Citrus Sinensis ID: 025606

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250
Protein Sequence
MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSISSSMGADS
Secondary Structure (PSIPRED)
ccccccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccccccccccccccccccccEEEcccHHHHHHHHccccccccEEHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccEEEEEEccEEEEEEccccccHHHHHHHHHHHHcccccHHHHHHHHcccccHHHHHHHHHHHcccccEEcccccccccEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccccccHHHHHHccccHHHHHHHHHHHHHHHHHccccccEcHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccEEEEEEccEEEEEEccHHccHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEcccccccEEEEccccccccccccccc
Coil and Loop (DISEMBL)
mrrrpgigglqSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHkndirknptfRSQFHEMCAKvgvdplasnkgFWAELLGIGDFYYELGVQIVEICLatrphnggliNLQELCNLLRQRRksnreavseDDCLRAISKLKVLGNGYEVISVGKkklvrsvptelnKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMvddghrdrkrrywfpcassisssmgads
Flexible Loop (DISEMBL)
mrrrpgigglqsaavardQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKsnreavseddclrAISKLkvlgngyevisvgkkklvrSVPTELNKDHNQILELaqaqgfvtvDEVERRLSWTSGRAIDALDILLEEGLAMVddghrdrkrrywfpcassisssmgads
Low Complexity Region (SEG)
MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAssisssMGADS
Disordered region (IsUnstruct)
**************VARDQYRLLGENVAKLRTDLMKEQLATFR******************TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQ**********EDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA***********
Disordered Region (DISOPRED)
*RRRPGIGGLQS*******************TDLMKEQLATFRSQLEDFA***********TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLL***********S*DDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASS*********
Disordered Region (DISEMBL)
***********SAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQR*********EDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS**********
Disordered Region (DISPRO)
****PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSISSSMGADS
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	250	2.2.26 [Sep-21-2011]
Q5M759	250	Vacuolar protein sorting-	yes	no	1.0	1.0	0.836	1e-127
Q5RJU0	257	Vacuolar-sorting protein	yes	no	0.944	0.918	0.514	1e-66
Q5U3V9	258	Vacuolar-sorting protein	yes	no	0.956	0.926	0.5	2e-63
Q96H20	258	Vacuolar-sorting protein	yes	no	0.944	0.914	0.493	7e-63
Q9CZ28	258	Vacuolar-sorting protein	yes	no	0.944	0.914	0.493	7e-63
Q5RK19	258	Vacuolar-sorting protein	yes	no	0.944	0.914	0.493	9e-63
Q54RC4	246	Vacuolar-sorting protein	yes	no	0.94	0.955	0.476	4e-55
Q9LIJ4	120	Putative vacuolar protein	no	no	0.468	0.975	0.820	4e-54
O94663	252	Vacuolar-sorting protein	yes	no	0.924	0.916	0.331	9e-38
Q12483	233	Vacuolar-sorting protein	yes	no	0.768	0.824	0.354	9e-30

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

 Score =  452 bits (1163), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 209/250 (83%), Positives = 234/250 (93%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ AA ARDQYRLLGENVAKLRTD+MKEQL+TFRSQLE+FARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQKAAAARDQYRLLGENVAKLRTDMMKEQLSTFRSQLEEFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FR+QFHEMCA +GVDPLASNKGFWAELLGIGDFYYELGVQI+E+C+ TR HNGGLI+L
Sbjct: 61  PAFRAQFHEMCANIGVDPLASNKGFWAELLGIGDFYYELGVQIIEVCMLTRSHNGGLISL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELCN LRQRRK +REAV+EDDCLRAISKLKVLG+G+EVI++GKKKLVRSVPTELNKDHN
Sbjct: 121 QELCNHLRQRRKKDREAVTEDDCLRAISKLKVLGSGFEVITIGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           QILELAQ QGFV V+EV+RRLSWTSGR IDAL+ LLEEGLAM+D+GH+D K RYWFPC S
Sbjct: 181 QILELAQGQGFVIVEEVQRRLSWTSGRVIDALETLLEEGLAMIDNGHKDGKCRYWFPCVS 240

Query: 241 SISSSMGADS 250
           S+ SS+G+D+
Sbjct: 241 SVYSSIGSDT 250

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  253 bits (645), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 122/237 (51%), Positives = 164/237 (69%), Gaps = 1/237 (0%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLLQMSKQLEMFKTNLEEFASKHKQEIRKNP 62

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA + HNGGLI L 
Sbjct: 63  QFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHHNGGLITLA 122

Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL   + + R    + VS+DD +RAI KLKVLGNG+ +I VG   LV+SVP ELN DH  
Sbjct: 123 ELHQHVLKGRGKLAQDVSQDDIIRAIKKLKVLGNGFGIIPVGGSYLVQSVPAELNMDHTV 182

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +L+LA+ +GFVTV+E++  L+W + RA   L+ LL+EGLA +D      + +YW P 
Sbjct: 183 VLQLAEKKGFVTVNEIKSSLNWETERAKHVLEHLLKEGLAWIDS-QAQGEAQYWLPA 238

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

Xenopus tropicalis (taxid: 8364)

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

 Score =  242 bits (618), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 120/240 (50%), Positives = 160/240 (66%), Gaps = 1/240 (0%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL TF++ LE+FA KHK +IRK+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGSVLAEDQIAQMSKQLDTFKTHLEEFASKHKQEIRKSS 62

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF EMCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L 
Sbjct: 63  QFRVQFQEMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLD 122

Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL + + + R    + VS+DD +RAI KLK +GNG+ +I VG   LV+SVP ELN DH  
Sbjct: 123 ELHHRVLKGRGKFAQDVSQDDLVRAIKKLKAMGNGFGMIPVGGTYLVQSVPAELNMDHTV 182

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASS 241
           +L+LA+ +G+VTV E+   L W   RA   LD LL+EGLA +D      + +YW P   S
Sbjct: 183 VLQLAEKKGYVTVSEIRESLKWEKERACHVLDHLLKEGLAWLDS-QAAGEPQYWLPALFS 241

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

Danio rerio (taxid: 7955)

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

 Score =  240 bits (612), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 117/237 (49%), Positives = 158/237 (66%), Gaps = 1/237 (0%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct: 123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P 
Sbjct: 183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPA 238

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

Homo sapiens (taxid: 9606)

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

 Score =  240 bits (612), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 117/237 (49%), Positives = 158/237 (66%), Gaps = 1/237 (0%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct: 123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P 
Sbjct: 183 VLQLAEKNGYVTVSEIKTSLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPA 238

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

Mus musculus (taxid: 10090)

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

 Score =  240 bits (612), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 117/237 (49%), Positives = 158/237 (66%), Gaps = 1/237 (0%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct: 123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P 
Sbjct: 183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPA 238

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

Rattus norvegicus (taxid: 10116)

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

 Score =  214 bits (545), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 114/239 (47%), Positives = 149/239 (62%), Gaps = 4/239 (1%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRR  GI   Q     + Q + + E +     + +KEQL  F+  LE FA KHK DI KN
Sbjct: 1   MRRGIGIQAAQKQTQTQKQLQNVSEQLNTENINKIKEQLLVFKENLEIFATKHKKDIIKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FR  F +MC  +GVDPLASNKGFW ++LG+GDFYY LGVQI+EICL  R  NGGL+ +
Sbjct: 61  PEFRKYFQDMCNMIGVDPLASNKGFWCQVLGVGDFYYTLGVQIIEICLKYRSSNGGLMEM 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISV-GKKKLVRSVPTELNKDH 179
             L   LR+ R  N + +S DD   +ISKLKVLGNG+ +I V G KKLV+SVP ELNKDH
Sbjct: 121 DTLAEHLRKLRGKNSQEISCDDIECSISKLKVLGNGFNIIKVSGGKKLVQSVPCELNKDH 180

Query: 180 NQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             I+ LAQ     +T   V  +L W+  R  + ++ LL+E +  +D+  +  +  YWFP
Sbjct: 181 TDIIILAQDNNASITQSLVISKLKWSEERINNVINFLLQESMIWIDE--QSNETIYWFP 237

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

Dictyostelium discoideum (taxid: 44689)

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

 Score =  211 bits (537), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 96/117 (82%), Positives = 110/117 (94%)

Query: 70  MCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQ 129
           MCA +GVDPLASNKGFWAELLGIGDFYYE+GVQI+E+C+ TR HNGGLI+LQELCN LRQ
Sbjct: 1   MCANIGVDPLASNKGFWAELLGIGDFYYEIGVQIIEVCMLTRSHNGGLISLQELCNHLRQ 60

Query: 130 RRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELA 186
           RRK++REAV+EDDCLRAISKLK+LG+ +EVI++GKKK VRSVPTELNKDHN ILELA
Sbjct: 61  RRKTDREAVTEDDCLRAISKLKLLGSRFEVITIGKKKFVRSVPTELNKDHNHILELA 117

Arabidopsis thaliana (taxid: 3702)

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

 Score =  157 bits (396), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 140/238 (58%), Gaps = 7/238 (2%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MR+R GIG L      + QY  +G  + + ++D +  QL+TF+  L+ FAR+H  +I++N
Sbjct: 1   MRKRIGIGALNDDEYLK-QYEEVGNELIEQQSDEIASQLSTFQEALKTFAREHATEIKQN 59

Query: 61  PTFRSQFHEMCAKVGVDPLAS--NKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLI 118
             FR+ F ++  K+G+DP  S  ++  WA + G+ +FYY++ V+++E+C AT+  NGGL+
Sbjct: 60  SQFRNTFVKLALKIGLDPFVSGSDESAWAAV-GMNEFYYQVAVRVIEVCYATQMENGGLL 118

Query: 119 NLQELCNLLRQRRKS-NREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNK 177
           ++ ++C  L +  ++   E + E D +RA+  L  LG G+ +  +  K+ +RS+P ELN 
Sbjct: 119 SVSQVCRFLNEENEAFGHEWLRETDVVRAVDSLAPLGPGFVLEKIAGKQYIRSLPLELNT 178

Query: 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYW 235
           D N +LE  +  G+VT+  +    +W   R I  L+ L+ + L  +D   +  +  YW
Sbjct: 179 DQNVVLEAVEILGYVTISILRDNYAWERSRCIQVLNDLVSKSLLWIDS--QGVEMAYW 234

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

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

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

 Score =  130 bits (327), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 73/206 (35%), Positives = 120/206 (58%), Gaps = 14/206 (6%)

Query: 35  MKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA---SNKGFWAELLG 91
           +++QL  F+ +L +FA+KH ++++ +P FRS+F  MC+ +G+DPL+    +K     L  
Sbjct: 32  LRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFDRDK----HLFT 87

Query: 92  IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK 151
           + DFYYE+ ++++EIC  T+  NGG+I+ QEL  +    RK N   V  DD  ++I  LK
Sbjct: 88  VNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKV--HFRKLN---VGLDDLEKSIDMLK 142

Query: 152 VLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDA 211
            L   +E+  +  KK +RSVP EL  D  +ILE+    G+ ++  ++  L W + R+  A
Sbjct: 143 SL-ECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSA 201

Query: 212 LDILLEEGLAMVDDGHRDRKRRYWFP 237
           LD ++  GL  + D     +  YW P
Sbjct: 202 LDEMVANGLLWI-DYQGGAEALYWDP 226

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

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

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	250
255563947	250	Vacuolar sorting protein SNF8, putative	0.996	0.996	0.923	1e-134
224126417	249	predicted protein [Populus trichocarpa]	0.952	0.955	0.928	1e-129
356527034	250	PREDICTED: vacuolar protein sorting-asso	1.0	1.0	0.884	1e-129
357459547	251	Vacuolar protein sorting-associated prot	1.0	0.996	0.888	1e-129
449470437	250	PREDICTED: vacuolar protein sorting-asso	1.0	1.0	0.864	1e-128
217074064	251	unknown [Medicago truncatula] gi|3884922	1.0	0.996	0.884	1e-128
356567363	250	PREDICTED: vacuolar protein sorting-asso	1.0	1.0	0.872	1e-127
225461026	252	PREDICTED: vacuolar protein sorting-asso	0.992	0.984	0.883	1e-126
42567176	250	ESCRT-II complex subunit VPS22 [Arabidop	1.0	1.0	0.836	1e-125
297799286	250	hypothetical protein ARALYDRAFT_913844 [	1.0	1.0	0.836	1e-125

>gi|255563947|ref|XP_002522973.1| Vacuolar sorting protein SNF8, putative [Ricinus communis] gi|223537785|gb|EEF39403.1| Vacuolar sorting protein SNF8, putative [Ricinus communis]

 Score =  483 bits (1242), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 230/249 (92%), Positives = 242/249 (97%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA ARDQYRLLGENVAKLRTDLMKEQL+TFRSQLE+FARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTAAAARDQYRLLGENVAKLRTDLMKEQLSTFRSQLEEFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           PTFR+QFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL
Sbjct: 61  PTFRAQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC LLRQ+RKS+R AVSEDDCLRAISKLK+LGNG+EVISVGKKKLVRSVPTELNKDHN
Sbjct: 121 QELCTLLRQKRKSDRGAVSEDDCLRAISKLKILGNGFEVISVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQAQGFVTVDEVERRLSWTSGRAIDALD LL+EGLAM+DDGH D KRRYWFPC S
Sbjct: 181 EILELAQAQGFVTVDEVERRLSWTSGRAIDALDTLLDEGLAMIDDGHGDGKRRYWFPCVS 240

Query: 241 SISSSMGAD 249
           SISSS+GAD
Sbjct: 241 SISSSVGAD 249

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126417|ref|XP_002319833.1| predicted protein [Populus trichocarpa] gi|222858209|gb|EEE95756.1| predicted protein [Populus trichocarpa]

 Score =  467 bits (1202), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 221/238 (92%), Positives = 233/238 (97%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA ARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTAAAARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           PTFR+QFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL
Sbjct: 61  PTFRTQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC LLRQ+RKS+REAVSEDDCLRAISKLK+LG+G+EVISVGK+KLVRSVPTELNKDHN
Sbjct: 121 QELCALLRQKRKSDREAVSEDDCLRAISKLKILGSGFEVISVGKRKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +ILELAQAQGFVTVDE+ERRLSWTSGRA DALD LL+EGLAM+DDGHRD KRRYWFPC
Sbjct: 181 EILELAQAQGFVTVDELERRLSWTSGRATDALDTLLDEGLAMIDDGHRDGKRRYWFPC 238

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356527034|ref|XP_003532119.1| PREDICTED: vacuolar protein sorting-associated protein 22 homolog 1-like [Glycine max]

 Score =  467 bits (1202), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 221/250 (88%), Positives = 239/250 (95%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+ A ARDQ+RLLGENVAK+RTDLMKEQLATFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTHAAARDQFRLLGENVAKIRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P+FRSQFHEMCAKVGVDPLASNKGFW+ELLG+GDFYYELGVQIV+ICLATR HNGGLI+L
Sbjct: 61  PSFRSQFHEMCAKVGVDPLASNKGFWSELLGLGDFYYELGVQIVDICLATRAHNGGLIDL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
            ELC+LLRQRRKS+RE VSEDDCLRAI KLKVLG+G+EVISVGKKKLVRSVPTELNKDHN
Sbjct: 121 HELCSLLRQRRKSDREVVSEDDCLRAIKKLKVLGSGFEVISVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQAQGFVTVDEVERRLSW+SGRAIDALD LL+EGLAM+DDGHRD +RRYWFPC S
Sbjct: 181 EILELAQAQGFVTVDEVERRLSWSSGRAIDALDTLLDEGLAMIDDGHRDGRRRYWFPCVS 240

Query: 241 SISSSMGADS 250
            ISSS+G DS
Sbjct: 241 PISSSIGVDS 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357459547|ref|XP_003600054.1| Vacuolar protein sorting-associated protein-like protein [Medicago truncatula] gi|355489102|gb|AES70305.1| Vacuolar protein sorting-associated protein-like protein [Medicago truncatula]

 Score =  465 bits (1197), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 222/250 (88%), Positives = 235/250 (94%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA ARDQY+ LGENVAK+RTD+MKEQL+TFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTAAAARDQYKKLGENVAKIRTDMMKEQLSTFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIV+ICLATRP NGGLINL
Sbjct: 61  PAFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVDICLATRPLNGGLINL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC LLRQRRKS+R  VSEDDCLRAISKLKVLG+G+EVISVGKKKLVRSVPTELNKDHN
Sbjct: 121 QELCQLLRQRRKSDRGVVSEDDCLRAISKLKVLGSGFEVISVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQ QGFVTVDEVERRLSWTSGRAIDALD LL+EGLAM+DDGH+D KRRYWFPC S
Sbjct: 181 EILELAQGQGFVTVDEVERRLSWTSGRAIDALDTLLDEGLAMIDDGHKDGKRRYWFPCVS 240

Query: 241 SISSSMGADS 250
            ISS  G DS
Sbjct: 241 PISSLTGIDS 250

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449470437|ref|XP_004152923.1| PREDICTED: vacuolar protein sorting-associated protein 22 homolog 1-like [Cucumis sativus] gi|449515265|ref|XP_004164670.1| PREDICTED: vacuolar protein sorting-associated protein 22 homolog 1-like [Cucumis sativus]

 Score =  463 bits (1192), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 216/250 (86%), Positives = 236/250 (94%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA ARDQYR LGENVAKLR D+MKEQL+TFRSQLEDFARKHK DI KN
Sbjct: 1   MRRRPGIGGLQTAAAARDQYRQLGENVAKLRADMMKEQLSTFRSQLEDFARKHKKDISKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYE+GVQIV+ICL+TRPHNGGLI+L
Sbjct: 61  PAFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYEIGVQIVDICLSTRPHNGGLISL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC LLRQRRKS+REAVSEDDCLRAISKLK+LG+G+EVI+VGKKKLVRSVPTELNKDHN
Sbjct: 121 QELCTLLRQRRKSDREAVSEDDCLRAISKLKILGSGFEVITVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQAQG+ TVDEVERRLSWTSGRA+DALD LL+EGLAM+DDGHRD +RRYWFPC S
Sbjct: 181 EILELAQAQGYATVDEVERRLSWTSGRAVDALDTLLDEGLAMIDDGHRDGRRRYWFPCVS 240

Query: 241 SISSSMGADS 250
            ISSS+  D+
Sbjct: 241 PISSSLTTDA 250

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074064|gb|ACJ85392.1| unknown [Medicago truncatula] gi|388492282|gb|AFK34207.1| unknown [Medicago truncatula]

 Score =  463 bits (1191), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 221/250 (88%), Positives = 234/250 (93%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA ARDQY+ LGENVAK RTD+M+EQL+TFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTAAAARDQYKKLGENVAKTRTDMMREQLSTFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIV+ICLATRP NGGLINL
Sbjct: 61  PAFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVDICLATRPLNGGLINL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC LLRQRRKS+R  VSEDDCLRAISKLKVLG+G+EVISVGKKKLVRSVPTELNKDHN
Sbjct: 121 QELCQLLRQRRKSDRGVVSEDDCLRAISKLKVLGSGFEVISVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQ QGFVTVDEVERRLSWTSGRAIDALD LL+EGLAM+DDGH+D KRRYWFPC S
Sbjct: 181 EILELAQGQGFVTVDEVERRLSWTSGRAIDALDTLLDEGLAMIDDGHKDGKRRYWFPCVS 240

Query: 241 SISSSMGADS 250
            ISS  G DS
Sbjct: 241 PISSLTGIDS 250

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567363|ref|XP_003551890.1| PREDICTED: vacuolar protein sorting-associated protein 22 homolog 1-like [Glycine max]

 Score =  461 bits (1185), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 218/250 (87%), Positives = 237/250 (94%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+ A ARDQ+RLLGENVAK+RTDLMKEQLATFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTHAAARDQFRLLGENVAKIRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FRSQFHEMCAKVGVDPLASNKGFW+ELLG+GDFYYELGVQIV+ICLATR HNGGLI+L
Sbjct: 61  PAFRSQFHEMCAKVGVDPLASNKGFWSELLGLGDFYYELGVQIVDICLATRVHNGGLIDL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELC+LLR RRK++RE VSEDDCLRAI KLKVLG+G+EVISVGKKKLVRSVPTELNKDHN
Sbjct: 121 QELCHLLRHRRKTDREVVSEDDCLRAIKKLKVLGSGFEVISVGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           +ILELAQAQGFVTVDEVERRLSW+SGRAIDALD LL+EGLAM+DDG +D +RRYWFPC S
Sbjct: 181 EILELAQAQGFVTVDEVERRLSWSSGRAIDALDTLLDEGLAMIDDGDKDGRRRYWFPCVS 240

Query: 241 SISSSMGADS 250
            ISSS+G DS
Sbjct: 241 PISSSIGVDS 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461026|ref|XP_002281130.1| PREDICTED: vacuolar protein sorting-associated protein 22 homolog 1 [Vitis vinifera] gi|297737408|emb|CBI26609.3| unnamed protein product [Vitis vinifera]

 Score =  455 bits (1171), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/249 (88%), Positives = 234/249 (93%), Gaps = 1/249 (0%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ+AA  RDQYRLLGENVAK+RTDLMKEQL TFRSQLEDFARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQTAAATRDQYRLLGENVAKIRTDLMKEQLTTFRSQLEDFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIV+ICLATR HNGGLI+L
Sbjct: 61  PAFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVDICLATRVHNGGLIDL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELCNLL QRRKS   AVSEDDCLRAISKLKVLG+G+EVISVGK+KLVRSVPTELNKDHN
Sbjct: 121 QELCNLLCQRRKSAHGAVSEDDCLRAISKLKVLGSGFEVISVGKRKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
            ILELAQAQGFVTV+EVERRLSW SGRA DAL+ LL+EGLAM+DDGHRD KRRYWFPCAS
Sbjct: 181 AILELAQAQGFVTVEEVERRLSWPSGRATDALETLLDEGLAMIDDGHRDGKRRYWFPCAS 240

Query: 241 SISSSMGAD 249
           S+ S++GAD
Sbjct: 241 SL-SAVGAD 248

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42567176|ref|NP_194434.2| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|186514003|ref|NP_001119065.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|186514006|ref|NP_001119066.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|186514008|ref|NP_001119067.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|332278132|sp|Q5M759.2|VP221_ARATH RecName: Full=Vacuolar protein sorting-associated protein 22 homolog 1; Short=AtVPS22-1; AltName: Full=ESCRT-II complex subunit VPS22 homolog 1 gi|332659887|gb|AEE85287.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|332659888|gb|AEE85288.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|332659889|gb|AEE85289.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana] gi|332659890|gb|AEE85290.1| ESCRT-II complex subunit VPS22 [Arabidopsis thaliana]

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 209/250 (83%), Positives = 234/250 (93%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ AA ARDQYRLLGENVAKLRTD+MKEQL+TFRSQLE+FARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQKAAAARDQYRLLGENVAKLRTDMMKEQLSTFRSQLEEFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FR+QFHEMCA +GVDPLASNKGFWAELLGIGDFYYELGVQI+E+C+ TR HNGGLI+L
Sbjct: 61  PAFRAQFHEMCANIGVDPLASNKGFWAELLGIGDFYYELGVQIIEVCMLTRSHNGGLISL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELCN LRQRRK +REAV+EDDCLRAISKLKVLG+G+EVI++GKKKLVRSVPTELNKDHN
Sbjct: 121 QELCNHLRQRRKKDREAVTEDDCLRAISKLKVLGSGFEVITIGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           QILELAQ QGFV V+EV+RRLSWTSGR IDAL+ LLEEGLAM+D+GH+D K RYWFPC S
Sbjct: 181 QILELAQGQGFVIVEEVQRRLSWTSGRVIDALETLLEEGLAMIDNGHKDGKCRYWFPCVS 240

Query: 241 SISSSMGADS 250
           S+ SS+G+D+
Sbjct: 241 SVYSSIGSDT 250

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799286|ref|XP_002867527.1| hypothetical protein ARALYDRAFT_913844 [Arabidopsis lyrata subsp. lyrata] gi|297313363|gb|EFH43786.1| hypothetical protein ARALYDRAFT_913844 [Arabidopsis lyrata subsp. lyrata]

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 209/250 (83%), Positives = 234/250 (93%)

Query: 1   MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
           MRRRPGIGGLQ AA ARDQYRLLGENVAKLRTD+MKEQLATFRSQLE+FARKHKNDIRKN
Sbjct: 1   MRRRPGIGGLQKAAAARDQYRLLGENVAKLRTDMMKEQLATFRSQLEEFARKHKNDIRKN 60

Query: 61  PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
           P FR+QFHEMC+ +GVDPLASNKGFWAELLGIGDFYYELGVQI+E+C+ TR HNGGLI+L
Sbjct: 61  PAFRAQFHEMCSNIGVDPLASNKGFWAELLGIGDFYYELGVQIIEVCMLTRSHNGGLISL 120

Query: 121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
           QELCN LRQRRK +REAV+EDDCLRAISKLKVLG+G+EVI++GKKKLVRSVPTELNKDHN
Sbjct: 121 QELCNHLRQRRKKDREAVTEDDCLRAISKLKVLGSGFEVITIGKKKLVRSVPTELNKDHN 180

Query: 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240
           QILELAQ QGFV V+EV+RRLSWTSGR IDAL+ LLEEGLAM+D+GH+D K RYWFPC S
Sbjct: 181 QILELAQGQGFVIVEEVQRRLSWTSGRVIDALETLLEEGLAMIDNGHKDGKCRYWFPCVS 240

Query: 241 SISSSMGADS 250
           S+ SS+G+D+
Sbjct: 241 SVYSSIGSDT 250

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	250
TAIR|locus:2116357	250	VPS22 "AT4G27040" [Arabidopsis	1.0	1.0	0.82	3.6e-112
ZFIN|ZDB-GENE-041114-117	258	snf8 "SNF8, ESCRT-II complex s	0.94	0.910	0.504	1.5e-58
UNIPROTKB|E1BZH7	258	SNF8 "Uncharacterized protein"	0.936	0.906	0.510	1.9e-58
UNIPROTKB|Q96H20	258	SNF8 "Vacuolar-sorting protein	0.94	0.910	0.495	6.6e-58
MGI|MGI:1343161	258	Snf8 "SNF8, ESCRT-II complex s	0.94	0.910	0.495	6.6e-58
RGD|1310144	258	Snf8 "SNF8, ESCRT-II complex s	0.94	0.910	0.495	6.6e-58
UNIPROTKB|I3L6X7	258	SNF8 "Uncharacterized protein"	0.94	0.910	0.491	8.4e-58
UNIPROTKB|E2RTF6	258	SNF8 "Uncharacterized protein"	0.94	0.910	0.491	1.4e-57
UNIPROTKB|Q08DR7	258	SNF8 "Uncharacterized protein"	0.94	0.910	0.491	1.7e-57
WB|WBGene00016167	269	vps-22 [Caenorhabditis elegans	0.94	0.873	0.462	7.8e-55

TAIR|locus:2116357 VPS22 "AT4G27040" [Arabidopsis thaliana (taxid:3702)]

 Score = 1107 (394.7 bits), Expect = 3.6e-112, P = 3.6e-112
 Identities = 205/250 (82%), Positives = 229/250 (91%)

Query:     1 MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKN 60
             MRRRPGIGGLQ AA ARDQYRLLGENVAKLRTD+MKEQL+TFRSQLE+FARKHKNDIRKN
Sbjct:     1 MRRRPGIGGLQKAAAARDQYRLLGENVAKLRTDMMKEQLSTFRSQLEEFARKHKNDIRKN 60

Query:    61 PTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINL 120
             P FR+QFHEMCA +GVDPLASNKGFWAELLGIGDFYYELGVQI+E+C+ TR HNGGLI+L
Sbjct:    61 PAFRAQFHEMCANIGVDPLASNKGFWAELLGIGDFYYELGVQIIEVCMLTRSHNGGLISL 120

Query:   121 QELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
             QELCN LRQRRK +REAV+EDDCLRAISKLKVLG+G+EVI++GKKKLVRSVPTELNKDHN
Sbjct:   121 QELCNHLRQRRKKDREAVTEDDCLRAISKLKVLGSGFEVITIGKKKLVRSVPTELNKDHN 180

Query:   181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAX 240
             QILELAQ QGFV V+EV+RRLSWTSGR IDAL+ LLEEGLAM+D+GH+D K RYWFPC  
Sbjct:   181 QILELAQGQGFVIVEEVQRRLSWTSGRVIDALETLLEEGLAMIDNGHKDGKCRYWFPCVS 240

Query:   241 XXXXXMGADS 250
                  +G+D+
Sbjct:   241 SVYSSIGSDT 250

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0016192 "vesicle-mediated transport" evidence=ISS

GO:0000814 "ESCRT II complex" evidence=ISS

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

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 119/236 (50%), Positives = 159/236 (67%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL TF++ LE+FA KHK +IRK+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGSVLAEDQIAQMSKQLDTFKTHLEEFASKHKQEIRKSS 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF EMCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L 
Sbjct:    63 QFRVQFQEMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLD 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL + + + R    + VS+DD +RAI KLK +GNG+ +I VG   LV+SVP ELN DH  
Sbjct:   123 ELHHRVLKGRGKFAQDVSQDDLVRAIKKLKAMGNGFGMIPVGGTYLVQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+ +G+VTV E+   L W   RA   LD LL+EGLA +D      + +YW P
Sbjct:   183 VLQLAEKKGYVTVSEIRESLKWEKERACHVLDHLLKEGLAWLDS-QAAGEPQYWLP 237

GO:0006810 "transport" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

 Score = 600 (216.3 bits), Expect = 1.9e-58, P = 1.9e-58
 Identities = 121/237 (51%), Positives = 164/237 (69%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCN-LLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHN 180
             EL   +L+ R K  +E VS+DD LRAI KLKVLG+G+ +I VG   L++SVP ELN DH 
Sbjct:   123 ELHQQVLKGRGKFAQE-VSQDDLLRAIKKLKVLGSGFGIIPVGGTYLIQSVPAELNMDHT 181

Query:   181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
              +L+LA+ +G+VTV E++  L W   RA   L+ LL+EG+A +D      + +YW P
Sbjct:   182 VVLQLAEKKGYVTVGEIKSSLKWEVERAKQILEHLLKEGMAWLDT-QAAGEPQYWLP 237

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0008134 "transcription factor binding" evidence=IEA

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

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 117/236 (49%), Positives = 158/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

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

GO:0015031 "protein transport" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IDA

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

GO:0008134 "transcription factor binding" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0016197 "endosomal transport" evidence=TAS

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

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 117/236 (49%), Positives = 158/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSEIKTSLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005768 "endosome" evidence=IEA

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

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

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

GO:0006810 "transport" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0015031 "protein transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

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

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 117/236 (49%), Positives = 158/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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

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

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

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

GO:0008150 "biological_process" evidence=ND

GO:0015031 "protein transport" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

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

 Score = 594 (214.2 bits), Expect = 8.4e-58, P = 8.4e-58
 Identities = 116/236 (49%), Positives = 158/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFSIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV +++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSDIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

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

 Score = 592 (213.5 bits), Expect = 1.4e-57, P = 1.4e-57
 Identities = 116/236 (49%), Positives = 158/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV +++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSDIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

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

 Score = 591 (213.1 bits), Expect = 1.7e-57, P = 1.7e-57
 Identities = 116/236 (49%), Positives = 157/236 (66%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
             EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct:   123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFSIIPVGGTYLIQSVPAELNMDHTV 182

Query:   182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +L+LA+  G+VTV  ++  L W + RA   L+ LL+EGLA +D      +  YW P
Sbjct:   183 VLQLAEKNGYVTVSAIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLP 237

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

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

 Score = 566 (204.3 bits), Expect = 7.8e-55, P = 7.8e-55
 Identities = 110/238 (46%), Positives = 163/238 (68%)

Query:     2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             RRR G+  +Q      +++   G+ +A  +     +QL    + LE FA++H+++I+KN 
Sbjct:     4 RRRIGVAAIQKKQETANKFAAKGDQMAGEQLVQFSQQLEQLSAGLEMFAQRHRDEIKKNS 63

Query:    62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
              FR  F EMCA VGVDPLAS+KGFWA+ LG GDFYYELG+QIVEICL+T   NGG++ ++
Sbjct:    64 QFRRHFQEMCASVGVDPLASSKGFWAKALGFGDFYYELGIQIVEICLSTTHINGGIMTVE 123

Query:   122 ELCN-LLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKK-LVRSVPTELNKDH 179
             E+ N L+R R ++ ++ +S DD LRA+ KLKVLGNG+E++ +G  + LV+SVP EL+ DH
Sbjct:   124 EIRNRLMRTRSRTRKDTISTDDILRAVDKLKVLGNGFELVPLGGGRFLVQSVPGELSMDH 183

Query:   180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
             +++L+LA+   +VT + +  +L W   RA  AL+ L++EGLA  D+   D  + YWFP
Sbjct:   184 SRVLQLAEDAAYVTKELIIDKLRWDEARASSALEHLVKEGLAWTDEQASDTTQ-YWFP 240

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9CZ28	SNF8_MOUSE	No assigned EC number	0.4936	0.944	0.9147	yes	no
O94663	SNF8_SCHPO	No assigned EC number	0.3319	0.924	0.9166	yes	no
Q5RK19	SNF8_RAT	No assigned EC number	0.4936	0.944	0.9147	yes	no
Q96H20	SNF8_HUMAN	No assigned EC number	0.4936	0.944	0.9147	yes	no
Q5U3V9	SNF8_DANRE	No assigned EC number	0.5	0.956	0.9263	yes	no
Q5RJU0	SNF8_XENTR	No assigned EC number	0.5147	0.944	0.9182	yes	no
Q54RC4	SNF8_DICDI	No assigned EC number	0.4769	0.94	0.9552	yes	no
Q5M759	VP221_ARATH	No assigned EC number	0.836	1.0	1.0	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.XIII.2975.1	hypothetical protein (249 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0029023702	hypothetical protein (179 aa)				•	•	•	•		0.989
	estExt_fgenesh4_pm.C_LG_X0978	hypothetical protein (447 aa)					•	•	•		0.968
	eugene3.00050070	hypothetical protein (222 aa)					•	•	•		0.906
	fgenesh4_pm.C_LG_VII000158	hypothetical protein (222 aa)					•	•	•		0.904
	estExt_Genewise1_v1.C_LG_VIII1654	hypothetical protein (229 aa)					•	•	•		0.899
	grail3.0145004603	hypothetical protein (207 aa)					•	•	•		0.864
	eugene3.00061076	hypothetical protein (253 aa)					•	•	•		0.862
	eugene3.01450002	hypothetical protein (223 aa)						•	•		0.841
	estExt_fgenesh4_pm.C_LG_I0430	hypothetical protein (226 aa)						•	•		0.840
	eugene3.00040221	SubName- Full=Putative uncharacterized protein; (209 aa)				•	•	•	•		0.656

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	250
pfam04157	219	pfam04157, EAP30, EAP30/Vps36 family	8e-68

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

 Score =  208 bits (531), Expect = 8e-68
 Identities = 103/223 (46%), Positives = 144/223 (64%), Gaps = 9/223 (4%)

Query: 6   GIGGLQSAAVARDQYRLLGENVAKLRTDL--MKEQLATFRSQLEDFARKHKNDIRKNPTF 63
           GI G++ +   + +Y  LG  +A    DL  + +Q   F   LE FA+KHK++I+ NP F
Sbjct: 2   GIAGIERSREEQRKYNDLGLQLA--FEDLEALMKQAKDFVELLESFAKKHKSEIKANPEF 59

Query: 64  RSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQEL 123
           R+QF  MCA +GVDPLAS KG  + L G+GDFYYEL VQIVEICLAT   NGG+I+LQ+L
Sbjct: 60  RAQFQSMCASLGVDPLASKKG--SVLGGVGDFYYELAVQIVEICLATLKENGGIISLQDL 117

Query: 124 CNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGK-KKLVRSVP-TELNKDHNQ 181
             L   R +   E VS +D L+A  KL+ LG G++++ +G    +V+SVP +EL++D  +
Sbjct: 118 YALY-NRARGGTELVSPEDLLKACKKLEKLGLGFKLVKIGSGVLVVQSVPKSELSEDQTK 176

Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224
           ILELA+  G VT  E+  +L W+ GRA + L+   +EGL   D
Sbjct: 177 ILELAEELGGVTASELAEKLGWSIGRAKEVLEKAEKEGLLWRD 219

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
KOG3341	249	consensus RNA polymerase II transcription factor c	100.0
PF04157	223	EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP	100.0
KOG2760	432	consensus Vacuolar sorting protein VPS36 [Intracel	100.0
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.77
PRK00135	188	scpB segregation and condensation protein B; Revie	96.46
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	96.15
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.99
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.9
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.59
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.27
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.2
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.79
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.63
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.05
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	93.95
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.94
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.71
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	93.68
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.07
PF04079	159	DUF387: Putative transcriptional regulators (Ypuh-	92.82
TIGR00281	186	segregation and condensation protein B. Shown to b	92.58
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	92.2
PRK11169	164	leucine-responsive transcriptional regulator; Prov	91.78
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	91.62
COG3355	126	Predicted transcriptional regulator [Transcription	91.21
PHA02943	165	hypothetical protein; Provisional	91.07
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	91.06
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	90.69
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	90.0
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	89.87
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	89.85
PRK15466	166	carboxysome structural protein EutK; Provisional	89.81
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	89.61
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	89.59
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	89.47
COG2345	218	Predicted transcriptional regulator [Transcription	89.31
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	89.25
PRK09334	86	30S ribosomal protein S25e; Provisional	89.16
PRK13509	251	transcriptional repressor UlaR; Provisional	89.08
COG2512	258	Predicted membrane-associated trancriptional regul	88.76
PF09107	50	SelB-wing_3: Elongation factor SelB, winged helix	88.48
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	88.48
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	88.45
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	88.31
PRK03573	144	transcriptional regulator SlyA; Provisional	88.11
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	88.06
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	88.04
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	87.84
PRK09954	362	putative kinase; Provisional	86.95
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	86.95
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	86.71
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	86.66
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	86.53
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	86.06
cd08767	126	Cdt1_c The C-terminal fold of replication licensin	86.05
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.0
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	85.99
COG1522	154	Lrp Transcriptional regulators [Transcription]	85.9
PRK06266	178	transcription initiation factor E subunit alpha; V	85.58
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	85.55
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	85.29
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	85.18
PRK03902	142	manganese transport transcriptional regulator; Pro	84.79
smart00843	63	Ftsk_gamma This domain directs oriented DNA transl	84.18
PLN02180	639	gamma-glutamyl transpeptidase 4	84.18
PLN02198	573	glutathione gamma-glutamylcysteinyltransferase	83.79
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	83.72
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	83.12
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	82.52
COG1846	126	MarR Transcriptional regulators [Transcription]	82.44
COG5126	160	FRQ1 Ca2+-binding protein (EF-Hand superfamily) [S	82.42
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	82.38
TIGR00066	516	g_glut_trans gamma-glutamyltranspeptidase. Also ca	82.35
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	82.34
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	82.13
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	81.85
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	81.53
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	81.44
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	81.44
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	80.59
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	80.45
PF01019	510	G_glu_transpept: Gamma-glutamyltranspeptidase; Int	80.22
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	80.05
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	80.05

>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]

Probab=100.00  E-value=5.1e-93  Score=616.46  Aligned_cols=244  Identities=59%  Similarity=0.974  Sum_probs=238.1

Q ss_pred             CCCCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC
Q 025606            1 MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA   80 (250)
Q Consensus         1 mrR~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~   80 (250)
                      ||||+|++||++++ +..+|++.|++++++|+.+|++||++|+.+|++||+||+.||++||+||++|+.||++||||||+
T Consensus         1 ~rrrvG~gAi~~~k-~~~ky~~~g~~l~e~Ql~q~~~Ql~~f~~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPla   79 (249)
T KOG3341|consen    1 MRRRVGLGAIQKKK-AAKKYKEVGTELAEQQLVQMSKQLEVFQEALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPLA   79 (249)
T ss_pred             CccchhhhHHhhHH-HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCccc
Confidence            89999999999987 89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEE
Q 025606           81 SNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVI  160 (250)
Q Consensus        81 s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi  160 (250)
                      |+||||++++|+|||||||+|||||||++|.+.|||+|++.||++++.+.|+...+.||+||++|||++|++||+||+|+
T Consensus        80 s~kgfw~~~lgvgdFYYelgVqviEvC~at~~~nGGlislqel~~~l~~~R~~~~e~vt~dD~lrAi~kLk~LG~gFev~  159 (249)
T KOG3341|consen   80 SGKGFWAELLGVGDFYYELGVQVIEVCLATKHTNGGLISLQELCNHLLQRRKKDHEAVTEDDLLRAIDKLKVLGSGFEVI  159 (249)
T ss_pred             cCcchHHHHhhhHHHHHHHhhHHHHHHHHhhcccCCeeeHHHHHHHHHHHhcccchhccHHHHHHHHHHhhccCCCeEEE
Confidence            99999999999999999999999999999999999999999999999999998889999999999999999999999999


Q ss_pred             EECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCcc
Q 025606          161 SVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS  240 (250)
Q Consensus       161 ~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~  240 (250)
                      +|||+++|||||.|||+||+.|||+|+..||||.+.|+++|+|+..||+.+|++|+++|++|+|.|+++ |..|||||+|
T Consensus       160 ~iggK~~vrSVP~ELn~Dht~ILela~~~gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~-e~~YW~ps~~  238 (249)
T KOG3341|consen  160 KIGGKKLVRSVPTELNMDHTVILELAEILGYVTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGD-EAAYWFPSLF  238 (249)
T ss_pred             EecCEEeeecCcchhcccHHHHHHHHHhcCceeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCc-ceeeechhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999965 9999999999


Q ss_pred             CCCccC
Q 025606          241 SISSSM  246 (250)
Q Consensus       241 ~~~~~~  246 (250)
                      ...-++
T Consensus       239 ~~~~~q  244 (249)
T KOG3341|consen  239 TDQYAQ  244 (249)
T ss_pred             hHHHhh
Confidence            865443

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

Probab=100.00  E-value=2.8e-66  Score=457.17  Aligned_cols=218  Identities=49%  Similarity=0.789  Sum_probs=187.6

Q ss_pred             cchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCc
Q 025606            5 PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKG   84 (250)
Q Consensus         5 ~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~   84 (250)
                      +||+||+++.+++++|++.+.+.+.+++++|..|+++|++.+++|+++|+++|++||+||++|++||++|||||+++++ 
T Consensus         1 ~GI~~l~~~~~~~~~~~~~~~~~a~~dl~~L~~qa~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~-   79 (223)
T PF04157_consen    1 VGIAGLQRRQEQKRQYNELGMQLAFQDLEALMSQAKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSK-   79 (223)
T ss_dssp             --------------------TCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTT-
T ss_pred             CchHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchh-
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999999998 


Q ss_pred             cccccc-ccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC
Q 025606           85 FWAELL-GIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG  163 (250)
Q Consensus        85 ~ws~~l-G~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig  163 (250)
                      +|++.+ |.++||||||+||+|||..+++.|||||+|+||+|++||+|+. ...|||+||++||++|++||.||++++++
T Consensus        80 ~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g-~~lISp~Di~~A~~~l~~lg~g~~l~~~~  158 (223)
T PF04157_consen   80 FWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGG-SELISPEDILRACKLLEVLGLGFRLRKFG  158 (223)
T ss_dssp             CCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTT-SST--HHHHHHHHHHHCCCTSSEEEEEET
T ss_pred             hhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhccc-CCCcCHHHHHHHHHHHHHcCCCeEEEEeC
Confidence            999999 9999999999999999999999999999999999999999931 57999999999999999999999999999


Q ss_pred             -CEEEEEecC-CccchhHHHHHHHH--HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          164 -KKKLVRSVP-TELNKDHNQILELA--QAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       164 -~~~~v~svp-~El~~D~~~vLela--~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                       |++||+++| .|++.||++||+++  +..||+|+.+|++++||+..||+++|+.|+++|++|||
T Consensus       159 sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~D  223 (223)
T PF04157_consen  159 SGVKVVQSVPYSELSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLWRD  223 (223)
T ss_dssp             TTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEeeC
Confidence             999999999 89999999999999  67999999999999999999999999999999999999

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

>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport]

Probab=100.00  E-value=9.6e-37  Score=284.42  Aligned_cols=224  Identities=20%  Similarity=0.266  Sum_probs=195.5

Q ss_pred             CCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHH------HHHHHHHHhcccccccChhHHHHHHHHHHHcCC
Q 025606            3 RRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFR------SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGV   76 (250)
Q Consensus         3 R~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~------~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV   76 (250)
                      |++||++|+|+.+++.+-++...+.+   |++|++.|+..+      +++.++.+..+++|.+|++.|  |+++..++||
T Consensus       196 r~vGI~giEr~~e~q~~~td~~i~~A---FqDLskLMs~Akemv~Lsk~~~~Km~~~~g~i~dDetv~--~ks~llsLGI  270 (432)
T KOG2760|consen  196 RMVGISGIERSLEEQLKKTDKTINNA---FQDLSKLMSLAKEMVSLSKSIAEKMKSKTGEIQDDETVR--FKSYLLSLGI  270 (432)
T ss_pred             eeechhHHHHHHHHHHHhcchhHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCchhhhh--hHHhhhhhcc
Confidence            57999999999999999999887777   777777777766      688899999999999999997  9999999999


Q ss_pred             CCCCCCCccccccccc--ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccC
Q 025606           77 DPLASNKGFWAELLGI--GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG  154 (250)
Q Consensus        77 DPL~s~k~~ws~~lG~--gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG  154 (250)
                      +...+..+     +|+  .-|+-+||.||.|+...+.++|||||+|.|+||++||+||  +++|||+|+.+||+.|+.||
T Consensus       271 ~dpvt~~n-----~~~s~~~Y~~~Lakqlse~l~~~lee~ggmisLtdvY~~~NRaRG--~eLiSPedl~~ACe~le~l~  343 (432)
T KOG2760|consen  271 LDPVTKDN-----FGLSLSLYHQELAKQLSEFLRLPLEENGGMISLTDVYCRYNRARG--TELISPEDLVNACELLEHLG  343 (432)
T ss_pred             CCcchhcc-----ccchHHHHHHHHHHHHHHHHhcchhhcCCEEEHHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHhcC
Confidence            74443422     231  5789999999999999999999999999999999999998  79999999999999999999


Q ss_pred             CCeEEEEEC-CEEEEEecCCccchhHHHHHHHHH---hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCC
Q 025606          155 NGYEVISVG-KKKLVRSVPTELNKDHNQILELAQ---AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDR  230 (250)
Q Consensus       155 ~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~---~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~  230 (250)
                      .|+++.+++ |..+||.-   -..|..+++.+.+   ..+.+|+++++..+||+...|+++|..++++|.+|+|++.   
T Consensus       344 ~pl~L~kf~SGvlvvqlK---s~~~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD~s~---  417 (432)
T KOG2760|consen  344 VPLRLRKFNSGVLVVQLK---SHSDEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRDDSV---  417 (432)
T ss_pred             CceEEEEcCCceEEEEee---ccchHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeeccCc---
Confidence            999999999 88888833   3444445555444   4678899999999999999999999999999999999999   


Q ss_pred             CcceeecCccCCCc
Q 025606          231 KRRYWFPCASSISS  244 (250)
Q Consensus       231 e~~Yw~P~l~~~~~  244 (250)
                      |++|||||+|.+..
T Consensus       418 eGL~fY~N~f~e~~  431 (432)
T KOG2760|consen  418 EGLRFYPNLFMESS  431 (432)
T ss_pred             cceeecccccccCC
Confidence            89999999998753

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=96.77  E-value=0.0045  Score=41.47  Aligned_cols=47  Identities=23%  Similarity=0.326  Sum_probs=40.0

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      ||.-+..||.+....|.+|..+|++.+|++..-+...|..|+++|++
T Consensus         1 l~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    1 LDETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             --HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            45667889999998899999999999999999999999999999975

...

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=96.46  E-value=0.031  Score=48.77  Aligned_cols=107  Identities=20%  Similarity=0.266  Sum_probs=83.9

Q ss_pred             HHHHHhhhhcccCCCc-eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecC----
Q 025606          102 QIVEICLATRPHNGGL-INLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVP----  172 (250)
Q Consensus       102 qIvevC~~tr~~nGGl-i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp----  172 (250)
                      .+||.++=.   .|-= +++.+|...+.         +++++|..+++.|..    -+.|++|+.++|.+.+++-|    
T Consensus         7 ~~iEA~LF~---sg~pgls~~~La~~l~---------~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~   74 (188)
T PRK00135          7 SIIEALLFV---SGEEGLSLEQLAEILE---------LEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENAD   74 (188)
T ss_pred             HHHHHHHHH---cCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHH
Confidence            345555443   3332 67888876542         567899999999953    48899999999988888732    


Q ss_pred             -----------CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          173 -----------TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       173 -----------~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                                 ..||.....+|.++.-++-||-.++.+..|-+.   -..|..|+..|++=.
T Consensus        75 ~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e  133 (188)
T PRK00135         75 YLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAKGLIKE  133 (188)
T ss_pred             HHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEE
Confidence                       269988888899888889999999999999985   788999999999864

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

Probab=96.15  E-value=0.084  Score=49.75  Aligned_cols=115  Identities=15%  Similarity=0.243  Sum_probs=87.9

Q ss_pred             hhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEec-----
Q 025606           97 YELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSV-----  171 (250)
Q Consensus        97 ~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~sv-----  171 (250)
                      .+++.+|.+.|.+.  ..+..++.+||...+        ...+..+++.|++.|-.-|. +++++-++....+-+     
T Consensus         8 ~~~~~~l~~~~~~~--~~~~~~~~~~L~~~~--------~~~~~~~~~~~in~Ll~~~~-~~~~~~~~~l~~~~~~~~~a   76 (327)
T PF05158_consen    8 SELEKKLLELCREN--PSPKGFSQEDLQQLI--------PGLDLQELVKAINELLSSGL-LKLLKKGGGLSYKAVSEEEA   76 (327)
T ss_dssp             HHHHHHHHHHHHH-----SS-EEHHHHHHH---------TTS-HHHHHHHHHHHHHHTS-EEEEE-SSSEEEEE--SSS-
T ss_pred             HHHHHHHHHHHHHh--cCCCCcCHHHHHhhc--------CCCCHHHHHHHHHHHHhCCC-EEEEEcCCEEEEEEeCHHHH
Confidence            57899999999987  667889999998773        34799999999999977554 888887776666666     


Q ss_pred             --CCccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          172 --PTELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       172 --p~El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                        ...|+.|+..|+.+++.  +-.+...+|+...|-.......+|..|+..+++=
T Consensus        77 ~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK  131 (327)
T PF05158_consen   77 KKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIK  131 (327)
T ss_dssp             ----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEE
T ss_pred             hhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEE
Confidence              34789999999999984  5568999999999999999999999999999863

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

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

Probab=95.99  E-value=0.018  Score=41.33  Aligned_cols=53  Identities=23%  Similarity=0.344  Sum_probs=47.5

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+..+.+|+...-..|..|+++|++.+|.+...+..+|+.|++.|++=+...
T Consensus         5 gLs~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~   57 (68)
T PF01978_consen    5 GLSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG   57 (68)
T ss_dssp             CHHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CcCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            46788888887766778999999999999999999999999999999988873

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

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

Probab=95.90  E-value=0.034  Score=40.40  Aligned_cols=55  Identities=20%  Similarity=0.259  Sum_probs=46.7

Q ss_pred             HHHHHHHHHhCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          179 HNQILELAQAQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       179 ~~~vLela~~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ...||++....|.  +|+.+|++.+|-++.-+...|..|.++|++..+.+.    +.+|.-
T Consensus         8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~----~~~W~i   64 (68)
T smart00550        8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGT----PPLWKL   64 (68)
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC----CCceEe
Confidence            3468998887777  999999999999999999999999999999887654    457753

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

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

Probab=95.59  E-value=0.036  Score=38.93  Aligned_cols=45  Identities=29%  Similarity=0.364  Sum_probs=41.6

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      +..|+++....|.+|+++|++.+|-|..=++.-|+.|.+.|++-+
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r   46 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKR   46 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            456899999999999999999999999999999999999999754

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

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

Probab=95.27  E-value=0.039  Score=40.00  Aligned_cols=44  Identities=18%  Similarity=0.293  Sum_probs=37.1

Q ss_pred             HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .|.++...+|.+|..+|+..+++++.-.+..|+.|++.|.+=.-
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~   47 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV   47 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            47788888999999999999999999999999999999987543

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

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.20  E-value=0.081  Score=35.69  Aligned_cols=53  Identities=28%  Similarity=0.313  Sum_probs=42.7

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      |+++.. .+.+|.+++++.++++..-+..+|+.|.+.|++......   ...||.++
T Consensus         2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~---~~~~~~~~   54 (66)
T smart00418        2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG---KRVYYSLT   54 (66)
T ss_pred             HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC---CEEEEEEc
Confidence            455555 678999999999999999999999999999999876432   45566544

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

Probab=94.79  E-value=0.1  Score=37.80  Aligned_cols=56  Identities=25%  Similarity=0.281  Sum_probs=43.5

Q ss_pred             HHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          181 QILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       181 ~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      .||++... .+.+|..++++.+|.+...|+.-|+.|+++|.+=..... .|-..||.-
T Consensus         4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~-rG~~~~W~l   60 (62)
T PF04703_consen    4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVR-RGKSTYWRL   60 (62)
T ss_dssp             CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-S-SSSS-EEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC-CCcceeeee
Confidence            48888886 888999999999999999999999999999988544433 235679964

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

Probab=94.63  E-value=0.087  Score=38.25  Aligned_cols=53  Identities=26%  Similarity=0.445  Sum_probs=41.3

Q ss_pred             ccchhHHHHHHHHH----hCCC-ccHHHHHHhcCCC-hHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQ----AQGF-VTVDEVERRLSWT-SGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~----~~g~-vt~~~L~~~l~W~-~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      +|+.-|..||+++.    ..|| .|+.+|++.+|++ ..-+...|..|++.|++=.+..
T Consensus         3 ~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~   61 (65)
T PF01726_consen    3 ELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG   61 (65)
T ss_dssp             ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence            57888999999876    2565 7999999999997 9999999999999999866643

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

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

Probab=94.05  E-value=0.17  Score=34.92  Aligned_cols=53  Identities=17%  Similarity=0.174  Sum_probs=44.0

Q ss_pred             cchhHHHHHHHHHhCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          175 LNKDHNQILELAQAQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       175 l~~D~~~vLela~~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |+.-|-.||-.....+-  +|+.+|++.++.++.-+...+..|++.|++-.....
T Consensus         3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~   57 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP   57 (62)
T ss_dssp             STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred             cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            56667778887776555  999999999999999999999999999999877544

...

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=93.95  E-value=0.2  Score=32.93  Aligned_cols=46  Identities=35%  Similarity=0.361  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      +..+++.....+.+|+.+|++.++.+..-+...|..|.++|++=..
T Consensus         2 ~~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~   47 (53)
T smart00420        2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV   47 (53)
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3457777776788999999999999999999999999999986443

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

Probab=93.94  E-value=0.15  Score=35.05  Aligned_cols=50  Identities=20%  Similarity=0.288  Sum_probs=43.4

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ||..|-.+|..+...|.+|..+|++.++-+..-.-..+..|++.|++=.-
T Consensus         1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~   50 (59)
T PF01047_consen    1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERE   50 (59)
T ss_dssp             STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            46678889988888788999999999999999999999999999987543

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.71  E-value=0.38  Score=35.53  Aligned_cols=54  Identities=22%  Similarity=0.280  Sum_probs=48.0

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .+++..+..+|.+....|.+|..+|++.++.+..-....|..|++.|++=....
T Consensus         6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347        6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence            367888889999988888899999999999999999999999999999965543

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=93.68  E-value=0.19  Score=46.26  Aligned_cols=160  Identities=16%  Similarity=0.223  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHHHHhhhhcccCCCce
Q 025606           40 ATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIVEICLATRPHNGGLI  118 (250)
Q Consensus        40 ~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIvevC~~tr~~nGGli  118 (250)
                      ..++.-|..|-.+++.   .||.|-  ++.+|..+|++|.    ++.+.++- -...--.-+.+|++++--+-.+.    
T Consensus         8 ~dYR~fl~d~ye~rk~---~~p~fS--~R~fa~~~G~ss~----s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~----   74 (271)
T TIGR02147         8 TDYRKYLRDYYEERKK---TDPAFS--WRFFAEKAGFSST----SYLNDIIKGKKNLTKRMIPKFAEALGLDEKEA----   74 (271)
T ss_pred             hhHHHHHHHHHHHHhc---cCcCcC--HHHHHHHhCCCCH----HHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHH----
Confidence            4566777777766663   799995  8999999999863    22222211 01111222333333332111110    


Q ss_pred             eHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCc--cchhHHHHHHHHHhCCCc-cHH
Q 025606          119 NLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTE--LNKDHNQILELAQAQGFV-TVD  195 (250)
Q Consensus       119 ~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~E--l~~D~~~vLela~~~g~v-t~~  195 (250)
                      +.-+++-.+++       .-|+++=.+|.+++..+-..-.+..+++.      -.+  -+=-|..|.+++.-.++- +++
T Consensus        75 ~yF~~lV~f~~-------ak~~~~k~~~~~~~~~~~~~~~~~~L~~~------~~~y~~~W~~~virel~~~~~~~~~~~  141 (271)
T TIGR02147        75 AYFEAMVNFGQ-------AKTDTEKQQFFEEMQALKPRPRLRVLAAD------QFEYYRHWYNSVIRELLGVMPFADDPE  141 (271)
T ss_pred             HHHHHHHHHhc-------cCCHHHHHHHHHHHHHHhhhchheeccHH------HHHHHHHHHHHHHHHHhhcCCCCCCHH
Confidence            00011112222       23555555555555543221111111110      000  023466788888865555 999


Q ss_pred             HHHHhcC--CChHHHHHHHHHHHHcCCceeec
Q 025606          196 EVERRLS--WTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       196 ~L~~~l~--W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|++.++  .+...++++|+-|++-|++=.|.
T Consensus       142 ~ia~~l~p~is~~ev~~sL~~L~~~glikk~~  173 (271)
T TIGR02147       142 ELAKRCFPKISAEQVKESLDLLERLGLIKKNE  173 (271)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC
Confidence            9999998  89999999999999999997774

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

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.07  E-value=0.27  Score=40.77  Aligned_cols=49  Identities=12%  Similarity=0.186  Sum_probs=44.6

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      |+.-..++|++.+..|..|.++|++.+|+|..-+..+++.|+.+|.+|.
T Consensus         7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179          7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            4555667999999899999999999999999999999999999999984

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

Probab=92.82  E-value=0.48  Score=40.23  Aligned_cols=96  Identities=24%  Similarity=0.344  Sum_probs=72.8

Q ss_pred             eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecCC---------------ccchh
Q 025606          118 INLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVPT---------------ELNKD  178 (250)
Q Consensus       118 i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp~---------------El~~D  178 (250)
                      +++++|...+        .  ++++|.++++.|+.    -+.|++|+.++|.+.+++-|.               .||..
T Consensus        14 vs~~~La~~l--------~--~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~LS~a   83 (159)
T PF04079_consen   14 VSIEELAEIL--------G--SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPKLSQA   83 (159)
T ss_dssp             B-HHHHHHHC--------T---HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHHHHHH
T ss_pred             CCHHHHHHHh--------C--CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCCCCHH
Confidence            6777775542        2  78999999999963    589999999999988888542               67877


Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      ...+|.++.=+.-||-.++.+--|-+   +..+|..|+..|++-+=..
T Consensus        84 alEtLAiIAY~QPiTr~eIe~IRGv~---s~~~i~~L~e~glI~~~gr  128 (159)
T PF04079_consen   84 ALETLAIIAYKQPITRAEIEEIRGVN---SDSVIKTLLERGLIEEVGR  128 (159)
T ss_dssp             HHHHHHHHHHH-SEEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHhcCCcCHHHHHHHcCCC---hHHHHHHHHHCCCEEecCc
Confidence            77788888767789999999988876   7889999999999877653

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

>TIGR00281 segregation and condensation protein B

Probab=92.58  E-value=1.5  Score=38.23  Aligned_cols=108  Identities=21%  Similarity=0.272  Sum_probs=78.9

Q ss_pred             HHHHHhhhhcccCCCc-eeHHHHHHHHHhhcCCCCCCCC-HHHHHHHHhhccc----cCCCeEEEEECCEEEEEecC---
Q 025606          102 QIVEICLATRPHNGGL-INLQELCNLLRQRRKSNREAVS-EDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVP---  172 (250)
Q Consensus       102 qIvevC~~tr~~nGGl-i~l~el~~~v~k~R~~~~~~IS-~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp---  172 (250)
                      .+||.++=..   |-= +++.++...+.         ++ ++++..+++.|+.    -+.|++|+.++|.+.+++-|   
T Consensus         4 ~~iEAlLF~s---g~pgls~~~La~il~---------~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~   71 (186)
T TIGR00281         4 AIIEALLFVS---GEPGVTLAELVRILG---------KEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFA   71 (186)
T ss_pred             HHHHHHHHHc---CCCCCCHHHHHHHhC---------CCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHH
Confidence            3455544433   332 67888876653         23 4567777777754    36799999999988888743   


Q ss_pred             -----------CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          173 -----------TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       173 -----------~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                                 ..||.....+|.++.=+.-||-.++.+-.|-+   +..+|..|+..|++=+-
T Consensus        72 ~~i~~~~~~~~~~LS~aaLEtLAIIAY~QPITr~eIe~IRGv~---s~~~l~~L~ergLI~~~  131 (186)
T TIGR00281        72 DYIHRFLPAKLKNLNSASLEVLAIIAYKQPITRARINEIRGVK---SYQIVDDLVEKGLVVEL  131 (186)
T ss_pred             HHHHHHhccccccCCHHHHHHHHHHHHcCCcCHHHHHHHcCCC---HHHHHHHHHHCCCeEec
Confidence                       13777777888888877899999999988887   67899999999988654

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

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

Probab=92.20  E-value=0.27  Score=38.26  Aligned_cols=64  Identities=23%  Similarity=0.388  Sum_probs=42.2

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee----ecCCCCCCcceeecCc
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV----DDGHRDRKRRYWFPCA  239 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv----D~q~~~~e~~Yw~P~l  239 (250)
                      ...++..|+.+.-..|.+|.++|+..+|.+.--.+..|..|..+|++-+    |++.+ -...|||.++
T Consensus        11 yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~-~~~~yw~i~~   78 (105)
T PF02002_consen   11 YGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERG-WTRYYWYIDY   78 (105)
T ss_dssp             S-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE---------EEEEE-TH
T ss_pred             cCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCc-EEEEEEEEcH
Confidence            3456778888888789999999999999999999999999999999843    32221 1357888764

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

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=91.78  E-value=0.35  Score=40.68  Aligned_cols=51  Identities=18%  Similarity=0.302  Sum_probs=46.3

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      ..|+.-..++|.+.+..|.+|.++|++.+|.|..-+..+++.|+++|.++.
T Consensus        10 ~~lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             hhHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            356666778999999999999999999999999999999999999999984

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=91.62  E-value=0.87  Score=35.60  Aligned_cols=56  Identities=16%  Similarity=0.238  Sum_probs=47.5

Q ss_pred             ccchhHHHHHHHHH----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQ----AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .++.-|-.+|....    ..|.+|..+|++.+++++.-.-..++.|++.|++..-....|
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D   81 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDD   81 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCccc
Confidence            56777877887666    468899999999999999999999999999999997655533

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

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=91.21  E-value=0.92  Score=37.34  Aligned_cols=48  Identities=27%  Similarity=0.327  Sum_probs=42.1

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .....+.+.+|-.|+++|++.++-++..+..+|+-|+..|++=+-...
T Consensus        31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~   78 (126)
T COG3355          31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVN   78 (126)
T ss_pred             HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence            334455667899999999999999999999999999999999998666

>PHA02943 hypothetical protein; Provisional

Probab=91.07  E-value=0.72  Score=39.31  Aligned_cols=58  Identities=22%  Similarity=0.298  Sum_probs=48.1

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      .+--..|||+. ..|+.|.+++++.+|-|...|+-.|..|+++|.+=.=...   ...||.-
T Consensus        10 ~~R~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G---~~tyw~l   67 (165)
T PHA02943         10 HTRMIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG---RAAIWCL   67 (165)
T ss_pred             HHHHHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec---ceEEEEE
Confidence            33345578888 7899999999999999999999999999999998774443   6788864

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

Probab=91.06  E-value=0.64  Score=35.84  Aligned_cols=49  Identities=27%  Similarity=0.394  Sum_probs=41.4

Q ss_pred             ccchhHHHHHHHHHh----CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          174 ELNKDHNQILELAQA----QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       174 El~~D~~~vLela~~----~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      .++.-+.+||+++..    .-.|++.+|.+.++.+....+.+|+.|..+|.+.
T Consensus        44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY   96 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY   96 (102)
T ss_dssp             -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence            477788999999885    3459999999999999999999999999999875

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

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

Probab=90.69  E-value=0.46  Score=42.87  Aligned_cols=46  Identities=30%  Similarity=0.417  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      -|..|+++.+..|.|++++|++.++-|..=.+.=|..|++.|++=+
T Consensus         6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R   51 (253)
T COG1349           6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR   51 (253)
T ss_pred             HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence            4788999999999999999999999999999999999999999866

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

Probab=90.00  E-value=0.93  Score=31.68  Aligned_cols=47  Identities=23%  Similarity=0.347  Sum_probs=36.9

Q ss_pred             cchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          175 LNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       175 l~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      |+..|..||..+. ..+..|..+|++.++-+..-+-..|+.|+..|++
T Consensus         1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv   48 (68)
T PF13463_consen    1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV   48 (68)
T ss_dssp             --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred             CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            3455777777776 7899999999999999999999999999999988

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=89.87  E-value=1.6  Score=35.44  Aligned_cols=56  Identities=20%  Similarity=0.202  Sum_probs=48.5

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |..|+.-|-.||......|.+|..+|++.++.++.-.-..|+.|++.|++=+-...
T Consensus        35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~   90 (144)
T PRK11512         35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   90 (144)
T ss_pred             ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence            44567778888887777788999999999999999999999999999999876544

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=89.85  E-value=1.5  Score=35.82  Aligned_cols=62  Identities=11%  Similarity=0.243  Sum_probs=47.7

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHh----cCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERR----LSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA  239 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~----l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l  239 (250)
                      |+.-+..|+++.=..|-+|+.++.+.    .+|+..-..+.|..|+++|++=++...   ...+|.|..
T Consensus         2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g---r~~~Y~p~v   67 (130)
T TIGR02698         2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEG---RKFIYTALV   67 (130)
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCC---CcEEEEecC
Confidence            45566778887766778999996655    489999999999999999998666332   466777753

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

>PRK15466 carboxysome structural protein EutK; Provisional

Probab=89.81  E-value=0.52  Score=40.41  Aligned_cols=39  Identities=26%  Similarity=0.371  Sum_probs=33.4

Q ss_pred             HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          184 ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       184 ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      .+++.+-..|+.++..++||+.++|+.+|++|..+|.+-
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (166)
T PRK15466        117 LLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR  155 (166)
T ss_pred             HHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence            445555566999999999999999999999999999764

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

Probab=89.61  E-value=0.95  Score=33.06  Aligned_cols=43  Identities=23%  Similarity=0.392  Sum_probs=36.1

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ..+.+++-..+.+|++.|+..|+.-=.||-..++.|+.+|++=
T Consensus         9 ~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs   51 (65)
T PF09397_consen    9 EEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVS   51 (65)
T ss_dssp             HHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE
T ss_pred             HHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCC
Confidence            3466666678999999999999999999999999999999873

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

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=89.59  E-value=1.8  Score=33.93  Aligned_cols=51  Identities=18%  Similarity=0.192  Sum_probs=45.2

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .++.-|-.+|......|.+|..+|++.++.++.-+-..|+.|+++|++=+-
T Consensus        25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~   75 (118)
T TIGR02337        25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRL   75 (118)
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence            456678788888887888999999999999999999999999999988764

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

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

Probab=89.47  E-value=1.2  Score=35.16  Aligned_cols=61  Identities=23%  Similarity=0.329  Sum_probs=45.9

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhc----CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRL----SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA  239 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l----~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l  239 (250)
                      +.-...|+++.=..|.+|+.++.+.+    +|+..=.++.|..|+++|++-++...   ...+|.|..
T Consensus         2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g---r~~~Y~p~i   66 (115)
T PF03965_consen    2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG---RAYVYSPLI   66 (115)
T ss_dssp             -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET---TCEEEEESS
T ss_pred             CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC---CceEEEeCC
Confidence            44456688887777779999888765    58899999999999999999999764   455666653

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

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=89.31  E-value=0.73  Score=41.25  Aligned_cols=57  Identities=28%  Similarity=0.351  Sum_probs=47.3

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC-CCcceee
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD-RKRRYWF  236 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~-~e~~Yw~  236 (250)
                      ..+|.++.+.|-+|+.+|++.||.++.-++.-|+.|+++|++=+-.+.++ |.+.+.|
T Consensus        14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y   71 (218)
T COG2345          14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLY   71 (218)
T ss_pred             HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceee
Confidence            45888888889999999999999999999999999999999877766542 3444444

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=89.25  E-value=1.1  Score=34.39  Aligned_cols=44  Identities=20%  Similarity=0.341  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ...||.+.+..|.+|.++|++.+|-+..-+...|..|+++|++-
T Consensus         5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            45688888888899999999999999999999999999999987

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

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=89.16  E-value=0.68  Score=35.68  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=34.9

Q ss_pred             hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc-eeecC
Q 025606          188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA-MVDDG  226 (250)
Q Consensus       188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~-WvD~q  226 (250)
                      ..-+||++.|++.++.....|+.+|.+|+.+|++ .|...
T Consensus        38 ~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~   77 (86)
T PRK09334         38 KEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKN   77 (86)
T ss_pred             cCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecC
Confidence            4578999999999999999999999999999998 66533

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=89.08  E-value=0.84  Score=41.08  Aligned_cols=46  Identities=35%  Similarity=0.432  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      -+..++++....|++|+++|++.+|.+..-++.-|..|+++|++=+
T Consensus         6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r   51 (251)
T PRK13509          6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKK   51 (251)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4677999999999999999999999999999999999999999854

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=88.76  E-value=0.95  Score=41.42  Aligned_cols=54  Identities=28%  Similarity=0.390  Sum_probs=48.2

Q ss_pred             CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      +..|+.|...|+++... +|-++.++|++.+|-++.-.-..|..|++.|++=+-.
T Consensus       190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K  244 (258)
T COG2512         190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEK  244 (258)
T ss_pred             cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEE
Confidence            46899999999998885 7779999999999999999999999999999975543

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

Probab=88.48  E-value=1.7  Score=30.08  Aligned_cols=43  Identities=33%  Similarity=0.314  Sum_probs=38.7

Q ss_pred             HHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          183 LELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       183 Lela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      -++++..|.+|+.++++.+|-|.--|...|+.|-+.|+.+++.
T Consensus         2 ~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~g   44 (50)
T PF09107_consen    2 RELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVG   44 (50)
T ss_dssp             HHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             hHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeC
Confidence            3566778999999999999999999999999999999999985

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

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

Probab=88.48  E-value=1.7  Score=30.81  Aligned_cols=44  Identities=27%  Similarity=0.407  Sum_probs=38.7

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      |+++.+.++.|+..+|++.+|-++.=+-+.|..|.++|++-.+.
T Consensus        13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~   56 (60)
T PF01325_consen   13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP   56 (60)
T ss_dssp             HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence            56666778999999999999999999999999999999987664

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

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

Probab=88.45  E-value=2.7  Score=28.73  Aligned_cols=49  Identities=27%  Similarity=0.277  Sum_probs=41.7

Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      ..+..|+..+...+ ++.+++++.++-+..-+...|+.|++.|++-....
T Consensus         7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~   55 (78)
T cd00090           7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE   55 (78)
T ss_pred             hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence            45667887766666 99999999999999999999999999999977543

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=88.31  E-value=0.95  Score=40.84  Aligned_cols=47  Identities=28%  Similarity=0.310  Sum_probs=42.5

Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .-+..|+++.+..|.+++.+|++.++-|..=++.-|..|+++|++=+
T Consensus         5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r   51 (256)
T PRK10434          5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR   51 (256)
T ss_pred             HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            34678999999999999999999999999999999999999997633

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=88.11  E-value=2.4  Score=34.25  Aligned_cols=56  Identities=20%  Similarity=0.190  Sum_probs=47.3

Q ss_pred             CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |..|+.-|-.+|..+.. .+..|..+|++.+++++.-.-..++.|++.|++-+-...
T Consensus        26 ~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~   82 (144)
T PRK03573         26 PLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA   82 (144)
T ss_pred             hcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC
Confidence            44667778778877764 467899999999999999999999999999999987554

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=88.06  E-value=2.1  Score=31.55  Aligned_cols=45  Identities=27%  Similarity=0.336  Sum_probs=39.5

Q ss_pred             HHHHHHHhC-CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          181 QILELAQAQ-GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       181 ~vLela~~~-g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+++.... +.+|+.+|++.+|.+..-+...|..|++.|++-.+.
T Consensus         9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~   54 (91)
T smart00346        9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG   54 (91)
T ss_pred             HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence            467766654 789999999999999999999999999999998763

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

Probab=88.04  E-value=0.95  Score=37.29  Aligned_cols=46  Identities=17%  Similarity=0.245  Sum_probs=43.1

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ...|+|++...|.+|..++....|-+..-++..+.+|+..|-++.=
T Consensus        14 k~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~   59 (127)
T PF06163_consen   14 KARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRH   59 (127)
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence            5668999999999999999999999999999999999999999874

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

Probab=87.84  E-value=1.3  Score=30.04  Aligned_cols=44  Identities=32%  Similarity=0.425  Sum_probs=36.0

Q ss_pred             HHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          181 QILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       181 ~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .||++.. ..+.+|..+|++.+|+++.-+...|..|+..|++=.|
T Consensus         7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence            3566555 3566899999999999999999999999999998655

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK09954 putative kinase; Provisional

Probab=86.95  E-value=1.4  Score=41.06  Aligned_cols=43  Identities=16%  Similarity=0.291  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      ..+||++.+..+++|..+|++.+|+++..++..|..|+++|.+
T Consensus         5 ~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954          5 EKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            3468999999999999999999999999999999999999975

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=86.95  E-value=2  Score=37.21  Aligned_cols=53  Identities=21%  Similarity=0.322  Sum_probs=48.6

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      ..++..+..+|.+....|.+|..+|++.++.+...+...|..|++.|++-.+.
T Consensus       139 ~~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~  191 (203)
T TIGR01884       139 AGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG  191 (203)
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            36788888999998887899999999999999999999999999999998885

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

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=86.71  E-value=0.98  Score=38.95  Aligned_cols=46  Identities=15%  Similarity=0.091  Sum_probs=42.5

Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      .-+..|++++...|++++.+|++.+|-|..-++.=|..|.++|++=
T Consensus         7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~   52 (185)
T PRK04424          7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE   52 (185)
T ss_pred             HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence            3577899999999999999999999999999999999999999873

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=86.66  E-value=2.4  Score=35.77  Aligned_cols=62  Identities=23%  Similarity=0.201  Sum_probs=48.3

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc----eeecCCCCCCcceeecC
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA----MVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~----WvD~q~~~~e~~Yw~P~  238 (250)
                      ..++..|+++.-..|-+|.++|+..+|.+..-.+..|..|..+|++    ..|+..+ --..||+.+
T Consensus        13 g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~g-w~~Y~w~i~   78 (158)
T TIGR00373        13 EEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETG-WYEYTWRIN   78 (158)
T ss_pred             ChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCC-cEEEEEEeC
Confidence            3456667776666789999999999999999999999999999998    4565542 135566543

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

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=86.53  E-value=1.4  Score=39.71  Aligned_cols=46  Identities=26%  Similarity=0.416  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      -+..++++....|.+|+.+|++.++-|..=++.-|..|+++|++=+
T Consensus         6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r   51 (252)
T PRK10906          6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR   51 (252)
T ss_pred             HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            4677999999999999999999999999999999999999999743

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

Probab=86.06  E-value=2.5  Score=29.19  Aligned_cols=36  Identities=28%  Similarity=0.183  Sum_probs=33.8

Q ss_pred             CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      +.+|..+|++.+|-+..-+...|..|.++|++..+.
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            579999999999999999999999999999998875

>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase

Probab=86.05  E-value=5.6  Score=32.36  Aligned_cols=78  Identities=17%  Similarity=0.184  Sum_probs=60.0

Q ss_pred             hhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCC-eEEEEECCEEEEEecCCccc
Q 025606           98 ELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNG-YEVISVGKKKLVRSVPTELN  176 (250)
Q Consensus        98 eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g-~~vi~ig~~~~v~svp~El~  176 (250)
                      +|+-.|--+|.+   ++-..|++++|+..+...   +...+|.+|+..-++.|.-+=.. +.++++++..||+..-.   
T Consensus        45 ~la~~v~~if~s---~~k~~l~~e~l~~kl~~S---~~~~~s~~E~E~~l~LL~el~P~Wis~~~~~~~~~lk~~k~---  115 (126)
T cd08767          45 ELARILRNIFVS---EKKTVLPLEELVYKLQAS---YPSILSRGEVEEHLRLLAELAPDWISEKSLRKGDYLKIDKK---  115 (126)
T ss_pred             HHHHHHHHHHHh---cccccccHHHHHHHHHHh---CCCCCCHHHHHHHHHHHHHhChHHheeeeeCCceEEEECcc---
Confidence            566666666766   778999999999999874   34679999999999999865533 67777888889987743   


Q ss_pred             hhHHHHHH
Q 025606          177 KDHNQILE  184 (250)
Q Consensus       177 ~D~~~vLe  184 (250)
                      .|...|.+
T Consensus       116 ~~~~~V~~  123 (126)
T cd08767         116 VDLEKVRK  123 (126)
T ss_pred             ccHHHHHH
Confidence            56666654

Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=86.00  E-value=2.7  Score=29.29  Aligned_cols=47  Identities=30%  Similarity=0.348  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      -..||.+....+..|+.+|++.+|.+..-+...|..|++.|++=+..
T Consensus        12 R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   12 RLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            34577777667889999999999999999999999999999975554

...

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

Probab=85.99  E-value=3  Score=28.15  Aligned_cols=40  Identities=25%  Similarity=0.285  Sum_probs=34.2

Q ss_pred             HHHHHHH-HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025606          180 NQILELA-QAQGFVTVDEVERRLSWTSGRAIDALDILLEEG  219 (250)
Q Consensus       180 ~~vLela-~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G  219 (250)
                      ..++.+. +..+++|.++|++.++-|.-=++.-|..|...|
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            4566666 667789999999999999999999999999998

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=85.90  E-value=2.2  Score=34.57  Aligned_cols=48  Identities=23%  Similarity=0.373  Sum_probs=44.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      .|+.-..++|++.+..|-.|..+|++.+|-|..-+..++..|+++|++
T Consensus         5 ~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522           5 KLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             cccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            466677889999998889999999999999999999999999999975

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=85.58  E-value=3.1  Score=35.92  Aligned_cols=44  Identities=20%  Similarity=0.157  Sum_probs=40.9

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      +..||.+.-..|.+|.++|+..+|.+..-++..|..|..+|++=
T Consensus        24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~   67 (178)
T PRK06266         24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD   67 (178)
T ss_pred             HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence            56688887788999999999999999999999999999999987

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=85.55  E-value=1.6  Score=29.26  Aligned_cols=33  Identities=24%  Similarity=0.258  Sum_probs=30.2

Q ss_pred             CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      ...+ |..+|++.+|.+..-++.+|..|.++|++
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i   50 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLV   50 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            4456 99999999999999999999999999985

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

Probab=85.29  E-value=1.8  Score=34.94  Aligned_cols=54  Identities=30%  Similarity=0.394  Sum_probs=49.4

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +..++.+|..|+++|..  ..|+.|++..++-...-+|-.+.+|+..|++=|-...
T Consensus        38 ~~~l~pE~~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~p~   91 (114)
T PF05331_consen   38 PAGLGPEHRAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRAPA   91 (114)
T ss_pred             CCCCCHHHHHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeCCC
Confidence            35799999999999998  8999999999999999999999999999999887554

The function of these proteins is unknown.

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

Probab=85.18  E-value=1.6  Score=34.84  Aligned_cols=36  Identities=25%  Similarity=0.219  Sum_probs=32.8

Q ss_pred             hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      ..-+||+..|++.|+.+...|+.+|.+|+..|++=.
T Consensus        56 ~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~   91 (105)
T PF03297_consen   56 KMKLITPSVLSERLKINGSLARKALRELESKGLIKP   91 (105)
T ss_dssp             TSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEE
T ss_pred             cCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEE
Confidence            356899999999999999999999999999998743

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

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=84.79  E-value=2.3  Score=34.71  Aligned_cols=43  Identities=16%  Similarity=0.300  Sum_probs=37.9

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ++.+....|++|+++|++.+++++.-+...|..|.+.|++-.+
T Consensus        13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            4455667899999999999999999999999999999998754

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

Probab=84.18  E-value=2.4  Score=30.77  Aligned_cols=43  Identities=28%  Similarity=0.302  Sum_probs=37.6

Q ss_pred             HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .+++++-..+.+|++.|++.|..-=.||-..++.|+.+|++=-
T Consensus         9 ~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p   51 (63)
T smart00843        9 EAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP   51 (63)
T ss_pred             HHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence            3566666778999999999999999999999999999999744

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

>PLN02180 gamma-glutamyl transpeptidase 4

Probab=84.18  E-value=1.7  Score=44.71  Aligned_cols=74  Identities=27%  Similarity=0.450  Sum_probs=48.8

Q ss_pred             HHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCccccc----c------cccccchh-hhHHHHHHHhhhhcc
Q 025606           44 SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAE----L------LGIGDFYY-ELGVQIVEICLATRP  112 (250)
Q Consensus        44 ~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~----~------lG~gdfy~-eLavqIvevC~~tr~  112 (250)
                      ..|.......+..+.++|.+|.-|..    =| .|+....-+...    +      -|...||. ++|.+|++-+.+   
T Consensus       215 ~~la~~l~~~~~~l~~~p~~~~~f~~----~G-~~~~~Gd~l~qp~LA~TLe~IA~~G~d~FY~G~iA~~iv~~~~~---  286 (639)
T PLN02180        215 PYLGKAISSHAAMILKDPGLRSVFSR----NG-QVLKPGETCYNPELAQSLETISEQGPGAFYNGTIGEKLVKDVKK---  286 (639)
T ss_pred             HHHHHHHHHHHHHHhcChhHHHHhCc----CC-ccCCCCCeeccHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHH---
Confidence            34555555666667778888766653    13 454322111111    1      25678888 999999999874   


Q ss_pred             cCCCceeHHHHHHH
Q 025606          113 HNGGLINLQELCNL  126 (250)
Q Consensus       113 ~nGGli~l~el~~~  126 (250)
                       +||+|+++||-..
T Consensus       287 -~GG~lT~eDLa~Y  299 (639)
T PLN02180        287 -AGGIITMDDLRSY  299 (639)
T ss_pred             -cCCCCCHHHHHhC
Confidence             8999999999755

>PLN02198 glutathione gamma-glutamylcysteinyltransferase

Probab=83.79  E-value=1.7  Score=44.07  Aligned_cols=74  Identities=22%  Similarity=0.275  Sum_probs=46.1

Q ss_pred             HHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccc----cc------cccccchh-hhHHHHHHHhhhhccc
Q 025606           45 QLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWA----EL------LGIGDFYY-ELGVQIVEICLATRPH  113 (250)
Q Consensus        45 ~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws----~~------lG~gdfy~-eLavqIvevC~~tr~~  113 (250)
                      .|.......+..|+.+|.+|+-|..    =| .|+....-+..    ++      -|...||. ++|.+|++-|.    .
T Consensus       166 ~la~~l~~~~~~l~~~p~~~~~f~~----~G-~~~~~Gd~l~~p~LA~TL~~iA~~G~~~FY~G~iA~~iv~~~~----~  236 (573)
T PLN02198        166 YLYMQMNATRSDILADKGLSDLFVS----NG-ELKKPGTICHNPKLALTLRLIGEYGPKAFYNGTVGVNLVRDIQ----K  236 (573)
T ss_pred             HHHHHHHHHHHHHhcChhHHHHcCc----CC-CcCCCCCeecCHHHHHHHHHHHHhCcccccCCHHHHHHHHHHH----H
Confidence            3444455556666677777766642    12 34332211110    11      25678887 79999999996    4


Q ss_pred             CCCceeHHHHHHHH
Q 025606          114 NGGLINLQELCNLL  127 (250)
Q Consensus       114 nGGli~l~el~~~v  127 (250)
                      +||+|+++||-..=
T Consensus       237 ~GG~lt~~DL~~y~  250 (573)
T PLN02198        237 SGGIITLKDLQSYR  250 (573)
T ss_pred             cCCCCCHHHHhhCC
Confidence            99999999997653

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=83.72  E-value=2.5  Score=37.88  Aligned_cols=47  Identities=15%  Similarity=0.211  Sum_probs=42.1

Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .-+..++++....+++|+++|++.+++|..-++.-|..|...|++=+
T Consensus         4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r   50 (240)
T PRK10411          4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR   50 (240)
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            34667999999899999999999999999999999999999998744

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

Probab=83.12  E-value=7.5  Score=35.80  Aligned_cols=94  Identities=19%  Similarity=0.301  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhhc-CCCCCCCCHHHHHHHHhhccccCCCeEEEEE-CCEEEEEecCCccchhHHHHH-HHHHhCCCccHHH
Q 025606          120 LQELCNLLRQRR-KSNREAVSEDDCLRAISKLKVLGNGYEVISV-GKKKLVRSVPTELNKDHNQIL-ELAQAQGFVTVDE  196 (250)
Q Consensus       120 l~el~~~v~k~R-~~~~~~IS~~DI~rAik~L~~LG~g~~vi~i-g~~~~v~svp~El~~D~~~vL-ela~~~g~vt~~~  196 (250)
                      +.+|...+.++- ......+|+-.++.=+.+|..++ .+.|+.. +|+-||  +|..|.   ..|- |+...+|.|+.-+
T Consensus         2 i~~L~~~~q~~Q~~~~~~rLSErnciEiv~kL~~~~-~ldli~T~dGkeyi--T~~~L~---~EI~~el~~~gGRv~~~d   75 (272)
T PF09743_consen    2 IEELQADFQRAQLASSSQRLSERNCIEIVNKLIEKK-LLDLIHTTDGKEYI--TPEQLE---KEIKDELYVHGGRVNLVD   75 (272)
T ss_pred             HHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHcC-CeeEEEECCCCEEE--CHHHHH---HHHHHHHHHcCCceEHHH
Confidence            455665555532 12357899999999999998887 4666655 577665  344442   3344 4445689999999


Q ss_pred             HHHhcCCChHHHHHHHHHHHHcC
Q 025606          197 VERRLSWTSGRAIDALDILLEEG  219 (250)
Q Consensus       197 L~~~l~W~~~Ra~~~L~~l~~~G  219 (250)
                      |...+|-+..-+...+..++++-
T Consensus        76 L~~~LnVd~~~ie~~~~~i~~~~   98 (272)
T PF09743_consen   76 LAQALNVDLDHIERRAQEIVKSD   98 (272)
T ss_pred             HHHhcCcCHHHHHHHHHHHHhCC
Confidence            99999999999999999988865

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

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

Probab=82.52  E-value=4.1  Score=27.03  Aligned_cols=40  Identities=33%  Similarity=0.442  Sum_probs=34.3

Q ss_pred             HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      .|+.+... |..++.+|++.+|-+..-...-|..|...|++
T Consensus         6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV   45 (47)
T PF01022_consen    6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLV   45 (47)
T ss_dssp             HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence            45655556 88999999999999999999999999999985

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=82.44  E-value=6  Score=29.82  Aligned_cols=55  Identities=25%  Similarity=0.254  Sum_probs=46.3

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      ++.-|..+|......+..+..+|++.++.++.-.-..|+.|++.|++.+-....|
T Consensus        20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~D   74 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPED   74 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccc
Confidence            6777888888777666666599999999999999999999999999998766543

>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]

Probab=82.42  E-value=5.1  Score=34.23  Aligned_cols=40  Identities=20%  Similarity=0.446  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC
Q 025606           36 KEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA   80 (250)
Q Consensus        36 ~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~   80 (250)
                      ..|.+.++++..-|..+..+-|..+     .|..|..++|-.|..
T Consensus        16 ~~qi~~lkeaF~l~D~d~~G~I~~~-----el~~ilr~lg~~~s~   55 (160)
T COG5126          16 EEQIQELKEAFQLFDRDSDGLIDRN-----ELGKILRSLGFNPSE   55 (160)
T ss_pred             HHHHHHHHHHHHHhCcCCCCCCcHH-----HHHHHHHHcCCCCcH
Confidence            4566778888888988888888876     688999999998864

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=82.38  E-value=3.1  Score=35.57  Aligned_cols=49  Identities=27%  Similarity=0.324  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHhCCCc-cHHHHHHhc--CCChHHHHHHHHHHHHcCCceeecC
Q 025606          178 DHNQILELAQAQGFV-TVDEVERRL--SWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       178 D~~~vLela~~~g~v-t~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      -|..|++++.-.++- ++..|++.+  +.+.+.++++|+-|++-|++=.|..
T Consensus        25 ~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~   76 (171)
T PF14394_consen   25 YHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD   76 (171)
T ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence            366788999976676 999999999  9999999999999999999988754

>TIGR00066 g_glut_trans gamma-glutamyltranspeptidase

Probab=82.35  E-value=3.3  Score=41.30  Aligned_cols=32  Identities=25%  Similarity=0.580  Sum_probs=27.5

Q ss_pred             ccccchh-hhHHHHHHHhhhhcccCCCceeHHHHHHH
Q 025606           91 GIGDFYY-ELGVQIVEICLATRPHNGGLINLQELCNL  126 (250)
Q Consensus        91 G~gdfy~-eLavqIvevC~~tr~~nGGli~l~el~~~  126 (250)
                      |...||. ++|.+|++-+.+    +||+|+++||...
T Consensus       191 G~~~FY~G~iA~~iv~~~~~----~GG~lt~~DL~~y  223 (516)
T TIGR00066       191 GPDAFYKGDIAESIIDTLQK----NGGIMTKKDLAAY  223 (516)
T ss_pred             CcccccCCHHHHHHHHHHHH----cCCCCCHHHHhhC
Confidence            5678888 999999998874    9999999999754

Also called gamma-glutamyltranspeptidase (ggt). Some members of this family have antibiotic synthesis or resistance activities. In the case of a cephalosporin acylase from Pseudomonas sp., the enzyme was shown to retain some gamma-glutamyltranspeptidase activity. Other, more distantly related proteins have ggt-related activities and score below the trusted cutoff.

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=82.34  E-value=2.7  Score=38.22  Aligned_cols=49  Identities=20%  Similarity=0.312  Sum_probs=43.6

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ..-+..|+++.+..|.+|+.+|++.|+-|..=++.=|..|+++|++=+-
T Consensus        16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~   64 (269)
T PRK09802         16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRA   64 (269)
T ss_pred             HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEE
Confidence            3457789999999999999999999999999999999999999998543

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=82.13  E-value=6.9  Score=36.13  Aligned_cols=71  Identities=17%  Similarity=0.255  Sum_probs=55.6

Q ss_pred             CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHH-HHHh--CCCccHHHHHHhcCCChHHHHHHH
Q 025606          136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILE-LAQA--QGFVTVDEVERRLSWTSGRAIDAL  212 (250)
Q Consensus       136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLe-la~~--~g~vt~~~L~~~l~W~~~Ra~~~L  212 (250)
                      ..||.+++..+++.+..   .               ...|+.-+...|. ++..  .|.++.+.++..+|++..-+..++
T Consensus       236 ~~I~~~~v~~~l~~~~~---~---------------~~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~  297 (328)
T PRK00080        236 GVITKEIADKALDMLGV---D---------------ELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVY  297 (328)
T ss_pred             CCCCHHHHHHHHHHhCC---C---------------cCCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHh
Confidence            57999999999976522   1               1234555566675 6664  788999999999999999999999


Q ss_pred             H-HHHHcCCceee
Q 025606          213 D-ILLEEGLAMVD  224 (250)
Q Consensus       213 ~-~l~~~Gl~WvD  224 (250)
                      + .|++.|+++..
T Consensus       298 e~~Li~~~li~~~  310 (328)
T PRK00080        298 EPYLIQQGFIQRT  310 (328)
T ss_pred             hHHHHHcCCcccC
Confidence            9 99999999743

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues

Probab=81.85  E-value=2.1  Score=37.48  Aligned_cols=117  Identities=15%  Similarity=0.218  Sum_probs=35.9

Q ss_pred             ccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCC
Q 025606           56 DIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNR  135 (250)
Q Consensus        56 eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~  135 (250)
                      +.+++++|    ..|=..+.|+-=.+   -|.    .++.-.+|-...|+......     ++.|.||-..++       
T Consensus        68 e~rE~eEy----~k~K~~f~veeeG~---~~~----~~~~~~~lL~~Fi~yIK~~K-----vv~ledla~~f~-------  124 (188)
T PF09756_consen   68 ERREQEEY----EKWKSAFSVEEEGE---DEE----EEEEESQLLQEFINYIKEHK-----VVNLEDLAAEFG-------  124 (188)
T ss_dssp             -------------------------------------------HHHHHHHHHHH-S-----EE-HHHHHHHH--------
T ss_pred             HHHHHHHH----HHHHHhccccccch---hHH----HhhHHHHHHHHHHHHHHHcc-----eeeHHHHHHHcC-------
Confidence            44455554    46666667763211   111    12332235555555555433     667888877765       


Q ss_pred             CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcC
Q 025606          136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLS  202 (250)
Q Consensus       136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~  202 (250)
                        ++..|++.-|+.|..-|.=.-|+.=.| +||--+|.||.    +|-.++..+|.||.++|....|
T Consensus       125 --l~t~~~i~ri~~L~~~g~ltGv~DdrG-kfIyIs~eE~~----~va~fi~~rGRvsi~el~~~~N  184 (188)
T PF09756_consen  125 --LRTQDVINRIQELEAEGRLTGVIDDRG-KFIYISEEEME----AVAKFIKQRGRVSISELAQESN  184 (188)
T ss_dssp             --S-HHHHHHHHHHHHHHSSS-EEE-TT---EEE---------------------------------
T ss_pred             --CCHHHHHHHHHHHHHCCCceeeEcCCC-CeEEecHHHHH----HHHHHHHHcCCccHHHHHHHHH
Confidence              799999999999999887666665447 58888888885    3667777899999999987654

They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=81.53  E-value=2.6  Score=27.15  Aligned_cols=34  Identities=26%  Similarity=0.248  Sum_probs=31.0

Q ss_pred             CccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .+|..+|++.+|.+..-+...|..|.++|++=.+
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4789999999999999999999999999998554

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

Probab=81.44  E-value=5.7  Score=27.77  Aligned_cols=43  Identities=21%  Similarity=0.353  Sum_probs=35.7

Q ss_pred             cchhHHHHHHHHHhCCC------ccHHHHHHhcCCChHHHHHHHHHHHH
Q 025606          175 LNKDHNQILELAQAQGF------VTVDEVERRLSWTSGRAIDALDILLE  217 (250)
Q Consensus       175 l~~D~~~vLela~~~g~------vt~~~L~~~l~W~~~Ra~~~L~~l~~  217 (250)
                      |+..|..+|..|=..||      +|.++|++.+|.++.=+-..|...++
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~   49 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAER   49 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            56778899999988887      78999999999999887777765543

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

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=81.44  E-value=1.8  Score=42.07  Aligned_cols=124  Identities=24%  Similarity=0.419  Sum_probs=83.8

Q ss_pred             HHHhhcHhHHHHH---------HHHHHHHHHHHHHHHHHHHHhccccccc------------ChhHHHHHHHH-------
Q 025606           19 QYRLLGENVAKLR---------TDLMKEQLATFRSQLEDFARKHKNDIRK------------NPTFRSQFHEM-------   70 (250)
Q Consensus        19 ~~~~~g~~l~~~~---------~~~l~~qL~~F~~~L~~Fa~~h~~eI~~------------dp~fR~~F~~m-------   70 (250)
                      +|+..|.+++.--         .-.|.+.|..+|+.+.   +..++.|++            ||.=-.-|.-+       
T Consensus       252 RftQAGsEVSalLGr~PSavGYQpTLatemg~lQERIt---stk~GSITSiQavyvPaDDlTDPapattFaHLDat~vLs  328 (468)
T COG0055         252 RFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERIT---STKKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLS  328 (468)
T ss_pred             HHhhcchHHHHHhccCccccccCchhHHHHHHHHHHHh---cCCCCceEEEEEEEeccccCCCcchhhhhhhcccceeee
Confidence            5667776665311         0157788888888774   466677764            77655556433       


Q ss_pred             --HHHcC----CCCCCCCCcccccccc---cccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHH
Q 025606           71 --CAKVG----VDPLASNKGFWAELLG---IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSED  141 (250)
Q Consensus        71 --C~siG----VDPL~s~k~~ws~~lG---~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~  141 (250)
                        .+++|    ||||.|++    .+|-   +|+=+|++|.++-.+.+..       .+|.|++..+    |  ++++|++
T Consensus       329 R~ia~~GIyPAvDPL~StS----r~l~p~ivGe~Hy~va~~vq~iLqrY-------keLqDIIaIL----G--mdELsee  391 (468)
T COG0055         329 RQIAALGIYPAVDPLDSTS----RALDPKIVGEEHYEVAREVQSILQRY-------KELQDIIAIL----G--MDELSEE  391 (468)
T ss_pred             HhHHhcCCCcccCcccccc----cccCcccccHHHHHHHHHHHHHHHHH-------HHHHHHHHHh----C--chhcChh
Confidence              45667    59999773    3443   6899999999999999984       3456665554    3  6899999


Q ss_pred             H---HHHHHhhccccCCCeEEEEE
Q 025606          142 D---CLRAISKLKVLGNGYEVISV  162 (250)
Q Consensus       142 D---I~rAik~L~~LG~g~~vi~i  162 (250)
                      |   |.||-+.=+=|.-+|-+-..
T Consensus       392 dk~~V~rArki~~FlSQpF~vAE~  415 (468)
T COG0055         392 DKLTVARARKIQRFLSQPFFVAEV  415 (468)
T ss_pred             HHHHHHHHHHHHHHhcCcchhhhe
Confidence            9   55666655667777765443

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=80.59  E-value=3.8  Score=35.46  Aligned_cols=45  Identities=24%  Similarity=0.243  Sum_probs=40.1

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ..||.+....|.+|+.+|++.+|.+..-+...|+.|+++|++=..
T Consensus         4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~   48 (203)
T TIGR02702         4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE   48 (203)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence            458887776677999999999999999999999999999998765

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

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

Probab=80.45  E-value=3  Score=31.52  Aligned_cols=38  Identities=24%  Similarity=0.323  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL  216 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~  216 (250)
                      ...+|.+...+.-||++.|+..+||+.++.+.+|..+-
T Consensus        26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p   63 (77)
T PF12324_consen   26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP   63 (77)
T ss_dssp             HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence            33456666667889999999999999999999998874

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

>PF01019 G_glu_transpept: Gamma-glutamyltranspeptidase; InterPro: IPR000101 Gamma-glutamyltranspeptidase (2

Probab=80.22  E-value=2.2  Score=42.35  Aligned_cols=76  Identities=26%  Similarity=0.396  Sum_probs=46.0

Q ss_pred             HHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccc----cc------cccccchh-hhHHHHHHHhhhhcc
Q 025606           44 SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWA----EL------LGIGDFYY-ELGVQIVEICLATRP  112 (250)
Q Consensus        44 ~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws----~~------lG~gdfy~-eLavqIvevC~~tr~  112 (250)
                      ..|..++++.+..|+.+|..|+-|..     +=.|+....-+-.    ++      -|...||- +||.+|++...+   
T Consensus       121 ~~la~~l~~~~~~l~~~~~~~~~f~~-----~G~~~~~Gd~l~~p~LA~TL~~ia~~G~~~FY~G~lA~~iv~~~~~---  192 (510)
T PF01019_consen  121 PSLARALARNADKLRRDPGSRALFLP-----DGRPPREGDILRQPELADTLERIAEEGPDAFYRGELAEKIVADVQA---  192 (510)
T ss_dssp             HHHHHHHHHHHHHHTTSHHHHHHHST-----TSSE--TTSEE--HHHHHHHHHHHHHTTHHHHSCHHHHHHHHHHHH---
T ss_pred             hhHHhHHHhHHHHHhhhhhHHHHhcc-----CCCcCCCCCEEEHHHHHHHHHHHHhcCchhhcCChHHHHHHHHHHh---
Confidence            57777788888888999999877743     1123332211100    01      25668888 799999998665   


Q ss_pred             cCCCceeHHHHHHHHH
Q 025606          113 HNGGLINLQELCNLLR  128 (250)
Q Consensus       113 ~nGGli~l~el~~~v~  128 (250)
                       +||+|+++|+-..-.
T Consensus       193 -~GG~lt~~Dla~Y~~  207 (510)
T PF01019_consen  193 -NGGLLTLEDLAAYQV  207 (510)
T ss_dssp             -TT-S--HHHHHH---
T ss_pred             -ccCCccHHHHhhcCC
Confidence             899999999976533

3.2.2 from EC) (GGT) [] catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification []. In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit. The sequences of mammalian and bacterial GGT show a number of regions of high similarity []. Pseudomonas cephalosporin acylases (3.5.1 from EC) that convert 7-beta-(4-carboxybutanamido)-cephalosporanic acid (GL-7ACA) into 7-aminocephalosporanic acid (7ACA) and glutaric acid are evolutionary related to GGT and also show some GGT activity []. Like GGT, these GL-7ACA acylases, are also composed of two subunits. As an autocatalytic peptidase GGT belongs to MEROPS peptidase family T3 (gamma-glutamyltransferase family, clan PB(T)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. The type example is gamma-glutamyltransferase 1 from Escherichia coli. ; GO: 0003840 gamma-glutamyltransferase activity; PDB: 2DBX_A 2Z8K_D 2Z8I_B 2DBU_D 2E0X_B 2DBW_B 2E0W_B 2DG5_A 2E0Y_C 2Z8J_C ....

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=80.05  E-value=5.9  Score=26.14  Aligned_cols=38  Identities=21%  Similarity=0.251  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL  216 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~  216 (250)
                      ..++|.+.+..|-.|..+|.+.+|+|..-+..++..|.
T Consensus         5 D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    5 DRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             HHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence            34688888988999999999999999999999998763

...

>TIGR00498 lexA SOS regulatory protein LexA

Probab=80.05  E-value=4.7  Score=34.49  Aligned_cols=52  Identities=25%  Similarity=0.458  Sum_probs=44.6

Q ss_pred             cchhHHHHHHHHHh----CCC-ccHHHHHHhcCCC-hHHHHHHHHHHHHcCCceeecC
Q 025606          175 LNKDHNQILELAQA----QGF-VTVDEVERRLSWT-SGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       175 l~~D~~~vLela~~----~g~-vt~~~L~~~l~W~-~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      |+.-|..||++.+.    .|+ .|+.+|++.+|-+ +.-+...|..|+++|++=.++.
T Consensus         4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~   61 (199)
T TIGR00498         4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPG   61 (199)
T ss_pred             cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCC
Confidence            67789999998883    455 8899999999998 9999999999999999877643

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	250
2zme_A	258	Integrated Structural And Functional Model Of The H		9e-64
3cuq_A	234	Integrated Structural And Functional Model Of The H		3e-61
1u5t_A	233	Structure Of The Escrt-Ii Endosomal Trafficking Com		7e-31

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

Iteration: 1
 Score =  239 bits (611), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 117/237 (49%), Positives = 158/237 (66%), Gaps = 1/237 (0%)
Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
           RR  G G +    +A  +Y+  G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62
Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
            FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122
Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
           EL   + + R    + VS+DD +RAI KLK LG G+ +I VG   L++SVP ELN DH  
Sbjct: 123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182
Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
           +L+LA+  G+VTV E++  L W + RA   L+ LL+EGLA +D      +  YW P 
Sbjct: 183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPA 238

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

Iteration: 1
 Score =  231 bits (589), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 109/204 (53%), Positives = 143/204 (70%), Gaps = 1/204 (0%)
Query: 35  MKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGD 94
           M +QL  F++ LE+FA KHK +IRKNP FR QF +MCA +GVDPLAS KGFW+E+LG+GD
Sbjct: 12  MSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGFWSEMLGVGD 71
Query: 95  FYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG 154
           FYYELGVQI+E+CLA +  NGGLI L+EL   + + R    + VS+DD +RAI KLK LG
Sbjct: 72  FYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG 131
Query: 155 NGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDI 214
            G+ +I VG   L++SVP ELN DH  +L+LA+  G+VTV E++  L W + RA   L+ 
Sbjct: 132 TGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSEIKASLKWETERARQVLEH 191
Query: 215 LLEEGLAMVDDGHRDRKRRYWFPC 238
           LL+EGLA +D      +  YW P 
Sbjct: 192 LLKEGLAWLDL-QAPGEAHYWLPA 214

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

Iteration: 1
 Score =  130 bits (327), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 74/222 (33%), Positives = 128/222 (57%), Gaps = 14/222 (6%)
Query: 19  QYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDP 78
           +Y  + + + + ++  +++QL  F+ +L +FA+KH ++++ +P FRS+F  MC+ +G+DP
Sbjct: 16  KYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDP 75
Query: 79  LA---SNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNR 135
           L+    +K     L  + DFYYE+ ++++EIC  T+  NGG+I+ QEL  +    RK N 
Sbjct: 76  LSLFDRDK----HLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKV--HFRKLN- 128
Query: 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVD 195
             V  DD  ++I  LK L   +E+  +  KK +RSVP EL  D  +ILE+    G+ ++ 
Sbjct: 129 --VGLDDLEKSIDMLKSL-ECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILGYSSIS 185
Query: 196 EVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
            ++  L W + R+  ALD ++  GL  + D     +  YW P
Sbjct: 186 LLKANLGWEAVRSKSALDEMVANGLLWI-DYQGGAEALYWDP 226

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	250
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	1e-109
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	1e-106
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	2e-26
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	1e-22
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	4e-20

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

 Score =  314 bits (806), Expect = e-109
 Identities = 113/229 (49%), Positives = 152/229 (66%), Gaps = 3/229 (1%)

Query: 24  GENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNK 83
           G  +A+ +   M +QL  F++ LE+FA KHK +IRKNP FR QF +MCA +GVDPLAS K
Sbjct: 1   GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGK 60

Query: 84  GFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDC 143
           GFW+E+LG+GDFYYELGVQI+E+CLA +  NGGLI L+EL   + + R    + VS+DD 
Sbjct: 61  GFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDVSQDDL 120

Query: 144 LRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSW 203
           +RAI KLK LG G+ +I VG   L++SVP ELN DH  +L+LA+  G+VTV E++  L W
Sbjct: 121 IRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSEIKASLKW 180

Query: 204 TSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC--ASSISSSMGADS 250
            + RA   L+ LL+EGLA +D      +  YW P       S  + A+ 
Sbjct: 181 ETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPALFTDLYSQEITAEE 228

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

 Score =  305 bits (783), Expect = e-106
 Identities = 71/235 (30%), Positives = 129/235 (54%), Gaps = 10/235 (4%)

Query: 3   RRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPT 62
           ++ G+           +Y  + + + + ++  +++QL  F+ +L +FA+KH ++++ +P 
Sbjct: 2   KQFGLAAFDELK--DGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPE 59

Query: 63  FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQE 122
           FRS+F  MC+ +G+DPL+        L  + DFYYE+ ++++EIC  T+  NGG+I+ QE
Sbjct: 60  FRSKFMHMCSSIGIDPLSL-FDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQE 118

Query: 123 LCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQI 182
           L  +  ++       V  DD  ++I  LK L   +E+  +  KK +RSVP EL  D  +I
Sbjct: 119 LEKVHFRKLN-----VGLDDLEKSIDMLKSLE-CFEIFQIRGKKFLRSVPNELTSDQTKI 172

Query: 183 LELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
           LE+    G+ ++  ++  L W + R+  ALD ++  GL  +D      +  YW P
Sbjct: 173 LEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDY-QGGAEALYWDP 226

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

 Score =  105 bits (263), Expect = 2e-26
 Identities = 36/237 (15%), Positives = 80/237 (33%), Gaps = 18/237 (7%)

Query: 2   RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
             R GI  L+ +   +     +  N A   TDL   +L +  + +E   +     ++   
Sbjct: 320 LSRIGISSLEKSRENQLLNNDILFNNA--LTDL--NKLMSLATSIERLYKNSNITMKTKT 375

Query: 62  TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRP-----HNGG 116
                   +       PL        + L    F  E+  +I E  L+         N  
Sbjct: 376 LNLQDESTVNEPKTRRPLLILD--REKFLNKELFLDEIAREIYEFTLSEFKDLNSDTNYM 433

Query: 117 LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELN 176
           +I L +L  +  +  +     +S  +   A  + + LG     +    K+++     + +
Sbjct: 434 IITLVDLYAMYNKSMRIGTGLISPMEMREACERFEHLGLNELKLVKVNKRILCVTSEKFD 493

Query: 177 KDHNQILELAQAQG-------FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226
               ++++L               +     + +WT G  ++ L   ++EG  ++D  
Sbjct: 494 VVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQ 550

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

 Score = 91.2 bits (226), Expect = 1e-22
 Identities = 37/198 (18%), Positives = 74/198 (37%), Gaps = 8/198 (4%)

Query: 32  TDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG 91
            DL   +L     ++ + ++   N I+      ++   +  K  +  +        E  G
Sbjct: 11  EDL--SKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYLLSMGIANPVTRETYG 68

Query: 92  IGDFYY-ELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKL 150
            G  Y+ +L  Q+  I        GG+++L E+  L+ + R    E +S +D + A   L
Sbjct: 69  SGTQYHMQLAKQLAGILQVPLEERGGIMSLTEVYCLVNRARGM--ELLSPEDLVNACKML 126

Query: 151 KVLGNGYEV--ISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRA 208
           + L     +     G   +      E  +     LE    +G +T +E  + +  +   A
Sbjct: 127 EALKLPLRLRVFDSGVMVIELQSHKE-EEMVASALETVSEKGSLTSEEFAKLVGMSVLLA 185

Query: 209 IDALDILLEEGLAMVDDG 226
            + L +  + G    DD 
Sbjct: 186 KERLLLAEKMGHLCRDDS 203

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

 Score = 83.5 bits (206), Expect = 4e-20
 Identities = 22/144 (15%), Positives = 54/144 (37%), Gaps = 12/144 (8%)

Query: 95  FYYELGVQIVEICLATRP-----HNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISK 149
           F  E+  +I E  L+         N  +I L +L  +  +  +     +S  +   A  +
Sbjct: 12  FLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGLISPMEMREACER 71

Query: 150 LKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQ-------AQGFVTVDEVERRLS 202
            + LG     +    K+++     + +    ++++L          +    +     + +
Sbjct: 72  FEHLGLNELKLVKVNKRILCVTSEKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSN 131

Query: 203 WTSGRAIDALDILLEEGLAMVDDG 226
           WT G  ++ L   ++EG  ++D  
Sbjct: 132 WTLGILMEVLQNCVDEGDLLIDKQ 155

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	100.0
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	100.0
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	100.0
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	100.0
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	100.0
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.05
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.85
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	95.81
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.74
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	95.72
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.55
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	95.47
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.29
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.26
2z99_A	219	Putative uncharacterized protein; winged helix dom	95.19
1t6s_A	162	Conserved hypothetical protein; A winged helix-tur	95.18
1p6r_A	82	Penicillinase repressor; transcription regulation,	94.92
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	94.66
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	94.36
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	94.35
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.35
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	94.32
3bja_A	139	Transcriptional regulator, MARR family, putative;	94.2
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	94.2
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.16
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	94.09
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.09
2gxg_A	146	146AA long hypothetical transcriptional regulator;	94.07
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	93.99
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	93.88
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	93.74
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	93.73
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	93.72
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	93.66
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.64
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	93.63
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.6
2pex_A	153	Transcriptional regulator OHRR; transcription regu	93.52
2nnn_A	140	Probable transcriptional regulator; structural gen	93.52
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.4
1sfx_A	109	Conserved hypothetical protein AF2008; structural	93.35
1z91_A	147	Organic hydroperoxide resistance transcriptional;	93.28
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	93.28
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.28
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	93.19
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.18
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	93.1
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	93.08
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	92.99
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	92.98
2kko_A	108	Possible transcriptional regulatory protein (possi	92.96
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	92.92
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	92.86
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	92.83
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	92.82
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	92.72
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	92.71
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	92.67
3s2w_A	159	Transcriptional regulator, MARR family; structural	92.66
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	92.63
3jth_A	98	Transcription activator HLYU; transcription factor	92.56
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	92.54
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	92.53
3r0a_A	123	Putative transcriptional regulator; structural gen	92.53
1ku9_A	152	Hypothetical protein MJ223; putative transcription	92.44
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	92.36
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	92.27
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	92.19
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	92.14
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	92.1
2w25_A	150	Probable transcriptional regulatory protein; trans	91.91
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	91.88
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	91.83
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	91.79
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	91.74
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	91.71
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	91.7
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	91.67
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	91.59
2eth_A	154	Transcriptional regulator, putative, MAR family; M	91.33
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	91.14
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	91.1
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	90.97
1okr_A	123	MECI, methicillin resistance regulatory protein ME	90.94
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	90.88
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	90.43
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	90.38
1lva_A	258	Selenocysteine-specific elongation factor; winged-	90.38
3nqo_A	189	MARR-family transcriptional regulator; structural	90.37
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	90.33
3f3x_A	144	Transcriptional regulator, MARR family, putative;	90.3
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	90.23
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	90.17
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.96
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	89.94
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	89.79
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	89.48
2lmt_A	148	Calmodulin-related protein 97A; spermatogenesis, m	89.44
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	89.41
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	89.28
2ovk_B	153	RLC, myosin regulatory light chain LC-2, mantle mu	89.16
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	89.05
2fxa_A	207	Protease production regulatory protein HPR; protea	88.84
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	88.23
3i5g_C	159	Myosin catalytic light chain LC-1, mantle muscle;	88.1
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	87.86
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	87.43
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	87.4
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	87.27
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	86.4
3fwb_A	161	Cell division control protein 31; gene gating, com	86.29
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.88
1bja_A	95	Transcription regulatory protein MOTA; activation	85.71
2pg4_A	95	Uncharacterized protein; structural genomics, join	85.64
1y0u_A	96	Arsenical resistance operon repressor, putative; s	85.6
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	85.32
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	84.78
3i5g_B	153	Myosin regulatory light chain LC-2, mantle muscle;	84.74
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	84.69
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	84.67
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	84.38
2mys_C	149	Myosin; muscle protein, motor protein; HET: MLY; 2	84.22
3ox6_A	153	Calcium-binding protein 1; EF-hand, calcium-sensor	84.05
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	83.79
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	83.78
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	83.7
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	83.7
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	83.23
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	83.06
2qac_A	146	Myosin A tail domain interacting protein MTIP; mal	82.68
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	82.37
1exr_A	148	Calmodulin; high resolution, disorder, metal trans	82.34
2h09_A	155	Transcriptional regulator MNTR; transcription regu	81.6
3qrx_A	169	Centrin; calcium-binding, EF-hand, cell division,	81.51
2vn2_A	128	DNAD, chromosome replication initiation protein; D	81.43
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	81.33
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	81.3
4fx0_A	148	Probable transcriptional repressor protein; helix-	80.6
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	80.57

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

Probab=100.00  E-value=1.4e-89  Score=608.13  Aligned_cols=231  Identities=31%  Similarity=0.621  Sum_probs=207.3

Q ss_pred             CCCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC-
Q 025606            2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA-   80 (250)
Q Consensus         2 rR~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~-   80 (250)
                      |||+||+||+  ++++++|+++|++++++|+++|++||++||++|++||++|++||++||+||++|++||++||||||+ 
T Consensus         1 rr~~G~~a~~--~~~~~~~~~~g~~l~~~~~~~l~~Ql~~F~~~L~~FA~kHk~eI~~dp~fR~~F~~mc~siGVDPLa~   78 (233)
T 1u5t_A            1 MKQFGLAAFD--ELKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSL   78 (233)
T ss_dssp             ---------------------CCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTTTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             CCCccHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhcccCHHHHHHHHHHHHHcCCCCCcc
Confidence            6889999999  7889999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             CCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEE
Q 025606           81 SNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVI  160 (250)
Q Consensus        81 s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi  160 (250)
                      |+||  +++||+|||||||||||||||++||++|||||+|+||+|+|+|+     +.||||||+|||++|++| +||+++
T Consensus        79 s~kg--~~~lg~gdfy~eLavqIvEvC~~tr~~nGGli~l~el~~~~~r~-----~~IS~dDi~rAik~L~~L-~gf~v~  150 (233)
T 1u5t_A           79 FDRD--KHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRK-----LNVGLDDLEKSIDMLKSL-ECFEIF  150 (233)
T ss_dssp             TTSS--GGGTTHHHHHHHHHHHHHHHHHHHTTTSSSCEEHHHHHHTTTTT-----TTCCHHHHHHHHHHHTTT-CCCCEE
T ss_pred             CCcc--ccccCcchHHHHHHHHHHHHHHHHHHhcCCeeEHHHHHHHHHhh-----cCCCHHHHHHHHHHhhhc-cCeEEE
Confidence            9999  89999999999999999999999999999999999999999996     789999999999999999 999999


Q ss_pred             EECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCcc
Q 025606          161 SVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS  240 (250)
Q Consensus       161 ~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~  240 (250)
                      ++||++||||||.|||+||+.||++|+..||||+++|++++||++.||+++|++|+++|++|||+|.++ |+.|||||+|
T Consensus       151 ~v~g~~~vqsvp~el~~D~~~vLe~a~~~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD~q~~~-e~~Yw~P~lf  229 (233)
T 1u5t_A          151 QIRGKKFLRSVPNELTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGA-EALYWDPSWI  229 (233)
T ss_dssp             EETTEEEECCSSSCCCTTHHHHHHTTTTTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSS-SCEEECGGGG
T ss_pred             EECCEEEEEeCCCccchHHHHHHHHHHhcCcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCCC-ccceechhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999853 8999999999


Q ss_pred             CCC
Q 025606          241 SIS  243 (250)
Q Consensus       241 ~~~  243 (250)
                      .+.
T Consensus       230 ~~~  232 (233)
T 1u5t_A          230 TRQ  232 (233)
T ss_dssp             GCC
T ss_pred             hcc
Confidence            853

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

Probab=100.00  E-value=2e-88  Score=600.74  Aligned_cols=221  Identities=51%  Similarity=0.877  Sum_probs=206.9

Q ss_pred             cHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHH
Q 025606           24 GENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQI  103 (250)
Q Consensus        24 g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqI  103 (250)
                      |.+++++|+++|++||++||++|++||+||++||++||+||++|++||++||||||+++||||+++||+|||||||||||
T Consensus         1 g~~l~~~~~~~~~~Ql~~F~~~L~~FA~kH~~eI~~dp~fR~~F~~mc~siGVDPlas~kg~ws~~lG~gdfy~eLavqI   80 (234)
T 3cuq_A            1 GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQI   80 (234)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTCCTTSCTTSHHHHHHCHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCHHHHHHHHHHHHHcCCCcccCCcchhhhhcCcchHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHH
Q 025606          104 VEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQIL  183 (250)
Q Consensus       104 vevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vL  183 (250)
                      ||||++||++|||||+|+||+|+|+|+||...+.||||||+|||++|++||+||+|+++||++||||||.|||+||++||
T Consensus        81 vEvC~~tr~~nGGli~L~el~~~~~r~Rg~~~~~IS~dDi~rAik~L~~LG~g~~v~~~~g~~~VqSvp~el~~D~~~vL  160 (234)
T 3cuq_A           81 IEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTVVL  160 (234)
T ss_dssp             HHHHHHHHHHHSSEEEHHHHHHHHHHTTTTCCSSCCHHHHHHHHHHHGGGBTTCEEEEETTEEEEECSCCCCCHHHHHHH
T ss_pred             HHHHHHHHHhcCCeeEHHHHHHHHHHhcCCccCccCHHHHHHHHHHHHhcCCCeEEEEECCEEEEEeCCCccchHHHHHH
Confidence            99999999999999999999999999999766899999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCCCcc
Q 025606          184 ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSISSS  245 (250)
Q Consensus       184 ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~~~~  245 (250)
                      ++|+..||||+++|++++||++.||+++|++|+++|++|||+|.+ +|+.|||||+|.+...
T Consensus       161 ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD~q~~-ge~~Yw~P~lf~~~~~  221 (234)
T 3cuq_A          161 QLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAP-GEAHYWLPALFTDLYS  221 (234)
T ss_dssp             HHHTTTSEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEESSSS-SSCEEECTTSSCCCCC
T ss_pred             HHHHhcCcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEeCCCC-Ccceeecchhhccccc
Confidence            999999999999999999999999999999999999999999985 5999999999986443

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

Probab=100.00  E-value=3.2e-57  Score=398.17  Aligned_cols=200  Identities=16%  Similarity=0.224  Sum_probs=174.3

Q ss_pred             HHHHHHHHHHHHHH------HHHHHHHhcccccccChhHHHHHHHHHHHcCCC-CCCCCCcccccccccccchhhhHHHH
Q 025606           31 RTDLMKEQLATFRS------QLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVD-PLASNKGFWAELLGIGDFYYELGVQI  103 (250)
Q Consensus        31 ~~~~l~~qL~~F~~------~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVD-PL~s~k~~ws~~lG~gdfy~eLavqI  103 (250)
                      -+++|++.|...++      ++....++.+++|++|++-  +|++||++|||| |+++ ++||+    .+||||||||||
T Consensus         9 af~DL~~LM~~Ak~mv~la~~~~~~~~~~~~~~~~~e~~--~f~~m~~slGvd~Pl~~-~~~~s----~~~f~~ELa~qi   81 (218)
T 3cuq_B            9 AFEDLSKLMIKAKEMVELSKSIANKIKDKQGDITEDETI--RFKSYLLSMGIANPVTR-ETYGS----GTQYHMQLAKQL   81 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHGGGCC----------CCSH--HHHHHHHHHTCCCHHHH-TTSSC----SCHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHH--HHHHHHHHcCCCCcchh-hccCc----ccHHHHHHHHHH
Confidence            36667777766663      3333444445566677764  699999999999 7775 69998    799999999999


Q ss_pred             HHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHH
Q 025606          104 VEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQI  182 (250)
Q Consensus       104 vevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~v  182 (250)
                      +|||.++++.|||||+|.||+|++||+||  .++|||+||++||++|++||.||++++++ |+++|||+|.+++.||++|
T Consensus        82 ~e~c~~~~~~~GG~I~L~dl~~~~nraRG--~~lVSp~Dl~~A~~~l~~Lg~~~~l~~~~sg~~vvqs~~~~~~~~~~~i  159 (218)
T 3cuq_B           82 AGILQVPLEERGGIMSLTEVYCLVNRARG--MELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQSHKEEEMVASA  159 (218)
T ss_dssp             HHHHHHHHHHTTSEEEHHHHHHHHHHTCS--SSCCCHHHHHHHHHTTTTTTCSEEEEECTTSBEEEEETTCCGGGGHHHH
T ss_pred             HHHHHHHHHhCCCeEEHHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHcCCCEEEEEECCCcEEEEcCCCchHHHHHHH
Confidence            99999999999999999999999999998  48999999999999999999999999998 8999999999999999999


Q ss_pred             HHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCC
Q 025606          183 LELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSI  242 (250)
Q Consensus       183 Lela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~  242 (250)
                      +++++..||||+++|++++||+..||+++|+.++++|++|||++.   |+.|||||+|.+
T Consensus       160 l~~~~~~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D~~~---eg~~y~pn~f~~  216 (218)
T 3cuq_B          160 LETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSV---EGLRFYPNLFMT  216 (218)
T ss_dssp             HHHHHHTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEESS---SCEEEEECGGGC
T ss_pred             HHHHHHCCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCC---CceEEehhhccc
Confidence            999999999999999999999999999999999999999999976   789999999985

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

Probab=100.00  E-value=3.3e-44  Score=350.87  Aligned_cols=221  Identities=17%  Similarity=0.168  Sum_probs=141.8

Q ss_pred             CCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHH------HHHHHHHHhcccccccChh--HHHHHHHHHHHc
Q 025606            3 RRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFR------SQLEDFARKHKNDIRKNPT--FRSQFHEMCAKV   74 (250)
Q Consensus         3 R~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~------~~L~~Fa~~h~~eI~~dp~--fR~~F~~mC~si   74 (250)
                      +++||+||+|+.+++.+-++...+-+   |++|++.|+..+      +.+...+++.+++|..|.+  =..+|+.++   
T Consensus       321 ~~~GI~gler~~e~~~~~~~~~i~~A---f~DL~~LM~~AkemV~La~~~~~~~~~~~~~~s~~~~~~e~~~~~s~L---  394 (566)
T 1w7p_D          321 SRIGISSLEKSRENQLLNNDILFNNA---LTDLNKLMSLATSIERLYKNSNITMKTKTLNLQDESTVNEPKTRRPLL---  394 (566)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccCcHHHHHHHHHHHHHHHHHHHHH---HHhHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCccchhhHhhHhhc---
Confidence            56899999999998888877766555   667777777766      4444555555566654422  112566665   


Q ss_pred             CCCCCCCCCcccccccc-cccchhhhHHHHHHHhhhhc----cc-CCCceeHHHHHHHHHhh-cCCCCCCCCHHHHHHHH
Q 025606           75 GVDPLASNKGFWAELLG-IGDFYYELGVQIVEICLATR----PH-NGGLINLQELCNLLRQR-RKSNREAVSEDDCLRAI  147 (250)
Q Consensus        75 GVDPL~s~k~~ws~~lG-~gdfy~eLavqIvevC~~tr----~~-nGGli~l~el~~~v~k~-R~~~~~~IS~~DI~rAi  147 (250)
                         |+. +     +++| .++||||||+||+|||.+++    ++ |||||+|.||++++||+ |+. .++|||+||++||
T Consensus       395 ---~Vt-r-----d~~~s~~~f~~ELA~qI~E~c~~~~~~~l~~~nGGmItL~DL~~~~NRa~R~g-~elISp~Dll~A~  464 (566)
T 1w7p_D          395 ---ILD-R-----EKFLNKELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIG-TGLISPMEMREAC  464 (566)
T ss_dssp             ----CC-S-----SCCCCHHHHHHHHHHHHHHHHHHTTCCSSCSCCCCEEEHHHHHHHHHHHTTTT-TCCCCHHHHHHHH
T ss_pred             ---ccc-h-----hhcCChhHHHHHHHHHHHHHHHhhhcccchhcCcCeEEHHHHHHHHHHhccCC-CCccCHHHHHHHH
Confidence               554 4     3444 48999999999999999999    88 99999999999999999 952 5899999999999


Q ss_pred             hhccccCCCeE-EEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcC-------CChHHHHHHHHHHHHcC
Q 025606          148 SKLKVLGNGYE-VISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLS-------WTSGRAIDALDILLEEG  219 (250)
Q Consensus       148 k~L~~LG~g~~-vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~-------W~~~Ra~~~L~~l~~~G  219 (250)
                      ++|++||.||. |++|++..+|+++|.+ +.|+++||++++..|+||+.+|++++|       |+..||+++|+.++++|
T Consensus       465 ~~le~Lg~~~~~L~~~~sgvlVvs~~~~-~~~~~~il~l~~~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~~~e~eG  543 (566)
T 1w7p_D          465 ERFEHLGLNELKLVKVNKRILCVTSEKF-DVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEG  543 (566)
T ss_dssp             TTGGGGTCTTCEEEECSSSCEEEESSCH-HHHHHHHHHHHTTSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCCeEEEEEECCEEEEEcCCCc-hHHHHHHHHHHHhcCCcCHHHHHHHhCCccccCcccHHHHHHHHHHHHHcC
Confidence            99999999999 9999866677799988 999999999999999999999999999       99999999999999999


Q ss_pred             CceeecCCCCCCcceeecCccCCC
Q 025606          220 LAMVDDGHRDRKRRYWFPCASSIS  243 (250)
Q Consensus       220 l~WvD~q~~~~e~~Yw~P~l~~~~  243 (250)
                      ++|||+|.   ++.|||||+|...
T Consensus       544 ~l~rDd~~---~G~~yypNlf~~~  564 (566)
T 1w7p_D          544 DLLIDKQL---SGIYYYKNSYWPS  564 (566)
T ss_dssp             SEEEEEET---TEEEEEECCSSCC
T ss_pred             CEEEECCC---CceEEehhhcccc
Confidence            99999998   6899999999753

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

Probab=100.00  E-value=1.4e-39  Score=276.15  Aligned_cols=143  Identities=20%  Similarity=0.296  Sum_probs=128.0

Q ss_pred             ccchhhhHHHHHHHhh---h-hcccCCC-ceeHHHHHHHHHhh-cCCCCCCCCHHHHHHHHhhccccCCC-eEEEEECCE
Q 025606           93 GDFYYELGVQIVEICL---A-TRPHNGG-LINLQELCNLLRQR-RKSNREAVSEDDCLRAISKLKVLGNG-YEVISVGKK  165 (250)
Q Consensus        93 gdfy~eLavqIvevC~---~-tr~~nGG-li~l~el~~~v~k~-R~~~~~~IS~~DI~rAik~L~~LG~g-~~vi~ig~~  165 (250)
                      .+||||||+||+|+|.   + +++.||| ||+|.||+|++||+ |+. .++|||+||++||++|++||.| |+++++++.
T Consensus        10 ~~f~~ELa~qi~e~c~~~~~~~~~~~GG~~I~L~dl~~~~nra~R~g-~~lISp~Dl~~A~~~l~~Lg~~~~~l~~~~sg   88 (169)
T 1u5t_B           10 ELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIG-TGLISPMEMREACERFEHLGLNELKLVKVNKR   88 (169)
T ss_dssp             TTHHHHHHHHHHHHHHTTTTTSSSCCCCCCEETTHHHHHHHHTTTSS-SCCCCHHHHHHHHTTTGGGTCCSCEEEEETTT
T ss_pred             hHHHHHHHHHHHHHHhhcchhhHHhcCceeEEHHHHHHHHHHhhcCC-CCccCHHHHHHHHHHHHhcCCCeEEEEEECCe
Confidence            7999999999999999   7 9999999 99999999999999 952 5899999999999999999999 999999954


Q ss_pred             EEEEecCCccchhH--HHHHHHHHhC-CC----ccHH-H-HHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          166 KLVRSVPTELNKDH--NQILELAQAQ-GF----VTVD-E-VERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       166 ~~v~svp~El~~D~--~~vLela~~~-g~----vt~~-~-L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      .+|+   .+.+.|+  ++++++++.. |+    ||++ + +++++||+..||+++|+.++++|++|||+|.   ++.+||
T Consensus        89 ~~V~---~~~~~d~~~~~il~~~~~~~g~d~~~vt~~~~~la~~~~ws~~~a~e~L~~~e~~G~l~~D~~~---~G~~y~  162 (169)
T 1u5t_B           89 ILCV---TSEKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQL---SGIYYY  162 (169)
T ss_dssp             EEEE---ESSCSHHHHHHHHHHHHHSCSBCHHHHHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECS---SCEEEE
T ss_pred             eEEE---eCCChhHHHHHHHHHHHhcCCCCcccccHHHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCC---CcceEE
Confidence            4444   2334444  8999999974 99    9999 9 9999999999999999999999999999998   457777


Q ss_pred             cCccCC
Q 025606          237 PCASSI  242 (250)
Q Consensus       237 P~l~~~  242 (250)
                      ||+|..
T Consensus       163 ~N~f~~  168 (169)
T 1u5t_B          163 KNSYWP  168 (169)
T ss_dssp             ECCSSC
T ss_pred             eeecCc
Confidence            999874

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

Probab=96.05  E-value=0.012  Score=41.35  Aligned_cols=60  Identities=15%  Similarity=0.160  Sum_probs=44.7

Q ss_pred             CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      |..++.-...||++... .+.+|.++|++.+|.++.-+...|..|.++|++-.   .   ..-||.+
T Consensus         5 ~~~m~~~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~---~---~~G~y~l   65 (67)
T 2heo_A            5 LSTGDNLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS---P---SPKYWSI   65 (67)
T ss_dssp             ----CHHHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE---E---ETTEEEE
T ss_pred             cccccHHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec---C---CCceEee
Confidence            65666445568888765 46899999999999999999999999999999533   2   2347765

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=95.85  E-value=0.02  Score=41.55  Aligned_cols=59  Identities=19%  Similarity=0.312  Sum_probs=48.3

Q ss_pred             ccchhH-HHHHHHHHhCC---CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          174 ELNKDH-NQILELAQAQG---FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       174 El~~D~-~~vLela~~~g---~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      .++.|. ..||++....|   .+|+.+|++.+|-++.-+...|..|+++|++-.-..    .+-||+
T Consensus        10 ~~~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~----~~~~W~   72 (77)
T 1qgp_A           10 SIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG----TPPLWK   72 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEECS----SSCEEE
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC----CCCceE
Confidence            445554 67889888877   999999999999999999999999999999876532    345665

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

Probab=95.81  E-value=0.036  Score=39.74  Aligned_cols=58  Identities=24%  Similarity=0.252  Sum_probs=47.9

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      ..||++....|.+|+.+|++.+|.+..-+...|..|+++|++=.+... .+.+.||...
T Consensus         3 ~~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~-~gr~~~y~l~   60 (81)
T 2htj_A            3 NEILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLR-RGMATYWFLK   60 (81)
T ss_dssp             HHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCS-SSSSCEEEES
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccC-CCCcEEEEEC
Confidence            457888877788999999999999999999999999999998765443 2356777754

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

Probab=95.74  E-value=0.03  Score=40.87  Aligned_cols=57  Identities=12%  Similarity=0.147  Sum_probs=48.3

Q ss_pred             HHHHHHHHHhC------CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          179 HNQILELAQAQ------GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       179 ~~~vLela~~~------g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      +..||++++..      +.+|+.+|++.+|.|..-++.-|..|+++|++=++-... +-+-+|+
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~ggr-~~~~~~~   68 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVNAGK-GVPGLWR   68 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESCSS-SSCCEEE
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCCC-CcHHHHH
Confidence            45688888754      889999999999999999999999999999999996443 3577776

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=95.72  E-value=0.018  Score=42.38  Aligned_cols=53  Identities=8%  Similarity=0.027  Sum_probs=45.5

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChH-HHHHHHHHHHHcCCceee
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSG-RAIDALDILLEEGLAMVD  224 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~-Ra~~~L~~l~~~Gl~WvD  224 (250)
                      |.++..=+.+||.+....|-.|+.+|++.+|.++. -++..|..|+++|++..-
T Consensus         6 ~~~~~~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A            6 SLDMAEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             SHHHHHHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             cccchhHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            33444446779999999999999999999999999 889999999999999843

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

Probab=95.55  E-value=0.025  Score=41.38  Aligned_cols=44  Identities=18%  Similarity=0.147  Sum_probs=41.2

Q ss_pred             HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .|+++.+..|.+|+++|++.|+-|..-.+.-|+.|+++|++=+-
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            48899999999999999999999999999999999999998665

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

Probab=95.47  E-value=0.024  Score=39.79  Aligned_cols=42  Identities=26%  Similarity=0.407  Sum_probs=34.9

Q ss_pred             HHH-HHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          182 ILE-LAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       182 vLe-la~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      +|. +++..-..|+.+++..+||+.++|+.+|+.|..+|.+--
T Consensus         8 LLall~s~~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRK   50 (68)
T 3i71_A            8 LLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRK   50 (68)
T ss_dssp             HHHHHHHCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhccccHHHHHHHhCCcHHHHHHHHHHHHhcchhhh
Confidence            443 455555679999999999999999999999999998743

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=95.29  E-value=0.053  Score=39.86  Aligned_cols=54  Identities=19%  Similarity=0.288  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhCC---CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          179 HNQILELAQAQG---FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       179 ~~~vLela~~~g---~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      +..||++....|   .+|+.+|++.+|-++.-++.+|..|.++|++..-..    .+-||+
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~----~~~~W~   68 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG----TPPLWK   68 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESS----SSCEEE
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC----CCCeeE
Confidence            456888888878   999999999999999999999999999999986532    245665

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

Probab=95.26  E-value=0.03  Score=42.01  Aligned_cols=44  Identities=14%  Similarity=0.122  Sum_probs=41.5

Q ss_pred             HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .|+++.+..|.||+++|++.|+-|..-.+.-|+.|++.|++=+-
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            48999999999999999999999999999999999999998775

>2z99_A Putative uncharacterized protein; winged helix domain, cell cycle, cell division, chromosome partition, cytoplasm; 2.30A {Mycobacterium tuberculosis}

Probab=95.19  E-value=0.29  Score=42.57  Aligned_cols=110  Identities=12%  Similarity=0.057  Sum_probs=86.9

Q ss_pred             HHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecCC---
Q 025606          101 VQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVPT---  173 (250)
Q Consensus       101 vqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp~---  173 (250)
                      ..+||..+=.-   |-=+++.+|...+.         +++++|..++..|+.    -+.||+|+.+++.+-+++-|.   
T Consensus        17 ~~~iEAlLf~a---~epvs~~~La~~l~---------~~~~~v~~~l~~L~~~y~~~~rGiel~~v~~gy~l~T~~e~~~   84 (219)
T 2z99_A           17 KRVLEALLLVI---DTPVTADALAAATE---------QPVYRVAAKLQLMADELTGRDSGIDLRHTSEGWRMYTRARFAP   84 (219)
T ss_dssp             HHHHHHHHHHC---SSCBCHHHHHHHHT---------SCHHHHHHHHHHHHHHHHHTTCSEEEEEETTEEEEEECGGGHH
T ss_pred             HHHHHHHHHHc---CCCCCHHHHHHHHC---------cCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHH
Confidence            45677666654   33388999877652         688999999999963    489999999999988888542   


Q ss_pred             ------------ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ------------ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 ------------El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                                  .||.-...+|.++.-++-||-.+|.+..|-+.   ..++..|+..|++-.-.
T Consensus        85 ~v~~~~~~~~~~~Ls~aaLEtLaiIAy~QPITR~eI~~irGv~~---~~~v~~Lle~gLI~e~G  145 (219)
T 2z99_A           85 YVEKLLLDGARTKLTRAALETLAVVAYRQPVTRARVSAVRGVNV---DAVMRTLLARGLITEVG  145 (219)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHHHHHHCSEEHHHHHHHHTSCC---HHHHHHHHHTTSEEEEE
T ss_pred             HHHHHhcccccCccCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCEEEcc
Confidence                        46655555787777779999999999999987   57899999999998764

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

Probab=95.18  E-value=0.077  Score=44.06  Aligned_cols=110  Identities=18%  Similarity=0.245  Sum_probs=83.8

Q ss_pred             HHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecCC----
Q 025606          102 QIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVPT----  173 (250)
Q Consensus       102 qIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp~----  173 (250)
                      .++|..+=.-   |-=+++++|...+.       ..+++++|..++..|+.    -+.||+|+.++|.+-+++-|.    
T Consensus        10 ~~iEAlLf~~---~~pvs~~~La~~~~-------~~~~~~~v~~~l~~L~~~y~~~~rg~~l~~v~~gy~l~t~~~~~~~   79 (162)
T 1t6s_A           10 RSLEALIFSS---EEPVNLQTLSQITA-------HKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADL   79 (162)
T ss_dssp             HHHHHHHHHC---SSCBCHHHHHHHTT-------CCCCHHHHHHHHHHHHHHHHHHTCSEEEEEETTEEEEEECGGGHHH
T ss_pred             HHHHHHHHHc---CCCCCHHHHHHHhC-------cCCCHHHHHHHHHHHHHHhhhCCCCEEEEEECCEEEEEEcHHHHHH
Confidence            4566555543   33388888876653       23799999999999963    389999999999999998764    


Q ss_pred             -----------ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          174 -----------ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       174 -----------El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                                 .||.-...+|.++.-++-||-.+|.+..|-+   +..++..|+..|++-.-
T Consensus        80 v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTR~eI~~irGv~---~~~~v~~L~e~glI~e~  138 (162)
T 1t6s_A           80 VRQLLAPVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGAS---PDYSIDRLLARGLIEVR  138 (162)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHHHHHHHCSEEHHHHHHHHTCC---CCSHHHHHHHTTSEEEE
T ss_pred             HHHHhcccccCccCHHHHHHHHHHHHcCCcCHHHHHHHHCCC---HHHHHHHHHHCCCEEEc
Confidence                       2333334466666667899999999999988   77899999999999863

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=94.92  E-value=0.061  Score=38.38  Aligned_cols=63  Identities=14%  Similarity=0.256  Sum_probs=52.3

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcC----CChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLS----WTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA  239 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~----W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l  239 (250)
                      .|+.-+..||.+....|.+|+.+|.+.++    |+..-....|+.|++.|++=+....   ...+|.|..
T Consensus         6 ~lt~~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~g---r~~~y~~~~   72 (82)
T 1p6r_A            6 QISDAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEG---RVFVYTPNI   72 (82)
T ss_dssp             CCCHHHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEET---TEEEEEESC
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEecC---CEEEEEeec
Confidence            57778888999888788999999999885    9999999999999999999887532   455666653

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

Probab=94.66  E-value=0.11  Score=39.54  Aligned_cols=54  Identities=15%  Similarity=0.164  Sum_probs=47.3

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..+|......|.+|..+|++.+++++.-+...|..|++.|++=+....
T Consensus        28 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~   81 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNP   81 (142)
T ss_dssp             SSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            456678888888877778999999999999999999999999999999887554

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

Probab=94.36  E-value=0.083  Score=40.64  Aligned_cols=53  Identities=25%  Similarity=0.392  Sum_probs=47.0

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      +..++.-+..||......| +|+.+|++.+|+++.-+...|+.|++.|++-+-.
T Consensus        33 ~~~lt~~~~~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~   85 (146)
T 3tgn_A           33 EVALTNTQEHILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSK   85 (146)
T ss_dssp             SSCCCHHHHHHHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             ccCCCHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEecc
Confidence            4567888999999888888 9999999999999999999999999999997643

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=94.35  E-value=0.16  Score=38.57  Aligned_cols=54  Identities=19%  Similarity=0.171  Sum_probs=46.9

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..+|......|.+|..+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        31 ~lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~   84 (138)
T 1jgs_A           31 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             TSCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCc
Confidence            457778888888777678999999999999999999999999999999886443

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

Probab=94.35  E-value=0.13  Score=39.64  Aligned_cols=55  Identities=18%  Similarity=0.209  Sum_probs=47.9

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      |..|+..|-.||......|.+|+.+|++.+++++.-+-..|+.|++.|++-+...
T Consensus        26 ~~~lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~   80 (145)
T 3g3z_A           26 QQDLNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEG   80 (145)
T ss_dssp             TTTCCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCC
T ss_pred             HcCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccC
Confidence            4456778888998887667799999999999999999999999999999987543

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

Probab=94.32  E-value=0.15  Score=39.00  Aligned_cols=54  Identities=17%  Similarity=0.049  Sum_probs=46.7

Q ss_pred             ccchhHHHHHHHH-HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELA-QAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela-~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..||... ...|.+|+.+|++.+++++.-+...|+.|++.|++=+....
T Consensus        34 ~l~~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~   88 (146)
T 2fbh_A           34 GLSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVA   88 (146)
T ss_dssp             CCTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCC
Confidence            3566677788888 67788999999999999999999999999999999886543

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

Probab=94.20  E-value=0.13  Score=38.93  Aligned_cols=53  Identities=8%  Similarity=0.244  Sum_probs=46.9

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .++..+..+|......|.+|+.+|++.+++++.-+...|..|++.|++=+...
T Consensus        30 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~   82 (139)
T 3bja_A           30 DISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKN   82 (139)
T ss_dssp             TCCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccC
Confidence            46777888998888788899999999999999999999999999999977543

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

Probab=94.20  E-value=0.092  Score=39.90  Aligned_cols=54  Identities=17%  Similarity=0.141  Sum_probs=47.5

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .++..+..+|......|.+|+.+|++.+++++.-+...|+.|++.|++=+....
T Consensus        26 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~   79 (138)
T 3bpv_A           26 NLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDP   79 (138)
T ss_dssp             TCCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            457778889988887789999999999999999999999999999999885433

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

Probab=94.16  E-value=0.16  Score=39.19  Aligned_cols=54  Identities=17%  Similarity=0.218  Sum_probs=47.4

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..||......|.+|+.+|++.+++++.-+...|+.|++.|++-+....
T Consensus        39 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   92 (150)
T 2rdp_A           39 PITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDE   92 (150)
T ss_dssp             SSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            567778888888777788999999999999999999999999999999886443

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=94.09  E-value=0.16  Score=38.81  Aligned_cols=55  Identities=15%  Similarity=0.125  Sum_probs=47.3

Q ss_pred             CccchhHHHHHHHHHhCC--CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          173 TELNKDHNQILELAQAQG--FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g--~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      ..++..|..||......|  .+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        27 ~~lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~   83 (139)
T 3eco_A           27 FDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDA   83 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCC
Confidence            356777888888877654  8999999999999999999999999999999887544

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

Probab=94.09  E-value=0.15  Score=39.16  Aligned_cols=55  Identities=15%  Similarity=0.163  Sum_probs=47.2

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      ..++..|..||......|.+|+.+|++.++.++.-+-..|+.|++.|++-+....
T Consensus        33 ~~lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   87 (143)
T 3oop_A           33 YDVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREIST   87 (143)
T ss_dssp             SSSCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCC
Confidence            3567778889988877789999999999999999999999999999999876443

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=94.07  E-value=0.23  Score=38.02  Aligned_cols=53  Identities=21%  Similarity=0.152  Sum_probs=46.3

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .++..+..||.... .|.+|+.+|++.+++++.-+...|..|++.|++=+....
T Consensus        34 ~l~~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   86 (146)
T 2gxg_A           34 NLSYLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDR   86 (146)
T ss_dssp             TCCHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCC
Confidence            45667888888877 889999999999999999999999999999999776443

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=93.99  E-value=0.18  Score=38.63  Aligned_cols=54  Identities=13%  Similarity=0.132  Sum_probs=47.3

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..+|......|.+|+.+|++.++.++.-+...|..|++.|++-+....
T Consensus        26 ~lt~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~   79 (144)
T 1lj9_A           26 SLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             TCTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            456678888888877788999999999999999999999999999999886544

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

Probab=93.88  E-value=0.12  Score=39.84  Aligned_cols=56  Identities=11%  Similarity=0.106  Sum_probs=47.7

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |..|+..|..||......|.+|..+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        35 ~~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   90 (148)
T 3nrv_A           35 KFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS   90 (148)
T ss_dssp             GGTCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             hcCCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            34678889899998888889999999999999999999999999999999876443

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=93.74  E-value=0.14  Score=39.79  Aligned_cols=54  Identities=15%  Similarity=0.161  Sum_probs=47.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..||.+....|.+|+.+|++.+++++.-+...|..|++.|++=+....
T Consensus        34 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   87 (155)
T 1s3j_A           34 GVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNT   87 (155)
T ss_dssp             TCCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            456668888888877778999999999999999999999999999999887544

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

Probab=93.73  E-value=0.086  Score=40.01  Aligned_cols=63  Identities=13%  Similarity=0.263  Sum_probs=51.9

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcC----CChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLS----WTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~----W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      ..|+.-+..||++.-..|.+|+.+|.+.++    |+..-....|+.|+++|++=+....   ....|+|.
T Consensus        31 ~~LT~~e~~VL~~L~~~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~g---R~~~Y~p~   97 (99)
T 2k4b_A           31 FNVSNAELIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEG---RKFVYRPL   97 (99)
T ss_dssp             CCCCCSCSHHHHHHHHHSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEET---TEEEEECC
T ss_pred             CCCCHHHHHHHHHHHhCCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeCC---CEEEEEEe
Confidence            356777777998887778899999999985    9999999999999999999887543   56666664

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

Probab=93.72  E-value=0.15  Score=37.86  Aligned_cols=53  Identities=19%  Similarity=0.280  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      -..||++....| +|+.+|++.+|.++.-++..|..|+++|++-.=...    +-.|+
T Consensus        19 ~~~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~~----PP~W~   71 (82)
T 1oyi_A           19 VCEAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDI----PPRWF   71 (82)
T ss_dssp             HHHHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSSS----SCEEE
T ss_pred             HHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC----CCcce
Confidence            345778777778 999999999999999999999999999999775433    44555

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=93.66  E-value=0.21  Score=38.31  Aligned_cols=56  Identities=18%  Similarity=0.099  Sum_probs=48.1

Q ss_pred             CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +..++..+..||..... .|.+|..+|++.+|+++.-+...|..|++.|++=+....
T Consensus        30 ~~~l~~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~   86 (147)
T 2hr3_A           30 ADPVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   86 (147)
T ss_dssp             CCHHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             ccCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCC
Confidence            34678888889888877 889999999999999999999999999999999876443

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=93.64  E-value=0.22  Score=38.49  Aligned_cols=54  Identities=15%  Similarity=0.046  Sum_probs=47.3

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .++..+..||......|.+|+.+|++.+++++.-+...|..|++.|++=+....
T Consensus        37 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~   90 (152)
T 3bj6_A           37 GVTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNP   90 (152)
T ss_dssp             TCCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence            356668888888887788999999999999999999999999999999886543

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

Probab=93.63  E-value=0.37  Score=37.21  Aligned_cols=107  Identities=13%  Similarity=0.085  Sum_probs=77.3

Q ss_pred             hhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccc
Q 025606           98 ELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELN  176 (250)
Q Consensus        98 eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~  176 (250)
                      .+..+|++.+.+     .| .+..|+...+         .++++.+.+.++.|...|.   |+.+. +..+-...   +.
T Consensus         7 ~l~~~i~~~~~~-----~p-~~~~~la~~~---------~~~~~~~~~~l~~l~~~G~---l~~i~~~~~~~~~~---~~   65 (121)
T 2pjp_A            7 AIWQKAEPLFGD-----EP-WWVRDLAKET---------GTDEQAMRLTLRQAAQQGI---ITAIVKDRYYRNDR---IV   65 (121)
T ss_dssp             HHHHHHGGGCSS-----SC-EEHHHHHHHT---------TCCHHHHHHHHHHHHHTTS---EEEEETTEEEEHHH---HH
T ss_pred             HHHHHHHHHHHh-----CC-CCHHHHHHHh---------CCCHHHHHHHHHHHHHCCC---EEEecCCceECHHH---HH
Confidence            445556666533     33 4777776553         3789999999999988775   55564 44332222   22


Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .=...+.++++..|.+|+.++++.+|-+.-.|...|+.|=+.|+.-+..
T Consensus        66 ~~~~~l~~~~~~~~~it~ae~Rd~lg~sRK~ai~lLE~~Dr~g~TrR~g  114 (121)
T 2pjp_A           66 EFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRG  114 (121)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEET
T ss_pred             HHHHHHHHHHHHCCCccHHHHHHHHCCcHHHHHHHHHHHhhcCCeEeeC
Confidence            2234467777888999999999999999999999999999999988763

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

Probab=93.60  E-value=0.23  Score=38.96  Aligned_cols=54  Identities=17%  Similarity=0.117  Sum_probs=46.9

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..+..||......|.+|..+|++.+++++.-+...|+.|++.|++-+....
T Consensus        49 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~  102 (162)
T 3cjn_A           49 GLSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDS  102 (162)
T ss_dssp             TCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCC
Confidence            356668888888887788999999999999999999999999999999886433

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

Probab=93.52  E-value=0.23  Score=38.54  Aligned_cols=53  Identities=19%  Similarity=0.173  Sum_probs=46.4

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+..+..||......|.+|+.+|++.+++++.-+...|..|++.|++-+...
T Consensus        44 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~   96 (153)
T 2pex_A           44 DLTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTRA   96 (153)
T ss_dssp             TCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             CCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCC
Confidence            45777888888887778899999999999999999999999999999988643

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

Probab=93.52  E-value=0.16  Score=38.54  Aligned_cols=53  Identities=13%  Similarity=0.093  Sum_probs=46.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .++..+..||......|.+|..+|++.+++++.-+...|+.|++.|++-+...
T Consensus        35 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~   87 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSAD   87 (140)
T ss_dssp             CCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            45777888888887777899999999999999999999999999999987543

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=93.40  E-value=0.15  Score=40.33  Aligned_cols=50  Identities=10%  Similarity=0.121  Sum_probs=45.4

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      +|+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++..
T Consensus         5 ~ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A            5 LIDNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             CCCHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcce
Confidence            45665678999999889999999999999999999999999999999985

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=93.35  E-value=0.2  Score=36.24  Aligned_cols=52  Identities=23%  Similarity=0.319  Sum_probs=45.3

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      ++.-+..||.+....|.+|+.+|++.+|.++.-+...|..|++.|++-....
T Consensus        18 l~~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           18 FKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee
Confidence            4556777888887668899999999999999999999999999999987644

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=93.28  E-value=0.24  Score=37.97  Aligned_cols=54  Identities=19%  Similarity=0.193  Sum_probs=46.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .++..+..||......|.+|..+|++.+++++.-+...|..|++.|++=+....
T Consensus        37 ~l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~   90 (147)
T 1z91_A           37 NITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSE   90 (147)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCS
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCC
Confidence            457778888888777778999999999999999999999999999999775443

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

Probab=93.28  E-value=0.14  Score=41.90  Aligned_cols=50  Identities=20%  Similarity=0.252  Sum_probs=45.0

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      |.+|+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++
T Consensus        12 ~~~ld~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I   61 (171)
T 2ia0_A           12 EIHLDDLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQERGVI   61 (171)
T ss_dssp             --CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             cCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            56677777789999998899999999999999999999999999999998

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=93.28  E-value=0.17  Score=36.94  Aligned_cols=55  Identities=13%  Similarity=0.165  Sum_probs=47.9

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHH----HHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEV----ERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L----~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      +..|+..|..||......|.+|..+|    ++.+++++.-+-..|+.|++.|++-+...
T Consensus         3 ~~~lt~~q~~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~   61 (99)
T 1tbx_A            3 STPFFYPEAIVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQE   61 (99)
T ss_dssp             CCSSBCHHHHHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            34678888889988887788999999    89999999999999999999999987643

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=93.19  E-value=0.41  Score=36.30  Aligned_cols=53  Identities=17%  Similarity=0.118  Sum_probs=45.5

Q ss_pred             ccchhHHHHHHHHHhCC--CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQG--FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g--~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .++..+..||.+....+  .+|+.+|++.+++++.-+...|+.|++.|++=+...
T Consensus        31 ~lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~   85 (141)
T 3bro_A           31 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVS   85 (141)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeCC
Confidence            45677888888777655  799999999999999999999999999999977543

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

Probab=93.18  E-value=0.19  Score=39.62  Aligned_cols=48  Identities=21%  Similarity=0.248  Sum_probs=44.2

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      |+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|+++|++.
T Consensus         7 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   54 (151)
T 2dbb_A            7 LDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR   54 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            566567899988888999999999999999999999999999999998

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=93.10  E-value=0.44  Score=35.48  Aligned_cols=78  Identities=17%  Similarity=0.192  Sum_probs=59.2

Q ss_pred             CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH
Q 025606          136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL  215 (250)
Q Consensus       136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l  215 (250)
                      ..++++++....+.++.|+++.                     ...||.+.. .|..|+.+|++.+|.+..-+...|..|
T Consensus         6 ~~~~~~~~~~~~~~~~~l~~~~---------------------r~~IL~~L~-~~~~~~~ela~~l~is~stvs~~L~~L   63 (106)
T 1r1u_A            6 SEINTDTLERVTEIFKALGDYN---------------------RIRIMELLS-VSEASVGHISHQLNLSQSNVSHQLKLL   63 (106)
T ss_dssp             ---CHHHHHHHHHHHHHTCSHH---------------------HHHHHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCHH---------------------HHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3578888888888888887422                     345776666 467899999999999999999999999


Q ss_pred             HHcCCceeecCCCCCCcceeecC
Q 025606          216 LEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       216 ~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      +..|++-.....   ...||..+
T Consensus        64 ~~~Glv~~~~~g---r~~~y~l~   83 (106)
T 1r1u_A           64 KSVHLVKAKRQG---QSMIYSLD   83 (106)
T ss_dssp             HHTTSEEEEEET---TEEEEEES
T ss_pred             HHCCCeEEEEeC---CEEEEEEC
Confidence            999999877532   45566543

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

Probab=93.08  E-value=0.3  Score=35.15  Aligned_cols=55  Identities=16%  Similarity=0.152  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      +..||.+....|.+|..+|++.+|.+..-+...|..|++.|++-.....   ...||.
T Consensus        26 ~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~---r~~~y~   80 (99)
T 3cuo_A           26 RLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDA---QRILYS   80 (99)
T ss_dssp             HHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECS---SCEEEE
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC---CEEEEE
Confidence            5568877777778999999999999999999999999999999877532   344544

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=92.99  E-value=0.15  Score=39.15  Aligned_cols=54  Identities=13%  Similarity=0.186  Sum_probs=43.2

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        34 ~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   87 (142)
T 3ech_A           34 DLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNP   87 (142)
T ss_dssp             CCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCC
Confidence            567778889988888788999999999999999999999999999999886544

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=92.98  E-value=0.37  Score=37.99  Aligned_cols=54  Identities=17%  Similarity=0.100  Sum_probs=47.8

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        43 glt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   96 (162)
T 3k0l_A           43 EISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDP   96 (162)
T ss_dssp             TCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCC
Confidence            467778889988887788999999999999999999999999999999876544

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

Probab=92.96  E-value=0.26  Score=37.08  Aligned_cols=77  Identities=22%  Similarity=0.180  Sum_probs=60.0

Q ss_pred             CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH
Q 025606          136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL  215 (250)
Q Consensus       136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l  215 (250)
                      ..++++++..+.+.++.|+.+.                     ...||.+... |.+|+.+|++.+|.++.-+...|..|
T Consensus         5 ~~~~~~~~~~~~~~~~al~~~~---------------------r~~IL~~L~~-~~~s~~eLa~~lgis~stvs~~L~~L   62 (108)
T 2kko_A            5 SDRKAALLDQVARVGKALANGR---------------------RLQILDLLAQ-GERAVEAIATATGMNLTTASANLQAL   62 (108)
T ss_dssp             CCTHHHHHHHHHHHHHHHTTST---------------------THHHHHHHTT-CCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CccChhhHHHHHHHHHHhCCHH---------------------HHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4467778888888888888422                     2347766654 78899999999999999999999999


Q ss_pred             HHcCCceeecCCCCCCcceeec
Q 025606          216 LEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       216 ~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ++.|++-.....   ...||..
T Consensus        63 ~~~GlV~~~~~g---r~~~y~l   81 (108)
T 2kko_A           63 KSGGLVEARREG---TRQYYRI   81 (108)
T ss_dssp             HHHTSEEEEEET---TEEEEEE
T ss_pred             HHCCCeEEEEeC---CEEEEEE
Confidence            999999877532   4556554

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

Probab=92.92  E-value=0.22  Score=38.79  Aligned_cols=52  Identities=12%  Similarity=0.089  Sum_probs=46.0

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+..|..||.+....|.+|+.+|++.+++++.-+...|+.|++.|++-+..
T Consensus        40 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~   91 (155)
T 3cdh_A           40 GLRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVA   91 (155)
T ss_dssp             TCCHHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CCCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            4566788888888777889999999999999999999999999999998753

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=92.86  E-value=0.3  Score=37.27  Aligned_cols=54  Identities=17%  Similarity=0.171  Sum_probs=46.8

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .++..+..||......|.+|+.+|++.++.++.-+...|..|++.|++=+....
T Consensus        34 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~   87 (142)
T 2bv6_A           34 NLTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSE   87 (142)
T ss_dssp             TCCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            356667788888887788999999999999999999999999999999776543

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

Probab=92.83  E-value=0.28  Score=34.76  Aligned_cols=53  Identities=17%  Similarity=0.242  Sum_probs=45.4

Q ss_pred             cchhHHHHHHHHHh-C-CCccHHHHHHhc-----CCChHHHHHHHHHHHHcCCceeecCC
Q 025606          175 LNKDHNQILELAQA-Q-GFVTVDEVERRL-----SWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       175 l~~D~~~vLela~~-~-g~vt~~~L~~~l-----~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      ++.-...||++... . +.+|+++|.+.+     +++..=+...|+.|++.|++-.....
T Consensus        15 ~t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~   74 (83)
T 2fu4_A           15 VTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFE   74 (83)
T ss_dssp             CCHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECG
T ss_pred             cCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeC
Confidence            35556778988875 3 799999999999     99999999999999999999887654

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

Probab=92.82  E-value=0.35  Score=38.52  Aligned_cols=54  Identities=11%  Similarity=0.057  Sum_probs=47.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-+..||......|.+|+.+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        42 ~lt~~~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   95 (168)
T 2nyx_A           42 NITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHP   95 (168)
T ss_dssp             SCCHHHHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            567778888888877788999999999999999999999999999999875433

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=92.72  E-value=0.22  Score=39.87  Aligned_cols=50  Identities=24%  Similarity=0.363  Sum_probs=45.5

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      +|+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++-.
T Consensus         7 ~ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   56 (162)
T 2p5v_A            7 TLDKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQ   56 (162)
T ss_dssp             CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEee
Confidence            56766778999999889999999999999999999999999999999863

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

Probab=92.71  E-value=0.37  Score=37.29  Aligned_cols=49  Identities=20%  Similarity=0.287  Sum_probs=44.3

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      |+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++-+
T Consensus        39 lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           39 LTIQQLAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             CCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4666777888887778899999999999999999999999999999988

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=92.67  E-value=0.22  Score=39.22  Aligned_cols=49  Identities=14%  Similarity=0.212  Sum_probs=43.9

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      |+.-+..+|++.+..|.+|..+|++.+|.+..-+...|..|++.|++-.
T Consensus         3 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   51 (144)
T 2cfx_A            3 LDQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQ   51 (144)
T ss_dssp             CCHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            4555667999888889999999999999999999999999999999863

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

Probab=92.66  E-value=0.26  Score=38.64  Aligned_cols=54  Identities=13%  Similarity=0.194  Sum_probs=46.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        47 ~lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~  100 (159)
T 3s2w_A           47 GIGSGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDE  100 (159)
T ss_dssp             TCCTTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            455567778888877788999999999999999999999999999999876443

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

Probab=92.63  E-value=0.26  Score=38.56  Aligned_cols=51  Identities=16%  Similarity=0.143  Sum_probs=44.5

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      |+..+..||......|.+|..+|++.+++++.-+...|+.|++.|++=+..
T Consensus        47 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~   97 (162)
T 2fa5_A           47 MAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRET   97 (162)
T ss_dssp             CCHHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeec
Confidence            466677888888878899999999999999999999999999999998753

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

Probab=92.56  E-value=0.33  Score=35.41  Aligned_cols=55  Identities=20%  Similarity=0.235  Sum_probs=45.1

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ...||.+... |.+|+.+|++.+|.+..-+...|..|++.|++-.....   ...||..
T Consensus        25 r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g---~~~~y~l   79 (98)
T 3jth_A           25 RLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEA---QTVYYTL   79 (98)
T ss_dssp             HHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT---TCCEEEE
T ss_pred             HHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC---CEEEEEE
Confidence            3457776666 89999999999999999999999999999999887554   4555543

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=92.54  E-value=0.23  Score=39.30  Aligned_cols=50  Identities=16%  Similarity=0.268  Sum_probs=45.0

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      +|+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++-.
T Consensus         4 ~ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   53 (151)
T 2cyy_A            4 PLDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKK   53 (151)
T ss_dssp             CCCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCC
T ss_pred             CcCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            46666778999999889999999999999999999999999999999853

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=92.53  E-value=0.2  Score=38.62  Aligned_cols=54  Identities=13%  Similarity=0.145  Sum_probs=46.9

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        33 glt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   86 (140)
T 3hsr_A           33 DLTYTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREE   86 (140)
T ss_dssp             TCCHHHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCC
Confidence            467778888888877789999999999999999999999999999999887544

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

Probab=92.53  E-value=0.33  Score=37.49  Aligned_cols=52  Identities=12%  Similarity=0.169  Sum_probs=43.6

Q ss_pred             ccchhHHHHHHHHHhC-CC-ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQAQ-GF-VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~~~-g~-vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+.-+..||.+.... |. +|+.+|++.+++++.-+...|+.|++.|++-+..
T Consensus        23 gLt~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           23 NLTKADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             TCCHHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeC
Confidence            4566677788776643 43 9999999999999999999999999999998864

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=92.44  E-value=0.46  Score=36.15  Aligned_cols=61  Identities=18%  Similarity=0.235  Sum_probs=47.7

Q ss_pred             cchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025606          175 LNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       175 l~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      ++.-+..+|.+.. ..|.+|+.+|++.+|.++.-+-..|..|++.|++-+....++ .+.|+.
T Consensus        24 l~~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~~d-~r~~~~   85 (152)
T 1ku9_A           24 LNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYE   85 (152)
T ss_dssp             CCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEE
T ss_pred             CChhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCC-ceEEEe
Confidence            4555777877765 357899999999999999999999999999999988753322 344544

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

Probab=92.36  E-value=0.26  Score=37.43  Aligned_cols=53  Identities=11%  Similarity=0.143  Sum_probs=45.9

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+..+..||......|.+|..+|++.+++++.-+...|+.|++.|++=+...
T Consensus        33 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~   85 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKA   85 (142)
T ss_dssp             TCCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecC
Confidence            35666778888877767899999999999999999999999999999987643

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=92.27  E-value=0.65  Score=34.94  Aligned_cols=82  Identities=15%  Similarity=0.199  Sum_probs=63.3

Q ss_pred             CCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHH
Q 025606          132 KSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDA  211 (250)
Q Consensus       132 ~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~  211 (250)
                      ++....++++++.+..+.++.|+.                     ..+..+|.+... |..|..+|++.+|.+..-+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~l~~---------------------~~~~~il~~L~~-~~~s~~ela~~l~is~stvsr~   65 (119)
T 2lkp_A            8 NRPSAPLDSQAAAQVASTLQALAT---------------------PSRLMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQ   65 (119)
T ss_dssp             CCCCSCCHHHHHHHHHHHHHHHCC---------------------HHHHHHHHHHHH-CCCCHHHHHHHHSSCHHHHHHH
T ss_pred             CccccccCHHHHHHHHHHHHHhCC---------------------HHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHH
Confidence            333456788888888888888764                     235667776666 7899999999999999999999


Q ss_pred             HHHHHHcCCceeecCCCCCCcceeecC
Q 025606          212 LDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       212 L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      |..|++.|++-.+...   ...||.+.
T Consensus        66 l~~Le~~Glv~~~~~~---r~~~~~~~   89 (119)
T 2lkp_A           66 LRVLRNLGLVVGDRAG---RSIVYSLY   89 (119)
T ss_dssp             HHHHHHHCSEEEEEET---TEEEEEES
T ss_pred             HHHHHHCCCEEEEecC---CEEEEEEc
Confidence            9999999999887533   45555544

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

Probab=92.19  E-value=0.26  Score=38.29  Aligned_cols=54  Identities=13%  Similarity=0.144  Sum_probs=45.7

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..|-.||......|.+|+.+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        38 ~lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   91 (149)
T 4hbl_A           38 GITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQ   91 (149)
T ss_dssp             TCCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC----
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCC
Confidence            467778889988887789999999999999999999999999999999876433

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=92.14  E-value=0.24  Score=38.42  Aligned_cols=48  Identities=17%  Similarity=0.311  Sum_probs=42.4

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      |+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|+++|++-
T Consensus         2 ld~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A            2 IDERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             CCSHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            344466788888888899999999999999999999999999999984

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=92.10  E-value=0.27  Score=37.50  Aligned_cols=53  Identities=13%  Similarity=0.083  Sum_probs=46.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+..+..||......|.+|..+|++.+++++.-+...|..|++.|++=+...
T Consensus        30 ~l~~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~   82 (145)
T 2a61_A           30 GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPD   82 (145)
T ss_dssp             TCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCC
Confidence            45667888888887778899999999999999999999999999999988643

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=91.91  E-value=0.3  Score=38.52  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=43.8

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      +|+.-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++-
T Consensus         4 ~ld~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A            4 ALDDIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3555566789888888999999999999999999999999999999995

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=91.88  E-value=0.39  Score=36.26  Aligned_cols=62  Identities=6%  Similarity=0.111  Sum_probs=51.7

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcC----CChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLS----WTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~----W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ..|+.-|..||.+.-..|.+|+.+|.+.++    |+..-....|+.|++.|++-+....   ....++|
T Consensus         6 ~~Lt~~q~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~---r~~~~~~   71 (126)
T 1sd4_A            6 VEISMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSE---NIYFYSS   71 (126)
T ss_dssp             CCCCHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEET---TEEEEEE
T ss_pred             CCCCHHHHHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCC---CeEEEEE
Confidence            467888989999888788899999999985    9999999999999999999987532   3444555

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

Probab=91.83  E-value=0.43  Score=37.51  Aligned_cols=54  Identities=22%  Similarity=0.227  Sum_probs=46.0

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        50 glt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~  103 (161)
T 3e6m_A           50 KLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISD  103 (161)
T ss_dssp             TCCHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCc
Confidence            356668888888877788999999999999999999999999999999876443

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=91.79  E-value=0.51  Score=36.07  Aligned_cols=55  Identities=11%  Similarity=0.157  Sum_probs=47.3

Q ss_pred             CCccchhHHHHHHHHHhC--CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          172 PTELNKDHNQILELAQAQ--GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       172 p~El~~D~~~vLela~~~--g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      +..|+..|..||......  +.+|+.+|++.++.++.-+-..|+.|++.|++-+...
T Consensus        32 ~~~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~   88 (127)
T 2frh_A           32 EFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRN   88 (127)
T ss_dssp             TTCCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCC
T ss_pred             HcCCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence            345677788888887765  8899999999999999999999999999999988533

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=91.74  E-value=0.44  Score=38.03  Aligned_cols=54  Identities=17%  Similarity=0.149  Sum_probs=45.3

Q ss_pred             ccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..|..||..... .+.+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        50 glt~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~  104 (166)
T 3deu_A           50 ELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA  104 (166)
T ss_dssp             TCCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCC
Confidence            456678888887775 678999999999999999999999999999999886443

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=91.71  E-value=0.35  Score=36.10  Aligned_cols=51  Identities=8%  Similarity=0.023  Sum_probs=46.9

Q ss_pred             CCccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          172 PTELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       172 p~El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      +..|+.+|..||.++..  ...+|..+|++.++-+..-....|+.|++.|++=
T Consensus        15 ~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIk   67 (91)
T 2dk5_A           15 MKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIK   67 (91)
T ss_dssp             CCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            56789999999999987  3489999999999999999999999999999998

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=91.70  E-value=0.84  Score=35.19  Aligned_cols=77  Identities=13%  Similarity=0.146  Sum_probs=60.5

Q ss_pred             CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025606          137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL  216 (250)
Q Consensus       137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~  216 (250)
                      ..+++++....+.++.|+.+                     -...||.+... |..|+.+|++.+|.+..-....|..|+
T Consensus        27 ~~~~~~~~~~~~~~kaL~~~---------------------~rl~IL~~L~~-~~~s~~ela~~lgis~stvs~~L~~Le   84 (122)
T 1r1t_A           27 AIAPEVAQSLAEFFAVLADP---------------------NRLRLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLR   84 (122)
T ss_dssp             CCCHHHHHHHHHHHHHHCCH---------------------HHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHhHHHHHHHHHHHhCCH---------------------HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46788888888888888742                     13457766654 678999999999999999999999999


Q ss_pred             HcCCceeecCCCCCCcceeecC
Q 025606          217 EEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       217 ~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      +.|++-.....   ...||.++
T Consensus        85 ~~Glv~~~~~g---r~~~y~l~  103 (122)
T 1r1t_A           85 NLRLVSYRKQG---RHVYYQLQ  103 (122)
T ss_dssp             HTTSEEEEEET---TEEEEEES
T ss_pred             HCCCeEEEEeC---CEEEEEEC
Confidence            99999987543   45566543

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

Probab=91.67  E-value=0.54  Score=36.70  Aligned_cols=62  Identities=16%  Similarity=0.195  Sum_probs=51.0

Q ss_pred             ccchhHHHHHHHHHh-CCCccHHHHHHhcC----CChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          174 ELNKDHNQILELAQA-QGFVTVDEVERRLS----WTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       174 El~~D~~~vLela~~-~g~vt~~~L~~~l~----W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      .|+.-|..||.+.-. .|.+|+.+|.+.++    |+..-....|+.|++.|++=+....   ...+++|.
T Consensus         6 ~lt~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~---r~~~~~~~   72 (138)
T 2g9w_A            6 RLGDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDD---RAHRYAPV   72 (138)
T ss_dssp             GCCHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC------CCEEEES
T ss_pred             cCCHHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecC---CeEEEEeC
Confidence            577888889998887 58999999999997    9999999999999999999987532   45555553

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=91.59  E-value=0.29  Score=39.50  Aligned_cols=46  Identities=13%  Similarity=0.273  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      -..++|.+.+..|.+|..+|++.+|.|..-+...|..|+++|++..
T Consensus         4 ~d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~   49 (162)
T 3i4p_A            4 LDRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRR   49 (162)
T ss_dssp             HHHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            3457899999899999999999999999999999999999999883

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=91.33  E-value=0.78  Score=35.65  Aligned_cols=53  Identities=17%  Similarity=0.186  Sum_probs=46.4

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+.-|..||......|.+|+.+|++.+++++.-+-..|+.|++.|++=+...
T Consensus        41 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~   93 (154)
T 2eth_A           41 DMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMD   93 (154)
T ss_dssp             HSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            46777888888887777899999999999999999999999999999977543

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=91.14  E-value=0.34  Score=37.78  Aligned_cols=54  Identities=11%  Similarity=0.180  Sum_probs=45.2

Q ss_pred             ccchhHHHHHHHH-HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELA-QAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela-~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..|..||.+. ...|.+|..+|++.+++++.-+-..|..|++.|++=+....
T Consensus        44 ~l~~~~~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~   98 (160)
T 3boq_A           44 GLSLAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSA   98 (160)
T ss_dssp             SCCHHHHHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC---
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            3566788888888 56778999999999999999999999999999999886433

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=91.10  E-value=0.28  Score=38.09  Aligned_cols=49  Identities=12%  Similarity=0.251  Sum_probs=44.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .++.-|-.||... ..|.+|+.+|++.+++++.-+-..|+.|++.|++-+
T Consensus        35 ~lt~~q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           35 GISAEQSHVLNML-SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             TCCHHHHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             CCCHHHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4566688888888 778999999999999999999999999999999997

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=90.94  E-value=0.25  Score=37.22  Aligned_cols=53  Identities=8%  Similarity=0.295  Sum_probs=47.0

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcC----CChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLS----WTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~----W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+.-+..||.+....|.+|+.+|.+.++    |++.-+...|+.|++.|++-+...
T Consensus         7 ~lt~~~~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~   63 (123)
T 1okr_A            7 EISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD   63 (123)
T ss_dssp             CCCHHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             cCCHHHHHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec
Confidence            57778888998887678899999999998    999999999999999999987643

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=90.88  E-value=0.38  Score=37.80  Aligned_cols=47  Identities=17%  Similarity=0.203  Sum_probs=42.2

Q ss_pred             hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .-+..+|.+.+..|.+|..+|++.+|.+..-+...|..|++.|++-.
T Consensus         3 ~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            3 EIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             HHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            34567888888888999999999999999999999999999999864

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=90.43  E-value=0.75  Score=34.19  Aligned_cols=45  Identities=18%  Similarity=0.247  Sum_probs=38.0

Q ss_pred             HHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          180 NQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       180 ~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ..|+.... .+..+|+.+|++.+|-+..-+..+|..|..+|++-..
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            34665543 4437999999999999999999999999999999877

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=90.38  E-value=0.73  Score=35.33  Aligned_cols=57  Identities=16%  Similarity=0.081  Sum_probs=44.2

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      ...||.+....|..|+.+|++.+|.+..-+...|..|+..|++-.....   ...||.++
T Consensus        44 rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~g---r~~~y~l~  100 (122)
T 1u2w_A           44 RAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEG---KLALYSLG  100 (122)
T ss_dssp             HHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-------CCEEEES
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEC---CEEEEEEC
Confidence            3457777765678999999999999999999999999999999886443   45566543

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=90.38  E-value=3.8  Score=35.55  Aligned_cols=113  Identities=12%  Similarity=0.086  Sum_probs=80.1

Q ss_pred             cccchhhhHHHHHHHhhhhcccCCCcee--HHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-CEEEE
Q 025606           92 IGDFYYELGVQIVEICLATRPHNGGLIN--LQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-KKKLV  168 (250)
Q Consensus        92 ~gdfy~eLavqIvevC~~tr~~nGGli~--l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v  168 (250)
                      ..+-+-.+..+|.+.+.+     +|+-+  +.|+...+         .+.++++...++.|...|.   |+.|. +..|-
T Consensus       135 ~~~~~~~~~~~i~~~~~~-----~g~~pp~~~dl~~~l---------~~~~~~~~~~l~~l~~~g~---lv~l~~~~~~~  197 (258)
T 1lva_A          135 FSETQKKLLKDLEDKYRV-----SRWQPPSFKEVAGSF---------NLDPSELEELLHYLVREGV---LVKINDEFYWH  197 (258)
T ss_dssp             CCHHHHHHHHHHHHHHHH-----HTTSCCBHHHHHHHT---------TCCHHHHHHHHHHHHHTTS---EEESSSSBEEE
T ss_pred             CCHHHHHHHHHHHHHHHH-----CCCCCCCHHHHHhHh---------CCCHHHHHHHHHHHHHCCC---EEEecCCeEEc
Confidence            345556666666666633     56543  45554332         3678888888888887775   66776 44443


Q ss_pred             EecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          169 RSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       169 ~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .....++   -..+.+++ ..|.+|+.++++.+|-|.-.|..-|+.|=+.|+.-+..
T Consensus       198 ~~~~~~~---~~~l~~~~-~~~~it~a~~Rd~lg~SRK~aIplLE~~Dr~g~TrR~g  250 (258)
T 1lva_A          198 RQALGEA---REVIKNLA-STGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVG  250 (258)
T ss_dssp             HHHHHHH---HHHHHHHH-TTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHH---HHHHHHHH-hcCCcCHHHHHHHhCCcHHHHHHHHHHHhhcCceeeeC
Confidence            3332222   44466777 78999999999999999999999999999999998874

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=90.37  E-value=0.78  Score=37.41  Aligned_cols=53  Identities=11%  Similarity=0.075  Sum_probs=46.5

Q ss_pred             cchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          175 LNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       175 l~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |+.-|-.||.....  .|.+|+.+|++.+++++.-+-..|..|++.|++-+....
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   93 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSP   93 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            67778888887764  678999999999999999999999999999999886544

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=90.33  E-value=0.26  Score=38.14  Aligned_cols=52  Identities=10%  Similarity=0.097  Sum_probs=38.7

Q ss_pred             ccchhHHHHHHHHHhC--CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQAQ--GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~~~--g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+.-|..||......  |.+|+.+|++.+++++.-+-..|+.|++.|++=+..
T Consensus        38 glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~   91 (148)
T 3jw4_A           38 GLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRI   91 (148)
T ss_dssp             TCCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC-
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeC
Confidence            4566788888877654  889999999999999999999999999999997654

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=90.30  E-value=0.52  Score=36.10  Aligned_cols=53  Identities=19%  Similarity=0.094  Sum_probs=45.5

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..|..||......|. |+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        34 ~lt~~~~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   86 (144)
T 3f3x_A           34 NLSYLDFSILKATSEEPR-SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDS   86 (144)
T ss_dssp             SCCHHHHHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence            456678888888877666 99999999999999999999999999999876433

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=90.23  E-value=0.44  Score=36.87  Aligned_cols=49  Identities=20%  Similarity=0.220  Sum_probs=43.0

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhc--CCChHHHHHHHHHHHHcCCcee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRL--SWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      ++.-...||++....|..|+.+|++.+  |.+..-+...|..|++.|++=.
T Consensus        11 md~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~   61 (111)
T 3b73_A           11 MTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQP   61 (111)
T ss_dssp             CCHHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEe
Confidence            444346799998877899999999999  9999999999999999999865

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=90.17  E-value=0.84  Score=32.67  Aligned_cols=46  Identities=15%  Similarity=0.207  Sum_probs=39.5

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      +..||.+....|.+|..+|++.+|.+..-....|..|++.|++-..
T Consensus        18 ~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~   63 (100)
T 1ub9_A           18 RLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4457776655578999999999999999999999999999999853

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=89.96  E-value=0.41  Score=34.60  Aligned_cols=54  Identities=15%  Similarity=0.262  Sum_probs=43.8

Q ss_pred             CccchhHHHHH-HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          173 TELNKDHNQIL-ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       173 ~El~~D~~~vL-ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      ..++..+..+| .+....+.+|+.+|++.+|.++.-+...|..|++.|++-....
T Consensus        17 ~~l~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           17 YKITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             HTCCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             hcCCHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence            34555565555 4454478899999999999999999999999999999988754

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

Probab=89.94  E-value=0.84  Score=33.71  Aligned_cols=47  Identities=17%  Similarity=0.102  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      +..||.+. ..|.+|+.+|++.+|+++.-....|..|++.|++-....
T Consensus        23 r~~IL~~L-~~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           23 RWEILTEL-GRADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             HHHHHHHH-HHSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec
Confidence            45577777 456799999999999999999999999999999987643

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

Probab=89.79  E-value=0.66  Score=32.23  Aligned_cols=43  Identities=19%  Similarity=0.407  Sum_probs=38.5

Q ss_pred             HHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          181 QILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       181 ~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      .+|+.+. .+|++.++..++++|-+++-...+|..|.++|++=+
T Consensus        14 ~lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           14 ELLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCeec
Confidence            3777666 689999999999999999999999999999999754

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=89.48  E-value=0.52  Score=39.06  Aligned_cols=52  Identities=23%  Similarity=0.316  Sum_probs=44.3

Q ss_pred             ccchhHHHHHHHHH----hCC-CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQ----AQG-FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~----~~g-~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      +|+.-|..+|+++.    ..| ..|..+|++.+|.+..-+...|..|+++|++=++.
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~~   58 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKN   58 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC-
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEecC
Confidence            57888999998865    346 48999999999999998999999999999997764

>2lmt_A Calmodulin-related protein 97A; spermatogenesis, metal binding protein; NMR {Drosophila melanogaster} PDB: 2lmu_A 2lmv_A

Probab=89.44  E-value=2.8  Score=31.99  Aligned_cols=93  Identities=19%  Similarity=0.480  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCC
Q 025606           37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGG  116 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGG  116 (250)
                      .|++.|+.....|=.++.+.|..++     |..++.++|.+|...                    .+..+....-..+.|
T Consensus         7 eqi~el~~~F~~~D~d~~G~I~~~E-----l~~~l~~~~~~~~~~--------------------~~~~~~~~~d~~~~g   61 (148)
T 2lmt_A            7 EQIAEFKDAFVQFDKEGTGKIATRE-----LGTLMRTLGQNPTEA--------------------ELQDLIAEAENNNNG   61 (148)
T ss_dssp             HHHHHHHHHHHHHHCSSCCEEEGGG-----HHHHHHHHTCCCCHH--------------------HHHHHHHHHHTTSTT
T ss_pred             HHHHHHHHHHHHHcCCCCCeECHHH-----HHHHHHhcCCCchHH--------------------HHHHHHHhcccCCCC
Confidence            3566778888888899999998774     668888899887431                    122233333345567


Q ss_pred             ceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025606          117 LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY  157 (250)
Q Consensus       117 li~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~  157 (250)
                      .++..|....+.....   ...+++++.+|.+.+-.=|+|+
T Consensus        62 ~i~~~ef~~~~~~~~~---~~~~~~~l~~aF~~~D~d~~G~   99 (148)
T 2lmt_A           62 QLNFTEFCGIMAKQMR---ETDTEEEMREAFKIFDRDGDGF   99 (148)
T ss_dssp             EEEHHHHHHHHHHTTT---TTTTHHHHHHHHHHHHSSCSSE
T ss_pred             cccHHHHHHHHHHHhc---ccCcHHHHHHHHHHHCCCCcCc
Confidence            7888887766655322   3456677777776666555554

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=89.41  E-value=0.47  Score=37.56  Aligned_cols=56  Identities=18%  Similarity=0.179  Sum_probs=44.6

Q ss_pred             CCccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +..|+.-|..||.+...  .+.+|+.+|++.+++++.-+-..|+.|++.|++-+....
T Consensus        41 ~~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           41 QFELSAQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             TTTCCHHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             hcCCCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCC
Confidence            34567778888887775  468999999999999999999999999999999876443

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=89.28  E-value=1.6  Score=31.74  Aligned_cols=50  Identities=12%  Similarity=0.074  Sum_probs=41.0

Q ss_pred             hHHHHHHHHH---hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          178 DHNQILELAQ---AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       178 D~~~vLela~---~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .+..|+.++.   ..+++|+.+|+..||-++--+..+|-.|.++|.+..=...
T Consensus        13 ~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~   65 (75)
T 1sfu_A           13 IFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   65 (75)
T ss_dssp             HHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCC
Confidence            4555555555   2556999999999999999999999999999999877555

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=89.05  E-value=1.5  Score=32.12  Aligned_cols=54  Identities=17%  Similarity=0.210  Sum_probs=43.6

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ..||.+... |.+|+.+|++.+|.+..-....|..|...|++-.....   ...||..
T Consensus        26 ~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g---~~~~y~l   79 (102)
T 3pqk_A           26 LMLVCTLVE-GEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNI---KQIFYRL   79 (102)
T ss_dssp             HHHHHHHHT-CCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSS---SCCEEEE
T ss_pred             HHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC---CEEEEEE
Confidence            346666644 67999999999999999999999999999999887644   4556654

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=88.84  E-value=0.9  Score=37.93  Aligned_cols=54  Identities=19%  Similarity=0.154  Sum_probs=46.6

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|-.||.+....|.+|+.+|++.+++++.-+-..|+.|++.|++=+....
T Consensus        45 gLt~~q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~   98 (207)
T 2fxa_A           45 DLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   98 (207)
T ss_dssp             TCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            456668888888877688999999999999999999999999999999887544

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=88.23  E-value=0.69  Score=40.29  Aligned_cols=53  Identities=11%  Similarity=0.168  Sum_probs=48.4

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      |..|+..+..+|+.....|.+|..+|++.+|.++.-+...|..|++.|++-.+
T Consensus       147 ~~~L~~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          147 MRDYSREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             HSCCCHHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            45788889999998766678999999999999999999999999999999987

>3i5g_C Myosin catalytic light chain LC-1, mantle muscle; rigor-like, squid, muscle myosin, contractIle protein; 2.60A {Todarodes pacificus} PDB: 3i5f_C 3i5h_C 3i5i_C

Probab=88.10  E-value=4.7  Score=31.66  Aligned_cols=94  Identities=13%  Similarity=0.287  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHH--hcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccC
Q 025606           37 EQLATFRSQLEDFAR--KHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHN  114 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~--~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~n  114 (250)
                      .|++.||.....|=.  .+.+.|..+     .|+.++.++|++|-..      +              |-++ ...-..+
T Consensus         6 eqi~elre~F~~fD~~~d~dG~I~~~-----El~~~lr~lG~~~t~~------e--------------l~~~-~~~d~~~   59 (159)
T 3i5g_C            6 DEIEEVREVFDLFDFWDGRDGDVDAA-----KVGDLLRCLGMNPTEA------Q--------------VHQH-GGTKKMG   59 (159)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSCEEGG-----GHHHHHHHTTCCCCHH------H--------------HHTT-TCCSSTT
T ss_pred             HHHHHHHHHHHHHCcCCCCCCeECHH-----HHHHHHHHcCCCCCHH------H--------------HHHH-HcccccC
Confidence            456667777777754  456778765     4668888999987420      1              1111 1223345


Q ss_pred             CCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025606          115 GGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY  157 (250)
Q Consensus       115 GGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~  157 (250)
                      .|-|++.|.+..+.+.... ...-++++|.+|.+.+-+=|+|+
T Consensus        60 ~g~i~f~eFl~~~~~~~~~-~~~~~~~~l~~aF~~fD~d~~G~  101 (159)
T 3i5g_C           60 EKAYKLEEILPIYEEMSSK-DTGTAADEFMEAFKTFDREGQGL  101 (159)
T ss_dssp             SCEECHHHHHHHHHHHTTC-CTTCCHHHHHHHHHHHCTTSSSE
T ss_pred             CCcccHHHHHHHHHHhhcc-cccchHHHHHHHHHHHhcCCCCc
Confidence            6788888888777664332 23456788888888877766665

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=87.86  E-value=0.83  Score=37.74  Aligned_cols=54  Identities=24%  Similarity=0.229  Sum_probs=46.4

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ..|||+.. .|.+|+..|++.+|-|-..|+-.|-.|++||++=-=...   ...||--
T Consensus        14 ~~ILE~Lk-~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~G---K~ayw~L   67 (165)
T 2vxz_A           14 RDILALLA-DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFG---NVALVCL   67 (165)
T ss_dssp             HHHHHHHT-TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEET---TEEEEES
T ss_pred             HHHHHHHH-hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEc---cEEEEEe
Confidence            45788888 899999999999999999999999999999998655443   6788864

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=87.43  E-value=0.47  Score=46.46  Aligned_cols=109  Identities=12%  Similarity=0.145  Sum_probs=28.5

Q ss_pred             ceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc--cC-CCeEEEEECCEEEEEec----CC-------------ccc
Q 025606          117 LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV--LG-NGYEVISVGKKKLVRSV----PT-------------ELN  176 (250)
Q Consensus       117 li~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~--LG-~g~~vi~ig~~~~v~sv----p~-------------El~  176 (250)
                      -|+.+++...++         +|+.++.++++.|..  ++ .|+ |...|+.++|..-    ..             .++
T Consensus       444 ~it~~~la~~l~---------~s~~~~~~~L~~L~~~~~~~~gl-ie~~g~~y~L~~~~~~~~~~~~~~~~~~~~~~~~~  513 (583)
T 3lmm_A          444 FITIDVVARGLQ---------SGKEAARNALEAARQTTVAGAPL-IIAHDGVWLLGNACREILRKVEPSPFSPVRYLSTD  513 (583)
T ss_dssp             SBCHHHHHHHHT---------SCHHHHHHHHHHHHTCEETTEES-EEEETTEEEECHHHHHHHTSCC-------------
T ss_pred             CcCHHHHHHHhC---------cCHHHHHHHHHHHHhhhccccce-EEEeCCEEEECHHHHHHhcccccccccccccccCC
Confidence            466666655543         799999999999975  33 444 3445665544331    00             011


Q ss_pred             hh--HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          177 KD--HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       177 ~D--~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      .+  ...|++++...|.+|..++++.+|-+...|+..|..|+++|++=.   .+.|...+|.+.
T Consensus       514 ~~~~~~~I~~~l~~~g~it~~di~~l~~ls~~qa~~~L~~Lv~~G~l~~---~G~gr~t~Y~~~  574 (583)
T 3lmm_A          514 QAELTNAAMLWLSEVGDLATSDLMAMCGVSRGTAKACVDGLVDEERVVA---VGGGRSRRYRLV  574 (583)
T ss_dssp             ----------------------------------------------------------------
T ss_pred             hhHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE---eCCCCceEEEEe
Confidence            11  235788888899999999999999999999999999999999622   222345555543

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=87.40  E-value=1.6  Score=32.06  Aligned_cols=61  Identities=11%  Similarity=0.064  Sum_probs=51.3

Q ss_pred             CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      |..++.-..+||++..+ ..-++..+|++.+|-++--.-.+|..|-++|.+-    .|  .+.||-|.
T Consensus        14 ~~~~~d~eekVLe~LkeaG~PlkageIae~~GvdKKeVdKaik~LKkEgkI~----SP--kRCyw~~~   75 (80)
T 2lnb_A           14 PGREGHLEQRILQVLTEAGSPVKLAQLVKECQAPKRELNQVLYRMKKELKVS----LT--SPATWCLG   75 (80)
T ss_dssp             SCHHHHHHHHHHHHHHHHTSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEE----EE--ETTEEEES
T ss_pred             CcccchHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCcc----CC--CCceeeCC
Confidence            55566557789999885 5679999999999999999999999999999953    22  68999986

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=87.27  E-value=0.84  Score=35.21  Aligned_cols=53  Identities=21%  Similarity=0.179  Sum_probs=43.2

Q ss_pred             ccchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025606          174 ELNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       174 El~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      .|+.-|..||.+.. ..+.+|+.+|++.+++++.-+-..|+.|++.|++-+...
T Consensus        36 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~   89 (150)
T 3fm5_A           36 GLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLD   89 (150)
T ss_dssp             TCCHHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC---
T ss_pred             CCCHHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCC
Confidence            45666888888765 445789999999999999999999999999999987543

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=86.40  E-value=0.98  Score=34.77  Aligned_cols=43  Identities=14%  Similarity=0.298  Sum_probs=37.4

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ++.+....|.+|+.+|++.+|.++.-+...|..|++.|++=+.
T Consensus        13 i~~l~~~~~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~   55 (142)
T 1on2_A           13 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHhhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3444555678999999999999999999999999999999776

>3fwb_A Cell division control protein 31; gene gating, complex, cell cycle, cell division, mitosis, MR transport, nuclear pore complex, nucleus, phosphoprotein; 2.50A {Saccharomyces cerevisiae} SCOP: a.39.1.5 PDB: 2gv5_A 2doq_A 3fwc_A

Probab=86.29  E-value=5.5  Score=29.87  Aligned_cols=36  Identities=6%  Similarity=0.063  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           39 LATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        39 L~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      +..++.....|-..+.+.|..+     .|..++..+|+.|.
T Consensus        22 ~~~l~~~F~~~D~~~~G~i~~~-----e~~~~l~~~~~~~~   57 (161)
T 3fwb_A           22 KQEIYEAFSLFDMNNDGFLDYH-----ELKVAMKALGFELP   57 (161)
T ss_dssp             HHHHHHHHHHHCTTSSSEECHH-----HHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHCCCCCCcCcHH-----HHHHHHHHcCCCCC
Confidence            3445555556666777777655     46777778887653

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.88  E-value=1.3  Score=33.83  Aligned_cols=52  Identities=13%  Similarity=0.224  Sum_probs=41.9

Q ss_pred             ccchhHHHHHHHH----HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELA----QAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela----~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .++.-+..+|...    +..+.+|..+|++.+|+++.-+...|..|+++|++-++.
T Consensus        10 ~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           10 NLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             -CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             hcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            4555565565543    346789999999999999999999999999999988764

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=85.71  E-value=1.9  Score=32.68  Aligned_cols=51  Identities=22%  Similarity=0.317  Sum_probs=45.5

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHH-hcCCChHHHHHHHHHHHHcCCce
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVER-RLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~-~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      +..|+.-|..+|-.....|++|+.+|.+ .++.++.-.-..|.-|+++|++=
T Consensus        11 ~~~L~~~QfsiL~~L~~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           11 NDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             TTSSCHHHHHHHHHHHHSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             hcCCCHHHHHHHHHHHHCCCCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee
Confidence            4567888888998888889999999999 99999998899999999999875

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=85.64  E-value=1.4  Score=31.79  Aligned_cols=46  Identities=15%  Similarity=0.127  Sum_probs=38.2

Q ss_pred             HHHHHHhCC-CccHHHHHHhcCCChHH-HHHHHHHHHHcCCceeecCC
Q 025606          182 ILELAQAQG-FVTVDEVERRLSWTSGR-AIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       182 vLela~~~g-~vt~~~L~~~l~W~~~R-a~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +|.+....| .+|+.+|++.++.++.- +-..|+.|++.|++-.|...
T Consensus        20 ~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~d   67 (95)
T 2pg4_A           20 TLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLS   67 (95)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEE
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCC
Confidence            444455555 79999999999999999 99999999999999855443

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=85.60  E-value=1.4  Score=32.04  Aligned_cols=45  Identities=16%  Similarity=0.046  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      ...||++.  .|.+|+.+|++.+|.+..-+...|..|++.|++-...
T Consensus        33 r~~Il~~L--~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           33 RRKILRML--DKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            45688877  4779999999999999999999999999999998764

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=85.32  E-value=1.2  Score=35.31  Aligned_cols=51  Identities=16%  Similarity=0.341  Sum_probs=41.7

Q ss_pred             ccchhHHHHHH-HHH----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          174 ELNKDHNQILE-LAQ----AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       174 El~~D~~~vLe-la~----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .||.++..+|- +..    ...+.|.++|++.+|.+..-+...|+.|+++|++=+.
T Consensus        29 gLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           29 GLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            45666665543 333    2578999999999999999999999999999999994

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=84.78  E-value=1.9  Score=33.60  Aligned_cols=54  Identities=19%  Similarity=0.239  Sum_probs=45.5

Q ss_pred             ccchhHHHHHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|-.+|.+..  ..|.+|+++|++.++.++.-.-..++.|++.|++=+-...
T Consensus        32 gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~   87 (147)
T 4b8x_A           32 GLTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNP   87 (147)
T ss_dssp             TCCHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecC
Confidence            35666777887664  4678999999999999999999999999999999876544

>3i5g_B Myosin regulatory light chain LC-2, mantle muscle; rigor-like, squid, muscle myosin, contractIle protein; 2.60A {Todarodes pacificus} PDB: 3i5f_B 3i5h_B 3i5i_B

Probab=84.74  E-value=2.2  Score=33.42  Aligned_cols=105  Identities=14%  Similarity=0.211  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCC-Ccccccc---cccccchhhhHH---------HH
Q 025606           37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASN-KGFWAEL---LGIGDFYYELGV---------QI  103 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~-k~~ws~~---lG~gdfy~eLav---------qI  103 (250)
                      .|+..|+.....|=.++.+.|..+     .|+..+.++|.+|.... ..+....   +...+|...++.         .+
T Consensus        13 ~qi~elk~~F~~~D~d~dG~I~~~-----El~~~l~~lg~~~~~~~~~~~~~~~~~~i~f~ef~~~~~~~~~~~~~~~~l   87 (153)
T 3i5g_B           13 RQMQELKEAFTMIDQDRDGFIGME-----DLKDMFSSLGRVPPDDELNAMLKECPGQLNFTAFLTLFGEKVSGTDPEDAL   87 (153)
T ss_dssp             HHHHHHHHHHHHHCCSTTSCCCHH-----HHHHHHHHTTSCCCHHHHHHHHHTSSSCCCSHHHHHTTTTTTTTCCCHHHH
T ss_pred             HHHHHHHHHHHHHCCCCCCeEcHH-----HHHHHHHHcCCCccHHHHHHHHHhccCCccHHHHHHHHHhhhcccccHHHH
Confidence            456667777888888888888865     47788889999886311 0011111   111233222211         22


Q ss_pred             HHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhc
Q 025606          104 VEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKL  150 (250)
Q Consensus       104 vevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L  150 (250)
                      .++-..-=..+-|.|+..||...+...    +..+|+++|..-++..
T Consensus        88 ~~aF~~fD~d~~G~I~~~el~~~l~~~----g~~ls~~ei~~~~~~~  130 (153)
T 3i5g_B           88 RNAFSMFDEDGQGFIPEDYLKDLLENM----GDNFSKEEIKNVWKDA  130 (153)
T ss_dssp             HHHHHTTCSSCSSCCCHHHHHHHHHSS----SSCCCHHHHHHHHTTC
T ss_pred             HHHHhccccCCCCeEeHHHHHHHHHHc----CCcCCHHHHHHHHHHh
Confidence            222222222334677777776655432    2456777766655543

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

Probab=84.69  E-value=3.4  Score=32.40  Aligned_cols=54  Identities=19%  Similarity=0.147  Sum_probs=44.7

Q ss_pred             ccchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|-.||.... ..+.+|+.+|++.++.++.-+-..++.|++.|++=+....
T Consensus        28 gLt~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~   82 (151)
T 4aik_A           28 ELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSA   82 (151)
T ss_dssp             CCCHHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCC
Confidence            45666777777665 4667899999999999999999999999999999876544

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.67  E-value=1.2  Score=33.69  Aligned_cols=50  Identities=8%  Similarity=0.033  Sum_probs=44.8

Q ss_pred             CccchhHHHHHHHHHhC--CCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          173 TELNKDHNQILELAQAQ--GFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       173 ~El~~D~~~vLela~~~--g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ..|+.++..|+.+++..  -.++..+|+...+.+.......|..|+..|++=
T Consensus        33 ~~Lt~~E~lVy~~I~~aGn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK   84 (95)
T 2yu3_A           33 KGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIK   84 (95)
T ss_dssp             CSCSHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEE
T ss_pred             cCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEE
Confidence            47899999999999964  449999999999999999999999999999863

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=84.38  E-value=0.64  Score=36.17  Aligned_cols=36  Identities=28%  Similarity=0.197  Sum_probs=33.0

Q ss_pred             CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .-+||+..|++.|+..-..|+.+|.+|+.+|++=.=
T Consensus        57 ~KlITpsvlseRlkI~gSLAR~aLreL~~kGlIk~V   92 (108)
T 3u5c_Z           57 YRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPI   92 (108)
T ss_dssp             CSSBSHHHHHHTTCCCTTHHHHHHHHHSSSSSCEEE
T ss_pred             CeEEeHHHhhhhhhhhHHHHHHHHHHHHHCCCEEEE
Confidence            568999999999999999999999999999997543

>2mys_C Myosin; muscle protein, motor protein; HET: MLY; 2.80A {Gallus gallus} SCOP: a.39.1.5 PDB: 1m8q_C* 1mvw_C* 1o18_F* 1o19_C* 1o1a_C* 1o1b_C* 1o1c_C* 1o1d_C* 1o1e_C* 1o1f_C* 1o1g_C*

Probab=84.22  E-value=3  Score=30.83  Aligned_cols=37  Identities=19%  Similarity=0.360  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           38 QLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        38 qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      ++..++.....|-.++.+.|..+     .|..++.++|..|-
T Consensus         6 ~~~~l~~~F~~~D~~~~G~i~~~-----el~~~l~~~~~~~~   42 (149)
T 2mys_C            6 AADDFKEAFLLFDRTGDAKITAS-----QVGDIARALGQNPT   42 (149)
T ss_pred             HHHHHHHHHHHhCCCCCCcCcHH-----HHHHHHHHhCCCCC
Confidence            45556666667777777777643     56677888887653

>3ox6_A Calcium-binding protein 1; EF-hand, calcium-sensor; 2.40A {Homo sapiens} PDB: 3ox5_A 2lan_A 2lap_A 2k7b_A 2k7c_A 2k7d_A

Probab=84.05  E-value=11  Score=27.77  Aligned_cols=37  Identities=14%  Similarity=0.336  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           38 QLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        38 qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      ++..++.....|-..+.+.|..+     .|+.++.++|..|.
T Consensus         9 ~~~~l~~~F~~~D~d~~G~i~~~-----el~~~l~~~~~~~~   45 (153)
T 3ox6_A            9 EIEELREAFREFDKDKDGYINCR-----DLGNCMRTMGYMPT   45 (153)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCCHH-----HHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHhCCCCCCcCcHH-----HHHHHHHHcCCCCC
Confidence            34555666666777888888754     57778888887653

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=83.79  E-value=1.1  Score=36.05  Aligned_cols=52  Identities=17%  Similarity=0.109  Sum_probs=44.3

Q ss_pred             ccchhHHHHHHHHHhCC---CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQAQG---FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~~~g---~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+.-+..||.+....|   .+|+.+|++.+++++.-+-..|+.|++.|++=+..
T Consensus        66 glt~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~  120 (181)
T 2fbk_A           66 GLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  120 (181)
T ss_dssp             TCCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecC
Confidence            45667888888777544   49999999999999999999999999999997753

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=83.78  E-value=2.8  Score=31.61  Aligned_cols=55  Identities=15%  Similarity=0.170  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ...||.+.. .|-+|+.+|++.+|.+..-+...|..|.+.|++-.....   ...||..
T Consensus        20 R~~Il~~L~-~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~g---r~~~y~l   74 (118)
T 3f6o_A           20 RRAVLGRLS-RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQG---RVRTCAI   74 (118)
T ss_dssp             HHHHHHHHH-TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEET---TEEEEEE
T ss_pred             HHHHHHHHH-hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecC---CEEEEEE
Confidence            344666665 478899999999999999999999999999999877554   4455543

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=83.70  E-value=1.9  Score=31.18  Aligned_cols=52  Identities=8%  Similarity=-0.029  Sum_probs=39.3

Q ss_pred             cchhHHHHHHHH-HhCC---CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          175 LNKDHNQILELA-QAQG---FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       175 l~~D~~~vLela-~~~g---~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |+.-+..+|... ...+   .+|+.+|++.++.++.-+-..|+.|++.|++ .|...
T Consensus        10 l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv-~~~~d   65 (95)
T 2qvo_A           10 FKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV-ECELE   65 (95)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE-EEEEE
T ss_pred             CchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc-cCCCC
Confidence            444455555443 3222   3999999999999999999999999999999 55443

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=83.70  E-value=0.96  Score=38.16  Aligned_cols=44  Identities=20%  Similarity=0.311  Sum_probs=38.6

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      |+.+.+..|.+|..+|++.+++++.-+...|..|+++|++=+..
T Consensus        11 I~~l~~~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~   54 (214)
T 3hrs_A           11 LYELGTRHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDK   54 (214)
T ss_dssp             HHHTTSSCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHhcCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEec
Confidence            45555568999999999999999999999999999999987653

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=83.23  E-value=0.82  Score=37.17  Aligned_cols=33  Identities=18%  Similarity=0.200  Sum_probs=31.4

Q ss_pred             CCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      -+||++.|++.|+.+-..|+.+|.+|+.+|++=
T Consensus        62 KlITpsvlseRlkI~gSLARkaLreL~~kGlIk   94 (143)
T 2xzm_8           62 KVLTVSTVVEKLKVNGSLARQLMRTMADRKLVE   94 (143)
T ss_dssp             SEECHHHHHHHHCBCHHHHHHHHHHHHHTTSEE
T ss_pred             eeecHHHHHHHhcchHHHHHHHHHHHHHCCCEE
Confidence            579999999999999999999999999999975

>2qac_A Myosin A tail domain interacting protein MTIP; malaria invasion, structural genomics, PSI, protein structur initiative, structural genomics of pathogenic protozoa CONS SGPP; 1.70A {Plasmodium falciparum} PDB: 2auc_A

Probab=82.68  E-value=4.4  Score=30.23  Aligned_cols=37  Identities=16%  Similarity=0.115  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHhc-ccccccChhHHHHHHHHHHHcCCCCC
Q 025606           38 QLATFRSQLEDFARKH-KNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        38 qL~~F~~~L~~Fa~~h-~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      ++..++.....|-.++ .+.|..+     .|+.++.++|.+|-
T Consensus        12 ~~~~l~~~F~~~D~d~~~G~i~~~-----el~~~l~~~g~~~~   49 (146)
T 2qac_A           12 EKVDESDVRIYFNEKSSGGKISID-----NASYNARKLGLAPS   49 (146)
T ss_dssp             HHSCHHHHHHHHHHHCBTTBEEHH-----HHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHhCccCCCCcccHH-----HHHHHHHHhCCCCC
Confidence            4455666677787887 7777654     56778888888764

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=82.37  E-value=2.3  Score=38.74  Aligned_cols=50  Identities=16%  Similarity=0.145  Sum_probs=45.4

Q ss_pred             cchhHHHHHH-----HHHhCCCccHHHHHHhc--CCChHHHHHHHHHHHHcCCceee
Q 025606          175 LNKDHNQILE-----LAQAQGFVTVDEVERRL--SWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       175 l~~D~~~vLe-----la~~~g~vt~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ++.-|..||+     +.+..+.|++.+|++.+  +.|..=.+.-|.+|+++|++=.=
T Consensus        15 l~eR~~~IL~~i~~~yl~~~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~   71 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQP   71 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEc
Confidence            5678889999     77788999999999998  99999999999999999998654

>1exr_A Calmodulin; high resolution, disorder, metal transport; 1.00A {Paramecium tetraurelia} SCOP: a.39.1.5 PDB: 1n0y_A 1osa_A 1clm_A 1mxe_A 2bbm_A 2bbn_A 4cln_A 4djc_A 2wel_D* 2x51_B 2vas_B* 2bkh_B 3gn4_B 3l9i_C 2ygg_B* 2w73_A 1lvc_D* 1wrz_A 2bki_B 2r28_A ...

Probab=82.34  E-value=11  Score=28.25  Aligned_cols=37  Identities=19%  Similarity=0.428  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           38 QLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        38 qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      ++..++..+..|-.++.+.|..+     .|..++.++|.+|-
T Consensus         8 ~~~~l~~~F~~~D~d~~G~i~~~-----el~~~l~~~g~~~~   44 (148)
T 1exr_A            8 QIAEFKEAFALFDKDGDGTITTK-----ELGTVMRSLGQNPT   44 (148)
T ss_dssp             HHHHHHHHHHHHCTTCSSEECHH-----HHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHHHHCCCCCCcCcHH-----HHHHHHHHcCCCCC
Confidence            34556666667777777777753     57778888888763

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=81.60  E-value=2  Score=33.55  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=35.3

Q ss_pred             HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          184 ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       184 ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      .+....|.+|+.+|++.+|.+..-...+|..|+++|++-+.
T Consensus        47 ~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~   87 (155)
T 2h09_A           47 DLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMI   87 (155)
T ss_dssp             HHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34445678999999999999999999999999999986554

>3qrx_A Centrin; calcium-binding, EF-hand, cell division, calcium binding, ME binding protein-toxin complex; 2.20A {Chlamydomonas reinhardtii} PDB: 2ggm_A 2ami_A 1zmz_A

Probab=81.51  E-value=12  Score=28.30  Aligned_cols=36  Identities=17%  Similarity=0.330  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCC
Q 025606           38 QLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDP   78 (250)
Q Consensus        38 qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDP   78 (250)
                      ++..++.....|-.++.+.|..+     .|..++.++|+.|
T Consensus        26 ~~~~l~~~F~~~D~d~~G~i~~~-----el~~~l~~~~~~~   61 (169)
T 3qrx_A           26 QKQEIREAFDLFDTDGSGTIDAK-----ELKVAMRALGFEP   61 (169)
T ss_dssp             HHHHHHHHHHHHCTTCCSEECHH-----HHHHHHHHTSCCC
T ss_pred             HHHHHHHHHHHhCCCCCCcCcHH-----HHHHHHHHcCCCC
Confidence            34556666667777777777754     5677788888765

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=81.43  E-value=3.4  Score=31.96  Aligned_cols=52  Identities=19%  Similarity=0.336  Sum_probs=42.2

Q ss_pred             ccchhHHHHHHHHH-----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQ-----AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~-----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .|+..+..||-...     ...++|+++|++.+|.+..-+..+|+.|+++|++=+..
T Consensus        29 gLt~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~   85 (128)
T 2vn2_A           29 GLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEE   85 (128)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            56666666654432     24569999999999999999999999999999998853

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=81.33  E-value=3  Score=33.40  Aligned_cols=76  Identities=20%  Similarity=0.315  Sum_probs=52.2

Q ss_pred             CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025606          137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL  216 (250)
Q Consensus       137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~  216 (250)
                      .+...|+..+.+.|+.|+++                     -...||.+.. .|-+|+.+|++.+|.+..-+...|..|.
T Consensus        39 ~~~~~~~~~~~~~l~aL~~p---------------------~R~~IL~~L~-~~~~t~~eLa~~lgls~stvs~hL~~L~   96 (151)
T 3f6v_A           39 ALVTTNVLVVLDQLEVAAEP---------------------TRRRLVQLLT-SGEQTVNNLAAHFPASRSAISQHLRVLT   96 (151)
T ss_dssp             ---------CCCHHHHHTSH---------------------HHHHHHHHGG-GCCEEHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             hhhhccHHHHHHHHHHhCCH---------------------HHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45666666666777776642                     2455777776 5779999999999999999999999999


Q ss_pred             HcCCceeecCCCCCCcceeec
Q 025606          217 EEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       217 ~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      +.|++......   ...||..
T Consensus        97 ~aGlV~~~~~G---r~~~y~l  114 (151)
T 3f6v_A           97 EAGLVTPRKDG---RFRYYRL  114 (151)
T ss_dssp             HTTSEEEEEET---TEEEEEE
T ss_pred             HCCCEEEEecC---CEEEEEE
Confidence            99999987543   4555553

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=81.30  E-value=5.1  Score=29.87  Aligned_cols=46  Identities=20%  Similarity=0.188  Sum_probs=38.7

Q ss_pred             HHHHHHHhCCCccHHHHHHhc-CCChHHHHHHHHHHHHcCCceeecCC
Q 025606          181 QILELAQAQGFVTVDEVERRL-SWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       181 ~vLela~~~g~vt~~~L~~~l-~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .||..... |.+|..+|++.+ +.+..-.-..|..|++.|++-+....
T Consensus        26 ~IL~~L~~-~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~   72 (112)
T 1z7u_A           26 SLMDELFQ-GTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFN   72 (112)
T ss_dssp             HHHHHHHH-SCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEEC
T ss_pred             HHHHHHHh-CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            35555444 789999999999 99999999999999999999876543

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=80.60  E-value=2.6  Score=33.03  Aligned_cols=48  Identities=17%  Similarity=0.230  Sum_probs=38.2

Q ss_pred             ccchhHHHHHHHHHh-----CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          174 ELNKDHNQILELAQA-----QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       174 El~~D~~~vLela~~-----~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      .|+.-|-.+|.....     .|.+|+.+|++.++.++.-.-..|+.|++.|++
T Consensus        30 gLt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glV   82 (148)
T 4fx0_A           30 GLTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLV   82 (148)
T ss_dssp             TCCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHTTSB
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCE
Confidence            356667778876653     356999999999999999999999999999987

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=80.57  E-value=4.9  Score=29.72  Aligned_cols=44  Identities=20%  Similarity=0.123  Sum_probs=37.8

Q ss_pred             HHHHHHhCCCccHHHHHHhc-CCChHHHHHHHHHHHHcCCceeecC
Q 025606          182 ILELAQAQGFVTVDEVERRL-SWTSGRAIDALDILLEEGLAMVDDG  226 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l-~W~~~Ra~~~L~~l~~~Gl~WvD~q  226 (250)
                      ||.... .|-.+..+|++.+ |.+..-.-..|..|++.|++=+-..
T Consensus        19 IL~~L~-~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~   63 (107)
T 2hzt_A           19 ILXHLT-HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVY   63 (107)
T ss_dssp             HHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHH-hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            555444 5789999999999 9999999999999999999986543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	250
d1u5ta1	145	a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8	9e-73
d1u5ta2	68	a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8	2e-23

>d1u5ta1 a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 145

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  216 bits (552), Expect = 9e-73
 Identities = 51/152 (33%), Positives = 92/152 (60%), Gaps = 7/152 (4%)

Query: 23  LGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASN 82
           + + + + ++  +++QL  F+ +L +FA+KH ++++ +P FRS+F  MC+ +G+DPL+  
Sbjct: 1   VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLF 60

Query: 83  KGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDD 142
                 L  + DFYYE+ ++++EIC  T+  NGG+I+ QEL  +  ++       V  DD
Sbjct: 61  DR-DKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRKLN-----VGLDD 114

Query: 143 CLRAISKLKVLGNGYEVISVGKKKLVRSVPTE 174
             ++I  LK L   +E+  +  KK +RSVP E
Sbjct: 115 LEKSIDMLKSLE-CFEIFQIRGKKFLRSVPNE 145

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 88.2 bits (219), Expect = 2e-23
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRY 234
           L  D  +ILE+    G+ ++  ++  L W + R+  ALD ++  GL  +D      +  Y
Sbjct: 1   LTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDY-QGGAEALY 59

Query: 235 WFPC 238
           W P 
Sbjct: 60  WDPS 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	250
d1u5ta1	145	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	100.0
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	99.94
d1u5tb1	94	Vacuolar protein sorting-associated protein VPS36	99.61
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.54
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.35
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.44
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.03
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	93.92
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	93.57
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	93.47
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	93.17
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	92.79
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.68
d1okra_	120	Methicillin resistance regulatory protein MecI {St	92.52
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.38
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	92.32
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	92.28
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	92.27
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	92.26
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	91.94
d2htja1	73	P fimbrial regulatory protein PapI {Escherichia co	91.64
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.32
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	91.06
d1wdcc_	152	Myosin Regulatory Chain {Bay scallop (Aequipecten	90.95
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	90.88
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	90.59
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	90.35
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	90.12
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	89.86
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	89.52
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	89.24
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	88.94
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	88.92
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	88.86
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	88.72
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	88.63
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	88.47
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	88.24
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	88.21
d1u5tb2	75	Vacuolar protein sorting-associated protein VPS36	88.04
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	87.85
d1t6sa1	85	Segregation and condensation protein B, ScpB {Chlo	87.24
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	86.85
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	86.74
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	86.53
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	86.31
d1wdcb_	142	Myosin Essential Chain {Bay scallop (Aequipecten i	85.97
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	85.97
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	85.81
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	85.75
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	85.71
d2mysb_	145	Myosin Essential Chain {Chicken (Gallus gallus) [T	85.29
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	85.19
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	84.93
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	84.81
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	84.38
d1lkja_	146	Calmodulin {Baker's yeast (Saccharomyces cerevisia	83.54
d1ggwa_	140	Cdc4p {Fission yeast (Schizosaccharomyces pombe) [	81.8
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	80.65
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	80.22

>d1u5ta1 a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.1e-63  Score=408.70  Aligned_cols=145  Identities=35%  Similarity=0.677  Sum_probs=138.2

Q ss_pred             hcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHH
Q 025606           23 LGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQ  102 (250)
Q Consensus        23 ~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavq  102 (250)
                      +|.+|.++|+++|++||++||++|++||++|++||++||+||++|++||++||||||+|+++ |+++||+||||||||||
T Consensus         1 l~~~l~e~q~~ql~~QL~vF~~~L~~FA~kH~~eI~~np~FR~~F~~MC~~iGVDPLas~~~-~~~~lg~gDFYyEL~Vq   79 (145)
T d1u5ta1           1 VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFDR-DKHLFTVNDFYYEVCLK   79 (145)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTTTCHHHHHHHHHHHHHHTCCHHHHTTS-SGGGTTHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhcCHHHHHHHHHHHHHhCCChhhcCCC-ccccccccchHHHHHHH
Confidence            47889999999999999999999999999999999999999999999999999999999988 55699999999999999


Q ss_pred             HHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCc
Q 025606          103 IVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTE  174 (250)
Q Consensus       103 IvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~E  174 (250)
                      |||||++||++|||||+|+||+.++.|++     .||++||+|||++|++|| ||+|+++||++||||||.|
T Consensus        80 IvEvC~~tr~~NGGli~l~el~~~~~~~~-----~is~dDi~rAi~~L~~Lg-G~~v~~iggk~~v~SVP~E  145 (145)
T d1u5ta1          80 VIEICRQTKDMNGGVISFQELEKVHFRKL-----NVGLDDLEKSIDMLKSLE-CFEIFQIRGKKFLRSVPNE  145 (145)
T ss_dssp             HHHHHHHHTTTSSSCEEHHHHHHTTTTTT-----TCCHHHHHHHHHHHTTTC-CCCEEEETTEEEECCSSSC
T ss_pred             HHHHHHHhhhcCCCEeEHHHHHHHHHhhc-----CCCHHHHHHHHHhhcccC-CcEEEEECCEEEEEeCCCC
Confidence            99999999999999999999998877754     499999999999999996 9999999999999999987

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=8.8e-28  Score=173.15  Aligned_cols=67  Identities=27%  Similarity=0.508  Sum_probs=64.3

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCC
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSI  242 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~  242 (250)
                      ||+||++||++|+..||||+++|++++||++.||+.+|++|+++|++|||+|++ +|+.|||||||..
T Consensus         1 Ls~Dqt~vLe~a~~~G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD~Q~~-~e~~YWfPsl~~~   67 (68)
T d1u5ta2           1 LTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGG-AEALYWDPSWITR   67 (68)
T ss_dssp             CCTTHHHHHHTTTTTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSS-SSCEEECGGGGGC
T ss_pred             CCchHHHHHHHHHHcCceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEecCCC-CCceeeChHhhcc
Confidence            699999999999999999999999999999999999999999999999999985 4999999999975

>d1u5tb1 a.4.5.54 (B:396-489) Vacuolar protein sorting-associated protein VPS36 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar protein sorting-associated protein VPS36
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.61  E-value=1e-15  Score=115.76  Aligned_cols=78  Identities=19%  Similarity=0.242  Sum_probs=71.5

Q ss_pred             ccchhhhHHHHHHHhhhhcccCCC-----ceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCC-CeEEEEEC-CE
Q 025606           93 GDFYYELGVQIVEICLATRPHNGG-----LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGN-GYEVISVG-KK  165 (250)
Q Consensus        93 gdfy~eLavqIvevC~~tr~~nGG-----li~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~-g~~vi~ig-~~  165 (250)
                      +-||-|||.||.|+|....+..||     ||+|.||+|++||+|+.+.+.|||+|+++||+.++.|+- ++++.+++ |.
T Consensus        10 ~lyh~ELArqlae~l~~~~k~~~g~~~~~mItL~Dly~~~NRaR~~G~eLiSP~D~~~Ac~~~e~l~L~p~~Lr~f~sgv   89 (94)
T d1u5tb1          10 ELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGLISPMEMREACERFEHLGLNELKLVKVNKRI   89 (94)
T ss_dssp             TTHHHHHHHHHHHHHHTTTTTSSSCCCCCCEETTHHHHHHHHTTTSSSCCCCHHHHHHHHTTTGGGTCCSCEEEEETTTE
T ss_pred             hHHHHHHHHHHHHHHHhhhhhhCCCCCcceeeHHHHHHHHHHhhhcCCcccCHHHHHHHHHHHHhCCCCceEEEEecCce
Confidence            689999999999999998887666     999999999999999544799999999999999999996 99999998 88


Q ss_pred             EEEEe
Q 025606          166 KLVRS  170 (250)
Q Consensus       166 ~~v~s  170 (250)
                      .+|||
T Consensus        90 lvv~s   94 (94)
T d1u5tb1          90 LCVTS   94 (94)
T ss_dssp             EEEES
T ss_pred             EEeeC
Confidence            88876

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.54  E-value=0.012  Score=43.15  Aligned_cols=50  Identities=24%  Similarity=0.379  Sum_probs=45.1

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      |+.-|..|+...-..|..|+.+|++.+|++...+..+|+.|++.|++=+-
T Consensus        18 lt~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          18 FKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEE
Confidence            46678888888878899999999999999999999999999999999754

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=95.35  E-value=0.016  Score=39.83  Aligned_cols=52  Identities=21%  Similarity=0.383  Sum_probs=44.6

Q ss_pred             ccchhHHHHHHHHH----hCC-CccHHHHHHhcCC-ChHHHHHHHHHHHHcCCceeec
Q 025606          174 ELNKDHNQILELAQ----AQG-FVTVDEVERRLSW-TSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       174 El~~D~~~vLela~----~~g-~vt~~~L~~~l~W-~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      -|+.-|..||+++.    ..| ..|..+|++.+|| |+.-+...|..|++.|++=.+.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCC
Confidence            47788999999877    245 4999999999999 7889999999999999887764

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.44  E-value=0.038  Score=36.51  Aligned_cols=43  Identities=19%  Similarity=0.316  Sum_probs=40.2

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      ..++|.+.+..|.+|.++|++.+|.+..-+..++..|+++|++
T Consensus         5 D~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI   47 (60)
T d1i1ga1           5 DKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGII   47 (60)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            4578998998999999999999999999999999999999986

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=94.03  E-value=0.063  Score=35.72  Aligned_cols=48  Identities=15%  Similarity=0.227  Sum_probs=43.1

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      |+.-..++|+..+..|.+|..+|++.+|.+..-+..++..|+++|.+-
T Consensus         3 lD~~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1           3 LDQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (63)
T ss_dssp             CCHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            455566789999989999999999999999999999999999999873

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.92  E-value=0.054  Score=36.12  Aligned_cols=43  Identities=12%  Similarity=0.191  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA  221 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~  221 (250)
                      ...+|++.+..+++|.++|++.+|-|..-+...|..|.+.|+.
T Consensus         7 ~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           7 PLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             HHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            4568999999999999999999999999999999999999974

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=93.57  E-value=0.12  Score=38.52  Aligned_cols=58  Identities=21%  Similarity=0.224  Sum_probs=49.7

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      |.+|+..|-.+|......|.+|+++|++.++.++.-+-..+..|++.|++-+-....+
T Consensus        29 ~~~Lt~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~D   86 (138)
T d1jgsa_          29 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPND   86 (138)
T ss_dssp             TTTSCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTC
T ss_pred             HcCCCHHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccCC
Confidence            4457888888998888778899999999999999999999999999999987544433

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=93.47  E-value=0.077  Score=35.16  Aligned_cols=44  Identities=11%  Similarity=0.170  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ..++|++.+..+..|..+|++.+|.|..-+..+++.|+++|++=
T Consensus         7 D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           7 DRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            45688888988999999999999999999999999999999763

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=93.17  E-value=0.11  Score=36.76  Aligned_cols=50  Identities=16%  Similarity=0.196  Sum_probs=43.6

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      +.-+..||.+....|.+|+.+|++.++++..-.-..|..|++.|++=.-.
T Consensus        15 ~p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~   64 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYK   64 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEE
Confidence            34466788888777899999999999999999999999999999996653

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.79  E-value=0.12  Score=35.30  Aligned_cols=49  Identities=24%  Similarity=0.346  Sum_probs=43.7

Q ss_pred             ccchhHHHHHHHHHh---CCCccHHHHHHhc-CCChHHHHHHHHHHHHcCCce
Q 025606          174 ELNKDHNQILELAQA---QGFVTVDEVERRL-SWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       174 El~~D~~~vLela~~---~g~vt~~~L~~~l-~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      -|+.-|.+||.+.+.   .-.+++.+|++.| |.+....+.+++.|..+|.+.
T Consensus         3 GLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IY   55 (69)
T d1dpua_           3 GLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY   55 (69)
T ss_dssp             CSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCcee
Confidence            477889999999884   3468999999999 899999999999999999998

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.68  E-value=0.12  Score=33.71  Aligned_cols=44  Identities=16%  Similarity=0.293  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ..++|++.+..+.+|..+|++.+|-+..-+..++..|+++|.+-
T Consensus         5 D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           5 DKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            35688999989999999999999999999999999999999864

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.52  E-value=0.13  Score=37.86  Aligned_cols=64  Identities=8%  Similarity=0.264  Sum_probs=53.6

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhc----CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRL----SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l----~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      +-+|+.-+..|+.+.=..|.+|+.++.+.+    +|+..=..+.|+.|++.|++=+....   ...+|+|.
T Consensus         2 ~~~lt~~E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~g---r~~~Y~~~   69 (120)
T d1okra_           2 TYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDN---KIFQYYSL   69 (120)
T ss_dssp             CCCCCHHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEET---TEEEEEES
T ss_pred             CCCCCHHHHHHHHHHHcCCCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEecC---CceEEeec
Confidence            346788888999988878899999977765    89999999999999999999887654   57777775

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.38  E-value=0.2  Score=37.39  Aligned_cols=61  Identities=16%  Similarity=0.214  Sum_probs=47.8

Q ss_pred             chhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          176 NKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       176 ~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      +.-+-.|+.+.- ..+.+|+.+|++.+|-++.-+-..|..|++.|++.+....++ .+.||.+
T Consensus        25 ~~~~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~d-rr~~~~~   86 (151)
T d1ku9a_          25 NKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYEA   86 (151)
T ss_dssp             CHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCC-CceeEEe
Confidence            334566776654 345699999999999999999999999999999998866643 4555553

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.32  E-value=0.31  Score=36.32  Aligned_cols=56  Identities=14%  Similarity=0.206  Sum_probs=48.8

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .|+.-|..||......+.+|+++|++.++.++.-+-..|+.|++.|++-......+
T Consensus        33 ~lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~~D   88 (141)
T d1lnwa_          33 DLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSD   88 (141)
T ss_dssp             CCCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSS
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccCCC
Confidence            56777888998887666689999999999999999999999999999988766544

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=92.28  E-value=0.36  Score=34.47  Aligned_cols=77  Identities=13%  Similarity=0.149  Sum_probs=61.7

Q ss_pred             CCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHH
Q 025606          135 REAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDI  214 (250)
Q Consensus       135 ~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~  214 (250)
                      ++.++|+.+....+.++.||.+-                     -..||.+... |-.|+.+|++.+|.+..-.-.-|..
T Consensus         2 ~~~~~pe~~~~la~~~kaL~~p~---------------------Rl~Il~~L~~-~~~~v~ela~~l~is~stvS~HL~~   59 (98)
T d1r1ta_           2 LQAIAPEVAQSLAEFFAVLADPN---------------------RLRLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRS   59 (98)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCCHH---------------------HHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHHhCCHH---------------------HHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            35688998888889999988643                     2346766654 5689999999999999999999999


Q ss_pred             HHHcCCceeecCCCCCCcceee
Q 025606          215 LLEEGLAMVDDGHRDRKRRYWF  236 (250)
Q Consensus       215 l~~~Gl~WvD~q~~~~e~~Yw~  236 (250)
                      |...|++....+.   ...||.
T Consensus        60 L~~aglV~~~r~G---~~~~Y~   78 (98)
T d1r1ta_          60 LRNLRLVSYRKQG---RHVYYQ   78 (98)
T ss_dssp             HHHTTSEEEEEET---TEEEEE
T ss_pred             HHHCCceEEEEEC---CEEEEE
Confidence            9999999887554   455665

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=92.27  E-value=0.12  Score=34.69  Aligned_cols=44  Identities=9%  Similarity=0.175  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ...||++....|.+|..+|++.+|-+..=+...+..|+++|++-
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            34689999988999999999999999999999999999999875

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=92.26  E-value=0.16  Score=36.54  Aligned_cols=54  Identities=15%  Similarity=0.251  Sum_probs=44.3

Q ss_pred             ccchhHHHHHH-HHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILE-LAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLe-la~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-+-.||. +.+..|.+|+++|++.++.++.-+...|+.|+..|++-.....
T Consensus        18 gLs~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~~   72 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE   72 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             CcCHHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEeecC
Confidence            35555666775 5566788999999999999999999999999999999776443

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.94  E-value=0.21  Score=36.98  Aligned_cols=64  Identities=16%  Similarity=0.177  Sum_probs=52.8

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      .|+..|-.+|......+.+|+++|++.++.++.-.-..++.|++.|++-+-....|+...|.++
T Consensus        31 glt~~q~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~l   94 (136)
T d2bv6a1          31 NLTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHL   94 (136)
T ss_dssp             TCCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEE
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCCcccchhhcc
Confidence            4677888899998888889999999999999999999999999999998766554433444443

>d2htja1 a.4.5.73 (A:1-73) P fimbrial regulatory protein PapI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FaeA-like
domain: P fimbrial regulatory protein PapI
species: Escherichia coli [TaxId: 562]

Probab=91.64  E-value=0.41  Score=32.44  Aligned_cols=57  Identities=25%  Similarity=0.272  Sum_probs=48.0

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      ..||++....+.-+..++++.+|.+...|+--|..|+++|++=+---- .|-.-|||-
T Consensus         3 n~Il~fl~~~~~~~T~EIAea~gvsaYQARyYL~~Lekegki~RsPlR-rGa~TlW~~   59 (73)
T d2htja1           3 NEILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLR-RGMATYWFL   59 (73)
T ss_dssp             HHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCS-SSSSCEEEE
T ss_pred             hHHHHHHHhcCCccHHHHHHHhhhHHHHHHHHHHHHHHhcCcccChhh-hhhHHHHHH
Confidence            458999887555589999999999999999999999999999887544 347889984

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=91.32  E-value=0.27  Score=36.37  Aligned_cols=57  Identities=18%  Similarity=0.174  Sum_probs=49.3

Q ss_pred             CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCC
Q 025606          172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHR  228 (250)
Q Consensus       172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~  228 (250)
                      |..|+..|-.+|......|.+|+.+|++.+++++.-.-.+++.|++.|++=+.....
T Consensus        28 ~~gLt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~   84 (137)
T d1z91a1          28 KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEE   84 (137)
T ss_dssp             TTCCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSS
T ss_pred             HcCcCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecCC
Confidence            346788888899888877889999999999999999999999999999997665543

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=91.06  E-value=0.18  Score=33.35  Aligned_cols=41  Identities=15%  Similarity=0.299  Sum_probs=37.1

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      |+++.+..|.|+..+|++.+|-++.=+-..+..|.++|++=
T Consensus        12 I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~   52 (61)
T d2ev0a1          12 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLI   52 (61)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            56666678999999999999999999999999999999863

>d1wdcc_ a.39.1.5 (C:) Myosin Regulatory Chain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Myosin Regulatory Chain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=90.95  E-value=0.89  Score=33.56  Aligned_cols=93  Identities=14%  Similarity=0.281  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHHH--hcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccC
Q 025606           37 EQLATFRSQLEDFAR--KHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHN  114 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~--~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~n  114 (250)
                      .|+..|++....|-.  .+.+.|..+     +|+.++.++|+.|-  .                  .+|-++ ...-..+
T Consensus         4 eqi~~l~~~F~~fD~~~~~dG~I~~~-----el~~~l~~lG~~~t--~------------------~e~~~~-~~~~~~~   57 (152)
T d1wdcc_           4 DEIDDLKDVFELFDFWDGRDGAVDAF-----KLGDVCRCLGINPR--N------------------EDVFAV-GGTHKMG   57 (152)
T ss_dssp             HHHHHHHHHHHHHHHHTCSSSCEEGG-----GHHHHHHHTTCCCC--H------------------HHHHHT-TCCSSTT
T ss_pred             HHHHHHHHHHHHHCcCCCCCCeECHH-----HHHHHHHHhccCcc--H------------------hhhhhh-hhhhccc
Confidence            456667777777754  445677665     45688889998872  1                  011122 2233445


Q ss_pred             CCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025606          115 GGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY  157 (250)
Q Consensus       115 GGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~  157 (250)
                      .|.|++.+.+..+.+...  ...-+.++|.+|.+.+-.=|+|+
T Consensus        58 ~~~i~~~eFl~~~~~~~~--~~~~~~~~l~~aF~~~D~~~~G~   98 (152)
T d1wdcc_          58 EKSLPFEEFLPAYEGLMD--CEQGTFADYMEAFKTFDREGQGF   98 (152)
T ss_dssp             SCEECHHHHHHHHHHHTT--SCCCCHHHHHHHHHTTCSSSSSE
T ss_pred             cccccccccccccccccc--cchhHHHhhhhhhhccccccCcc
Confidence            678999999888776543  24567889999999888777775

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.88  E-value=0.2  Score=37.04  Aligned_cols=54  Identities=11%  Similarity=0.134  Sum_probs=47.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+..|-.+|......|.+|+.+|++.+++++.-+-..|+.|++.|++-.-...
T Consensus        27 glt~~q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~   80 (136)
T d2fbia1          27 GLTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP   80 (136)
T ss_dssp             TCCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            467778889988887889999999999999999999999999999999655433

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=90.59  E-value=0.42  Score=32.73  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=36.5

Q ss_pred             CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      ..++|+-.|+.++|.++-.+-.+|-.|.+.|.+..-...
T Consensus        22 ~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~t   60 (70)
T d1sfua_          22 NDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   60 (70)
T ss_dssp             TCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             CCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCCc
Confidence            679999999999999999999999999999999988776

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=90.35  E-value=0.47  Score=35.00  Aligned_cols=57  Identities=18%  Similarity=0.191  Sum_probs=50.0

Q ss_pred             CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .+|+..|..+|......|.+|+.+|++.++-++.-+-..+..|++.|++-+=....|
T Consensus        28 ~~lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D   84 (140)
T d2etha1          28 SDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVD   84 (140)
T ss_dssp             HHSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTT
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccc
Confidence            367888888998888778899999999999999999999999999999987655544

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=90.12  E-value=0.64  Score=33.90  Aligned_cols=56  Identities=18%  Similarity=0.147  Sum_probs=46.7

Q ss_pred             ccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .|+..|-.||.+...  .+.+|+.+|++.++.++..+-.+|+.|++.|++-+-....+
T Consensus        26 glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D   83 (135)
T d3broa1          26 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKD   83 (135)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhhh
Confidence            567888888876663  46699999999999999999999999999999976654433

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=89.86  E-value=0.54  Score=34.45  Aligned_cols=55  Identities=18%  Similarity=0.073  Sum_probs=45.1

Q ss_pred             cchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          175 LNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       175 l~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      |+.-|-.+|-... ..+.+|+++|++.+++++.-+-..++.|++.|++-.-....|
T Consensus        26 lt~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~D   81 (137)
T d2fbha1          26 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAED   81 (137)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTT
T ss_pred             CCHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCCC
Confidence            4556777775554 455689999999999999999999999999999997765543

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.52  E-value=0.46  Score=34.97  Aligned_cols=56  Identities=7%  Similarity=0.167  Sum_probs=48.5

Q ss_pred             ccchhHHHHHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      +|+..|..||....  ..|.+|+.+|++.+++++..+-..|+.|++.|++=+-....|
T Consensus        31 ~Lt~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D   88 (125)
T d1p4xa1          31 DMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKID   88 (125)
T ss_dssp             SSCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSS
T ss_pred             CCCHHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeecccCC
Confidence            68888999988765  356799999999999999999999999999999988766544

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.24  E-value=0.39  Score=31.93  Aligned_cols=44  Identities=16%  Similarity=0.189  Sum_probs=38.7

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      |+++-+..|.|+..+|++.+|-++.=+-..+..|.++|++=.+.
T Consensus        14 I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          14 IYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEEcC
Confidence            55666678999999999999999999999999999999886553

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.94  E-value=0.42  Score=31.96  Aligned_cols=44  Identities=16%  Similarity=0.182  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ...||.+....|.+|..+|++.+|-+..-....+++|+++|++=
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~   50 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQ   50 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44589999999999999999999999999999999999999764

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=88.92  E-value=1  Score=31.05  Aligned_cols=63  Identities=11%  Similarity=0.217  Sum_probs=50.7

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHH----hcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVER----RLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA  239 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~----~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l  239 (250)
                      .|+.-...|+++.=.+|-+|+.++.+    ..+|+..=.++.|..|++.|++=++.+.   ...+|.|..
T Consensus         6 ~Ls~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~g---r~~~Y~p~i   72 (82)
T d1p6ra_           6 QISDAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEG---RVFVYTPNI   72 (82)
T ss_dssp             CCCHHHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEET---TEEEEEESC
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEecC---CeEEEEecC
Confidence            57777778888877788999999754    4599999999999999999999888765   455555543

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=88.86  E-value=0.32  Score=35.97  Aligned_cols=53  Identities=13%  Similarity=0.081  Sum_probs=45.9

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |+.-|-.+|......|.+|+++|++.++.++.-.-..|+.|++.|++-.=...
T Consensus        28 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~   80 (139)
T d2a61a1          28 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDP   80 (139)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeecc
Confidence            46668888888877788999999999999999999999999999999765443

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.72  E-value=0.71  Score=34.04  Aligned_cols=56  Identities=16%  Similarity=0.255  Sum_probs=47.5

Q ss_pred             ccchhHHHHHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .|+..|-.||....  ..+.+|+.+|++.+++++..+-..++.|++.|++-+-....|
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D   87 (125)
T d1p4xa2          30 TLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTED   87 (125)
T ss_dssp             SSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSS
T ss_pred             CCCHHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCC
Confidence            57777888888775  456799999999999999999999999999999987655533

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.63  E-value=0.29  Score=35.66  Aligned_cols=76  Identities=16%  Similarity=0.099  Sum_probs=57.6

Q ss_pred             CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025606          138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE  217 (250)
Q Consensus       138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~  217 (250)
                      +.++|+.++.+.++.||++-                     -..||......|-.|+.+|++.+|.+..-+-.-|..|..
T Consensus        13 l~~~d~~~~~~~~kaLadp~---------------------Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~   71 (108)
T d1u2wa1          13 LQTVDISGVSQILKAIADEN---------------------RAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYK   71 (108)
T ss_dssp             HHTTTHHHHHHHHHHHHSHH---------------------HHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cChhhHHHHHHHHHHhCCHH---------------------HHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHH
Confidence            56778888889989888632                     334776544457789999999999999999999999999


Q ss_pred             cCCceeecCCCCCCcceeec
Q 025606          218 EGLAMVDDGHRDRKRRYWFP  237 (250)
Q Consensus       218 ~Gl~WvD~q~~~~e~~Yw~P  237 (250)
                      .|++=.-.+.   ...||..
T Consensus        72 aGlv~~~r~G---~~~~Y~l   88 (108)
T d1u2wa1          72 QGVVNFRKEG---KLALYSL   88 (108)
T ss_dssp             TTSEEEC-------CCEEEE
T ss_pred             CCeeEEEEEC---CEEEEEE
Confidence            9998776544   5666654

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.47  E-value=0.68  Score=34.32  Aligned_cols=56  Identities=18%  Similarity=0.095  Sum_probs=46.5

Q ss_pred             CCccchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +..++.-|-.+|.... ..|-+|+.+|++.+|+++.-+-..|+.|++.|++=+-...
T Consensus        29 ~~glt~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~   85 (145)
T d2hr3a1          29 ADPVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   85 (145)
T ss_dssp             CCHHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             hcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCc
Confidence            4567777888887665 4577999999999999999999999999999999766544

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.24  E-value=0.72  Score=33.36  Aligned_cols=58  Identities=17%  Similarity=0.121  Sum_probs=48.5

Q ss_pred             CCccchhHHHHHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          172 PTELNKDHNQILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       172 p~El~~D~~~vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      +-.|+..|-.||....  ..+.+|+.+|++.++.++..+-.+|+.|++.|++=+-....|
T Consensus        27 ~~~Lt~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~D   86 (115)
T d1hsja1          27 KFNLNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQD   86 (115)
T ss_dssp             SCCCCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSS
T ss_pred             hcCCCHHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecCC
Confidence            4467888888888765  467899999999999999999999999999999986655433

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.21  E-value=0.65  Score=34.10  Aligned_cols=56  Identities=18%  Similarity=0.175  Sum_probs=45.0

Q ss_pred             CCccchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          172 PTELNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       172 p~El~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      |..++..|-.+|.... ..+.+|+.+|.+.++.++.-+-..|..|++.|++-+=...
T Consensus        26 ~~glt~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~   82 (140)
T d3deua1          26 PLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA   82 (140)
T ss_dssp             TTTCCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             HcCCCHHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccC
Confidence            3356777877887665 4678999999999999999999999999999999854433

>d1u5tb2 a.4.5.54 (B:490-564) Vacuolar protein sorting-associated protein VPS36 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar protein sorting-associated protein VPS36
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.04  E-value=0.87  Score=31.06  Aligned_cols=58  Identities=17%  Similarity=0.303  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhc-------CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          179 HNQILELAQAQGFVTVDEVERRL-------SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l-------~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      ..+++.+++....+..-.|...|       +|+..-..++|.--+++|-+-+|+|.+  ...||+-+
T Consensus         7 k~ki~~~i~~~pG~DlLqlT~~ln~~~~~nnW~iGvi~EVlqncv~eG~lliDeQiS--Gi~YY~N~   71 (75)
T d1u5tb2           7 KEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLS--GIYYYKNS   71 (75)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECSS--CEEEEECC
T ss_pred             HHHHHHHHhcCCCccHHHHHHHHcccCCcccchHHHHHHHHHHHHhccceeeehhhc--ceeeeeec
Confidence            45688888865555555554443       599999999999999999999999994  24444433

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=87.85  E-value=0.34  Score=37.54  Aligned_cols=54  Identities=19%  Similarity=0.154  Sum_probs=47.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      .|+.-|-.||.+....|.+|+.+|++.++.++.-+-.++..|++.|++=+-...
T Consensus        38 ~Lt~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~   91 (162)
T d2fxaa1          38 DLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   91 (162)
T ss_dssp             TCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCCHHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeeccc
Confidence            557778889988887788999999999999999999999999999999775443

>d1t6sa1 a.4.5.60 (A:1-85) Segregation and condensation protein B, ScpB {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ScpB/YpuH-like
domain: Segregation and condensation protein B, ScpB
species: Chlorobium tepidum [TaxId: 1097]

Probab=87.24  E-value=0.6  Score=32.41  Aligned_cols=61  Identities=15%  Similarity=0.257  Sum_probs=47.7

Q ss_pred             HHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecC
Q 025606          102 QIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVP  172 (250)
Q Consensus       102 qIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp  172 (250)
                      ++||.++=.   .|.=+++++|...+.       ..+|+++|..+++.|+.    -+.||+|+.++|.+-+++-|
T Consensus        10 ~~IEAlLFa---s~~Pls~~~L~~~l~-------~~~~~~~i~~~l~~L~~~y~~~~~g~el~~~~~gy~~~tk~   74 (85)
T d1t6sa1          10 RSLEALIFS---SEEPVNLQTLSQITA-------HKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEP   74 (85)
T ss_dssp             HHHHHHHHH---CSSCBCHHHHHHHTT-------CCCCHHHHHHHHHHHHHHHHHHTCSEEEEEETTEEEEEECG
T ss_pred             HHHHHHHHh---cCCCCCHHHHHHHHc-------cCCCHHHHHHHHHHHHHHHhcCCCcEEEEEECCEEEEEEhH
Confidence            456665554   355688889876654       25899999999999873    57899999999998888887

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=86.85  E-value=0.27  Score=34.27  Aligned_cols=38  Identities=13%  Similarity=0.116  Sum_probs=35.3

Q ss_pred             hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .+|.+|+.+|++.++.++...-..|+.|+++|++-+..
T Consensus        18 ~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~   55 (85)
T d3ctaa1          18 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTV   55 (85)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeec
Confidence            36899999999999999999999999999999999853

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.74  E-value=0.8  Score=31.47  Aligned_cols=53  Identities=9%  Similarity=0.016  Sum_probs=45.7

Q ss_pred             chhHHHHHHHHHhCCCccHHHHHHhcCCChHH-HHHHHHHHHHcCCceeecCCC
Q 025606          176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGR-AIDALDILLEEGLAMVDDGHR  228 (250)
Q Consensus       176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~R-a~~~L~~l~~~Gl~WvD~q~~  228 (250)
                      ..-+.+|+++....|--|+-.|+.++|-++.+ .-.+|-.|.+.|.+...+..|
T Consensus         4 ~d~eekI~~~L~~~g~~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~~~tP   57 (73)
T d1xmka1           4 AEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTP   57 (73)
T ss_dssp             HHHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECSSS
T ss_pred             HHHHHHHHHHHHHcCCchHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecCCCCC
Confidence            34466799999988889999999999999976 888999999999999876653

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=86.53  E-value=1.1  Score=33.30  Aligned_cols=56  Identities=13%  Similarity=0.140  Sum_probs=48.1

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD  229 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~  229 (250)
                      .|+..|-.+|......+.+|+.+|++.++.++.-.-..|..|++.|++-+-....|
T Consensus        26 ~lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~D   81 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASN   81 (144)
T ss_dssp             TCTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCCCC
Confidence            56777888887777667799999999999999999999999999999987765533

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MerB N-terminal domain-like
domain: Alkylmercury lyase MerB
species: Escherichia coli [TaxId: 562]

Probab=86.31  E-value=0.23  Score=33.02  Aligned_cols=35  Identities=17%  Similarity=0.223  Sum_probs=29.7

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL  216 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~  216 (250)
                      +|.....+.-||++.|+..+||+.++.+.+|+.|-
T Consensus         7 LLr~LA~G~PVs~~~LA~alg~~~~eV~~aL~~~p   41 (60)
T d1s6la1           7 LLRELAKGRPVSRTTLAGILDWPAERVAAVLEQAT   41 (60)
T ss_dssp             HHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             HHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHhCC
Confidence            45555566789999999999999999999998764

>d1wdcb_ a.39.1.5 (B:) Myosin Essential Chain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Myosin Essential Chain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=85.97  E-value=1.9  Score=31.34  Aligned_cols=90  Identities=11%  Similarity=0.207  Sum_probs=59.2

Q ss_pred             HHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCC
Q 025606           36 KEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNG  115 (250)
Q Consensus        36 ~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nG  115 (250)
                      .+|++.|+.....|=..+.+.|..+     .|+.+..++|.+|-..      +              |-++.    ..+.
T Consensus         3 ~~qi~e~~~~F~~~D~d~~G~I~~~-----el~~~l~~lg~~~~~~------e--------------l~~~~----~~~~   53 (142)
T d1wdcb_           3 QKQIQEMKEAFSMIDVDRDGFVSKE-----DIKAISEQLGRAPDDK------E--------------LTAML----KEAP   53 (142)
T ss_dssp             HHHHHHHHHHHHHHCTTCSSSCCHH-----HHHHHHHHHSSCCCHH------H--------------HHHHH----TTSS
T ss_pred             HHHHHHHHHHHHHHcCCCCCcCChH-----HHHHHHHHhhcCCCHH------H--------------HHHHH----Hhcc
Confidence            3578888888889988999888875     5778888999987420      1              11111    2345


Q ss_pred             CceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025606          116 GLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY  157 (250)
Q Consensus       116 Gli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~  157 (250)
                      |-|+..+.+..+.+...   ..-++++|.+|.+.+-.=|+|+
T Consensus        54 ~~i~~~eF~~~~~~~~~---~~~~~~~l~~aF~~~D~d~~G~   92 (142)
T d1wdcb_          54 GPLNFTMFLSIFSDKLS---GTDSEETIRNAFAMFDEQETKK   92 (142)
T ss_dssp             SCCCHHHHHHHHHHHTC---SCCCHHHHHHHHHTTCTTCCSC
T ss_pred             Ccccccccccccccccc---ccchhhhHHHhhhhhcccCCCc
Confidence            67888887777665422   2345677777777765555554

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.97  E-value=0.7  Score=30.31  Aligned_cols=42  Identities=14%  Similarity=0.197  Sum_probs=36.8

Q ss_pred             HHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCC
Q 025606          179 HNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGL  220 (250)
Q Consensus       179 ~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl  220 (250)
                      +..+|++.. ..++||+.+|++.+|-|..=++.-|+.|.+.|.
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            456787765 468999999999999999999999999999996

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.81  E-value=1  Score=31.66  Aligned_cols=54  Identities=15%  Similarity=0.138  Sum_probs=43.9

Q ss_pred             ccchhHHHHHHHHH-----hCCCccHHHHHHh--cCCChHHHHHHHHHHHHcCCceeecCC
Q 025606          174 ELNKDHNQILELAQ-----AQGFVTVDEVERR--LSWTSGRAIDALDILLEEGLAMVDDGH  227 (250)
Q Consensus       174 El~~D~~~vLela~-----~~g~vt~~~L~~~--l~W~~~Ra~~~L~~l~~~Gl~WvD~q~  227 (250)
                      +|+.-|..||..+-     .+--|+..+|++.  +++|..=++..|..|+++|++--+.-.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~h~s   61 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHTS   61 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSSC
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCCCCC
Confidence            57778888887543     3556999999998  557999999999999999999776543

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.75  E-value=1  Score=33.04  Aligned_cols=62  Identities=6%  Similarity=0.075  Sum_probs=50.5

Q ss_pred             ccchhHHHHHHHHHhCCCccHHHHHHh----cCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025606          174 ELNKDHNQILELAQAQGFVTVDEVERR----LSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       174 El~~D~~~vLela~~~g~vt~~~L~~~----l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~  238 (250)
                      +|+.-...|++++=..|-+|+.++.+.    .+|+..=..+.|..|++.|++=+..+.   ...+|.|.
T Consensus         3 ~ls~~E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~g---r~~~Y~~~   68 (122)
T d1sd4a_           3 EISMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSE---NIYFYSSN   68 (122)
T ss_dssp             CCCHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEET---TEEEEEEC
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeeccC---CeEEEeec
Confidence            456667778888888889999988776    489999999999999999999887665   45566664

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=85.71  E-value=1  Score=33.13  Aligned_cols=50  Identities=16%  Similarity=0.176  Sum_probs=43.9

Q ss_pred             cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025606          175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD  224 (250)
Q Consensus       175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD  224 (250)
                      ++.-|-.+|......|.+|+.+|++.++.++.-+-..++.|++.|++=+-
T Consensus        33 lt~~q~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~   82 (143)
T d1s3ja_          33 VTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   82 (143)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheee
Confidence            56668888888777778999999999999999999999999999999544

>d2mysb_ a.39.1.5 (B:) Myosin Essential Chain {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Myosin Essential Chain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=85.29  E-value=1.4  Score=32.19  Aligned_cols=38  Identities=16%  Similarity=0.285  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      +|++.|++....|-..+.+.|...     .|..+..++|..|.
T Consensus         4 ~qi~el~e~F~~~D~~~~G~I~~~-----e~~~~l~~lg~~~~   41 (145)
T d2mysb_           4 TEIEDFKEAFTVIDQNADGIIDKD-----DLRETFAAMGRLNV   41 (145)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHH-----HHHHHHHHhCCCcc
Confidence            566777888888888888888765     57788888997764

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=85.19  E-value=1  Score=29.59  Aligned_cols=49  Identities=14%  Similarity=0.292  Sum_probs=40.3

Q ss_pred             cchhHHHHHHHHH----hCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025606          175 LNKDHNQILELAQ----AQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMV  223 (250)
Q Consensus       175 l~~D~~~vLela~----~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv  223 (250)
                      ||.||..+.+-++    ..|+  -++.+|.+.+|-+...++..|..|.++|.+-.
T Consensus         1 ls~~q~~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvk   55 (64)
T d1lvaa3           1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVK   55 (64)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            5777877766554    2343  78999999999999999999999999999863

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=84.93  E-value=1.1  Score=30.04  Aligned_cols=45  Identities=22%  Similarity=0.408  Sum_probs=39.4

Q ss_pred             HHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          181 QILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       181 ~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      .||++.. ..+.+|.++|++.+|.++..+...|..|++.|++=.|+
T Consensus         9 ~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~   54 (75)
T d1mkma1           9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK   54 (75)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            4666655 46779999999999999999999999999999998874

>d2ve8a1 a.4.5.67 (A:745-811) DNA translocase FtsK {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.81  E-value=0.84  Score=30.84  Aligned_cols=43  Identities=14%  Similarity=0.286  Sum_probs=38.2

Q ss_pred             HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ..+.+++...+..|.+.|++.|+.-=.||-..++.|+.+|++=
T Consensus         7 ~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVs   49 (67)
T d2ve8a1           7 DEAVRFVTESRRASISAVQRKLKIGYNRAARMIEAMEMAGVVT   49 (67)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBC
T ss_pred             HHHHHHHHHhCcccHHHHHHHHhcchHHHHHHHHHHHHCcCCC
Confidence            3467777777899999999999999999999999999999974

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.38  E-value=2.9  Score=29.23  Aligned_cols=74  Identities=18%  Similarity=0.191  Sum_probs=57.5

Q ss_pred             HHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025606          140 EDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEG  219 (250)
Q Consensus       140 ~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G  219 (250)
                      +|.+.+..+.++.||.+-                     -..||.+... |-.|+.+|++.+|.+..-.-.-|..|...|
T Consensus         2 ~d~~e~~a~~fkaL~d~~---------------------Rl~Il~~L~~-~~~~v~el~~~l~~s~~~vS~HL~~L~~~g   59 (94)
T d1r1ua_           2 TDTLERVTEIFKALGDYN---------------------RIRIMELLSV-SEASVGHISHQLNLSQSNVSHQLKLLKSVH   59 (94)
T ss_dssp             HHHHHHHHHHHHHTCSHH---------------------HHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHhCCHH---------------------HHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            577788888888888643                     2336666654 668999999999999999999999999999


Q ss_pred             CceeecCCCCCCcceeecC
Q 025606          220 LAMVDDGHRDRKRRYWFPC  238 (250)
Q Consensus       220 l~WvD~q~~~~e~~Yw~P~  238 (250)
                      ++=.-...   ...||..+
T Consensus        60 lv~~~r~G---~~~~Y~l~   75 (94)
T d1r1ua_          60 LVKAKRQG---QSMIYSLD   75 (94)
T ss_dssp             SEEEEEET---TEEEEEES
T ss_pred             ceEEEEEC---CEEEEEEC
Confidence            99776544   56666543

>d1lkja_ a.39.1.5 (A:) Calmodulin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Calmodulin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.54  E-value=3.5  Score=29.63  Aligned_cols=106  Identities=17%  Similarity=0.318  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCC-Cccccc----ccc---cccchhhh---------
Q 025606           37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASN-KGFWAE----LLG---IGDFYYEL---------   99 (250)
Q Consensus        37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~-k~~ws~----~lG---~gdfy~eL---------   99 (250)
                      .|+..|++....|-..+.+.|.-+     .|+.++...|.+|.... ..++..    ..+   ..+|...+         
T Consensus         7 ~~i~~l~~~F~~~D~d~~G~i~~~-----e~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (146)
T d1lkja_           7 EQIAEFKEAFALFDKDNNGSISSS-----ELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLKSNDS   81 (146)
T ss_dssp             HHHHHHHHHHHHHCCSSSSEEEHH-----HHHHHHHHHTCCCCHHHHHHHHHHHCSSSCCEEEHHHHHHHHHHHTCCCCH
T ss_pred             HHHHHHHHHHHHHCCCCCCcEeHH-----HHHHHHHhcCCCCCHHHHHHHHHHhccCCcccccHHHHHHHHHHhhccccH
Confidence            345557777777877777777754     57788888898875211 000000    001   11222211         


Q ss_pred             HHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc
Q 025606          100 GVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK  151 (250)
Q Consensus       100 avqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~  151 (250)
                      ..++.+++..-=..+-|.|++.|+...+...    ...++++++..-++.+.
T Consensus        82 ~~~~~~aF~~~D~d~~G~I~~~el~~~l~~~----g~~~~~~~~~~~~~~~d  129 (146)
T d1lkja_          82 EQELLEAFKVFDKNGDGLISAAELKHVLTSI----GEKLTDAEVDDMLREVS  129 (146)
T ss_dssp             HHHHHHHHHHHCSSSSCEEEHHHHHHHHHHH----TCSCCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCCCCCCcCcHHHHHHHHHHc----CCcccHHHHHHHHHhcc
Confidence            1245555555545555777777776665543    24567766666555543

>d1ggwa_ a.39.1.5 (A:) Cdc4p {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Cdc4p
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=81.80  E-value=0.88  Score=33.25  Aligned_cols=35  Identities=17%  Similarity=0.394  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025606           40 ATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL   79 (250)
Q Consensus        40 ~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL   79 (250)
                      +.||.....|=..+.+.|..+     +|+.++.++|.+|-
T Consensus         5 ~~fke~F~~~D~d~dG~I~~~-----el~~~l~~lg~~~t   39 (140)
T d1ggwa_           5 SPYKQAFSLFDRHGTGRIPKT-----SIGDLLRACGQNPT   39 (140)
T ss_dssp             TTTHHHHHHTCSSSSSEECHH-----HHHHHHHHTSCCCC
T ss_pred             HHHHHHHHHHCCCCCCeECHH-----HHHHHHHHHHhhhH
Confidence            458888888888888888765     57788889998874

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=80.65  E-value=0.77  Score=30.03  Aligned_cols=43  Identities=23%  Similarity=0.285  Sum_probs=37.2

Q ss_pred             HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025606          182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD  225 (250)
Q Consensus       182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~  225 (250)
                      ||.+... |-+|..+|++.+|-+..-....+++|+.+|++---.
T Consensus         4 Il~~i~~-~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1           4 ILKRIMK-SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             SHHHHHH-SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHH-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            5666665 459999999999999999999999999999986543

>d2j5pa1 a.4.5.67 (A:1261-1329) DNA translocase FtsK {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Escherichia coli [TaxId: 562]

Probab=80.22  E-value=1.8  Score=29.23  Aligned_cols=44  Identities=14%  Similarity=0.293  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025606          179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM  222 (250)
Q Consensus       179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W  222 (250)
                      ...+.+++-..+..|++.|++.|+.-=.||-..++.|+.+|++=
T Consensus         9 y~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVs   52 (69)
T d2j5pa1           9 FDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEAQGIVS   52 (69)
T ss_dssp             HHHHHHHHHHTTEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSBC
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHhccchHHHHHHHHHHHCCcCC
Confidence            44577777778899999999999999999999999999999963