---~~l~~l-~~-~~~~~~v~~n~~  180 (184)
                         +.+.++ .+ ...+++||+..|
T Consensus       187 ~~~~~~~~~~l~~~~~~~ai~~~nd  211 (305)
T 3huu_A          187 DLRDFIKQYCIDASHMPSVIITSDV  211 (305)
T ss_dssp             HHHHHC--------CCCSEEEESSH
T ss_pred             HHHHHHHHhhhcCCCCCCEEEECCh
Confidence               344455 44 347899998765

>3s3t_A Nucleotide-binding protein, universal stress PROT family; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; HET: ATP; 1.90A {Lactobacillus plantarum} SCOP: c.26.2.0

Probab=89.73  E-value=3.1  Score=27.56  Aligned_cols=73  Identities=7%  Similarity=0.033  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHHHhcCC---eEEEEECChHHHHHH-HHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEEE
Q psy17626         15 FLLECLADLDRQLKSHGG---QLFIVQGSPISIFQK-LKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVKE   87 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~---~L~v~~g~~~~~l~~-l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~~   87 (184)
                      -..+.|..+.+.+.+.|+   ...+..|++.+.|.+ .+++.+++-|+.-..- +...+. .-....+.+...++++..
T Consensus        66 ~~~~~l~~~~~~~~~~g~~~~~~~~~~g~~~~~I~~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pVlv  144 (146)
T 3s3t_A           66 HAKDAMRQRQQFVATTSAPNLKTEISYGIPKHTIEDYAKQHPEIDLIVLGATGTNSPHRVAVGSTTSYVVDHAPCNVIV  144 (146)
T ss_dssp             HHHHHHHHHHHHHTTSSCCCCEEEEEEECHHHHHHHHHHHSTTCCEEEEESCCSSCTTTCSSCHHHHHHHHHCSSEEEE
T ss_pred             HHHHHHHHHHHHHHhcCCcceEEEEecCChHHHHHHHHHhhcCCCEEEECCCCCCCcceEEEcchHHHHhccCCCCEEE
Confidence            445567777777877777   567889999999999 9999999999997532 221111 112334455666777654

>1tq8_A Hypothetical protein RV1636; MTCY01B2.28, structural target, NYSGXRC, PSI, protein structure initiative; 2.40A {Mycobacterium tuberculosis} SCOP: c.26.2.4

Probab=89.64  E-value=1  Score=31.21  Aligned_cols=71  Identities=14%  Similarity=0.131  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHhcCCe---EEEEECChHHHHHHHHHHcCcceEEEeecc-cchhHHH-HHHHHHHHHhCCCeEEEe
Q psy17626         18 ECLADLDRQLKSHGGQ---LFIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHKR-DKKVKKWCAENNITVKEF   88 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~---L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~r-d~~v~~~l~~~gi~~~~~   88 (184)
                      +.|.++.+.+.+.|++   ..+..|+|.+.|.+.+++.+++-|++-..- ....+-. -....+.+....+++..+
T Consensus        81 ~~l~~~~~~~~~~gv~~v~~~v~~G~~~~~I~~~a~~~~~DLIV~G~~g~~~~~~~~lGSva~~vl~~a~~PVlvV  156 (163)
T 1tq8_A           81 EILHDAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIV  156 (163)
T ss_dssp             HHHHHHHHHHHTTTCCEEEEEEECSSHHHHHHHHHHHTTCSEEEEECCCCCSHHHHHTBBHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHHHcCCCeEEEEEecCCHHHHHHHHHHhcCCCEEEECCCCCCcccceeeccHHHHHHHhCCCCEEEE
Confidence            4566677777777876   567789999999999999999999987542 2221111 122344556667887754

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=89.63  E-value=1.6  Score=34.88  Aligned_cols=154  Identities=8%  Similarity=-0.008  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEecCce
Q psy17626         13 FRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVSHT   92 (184)
Q Consensus        13 ~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~~~~   92 (184)
                      ..|..+-+..+.+.+++.|..+.+...+......+.+...+++.|+...    .    +..+.+.+.+.|+++..++...
T Consensus        36 ~~f~~~l~~gi~~~a~~~g~~~~i~~~~~~~~~i~~l~~~~vDGiIi~~----~----~~~~~~~l~~~~iPvV~i~~~~  107 (412)
T 4fe7_A           36 KAYDRQVVEGVGEYLQASQSEWDIFIEEDFRARIDKIKDWLGDGVIADF----D----DKQIEQALADVDVPIVGVGGSY  107 (412)
T ss_dssp             SHHHHHHHHHHHHHHHHHTCCEEEEECC-CC--------CCCSEEEEET----T----CHHHHHHHTTCCSCEEEEEECC
T ss_pred             chhhHHHHHHHHHHHHhcCCCeEEEecCCccchhhhHhcCCCCEEEEec----C----ChHHHHHHhhCCCCEEEecCCc
Confidence            3477778888889999999998888765444344555667899998832    1    1234455677899998776432


Q ss_pred             ee-----cccccccccCCCCchhHHHHHHHhhh---cccccc----Ccchh--HHHHHHHHHHHHHHHhCCCeEEEEeCC
Q psy17626         93 LW-----DPEVVIQTNGNVPPLTYKMYLHTVSC---IGTMHI----GYNRF--RFLLECLADLDRQLKSHGGQLFIVQGS  158 (184)
Q Consensus        93 L~-----~p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~~----~~~r~--~fl~~~L~~L~~~L~~~g~~L~v~~g~  158 (184)
                      --     ....|..+       .+..-+...+.   .+-.+.    ++...  .+..+.+.-..+.|++.|++..+..+.
T Consensus       108 ~~~~~~~~~~~V~~D-------~~~~g~~a~~~L~~~G~r~I~~i~~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~  180 (412)
T 4fe7_A          108 HLAESYPPVHYIATD-------NYALVESAFLHLKEKGVNRFAFYGLPESSGKRWATEREYAFRQLVAEEKYRGVVYQGL  180 (412)
T ss_dssp             SSGGGSCSSEEEEEC-------HHHHHHHHHHHHHHTTCCEEEEECCCTTSCCHHHHHHHHHHHHHHTTSSSCCEEECCS
T ss_pred             cccccCCCCCEEEeC-------HHHHHHHHHHHHHHcCCceEEEecccccccccHHHHHHHHHHHHHHHcCCCccccccc
Confidence            11     01111111       11111111111   111111    11111  245667778888899999887666532


Q ss_pred             ---------hhHHHHHHHHH-cCcCeEEEcccc
Q psy17626        159 ---------PISIFQKLKRE-LNFTKLCFEQDC  181 (184)
Q Consensus       159 ---------~~~~l~~l~~~-~~~~~v~~n~~~  181 (184)
                               ..+.+.++.+. ..+++||+..|.
T Consensus       181 ~~~~~~~~~~~~~~~~~l~~~~~~~aI~~~nD~  213 (412)
T 4fe7_A          181 ETAPENWQHAQNRLADWLQTLPPQTGIIAVTDA  213 (412)
T ss_dssp             CSSCSSHHHHHHHHHHHHHHSCTTEEEEESSHH
T ss_pred             cccccchhhHHHHHHHHHHhCCCCeEEEEEecH
Confidence                     23455566655 478999987653

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}

Probab=89.16  E-value=4.3  Score=30.34  Aligned_cols=155  Identities=10%  Similarity=0.014  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECC----hHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGS----PISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~----~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .|..+-+..+.+.+++.|..+.+...+    ....+.+++...+++.|++.... ...     ...+.+.+.|+++..++
T Consensus        23 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~-~~~-----~~~~~l~~~~iPvV~i~   96 (288)
T 3gv0_A           23 GFTSQMVFGITEVLSTTQYHLVVTPHIHAKDSMVPIRYILETGSADGVIISKIE-PND-----PRVRFMTERNMPFVTHG   96 (288)
T ss_dssp             CHHHHHHHHHHHHHTTSSCEEEECCBSSGGGTTHHHHHHHHHTCCSEEEEESCC-TTC-----HHHHHHHHTTCCEEEES
T ss_pred             HHHHHHHHHHHHHHHHcCCEEEEecCCcchhHHHHHHHHHHcCCccEEEEecCC-CCc-----HHHHHHhhCCCCEEEEC
Confidence            477888889999999999999887532    23456666777899998875321 111     22334566799998876


Q ss_pred             Cceeec-ccccccccCCCCchhHHHHHHHhhh---ccccc----cCcchhHHHHHHHHHHHHHHHhCCCeEEEE---eCC
Q psy17626         90 SHTLWD-PEVVIQTNGNVPPLTYKMYLHTVSC---IGTMH----IGYNRFRFLLECLADLDRQLKSHGGQLFIV---QGS  158 (184)
Q Consensus        90 ~~~L~~-p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~----~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~---~g~  158 (184)
                      ...--+ ...|..+       .+..-+...+.   .+-.+    .+........+.+.-..+.+++.|+++...   .++
T Consensus        97 ~~~~~~~~~~V~~D-------~~~~g~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~  169 (288)
T 3gv0_A           97 RSDMGIEHAFHDFD-------NEAYAYEAVERLAQCGRKRIAVIVPPSRFSFHDHARKGFNRGIRDFGLTEFPIDAVTIE  169 (288)
T ss_dssp             CCCSSCCCEEEEEC-------HHHHHHHHHHHHHHTTCCEEEEECCCTTSHHHHHHHHHHHHHHHHTTCEECCCCSCCTT
T ss_pred             CcCCCCCCcEEEeC-------cHHHHHHHHHHHHHCCCCeEEEEcCCcccchHHHHHHHHHHHHHHcCCCcchhheeccc
Confidence            542110 0111111       11111111111   11111    122223345567777888899989875532   222


Q ss_pred             --h---hHHHHHHHHHc-CcCeEEEcccc
Q psy17626        159 --P---ISIFQKLKREL-NFTKLCFEQDC  181 (184)
Q Consensus       159 --~---~~~l~~l~~~~-~~~~v~~n~~~  181 (184)
                        .   .+.+.++.++. .+++||+..|.
T Consensus       170 ~~~~~~~~~~~~~l~~~~~~~ai~~~~d~  198 (288)
T 3gv0_A          170 TPLEKIRDFGQRLMQSSDRPDGIVSISGS  198 (288)
T ss_dssp             SCHHHHHHHHHHHTTSSSCCSEEEESCHH
T ss_pred             cchHHHHHHHHHHHhCCCCCcEEEEcCcH
Confidence              1   24566666654 68999987653

>1mjh_A Protein (ATP-binding domain of protein MJ0577); hypothetical protein, structural genomics, functional assignment; HET: ATP; 1.70A {Methanocaldococcus jannaschii} SCOP: c.26.2.4

Probab=88.91  E-value=1.4  Score=30.06  Aligned_cols=73  Identities=14%  Similarity=0.117  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHhcCCe--EEEEECChHHHHHHHHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEEEec
Q psy17626         17 LECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .+.|..+.+.+...|++  ..+..|++.+.|.+.+++.+++.|+.-..- +...+- .-....+.+....+++..+.
T Consensus        82 ~~~l~~~~~~~~~~g~~~~~~v~~G~~~~~I~~~a~~~~~dlIV~G~~g~~~~~~~~~GSv~~~vl~~~~~pVlvv~  158 (162)
T 1mjh_A           82 KNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK  158 (162)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCSSCCTTCSSCHHHHHHHHHCCSCEEEEC
T ss_pred             HHHHHHHHHHHHHcCCceEEEEcCCCHHHHHHHHHHHcCCCEEEEcCCCCCCccceEecchHHHHHHhCCCCEEEEe
Confidence            34566677777777876  457789999999999999999999987542 221111 11233445566678877553

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}

Probab=88.66  E-value=5.8  Score=29.27  Aligned_cols=153  Identities=10%  Similarity=-0.016  Sum_probs=82.1

Q ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEECC--hHH--HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         13 FRFLLECLADLDRQLKSHGGQLFIVQGS--PIS--IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        13 ~~fl~~sL~~L~~~L~~~g~~L~v~~g~--~~~--~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      ..|..+-+..+.+.++++|..+.+...+  +..  .+.+.+...+++.|+..-   ..    +..++..+.+.|+++..+
T Consensus        20 ~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~~dgiIi~~---~~----~~~~~~~l~~~~iPvV~~   92 (277)
T 3e61_A           20 NPFFTLIARGVEDVALAHGYQVLIGNSDNDIKKAQGYLATFVSHNCTGMISTA---FN----ENIIENTLTDHHIPFVFI   92 (277)
T ss_dssp             SHHHHHHHHHHHHHHHHTTCCEEEEECTTCHHHHHHHHHHHHHTTCSEEEECG---GG----HHHHHHHHHHC-CCEEEG
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEec---CC----hHHHHHHHHcCCCCEEEE
Confidence            3477888888999999999999887643  322  234444557899998854   11    222331566789999987


Q ss_pred             cCceeecccccccccCCCCchhHHHHHHHhh---hcccccc----CcchhHHHHHHHHHHHHHHHhCCCeEE-EEeCC--
Q psy17626         89 VSHTLWDPEVVIQTNGNVPPLTYKMYLHTVS---CIGTMHI----GYNRFRFLLECLADLDRQLKSHGGQLF-IVQGS--  158 (184)
Q Consensus        89 ~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~---~~~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~-v~~g~--  158 (184)
                      +...--.. .+..++       +..-....+   +.+-.+.    +..........+.-+.+.+++.|++.. +..++  
T Consensus        93 ~~~~~~~~-~V~~D~-------~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~  164 (277)
T 3e61_A           93 DRINNEHN-GISTNH-------FKGGQLQAEVVRKGKGKNVLIVHENLLIDAFHQRVQGIKYILDQQRIDYKMLEATLLD  164 (277)
T ss_dssp             GGCC----------H-------HHHHHHHHHHHHHTTCCSEEEEESCTTSHHHHHHHHHHHHHHHC---CEEEEEGGGGG
T ss_pred             eccCCCCC-eEEech-------HHHHHHHHHHHHHCCCCeEEEEeCCCCCccHHHHHHHHHHHHHHcCCCccceecCCCC
Confidence            65432211 222211       111111111   1121111    222334555677778888998898766 44332  


Q ss_pred             hhHHHHHHHHHcCcCeEEEccc
Q psy17626        159 PISIFQKLKRELNFTKLCFEQD  180 (184)
Q Consensus       159 ~~~~l~~l~~~~~~~~v~~n~~  180 (184)
                      .......+.+...+++||+..|
T Consensus       165 ~~~~~~~l~~~~~~~ai~~~~d  186 (277)
T 3e61_A          165 NDKKFIDLIKELSIDSIICSND  186 (277)
T ss_dssp             SHHHHHHHHHHHTCCEEEESSH
T ss_pred             HHHHHHHhhcCCCCCEEEECCc
Confidence            2344444655678999998765

>3fdx_A Putative filament protein / universal stress PROT; structural genomics, APC60640.1, universal protein F, PSI-2; HET: MSE ATP; 1.58A {Klebsiella pneumoniae subsp} PDB: 3fh0_A*

Probab=88.10  E-value=1.8  Score=28.67  Aligned_cols=72  Identities=11%  Similarity=0.065  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHhcCC-----eEEEEECChHHHHHHHHHHcCcceEEEeecccchhHH--HHHHHHHHHHhCCCeEEE
Q psy17626         15 FLLECLADLDRQLKSHGG-----QLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHK--RDKKVKKWCAENNITVKE   87 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~-----~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~--rd~~v~~~l~~~gi~~~~   87 (184)
                      ...+.+..+++-+++.|.     ...+..|++.+.|.+.+++.+++-|++-.. .....+  .-....+.+...++++..
T Consensus        63 ~~~~~~~~l~~~~~~~~~~~~~v~~~~~~g~~~~~I~~~a~~~~~dliV~G~~-~~~~~~~~~Gs~~~~v~~~~~~pVlv  141 (143)
T 3fdx_A           63 LREGSETQLKEIAKKFSIPEDRMHFHVAEGSPKDKILALAKSLPADLVIIASH-RPDITTYLLGSNAAAVVRHAECSVLV  141 (143)
T ss_dssp             HHHHHHHHHHHHHTTSCCCGGGEEEEEEESCHHHHHHHHHHHTTCSEEEEESS-CTTCCSCSSCHHHHHHHHHCSSEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCCCceEEEEEecChHHHHHHHHHHhCCCEEEEeCC-CCCCeeeeeccHHHHHHHhCCCCEEE
Confidence            455667777777777775     467889999999999999999999999875 322111  112334455666777654

>3hgm_A Universal stress protein TEAD; rossman fold, signaling protein; HET: ATP; 1.90A {Halomonas elongata} SCOP: c.26.2.0

Probab=87.62  E-value=3.8  Score=27.12  Aligned_cols=73  Identities=10%  Similarity=0.107  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHHhcCC-----eEEEEECChHHHHHHHHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEE
Q psy17626         14 RFLLECLADLDRQLKSHGG-----QLFIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVK   86 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~-----~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~   86 (184)
                      .-..+.|..+.+.+++.|+     ...+..|++.+.|.+.+++.+++-|+.-..- +...+- .-....+.+...++++.
T Consensus        66 ~~~~~~l~~~~~~~~~~g~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pVl  145 (147)
T 3hgm_A           66 DYATEIAVQAKTRATELGVPADKVRAFVKGGRPSRTIVRFARKRECDLVVIGAQGTNGDKSLLLGSVAQRVAGSAHCPVL  145 (147)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCGGGEEEEEEESCHHHHHHHHHHHTTCSEEEECSSCTTCCSCCCCCHHHHHHHHHCSSCEE
T ss_pred             HHHHHHHHHHHHHHHhcCCCccceEEEEecCCHHHHHHHHHHHhCCCEEEEeCCCCccccceeeccHHHHHHhhCCCCEE
Confidence            3455667777888887785     4577899999999999999999999987532 111111 11233444555566654

>3n28_A Phosphoserine phosphatase; HAD family hydrolase, structural genomics, PSI, protein STRU initiative, nysgrc; 2.30A {Vibrio cholerae}

Probab=87.57  E-value=3.6  Score=31.89  Aligned_cols=43  Identities=21%  Similarity=0.190  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcc
Q psy17626        137 CLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ  179 (184)
Q Consensus       137 ~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~  179 (184)
                      ...++-+.|++.|.++.++.++.......+.++.|++.++.+.
T Consensus       182 g~~~~l~~L~~~g~~~~ivS~~~~~~~~~~~~~lgl~~~~~~~  224 (335)
T 3n28_A          182 ELPELVATLHAFGWKVAIASGGFTYFSDYLKEQLSLDYAQSNT  224 (335)
T ss_dssp             THHHHHHHHHHTTCEEEEEEEEEHHHHHHHHHHHTCSEEEEEE
T ss_pred             CHHHHHHHHHHCCCEEEEEeCCcHHHHHHHHHHcCCCeEEeee
Confidence            3445666778889999999999988899999999999887653

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}

Probab=87.48  E-value=7.3  Score=29.01  Aligned_cols=154  Identities=11%  Similarity=0.018  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEC--ChHH--HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQG--SPIS--IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g--~~~~--~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .|..+-+..+.+.+++.|..+.+...  ++..  .+.+.+...+++.|++.....      .....+.+.+.|+++..++
T Consensus        21 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~------~~~~~~~~~~~~iPvV~~~   94 (291)
T 3egc_A           21 VFFAEVASGVESEARHKGYSVLLANTAEDIVREREAVGQFFERRVDGLILAPSEG------EHDYLRTELPKTFPIVAVN   94 (291)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHTTCSEEEECCCSS------CCHHHHHSSCTTSCEEEES
T ss_pred             hHHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCC------ChHHHHHhhccCCCEEEEe
Confidence            47778888899999999999988864  3332  233444556899888754322      1123334556799998876


Q ss_pred             Cceeec-ccccccccCCCCchhHHHHHHHhhh---cccccc----CcchhHHHHHHHHHHHHHHHhCCCeEE---EEe--
Q psy17626         90 SHTLWD-PEVVIQTNGNVPPLTYKMYLHTVSC---IGTMHI----GYNRFRFLLECLADLDRQLKSHGGQLF---IVQ--  156 (184)
Q Consensus        90 ~~~L~~-p~~i~~~~~~~~~~v~~~F~~~~~~---~~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~---v~~--  156 (184)
                      ...--+ ...+..       ..+..-+...+.   .+-.+.    +........+.+.-..+.+++.|+++.   +..  
T Consensus        95 ~~~~~~~~~~V~~-------D~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~~  167 (291)
T 3egc_A           95 RELRIPGCGAVLS-------ENVRGARTAVEYLIARGHTRIGAIVGSAGLMTSRERLKGFRAAMSAAGLPVRQEWIAAGG  167 (291)
T ss_dssp             SCCCCTTCEEEEE-------CHHHHHHHHHHHHHHTTCCSEEEECSCTTSHHHHHHHHHHHHHHHHTTCCCCGGGEEC--
T ss_pred             cccCCCCCCEEEE-------CcHHHHHHHHHHHHHcCCCEEEEEeCCCCCcCHHHHHHHHHHHHHHcCCCCCHHHeEeCC
Confidence            543210 111111       111111111111   121111    222234455677778888888887642   322  


Q ss_pred             ---CChhHHHHHHHHH-cCcCeEEEccc
Q psy17626        157 ---GSPISIFQKLKRE-LNFTKLCFEQD  180 (184)
Q Consensus       157 ---g~~~~~l~~l~~~-~~~~~v~~n~~  180 (184)
                         .+..+.+.++.++ ..+++||+..|
T Consensus       168 ~~~~~~~~~~~~~l~~~~~~~ai~~~~d  195 (291)
T 3egc_A          168 VRADNGRDGAIKVLTGADRPTALLTSSH  195 (291)
T ss_dssp             ----CCHHHHHHHHTC-CCCSEEEESSH
T ss_pred             CChhHHHHHHHHHHhCCCCCcEEEECCc
Confidence               2334566777654 47899998765

>3k4h_A Putative transcriptional regulator; structural genomics, protein structure INI NEW YORK structural genomix research consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh 391-98}

Probab=87.19  E-value=7.5  Score=28.86  Aligned_cols=154  Identities=15%  Similarity=0.112  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECCh-H---HHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGSP-I---SIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~~-~---~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .|..+-+..+.+.++++|..+.+...+. .   ..+.+.+...+++.|++......     + ...+.+.+.|+++..++
T Consensus        26 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~-----~-~~~~~l~~~~iPvV~~~   99 (292)
T 3k4h_A           26 PFFPEVIRGISSFAHVEGYALYMSTGETEEEIFNGVVKMVQGRQIGGIILLYSREN-----D-RIIQYLHEQNFPFVLIG   99 (292)
T ss_dssp             THHHHHHHHHHHHHHHTTCEEEECCCCSHHHHHHHHHHHHHTTCCCEEEESCCBTT-----C-HHHHHHHHTTCCEEEES
T ss_pred             HHHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEeCCCCC-----h-HHHHHHHHCCCCEEEEC
Confidence            4778888889999999999998876532 2   23444555678999887532111     1 23445567799998876


Q ss_pred             Cceeec--ccccccccCCCCchhHHHHHHHhhhc---cccc----cCcchhHHHHHHHHHHHHHHHhCCCeE---EEEeC
Q psy17626         90 SHTLWD--PEVVIQTNGNVPPLTYKMYLHTVSCI---GTMH----IGYNRFRFLLECLADLDRQLKSHGGQL---FIVQG  157 (184)
Q Consensus        90 ~~~L~~--p~~i~~~~~~~~~~v~~~F~~~~~~~---~~~~----~~~~r~~fl~~~L~~L~~~L~~~g~~L---~v~~g  157 (184)
                      ...--.  ...|..       ..+..-+...+.+   +..+    .+........+.+.-..+.|++.|+++   .+..+
T Consensus       100 ~~~~~~~~~~~V~~-------D~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~g~~~~~~~~~~~  172 (292)
T 3k4h_A          100 KPYDRKDEITYVDN-------DNYTAAREVAEYLISLGHKQIAFIGGGSDLLVTRDRLAGMSDALKLADIVLPKEYILHF  172 (292)
T ss_dssp             CCSSCTTTSCEEEC-------CHHHHHHHHHHHHHHTTCCCEEEEESCTTBHHHHHHHHHHHHHHHHTTCCCCGGGEEEC
T ss_pred             CCCCCCCCCCEEEE-------CcHHHHHHHHHHHHHCCCceEEEEeCcccchhHHHHHHHHHHHHHHcCCCCChheEEec
Confidence            542111  111111       1111111121111   1111    122223344566778888899888763   23333


Q ss_pred             C-----hhHHHHHHHHHc-CcCeEEEccc
Q psy17626        158 S-----PISIFQKLKREL-NFTKLCFEQD  180 (184)
Q Consensus       158 ~-----~~~~l~~l~~~~-~~~~v~~n~~  180 (184)
                      +     ..+.+.++.++. .+++||+..|
T Consensus       173 ~~~~~~~~~~~~~~l~~~~~~~ai~~~~d  201 (292)
T 3k4h_A          173 DFSRESGQQAVEELMGLQQPPTAIMATDD  201 (292)
T ss_dssp             CSSHHHHHHHHHHHHTSSSCCSEEEESSH
T ss_pred             CCCHHHHHHHHHHHHcCCCCCcEEEEcCh
Confidence            2     234566676665 7899998765

>3h75_A Periplasmic sugar-binding domain protein; protein structure initiative II (PSI II), sugar binding PROT alpha/beta fold; 1.60A {Pseudomonas fluorescens pf-5}

Probab=86.80  E-value=9.1  Score=29.45  Aligned_cols=73  Identities=12%  Similarity=0.057  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEC--ChH---HHHHHHHHH-cCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEE
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQG--SPI---SIFQKLKRE-LNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKE   87 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g--~~~---~~l~~l~~~-~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~   87 (184)
                      .|..+-+..+++.++++|..+.+...  ++.   +.+..+.+. .+++.|++.-+..     ....+.+.+.+.||++..
T Consensus        17 ~f~~~~~~g~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~i~~~~~vDgiIi~~~~~-----~~~~~~~~~~~~giPvV~   91 (350)
T 3h75_A           17 TFWVSYSQFMQAAARDLGLDLRILYAERDPQNTLQQARELFQGRDKPDYLMLVNEQY-----VAPQILRLSQGSGIKLFI   91 (350)
T ss_dssp             HHHHHHHHHHHHHHHHHTCEEEEEECTTCHHHHHHHHHHHHHSSSCCSEEEEECCSS-----HHHHHHHHHTTSCCEEEE
T ss_pred             hHHHHHHHHHHHHHHHcCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEeCchh-----hHHHHHHHHHhCCCcEEE
Confidence            47777888888889999999988864  333   346667766 7899998864211     122334455678999998


Q ss_pred             ecCc
Q psy17626         88 FVSH   91 (184)
Q Consensus        88 ~~~~   91 (184)
                      ++..
T Consensus        92 ~~~~   95 (350)
T 3h75_A           92 VNSP   95 (350)
T ss_dssp             EESC
T ss_pred             EcCC
Confidence            7654

>3dlo_A Universal stress protein; unknown function, structural genomics, PSI-2, protein struct initiative, midwest center for structural genomics; HET: MSE; 1.97A {Archaeoglobus fulgidus} PDB: 3qtb_A*

Probab=86.16  E-value=1.5  Score=29.95  Aligned_cols=74  Identities=9%  Similarity=-0.084  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEE----EECChHHHHHHHHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEEE
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFI----VQGSPISIFQKLKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVKE   87 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v----~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~~   87 (184)
                      .-..+.|.++.+.+++.|.+..+    ..|+|.+.|.+.+++.+++-|+.-..- +...+- .-....+.+....+++..
T Consensus        74 ~~~~~~l~~~~~~~~~~g~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIV~G~~g~~~~~~~~lGSv~~~vl~~a~~PVLv  153 (155)
T 3dlo_A           74 IEAKETLSWAVSIIRKEGAEGEEHLLVRGKEPPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVIC  153 (155)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEEEESSSCHHHHHHHHHHHTTCSEEEEECCEECTTSCEECCHHHHHHHHHCSSCEEE
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHHcCCCEEEECCCCCCCCCCEEeccHHHHHHHhCCCCEEE
Confidence            34556677788888888887653    349999999999999999999986432 111111 122334455566676654

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}

Probab=86.10  E-value=8.6  Score=28.49  Aligned_cols=158  Identities=11%  Similarity=0.031  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEC--ChH---HHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEe
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQG--SPI---SIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEF   88 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g--~~~---~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~   88 (184)
                      .|..+-+..+.+.++++|..+.+...  ++.   +.+..+ ...+++.|+..-..   ....+ ...+.+.+.||++..+
T Consensus        18 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l-~~~~vdgiIi~~~~---~~~~~-~~~~~~~~~~iPvV~~   92 (291)
T 3l49_A           18 DWDLKAYQAQIAEIERLGGTAIALDAGRNDQTQVSQIQTL-IAQKPDAIIEQLGN---LDVLN-PWLQKINDAGIPLFTV   92 (291)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHH-HHHCCSEEEEESSC---HHHHH-HHHHHHHHTTCCEEEE
T ss_pred             hHHHHHHHHHHHHHHHcCCEEEEEcCCCCHHHHHHHHHHH-HHcCCCEEEEeCCC---hhhhH-HHHHHHHHCCCcEEEe
Confidence            47778888999999999999988854  332   233333 34689998875321   11222 2334456679999888


Q ss_pred             cCceeecccccccccCCCCch-hHHHHHHHhhh-ccccc----cCcchhHHHHHHHHHHHHHHHhC-CCeEE----EEeC
Q psy17626         89 VSHTLWDPEVVIQTNGNVPPL-TYKMYLHTVSC-IGTMH----IGYNRFRFLLECLADLDRQLKSH-GGQLF----IVQG  157 (184)
Q Consensus        89 ~~~~L~~p~~i~~~~~~~~~~-v~~~F~~~~~~-~~~~~----~~~~r~~fl~~~L~~L~~~L~~~-g~~L~----v~~g  157 (184)
                      +...   ++.+..= +.+.+. .+..-...... .+..+    .+........+.+.-..+.+++. |+++.    +..+
T Consensus        93 ~~~~---~~~~~~V-~~D~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~  168 (291)
T 3l49_A           93 DTAT---PHAINNT-TSNNYSIGAELALQMVADLGGKGNVLVFNGFYSVPVCKIRYDQMKYVLEAFPDVKIIEPELRDVI  168 (291)
T ss_dssp             SCCC---TTCSEEE-EECHHHHHHHHHHHHHHHHTTCEEEEEECSCTTSHHHHHHHHHHHHHHHTCTTEEECSSCBCCCS
T ss_pred             cCCC---CCcCceE-ecChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHCCCCEEEeeeccCCC
Confidence            6542   1111110 000111 11111111111 11111    12222334455677788888887 45421    1122


Q ss_pred             -----ChhHHHHHHHHHc----CcCeEEEccc
Q psy17626        158 -----SPISIFQKLKREL----NFTKLCFEQD  180 (184)
Q Consensus       158 -----~~~~~l~~l~~~~----~~~~v~~n~~  180 (184)
                           ...+.+.++.+++    +++.||+..|
T Consensus       169 ~~~~~~~~~~~~~~l~~~~~~~~~~ai~~~~d  200 (291)
T 3l49_A          169 PNTIQSAYSNVTDMLTKYPNEGDVGAIWACWD  200 (291)
T ss_dssp             SSHHHHHHHHHHHHHHHCCSTTSCCEEEESSH
T ss_pred             CCCHHHHHHHHHHHHHhCCCcCCcCEEEECCC
Confidence                 1234677777776    5999998765

>3ksm_A ABC-type sugar transport system, periplasmic COMP; periplasmic component, PSI- 11023L, structural genomics, protein structure initiative; HET: BDR; 1.90A {Hahella chejuensis}

Probab=85.54  E-value=8.8  Score=28.09  Aligned_cols=159  Identities=11%  Similarity=-0.011  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEE----CChHH---HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQ----GSPIS---IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~----g~~~~---~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      .|..+-+..+.+.++++|..+.+..    +++..   .+..+.+..+++.|+....-.   ...+ ...+.+.+.|+++.
T Consensus        13 ~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~~vdgii~~~~~~---~~~~-~~~~~~~~~~ipvV   88 (276)
T 3ksm_A           13 AYWRQVYLGAQKAADEAGVTLLHRSTKDDGDIAGQIQILSYHLSQAPPDALILAPNSA---EDLT-PSVAQYRARNIPVL   88 (276)
T ss_dssp             THHHHHHHHHHHHHHHHTCEEEECCCSSTTCHHHHHHHHHHHHHHSCCSEEEECCSST---TTTH-HHHHHHHHTTCCEE
T ss_pred             hHHHHHHHHHHHHHHHcCCEEEEECCCCCCCHHHHHHHHHHHHHhCCCCEEEEeCCCH---HHHH-HHHHHHHHCCCcEE
Confidence            3777778888899999999998875    34432   455555543399998864211   1112 22334567799999


Q ss_pred             EecCceeecc--cccccccCCCCch-hHHHHHHHhhhc---cccc----cCcchhHHHHHHHHHHHHHHHhC-CCeEEE-
Q psy17626         87 EFVSHTLWDP--EVVIQTNGNVPPL-TYKMYLHTVSCI---GTMH----IGYNRFRFLLECLADLDRQLKSH-GGQLFI-  154 (184)
Q Consensus        87 ~~~~~~L~~p--~~i~~~~~~~~~~-v~~~F~~~~~~~---~~~~----~~~~r~~fl~~~L~~L~~~L~~~-g~~L~v-  154 (184)
                      .++...--+.  ..+..+    .+. .+..-......+   +..+    .+..........+.-..+.+++. |+++.. 
T Consensus        89 ~~~~~~~~~~~~~~V~~d----~~~~g~~~~~~l~~~~~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~  164 (276)
T 3ksm_A           89 VVDSDLAGDAHQGLVATD----NYAAGQLAARALLATLDLSKERNIALLRLRAGNASTDQREQGFLDVLRKHDKIRIIAA  164 (276)
T ss_dssp             EESSCCSSSCSSEEEECC----HHHHHHHHHHHHHHHSCTTSCEEEEECBCCTTCHHHHHHHHHHHHHHTTCTTEEEEEC
T ss_pred             EEecCCCCCCcceEEccC----HHHHHHHHHHHHHHhcCcCCCceEEEEEcCCCchhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            8865431110  011111    111 111111111111   1111    12222344556777788888888 776542 


Q ss_pred             EeC--C---hhHHHHHHHHHc-CcCeEEEccc
Q psy17626        155 VQG--S---PISIFQKLKREL-NFTKLCFEQD  180 (184)
Q Consensus       155 ~~g--~---~~~~l~~l~~~~-~~~~v~~n~~  180 (184)
                      ..+  +   ..+.+.++.+++ .++.||+..+
T Consensus       165 ~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d  196 (276)
T 3ksm_A          165 PYAGDDRGAARSEMLRLLKETPTIDGLFTPNE  196 (276)
T ss_dssp             CBCCSSHHHHHHHHHHHHHHCSCCCEEECCSH
T ss_pred             ecCCCcHHHHHHHHHHHHHhCCCceEEEECCc
Confidence            222  1   234566777776 7899998755

>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein, USP domain, nucleotide binding domain, AMP; HET: MSE AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4

Probab=85.39  E-value=2.7  Score=29.04  Aligned_cols=72  Identities=10%  Similarity=-0.000  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHHhcCCeE--EEEECChHHHHHHHHHHcCcceEEEeeccc-chhHHH-HHHHHHHHHhCCCeEEEec
Q psy17626         18 ECLADLDRQLKSHGGQL--FIVQGSPISIFQKLKRELNFTKLCFEQDCE-ALWHKR-DKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~L--~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~-~~~~~r-d~~v~~~l~~~gi~~~~~~   89 (184)
                      +.|..+.+.+...|++.  .+..|++.+.|.+.+++.+++.|++-..-. ...+-. -....+.+....+++..+.
T Consensus        87 ~~l~~~~~~~~~~g~~~~~~v~~G~~~~~I~~~a~~~~~DLIVmG~~g~~~~~~~~~Gsva~~vl~~a~~pVlvv~  162 (175)
T 2gm3_A           87 HLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIK  162 (175)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEEESCHHHHHHHHHHHHCCSEEEEEECCCC--------CHHHHHHHHCSSCEEEEE
T ss_pred             HHHHHHHHHHHHCCCceEEEEecCCHHHHHHHHHHHhCCCEEEEeCCCCChhhhhhcCchHHHHHhCCCCCEEEEc
Confidence            45666666677778764  577899999999999999999999875422 111111 1233455666778887543

>3fg9_A Protein of universal stress protein USPA family; APC60691, nucleotide- binding, lactobacillus plantarum WCFS1, structural genomics PSI-2; 1.47A {Lactobacillus plantarum}

Probab=84.92  E-value=4  Score=27.46  Aligned_cols=73  Identities=12%  Similarity=0.074  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHHhcCC---eEEEEE-CChHHHHHHH-HHHcCcceEEEeecccc-hhHHHHHHHHHHHHhCCCeEEE
Q psy17626         15 FLLECLADLDRQLKSHGG---QLFIVQ-GSPISIFQKL-KRELNFTKLCFEQDCEA-LWHKRDKKVKKWCAENNITVKE   87 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~---~L~v~~-g~~~~~l~~l-~~~~~~~~v~~~~~~~~-~~~~rd~~v~~~l~~~gi~~~~   87 (184)
                      -..+.|..+.+.+.+.|+   ...+.. |++.+.|.+. +++.+++-|+.-..-.. ..+-.-....+.+....+++..
T Consensus        76 ~~~~~l~~~~~~~~~~g~~~~~~~v~~~g~~~~~I~~~~a~~~~~DlIV~G~~g~~~~~~~~Gs~~~~vl~~a~~PVlv  154 (156)
T 3fg9_A           76 HVEDVVAEYVQLAEQRGVNQVEPLVYEGGDVDDVILEQVIPEFKPDLLVTGADTEFPHSKIAGAIGPRLARKAPISVIV  154 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCSSEEEEEEECSCHHHHHHHTHHHHHCCSEEEEETTCCCTTSSSCSCHHHHHHHHCSSEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCceEEEEEeCCCHHHHHHHHHHHhcCCCEEEECCCCCCccceeecchHHHHHHhCCCCEEE
Confidence            345667777777777787   356778 9999999998 99999999998754221 1111112234455566677654

>2dum_A Hypothetical protein PH0823; conserved hypothetical protein, putative universal protein A structural genomics, NPPSFA; 2.75A {Pyrococcus horikoshii}

Probab=84.34  E-value=2.1  Score=29.42  Aligned_cols=74  Identities=16%  Similarity=0.097  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHhcCCe--E--EEEECChHHHHHHHHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEEEec
Q psy17626         16 LLECLADLDRQLKSHGGQ--L--FIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        16 l~~sL~~L~~~L~~~g~~--L--~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~~~~   89 (184)
                      ..+.|..+.+.+...|++  .  .+..|++.+.|.+.+++.+++.|+.-..- ....+. .-....+.+...++++..+.
T Consensus        76 ~~~~l~~~~~~~~~~g~~~~~~~~~~~g~~~~~I~~~a~~~~~DlIV~G~~g~~~~~~~~~Gsv~~~vl~~~~~PVlvv~  155 (170)
T 2dum_A           76 ASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIK  155 (170)
T ss_dssp             HHHHHHHHHHHHHHHTTCSEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCCCC--TTCCCHHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHHHHHHHHHcCCceeeeeEEecCChHHHHHHHHHHcCCCEEEECCCCCCccccceechHHHHHHHhCCCCEEEEc
Confidence            344566666666666764  4  67789999999999999999999987542 211111 11234455666788887654

>3vni_A Xylose isomerase domain protein TIM barrel; D-psicose 3-epimerase, ketohexose; 1.98A {Clostridium cellulolyticum} PDB: 3vnj_A* 3vnl_A* 3vnk_A* 3vnm_A*

Probab=83.65  E-value=4.9  Score=30.22  Aligned_cols=135  Identities=10%  Similarity=0.055  Sum_probs=72.7

Q ss_pred             hHHHHHHHHHHcCcceEEEeecc-cchhHHHHHHHHHHHHhCCCeEEEecCceeecccccccccCCCCc-------hhHH
Q psy17626         41 PISIFQKLKRELNFTKLCFEQDC-EALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPP-------LTYK  112 (184)
Q Consensus        41 ~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~rd~~v~~~l~~~gi~~~~~~~~~L~~p~~i~~~~~~~~~-------~v~~  112 (184)
                      +.+...+.+++.|++.|=..... .......-+.+++.+++.|+++....+    ++..+... . .-+       ..+.
T Consensus        18 ~~~~~l~~~~~~G~~~vEl~~~~~~~~~~~~~~~~~~~l~~~gl~i~~~~~----~~~~~~l~-~-~d~~~r~~~~~~~~   91 (294)
T 3vni_A           18 DYKYYIEKVAKLGFDILEIAASPLPFYSDIQINELKACAHGNGITLTVGHG----PSAEQNLS-S-PDPDIRKNAKAFYT   91 (294)
T ss_dssp             CHHHHHHHHHHHTCSEEEEESTTGGGCCHHHHHHHHHHHHHTTCEEEEEEC----CCGGGCTT-C-SCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCEEEecCcccCCcCHHHHHHHHHHHHHcCCeEEEeec----CCCCcCCC-C-CCHHHHHHHHHHHH
Confidence            45555666677788877554321 111233345778888888888776221    11111110 0 011       1122


Q ss_pred             HHHHHhhhcccccc--------C------c---chhHHHHHHHHHHHHHHHhCCCeEEEEeC--------ChhHHHHHHH
Q psy17626        113 MYLHTVSCIGTMHI--------G------Y---NRFRFLLECLADLDRQLKSHGGQLFIVQG--------SPISIFQKLK  167 (184)
Q Consensus       113 ~F~~~~~~~~~~~~--------~------~---~r~~fl~~~L~~L~~~L~~~g~~L~v~~g--------~~~~~l~~l~  167 (184)
                      ........++.+..        +      .   ..+..+.++|..+....++.|+.|.+-.-        ...+.+.+++
T Consensus        92 ~~i~~a~~lG~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~~Gv~l~lEn~~~~~~~~~~~~~~~~~l~  171 (294)
T 3vni_A           92 DLLKRLYKLDVHLIGGALYSYWPIDYTKTIDKKGDWERSVESVREVAKVAEACGVDFCLEVLNRFENYLINTAQEGVDFV  171 (294)
T ss_dssp             HHHHHHHHHTCCEEEESTTSCSSCCTTSCCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEECCCTTTCSSCCSHHHHHHHH
T ss_pred             HHHHHHHHhCCCeeeccccCCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCEEEEEecCcccCcccCCHHHHHHHH
Confidence            22333333332111        0      1   12355678888888888899998887632        2355677888


Q ss_pred             HHcCcCeEEEcccc
Q psy17626        168 RELNFTKLCFEQDC  181 (184)
Q Consensus       168 ~~~~~~~v~~n~~~  181 (184)
                      ++.+-..|-..-|.
T Consensus       172 ~~v~~~~vg~~~D~  185 (294)
T 3vni_A          172 KQVDHNNVKVMLDT  185 (294)
T ss_dssp             HHHCCTTEEEEEEH
T ss_pred             HHcCCCCEEEEEEh
Confidence            88877666665554

>3ij5_A 3-deoxy-D-manno-octulosonate 8-phosphate phosphat; IDP022 hydrolase, lipopolysaccharide biosynthesis, magnesium, STRU genomics; 1.95A {Yersinia pestis}

Probab=83.15  E-value=1.7  Score=31.72  Aligned_cols=55  Identities=16%  Similarity=0.093  Sum_probs=41.8

Q ss_pred             HHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626         23 LDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus        23 L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +=+.|++.|+++.|..|++...+..+++..+++.++...  .+    .-..++.++++.|+
T Consensus        84 ~L~~L~~~G~~l~I~T~~~~~~~~~~l~~lgi~~~f~~~--k~----K~~~l~~~~~~lg~  138 (211)
T 3ij5_A           84 GIRCLITSDIDVAIITGRRAKLLEDRANTLGITHLYQGQ--SD----KLVAYHELLATLQC  138 (211)
T ss_dssp             HHHHHHHTTCEEEEECSSCCHHHHHHHHHHTCCEEECSC--SS----HHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCEEEEEeCCCHHHHHHHHHHcCCchhhccc--CC----hHHHHHHHHHHcCc
Confidence            446677889999999999999999999999999887654  11    12355666666565

>3n07_A 3-deoxy-D-manno-octulosonate 8-phosphate phosphat; structural genomics, phosphatase, PSI-2, protein structure initiative; HET: MSE; 1.76A {Vibrio cholerae}

Probab=82.73  E-value=1.9  Score=30.95  Aligned_cols=53  Identities=17%  Similarity=0.273  Sum_probs=40.1

Q ss_pred             HHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626         25 RQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus        25 ~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +.|++.|+++.|+.|++...+..++++.+++.++...      ...-..++.++++.|+
T Consensus        62 ~~L~~~G~~~~ivT~~~~~~~~~~l~~lgi~~~~~~~------k~k~~~~~~~~~~~~~  114 (195)
T 3n07_A           62 KALMNAGIEIAIITGRRSQIVENRMKALGISLIYQGQ------DDKVQAYYDICQKLAI  114 (195)
T ss_dssp             HHHHHTTCEEEEECSSCCHHHHHHHHHTTCCEEECSC------SSHHHHHHHHHHHHCC
T ss_pred             HHHHHCCCEEEEEECcCHHHHHHHHHHcCCcEEeeCC------CCcHHHHHHHHHHhCC
Confidence            4567789999999999999999999999999887654      1122355566666565

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=82.57  E-value=14  Score=28.21  Aligned_cols=148  Identities=11%  Similarity=0.114  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECChHH---HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEecC
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGSPIS---IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVS   90 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~---~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~~   90 (184)
                      .|..+-+..+.+.+++.|..+.+...+..+   .+.+.+...+++.|+....            .+.+.+.|+++..++.
T Consensus        77 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~------------~~~~~~~~iPvV~~~~  144 (333)
T 3jvd_A           77 EYYSESLQTIQQDLKAAGYQMLVAEANSVQAQDVVMESLISIQAAGIIHVPV------------VGSIAPEGIPMVQLTR  144 (333)
T ss_dssp             HHHHHHHHHHHHHHHHHTCEEEEEECCSHHHHHHHHHHHHHHTCSEEEECCC------------TTCCC-CCSCEEEECC
T ss_pred             hHHHHHHHHHHHHHHHCCCEEEEECCCChHHHHHHHHHHHhCCCCEEEEcch------------HHHHhhCCCCEEEECc
Confidence            477788888888999999998887644222   2333344568888887643            1223456899887765


Q ss_pred             ceeec-ccccccccCCCCchhHHHHHHHhhhc---cccc----cCcchhHHHHHHHHHHHHHHHhCCCeEEEEe-CC---
Q psy17626         91 HTLWD-PEVVIQTNGNVPPLTYKMYLHTVSCI---GTMH----IGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GS---  158 (184)
Q Consensus        91 ~~L~~-p~~i~~~~~~~~~~v~~~F~~~~~~~---~~~~----~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-g~---  158 (184)
                      ..--+ ...+.       ...+..-+...+.+   +-.+    .++.......+.++-..+.|++.|++ .+.. ++   
T Consensus       145 ~~~~~~~~~V~-------~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~-~~~~~~~~~~  216 (333)
T 3jvd_A          145 GELGPGFPRVL-------CDDEAGFFQLTESVLGGSGMNIAALVGEESLSTTQERMRGISHAASIYGAE-VTFHFGHYSV  216 (333)
T ss_dssp             ----CCSCEEE-------ECHHHHHHHHHHHHCCSSSCEEEEEESCTTSHHHHHHHHHHHHHHHHTTCE-EEEEECCSSH
T ss_pred             cCCCCCCCEEE-------EChHHHHHHHHHHHHHCCCCeEEEEeCCCCCccHHHHHHHHHHHHHHCCCC-EEEecCCCCH
Confidence            32110 11111       11122222222222   1111    12222334556778888899999998 4444 32   


Q ss_pred             --hhHHHHHHHHHcCcCeEEEcccc
Q psy17626        159 --PISIFQKLKRELNFTKLCFEQDC  181 (184)
Q Consensus       159 --~~~~l~~l~~~~~~~~v~~n~~~  181 (184)
                        ..+.+.++.++..+++||+..|.
T Consensus       217 ~~~~~~~~~ll~~~~~~ai~~~nd~  241 (333)
T 3jvd_A          217 ESGEEMAQVVFNNGLPDALIVASPR  241 (333)
T ss_dssp             HHHHHHHHHHHHTCCCSEEEECCHH
T ss_pred             HHHHHHHHHHhcCCCCcEEEECCHH
Confidence              23456777777779999987663

>3mmz_A Putative HAD family hydrolase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.84A {Streptomyces avermitilis}

Probab=82.48  E-value=2.5  Score=29.60  Aligned_cols=54  Identities=20%  Similarity=0.418  Sum_probs=39.2

Q ss_pred             HHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626         23 LDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus        23 L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +=+.|++.|+++.|+.|++...+..+++..+++ ++...  .    ..-..++.++++.|+
T Consensus        47 ~l~~L~~~g~~~~i~T~~~~~~~~~~~~~lgi~-~~~~~--~----~k~~~l~~~~~~~~~  100 (176)
T 3mmz_A           47 GIAALRKSGLTMLILSTEQNPVVAARARKLKIP-VLHGI--D----RKDLALKQWCEEQGI  100 (176)
T ss_dssp             HHHHHHHTTCEEEEEESSCCHHHHHHHHHHTCC-EEESC--S----CHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCeEEEEECcChHHHHHHHHHcCCe-eEeCC--C----ChHHHHHHHHHHcCC
Confidence            445677889999999999999999999999999 54432  1    122355556666564

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=82.34  E-value=15  Score=28.18  Aligned_cols=154  Identities=11%  Similarity=0.001  Sum_probs=83.9

Q ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEC--ChHHH--HHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEecC
Q psy17626         15 FLLECLADLDRQLKSHGGQLFIVQG--SPISI--FQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFVS   90 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~~L~v~~g--~~~~~--l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~~   90 (184)
                      |..+-+..+.+.++++|..+.+...  ++...  +.+.+...+++.|++..... ..     ...+.+.+.|+++..+++
T Consensus        82 ~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdGiIi~~~~~-~~-----~~~~~l~~~~iPvV~i~~  155 (344)
T 3kjx_A           82 VFPEVLTGINQVLEDTELQPVVGVTDYLPEKEEKVLYEMLSWRPSGVIIAGLEH-SE-----AARAMLDAAGIPVVEIMD  155 (344)
T ss_dssp             SHHHHHHHHHHHHTSSSSEEEEEECTTCHHHHHHHHHHHHTTCCSEEEEECSCC-CH-----HHHHHHHHCSSCEEEEEE
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEECCCC-CH-----HHHHHHHhCCCCEEEEeC
Confidence            6677788899999999999988754  33322  22233346889888753211 11     234456678999988753


Q ss_pred             ceeeccc-ccccccCCCCchhHHHHHHHhhh---cccccc----Ccc-hhHHHHHHHHHHHHHHHhCCCeE---EEEeCC
Q psy17626         91 HTLWDPE-VVIQTNGNVPPLTYKMYLHTVSC---IGTMHI----GYN-RFRFLLECLADLDRQLKSHGGQL---FIVQGS  158 (184)
Q Consensus        91 ~~L~~p~-~i~~~~~~~~~~v~~~F~~~~~~---~~~~~~----~~~-r~~fl~~~L~~L~~~L~~~g~~L---~v~~g~  158 (184)
                      ..--+.. .+..+       .+..-+...+.   .+-.+.    ++. ......+.+.-..+.|++.|+++   .+..++
T Consensus       156 ~~~~~~~~~V~~D-------~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~  228 (344)
T 3kjx_A          156 SDGKPVDAMVGIS-------HRRAGREMAQAILKAGYRRIGFMGTKMPLDYRARKRFEGFTEVLGKNGVEIEDREFYSGG  228 (344)
T ss_dssp             CSSCCSSEEEEEC-------HHHHHHHHHHHHHHHTCCSCCEEESSTTTCHHHHHHHHHHHHHHHHTTCCCSCEEECSSC
T ss_pred             CCCCCCCCEEEEC-------cHHHHHHHHHHHHHCCCCeEEEEecCcccCccHHHHHHHHHHHHHHcCCCCChheEEeCC
Confidence            2111110 12111       11111111111   111111    111 11344566777888999988764   333332


Q ss_pred             -----hhHHHHHHHHHc-CcCeEEEcccc
Q psy17626        159 -----PISIFQKLKREL-NFTKLCFEQDC  181 (184)
Q Consensus       159 -----~~~~l~~l~~~~-~~~~v~~n~~~  181 (184)
                           ..+.+.++.++. .+++||+..|.
T Consensus       229 ~~~~~~~~~~~~ll~~~~~~~ai~~~nd~  257 (344)
T 3kjx_A          229 SALAKGREMTQAMLERSPDLDFLYYSNDM  257 (344)
T ss_dssp             CCHHHHHHHHHHHHHHSTTCCEEEESSHH
T ss_pred             CCHHHHHHHHHHHHhcCCCCCEEEECCHH
Confidence                 234667777766 89999987653

>3mn1_A Probable YRBI family phosphatase; structural genomics, PSI, protein structure initiative, NYSG phosphatase; 1.80A {Pseudomonas syringae PV} PDB: 3nrj_A

Probab=82.05  E-value=2  Score=30.48  Aligned_cols=55  Identities=20%  Similarity=0.167  Sum_probs=41.8

Q ss_pred             HHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626         23 LDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus        23 L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +=+.|++.|+++.|..|++...+..+++..+++.++...     ..+ -+.+..++++.|+
T Consensus        54 ~l~~L~~~g~~~~i~T~~~~~~~~~~~~~lgl~~~f~~~-----~~K-~~~~~~~~~~~g~  108 (189)
T 3mn1_A           54 GIKMLIASGVTTAIISGRKTAIVERRAKSLGIEHLFQGR-----EDK-LVVLDKLLAELQL  108 (189)
T ss_dssp             HHHHHHHTTCEEEEECSSCCHHHHHHHHHHTCSEEECSC-----SCH-HHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCEEEEEECcChHHHHHHHHHcCCHHHhcCc-----CCh-HHHHHHHHHHcCC
Confidence            445677889999999999999999999999999887654     111 1466666666665

>3tnj_A Universal stress protein (USP); structural genomics, PSI-biology, midwest center for structu genomics, MCSG, chaperone; HET: AMP; 2.00A {Nitrosomonas europaea} PDB: 2pfs_A*

Probab=82.01  E-value=7.1  Score=25.88  Aligned_cols=71  Identities=10%  Similarity=0.007  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHhcCC---eEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHH-HHHHHHHHHhCCCeEEEe
Q psy17626         18 ECLADLDRQLKSHGG---QLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKR-DKKVKKWCAENNITVKEF   88 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~---~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~r-d~~v~~~l~~~gi~~~~~   88 (184)
                      +....|++-.++.|.   ...+..|++.+.|.+.+++.+++-|+.-..-....... -....+.+....+++..+
T Consensus        71 ~~~~~l~~~~~~~~~~~~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~Gs~~~~vl~~~~~pVlvv  145 (150)
T 3tnj_A           71 VEKQKLSQIGNTLGIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHGRHGLALLLGSTANSVLHYAKCDVLAV  145 (150)
T ss_dssp             HHHHHHHHHHHHHTCCGGGEEEEESCHHHHHHHHHHHTTCSEEEEEEC--------CCCHHHHHHHHCSSEEEEE
T ss_pred             HHHHHHHHHHHHcCCCcceEEEecCCHHHHHHHHHHHcCCCEEEEecCCCCCcCeEecchHHHHHHhCCCCEEEE
Confidence            333334333344454   47888999999999999999999999875321111111 122345566667887654

>3idf_A USP-like protein; universal, stress, PSI, MCSG, structural genomics, midwest center for structural genomics structure initiative; 2.00A {Wolinella succinogenes}

Probab=81.97  E-value=4.7  Score=26.39  Aligned_cols=45  Identities=11%  Similarity=0.236  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHhcCCe--EEEEECChHHHHHHHHHHcCcceEEEeec
Q psy17626         16 LLECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        16 l~~sL~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      ..+.|..+.+.+.+.|++  ..+..|++.+.|.+.++  +++-|+.-..
T Consensus        64 ~~~~l~~~~~~~~~~g~~~~~~v~~g~~~~~I~~~a~--~~dliV~G~~  110 (138)
T 3idf_A           64 AKLLTQKFSTFFTEKGINPFVVIKEGEPVEMVLEEAK--DYNLLIIGSS  110 (138)
T ss_dssp             HHHHHHHHHHHHHTTTCCCEEEEEESCHHHHHHHHHT--TCSEEEEECC
T ss_pred             HHHHHHHHHHHHHHCCCCeEEEEecCChHHHHHHHHh--cCCEEEEeCC
Confidence            345667777777777766  67789999999999999  9999988753

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}

Probab=81.89  E-value=14  Score=27.47  Aligned_cols=152  Identities=13%  Similarity=-0.051  Sum_probs=81.4

Q ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEC--Ch---HHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         15 FLLECLADLDRQLKSHGGQLFIVQG--SP---ISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        15 fl~~sL~~L~~~L~~~g~~L~v~~g--~~---~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      |..+-+..+.+.+++.|..+.+...  ++   .+.+.. +...+++.|+...... ..    ..+ +.+.+.|+++..++
T Consensus        22 ~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~-l~~~~vdgiIi~~~~~-~~----~~~-~~l~~~~iPvV~~~   94 (287)
T 3bbl_A           22 ILDQFLSSMVREAGAVNYFVLPFPFSEDRSQIDIYRDL-IRSGNVDGFVLSSINY-ND----PRV-QFLLKQKFPFVAFG   94 (287)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEECCCCSSTTCCHHHHHH-HHTTCCSEEEECSCCT-TC----HHH-HHHHHTTCCEEEES
T ss_pred             hHHHHHHHHHHHHHHcCCEEEEEeCCCchHHHHHHHHH-HHcCCCCEEEEeecCC-Cc----HHH-HHHHhcCCCEEEEC
Confidence            6777788888899999999887642  22   233444 4456899888753211 11    223 33456799998876


Q ss_pred             Cceee-cccccccccCCCCchhHHHHHHHhh---hcccccc----CcchhHHHHHHHHHHHHHHHhCCCeEE---EEeCC
Q psy17626         90 SHTLW-DPEVVIQTNGNVPPLTYKMYLHTVS---CIGTMHI----GYNRFRFLLECLADLDRQLKSHGGQLF---IVQGS  158 (184)
Q Consensus        90 ~~~L~-~p~~i~~~~~~~~~~v~~~F~~~~~---~~~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~---v~~g~  158 (184)
                      ...-- ....+..+       .+..-+...+   +.+-.+.    +........+.+.-..+.|++.|+++.   +..++
T Consensus        95 ~~~~~~~~~~V~~D-------~~~~g~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~  167 (287)
T 3bbl_A           95 RSNPDWDFAWVDID-------GTAGTRQAVEYLIGRGHRRIAILAWPEDSRVGNDRLQGYLEAMQTAQLPIETGYILRGE  167 (287)
T ss_dssp             CCSTTCCCCEEEEC-------HHHHHHHHHHHHHHHTCCCEEEEECCTTCHHHHHHHHHHHHHHHHTTCCCCGGGEEECC
T ss_pred             CcCCCCCCCEEEec-------cHHHHHHHHHHHHHCCCCeEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEEeCC
Confidence            53210 00111111       1111111111   1121111    122223445667778888888887542   34432


Q ss_pred             --h---hHHHHHHHH-Hc--CcCeEEEccc
Q psy17626        159 --P---ISIFQKLKR-EL--NFTKLCFEQD  180 (184)
Q Consensus       159 --~---~~~l~~l~~-~~--~~~~v~~n~~  180 (184)
                        .   .+.+.++.+ +.  .+++||+..|
T Consensus       168 ~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d  197 (287)
T 3bbl_A          168 GTFEVGRAMTLHLLDLSPERRPTAIMTLND  197 (287)
T ss_dssp             SSHHHHHHHHHHHHTSCTTTSCSEEEESSH
T ss_pred             CCHHHHHHHHHHHHhhCCCCCCcEEEECCc
Confidence              2   245667776 54  6899998765

>3fvv_A Uncharacterized protein; unknown function, structural genomics, PSI,MCSG, protein STR initiative, midwest center for structural genomics; 2.10A {Bordetella pertussis}

Probab=81.69  E-value=4.8  Score=28.80  Aligned_cols=45  Identities=13%  Similarity=0.096  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcc
Q psy17626        135 LECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ  179 (184)
Q Consensus       135 ~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~  179 (184)
                      .....++-+.|++.|+++.|+.+.+...+..+++.+|++.++.+.
T Consensus        94 ~~g~~~~l~~l~~~g~~~~ivS~~~~~~~~~~~~~~g~~~~~~~~  138 (232)
T 3fvv_A           94 TVQAVDVVRGHLAAGDLCALVTATNSFVTAPIARAFGVQHLIATD  138 (232)
T ss_dssp             CHHHHHHHHHHHHTTCEEEEEESSCHHHHHHHHHHTTCCEEEECE
T ss_pred             CHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHHHHcCCCEEEEcc
Confidence            345556667788889999999999999999999999999887653

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=81.02  E-value=14  Score=26.97  Aligned_cols=156  Identities=15%  Similarity=0.102  Sum_probs=87.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEECC--hHH--HHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         14 RFLLECLADLDRQLKSHGGQLFIVQGS--PIS--IFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        14 ~fl~~sL~~L~~~L~~~g~~L~v~~g~--~~~--~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      .|..+-+..+.+.++++|..+.+...+  +..  .+.+.+...+++.|+....... .   + ...+.+.+.|+++..++
T Consensus        15 ~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~-~---~-~~~~~~~~~~iPvV~~~   89 (272)
T 3o74_A           15 PSYARIAKQLEQGARARGYQLLIASSDDQPDSERQLQQLFRARRCDALFVASCLPP-E---D-DSYRELQDKGLPVIAID   89 (272)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHTTCSEEEECCCCCS-S---C-CHHHHHHHTTCCEEEES
T ss_pred             hhHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecCccc-c---H-HHHHHHHHcCCCEEEEc
Confidence            477778888999999999999888643  322  2333344568998888643211 1   1 12234566799998876


Q ss_pred             CceeecccccccccCCCCchhHHHHHHHhhhc---ccccc----CcchhHHHHHHHHHHHHHHHhCCCeEEEEe-C--Ch
Q psy17626         90 SHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI---GTMHI----GYNRFRFLLECLADLDRQLKSHGGQLFIVQ-G--SP  159 (184)
Q Consensus        90 ~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~---~~~~~----~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-g--~~  159 (184)
                      ...-  ...+..=    ....+..-+...+.+   +..+.    +........+.+.-..+.+++.|++..... +  +.
T Consensus        90 ~~~~--~~~~~~V----~~d~~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~  163 (272)
T 3o74_A           90 RRLD--PAHFCSV----ISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRRYQGEAFSR  163 (272)
T ss_dssp             SCCC--TTTCEEE----EECHHHHHHHHHHHHHTTCCSEEEEEEECTTSHHHHHHHHHHHHHTTTCCSEEEEEEESSSSH
T ss_pred             cCCC--ccccCEE----EEchHHHHHHHHHHHHHCCCcEEEEEecCCCCccHHHHHHHHHHHHHHcCCChheeecCCCCH
Confidence            5321  1111000    011111111121111   21111    222233456677888889999998765443 2  22


Q ss_pred             ---hHHHHHHHHHcC--cCeEEEccc
Q psy17626        160 ---ISIFQKLKRELN--FTKLCFEQD  180 (184)
Q Consensus       160 ---~~~l~~l~~~~~--~~~v~~n~~  180 (184)
                         .+.+.++.+++.  +++||+..+
T Consensus       164 ~~~~~~~~~~l~~~~~~~~ai~~~~d  189 (272)
T 3o74_A          164 ECGQRLMQQLIDDLGGLPDALVTTSY  189 (272)
T ss_dssp             HHHHHHHHHHHHHHTSCCSEEEESSH
T ss_pred             HHHHHHHHHHHhcCCCCCcEEEEeCc
Confidence               346777777775  999998765

>2p9j_A Hypothetical protein AQ2171; secsg, riken, PSI, structural GENO protein structure initiative, southeast collaboratory for S genomics; 2.40A {Aquifex aeolicus}

Probab=80.26  E-value=11  Score=25.41  Aligned_cols=57  Identities=14%  Similarity=0.086  Sum_probs=40.1

Q ss_pred             HHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCe
Q psy17626         22 DLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNIT   84 (184)
Q Consensus        22 ~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~   84 (184)
                      ++=+.|++.|.++.|+.|.+...+..+++..++...+-..      ......+...+++.|+.
T Consensus        43 ~~l~~l~~~g~~~~i~T~~~~~~~~~~l~~~gl~~~~~~~------kp~~~~~~~~~~~~~~~   99 (162)
T 2p9j_A           43 IGIKLLQKMGITLAVISGRDSAPLITRLKELGVEEIYTGS------YKKLEIYEKIKEKYSLK   99 (162)
T ss_dssp             HHHHHHHTTTCEEEEEESCCCHHHHHHHHHTTCCEEEECC--------CHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHCCCEEEEEeCCCcHHHHHHHHHcCCHhhccCC------CCCHHHHHHHHHHcCCC
Confidence            4445567789999999999999999999999998655331      12233555666666653

>3loq_A Universal stress protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: AMP; 2.32A {Archaeoglobus fulgidus}

Probab=80.11  E-value=16  Score=27.28  Aligned_cols=72  Identities=13%  Similarity=0.139  Sum_probs=48.0

Q ss_pred             HHHHHHHHHHHhcCCe--EEEEECChHHHHHHHHHHcCcceEEEeecc-cchhHH-HHHHHHHHHHhCCCeEEEec
Q psy17626         18 ECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHK-RDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~-rd~~v~~~l~~~gi~~~~~~   89 (184)
                      +.+.++.+.|++.|++  ..+..|++.+.|.+.+++.+++-|++-..- +...+- .-...++.+....+++..+.
T Consensus       214 ~~l~~~~~~l~~~~~~~~~~~~~g~~~~~I~~~a~~~~~dLlV~G~~~~~~~~~~~~Gs~~~~vl~~~~~pvLvv~  289 (294)
T 3loq_A          214 ADLRVMEEVIGAEGIEVHVHIESGTPHKAILAKREEINATTIFMGSRGAGSVMTMILGSTSESVIRRSPVPVFVCK  289 (294)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEECSCHHHHHHHHHHHTTCSEEEEECCCCSCHHHHHHHCHHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHHHHHHHcCCcEEEEEecCCHHHHHHHHHHhcCcCEEEEeCCCCCCccceeeCcHHHHHHhcCCCCEEEEC
Confidence            4566777778777875  566789999999999999999988886432 221111 12233455666778776543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	184
d1u3da2	185	Cryptochrome {Thale cress (Arabidopsis thaliana) [	99.96
d1np7a2	204	Cryptochrome {Synechocystis sp., pcc 6803 [TaxId:	99.95
d1owla2	202	DNA photolyase {Synechococcus elongatus [TaxId: 32	99.95
d1dnpa2	200	DNA photolyase {Escherichia coli [TaxId: 562]}	99.93
d2j07a2	170	DNA photolyase {Thermus thermophilus [TaxId: 274]}	99.92
d1owla2	202	DNA photolyase {Synechococcus elongatus [TaxId: 32	99.33
d2j07a2	170	DNA photolyase {Thermus thermophilus [TaxId: 274]}	99.31
d1u3da2	185	Cryptochrome {Thale cress (Arabidopsis thaliana) [	99.3
d1np7a2	204	Cryptochrome {Synechocystis sp., pcc 6803 [TaxId:	99.29
d1dnpa2	200	DNA photolyase {Escherichia coli [TaxId: 562]}	99.19
d2b8ea1	135	Cation-transporting ATPase {Archaeon Archaeoglobus	92.34
d2b8ea1	135	Cation-transporting ATPase {Archaeon Archaeoglobus	90.96
d1mjha_	160	"Hypothetical" protein MJ0577 {Archaeon Methanococ	88.77
d1mjha_	160	"Hypothetical" protein MJ0577 {Archaeon Methanococ	87.93
d2gm3a1	171	Putative ethylene-responsive protein AT3g01520/F4P	85.18
d1ykga1	146	Sulfite reductase alpha-component CysJ N-terminal	84.93
d1q77a_	138	Hypothetical protein Aq_178 {Aquifex aeolicus [Tax	84.04
d2z3va1	135	Hypothetical protein TTHA0895 {Thermus thermophilu	83.73
d1nnla_	217	Phosphoserine phosphatase {Human (Homo sapiens) [T	83.44
d2c4va1	158	Type II 3-dehydroquinate dehydratase {Helicobacter	80.3

>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.96  E-value=4.5e-28  Score=177.90  Aligned_cols=118  Identities=21%  Similarity=0.319  Sum_probs=111.3

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEE-CChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENN   82 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~g   82 (184)
                      +..+.|++|.+|+++||.+|+++|+++|++|+++. |++.++|.+|+++++|++||+|++|++++++||++|+++|++.|
T Consensus        39 ~~~~~~~~~~~fl~~sL~~L~~~L~~~g~~L~v~~~g~~~~~l~~l~~~~~i~~v~~n~~~~~~e~~rd~~v~~~l~~~g  118 (185)
T d1u3da2          39 GHYHPGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVLTAQG  118 (185)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHHHHHHHHHTCCEEEEECCCSHHHHHHHHHHHHHHHTTT
T ss_pred             cccChHHHHHHHHHHHHHHHHHHHHhcCCcceEeeccchHHHHHHHHHhcCCceEEEeccccHHHHHHHHHHHHHHHHcC
Confidence            45678999999999999999999999999999986 89999999999999999999999999999999999999999999


Q ss_pred             CeEEEecCceeecccccccccCCCCchhHHHHHHHhhhcc
Q psy17626         83 ITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIG  122 (184)
Q Consensus        83 i~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~  122 (184)
                      |.++.+++++|++|+++++++| ++|+|||+|++.+.+..
T Consensus       119 i~~~~~~~~~L~~p~~i~~~~g-~~y~vFTpF~k~~~~~~  157 (185)
T d1u3da2         119 IAVRSFNADLLYEPWEVTDELG-RPFSMFAAFWERCLSMP  157 (185)
T ss_dssp             CEEEEECCSCSSCGGGCCCSSS-CCCSSHHHHHHHHHTCS
T ss_pred             CceeecCCceecCccccccCCC-CCCcccHHHHHHHHhCc
Confidence            9999999999999999998765 79999999999987753

>d1np7a2 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Synechocystis sp., pcc 6803 [TaxId: 1143]

Probab=99.95  E-value=2.8e-28  Score=181.57  Aligned_cols=117  Identities=17%  Similarity=0.272  Sum_probs=111.8

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      |...+|++|.+|+++||.+|+++|+++|++|+|++|++.++|.+|+++++|++||+|++|++++++||+.|++.|++.||
T Consensus        51 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~G~~~~~l~~l~~~~~i~~V~~n~~~~~~e~~rd~~v~~~l~~~~i  130 (204)
T d1np7a2          51 GFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGI  130 (204)
T ss_dssp             SCBSSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTEEEEEEECCCSHHHHHHHHHHHHHHHHHTC
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHhccchhhhhhhhhHHHHHHHHHHhhhhheeeeccccHHHHHHHHHHhhhhcccee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHHhhhc
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCI  121 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~  121 (184)
                      .++.+++++|++|++++++.+ ++|+|||+|++.+++.
T Consensus       131 ~~~~~~~~~L~~p~~l~~~~~-~~~~vFTpFrk~~e~~  167 (204)
T d1np7a2         131 EAKGYWGSTLCHPEDLPFSIQ-DLPDLFTKFRKDIEKK  167 (204)
T ss_dssp             EEEEECCSSSSCGGGSSSCGG-GCCSSHHHHHHHHHTT
T ss_pred             eeEeccCccccChhhccCCCC-CCCccchHHHHHHHhc
Confidence            999999999999999999865 7999999999999764

>d1owla2 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Synechococcus elongatus [TaxId: 32046]

Probab=99.95  E-value=6.7e-28  Score=179.29  Aligned_cols=120  Identities=19%  Similarity=0.364  Sum_probs=113.9

Q ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCC
Q psy17626          4 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNI   83 (184)
Q Consensus         4 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi   83 (184)
                      +.++.|++|++|+++||.+|+++|+++|++|.|++|++.++|+++++++++++||+|++|++++++||+.+++.|++.||
T Consensus        41 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~i~~G~~~~~l~~l~~~~~i~~v~~~~~~~~~~~~rd~~i~~~~~~~~i  120 (202)
T d1owla2          41 QSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGI  120 (202)
T ss_dssp             TCTTCCHHHHHHHHHHHHHHHHHHHHHTSCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHHHHHHHHHHHHHHHHTTC
T ss_pred             cchhhhHHHHHHHHHHHHHHHHhhhccccceEEEEeeeeccchhhccccccceeEEeeeccchhhhHHHHHhhhhhhccc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEecCceeecccccccccCCCCchhHHHHHHHhhhcccc
Q psy17626         84 TVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTM  124 (184)
Q Consensus        84 ~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~~  124 (184)
                      .++.+++++|++|+++.++. +++|+|||+|++.+++...+
T Consensus       121 ~~~~~~~~~L~~p~~v~~~~-g~~~~vFTpF~k~~~~~~~~  160 (202)
T d1owla2         121 RAVQLWDQLLHSPDQILSGS-GNPYSVYGPFWKNWQAQPKP  160 (202)
T ss_dssp             EEEEECCSSSSCTTTCCCTT-SCCCSSHHHHHHHHHHSCCC
T ss_pred             cccccccccccCcccccCCC-CCchhhhHHHHHHHHhcCCC
Confidence            99999999999999999875 47999999999999887653

>d1dnpa2 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=2.7e-25  Score=164.80  Aligned_cols=113  Identities=17%  Similarity=0.195  Sum_probs=105.5

Q ss_pred             CCCCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECC----hHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHh
Q psy17626          5 TMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGS----PISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAE   80 (184)
Q Consensus         5 ~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~----~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~   80 (184)
                      .+..|++|.+|+.+||.+|+++|+++|++|+|+.|+    +.++|.+++++++|++||+|++|++++++||++|++.|  
T Consensus        43 ~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~~~~~l~~l~~~~~i~~v~~n~~~~~~~~~rd~~v~~~l--  120 (200)
T d1dnpa2          43 THNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERAL--  120 (200)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHTCCEEEEECCCSHHHHHHHHHHHHHC--
T ss_pred             ccCcchhhhhhHHHHHHHHHhhhhhccceeEEEEecccccchhHHHHHHHhcCCcEEEEeccccHHHHHHHHHHHHHh--
Confidence            357899999999999999999999999999999998    67789999999999999999999999999999999998  


Q ss_pred             CCCeEEEecCceeecccccccccCCCCchhHHHHHHHhhh
Q psy17626         81 NNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSC  120 (184)
Q Consensus        81 ~gi~~~~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~  120 (184)
                      .||.++.+++++|++|++|.++.| ++|+|||+|++.+.+
T Consensus       121 ~~i~~~~~~~~~L~~p~~v~~~~g-~~y~VFTpF~k~~~~  159 (200)
T d1dnpa2         121 RNVVCEGFDDSVILPPGAVMTGNH-EMYKVFTPFKNAWLK  159 (200)
T ss_dssp             TTSEEEEECCSSSSCTTSSCCTTS-CCCSSHHHHHHHHHH
T ss_pred             hhhcccccCceeeccccccccCCC-CCCccCCHHHHHHHH
Confidence            489999999999999999999764 799999999998865

>d2j07a2 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=1.5e-25  Score=162.11  Aligned_cols=109  Identities=17%  Similarity=0.189  Sum_probs=99.5

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEeecccchhHHHHHHHHHHHHhCCCeEE
Q psy17626          7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRDKKVKKWCAENNITVK   86 (184)
Q Consensus         7 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~   86 (184)
                      ..|++|.+|+++||.+|+++|+++|++|+|++|++.++|++|+++++|++||+|++|++++++||+.|++.+   +    
T Consensus        40 ~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~G~~~~~l~~l~~~~~i~~V~~n~~~~~~~~~rd~~v~~~l---~----  112 (170)
T d2j07a2          40 KTTPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREAL---P----  112 (170)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHHHHHHHHHHHHHC---S----
T ss_pred             hhhHHHHHHHHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHHhhhhHHHhhccchhhhhHHHHHHHhhh---c----
Confidence            458899999999999999999999999999999999999999999999999999999999999999999765   2    


Q ss_pred             EecCceeecccccccccCCCCchhHHHHHHHhhhcccc
Q psy17626         87 EFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTVSCIGTM  124 (184)
Q Consensus        87 ~~~~~~L~~p~~i~~~~~~~~~~v~~~F~~~~~~~~~~  124 (184)
                       +.+++|++|+.++++.+ ++|+|||+|++.+++...+
T Consensus       113 -~~~~~l~~p~~v~~~~~-~~y~VFTpF~k~~~~~~~p  148 (170)
T d2j07a2         113 -VPLHLLPAPHLLPPDLP-RAYRVYTPFSRLYRGAAPP  148 (170)
T ss_dssp             -SCEEEECCCCSSCTTCS-SCCSSHHHHHTTCCCCCCC
T ss_pred             -cCceeecccCeeeCCcC-CCCCccCHHHHHHhccCCC
Confidence             56788999999988764 7999999999999876543

>d1owla2 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Synechococcus elongatus [TaxId: 32046]

Probab=99.33  E-value=1.7e-13  Score=100.60  Aligned_cols=68  Identities=24%  Similarity=0.538  Sum_probs=62.5

Q ss_pred             HhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        117 TVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       117 ~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      .+..+..+..+.+|..|+.+||.+|+++|+++|++|.|+.|++.++|.++++++++++||+|++|+++
T Consensus        36 dp~~~~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~i~~G~~~~~l~~l~~~~~i~~v~~~~~~~~~  103 (202)
T d1owla2          36 DPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPY  103 (202)
T ss_dssp             CHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHTSCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHH
T ss_pred             cchHhcchhhhHHHHHHHHHHHHHHHHhhhccccceEEEEeeeeccchhhccccccceeEEeeeccch
Confidence            34455667789999999999999999999999999999999999999999999999999999999864

>d2j07a2 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Thermus thermophilus [TaxId: 274]

Probab=99.31  E-value=1.4e-12  Score=93.22  Aligned_cols=58  Identities=21%  Similarity=0.366  Sum_probs=55.3

Q ss_pred             CcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       127 ~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +.++..|+.+||.+|+++|+++|++|.|+.|++.++|++|+++++|++||+|++|+++
T Consensus        42 ~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~G~~~~~l~~l~~~~~i~~V~~n~~~~~~   99 (170)
T d2j07a2          42 TPRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPY   99 (170)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTCSEEEEECCCSHH
T ss_pred             hHHHHHHHHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHHhhhhHHHhhccchhh
Confidence            5678899999999999999999999999999999999999999999999999999874

>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.30  E-value=4.6e-13  Score=96.97  Aligned_cols=68  Identities=19%  Similarity=0.260  Sum_probs=61.5

Q ss_pred             HhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEe-CChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        117 TVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQ-GSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       117 ~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~-g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      .+.+|+.+..+.++.+|+.+||.+|+++|+++|++|+++. |++.++|.+++++++|++||+|++|+++
T Consensus        34 dp~~~~~~~~~~~~~~fl~~sL~~L~~~L~~~g~~L~v~~~g~~~~~l~~l~~~~~i~~v~~n~~~~~~  102 (185)
T d1u3da2          34 APEEEGHYHPGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPL  102 (185)
T ss_dssp             CGGGGTTCCCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHHHHHHHHHTCCEEEEECCCSHH
T ss_pred             cchHhcccChHHHHHHHHHHHHHHHHHHHHhcCCcceEeeccchHHHHHHHHHhcCCceEEEeccccHH
Confidence            3445667778889999999999999999999999999986 8999999999999999999999999874

>d1np7a2 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: Cryptochrome
species: Synechocystis sp., pcc 6803 [TaxId: 1143]

Probab=99.29  E-value=1.7e-12  Score=95.25  Aligned_cols=63  Identities=19%  Similarity=0.433  Sum_probs=59.3

Q ss_pred             cccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       122 ~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      +.+..+.++..|+.+||.+|+++|+++|++|.++.|++.++|.+|+++++|++||+|++|+++
T Consensus        51 ~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~G~~~~~l~~l~~~~~i~~V~~n~~~~~~  113 (204)
T d1np7a2          51 GFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQE  113 (204)
T ss_dssp             SCBSSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHTTEEEEEEECCCSHH
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHhccchhhhhhhhhHHHHHHHHHHhhhhheeeeccccHH
Confidence            456678899999999999999999999999999999999999999999999999999999863

>d1dnpa2 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Cryptochrome/photolyase, N-terminal domain
superfamily: Cryptochrome/photolyase, N-terminal domain
family: Cryptochrome/photolyase, N-terminal domain
domain: DNA photolyase
species: Escherichia coli [TaxId: 562]

Probab=99.19  E-value=2.4e-12  Score=94.25  Aligned_cols=71  Identities=18%  Similarity=0.229  Sum_probs=62.2

Q ss_pred             HHHHhhhccccccCcchhHHHHHHHHHHHHHHHhCCCeEEEEeCC----hhHHHHHHHHHcCcCeEEEcccccCC
Q psy17626        114 YLHTVSCIGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGS----PISIFQKLKRELNFTKLCFEQDCEAY  184 (184)
Q Consensus       114 F~~~~~~~~~~~~~~~r~~fl~~~L~~L~~~L~~~g~~L~v~~g~----~~~~l~~l~~~~~~~~v~~n~~~~~~  184 (184)
                      |...+..+..+..+.++..|+.+||.+|+++|+++|++|.|+.|+    +.++|.+++++++|++||+|++|+++
T Consensus        34 yi~dp~~~~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~g~~~~~~~~~l~~l~~~~~i~~v~~n~~~~~~  108 (200)
T d1dnpa2          34 YIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVN  108 (200)
T ss_dssp             EEECHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHTCCEEEEECCCSHH
T ss_pred             EEEcchhhcccCcchhhhhhHHHHHHHHHhhhhhccceeEEEEecccccchhHHHHHHHhcCCcEEEEeccccHH
Confidence            333445566677899999999999999999999999999999987    56789999999999999999999874

>d2b8ea1 c.108.1.7 (A:416-434,A:548-663) Cation-transporting ATPase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Meta-cation ATPase, catalytic domain P
domain: Cation-transporting ATPase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.34  E-value=0.12  Score=33.71  Aligned_cols=41  Identities=22%  Similarity=0.248  Sum_probs=35.4

Q ss_pred             HHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcceEEEee
Q psy17626         21 ADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ   61 (184)
Q Consensus        21 ~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~   61 (184)
                      .+.-+.|++.|+.++++.|+..+....++++.+++.++.+-
T Consensus        27 ~~~I~~L~~~Gi~v~ilTGD~~~~a~~ia~~lgI~~v~~~~   67 (135)
T d2b8ea1          27 KPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEV   67 (135)
T ss_dssp             HHHHHHHHHTTCEEEEECSSCHHHHHHHHHHHTCSEEECSC
T ss_pred             HHHHHHHHHcCCEEEEEcCcchhhhhHHHhhhhhhhhcccc
Confidence            34556678889999999999999999999999999998754

>d2b8ea1 c.108.1.7 (A:416-434,A:548-663) Cation-transporting ATPase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Meta-cation ATPase, catalytic domain P
domain: Cation-transporting ATPase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.96  E-value=0.25  Score=32.15  Aligned_cols=40  Identities=23%  Similarity=0.230  Sum_probs=34.3

Q ss_pred             HHHHHHhCCCeEEEEeCChhHHHHHHHHHcCcCeEEEccc
Q psy17626        141 LDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQD  180 (184)
Q Consensus       141 L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~v~~n~~  180 (184)
                      .-+.|++.|+...++.||.......++++.|++.+|.+..
T Consensus        29 ~I~~L~~~Gi~v~ilTGD~~~~a~~ia~~lgI~~v~~~~~   68 (135)
T d2b8ea1          29 AVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVL   68 (135)
T ss_dssp             HHHHHHHTTCEEEEECSSCHHHHHHHHHHHTCSEEECSCC
T ss_pred             HHHHHHHcCCEEEEEcCcchhhhhHHHhhhhhhhhccccc
Confidence            4455777799999999999999999999999999987643

>d1mjha_ c.26.2.4 (A:) "Hypothetical" protein MJ0577 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: "Hypothetical" protein MJ0577
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=88.77  E-value=0.68  Score=30.04  Aligned_cols=72  Identities=14%  Similarity=0.121  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHhcCCe--EEEEECChHHHHHHHHHHcCcceEEEee-cccchhHHH-HHHHHHHHHhCCCeEEEe
Q psy17626         17 LECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFEQ-DCEALWHKR-DKKVKKWCAENNITVKEF   88 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~~~-~~~~~~~~r-d~~v~~~l~~~gi~~~~~   88 (184)
                      .+.|.++.+.+...|++  ..+..|+|.+.|.+++++.+++-|+.-. ..++..+-. -....+.+...++++..+
T Consensus        80 ~~~l~~~~~~~~~~gv~~~~~~~~G~~~~~I~~~a~~~~~dliV~G~~~~~~~~~~~~GS~a~~vl~~s~~pVlvV  155 (160)
T d1mjha_          80 KNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV  155 (160)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTTCSEEEEESCCSSCCTTCSSCHHHHHHHHHCCSCEEEE
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEEeccHHHHHhhhhhccccceEEeccCCCCcccccccCcHHHHHHhcCCCCEEEE
Confidence            45666777788888876  5778999999999999999999999853 222222211 123344556677887654

>d1mjha_ c.26.2.4 (A:) "Hypothetical" protein MJ0577 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: "Hypothetical" protein MJ0577
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=87.93  E-value=2.1  Score=27.45  Aligned_cols=45  Identities=16%  Similarity=0.231  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHhCCCe--EEEEeCChhHHHHHHHHHcCcCeEEEc
Q psy17626        134 LLECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFE  178 (184)
Q Consensus       134 l~~~L~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~n  178 (184)
                      ..+.|+++...+...|++  ..+..|++.+.+.+++++.+++-|+..
T Consensus        79 ~~~~l~~~~~~~~~~gv~~~~~~~~G~~~~~I~~~a~~~~~dliV~G  125 (160)
T d1mjha_          79 AKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMG  125 (160)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHHHHTTCSEEEEE
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEEeccHHHHHhhhhhccccceEEec
Confidence            446677777888888876  456679999999999999999999864

>d2gm3a1 c.26.2.4 (A:5-175) Putative ethylene-responsive protein AT3g01520/F4P13_7 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Putative ethylene-responsive protein AT3g01520/F4P13 7
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.18  E-value=1.5  Score=28.71  Aligned_cols=72  Identities=11%  Similarity=0.026  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHhcCCe--EEEEECChHHHHHHHHHHcCcceEEEeecc-cchhHHHHHH-HHHHHHhCCCeEEEe
Q psy17626         17 LECLADLDRQLKSHGGQ--LFIVQGSPISIFQKLKRELNFTKLCFEQDC-EALWHKRDKK-VKKWCAENNITVKEF   88 (184)
Q Consensus        17 ~~sL~~L~~~L~~~g~~--L~v~~g~~~~~l~~l~~~~~~~~v~~~~~~-~~~~~~rd~~-v~~~l~~~gi~~~~~   88 (184)
                      .+-|..+...+...|++  ..+..|++.+.|.+++++.+++.|+.-..- +...+..--. ....++...+++..+
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~dlIV~G~~g~~~~~~~~lGSv~~~vi~~~~cpVlvV  157 (171)
T d2gm3a1          82 LHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTI  157 (171)
T ss_dssp             HHHHHHHHHHHHHHTCEEEEEEEESCHHHHHHHHHHHHCCSEEEEEECCCC--------CHHHHHHHHCSSCEEEE
T ss_pred             HHHHHHHHHHHHhcCCceEEEEEeCChHHHHHHHHhhcCCcEEEeccCCccccccCccCcHHHHHHhCCCCCEEEE
Confidence            34456667777777755  567899999999999999999999987542 2222221112 233445566777643

>d1ykga1 c.23.5.2 (A:63-208) Sulfite reductase alpha-component CysJ N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Cytochrome p450 reductase N-terminal domain-like
domain: Sulfite reductase alpha-component CysJ N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.93  E-value=3.4  Score=26.64  Aligned_cols=64  Identities=14%  Similarity=0.167  Sum_probs=40.7

Q ss_pred             CCCchhHHHHHHHhhhcccccc----------CcchhHHHHHHHHHHHHHHHhCCCe----EEEEeCChhHHHHHHHH
Q psy17626        105 NVPPLTYKMYLHTVSCIGTMHI----------GYNRFRFLLECLADLDRQLKSHGGQ----LFIVQGSPISIFQKLKR  168 (184)
Q Consensus       105 ~~~~~v~~~F~~~~~~~~~~~~----------~~~r~~fl~~~L~~L~~~L~~~g~~----L~v~~g~~~~~l~~l~~  168 (184)
                      |++|.....|+........+..          |.............+.+.|+++|..    +.....+..+.+..+..
T Consensus        59 G~~P~~~~~f~~~l~~~~~~~l~~~~~aVfGlGds~Y~~Fc~~~~~l~~~l~~lGa~~i~~~~~~D~~~e~~~~~W~~  136 (146)
T d1ykga1          59 GEPPEEAVALHKFLFSKKAPKLENTAFAVFSLGDTSYEFFCQSGKDFDSKLAELGGERLLDRVDADVEYQAAASEWRA  136 (146)
T ss_dssp             GBCCGGGHHHHHHHTSTTCCCCTTCEEEEEEECCTTSSSTTHHHHHHHHHHHHHTCEESSCCEEECTTCHHHHHHHHH
T ss_pred             CcCchhHHHHHHHHHcccccccCCCeEEEEcCcchhHHHHHHHHHHHHHHHHHCCCcEeeCceecCCCCHHHHHHHHH
Confidence            4788888888876654433321          3334455677889999999999974    33334455555555544

>d1q77a_ c.26.2.4 (A:) Hypothetical protein Aq_178 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein Aq 178
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.04  E-value=1.6  Score=27.16  Aligned_cols=47  Identities=9%  Similarity=0.031  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHhcCC--eEEEEECChHHHHHHHHHHcCcceEEEeec
Q psy17626         16 LLECLADLDRQLKSHGG--QLFIVQGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        16 l~~sL~~L~~~L~~~g~--~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      ..+.|.++.+.+...|.  ...+..|+|.+.|.+.+++.+++-|++-..
T Consensus        70 ~~~~l~~~~~~~~~~~~~~~~~v~~G~~~~~I~~~a~~~~~DLIV~Gs~  118 (138)
T d1q77a_          70 IERRLREVWEKLTGSTEIPGVEYRIGPLSEEVKKFVEGKGYELVVWACY  118 (138)
T ss_dssp             HHHHHHHHHHHHHSCCCCCCEEEECSCHHHHHHHHHTTSCCSEEEECSC
T ss_pred             ccccchhhcccccccceeEEEeeecchhHHHHHHhhhhccCCEEEEecC
Confidence            34444444555554454  468889999999999999999999999753

>d2z3va1 c.26.2.4 (A:2-136) Hypothetical protein TTHA0895 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Adenine nucleotide alpha hydrolases-like
family: Universal stress protein-like
domain: Hypothetical protein TTHA0895
species: Thermus thermophilus [TaxId: 274]

Probab=83.73  E-value=1.8  Score=26.86  Aligned_cols=31  Identities=10%  Similarity=0.216  Sum_probs=26.5

Q ss_pred             CeEEEEECChHHHHHHHHHHcCcceEEEeec
Q psy17626         32 GQLFIVQGSPISIFQKLKRELNFTKLCFEQD   62 (184)
Q Consensus        32 ~~L~v~~g~~~~~l~~l~~~~~~~~v~~~~~   62 (184)
                      ....+..|++.++|.+.+++.+++-|+....
T Consensus        77 ~~~~~~~g~~~~~I~~~a~~~~~dliV~G~~  107 (135)
T d2z3va1          77 EDALLLEGVPAEAILQAARAEKADLIVMGTR  107 (135)
T ss_dssp             GGEEEEESCHHHHHHHHHHHTTCSEEEEESS
T ss_pred             EEEEEEcCChHHHHHHHhhhhheeeEEeccC
Confidence            3467788999999999999999999888643

>d1nnla_ c.108.1.4 (A:) Phosphoserine phosphatase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: HAD-like
superfamily: HAD-like
family: Phosphoserine phosphatase
domain: Phosphoserine phosphatase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.44  E-value=0.91  Score=31.28  Aligned_cols=43  Identities=21%  Similarity=0.365  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhcCCeEEEEECChHHHHHHHHHHcCcc--eEEEe
Q psy17626         18 ECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFT--KLCFE   60 (184)
Q Consensus        18 ~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~--~v~~~   60 (184)
                      ....++-+.|++.|.++.|+.|.....+..+++.++++  .|++|
T Consensus        85 pg~~~~i~~lk~~G~~~~ivS~~~~~~v~~i~~~lgi~~~~v~an  129 (217)
T d1nnla_          85 PGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFAN  129 (217)
T ss_dssp             TTHHHHHHHHHHTTCEEEEEEEEEHHHHHHHHHHTTCCGGGEEEE
T ss_pred             HHHHHHHHHHHhCCCEEEEECCCchHHHHHHHHHhCCcccceeee
Confidence            34456666677777777777777777777777777765  34443

>d2c4va1 c.23.13.1 (A:1-158) Type II 3-dehydroquinate dehydratase {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Type II 3-dehydroquinate dehydratase
family: Type II 3-dehydroquinate dehydratase
domain: Type II 3-dehydroquinate dehydratase
species: Helicobacter pylori [TaxId: 210]

Probab=80.30  E-value=5.9  Score=26.04  Aligned_cols=79  Identities=9%  Similarity=-0.013  Sum_probs=54.3

Q ss_pred             HHHHHHHHH----h--cCCeEEEEECChHHHHHHHHHHc---CcceEEEeec-ccchhHHHHHHHHHHHHhCCCeEEEec
Q psy17626         20 LADLDRQLK----S--HGGQLFIVQGSPISIFQKLKREL---NFTKLCFEQD-CEALWHKRDKKVKKWCAENNITVKEFV   89 (184)
Q Consensus        20 L~~L~~~L~----~--~g~~L~v~~g~~~~~l~~l~~~~---~~~~v~~~~~-~~~~~~~rd~~v~~~l~~~gi~~~~~~   89 (184)
                      |.++.+.++    +  +|+.+.+++-+.+..+-....+.   +++.|..|.. |+.+..    .++..+...++++.+++
T Consensus        27 L~~i~~~~~~~a~~~~l~v~l~~~QSN~EgelId~I~~a~~~~~dgiIINPga~ThtS~----al~DAl~~~~~P~iEVH  102 (158)
T d2c4va1          27 LDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSI----AIADAIMLAGKPVIEVH  102 (158)
T ss_dssp             HHHHHHHHHHHHHHHTCCCEEEEEECSCHHHHHHHHHHTTSTTEEEEEEECGGGGGTCH----HHHHHHHHSSSCEEEEE
T ss_pred             HHHHHHHHHHHHHHcCCceehhhHHHhHHHHHHHHHHHHhCCCcceEEecchhheeeee----ehHHHHHhcCCCEEEEE
Confidence            555555553    2  67899999999887777777653   5788999953 344443    44555666789999888


Q ss_pred             Cceeecccccccc
Q psy17626         90 SHTLWDPEVVIQT  102 (184)
Q Consensus        90 ~~~L~~p~~i~~~  102 (184)
                      =...+..+..+..
T Consensus       103 lSNi~~RE~fR~~  115 (158)
T d2c4va1         103 LTNIQAREEFRKN  115 (158)
T ss_dssp             SSCTTSSCGGGSC
T ss_pred             ccCcccccccccc
Confidence            7777777766553