Psyllid ID: psy16234

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------61
Protein Sequence
MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHHccccccHHHcccccccHHHHccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHcccccEEEEcccccEEEEEEEEccccEEEEEcHHHHHHHHHHcccccccHHHHHHHHcccHHHHHHHHHHHHHcccccccccccccccEEEEcccccccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccEEcccccccEEEcc
Secondary Structure Prediction (SSPRO)
ccccccEEcHHHHHHHHHHHHHHHHcccccccccHcccHHHHHHHHHcccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHcccccEEEEEcccccEEEEEEcccccEEEEEEHHHHHHHHHHcccccccHHHHHHHccccHHHHHHHHHHHHHcHHccccccccccccEEEEEccccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccccEEEcc
Coil and Loop (DISEMBL)
mslkpkqvdfnktWGSLQETIQGVITLgnvrratwndrfSDIYSLcvaypepladrLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFlqgecvpmvaEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAisglsgdniSTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSvinhkfdpkmpskspeyLAKYCDMLLKksskglsesemddKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDikisgglnekfhsefvktneidlgiHFSINIlqagswplgptvissfsvpQELEKCIHMFEKfyhgqfngrklsWLHNISQVELKlsylkrpyfvTMQTFQMAILLLFEkndamtcgdiQTVLSLSQDQIGRHIASLVECKLLtsnkeeltEDTEIRLNlgynnkrtklkisgavqketpqeIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSqsksfapsISMIKKCIESLIDKnyvertanstdeysyva
Flexible Loop (DISEMBL)
MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLltsnkeeltedteirlnlgynnkrtklkisgavqketpqeiertvssvdedrKLYLQAAIVRIMKSRKQIRHNALIQEVlsqsksfapsiSMIKKCIESlidknyvertanstdeysyva
Low Complexity Region (SEG)
MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMllkksskglsESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Disordered region (IsUnstruct)
*********FNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK***********YLAKYCDMLL******************SITVFKYIDDKDVFHKFYAKMLAKRLIHQ********EAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNN*****************************RKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE*************
Disordered Region (DISOPRED)
**LKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKK**********DDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLK***********************RKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Disordered Region (DISEMBL)
MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKS***********KLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN*********
Disordered Region (DISPRO)
**LKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETP*EIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
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	609	2.2.26 [Sep-21-2011]
Q9D4H8	745	Cullin-2 OS=Mus musculus	yes	N/A	0.885	0.723	0.545	1e-172
Q5RCF3	745	Cullin-2 OS=Pongo abelii	yes	N/A	0.886	0.724	0.544	1e-169
Q13617	745	Cullin-2 OS=Homo sapiens	yes	N/A	0.886	0.724	0.544	1e-169
Q17390	850	Cullin-2 OS=Caenorhabditi	yes	N/A	0.886	0.635	0.422	1e-125
Q9WTX6	776	Cullin-1 OS=Mus musculus	no	N/A	0.881	0.692	0.431	1e-119
Q5R4G6	776	Cullin-1 OS=Pongo abelii	no	N/A	0.881	0.692	0.431	1e-119
Q13616	776	Cullin-1 OS=Homo sapiens	no	N/A	0.881	0.692	0.431	1e-119
Q9XZJ3	771	Cullin-2 OS=Dictyostelium	yes	N/A	0.889	0.702	0.386	1e-115
O60999	770	Cullin-1 OS=Dictyostelium	no	N/A	0.888	0.702	0.4	1e-111
Q24311	774	Cullin homolog 1 OS=Droso	no	N/A	0.883	0.695	0.391	1e-105

>sp|Q9D4H8|CUL2_MOUSE Cullin-2 OS=Mus musculus GN=Cul2 PE=1 SV=2

 Score =  604 bits (1558), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 298/546 (54%), Positives = 407/546 (74%), Gaps = 7/546 (1%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
            Y  IF + FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY K
Sbjct: 202 FYQGIFVSPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTK 261

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V  +C+Q MVADHL FL  EC  ++ +ER++D+ANMY LLR+V  G+  +I+ ++ HI  
Sbjct: 262 VIHECQQRMVADHLQFLHSECHSIIQQERKNDMANMYVLLRAVSSGLPHMIEELQKHIHD 321

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GL A S L+ +++ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +
Sbjct: 322 EGLRATSNLTQEHMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-E 380

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
           PK   K+PE LAKYCD LLKKS+KG++E+E++DKL+  ITVFKYIDDKDVF KFYA+MLA
Sbjct: 381 PKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLA 440

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE- 367
           KRLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F++  + 
Sbjct: 441 KRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIRNQDT 499

Query: 368 -IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNI 426
            IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH +
Sbjct: 500 VIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYL 559

Query: 427 SQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVE 486
              E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++
Sbjct: 560 CTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLD 619

Query: 487 CKLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLY 544
            K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+Y
Sbjct: 620 VKMINHDSEKEDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMY 679

Query: 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTD 603
           LQAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S D
Sbjct: 680 LQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASAD 739

Query: 604 EYSYVA 609
           EYSYVA
Sbjct: 740 EYSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).
Mus musculus (taxid: 10090)

>sp|Q5RCF3|CUL2_PONAB Cullin-2 OS=Pongo abelii GN=CUL2 PE=2 SV=1

 Score =  596 bits (1537), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 297/545 (54%), Positives = 406/545 (74%), Gaps = 5/545 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
            Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY K
Sbjct: 202 FYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTK 261

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V  +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  
Sbjct: 262 VIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHD 321

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +
Sbjct: 322 EGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-E 380

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
           PK   K+PE LAKYCD LLKKS+KG++E+E++D+L+  ITVFKYIDDKDVF KFYA+MLA
Sbjct: 381 PKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLA 440

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE- 367
           KRLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++     +  
Sbjct: 441 KRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTV 500

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct: 501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct: 561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query: 488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
           K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct: 621 KMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 680

Query: 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
           QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct: 681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query: 605 YSYVA 609
           YSYVA
Sbjct: 741 YSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).

Pongo abelii (taxid: 9601)

>sp|Q13617|CUL2_HUMAN Cullin-2 OS=Homo sapiens GN=CUL2 PE=1 SV=2

 Score =  596 bits (1537), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 297/545 (54%), Positives = 406/545 (74%), Gaps = 5/545 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
            Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY K
Sbjct: 202 FYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTK 261

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V  +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  
Sbjct: 262 VIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHD 321

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +
Sbjct: 322 EGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-E 380

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
           PK   K+PE LAKYCD LLKKS+KG++E+E++D+L+  ITVFKYIDDKDVF KFYA+MLA
Sbjct: 381 PKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLA 440

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE- 367
           KRLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++     +  
Sbjct: 441 KRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTV 500

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct: 501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct: 561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query: 488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
           K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct: 621 KMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 680

Query: 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
           QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct: 681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query: 605 YSYVA 609
           YSYVA
Sbjct: 741 YSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).

Homo sapiens (taxid: 9606)

>sp|Q17390|CUL2_CAEEL Cullin-2 OS=Caenorhabditis elegans GN=cul-2 PE=1 SV=3

 Score =  447 bits (1151), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 236/558 (42%), Positives = 353/558 (63%), Gaps = 18/558 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
            Y + FE   L  + ++Y + A K+L   + S+YME+V+ +L +E  R+ ++LH SS  K
Sbjct: 294 FYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEK 353

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V   C++ M+  H + L   C  ++  E   DL NMY LL+ ++ G+++++    +++ K
Sbjct: 354 VITLCQKVMIKAHKDKLHAVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKK 413

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GLEA+S L+G+N+  QFVEN+L V+ K+      +F  D  F   LDKA   V+N K  
Sbjct: 414 KGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEP 473

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
            +   K+ E LA+Y D LLKKS+KGLSE++++ KL  +I +F+YI+DKD+F KFY+KMLA
Sbjct: 474 GQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLA 533

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKF--HSEFVKTN 366
            RLI   S SMD EE MINKLKQACGYEFT+K  RM TDI +S  L+  F  H   +KT 
Sbjct: 534 NRLIASTSISMDAEELMINKLKQACGYEFTSKLSRMFTDIGLSQELSNNFDKHIADIKTV 593

Query: 367 EIDLG-IHFSINILQAGSWPL-GPTV-----------ISSFSVPQELEKCIHMFEKFYHG 413
           + D+  +     ILQAGSWPL  P +           +++F +P+ L+  I  FEKFY G
Sbjct: 594 QPDVKFVPTQTMILQAGSWPLNAPQLSTNSNNQTAQDVANFHLPRILQPVIQEFEKFYTG 653

Query: 414 QFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLS 473
           + NGRKL+WL N+SQ +++L+YL + Y   M  +QMA LL FE+ DA+   DI   + +S
Sbjct: 654 KHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVS 713

Query: 474 QDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGA-VQKETPQEIER 532
            D + + I ++++  LLT + + LT D+ +RLN+   +KR K ++    V K   +E E 
Sbjct: 714 GDYLLKTIRTILDVTLLTCDDQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEA 773

Query: 533 TVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLID 591
             ++V +DRK Y++ AIVRIMK+RK ++HNAL+ E++ Q+K  F+P +  IKK IE LI+
Sbjct: 774 VANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIE 833

Query: 592 KNYVERTANSTDEYSYVA 609
           K Y++RT +  DEY Y+A
Sbjct: 834 KMYIQRT-DQNDEYQYLA 850

Positive cell-cycle regulator that is required at two distinct points in the cell cycle; the G1-to-S-phase transition and mitosis. Also required for proper cytoskeletal movement and mitotic chromosome condensation. Core component of multiple cullin-RING-based CBC (Cul2-ElonginB-ElonginC) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. As a scaffold protein may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The functional specificity of the CBC complex depends on the variable substrate recognition component (By similarity). May function in ubiquitin-mediated degradation of CKIs to target cki-1 for degradation. CBC(zif-1) may ensure germline precursor cell asymmetry by targeting germline proteins for destruction if expressed in non-germline cells. CBC(fem-1) directs ubiquitination of tra-1.

Caenorhabditis elegans (taxid: 6239)

>sp|Q9WTX6|CUL1_MOUSE Cullin-1 OS=Mus musculus GN=Cul1 PE=1 SV=1

 Score =  431 bits (1107), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 239/554 (43%), Positives = 335/554 (60%), Gaps = 17/554 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 227 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 286

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 287 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 346

Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 347 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 406

Query: 247 FDPKMP---SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFY 303
              KM    SKSPE LA+YCD LLKKSSK   E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 407 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 466

Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 467 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 526

Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +DL   FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 527 NSEPLDLD--FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWL 582

Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 583 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 642

Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 643 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 702

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+
Sbjct: 703 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 762

Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 763 ERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53 (By similarity). SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Mus musculus (taxid: 10090)

>sp|Q5R4G6|CUL1_PONAB Cullin-1 OS=Pongo abelii GN=CUL1 PE=2 SV=1

 Score =  431 bits (1107), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 239/554 (43%), Positives = 335/554 (60%), Gaps = 17/554 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 227 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 286

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 287 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 346

Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 347 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 406

Query: 247 FDPKMP---SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFY 303
              KM    SKSPE LA+YCD LLKKSSK   E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 407 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 466

Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 467 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 526

Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +DL   FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 527 NSEPLDLD--FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWL 582

Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 583 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 642

Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 643 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 702

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+
Sbjct: 703 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 762

Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 763 ERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participates in Wnt signaling. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Pongo abelii (taxid: 9601)

>sp|Q13616|CUL1_HUMAN Cullin-1 OS=Homo sapiens GN=CUL1 PE=1 SV=2

 Score =  431 bits (1107), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 239/554 (43%), Positives = 335/554 (60%), Gaps = 17/554 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 227 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 286

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 287 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 346

Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 347 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 406

Query: 247 FDPKMP---SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFY 303
              KM    SKSPE LA+YCD LLKKSSK   E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 407 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 466

Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 467 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 526

Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +DL   FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 527 NSEPLDLD--FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWL 582

Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 583 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 642

Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 643 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 702

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+
Sbjct: 703 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 762

Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 763 ERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Homo sapiens (taxid: 9606)

>sp|Q9XZJ3|CUL2_DICDI Cullin-2 OS=Dictyostelium discoideum GN=culB PE=2 SV=1

 Score =  417 bits (1073), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 226/584 (38%), Positives = 348/584 (59%), Gaps = 42/584 (7%)

Query: 66  DQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSS 125
           D+ LY+  +E  +LE + ++Y  E+   + +  +S YM++    + EE  RS ++L+ SS
Sbjct: 190 DRTLYLIEYEASYLENTRQFYTRESVAFIASSGISSYMKKAETRIDEEEQRSQKYLNSSS 249

Query: 126 YPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDH 185
           + K++      ++  H   LQ EC+  + +E+  ++ NMY LL  +  G+  +++ V+ +
Sbjct: 250 HDKMRRLLHSILIEKHKELLQSECINYLKDEKLDEIYNMYKLLSRIEGGLAPVLETVQKY 309

Query: 186 ICKQGLEAISGLSGDNISTQ--FVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVI 243
           I   G++AI  +   N      +VE +L ++ ++ + +K+ F+ D SF+  LD AC  + 
Sbjct: 310 IQHVGIDAIKSIPDRNNPDPKIYVETLLKIYLQFSSIIKKSFNNDVSFITVLDLACHKIF 369

Query: 244 NHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFY 303
           N     +  +KSPE LAKYCDMLLKK +K   E E+++KL Q I +FKY+DDKDVF KFY
Sbjct: 370 NQNHITRNTTKSPELLAKYCDMLLKKGNKQHEEIELEEKLGQIIVLFKYVDDKDVFQKFY 429

Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           +KML++RLI+  S S D E+ MI  LKQACG+E+T+KF RM  DI +S   NE+F +  +
Sbjct: 430 SKMLSRRLINGTSVSDDIEKFMITGLKQACGFEYTSKFQRMFNDITLSAETNEEFKNHLI 489

Query: 364 KTNEIDLG-IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSW 422
           K N + +G I FSI +L +GSW L     SSF VPQEL  CI  F+++Y  Q  GRKL+W
Sbjct: 490 K-NSLSIGKIDFSILVLTSGSWSLHSQT-SSFIVPQELTLCISAFQQYYSTQHQGRKLNW 547

Query: 423 LHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIA 482
           LH++ + E K  + K+ Y   +  FQ+ ILL+F   ++++  +I    +L+++++ R + 
Sbjct: 548 LHHLCKAEAKSFFAKKSYDFQVTNFQLGILLIFNTQESVSLEEITKFTNLNENELSRTLQ 607

Query: 483 SLVECKLLTSNKEE------------------------------------LTEDTEIRLN 506
           SL+E K+L S K++                                     +   E  +N
Sbjct: 608 SLIEAKILISKKKDQNSINNNNNNNNNNNNNGEGNNSLVDSANNMQPSSSSSSTQEYTVN 667

Query: 507 LGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQ 566
             Y+NKR+K+K+S ++QKETP + E T   +DEDRKLYLQA+IVRIMK+RK + H +LIQ
Sbjct: 668 SAYSNKRSKVKVSSSLQKETPLQNEETYKGIDEDRKLYLQASIVRIMKARKTMNHVSLIQ 727

Query: 567 EVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
           EV+  S+  F P+I MIKKCIE LI+K Y+ R    +D Y Y A
Sbjct: 728 EVIEHSRLRFQPNIPMIKKCIEQLIEKEYITRAEGESDRYLYAA 771

Probable core component of cullin-based SCF-like E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit (By similarity). Appears to ensure that the proper number of prestalk cells differentiate at the appropriate time in development. May govern prestalk cell differentiation.

Dictyostelium discoideum (taxid: 44689)

>sp|O60999|CUL1_DICDI Cullin-1 OS=Dictyostelium discoideum GN=culA PE=1 SV=1

 Score =  403 bits (1036), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 222/555 (40%), Positives = 334/555 (60%), Gaps = 14/555 (2%)

Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
            +Y   FE  FL  +  +Y +E++K +   +V+ YM++V   L+EE  R  ++LH ++  
Sbjct: 217 QVYKSGFEELFLTATENYYTNESAKFISENSVADYMKKVETRLNEEVKRVQQYLHQNTES 276

Query: 128 KVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHIC 187
           ++ AKCE+ ++  H+  +  E   ++ +++  DL  MY LL  +  G+  L   +  H+ 
Sbjct: 277 ELIAKCEKVLIEKHVEVIWNEFQTLLEKDKIPDLTRMYSLLSRIPRGLEPLRTTLEKHVQ 336

Query: 188 KQGLEAISGLSGDNI--STQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINH 245
             GL+A+S ++ + +     ++E +L V KKY   V   F  D  F+ +LDKAC   IN 
Sbjct: 337 NVGLQAVSSIATNGVIEPKVYIETLLKVFKKYNELVTGAFRSDTGFVASLDKACRRFINE 396

Query: 246 K---FDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKF 302
                  K  SKSPE LA++ D LLKKS     ESEM+  L+  + VFKYI+DKDVF  F
Sbjct: 397 NAVTIAAKSSSKSPELLARFTDFLLKKSPNNPEESEMEQLLNDVMIVFKYIEDKDVFQDF 456

Query: 303 YAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEF 362
           Y+KMLAKRLIH  STS D E  MI KLK  CGYE+T+K  RM TD+ +S  L ++F++  
Sbjct: 457 YSKMLAKRLIHGTSTSEDLEGTMIGKLKSTCGYEYTSKLQRMFTDMSLSRELLDRFNNHI 516

Query: 363 VKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSW 422
            +     L I FS+ +L  GSWPL P   ++FS+P+EL+ C  +F+KFY  Q +GRKL+W
Sbjct: 517 EQVERSSLNIDFSVLVLATGSWPLQPPS-TNFSIPKELQACEQLFQKFYQNQHSGRKLNW 575

Query: 423 LHNISQVELKLSYL---KRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGR 479
           LH++S+ ELK  YL   K  Y +   T+Q+ +LL F + + +T  +IQ    L    +  
Sbjct: 576 LHHLSKGELKTKYLQTSKSGYTLQCSTYQIGVLLQFNQYETLTSEEIQESTQLIDSVLKG 635

Query: 480 HIASLVECKLLTSNK----EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVS 535
            + SL + K+L ++     EE+ + T+  LN  + NK+TK+ I+  V  +  +EI+    
Sbjct: 636 TLTSLAKSKILLADPPLDDEEIAKTTKFSLNKQFKNKKTKIFINVPVLTQVKEEIDSIHK 695

Query: 536 SVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNY 594
           +V+EDRKL +QAAIVRIMK RKQ+ H+ L+ EV+SQ ++ F P +++IKKCI+ LI+K Y
Sbjct: 696 TVEEDRKLQIQAAIVRIMKMRKQLAHSGLMTEVISQLQTRFNPKVNIIKKCIDILIEKEY 755

Query: 595 VERTANSTDEYSYVA 609
           + R     D YSYVA
Sbjct: 756 LMRVEGKKDHYSYVA 770

Probable core component of cullin-based SCF-like E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit (By similarity). Required at several stages during development. CulA and fbxA regulate multicellular development by targeting regA for degradation via a pathway that requires erkB function, leading to an increase in cAMP and PKA activity.

Dictyostelium discoideum (taxid: 44689)

>sp|Q24311|CUL1_DROME Cullin homolog 1 OS=Drosophila melanogaster GN=lin19 PE=1 SV=2

 Score =  382 bits (981), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 219/560 (39%), Positives = 322/560 (57%), Gaps = 22/560 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNR--------SVRF 120
           +Y   FE +F+  +  +Y+ E+   L T  V++Y++ V   L EET R         + +
Sbjct: 218 VYKQNFENKFIADTSAFYEKESDAFLSTNTVTEYLKHVENRLEEETQRVRGFNSKNGLSY 277

Query: 121 LHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILID 180
           LH ++   +K+ CE+ ++  HL     E   ++  +R  DL  MY L+    + +  L  
Sbjct: 278 LHETTADVLKSTCEEVLIEKHLKIFHTEFQNLLNADRNDDLKRMYSLVALSSKNLTDLKS 337

Query: 181 AVRDHICKQGLEAIS---GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDK 237
            + +HI  QG EAI+        N    +V+ +L VHKKY A V   F+ D  F+ ALDK
Sbjct: 338 ILENHILHQGTEAIAKCCTTDAANDPKTYVQTILDVHKKYNALVLTAFNNDNGFVAALDK 397

Query: 238 ACSSVINHKFD--PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDD 295
           AC   IN          SKSPE LAKYCD+LLKKSSK   + E++D L+Q + VFKYI+D
Sbjct: 398 ACGKFINSNVVTIANSASKSPELLAKYCDLLLKKSSKNPEDKELEDNLNQVMVVFKYIED 457

Query: 296 KDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLN 355
           KDVF K+Y+KMLAKRL++  S S D E  MI+KLKQ CGYE+T K  RM  DI +S  LN
Sbjct: 458 KDVFQKYYSKMLAKRLVNHTSASDDAEAMMISKLKQTCGYEYTVKLQRMFQDIGVSKDLN 517

Query: 356 EKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQF 415
             F     + N + + I F I +L +GSWP   +  ++F +P ELE+ +  F +FY  + 
Sbjct: 518 SYFKQYLAEKN-LTMEIDFGIEVLSSGSWPFQLS--NNFLLPSELERSVRQFNEFYAARH 574

Query: 416 NGRKLSWLHNISQVELKLSYLKR---PYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSL 472
           +GRKL+WL+ + + EL ++  +     Y +   TFQM++LL F    + T   +Q     
Sbjct: 575 SGRKLNWLYQMCKGELIMNVNRNNSSTYTLQASTFQMSVLLQFNDQLSFTVQQLQDNTQT 634

Query: 473 SQDQIGRHIASLVECKLLTS--NKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEI 530
            Q+ + + +  L++ K+LTS  N+  LT ++ + L L Y NK+ ++ I+  ++ E   E 
Sbjct: 635 QQENLIQVLQILLKAKVLTSSDNENSLTPESTVELFLDYKNKKRRININQPLKTELKVEQ 694

Query: 531 ERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESL 589
           E     ++EDRKL +QAAIVRIMK RK++ H  LI EVL+Q S  F P + +IKKCI+ L
Sbjct: 695 ETVHKHIEEDRKLLIQAAIVRIMKMRKRLNHTNLISEVLNQLSTRFKPKVPVIKKCIDIL 754

Query: 590 IDKNYVERTANSTDEYSYVA 609
           I+K Y+ER     D YSY+A
Sbjct: 755 IEKEYLERMEGHKDTYSYLA 774

Core component of multiple SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme.

Drosophila melanogaster (taxid: 7227)

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	609
91084625	743	PREDICTED: similar to cullin [Tribolium	0.885	0.725	0.636	0.0
193638906	737	PREDICTED: cullin-2-like isoform 1 [Acyr	0.876	0.724	0.593	0.0
443700766	660	hypothetical protein CAPTEDRAFT_175514 [	0.886	0.818	0.568	0.0
156553060	752	PREDICTED: cullin-2-like isoform 1 [Naso	0.904	0.732	0.582	0.0
195384726	756	GJ14230 [Drosophila virilis] gi|19414752	0.883	0.711	0.578	0.0
158291834	766	AGAP003605-PA [Anopheles gambiae str. PE	0.883	0.702	0.583	0.0
157114617	754	cullin [Aedes aegypti] gi|108877199|gb|E	0.883	0.713	0.593	0.0
322800724	752	hypothetical protein SINV_05339 [Solenop	0.889	0.720	0.591	0.0
195030360	756	GH10784 [Drosophila grimshawi] gi|193904	0.883	0.711	0.578	0.0
195155674	756	GL25796 [Drosophila persimilis] gi|19847	0.883	0.711	0.574	0.0

>gi|91084625|ref|XP_974579.1| PREDICTED: similar to cullin [Tribolium castaneum] gi|270008911|gb|EFA05359.1| hypothetical protein TcasGA2_TC015524 [Tribolium castaneum]

 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 345/542 (63%), Positives = 436/542 (80%), Gaps = 3/542 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY ++FE  FL+ SGE +K +A+KLLQ  NVS YMERV   + EE  R+ RFLH SS PK
Sbjct: 204 LYQELFEEPFLKESGEHFKRDAAKLLQEKNVSLYMERVKGRIEEELLRARRFLHTSSLPK 263

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V  +CE HMVA+HL+FL  ECV MV  ER+ DL+NMY LL+SV+  + +L+D V DHI  
Sbjct: 264 VSQRCETHMVAEHLDFLYSECVAMVQGERKKDLSNMYDLLKSVQNAMVVLVDTVLDHIKT 323

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           QGL A+  +  +NI   FVENMLAV+KKYK  ++E+F  DQ+FMGALDKACSSVINHKF 
Sbjct: 324 QGLTAVGNIDTENIHITFVENMLAVYKKYKLLIQEVFKSDQNFMGALDKACSSVINHKFG 383

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
            K   KSPE+LAKYCD LL+KSSKG+S+SE+D+KL++SIT+FKYIDDKDVF KFY++MLA
Sbjct: 384 -KPVCKSPEFLAKYCDALLRKSSKGISDSEVDEKLAESITIFKYIDDKDVFQKFYSRMLA 442

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI 368
           KRLIHQQ+ SMD EEAMIN+LKQACGYEFT+K HRM TD+ +S  LN KF++ F+K + I
Sbjct: 443 KRLIHQQTQSMDAEEAMINRLKQACGYEFTSKLHRMFTDMSVSADLNNKFNA-FLKQDNI 501

Query: 369 DLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
           DLGI+FSI +LQAG+WPLG TV + F+ P++LEK + MFE FYH +FNGRKL+WLHN+ Q
Sbjct: 502 DLGINFSIYVLQAGAWPLGQTVTTPFTYPRQLEKSVQMFENFYHNRFNGRKLTWLHNLCQ 561

Query: 429 VELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488
            ELKL +LK+ Y VTMQTFQMA LLLFE  D++T  +I+  L L+ +Q  R+ ASL++CK
Sbjct: 562 AELKLGHLKKSYLVTMQTFQMATLLLFEHTDSLTFREIRESLQLTAEQYHRYAASLIDCK 621

Query: 489 LLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAA 548
           LL ++  +L  +T +RLN+ YNNKRTK +I+ AVQKE+PQEIE+T++SV+EDRK+YLQAA
Sbjct: 622 LLIADSTDLKPETVLRLNMEYNNKRTKFRINAAVQKESPQEIEQTMNSVEEDRKMYLQAA 681

Query: 549 IVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607
           IVRIMKSRK ++HNALIQEV +QSK SFAPS+ +IKKCIESLIDK Y+ERT +S++EYSY
Sbjct: 682 IVRIMKSRKILKHNALIQEVYAQSKVSFAPSVQLIKKCIESLIDKQYIERTPHSSEEYSY 741

Query: 608 VA 609
           VA
Sbjct: 742 VA 743

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193638906|ref|XP_001946605.1| PREDICTED: cullin-2-like isoform 1 [Acyrthosiphon pisum] gi|328718067|ref|XP_003246377.1| PREDICTED: cullin-2-like isoform 2 [Acyrthosiphon pisum]

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/541 (59%), Positives = 409/541 (75%), Gaps = 7/541 (1%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY   FE  FLE S E +K EA++LLQ   VS YM +VLQ+L EE  RS ++LH S+Y K
Sbjct: 204 LYQSYFEQPFLEQSSEHFKREAARLLQESTVSDYMVKVLQILKEEGIRSKKYLHDSTYVK 263

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           ++ +C QHMVADHLNFL GE   M+ EERR+D+ N+Y LLR +++G+  L+D  R+HI +
Sbjct: 264 LRGRCRQHMVADHLNFLHGESEAMIKEERRNDMHNIYLLLREIKDGMTSLVDIFREHIKQ 323

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
            G+  I  L  + I   FVE +L VHKKYK+ V ++F+ D  F GALDKA + +IN+K  
Sbjct: 324 HGIRVIESLRQEQIYVHFVEEVLKVHKKYKSIVVDVFNNDLCFSGALDKAFTVIINYKQV 383

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
              PSKSPEYL+KYCD LLKKSSKG+ E E+D KL QSIT+FKY+DDKD+F +FY + LA
Sbjct: 384 KNQPSKSPEYLSKYCDNLLKKSSKGMCEGEIDQKLLQSITIFKYVDDKDIFQRFYQRHLA 443

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI 368
           KRLIHQQS SMDGEE MINKLKQACGYEFTNK HRM TDI++S GLN KFHSEF+K  + 
Sbjct: 444 KRLIHQQSQSMDGEEGMINKLKQACGYEFTNKLHRMFTDIRVSEGLNAKFHSEFLKPTD- 502

Query: 369 DLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
            L + FS+ +LQ G+WPLG +++SSF +PQ+L  CI  FE FY  +FNGRKL+WLH+  Q
Sbjct: 503 KLNVSFSMYVLQTGAWPLGSSIVSSFVIPQQLIPCIQYFEAFYKEKFNGRKLTWLHHHCQ 562

Query: 429 VELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488
            ELKL+YL++ Y VTMQTFQM+I+LLFE  D +   +I  +L L+ DQ  +HI SL+ECK
Sbjct: 563 GELKLNYLQKVYIVTMQTFQMSIMLLFEDRDTINYTEIHEILQLTSDQFQKHINSLIECK 622

Query: 489 LLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAA 548
           LL      L +   + LN+ Y NKRTKL+I+ A+QKETPQE+E+TV+SV++DRK YLQAA
Sbjct: 623 LL------LIDGDNVSLNMAYTNKRTKLRITSALQKETPQEVEQTVNSVEDDRKTYLQAA 676

Query: 549 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 608
           IVRIMKSRK +RHN L+ E+LSQS++FAPSI++IKK IE+LIDK Y+ERT NS+D YSYV
Sbjct: 677 IVRIMKSRKILRHNQLVNEILSQSQTFAPSIALIKKSIETLIDKGYLERTPNSSDGYSYV 736

Query: 609 A 609
           A
Sbjct: 737 A 737

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443700766|gb|ELT99573.1| hypothetical protein CAPTEDRAFT_175514 [Capitella teleta]

 Score =  656 bits (1693), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 308/542 (56%), Positives = 418/542 (77%), Gaps = 2/542 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY D+FE +FL  +GE+Y  EA +LL  C  S+YM++V+Q L +E  RS +FLH SSY K
Sbjct: 120 LYEDVFEVKFLRETGEYYHREALQLLDDCTCSEYMDKVIQRLDDEDMRSRKFLHPSSYCK 179

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           V  +CEQ MVADHL FL  EC  MVA+E+RHD++N+Y LL  + +G++I +  V++HI +
Sbjct: 180 VTKECEQKMVADHLAFLHSECRNMVAKEKRHDMSNLYRLLCPISKGLDIFVQDVKEHIKQ 239

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GL A++ L GD++ +QFVE++L VH KY   + E+F GDQ F+GALDKA ++VINH+ +
Sbjct: 240 EGLTAVASLKGDSVPSQFVESLLEVHAKYSDLITEVFKGDQHFIGALDKAFAAVINHRSN 299

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
            K   +SPE +AKYCD LLKK++KG+SE+E+DDKLSQSIT+F+Y+DDKD++ +FYA+MLA
Sbjct: 300 FKSNCRSPELVAKYCDSLLKKTAKGMSETEIDDKLSQSITIFRYLDDKDIYQRFYARMLA 359

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI 368
           KRLI+ Q  SMD EE+MIN+LKQACGYEFTNK HRM TD+ IS  LN KF S+F K +  
Sbjct: 360 KRLIYTQFHSMDAEESMINRLKQACGYEFTNKLHRMFTDMSISSDLNSKF-SDFCKEDST 418

Query: 369 DLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
           DLGI+FSI +LQAG+WP+G   + +F++PQELEK + MFE FY   FNGRKL+W+H+   
Sbjct: 419 DLGINFSILVLQAGAWPIGQNNLPTFAIPQELEKSVRMFEVFYGRHFNGRKLTWMHSFCN 478

Query: 429 VELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488
            ELKL+YLKRPY VT+ TF MA+LL F  + +++  D+  +  L + ++ + +  L++ K
Sbjct: 479 AELKLTYLKRPYIVTLGTFHMALLLPFNSSHSVSFRDLVDISRLPEKELLKQVQVLLDAK 538

Query: 489 LLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAA 548
           ++ SN+   T D    LNL Y NKRTK KI  +VQ+ETPQE+E+T+S+VDEDRK+Y+QAA
Sbjct: 539 IIVSNESTATMDGVFSLNLEYTNKRTKFKIITSVQRETPQEVEQTMSNVDEDRKMYVQAA 598

Query: 549 IVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607
           IVR MK+RK ++HNALIQEV+SQS++ FAPSISMIKKCIE+LIDK Y+ER++ STDEYSY
Sbjct: 599 IVRTMKARKVLKHNALIQEVISQSRARFAPSISMIKKCIETLIDKQYIERSSTSTDEYSY 658

Query: 608 VA 609
           +A
Sbjct: 659 IA 660

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|156553060|ref|XP_001599116.1| PREDICTED: cullin-2-like isoform 1 [Nasonia vitripennis] gi|345484337|ref|XP_003425008.1| PREDICTED: cullin-2-like [Nasonia vitripennis]

 Score =  655 bits (1691), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/556 (58%), Positives = 417/556 (75%), Gaps = 5/556 (0%)

Query: 59  QETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSV 118
           +E K+    +LY +IFE  FL+ SGE+Y  EAS+LLQ  +V++YMERV   L +E  R+ 
Sbjct: 197 EEYKMKGQLNLYQEIFEGPFLKQSGEFYLREASELLQQSDVTRYMERVTWRLSQEELRAH 256

Query: 119 RFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINIL 178
           +FLH++S PKV+  CE+ MVA H+ +L  E   MV  ERR DLA +YPLLR +  G+  L
Sbjct: 257 KFLHITSVPKVRQCCEEKMVAAHVAWLHTEVDAMVENERRKDLALIYPLLRPLPSGLAHL 316

Query: 179 IDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKA 238
           +  + +HI  +GL+AI  L G+N+ T FVE+ML VH KY   +KELF GDQ+F+GALDKA
Sbjct: 317 VQKLTEHITNEGLQAIGSLHGENVHTLFVESMLDVHSKYSDLIKELFKGDQAFIGALDKA 376

Query: 239 CSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDV 298
           CS+V+NH+  P+ P+++PE LAKYCD LLKKS+K  SESE+++KL++SITVFKY+DDKDV
Sbjct: 377 CSAVVNHRPAPRQPARAPELLAKYCDSLLKKSAKVASESEIEEKLARSITVFKYVDDKDV 436

Query: 299 FHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKF 358
           F KFYA+MLAKRLIHQQS SMD EEAMI++LKQACGYEFTNK HRM TD+ +S  LN KF
Sbjct: 437 FQKFYARMLAKRLIHQQSQSMDAEEAMIDRLKQACGYEFTNKLHRMFTDMSVSADLNTKF 496

Query: 359 HSEFVKT--NEIDLGIHFSINILQAGSW-PLGPTVISSFSVPQELEKCIHMFEKFYHGQF 415
            +   +    +   GI F + +LQAG+W    P     F VPQ+LEK +  FE FYH QF
Sbjct: 497 TASLREREGEKHQFGIGFVVYVLQAGAWPLGLPPSPGPFHVPQQLEKSVQAFESFYHAQF 556

Query: 416 NGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQD 475
           +GRKL+WLH++ Q ELKL+YLK+PY VT+QT+QMA+LLLFE  D+++C +    L LS D
Sbjct: 557 SGRKLTWLHHLCQGELKLNYLKKPYLVTVQTYQMALLLLFEHCDSISCKEAAVSLRLSHD 616

Query: 476 QIGRHIASLVECKLL-TSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTV 534
           Q+ +H  SLV+CK+L  S +E+L EDT + LN  Y NKRTK +I+GA+Q++ P + E T 
Sbjct: 617 QLVKHAVSLVDCKILKKSTEEDLEEDTILTLNFEYYNKRTKFRITGALQRDAPHDTEATH 676

Query: 535 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKN 593
            SVD+DRKLYLQAAIVRIMKSRK +RHN L+QEVL QSK +FAPSI MIKKCIE+LIDK 
Sbjct: 677 RSVDDDRKLYLQAAIVRIMKSRKVLRHNQLVQEVLGQSKVTFAPSIGMIKKCIENLIDKQ 736

Query: 594 YVERTANSTDEYSYVA 609
           Y+ERT+NS DEYSYVA
Sbjct: 737 YIERTSNSADEYSYVA 752

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195384726|ref|XP_002051063.1| GJ14230 [Drosophila virilis] gi|194147520|gb|EDW63218.1| GJ14230 [Drosophila virilis]

 Score =  655 bits (1690), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 314/543 (57%), Positives = 410/543 (75%), Gaps = 5/543 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY ++FE   LE SG +Y +EA+KLLQ C+VSQYM+ V+++L  E+ R+ +FLHVSS PK
Sbjct: 217 LYQELFEGPMLEASGTYYTNEANKLLQRCSVSQYMQEVIKILEYESKRAQKFLHVSSLPK 276

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINI-LIDAVRDHIC 187
           ++ +CE+  + D L F+  EC  MV++ERR DL NMY +L+ + + +   LI    +HI 
Sbjct: 277 LRKQCEEKFINDRLGFIYSECRDMVSDERRQDLRNMYIVLKPIPDNLKAELIQTFLEHIK 336

Query: 188 KQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF 247
            +GLE +  L G+NI   FVENML VH KY+  + ++F  D  F+ ALDKAC+SVIN + 
Sbjct: 337 NEGLETVYALKGENIHIAFVENMLKVHHKYQELIADVFENDSLFLSALDKACASVINRRP 396

Query: 248 DPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKML 307
             + P +S EY+AKYCD LLKKS     E+E+D KL+ +IT+FKYI+DKDV+ KFY+++L
Sbjct: 397 SERQPCRSAEYVAKYCDTLLKKSKT--CEAEIDQKLTNNITIFKYIEDKDVYQKFYSRLL 454

Query: 308 AKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE 367
           AKRLIH+QS SMD EE MIN+LKQACGYEFTNK HRM TDI +S  LN KF++  +K N+
Sbjct: 455 AKRLIHEQSQSMDAEEGMINRLKQACGYEFTNKLHRMFTDISVSTDLNNKFNNH-LKDND 513

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           IDLGI+ SI +LQAG+WPLG T +  F+VPQE EK I MFE +YH  F+GRKL+WLH++ 
Sbjct: 514 IDLGINLSIKVLQAGAWPLGSTQVIPFAVPQEFEKSIKMFEDYYHNLFSGRKLTWLHHMC 573

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             ELKLS+LK+ Y VTMQT+QMAI+LLFE  D ++C +IQ  L L+ +   +H+  ++E 
Sbjct: 574 HGELKLSHLKKSYIVTMQTYQMAIILLFETCDTLSCREIQNTLQLNDETYQKHMQPMIES 633

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
           KLL ++ E L+ DT I LN  Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQA
Sbjct: 634 KLLNASSENLSGDTRIELNFDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQA 693

Query: 548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
           AIVRIMK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYS
Sbjct: 694 AIVRIMKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYS 753

Query: 607 YVA 609
           Y+A
Sbjct: 754 YMA 756

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158291834|ref|XP_313365.4| AGAP003605-PA [Anopheles gambiae str. PEST] gi|157017477|gb|EAA08832.5| AGAP003605-PA [Anopheles gambiae str. PEST]

 Score =  654 bits (1688), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/543 (58%), Positives = 413/543 (76%), Gaps = 5/543 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY ++FET+ LE SG+ ++  AS+LLQ C+VSQYMER+++   EE   +  +LH SS PK
Sbjct: 227 LYQELFETRMLEESGQNFRIVASELLQVCSVSQYMERIIKKFEEEEKLAKIYLHESSLPK 286

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           ++  CE+ MV  H+NFL  EC  MVA E+  DL N+Y LL+ V +G+  LI+   +HI +
Sbjct: 287 LRKVCEEEMVTKHMNFLYSECKEMVATEKSADLRNLYILLKPVTDGLKRLIEVFLEHIKE 346

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           QG + IS + GD++  QFVENML VH+KY+  +   F  D  F+GALDKAC+ +IN K  
Sbjct: 347 QGKKTISCMKGDSVHIQFVENMLDVHRKYEELIHTTFKSDPLFLGALDKACARIINEKHS 406

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
                +S E +AKYCD LLKKS    +E E+D KL++SI +FKYI+DKDV+ KFY++MLA
Sbjct: 407 NNQVCRSAELVAKYCDSLLKKSKT--TEGEIDQKLTRSIIIFKYIEDKDVYQKFYSRMLA 464

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI 368
           KRLIH+QS SMD EE MINKLKQACGYEFTNK HRM TDI +S  LN KF S+++  N+ 
Sbjct: 465 KRLIHEQSQSMDAEELMINKLKQACGYEFTNKLHRMFTDISVSTDLNAKF-SKYLNDNKH 523

Query: 369 DLGIHFSINILQAGSWPLGPT-VISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           + GI+FS+ +LQAG+WPLGPT V++SF++PQE EK I +FE+FYH  F+GRKL+WLH++ 
Sbjct: 524 ETGINFSVKVLQAGAWPLGPTQVVASFAIPQEFEKSIRLFEEFYHINFSGRKLTWLHHLC 583

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             E+KLS+ KR Y VTMQT+QMAILL+FE  D  TC ++QT L L Q+   RH+ SLVE 
Sbjct: 584 HGEMKLSFEKRNYIVTMQTYQMAILLMFENTDKYTCKELQTSLQLQQEIFQRHLQSLVEA 643

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
           K+L  N+E++ +DTE+ +N+ Y+NKRTK KI+  +QKETPQE+E T+++VDEDRK+YLQA
Sbjct: 644 KILLLNEEKMNDDTEVSINVNYSNKRTKFKITTNLQKETPQEVEHTMNAVDEDRKMYLQA 703

Query: 548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
           AIVRIMKSRK +RHN LIQE+LSQSK SFAP++SMIKKCIESLIDK Y+ERT NS DEYS
Sbjct: 704 AIVRIMKSRKVLRHNTLIQEILSQSKVSFAPNVSMIKKCIESLIDKQYIERTPNSGDEYS 763

Query: 607 YVA 609
           YVA
Sbjct: 764 YVA 766

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157114617|ref|XP_001652340.1| cullin [Aedes aegypti] gi|108877199|gb|EAT41424.1| AAEL006929-PA [Aedes aegypti]

 Score =  654 bits (1687), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/543 (59%), Positives = 409/543 (75%), Gaps = 5/543 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY   FE   L+ SGE+YK EA++LLQ C VS YME V++ L EE  R++++LH SS PK
Sbjct: 215 LYQQTFEAPLLQDSGEFYKLEANRLLQVCTVSSYMEEVIKKLDEENRRALKYLHNSSIPK 274

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           ++ +CEQ M+ DHL+FL  EC  MV+ E+R DL N+Y +L+ + + +  L+    +HI  
Sbjct: 275 LRKECEQRMITDHLDFLYSECSEMVSTEKRKDLKNLYTILKPIPDALKALVQTFMEHIRN 334

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +G++ IS L G+ I  QFVE ML VH+KY+A + + F+ D  F+ ALDKACS+VIN K  
Sbjct: 335 EGIQMISTLKGETIHVQFVEGMLQVHEKYEALIADTFNSDPVFLSALDKACSNVINSKLC 394

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
            K PSKS E +AKYCD LLKKS    +E E++ KL++SIT+FKYI+DKD + KFY++MLA
Sbjct: 395 EKQPSKSAELVAKYCDSLLKKSKT--TEIEIESKLTKSITIFKYIEDKDFYQKFYSRMLA 452

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI 368
           KRLIH QS SMD EE MINKLKQACGYEFTNK HRM TDI +S  LN KF + ++K    
Sbjct: 453 KRLIHDQSQSMDAEEMMINKLKQACGYEFTNKLHRMFTDISVSADLNTKF-AHYLKQQNK 511

Query: 369 DLGIHFSINILQAGSWPLGPTVISS-FSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           +LGI+ SI ILQAG+WPLGPT I+S F+VPQE EK I +FE FYH  F+GRKL+WL+++ 
Sbjct: 512 ELGINLSIKILQAGAWPLGPTQITSGFAVPQEFEKPIRLFESFYHVNFSGRKLTWLNHLC 571

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             ELK+S+  R Y VTMQT+QMAILLLFE  D++   +IQ  L L++D + +HI SLVE 
Sbjct: 572 HGELKISFADRNYMVTMQTYQMAILLLFESTDSLHYKEIQDSLQLNKDMLQKHILSLVES 631

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
           KLL S+ E + E++++ LN  Y NKRTK KI+ A+QKETPQEIE T++SVDEDRK+YLQA
Sbjct: 632 KLLLSDTEGVDENSKLSLNKNYINKRTKFKITAALQKETPQEIENTINSVDEDRKMYLQA 691

Query: 548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
            IVRIMKSRK +RHNALIQE+L+QSK SFAPSI MIKKCIESLIDK Y+ERT NS DEYS
Sbjct: 692 TIVRIMKSRKVLRHNALIQEILAQSKVSFAPSIGMIKKCIESLIDKQYIERTPNSGDEYS 751

Query: 607 YVA 609
           YVA
Sbjct: 752 YVA 754

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322800724|gb|EFZ21628.1| hypothetical protein SINV_05339 [Solenopsis invicta]

 Score =  654 bits (1686), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/546 (59%), Positives = 409/546 (74%), Gaps = 4/546 (0%)

Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
           +LY +IFE  FL+ SGE+Y +EAS LLQ  +V++Y+E+V   L +E  R+ +FLH SS  
Sbjct: 207 NLYQEIFEEPFLKASGEFYTAEASSLLQQSDVTRYIEKVTWRLAQEEARAYKFLHKSSVA 266

Query: 128 KVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHIC 187
           KVKA CE  MVA H++ L  E   M+  E R DLA +YPLLRS+  G++ L+  +  HI 
Sbjct: 267 KVKACCEDKMVAAHVDLLHAEAELMIKNESRRDLALLYPLLRSLPGGLDPLVQHLTRHIT 326

Query: 188 KQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF 247
            QGL+AI  L G+N+  QFVENML VH KY   +KE+F+ DQSF+GALDKACS+++N++ 
Sbjct: 327 LQGLQAIGPLQGENVYMQFVENMLNVHSKYSEMIKEVFNSDQSFVGALDKACSAIVNYRP 386

Query: 248 DPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKML 307
            PK P ++PE LAKYCD LLKKS +  SESE++DKL +SITVFKY+DDKDVF KFY++ML
Sbjct: 387 APKQPVRAPELLAKYCDTLLKKSPRAASESEIEDKLKRSITVFKYVDDKDVFQKFYSRML 446

Query: 308 AKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN- 366
           AKRLIHQQS SMD EE MI+ LK+ACGYEFTNK HRM TD+ +S  LN KF +   + + 
Sbjct: 447 AKRLIHQQSQSMDAEEMMIDDLKRACGYEFTNKLHRMFTDMSVSADLNAKFTTTLREGDG 506

Query: 367 EIDLGIHFSINILQAGSW-PLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHN 425
           E  LG  F++ +LQAG+W    P     F VPQ+LEK I  FE FYH QF+GRKL+WLH+
Sbjct: 507 ENQLGTGFAVKVLQAGAWPLGLPPSPGPFHVPQQLEKSIQAFETFYHMQFSGRKLTWLHH 566

Query: 426 ISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485
           +SQ ELK +YLK+PY VT+QT+QMA+LLLFE  DA+ C +    L LS DQ+ +H ASLV
Sbjct: 567 LSQGELKFNYLKKPYLVTVQTYQMALLLLFEHCDAIPCKEAAASLRLSHDQLVKHAASLV 626

Query: 486 ECKLLT-SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLY 544
           +CK+L  SN  EL EDT + LN  Y+NKRTK +++G +Q++ PQ+ E T  SVDEDRK++
Sbjct: 627 DCKILNKSNDGELEEDTILTLNFSYSNKRTKFRVTGVLQRDAPQDAEATHRSVDEDRKMF 686

Query: 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTD 603
           LQAAIVRIMKSRK +RHN LIQEVLSQSK +FAPSI MIKKCIE+LIDK Y+ERTANS D
Sbjct: 687 LQAAIVRIMKSRKLLRHNQLIQEVLSQSKVTFAPSIGMIKKCIETLIDKQYIERTANSAD 746

Query: 604 EYSYVA 609
           EYSY+A
Sbjct: 747 EYSYIA 752

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195030360|ref|XP_001988036.1| GH10784 [Drosophila grimshawi] gi|193904036|gb|EDW02903.1| GH10784 [Drosophila grimshawi]

 Score =  653 bits (1685), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 314/543 (57%), Positives = 409/543 (75%), Gaps = 5/543 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY ++FE   LE SG +Y +EA+KLLQ C+VSQYM+ V+++L  E+ R+ +FLHVSS PK
Sbjct: 217 LYQELFEQPMLEASGTYYTNEANKLLQRCSVSQYMQEVIKILEFESKRAQKFLHVSSLPK 276

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINI-LIDAVRDHIC 187
           ++  CE   + D L F+  EC  MV++ERR DL NMY +L+ + + +   LI    +HI 
Sbjct: 277 LRKMCEWKFINDRLGFIYSECRDMVSDERRQDLRNMYIVLKPIPDNLKAELIQTFLEHIK 336

Query: 188 KQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF 247
            +GLE +  L G+NI   FVENML VH KY+  + ++F  D  F+ ALDKAC+SVIN + 
Sbjct: 337 NEGLETVYALKGENIHIAFVENMLKVHHKYQELIADVFENDSLFLSALDKACASVINRRP 396

Query: 248 DPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKML 307
             + P +S EY+AKYCD LLKKS     E+E+D KL+ +IT+FKYI+DKDV+ KFY+++L
Sbjct: 397 SERQPCRSAEYVAKYCDTLLKKSKT--CEAEIDQKLTNNITIFKYIEDKDVYQKFYSRLL 454

Query: 308 AKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE 367
           AKRLIH+QS SMD EE MIN+LKQACGYEFTNK HRM TDI +S  LN KF++  +K N+
Sbjct: 455 AKRLIHEQSQSMDAEEGMINRLKQACGYEFTNKLHRMFTDISVSTDLNNKFNNH-LKDND 513

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           IDLGI+ SI +LQAG+WPLG T +  F+VPQE EK I MFE +YH  F+GRKL+WLH++ 
Sbjct: 514 IDLGINLSIKVLQAGAWPLGSTQVIPFAVPQEFEKSIKMFEDYYHNLFSGRKLTWLHHMC 573

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             ELKLS+LK+ Y VTMQT+QMAI+LLFE  D ++C +IQ  L L+ +   +H+  ++E 
Sbjct: 574 HGELKLSHLKKSYIVTMQTYQMAIILLFETCDTLSCREIQNTLQLNDETYQKHMQPMIES 633

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
           KLL ++ E L+ DT I LN+ Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQA
Sbjct: 634 KLLNASSENLSGDTRIELNMDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQA 693

Query: 548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
           AIVRIMK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYS
Sbjct: 694 AIVRIMKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYS 753

Query: 607 YVA 609
           Y+A
Sbjct: 754 YMA 756

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195155674|ref|XP_002018726.1| GL25796 [Drosophila persimilis] gi|198476633|ref|XP_001357419.2| GA13508 [Drosophila pseudoobscura pseudoobscura] gi|194114879|gb|EDW36922.1| GL25796 [Drosophila persimilis] gi|198137786|gb|EAL34488.2| GA13508 [Drosophila pseudoobscura pseudoobscura]

 Score =  651 bits (1680), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 312/543 (57%), Positives = 409/543 (75%), Gaps = 5/543 (0%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           LY D+FE   LE SG +Y  EA+KLLQ C VSQYM+ V+++L  E+ R+ +FLHVSS  K
Sbjct: 217 LYQDLFEAPMLEASGAYYTDEANKLLQRCTVSQYMQEVIRILEYESRRAQKFLHVSSLAK 276

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINI-LIDAVRDHIC 187
           ++ +CE+  + D L F+  EC  MV+EERR DL NMY +L+ + + +   LI    +HI 
Sbjct: 277 LRKQCEEKFINDRLGFIYSECREMVSEERRQDLRNMYIVLKPIPDHLKSELIQTFLEHIK 336

Query: 188 KQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF 247
            +GLE +S L G+NI   FVENML VH+KY+  + ++F  D  F+ ALDKAC+SVIN + 
Sbjct: 337 NEGLETVSALKGENIHISFVENMLKVHQKYQELIGDVFENDSLFLSALDKACASVINRRP 396

Query: 248 DPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKML 307
             ++P +S EY+A+YCD LLKKS     E+E+D KL+ +IT+FKYI+DKDV+ KFY+++L
Sbjct: 397 SERVPCRSAEYVARYCDTLLKKSKT--CEAEIDQKLTNNITIFKYIEDKDVYQKFYSRLL 454

Query: 308 AKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE 367
           AKRLIH+QS SMD EE MIN+LKQACGYEFTNK HRM TDI +S  LN KF++    TN 
Sbjct: 455 AKRLIHEQSQSMDAEEGMINRLKQACGYEFTNKLHRMFTDISVSTDLNNKFNTHLKDTN- 513

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           ++LGI+ SI +LQAG+WPLG T +  F+VPQE EK I MFE +YH  F+GRKL+WLH++ 
Sbjct: 514 VELGINLSIKVLQAGAWPLGSTQVIPFAVPQEFEKSIKMFEDYYHKLFSGRKLTWLHHMC 573

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
             ELKLS+LK+ Y VTMQT+QMAI+LLFE  D+++C +IQ  L L+ +   +H+  ++E 
Sbjct: 574 HGELKLSHLKKSYIVTMQTYQMAIILLFETCDSLSCREIQNTLQLNDETFQKHMQPMIES 633

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
           KLL ++ E L  +T I LN+ Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQA
Sbjct: 634 KLLNASSENLAGETRIDLNMDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQA 693

Query: 548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
           AIVRIMK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYS
Sbjct: 694 AIVRIMKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYS 753

Query: 607 YVA 609
           Y+A
Sbjct: 754 YMA 756

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	609
FB|FBgn0032956	753	Cul-2 "Cullin-2" [Drosophila m	0.883	0.714	0.563	5.9e-187
UNIPROTKB|E2QRU7	745	CUL2 "Uncharacterized protein"	0.883	0.722	0.537	4.5e-178
UNIPROTKB|Q08DE9	745	CUL2 "Uncharacterized protein"	0.883	0.722	0.537	5.7e-178
UNIPROTKB|Q13617	745	CUL2 "Cullin-2" [Homo sapiens	0.883	0.722	0.535	9.2e-178
ZFIN|ZDB-GENE-030131-8032	764	cul2 "cullin 2" [Danio rerio (	0.973	0.776	0.503	2.4e-177
MGI|MGI:1918995	745	Cul2 "cullin 2" [Mus musculus	0.883	0.722	0.533	2.4e-177
UNIPROTKB|D4A0H4	725	Cul2 "Cullin 2 (Predicted), is	0.574	0.482	0.561	8.3e-171
RGD|1310644	706	Cul2 "cullin 2" [Rattus norveg	0.758	0.654	0.491	1.6e-159
UNIPROTKB|F1N829	747	CUL2 "Uncharacterized protein"	0.973	0.793	0.508	1.3e-153
UNIPROTKB|Q5T2B7	688	CUL2 "Cullin-2" [Homo sapiens	0.883	0.781	0.535	9.5e-153

FB|FBgn0032956 Cul-2 "Cullin-2" [Drosophila melanogaster (taxid:7227)]

 Score = 1615 (573.6 bits), Expect = 5.9e-187, Sum P(2) = 5.9e-187
 Identities = 306/543 (56%), Positives = 404/543 (74%)

Query:    69 LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
             LY ++FE   LE SG +Y  EA+KLL  C+VS+YM+ V+++L  E+ R+ +FLHVSS PK
Sbjct:   214 LYQELFEGPMLEASGAYYTDEANKLLHRCSVSEYMQEVIRILEYESRRAQKFLHVSSLPK 273

Query:   129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINI-LIDAVRDHIC 187
             ++ +CE+  + D L F+  EC  MV+EERR DL NMY +L+ + + +   LI    DHI 
Sbjct:   274 LRKECEEKFINDRLGFIYSECREMVSEERRQDLRNMYVVLKPIPDNLKSELITTFLDHIK 333

Query:   188 KQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF 247
              +GL+ +S L G+NI   FVENML VH KY+  + ++F  D  F+ ALDKAC+SVIN + 
Sbjct:   334 SEGLQTVSALKGENIHIAFVENMLKVHHKYQELIADVFENDSLFLSALDKACASVINRRP 393

Query:   248 DPKMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKML 307
               + P +S EY+AKYCD           E+E+D KL+ +IT+FKYI+DKDV+ KFY+++L
Sbjct:   394 TERQPCRSAEYVAKYCD--TLLKKSKTCEAEIDQKLTNNITIFKYIEDKDVYQKFYSRLL 451

Query:   308 AKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE 367
             AKRLIH+QS SMD EE MIN+LKQACGYEFTNK HRM TDI +S  LN KF++  +K + 
Sbjct:   452 AKRLIHEQSQSMDAEEGMINRLKQACGYEFTNKLHRMFTDISVSVDLNNKFNTH-LKDSN 510

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             +DLGI+ +I +LQAG+WPLG T +  F+VPQE EK I MFE +YH  F+GRKL+WLH++ 
Sbjct:   511 VDLGINLAIKVLQAGAWPLGSTQVIPFAVPQEFEKSIKMFEDYYHKLFSGRKLTWLHHMC 570

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               ELKLS+LK+ Y VTMQT+QMAI+LLFE  D+++C +IQ  L L+ +   +H+  ++E 
Sbjct:   571 HGELKLSHLKKSYIVTMQTYQMAIILLFETCDSLSCREIQNTLQLNDETFQKHMQPIIES 630

Query:   488 KLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 547
             KLL ++ E L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQA
Sbjct:   631 KLLNASSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQA 690

Query:   548 AIVRIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606
             AIVRIMK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYS
Sbjct:   691 AIVRIMKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYS 750

Query:   607 YVA 609
             Y+A
Sbjct:   751 YMA 753

GO:0000152 "nuclear ubiquitin ligase complex" evidence=ISS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

GO:0007295 "growth of a germarium-derived egg chamber" evidence=IMP

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=IMP

UNIPROTKB|E2QRU7 CUL2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1493 (530.6 bits), Expect = 4.5e-178, Sum P(2) = 4.5e-178
 Identities = 293/545 (53%), Positives = 399/545 (73%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   203 YQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 262

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  +
Sbjct:   263 IHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIQDE 322

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   323 GLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 381

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   382 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAK 441

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+K  +  
Sbjct:   442 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIKNQDTV 500

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct:   621 KMINHDSEKEDIDTESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 680

Query:   546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
             QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct:   681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query:   605 YSYVA 609
             YSYVA
Sbjct:   741 YSYVA 745

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|Q08DE9 CUL2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 1492 (530.3 bits), Expect = 5.7e-178, Sum P(2) = 5.7e-178
 Identities = 293/545 (53%), Positives = 399/545 (73%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   203 YQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 262

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  +
Sbjct:   263 IHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDE 322

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   323 GLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 381

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   382 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAK 441

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+K  +  
Sbjct:   442 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIKNQDTV 500

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct:   621 KMINHDSEKEDIDVESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 680

Query:   546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
             QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct:   681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query:   605 YSYVA 609
             YSYVA
Sbjct:   741 YSYVA 745

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|Q13617 CUL2 "Cullin-2" [Homo sapiens (taxid:9606)]

 Score = 1490 (529.6 bits), Expect = 9.2e-178, Sum P(2) = 9.2e-178
 Identities = 292/545 (53%), Positives = 399/545 (73%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   203 YQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 262

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  +
Sbjct:   263 IHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDE 322

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   323 GLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 381

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++D+L+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   382 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAK 441

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+K  +  
Sbjct:   442 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIKNQDTV 500

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct:   621 KMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 680

Query:   546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
             QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct:   681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query:   605 YSYVA 609
             YSYVA
Sbjct:   741 YSYVA 745

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0031625 "ubiquitin protein ligase binding" evidence=IDA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IDA

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0008285 "negative regulation of cell proliferation" evidence=TAS

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=TAS

GO:0007050 "cell cycle arrest" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0033554 "cellular response to stress" evidence=TAS

GO:0061418 "regulation of transcription from RNA polymerase II promoter in response to hypoxia" evidence=TAS

GO:0071456 "cellular response to hypoxia" evidence=TAS

ZFIN|ZDB-GENE-030131-8032 cul2 "cullin 2" [Danio rerio (taxid:7955)]

 Score = 1491 (529.9 bits), Expect = 2.4e-177, Sum P(2) = 2.4e-177
 Identities = 303/602 (50%), Positives = 419/602 (69%)

Query:    14 WGSLQ-ETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVD 72
             W  L  E +Q ++ +G + +   NDR  +  +  V +    +    ++ K       Y +
Sbjct:   166 WRKLMIEPLQPML-IGKLLKEIKNDRCGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQE 224

Query:    73 IFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAK 132
             IFE  FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV  +
Sbjct:   225 IFEGPFLTKTGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEVRCRKYLHPSSYSKVIHE 284

Query:   133 CEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLE 192
             C+Q MVADHL FL GEC  ++ +E+R D+ANMY LLR+V  G+  +I  ++ HI  +G+ 
Sbjct:   285 CQQRMVADHLQFLHGECQNIIRQEKRDDMANMYTLLRAVSSGLPHMIQELQVHIHDEGIR 344

Query:   193 AISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMP 252
             A   LS +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +PK  
Sbjct:   345 ATINLSQENMPTLFVESVLEVHSKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EPKSI 403

Query:   253 SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLI 312
              K+PE LAKYCD           E+E++DKL+  ITVFKYIDDKDVF K YA+MLAKRLI
Sbjct:   404 CKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKIYARMLAKRLI 463

Query:   313 HQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE--IDL 370
             H  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+KT E  +DL
Sbjct:   464 HGLSLSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSTDLNNKFNN-FIKTQETVVDL 522

Query:   371 GIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVE 430
             GI F I +LQAG+WPL     S+F++PQELEK + MFE FY+  F+GRKL+WLH +   E
Sbjct:   523 GISFQIYVLQAGAWPLTHVPSSTFAIPQELEKSVQMFELFYNQHFSGRKLTWLHYLCTGE 582

Query:   431 LKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLL 490
             +K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ K++
Sbjct:   583 VKMNYLSKPYVAVVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELQKTIKSLLDVKMI 642

Query:   491 TSN--KEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAA 548
             + +  KEE+  ++   L + + +KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAA
Sbjct:   643 SHDLQKEEIEPESTFSLIMSFTSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYLQAA 702

Query:   549 IVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607
             IVRIMK+RK +RHNALIQEV++QSK+ F PSISMIKKCIE LIDK Y+ER+ +S DEYSY
Sbjct:   703 IVRIMKARKVLRHNALIQEVINQSKARFNPSISMIKKCIEVLIDKQYIERSQSSADEYSY 762

Query:   608 VA 609
             VA
Sbjct:   763 VA 764

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0001944 "vasculature development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

MGI|MGI:1918995 Cul2 "cullin 2" [Mus musculus (taxid:10090)]

 Score = 1481 (526.4 bits), Expect = 2.4e-177, Sum P(2) = 2.4e-177
 Identities = 291/545 (53%), Positives = 397/545 (72%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y  IF + FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   203 YQGIFVSPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 262

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++ +ER++D+ANMY LLR+V  G+  +I+ ++ HI  +
Sbjct:   263 IHECQQRMVADHLQFLHSECHSIIQQERKNDMANMYVLLRAVSSGLPHMIEELQKHIHDE 322

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +++ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   323 GLRATSNLTQEHMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 381

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   382 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAK 441

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F++  +  
Sbjct:   442 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIRNQDTV 500

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct:   621 KMINHDSEKEDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYL 680

Query:   546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
             QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct:   681 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 740

Query:   605 YSYVA 609
             YSYVA
Sbjct:   741 YSYVA 745

GO:0005515 "protein binding" evidence=IPI

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IMP

GO:0030891 "VCB complex" evidence=ISO

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=ISO

GO:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

UNIPROTKB|D4A0H4 Cul2 "Cullin 2 (Predicted), isoform CRA_a" [Rattus norvegicus (taxid:10116)]

 Score = 1030 (367.6 bits), Expect = 8.3e-171, Sum P(3) = 8.3e-171
 Identities = 200/356 (56%), Positives = 268/356 (75%)

Query:   259 LAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTS 318
             LAKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAKRLIH  S S
Sbjct:   371 LAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMS 430

Query:   319 MDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE--IDLGIHFSI 376
             MD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F++  +  IDLGI F I
Sbjct:   431 MDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIRNQDTVIDLGISFQI 489

Query:   377 NILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYL 436
              +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH +   E+K++YL
Sbjct:   490 YVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYL 549

Query:   437 KRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT--SNK 494
              +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ K++   S K
Sbjct:   550 GKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEK 609

Query:   495 EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 554
             E++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   610 EDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYLQAAIVRIMK 669

Query:   555 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   670 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 725

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

RGD|1310644 Cul2 "cullin 2" [Rattus norvegicus (taxid:10116)]

 Score = 1177 (419.4 bits), Expect = 1.6e-159, Sum P(3) = 1.6e-159
 Identities = 230/468 (49%), Positives = 326/468 (69%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y  IF + FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   203 YQGIFVSPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 262

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++  ER++D+ANMY LLR+V  G+  +I+ ++ HI  +
Sbjct:   263 IHECQQRMVADHLQFLHSECHSIIRHERKNDMANMYVLLRAVSSGLPHMIEELQRHIHDE 322

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +++ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   323 GLRATSNLTQEHMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 381

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   382 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAK 441

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F++  +  
Sbjct:   442 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIRNQDTV 500

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   501 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 560

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   561 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 620

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERT 533
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQ I ++
Sbjct:   621 KMINHDSEKEDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQVISQS 668

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0030163 "protein catabolic process" evidence=ISO

GO:0030891 "VCB complex" evidence=IDA

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=ISO

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA;ISO

GO:0032403 "protein complex binding" evidence=IPI

GO:0004842 "ubiquitin-protein ligase activity" evidence=IC

UNIPROTKB|F1N829 CUL2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 1498 (532.4 bits), Expect = 1.3e-153, P = 1.3e-153
 Identities = 307/604 (50%), Positives = 422/604 (69%)

Query:    14 WGSLQ-ETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHLYVD 72
             W  L  E +Q ++ +  + R   NDR  +  +  V +    +    ++ K  L    Y +
Sbjct:   147 WRKLMIEPLQAIL-IRMLLREIKNDRCGEDPNQKVIHGVINSFVHVEQYKKKLPLKFYQE 205

Query:    73 IFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAK 132
             IFE  FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV  +
Sbjct:   206 IFECPFLNETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEMRCRKYLHPSSYGKVIHE 265

Query:   133 CEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLE 192
             C+Q MVADHL FL  EC  ++ +E+R+D+ANMY LLR+V  G+  +I  +++HI  +GL 
Sbjct:   266 CQQRMVADHLQFLHAECHNIIRQEKRNDMANMYTLLRAVSSGLPHMIQELQNHIHDEGLR 325

Query:   193 AISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMP 252
             A S LS +N+ TQFVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +PK  
Sbjct:   326 ATSNLSQENMPTQFVESVLEVHSKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EPKSI 384

Query:   253 SKSPEYL--AKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKR 310
              K+PE L  AKYCD           E+E++DKL+  ITVFKYIDDKDVF KFYA+MLAKR
Sbjct:   385 CKAPELLELAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYIDDKDVFQKFYARMLAKR 444

Query:   311 LIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE--I 368
             LIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+K  +  I
Sbjct:   445 LIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIKNQDTII 503

Query:   369 DLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
             DLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH +  
Sbjct:   504 DLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCT 563

Query:   429 VELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488
              E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ K
Sbjct:   564 GEVKMNYLCKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVK 623

Query:   489 LLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQ 546
             ++   S+KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQ
Sbjct:   624 MINHDSDKEDVEAESTFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQ 683

Query:   547 AAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEY 605
             AAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEY
Sbjct:   684 AAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEY 743

Query:   606 SYVA 609
             SYVA
Sbjct:   744 SYVA 747

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

UNIPROTKB|Q5T2B7 CUL2 "Cullin-2" [Homo sapiens (taxid:9606)]

 Score = 1490 (529.6 bits), Expect = 9.5e-153, P = 9.5e-153
 Identities = 292/545 (53%), Positives = 399/545 (73%)

Query:    70 YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKV 129
             Y +IFE+ FL  +GE+YK EAS LLQ  N SQYME+VL  L +E  R  ++LH SSY KV
Sbjct:   146 YQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKV 205

Query:   130 KAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQ 189
               +C+Q MVADHL FL  EC  ++ +E+++D+ANMY LLR+V  G+  +I  +++HI  +
Sbjct:   206 IHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDE 265

Query:   190 GLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
             GL A S L+ +N+ T FVE++L VH K+   +  + +GDQ FM ALDKA +SV+N++ +P
Sbjct:   266 GLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYR-EP 324

Query:   250 KMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAK 309
             K   K+PE LAKYCD           E+E++D+L+  ITVFKYIDDKDVF KFYA+MLAK
Sbjct:   325 KSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAK 384

Query:   310 RLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNE-- 367
             RLIH  S SMD EEAMINKLKQACGYEFT+K HRM TD+ +S  LN KF++ F+K  +  
Sbjct:   385 RLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNN-FIKNQDTV 443

Query:   368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
             IDLGI F I +LQAG+WPL     S+F++PQELEK + MFE FY   F+GRKL+WLH + 
Sbjct:   444 IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC 503

Query:   428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
               E+K++YL +PY   + T+QMA+LL F  ++ ++  ++Q    +++ ++ + I SL++ 
Sbjct:   504 TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDV 563

Query:   488 KLLT--SNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             K++   S KE++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YL
Sbjct:   564 KMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYL 623

Query:   546 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 604
             QAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DE
Sbjct:   624 QAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADE 683

Query:   605 YSYVA 609
             YSYVA
Sbjct:   684 YSYVA 688

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O13790	CUL1_SCHPO	No assigned EC number	0.3321	0.8752	0.6949	yes	N/A
Q13617	CUL2_HUMAN	No assigned EC number	0.5449	0.8866	0.7248	yes	N/A
Q9C9L0	CUL3B_ARATH	No assigned EC number	0.3202	0.8817	0.7336	yes	N/A
Q17390	CUL2_CAEEL	No assigned EC number	0.4229	0.8866	0.6352	yes	N/A
Q9XZJ3	CUL2_DICDI	No assigned EC number	0.3869	0.8899	0.7029	yes	N/A
Q9D4H8	CUL2_MOUSE	No assigned EC number	0.5457	0.8850	0.7234	yes	N/A
Q5RCF3	CUL2_PONAB	No assigned EC number	0.5449	0.8866	0.7248	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	609
pfam00888	603	pfam00888, Cullin, Cullin family	1e-139
COG5647	773	COG5647, COG5647, Cullin, a subunit of E3 ubiquiti	1e-105
smart00182	143	smart00182, CULLIN, Cullin	3e-48
pfam10557	68	pfam10557, Cullin_Nedd8, Cullin protein neddylatio	8e-28
smart00884	68	smart00884, Cullin_Nedd8, Cullin protein neddylati	4e-26
pfam12840	61	pfam12840, HTH_20, Helix-turn-helix domain	0.003

>gnl|CDD|216175 pfam00888, Cullin, Cullin family

 Score =  416 bits (1071), Expect = e-139
 Identities = 188/447 (42%), Positives = 263/447 (58%), Gaps = 8/447 (1%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE  FLE + E+YK E+SK LQ  +VS+YM++V + L EE  R   +LH S+  K
Sbjct: 164 VYKEDFEKPFLEATSEFYKKESSKFLQENSVSEYMKKVEERLEEEEERVRLYLHSSTEKK 223

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +   CE+ ++  HL FL  E   ++  E+  DL  MY LL  V  G+  L      HI K
Sbjct: 224 LIEVCEKVLIEKHLEFLHSEFQRLLDNEKIEDLRRMYRLLSRVPNGLEPLRKYFEKHIKK 283

Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
           +GL A+S L+ +     +V+ +L +H KY + V E F+ D  F+ ALDKA    IN    
Sbjct: 284 EGLAAVSDLAVETDPKDYVQTLLELHDKYDSLVNEAFNNDALFLNALDKAFEEFIN---- 339

Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
               SKS E LAKYCD LLKKS KGL+E E+++KL + I +FKYI+DKDVF KFY KMLA
Sbjct: 340 -SNSSKSAELLAKYCDSLLKKSLKGLNEEELEEKLDKIIVLFKYIEDKDVFEKFYRKMLA 398

Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN-E 367
           KRL++  S S D E+ MI KLKQ CGY+FT+K  RM  DI +S  LN  F +        
Sbjct: 399 KRLLNGTSASDDAEKKMIEKLKQECGYQFTSKLERMFKDISLSKELNNSFKNHLENNLDL 458

Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
           +  GI  S+ +L  G WP  PT    FS+P+ELEK +  FE+FY  + +GRKL+WLH++ 
Sbjct: 459 LSEGIDLSVLVLSTGFWPTLPT--EPFSLPEELEKALEKFEEFYSKKHSGRKLTWLHSLG 516

Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
           + ELK  +  + Y +T+ T+QMA+LLLF   + +T  ++     LS D + R + SL++ 
Sbjct: 517 RGELKAEFNDKTYELTVSTYQMAVLLLFNDQEELTVEELSEATGLSDDLLRRTLQSLLKA 576

Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRT 514
           K+L   K    E+         N+  T
Sbjct: 577 KVLLLTKIPKGEEFSPNTVFSLNSDFT 603

Length = 603

>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score =  334 bits (858), Expect = e-105
 Identities = 180/568 (31%), Positives = 297/568 (52%), Gaps = 30/568 (5%)

Query: 65  LDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVS 124
            +   Y  +FE  FLE + E+Y+ E+S++++  +V++Y+E+  ++L  E      +L VS
Sbjct: 213 ENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVS 272

Query: 125 SYPKVKAKCEQHMVADHLNFL---QGECVPMVAEERRHDLANMYPLLRSVREGINILIDA 181
           +   +    E  ++  HL+ L          +       L  +Y LL   + G+  L + 
Sbjct: 273 TKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPLQEV 332

Query: 182 VRDHICKQGLEA------------ISGLSGDN--ISTQFVENMLAVHKKYKAFVKELFSG 227
              ++  +G+                G  G    +   +V+ +L+ H  + + V E F G
Sbjct: 333 FERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEG 392

Query: 228 DQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSI 287
           D S + AL  A  + IN        S   EYLAKY D LLKK  K     ++ D L   I
Sbjct: 393 DGSIVKALGNAFKTFINGNESAD--SGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDII 450

Query: 288 TVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTD 347
           T+F+Y+++KDVF K+Y K+LAKRL++ +S S   E  MI+ LK+ CG EFT+K   M  D
Sbjct: 451 TLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRD 510

Query: 348 IKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMF 407
           I +S    E F       N+    +   + +L    WPL P  + S  +P+EL   +  F
Sbjct: 511 ISLSSEFTEAFQHSPQSYNK---YLDLFVWVLTQAYWPLSPEEV-SIRLPKELVPILEGF 566

Query: 408 EKFYHGQFNGRKLSWLHNISQVELKLSYLKR---PYFVTMQTFQMAILLLFEKNDAMTCG 464
           +KFY  + NGRKL W  ++   E+K  + +        T   +Q+ + LLF  ++ +T  
Sbjct: 567 KKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFE 626

Query: 465 DIQTVLSLSQDQIGRHIASLVECKL--LTSNKEELTEDTEIRLNLGYNNKRTKLKISGAV 522
           +I  +  LS D + R + SL   KL  L  + + ++ +T+  +N  +++K  ++KI+   
Sbjct: 627 EILELTKLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIA 686

Query: 523 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISM 581
           + E  Q+   T  +V+EDR+  LQA IVRIMK+RK+++H  L++EV++Q KS F P +SM
Sbjct: 687 ESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSM 746

Query: 582 IKKCIESLIDKNYVERTANSTDEYSYVA 609
           +K+ IE+LI+K Y+ER A+  + Y Y+A
Sbjct: 747 VKRAIETLIEKEYLERQADD-EIYVYLA 773

Length = 773

>gnl|CDD|214545 smart00182, CULLIN, Cullin

 Score =  164 bits (418), Expect = 3e-48
 Identities = 66/141 (46%), Positives = 87/141 (61%), Gaps = 1/141 (0%)

Query: 292 YIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKIS 351
           YI DKDVF K+Y K LAKRLI  +S S D EE MI KLKQ CGYEFT+K  RM  DI +S
Sbjct: 1   YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLS 60

Query: 352 GGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFY 411
             LN+ F             I  ++ +L +G WP   T +   ++PQELE  +  FE+FY
Sbjct: 61  KDLNQSFKDMLENNPSAKPIIDLNVRVLTSGYWPTSSTEV-EINLPQELEDALEEFEEFY 119

Query: 412 HGQFNGRKLSWLHNISQVELK 432
             + +GRKL+WLH++ + E+K
Sbjct: 120 LAKHSGRKLTWLHSLGRGEVK 140

Length = 143

>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain

 Score =  105 bits (265), Expect = 8e-28
 Identities = 40/68 (58%), Positives = 51/68 (75%), Gaps = 1/68 (1%)

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 595
           V+EDRKL +QAAIVRIMKSRK + HN L+ EV+ Q K  F PS++ IKK IESLI+K Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIEKEYL 60

Query: 596 ERTANSTD 603
           ER  +  +
Sbjct: 61  ERDEDDRN 68

This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. Length = 68

>gnl|CDD|214883 smart00884, Cullin_Nedd8, Cullin protein neddylation domain

 Score =  101 bits (253), Expect = 4e-26
 Identities = 39/68 (57%), Positives = 51/68 (75%), Gaps = 1/68 (1%)

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 595
           V+EDRKL +QAAIVRIMKSRK + H+ L+ EV+ Q K  F PS+S IKK IESLI++ Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHSELVSEVIEQLKKRFKPSVSDIKKRIESLIEREYL 60

Query: 596 ERTANSTD 603
           ER  +  +
Sbjct: 61  ERDEDDPN 68

This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. Length = 68

>gnl|CDD|205100 pfam12840, HTH_20, Helix-turn-helix domain

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 9/48 (18%), Positives = 20/48 (41%)

Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEE 496
           + IL      + +T  ++   L + +  +  H+  L E  L+   +E 
Sbjct: 13  LRILRALMGGEPLTASELAERLGIPKQTLSYHLRKLEEAGLVEVVREG 60

This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins. Length = 61

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	609
KOG2284|consensus	728		100.0
KOG2166|consensus	725		100.0
COG5647	773	Cullin, a subunit of E3 ubiquitin ligase [Posttran	100.0
KOG2167|consensus	661		100.0
KOG2285|consensus	777		100.0
PF00888	588	Cullin: Cullin family; InterPro: IPR001373 Cullins	100.0
smart00182	142	CULLIN Cullin.	100.0
KOG2165|consensus	765		99.97
PF10557	68	Cullin_Nedd8: Cullin protein neddylation domain; I	99.79
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	96.23
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.05
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.83
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	95.43
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.85
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	94.47
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	94.14
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	94.13
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.1
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	93.51
COG3355	126	Predicted transcriptional regulator [Transcription	93.26
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	92.95
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	92.5
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	92.26
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	91.79
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	91.75
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	91.52
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	91.16
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	90.98
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	90.83
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	90.78
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	90.19
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	90.15
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	89.5
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	89.46
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	89.37
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	88.82
COG1414	246	IclR Transcriptional regulator [Transcription]	88.81
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	88.55
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	88.48
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	87.85
PRK11569	274	transcriptional repressor IclR; Provisional	87.76
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	87.61
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	87.51
COG1959	150	Predicted transcriptional regulator [Transcription	87.51
PRK13777	185	transcriptional regulator Hpr; Provisional	87.37
PF13730	55	HTH_36: Helix-turn-helix domain	87.18
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	86.8
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	86.47
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	86.21
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	85.81
PHA00738	108	putative HTH transcription regulator	85.68
PRK03573	144	transcriptional regulator SlyA; Provisional	85.5
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	85.4
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	85.2
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	85.09
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	85.06
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	84.78
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	84.4
COG3682	123	Predicted transcriptional regulator [Transcription	84.12
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	84.1
PRK10870	176	transcriptional repressor MprA; Provisional	83.53
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	83.4
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	82.03
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	81.73
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	81.68
COG2345	218	Predicted transcriptional regulator [Transcription	81.33
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	81.15
COG1846	126	MarR Transcriptional regulators [Transcription]	80.86
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	80.83
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	80.52
PRK11014	141	transcriptional repressor NsrR; Provisional	80.5
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	80.34

>KOG2284|consensus

Probab=100.00  E-value=1e-120  Score=901.79  Aligned_cols=577  Identities=43%  Similarity=0.769  Sum_probs=561.8

Q ss_pred             CCCCCCccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh------------
Q psy16234          1 MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH------------   68 (609)
Q Consensus         1 ~~~~~~~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~------------   68 (609)
                      |||+|+.+|||++|..|.++|..++.++++++..|..+|++||++|++.|.|+|+.||+.++.++.+|            
T Consensus         2 ~slkp~vv~fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~   81 (728)
T KOG2284|consen    2 YSLKPKVVEFDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVD   81 (728)
T ss_pred             CCCCceeeeHHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999887            


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        82 p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~i~~~l  161 (728)
T KOG2284|consen   82 PDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKTILPQL  161 (728)
T ss_pred             HHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------ccHHhhHHHHHHHHHHHHHHHHHH
Q psy16234         69 --------------------------------------------------------LYVDIFETQFLEMSGEWYKSEASK   92 (609)
Q Consensus        69 --------------------------------------------------------~Y~~~FE~~~L~~t~~yY~~~s~~   92 (609)
                                                                              +|++.||.|||-+|..||+.+|+.
T Consensus       162 v~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~  241 (728)
T KOG2284|consen  162 VKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQK  241 (728)
T ss_pred             HHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHH
Confidence                                                                    899999999999999999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhccc
Q psy16234         93 LLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVR  172 (609)
Q Consensus        93 ~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~  172 (609)
                      .+.+.+|++||.+|..++++|+-||..|||+||..|++..|++++|.+|.+.++..|..++++++..||+.||.|++.+.
T Consensus       242 ~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~lha~ch~~i~~e~~~d~~nmy~ll~~i~  321 (728)
T KOG2284|consen  242 MLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKLHAVCHDLITNEENKDLRNMYRLLKPIQ  321 (728)
T ss_pred             HHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCC
Q psy16234        173 EGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMP  252 (609)
Q Consensus       173 ~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~  252 (609)
                      .|++.+...|++||.++|.++++.+++.+.|..||+.+|.+|.||.+++...|++|..|..++|+|+..++|....+++.
T Consensus       322 ~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv  401 (728)
T KOG2284|consen  322 AGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSV  401 (728)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998666777


Q ss_pred             CCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHH
Q psy16234        253 SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQA  332 (609)
Q Consensus       253 ~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~  332 (609)
                      +++||.||+|||.+|||+.||+++.|++.+|+..+.+|+|++|||+|+++|.++||+|||.+.|.|+|.|+.||++||+.
T Consensus       402 ~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqa  481 (728)
T KOG2284|consen  402 PKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQA  481 (728)
T ss_pred             cchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHh
Q psy16234        333 CGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYH  412 (609)
Q Consensus       333 ~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~  412 (609)
                      ||++||+++.  +.|++.|.+++++| .+.+                            .+|.+|.+|+...+.|+.||.
T Consensus       482 cgyefts~~~--~td~~~s~~lnn~f-~~~i----------------------------~nf~~pq~l~~~iq~fe~fyt  530 (728)
T KOG2284|consen  482 CGYEFTSSWP--LTDPQLSTNLNNQF-AQDI----------------------------ANFHLPQILQPVIQEFEKFYT  530 (728)
T ss_pred             hCceecccCC--CCChhhccccchhH-HHHH----------------------------HhccchHHHHHHHHHHHHHhc
Confidence            9999999999  99999999999999 5533                            258999999999999999999


Q ss_pred             hcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        413 GQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       413 ~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++|+||+|+|++.+|+++++++|.++.|.-.|.+|||++||+||..+.+++.+|.+.+|++.+.|.+.+.++.+.++|..
T Consensus       531 ~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tildv~~~~~  610 (728)
T KOG2284|consen  531 GKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILDVTLLTC  610 (728)
T ss_pred             cccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHhceeecc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCEEEEecCCCCCcceEEecccc-ccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHh
Q psy16234        493 NKEELTEDTEIRLNLGYNNKRTKLKISGAV-QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ  571 (609)
Q Consensus       493 ~~~~~~~~~~f~lN~~F~~~~~ki~i~~~~-~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~  571 (609)
                      ++.++..+..|++|++|++++.|+++.+|+ ++.+++|.+.+...+.+||+.+++||||||||+||.+.|+.|+++|+.|
T Consensus       611 d~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~q  690 (728)
T KOG2284|consen  611 DDQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQ  690 (728)
T ss_pred             cccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHh
Confidence            887888889999999999999999999876 8889999999999999999999999999999999999999999999999


Q ss_pred             hcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        572 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       572 l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      .++ |.|++++||+|||.||+|.||+|.+.+ +.|.|+|
T Consensus       691 t~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a  728 (728)
T KOG2284|consen  691 TKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA  728 (728)
T ss_pred             hcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence            999 999999999999999999999999887 9999997

>KOG2166|consensus

Probab=100.00  E-value=3.8e-106  Score=890.17  Aligned_cols=587  Identities=32%  Similarity=0.601  Sum_probs=530.3

Q ss_pred             CCCccChHhhHHHHHHHHHHHHhcC-CCChhhhhhhhhhhhhhcc------cCC-cccHHHHHHHHHhhhhhh-------
Q psy16234          4 KPKQVDFNKTWGSLQETIQGVITLG-NVRRATWNDRFSDIYSLCV------AYP-EPLADRLYQETKLFLDQH-------   68 (609)
Q Consensus         4 ~~~~~~fe~~W~~l~~~i~~i~~~~-~~~~~~~~~~y~~vy~~c~------~~~-~~~~~~Ly~~~~~~l~~~-------   68 (609)
                      .+++++|+.+|+.+++|+..+.+.. .++ ..+|..|+.+|.+|+      +.+ .+.+++||+++++++.+|       
T Consensus         4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s-~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~   82 (725)
T KOG2166|consen    4 APKEIDLEVGWSYIETGITKLKRIIEGLS-EPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLP   82 (725)
T ss_pred             cccccchhccHHHHHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999988863 444 455666666555555      332 234499999998888766       


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        83 ~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~  162 (725)
T KOG2166|consen   83 ALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIH  162 (725)
T ss_pred             HHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhh
Q psy16234         69 -----------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVR  119 (609)
Q Consensus        69 -----------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~  119 (609)
                                                   +|..+||++|+++|..||..++..|+...++.+||.+|+.++.+|..|+..
T Consensus       163 ~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~  242 (725)
T KOG2166|consen  163 KEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTH  242 (725)
T ss_pred             hhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHh
Confidence                                         799999999999999999999999999999999999999999999999998


Q ss_pred             hcCCCchhHHHHHHHHHHHHHH----HHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhh
Q psy16234        120 FLHVSSYPKVKAKCEQHMVADH----LNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAIS  195 (609)
Q Consensus       120 yL~~~t~~kl~~~l~~~LI~~~----~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~  195 (609)
                      ||+..+..++.+.++..++..|    .+.+++||..|+++++.+||.+||+|+++++.|++++.+.|+.|++.+|..++.
T Consensus       243 yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~  322 (725)
T KOG2166|consen  243 YLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVA  322 (725)
T ss_pred             hhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhh
Confidence            8877766666666666665555    455569999999999999999999999999999999999999999999988888


Q ss_pred             cccCC--CchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCC
Q psy16234        196 GLSGD--NISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKG  273 (609)
Q Consensus       196 ~~~~~--~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~  273 (609)
                      .....  ..|..+|..+++++++|..++..||.++..|..+++.||..|+|.+..     ..+|+||+|||.+||++.++
T Consensus       323 r~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~-----~~~E~la~y~D~~lkk~~k~  397 (725)
T KOG2166|consen  323 RPAETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA-----TSAELLATYCDDILKKGSKK  397 (725)
T ss_pred             hhhhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC-----CcHHHHHHHhHHHhcccccC
Confidence            66433  689999999999999999999999999999999999999999998842     22699999999999999999


Q ss_pred             CChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHH
Q psy16234        274 LSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGG  353 (609)
Q Consensus       274 ~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~  353 (609)
                      .++.+++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|+|+|++||++|+++||.+||.||++|++|+..|++
T Consensus       398 ~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~  477 (725)
T KOG2166|consen  398 LSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRE  477 (725)
T ss_pred             CchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEE
Q psy16234        354 LNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKL  433 (609)
Q Consensus       354 l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~  433 (609)
                      ++..| +++ .+.+...+++|.|.|||+|+||.+++  .++.||++|.++++.|..||.++|+||+|+|+|++|+|+|.+
T Consensus       478 l~~~F-~~~-~~~~~~~~~df~v~VLt~g~WP~~~~--~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~  553 (725)
T KOG2166|consen  478 LQTAF-ADY-ANYSANLGIDFTVTVLTTGFWPSYKS--TDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEING  553 (725)
T ss_pred             HHHHH-Hhh-hchhccCCCceeEEEeecCCcCCccC--CCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEE
Confidence            99999 765 22333367999999999999999775  469999999999999999999999999999999999999999


Q ss_pred             EEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc--CccccCC--CCCCCCCEEEEecCC
Q psy16234        434 SYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC--KLLTSNK--EELTEDTEIRLNLGY  509 (609)
Q Consensus       434 ~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~--~iL~~~~--~~~~~~~~f~lN~~F  509 (609)
                      +|.+++|+++||++||+||++||+.+.+|+++|.++|+++.+++.++|+||...  +++.. |  +. ++++.|.+|.+|
T Consensus       554 ~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f  631 (725)
T KOG2166|consen  554 KFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKF  631 (725)
T ss_pred             EecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccc
Confidence            999999999999999999999999999999999999999999999999999543  34444 3  33 789999999999


Q ss_pred             CCCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHH
Q psy16234        510 NNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIES  588 (609)
Q Consensus       510 ~~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~  588 (609)
                      +++..|++++.+..+    |.+.+.+.+++||+.+|+||||||||+||.|.|++|+.||++|+++ |.|++.+||+|||.
T Consensus       632 ~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~  707 (725)
T KOG2166|consen  632 TSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIED  707 (725)
T ss_pred             cCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHH
Confidence            999999999876544    6778889999999999999999999999999999999999999999 99999999999999


Q ss_pred             hhhhccccccCCCCCceee
Q psy16234        589 LIDKNYVERTANSTDEYSY  607 (609)
Q Consensus       589 LIekeyl~r~~~~~~~y~Y  607 (609)
                      |||||||+|| +|+++|+|
T Consensus       708 LIEkeYleR~-~~~~~Y~Y  725 (725)
T KOG2166|consen  708 LIEREYLERD-ENPNIYRY  725 (725)
T ss_pred             HHHHHHHhcc-CCCCcccC
Confidence            9999999999 89999998

>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.3e-106  Score=854.98  Aligned_cols=597  Identities=32%  Similarity=0.536  Sum_probs=539.8

Q ss_pred             CccChHhhHHHHHHHHHHHHhc--CCCChhhhhhhhhhhhhhcccCCc-------------ccHHHHHHHHHhhhhhh--
Q psy16234          6 KQVDFNKTWGSLQETIQGVITL--GNVRRATWNDRFSDIYSLCVAYPE-------------PLADRLYQETKLFLDQH--   68 (609)
Q Consensus         6 ~~~~fe~~W~~l~~~i~~i~~~--~~~~~~~~~~~y~~vy~~c~~~~~-------------~~~~~Ly~~~~~~l~~~--   68 (609)
                      ...||+.+|+.++.||.+|...  .++....+|+.|+.+|++|+....             .+++.||+++..+.+++  
T Consensus        16 ~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~i~   95 (773)
T COG5647          16 SEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNYIE   95 (773)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4688999999999999999954  567788999999999999995422             26777888885444332  


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        96 ~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~~lin~  175 (773)
T COG5647          96 EYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVDSLINP  175 (773)
T ss_pred             HhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Q psy16234         69 -----------------------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVL  107 (609)
Q Consensus        69 -----------------------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~  107 (609)
                                                               +|...||++||+.|.+||..+++..+..+++.+||.+|.
T Consensus       176 LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL~ka~  255 (773)
T COG5647         176 LLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAH  255 (773)
T ss_pred             HHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHH
Confidence                                                     799999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHh---hhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHH
Q psy16234        108 QVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQG---ECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD  184 (609)
Q Consensus       108 ~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~---~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~  184 (609)
                      .++++|..++..|++.++..++.++++++||+.|.+.+..   ++..+++..+.+.|+.||+++++++.|+.+|.+.|++
T Consensus       256 ~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~~~f~~  335 (773)
T COG5647         256 KILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPLQEVFER  335 (773)
T ss_pred             HHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHH
Confidence            9999999999999999999999999999999999999975   9999999999999999999999999999999999999


Q ss_pred             HHHHHH--H-HHhhc---cc--------CCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCC
Q psy16234        185 HICKQG--L-EAISG---LS--------GDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPK  250 (609)
Q Consensus       185 ~i~~~g--~-~~~~~---~~--------~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~  250 (609)
                      ||++.|  . .....   .+        ....|..||+.++.+|+.+..++...|.+|..+.+++++||+.|+|.+..  
T Consensus       336 yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~s--  413 (773)
T COG5647         336 YVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNES--  413 (773)
T ss_pred             HHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccc--
Confidence            999999  1 11110   01        12368899999999999999999999999999999999999999998632  


Q ss_pred             CCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Q psy16234        251 MPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLK  330 (609)
Q Consensus       251 ~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk  330 (609)
                      ....+||+||+|+|.+||++.+.....+++..+.+++.||+|+.+||+|+++|++.||||||+++|+|.++|.+||++||
T Consensus       414 a~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LK  493 (773)
T COG5647         414 ADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLK  493 (773)
T ss_pred             cccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHH
Confidence            22578999999999999998865555678888999999999999999999999999999999999999999999999999


Q ss_pred             HHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHH
Q psy16234        331 QACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKF  410 (609)
Q Consensus       331 ~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~  410 (609)
                      +.||.+||+|+++||+||+.|.++...|++.  ++. ....+|+.|.||+..+||.+++ ...++||++|.+.++.|++|
T Consensus       494 k~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s--~~s-~~~~~Dl~v~VLt~a~WP~sp~-~~~~~lP~~l~p~le~f~~~  569 (773)
T COG5647         494 KVCGQEFTSKLEGMFRDISLSSEFTEAFQHS--PQS-YNKYLDLFVWVLTQAYWPLSPE-EVSIRLPKELVPILEGFKKF  569 (773)
T ss_pred             HHhhhHHHHHHHHHHHhcchhHHHHHHHhhC--chh-hccccchhHHHHHHhcCCCCcc-ccccCCChHHHHHHHHHHHH
Confidence            9999999999999999999999999999333  221 1257899999999999998876 46999999999999999999


Q ss_pred             HhhcCCCcceeeecccceEEEEEEEeCccE---EEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc
Q psy16234        411 YHGQFNGRKLSWLHNISQVELKLSYLKRPY---FVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC  487 (609)
Q Consensus       411 Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~---~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~  487 (609)
                      |.+||+||+|.|.||||+|+|+++|+.+.+   ..+++++|+.|+++||+++++|+++|.+.|+|+.++++++|+||+++
T Consensus       570 Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~a  649 (773)
T COG5647         570 YSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCA  649 (773)
T ss_pred             HHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhh
Confidence            999999999999999999999999987653   33478999999999999999999999999999999999999999998


Q ss_pred             CccccCC--CCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHH
Q psy16234        488 KLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALI  565 (609)
Q Consensus       488 ~iL~~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~  565 (609)
                      +++...+  +.++|++.|.+|.+|+++..+|+++.+...+..++..++++.+++||+..+|||||||||+||.|+|++|+
T Consensus       650 k~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv  729 (773)
T COG5647         650 KLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLV  729 (773)
T ss_pred             heeeeccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHH
Confidence            8765443  67889999999999999999999998876666667788889999999999999999999999999999999


Q ss_pred             HHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        566 QEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       566 ~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      ++|+.|.++ |.|++.+||++|+.|||||||+|.++| ..|+|+|
T Consensus       730 ~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa  773 (773)
T COG5647         730 KEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA  773 (773)
T ss_pred             HHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence            999999999 999999999999999999999999988 8999997

>KOG2167|consensus

Probab=100.00  E-value=1.9e-97  Score=768.24  Aligned_cols=532  Identities=31%  Similarity=0.539  Sum_probs=500.6

Q ss_pred             HhhhhhhccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHH
Q psy16234         62 KLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADH  141 (609)
Q Consensus        62 ~~~l~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~  141 (609)
                      +.+...++|.+.|+..|++.+.++|.+++.+..++..+++||++++.++.+|..|+..|++.+|..++..+++.+|+..|
T Consensus       122 ~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~h  201 (661)
T KOG2167|consen  122 KMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRH  201 (661)
T ss_pred             HHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHH
Confidence            34444559999999999999999999999999999999999999999999999999999999997779999999999999


Q ss_pred             HHHHH-hhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHH
Q psy16234        142 LNFLQ-GECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAF  220 (609)
Q Consensus       142 ~~~l~-~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~l  220 (609)
                      ++.+. .|+..+++.++..|+.+||.|++++.+|...++..|.+|+++-|..++....+   ...+|..++.++++.+-+
T Consensus       202 L~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~k---Dk~mVqELL~FK~k~Dii  278 (661)
T KOG2167|consen  202 LDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEK---DKDMVQELLDFKKKVDII  278 (661)
T ss_pred             HHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchh---hHHHHHHHHHHHHHhhHH
Confidence            99975 79999999999999999999999999899999999999999999999876543   356999999999999999


Q ss_pred             HHHhcCCC--hhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHH
Q psy16234        221 VKELFSGD--QSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDV  298 (609)
Q Consensus       221 i~~~F~~~--~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~  298 (609)
                      +..+|..+  ..|..++.+||+.|+|..     ..++||++|+|.|.+|+.|+++.++++++..++.++.||+||..||+
T Consensus       279 ~~~sF~~~v~e~f~~~~~~afe~fink~-----~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdv  353 (661)
T KOG2167|consen  279 VDESFLKYVAEKFLNSMSKAFETFINKR-----RNRPAELIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDV  353 (661)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHhcc-----cCCHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHH
Confidence            99999999  899999999999999965     37899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhcc-CCCCCcceEEE
Q psy16234        299 FHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN-EIDLGIHFSIN  377 (609)
Q Consensus       299 F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~-~~~~~~~f~~~  377 (609)
                      |+.+|++-||+|||.++|+|.|+|.+|+.+||.+||..||+||++||+||..|++++..| +++...+ ....++ +.+.
T Consensus       354 feA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f-~~~~~~~~~~~~~l-~~v~  431 (661)
T KOG2167|consen  354 FEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAF-KQSKGANNRLEGNL-LTVN  431 (661)
T ss_pred             HHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHH-HHHHHhhccCcCCc-eEEE
Confidence            999999999999999999999999999999999999999999999999999999999999 7764333 333445 9999


Q ss_pred             eeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcC
Q psy16234        378 ILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEK  457 (609)
Q Consensus       378 VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~  457 (609)
                      |||.|+||.+++  ..+.||++|..+++.|..||-.+|.||+|.|.+.+|+|.+++.|..|+.++.+|++|++||++||+
T Consensus       432 vlt~~yWpty~~--~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~  509 (661)
T KOG2167|consen  432 VLTMGYWPTYPP--MEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNE  509 (661)
T ss_pred             eecccccCCCCc--hhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCC
Confidence            999999999987  689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHh--cCccccCC--CCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhh
Q psy16234        458 NDAMTCGDIQTVLSLSQDQIGRHIASLVE--CKLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERT  533 (609)
Q Consensus       458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~--~~iL~~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~  533 (609)
                      ++.+|++||.+.|+|.+-+|.++|++|.+  .++|.+.|  +.+.+++.|.+|.+|+.|..||+|+++..|++.+|...|
T Consensus       510 ~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~  589 (661)
T KOG2167|consen  510 GEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKST  589 (661)
T ss_pred             CCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhh
Confidence            99999999999999999999999999996  46888887  678899999999999999999999999989999999999


Q ss_pred             hhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        534 VSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       534 ~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      .++|.+||.+.|+||||||||+||+|+|+.|+.++.+|++ |++.+ ++|++||+||+|||++|| +| +.|+|||
T Consensus       590 ~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk-fpv~~-d~kkriesli~rey~erd-~n-~~y~yva  661 (661)
T KOG2167|consen  590 TERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK-FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA  661 (661)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC-CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence            9999999999999999999999999999999999999999 99888 999999999999999999 44 9999998

>KOG2285|consensus

Probab=100.00  E-value=1.6e-90  Score=692.78  Aligned_cols=600  Identities=32%  Similarity=0.543  Sum_probs=537.1

Q ss_pred             ccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccC---CcccHHHHHHHHHhhhhhh---------------
Q psy16234          7 QVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAY---PEPLADRLYQETKLFLDQH---------------   68 (609)
Q Consensus         7 ~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~---~~~~~~~Ly~~~~~~l~~~---------------   68 (609)
                      ...||+.|+..++.|.++++.+++++..|.++|.+||..|+|.   |..+.+-|-..+.+|+.+-               
T Consensus        10 r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL~   89 (777)
T KOG2285|consen   10 RDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTDGALLI   89 (777)
T ss_pred             hhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence            3479999999999999999999999999999999999999986   3334444555555554321               


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        90 ~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklVhaER~G~a  169 (777)
T KOG2285|consen   90 GYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLVHAERDGNA  169 (777)
T ss_pred             HHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccch
Confidence                                                                                            


Q ss_pred             -------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCC
Q psy16234         69 -------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHV  123 (609)
Q Consensus        69 -------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~  123 (609)
                                               +|.+.||..||+.|.+||+..+..+++++++.+||+.|...+++|+.|+.+||.+
T Consensus       170 ~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~  249 (777)
T KOG2285|consen  170 IDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEM  249 (777)
T ss_pred             hhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhcc
Confidence                                     8999999999999999999999999999999999999999999999999999977


Q ss_pred             --CchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcc--cC
Q psy16234        124 --SSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGL--SG  199 (609)
Q Consensus       124 --~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~--~~  199 (609)
                        .|..++++.|.+.||.+|.+.|+.+|..|+...+++-|++||+|+.+++.|++++...+..||...|.+-+...  .-
T Consensus       250 ~~~s~~~lme~~VnaLv~sf~~tIlAEC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~i  329 (777)
T KOG2285|consen  250 NSPSSGKLMEKAVNALVESFEDTILAECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENI  329 (777)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhc
Confidence              68899999999999999999999999999999999999999999999999999999999999999999877533  22


Q ss_pred             CCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCC-------------C--CCCCchhHhHHHHH
Q psy16234        200 DNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP-------------K--MPSKSPEYLAKYCD  264 (609)
Q Consensus       200 ~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~-------------~--~~~~~~e~La~y~D  264 (609)
                      ..++..||+.||.++++|.+++.++|..|+.|..+-|.||+.++|.....             +  -..++||+||.|||
T Consensus       330 ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCD  409 (777)
T KOG2285|consen  330 TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCD  409 (777)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHH
Confidence            35788999999999999999999999999999999999999999986321             1  24689999999999


Q ss_pred             HHHhccC--CCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCc--hhHHH
Q psy16234        265 MLLKKSS--KGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGY--EFTNK  340 (609)
Q Consensus       265 ~~lkk~~--k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~--~~t~k  340 (609)
                      .+||+..  |.++.++++.+|.+++-+++|+++||+|..+++.+|++|||.+.|++.+.|+.|+..|+ +||.  +|++|
T Consensus       410 mLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNk  488 (777)
T KOG2285|consen  410 MLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNK  488 (777)
T ss_pred             HHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHH
Confidence            9999974  67788999999999999999999999999999999999999999999999999999998 5885  89999


Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHhhcc-CCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcc
Q psy16234        341 FHRMLTDIKISGGLNEKFHSEFVKTN-EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRK  419 (609)
Q Consensus       341 l~~M~~Di~~S~~l~~~f~~~~~~~~-~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~Rk  419 (609)
                      |.+||+||+.|+++++.| +..+... +....-.+++.||+.|.|...+. ...+.||.+|++.+-..+.||+++|+||+
T Consensus       489 LaRMfQDIkvseDlN~~F-k~~~~~~~~~~~aDsiNiKiLNaGAW~R~SE-rv~vSLP~ELED~iPdveEfykk~hsgrk  566 (777)
T KOG2285|consen  489 LARMFQDIKVSEDLNSSF-KKALTGTNNNSIADSINIKILNAGAWGRGSE-RVRVSLPRELEDFIPDVEEFYKKKHSGRK  566 (777)
T ss_pred             HHHHHhhccccHHHHHHH-HHHHhCCCCCCcccceeeeeecccccccccc-eEEEeCchhHHHhCccHHHHHhcccCccc
Confidence            999999999999999999 5545433 33334567899999999998865 46899999999999999999999999999


Q ss_pred             eeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----cCcccc
Q psy16234        420 LSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVE-----CKLLTS  492 (609)
Q Consensus       420 L~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~-----~~iL~~  492 (609)
                      |.|.|++|.++|++.-.-|.|.+.|+|+||+||.+||+  ++.+|++.+.-+|.+|+.+|.+.|-||+.     ..||..
T Consensus       567 l~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~  646 (777)
T KOG2285|consen  567 LQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLC  646 (777)
T ss_pred             hhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeee
Confidence            99999999999988666689999999999999999997  58999999999999999999999999984     457666


Q ss_pred             CC------CCCCCCCEEEEecCCC-------CCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCC
Q psy16234        493 NK------EELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI  559 (609)
Q Consensus       493 ~~------~~~~~~~~f~lN~~F~-------~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l  559 (609)
                      +|      +++.++..|.+|.+|.       .+++|+++....+-.+....++.++.+-+-|....|-+||+|||.||++
T Consensus       647 ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~  726 (777)
T KOG2285|consen  647 EPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTY  726 (777)
T ss_pred             cCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHh
Confidence            54      6788899999999995       4567788766555544444445567788899999999999999999999


Q ss_pred             ChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        560 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       560 ~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +..+|..+.++.++. |-|+..+||++||.|||..|++||++|-++|+|+|
T Consensus       727 ~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia  777 (777)
T KOG2285|consen  727 TNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA  777 (777)
T ss_pred             hHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence            999999999999999 99999999999999999999999999999999997

>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3)

Probab=100.00  E-value=3.3e-80  Score=698.05  Aligned_cols=483  Identities=36%  Similarity=0.667  Sum_probs=431.9

Q ss_pred             HHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-------------------------
Q psy16234         14 WGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-------------------------   68 (609)
Q Consensus        14 W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-------------------------   68 (609)
                      |+.|++||..|+ .+.+++..||++|+.||++|...   .|++||+.+++++..|                         
T Consensus         1 W~~l~~~i~~i~-~~~~~~~~~~~lY~~vy~l~~~~---~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~   76 (588)
T PF00888_consen    1 WEILEEAIDQIF-KKSISKLSYMELYTCVYNLCDNK---YGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWE   76 (588)
T ss_dssp             HHHHHHHHHHHH-TT-GCCSHHHHHHHHHHHHHHTT---THHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHH-cCCCChhHHHHHHHHHHhhcCCc---ccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHH
Confidence            999999999999 45778999999999999996544   8899999998777655                         


Q ss_pred             --------------------------------------------------------------------------ccHHhh
Q psy16234         69 --------------------------------------------------------------------------LYVDIF   74 (609)
Q Consensus        69 --------------------------------------------------------------------------~Y~~~F   74 (609)
                                                                                                +|.+.|
T Consensus        77 ~~~~~~~~i~~if~yLdr~yv~~~~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~~~~~y~~~f  156 (588)
T PF00888_consen   77 KYKKAIKYISDIFSYLDRNYVKRNLFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELGSLEVYEEEF  156 (588)
T ss_dssp             HHHHHHHHHHHHTHHHHHTSTTTTHHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTTHTHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccchHHhhHHHH
Confidence                                                                                      489999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHh
Q psy16234         75 ETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVA  154 (609)
Q Consensus        75 E~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~  154 (609)
                      |++||+.|.+||+.++   +++.++.+||.+|+.++++|.+|+..||+++|..++.+++.++||.+|.+.|.+++..|++
T Consensus       157 e~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l~~~~~~ll~  233 (588)
T PF00888_consen  157 EKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDELSSGFRDLLE  233 (588)
T ss_dssp             HHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999   7777999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHH
Q psy16234        155 EERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGA  234 (609)
Q Consensus       155 ~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~  234 (609)
                      +++.++|++||+|+++++++++.+++.|++||.+.|.++++.......|..||+.++++|++|..++..||++++.|..+
T Consensus       234 ~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~  313 (588)
T PF00888_consen  234 EDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKA  313 (588)
T ss_dssp             TT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHH
T ss_pred             hhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHH
Confidence            99999999999999999999999999999999999999999876556788999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCC
Q psy16234        235 LDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQ  314 (609)
Q Consensus       235 l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~  314 (609)
                      +++||+.++|.+     ..++|++||+|||.+++++.++.++++++..++.++.||+|+++||+|+.+|+++||+|||.+
T Consensus       314 l~~af~~~~n~~-----~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~  388 (588)
T PF00888_consen  314 LDEAFEEFLNKN-----NNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSN  388 (588)
T ss_dssp             HHHHHHHHHHCS-----TSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHhHHHHHHcC-----CcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcc
Confidence            999999999986     378999999999999999987778888999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCC--CcceEEEeeecCCCCCCCCCCC
Q psy16234        315 QSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDL--GIHFSINILQAGSWPLGPTVIS  392 (609)
Q Consensus       315 ~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~--~~~f~~~VLt~~~WP~~~~~~~  392 (609)
                      ++.+.+.|+.+|++|+.+||.++|++|++|++|+..|+++++.| ++.....+...  +++|+|.||++|+||..+.. .
T Consensus       389 ~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f-~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~-~  466 (588)
T PF00888_consen  389 KSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEF-KQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSE-N  466 (588)
T ss_dssp             -BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTT-SS--CCEEEEEEEETTTS-S-S-S-S
T ss_pred             cccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHH-HHHhhhccccccCCCceEEEEecCCCCCCCCCC-c
Confidence            99999999999999999999999999999999999999999999 77666554333  89999999999999999863 2


Q ss_pred             CccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCC
Q psy16234        393 SFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSL  472 (609)
Q Consensus       393 ~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i  472 (609)
                      ++.+|++|+.+++.|++||+++|+||+|+|++++|+|+|+++++++.++++||++||+||++||+++++|+++|++.||+
T Consensus       467 ~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~  546 (588)
T PF00888_consen  467 NIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGI  546 (588)
T ss_dssp             -----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC--
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCc
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHhcCccc--cCC--CCCCCCCEEEEecCCC
Q psy16234        473 SQDQIGRHIASLVECKLLT--SNK--EELTEDTEIRLNLGYN  510 (609)
Q Consensus       473 ~~~~l~~~L~~L~~~~iL~--~~~--~~~~~~~~f~lN~~F~  510 (609)
                      ++++++++|.+|++.|++.  +.+  +++.+++.|.+|.+|+
T Consensus       547 ~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~  588 (588)
T PF00888_consen  547 SEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT  588 (588)
T ss_dssp             -HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred             CHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence            9999999999999999987  333  6789999999999996

Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....

>smart00182 CULLIN Cullin

Probab=100.00  E-value=2.6e-34  Score=263.08  Aligned_cols=142  Identities=47%  Similarity=0.845  Sum_probs=132.1

Q ss_pred             ccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCC
Q psy16234        292 YIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLG  371 (609)
Q Consensus       292 ~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~  371 (609)
                      |++|||+|+.+|+++||+|||..++++.+.|..||++||.+||.++|++|++|++|+..|+++++.| ++++..++...+
T Consensus         1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f-~~~~~~~~~~~~   79 (142)
T smart00182        1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSF-KDMLENNSNKPI   79 (142)
T ss_pred             CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhccCCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999 776655433367


Q ss_pred             cceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEE
Q psy16234        372 IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSY  435 (609)
Q Consensus       372 ~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~  435 (609)
                      ++|+|.|||+++||..+.. .++.||++|+.+++.|++||.++|+||+|+|+|++|+|+|+++|
T Consensus        80 ~~~~~~VLs~~~WP~~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~  142 (142)
T smart00182       80 IDLNVRVLTSGYWPTSSTE-VEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF  142 (142)
T ss_pred             CceEEEECCCCCCCCCCCC-CceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence            8999999999999988753 58999999999999999999999999999999999999999875

>KOG2165|consensus

Probab=99.97  E-value=1.5e-28  Score=260.39  Aligned_cols=306  Identities=20%  Similarity=0.282  Sum_probs=243.8

Q ss_pred             eeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHH-Hhhc-c
Q psy16234        289 VFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSE-FVKT-N  366 (609)
Q Consensus       289 lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~-~~~~-~  366 (609)
                      |...+.+|+.|.+.||.+||.||++....+.+.|..-++.||-.+|....+.|++|++|+..|+++++.+|+. .... .
T Consensus       445 LVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~~  524 (765)
T KOG2165|consen  445 LVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRGA  524 (765)
T ss_pred             HHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhccc
Confidence            3445599999999999999999999999999999999999999999999999999999999999999999553 2211 1


Q ss_pred             CCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecH
Q psy16234        367 EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQT  446 (609)
Q Consensus       367 ~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~  446 (609)
                      ...+.+.+++.||++.+||....  ..+.+|..++..++.+.+-|.+...+|+|.|++++|+|++++++.+++.+++||+
T Consensus       525 e~~~~~~i~~~IlS~~fWP~~~~--~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp  602 (765)
T KOG2165|consen  525 EEVPDFGISATILSSLFWPPLCD--EAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSP  602 (765)
T ss_pred             ccCCCCchhhhhhhhhcCCcccc--ccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCH
Confidence            11235788999999999998765  6899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCcceEEeccccccCC
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKET  526 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~  526 (609)
                      .||+|+.+|.+.++||++++++.+|+|...+++.|..|++.|+|..+|. +++.++|++++.=.+.   .+-+....-+.
T Consensus       603 ~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~-~s~tgt~T~iEse~d~---~q~~~~~~~e~  678 (765)
T KOG2165|consen  603 EQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPI-ISDTGTLTVIESEMDF---DQAEGTVLLEA  678 (765)
T ss_pred             HHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCC-CCCCceeeeccccccc---cccCCCccccc
Confidence            9999999999999999999999999999999999999999999998863 3778999999853322   22111111121


Q ss_pred             hhHHhh--hhhhHHHHh--hhhhhhhhhhhhccccCCChHHHHHHHHHhhc--C-CCCChHHHHHHHHHhhhhccccccC
Q psy16234        527 PQEIER--TVSSVDEDR--KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSK--S-FAPSISMIKKCIESLIDKNYVERTA  599 (609)
Q Consensus       527 ~~e~~~--~~~~v~~~R--~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~--~-F~~~~~~ik~~Ie~LIekeyl~r~~  599 (609)
                      .++..+  ....+++-+  -..-...||-.+-.-+.|+.+-+.+...--..  + ..++-++++..+..++..|-|+-.+
T Consensus       679 eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~~  758 (765)
T KOG2165|consen  679 EEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFIA  758 (765)
T ss_pred             ccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEec
Confidence            111111  112222211  12334578887777788988777754322221  1 5567788999999999888888766


Q ss_pred             C
Q psy16234        600 N  600 (609)
Q Consensus       600 ~  600 (609)
                      +
T Consensus       759 G  759 (765)
T KOG2165|consen  759 G  759 (765)
T ss_pred             c
Confidence            3

>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain

Probab=99.79  E-value=5e-20  Score=145.27  Aligned_cols=67  Identities=51%  Similarity=0.819  Sum_probs=61.2

Q ss_pred             HHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCC
Q psy16234        537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTD  603 (609)
Q Consensus       537 v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~  603 (609)
                      |+++|...|+|+||||||++|+++|++|+.+|.+++++ |.|+..+||++||.||++|||+||++|+|
T Consensus         1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n   68 (68)
T PF10557_consen    1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN   68 (68)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred             CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence            35789999999999999999999999999999999997 99999999999999999999999999875

With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....

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

Probab=96.23  E-value=0.014  Score=49.24  Aligned_cols=65  Identities=18%  Similarity=0.231  Sum_probs=54.9

Q ss_pred             EEecHHHHHHHHhhc--------CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCC
Q psy16234        442 VTMQTFQMAILLLFE--------KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYN  510 (609)
Q Consensus       442 l~~s~~Q~~iLllFn--------~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~  510 (609)
                      ..++.-|+.+|+..-        ..+.+|-.||++.+|++.+.+.+.|..|.+.|+|....    ....|++|.+++
T Consensus        21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~----~~~~~~~n~~~~   93 (95)
T TIGR01610        21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG----MMGIVGVNTPLS   93 (95)
T ss_pred             CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec----CCceeecCCCcc
Confidence            457788898888655        46789999999999999999999999999999998652    247899998864

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

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

Probab=96.05  E-value=0.01  Score=43.90  Aligned_cols=46  Identities=22%  Similarity=0.369  Sum_probs=39.7

Q ss_pred             HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        449 MAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       449 ~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +.||..|.+.+ .+|+.||++.+|+|...+.+.|..|...|++.++|
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecCc
Confidence            46888888765 48999999999999999999999999999998764

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.

>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=95.83  E-value=0.022  Score=41.30  Aligned_cols=46  Identities=24%  Similarity=0.319  Sum_probs=39.7

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLL  490 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL  490 (609)
                      +..+..||....+++.+|..+|++.+|++...+.++|..|.+.|++
T Consensus         2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            4567788988888899999999999999999999999999999987

...

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

Probab=95.43  E-value=0.05  Score=44.57  Aligned_cols=59  Identities=15%  Similarity=0.261  Sum_probs=43.5

Q ss_pred             HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        447 FQMAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       447 ~Q~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      +++.+.+..+..+ .+|.++|++.+++|...+.+.++.|.+.|++....   .+++.|.++.+
T Consensus        11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~---G~~GGy~L~~~   70 (83)
T PF02082_consen   11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSR---GRGGGYRLARP   70 (83)
T ss_dssp             HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET---STTSEEEESS-
T ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC---CCCCceeecCC
Confidence            3444555544443 49999999999999999999999999999987543   23577888764

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

>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=94.85  E-value=0.045  Score=41.84  Aligned_cols=50  Identities=16%  Similarity=0.337  Sum_probs=44.4

Q ss_pred             ecHHHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDA--MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|+.|+.||..+...+.  +|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus         3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~   54 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE   54 (62)
T ss_dssp             STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            47789999988887776  999999999999999999999999999999765

...

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

Probab=94.47  E-value=0.1  Score=39.37  Aligned_cols=46  Identities=20%  Similarity=0.318  Sum_probs=41.7

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      |..|+...++++.+|+++|++.+|++...+++-|..|.+.|++.+.
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4467888888999999999999999999999999999999998765

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

>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=94.14  E-value=0.15  Score=39.61  Aligned_cols=50  Identities=24%  Similarity=0.324  Sum_probs=40.7

Q ss_pred             ecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||.... ....++..+|++.++++...+.+.+..|+..|+|.+.
T Consensus         1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~   51 (68)
T PF13463_consen    1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE   51 (68)
T ss_dssp             --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            3677899998888 7789999999999999999999999999999999655

>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=94.13  E-value=0.13  Score=37.14  Aligned_cols=44  Identities=27%  Similarity=0.465  Sum_probs=37.4

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      ...-||.++-+ .+.++.||++.+|++...+.++|..|.+.|++.
T Consensus         3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence            34567777766 679999999999999999999999999999875

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 ....

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

Probab=94.10  E-value=0.065  Score=40.55  Aligned_cols=50  Identities=22%  Similarity=0.334  Sum_probs=44.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|+.+|....+.+.+|..+|++.++++...+.+.+..|.+.|++.+.
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            36789999998888888999999999999999999999999999999765

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 ....

>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=93.51  E-value=0.16  Score=38.85  Aligned_cols=49  Identities=27%  Similarity=0.434  Sum_probs=42.3

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.-..||.++...+.+|+.+|++.+|++...+..+|..|.+.|++...
T Consensus         9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~   57 (61)
T PF12840_consen    9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE   57 (61)
T ss_dssp             SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            4566778888877789999999999999999999999999999998643

...

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=93.26  E-value=0.22  Score=43.90  Aligned_cols=38  Identities=24%  Similarity=0.456  Sum_probs=35.5

Q ss_pred             cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        456 EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       456 n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +.++.+|+++|++.++.+...+.+.|+.|+.+|++.+.
T Consensus        38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re   75 (126)
T COG3355          38 EENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE   75 (126)
T ss_pred             hhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence            36789999999999999999999999999999999876

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

Probab=92.95  E-value=0.2  Score=39.38  Aligned_cols=47  Identities=19%  Similarity=0.251  Sum_probs=41.0

Q ss_pred             HHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        447 FQMAILLLFEKNDA--MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       447 ~Q~~iLllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..-.||.++.+...  +|..+|++.+|++...+.++|..|.+.|++...
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~   55 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ   55 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            44567777777655  999999999999999999999999999999775

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

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=92.50  E-value=0.23  Score=43.58  Aligned_cols=52  Identities=17%  Similarity=0.189  Sum_probs=47.3

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .++..|+.||..+..++.+|..+|++.++++...+.+.+..|.+.|++...+
T Consensus        25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~   76 (118)
T TIGR02337        25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK   76 (118)
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence            4578899999998888899999999999999999999999999999998753

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=92.26  E-value=0.42  Score=39.52  Aligned_cols=55  Identities=20%  Similarity=0.329  Sum_probs=44.1

Q ss_pred             HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      ..||..+... +.+|..+|++.+|++...+.+.|..|.+.|+|...+    .++.|.+..
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~----~~~~y~l~~   63 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG----QNGRYRLGP   63 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC----CCCceeecH
Confidence            4567777766 689999999999999999999999999999997653    234565543

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

Probab=91.79  E-value=0.16  Score=39.80  Aligned_cols=49  Identities=24%  Similarity=0.296  Sum_probs=42.0

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      |-.++.|+..+-..+..|..+|++.+|++...+.+.|..|.+.|++...
T Consensus         7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~   55 (68)
T PF01978_consen    7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE   55 (68)
T ss_dssp             HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4456666666557788999999999999999999999999999999765

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.

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=91.75  E-value=0.62  Score=39.55  Aligned_cols=61  Identities=21%  Similarity=0.393  Sum_probs=47.9

Q ss_pred             ecHHHHHHHHh-------hcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCC
Q psy16234        444 MQTFQMAILLL-------FEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYN  510 (609)
Q Consensus       444 ~s~~Q~~iLll-------Fn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~  510 (609)
                      +|.-|..|++.       ||. .+.+|..++++.||++...+.+++..|++.|+|..+      +..+.+|.+.+
T Consensus        30 ls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~------g~~~G~N~~i~   98 (100)
T PF04492_consen   30 LSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRD------GKRIGVNKNIS   98 (100)
T ss_pred             ccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC------CcEEeeecccc
Confidence            44455555544       554 478999999999999999999999999999999776      46777777653

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=91.52  E-value=0.37  Score=43.86  Aligned_cols=52  Identities=17%  Similarity=0.179  Sum_probs=46.8

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .++..|+.||......+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~   88 (144)
T PRK11512         37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP   88 (144)
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            4677899999887777889999999999999999999999999999998763

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=91.16  E-value=0.47  Score=47.83  Aligned_cols=56  Identities=13%  Similarity=0.245  Sum_probs=47.1

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      +.||.+|.+...+|+.||++.+|+|...+.+.|..|+..|+|.+++    .++.|.+-..
T Consensus        17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~----~~~~Y~lG~~   72 (257)
T PRK15090         17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEG----ESEKYSLTLK   72 (257)
T ss_pred             HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEEecHH
Confidence            4688889887789999999999999999999999999999997753    2456666544

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=90.98  E-value=0.56  Score=39.17  Aligned_cols=52  Identities=13%  Similarity=0.262  Sum_probs=46.9

Q ss_pred             EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +.++..+..||......+.+|..+|++.++++...+.++|..|.+.|++...
T Consensus         6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~   57 (101)
T smart00347        6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL   57 (101)
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence            4567889999988888788999999999999999999999999999999764

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=90.83  E-value=0.76  Score=42.90  Aligned_cols=58  Identities=12%  Similarity=0.114  Sum_probs=43.8

Q ss_pred             HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .+++.+.|+. ...+|.++|++.+++|...+.+.|..|.++||+....   .+++.|.+..+
T Consensus        12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~r---G~~GGy~Lar~   70 (164)
T PRK10857         12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVR---GPGGGYLLGKD   70 (164)
T ss_pred             HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC---CCCCCeeccCC
Confidence            3444555665 3589999999999999999999999999999997531   12445666543

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=90.78  E-value=0.74  Score=42.47  Aligned_cols=56  Identities=16%  Similarity=0.193  Sum_probs=43.1

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      +.+.|..+..+.+|..+|++..++|...|.+.|..|.++||+....   ..++-|.++.
T Consensus        13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r---G~~GGy~La~   68 (153)
T PRK11920         13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR---GRNGGVRLGR   68 (153)
T ss_pred             HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec---CCCCCeeecC
Confidence            3344555555678999999999999999999999999999987542   2345566654

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=90.19  E-value=0.73  Score=32.82  Aligned_cols=34  Identities=21%  Similarity=0.423  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..+|++.+|++...+.+.|..|.+.|++...
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            4789999999999999999999999999999765

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=90.15  E-value=0.74  Score=33.37  Aligned_cols=44  Identities=27%  Similarity=0.382  Sum_probs=37.9

Q ss_pred             HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .|+..+.++..+|..+|++.++++...+.+.|..|.+.|++...
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~   47 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV   47 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45656666677999999999999999999999999999988654

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=89.50  E-value=0.99  Score=40.63  Aligned_cols=56  Identities=18%  Similarity=0.185  Sum_probs=41.4

Q ss_pred             HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      +.+.+.++.. ..+|.++|++.+++|...+.+.|..|.++||+....   ..++.|.+..
T Consensus        13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~---G~~Ggy~l~~   69 (135)
T TIGR02010        13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVR---GPGGGYQLGR   69 (135)
T ss_pred             HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEe---CCCCCEeccC
Confidence            3444555543 479999999999999999999999999999986431   1234465554

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

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=89.46  E-value=0.9  Score=39.22  Aligned_cols=52  Identities=15%  Similarity=0.243  Sum_probs=45.2

Q ss_pred             EecHHHHHHHHhhc----CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFE----KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn----~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .+|..|..||....    ..+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~   77 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER   77 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence            45778888887665    55789999999999999999999999999999998763

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.

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

Probab=89.37  E-value=0.87  Score=34.97  Aligned_cols=44  Identities=20%  Similarity=0.194  Sum_probs=36.3

Q ss_pred             HHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      ||-.+++ +.++|..||++++|++.......|..|.+.|.+...|
T Consensus         5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen    5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4555565 6789999999999999999999999999999887655

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

Probab=88.82  E-value=0.51  Score=38.35  Aligned_cols=45  Identities=24%  Similarity=0.449  Sum_probs=37.3

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..|+...+..+.+++.+|.+.+|+++..+.++|..|.+.|++...
T Consensus         3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~   47 (80)
T PF13601_consen    3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE   47 (80)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence            456666666788999999999999999999999999999998643

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=88.81  E-value=0.93  Score=45.38  Aligned_cols=56  Identities=25%  Similarity=0.401  Sum_probs=46.3

Q ss_pred             HHHHHhhcCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        449 MAILLLFEKNDA-MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       449 ~~iLllFn~~~~-lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      +.||.+|...+. +++.||++.+|+|...+.+.|..|+..|++..++    .++.|.+-..
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~----~~g~Y~Lg~~   63 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP----EDGRYRLGPR   63 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEeehHH
Confidence            468888987654 7899999999999999999999999999999875    2346776443

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=88.55  E-value=1.2  Score=35.03  Aligned_cols=46  Identities=15%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..|. ||+..... +.|+++|.+.||++...+...|..|.+.|++...
T Consensus         6 ~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen    6 VTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             HHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence            3444 44444444 8999999999999999999999999999999764

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

Probab=88.48  E-value=0.44  Score=37.46  Aligned_cols=46  Identities=24%  Similarity=0.416  Sum_probs=36.7

Q ss_pred             hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234        548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN  600 (609)
Q Consensus       548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~  600 (609)
                      .|-.+|+.++.++..+|-.+       |..+++.+..-|+.|+.+|||++.+.
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~-------~~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELARE-------FGISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHH-------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            35567899999999887754       88999999999999999999998764

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

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

Probab=87.85  E-value=1.2  Score=44.50  Aligned_cols=54  Identities=22%  Similarity=0.301  Sum_probs=45.1

Q ss_pred             HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        449 MAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       449 ~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      ..||.+|.. ...+|+.||++.+|+|...+.+.|..|+..|.|..+      +..|.+-..
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~------~~~Y~lG~~   66 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD------GRLFWLTPR   66 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC------CCEEEecHH
Confidence            468888986 567999999999999999999999999999999764      356766443

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

>PRK11569 transcriptional repressor IclR; Provisional

Probab=87.76  E-value=1.1  Score=45.58  Aligned_cols=53  Identities=8%  Similarity=0.148  Sum_probs=44.6

Q ss_pred             HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEE
Q psy16234        449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRL  505 (609)
Q Consensus       449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~l  505 (609)
                      ..||.+|.+. ..+|+.||++.+|++...+.+.|.+|+..|+|..++    .++.|.+
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~----~~~~Y~l   84 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG----ELGHWAI   84 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEec
Confidence            4688889874 579999999999999999999999999999998753    2456665

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=87.61  E-value=0.74  Score=42.98  Aligned_cols=49  Identities=20%  Similarity=0.263  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCc
Q psy16234        460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKR  513 (609)
Q Consensus       460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~  513 (609)
                      .+|.++|++.+|++...+.+.+..|.+.++|.+..     .+.|.||++|--+.
T Consensus        75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~-----~G~Y~iNP~~~~kG  123 (165)
T PF05732_consen   75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR-----NGAYMINPNFFFKG  123 (165)
T ss_pred             EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc-----CCeEEECcHHheeC
Confidence            36889999999999999999999999999998763     57999999975443

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=87.51  E-value=1.3  Score=45.09  Aligned_cols=56  Identities=23%  Similarity=0.282  Sum_probs=46.4

Q ss_pred             HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      ..||.+|... ..+|+.||++.+|+|...+.+.|.+|+..|.|..++    .++.|.+...
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~----~~~~Y~lG~~   84 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS----QLGWWHIGLG   84 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEEecHH
Confidence            4688889865 579999999999999999999999999999998763    2456766544

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=87.51  E-value=1.5  Score=40.37  Aligned_cols=59  Identities=14%  Similarity=0.211  Sum_probs=44.7

Q ss_pred             HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        447 FQMAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       447 ~Q~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      +.+.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|.++|++....   .+++-|.++..
T Consensus        11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~r---G~~GGy~Lar~   70 (150)
T COG1959          11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVR---GKGGGYRLARP   70 (150)
T ss_pred             HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeec---CCCCCccCCCC
Confidence            3444555555544 68899999999999999999999999999997543   23566777653

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=87.37  E-value=1.3  Score=42.10  Aligned_cols=52  Identities=13%  Similarity=0.029  Sum_probs=47.4

Q ss_pred             EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +.++..|..||.....++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~   92 (185)
T PRK13777         41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS   92 (185)
T ss_pred             CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence            3466789999999998899999999999999999999999999999999875

>PF13730 HTH_36: Helix-turn-helix domain

Probab=87.18  E-value=1.8  Score=32.07  Aligned_cols=29  Identities=24%  Similarity=0.302  Sum_probs=27.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234        462 TCGDIQTVLSLSQDQIGRHIASLVECKLL  490 (609)
Q Consensus       462 t~~ei~~~t~i~~~~l~~~L~~L~~~~iL  490 (609)
                      |.+.|++.+|++...+.+++..|.+.|+|
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            89999999999999999999999999875

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=86.80  E-value=1.7  Score=38.73  Aligned_cols=46  Identities=13%  Similarity=0.212  Sum_probs=36.8

Q ss_pred             HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.+.+.-++ ...+|.++|++.+++|...+.+.|..|.+.|+|...
T Consensus        12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            3344444333 348999999999999999999999999999998653

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

>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=86.47  E-value=1.7  Score=32.20  Aligned_cols=39  Identities=31%  Similarity=0.445  Sum_probs=31.9

Q ss_pred             HHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcC
Q psy16234        450 AILLLF-EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK  488 (609)
Q Consensus       450 ~iLllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~  488 (609)
                      .||.++ +..+.+|.++|++.+|++...+.+.|..|-..+
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            344444 666669999999999999999999999998877

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 ....

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=86.21  E-value=2.1  Score=31.84  Aligned_cols=40  Identities=13%  Similarity=0.250  Sum_probs=34.6

Q ss_pred             hcCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        455 FEKNDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       455 Fn~~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +...+.+ |..+|++.+|++...+.++|..|.+.|+|...+
T Consensus        14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4455667 999999999999999999999999999986543

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=85.81  E-value=1.6  Score=37.40  Aligned_cols=46  Identities=15%  Similarity=0.274  Sum_probs=40.9

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ..-.||..+..+...|+.+|++.+|++...+.+.+..|.+.|++..
T Consensus         4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~   49 (108)
T smart00344        4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence            3456788888878899999999999999999999999999999873

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

>PHA00738 putative HTH transcription regulator

Probab=85.68  E-value=2.1  Score=36.54  Aligned_cols=67  Identities=19%  Similarity=0.157  Sum_probs=52.2

Q ss_pred             EEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234        441 FVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY  509 (609)
Q Consensus       441 ~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F  509 (609)
                      ++...+.=-.||.++.+++.+++.+|++.++++...+-++|..|-.+||+....  ....-.|++|.+-
T Consensus         7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK--~Gr~vyY~Ln~~~   73 (108)
T PHA00738          7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYK--EGRTLYAKIRENS   73 (108)
T ss_pred             cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEE--ECCEEEEEECCCc
Confidence            455566666778777777789999999999999999999999999999997542  0113457777764

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=85.50  E-value=1.6  Score=39.66  Aligned_cols=53  Identities=11%  Similarity=0.149  Sum_probs=45.8

Q ss_pred             EEecHHHHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        442 VTMQTFQMAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +.++..|..||...... +..|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~   80 (144)
T PRK03573         27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT   80 (144)
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence            34677898888887754 568999999999999999999999999999998763

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=85.40  E-value=1.4  Score=42.60  Aligned_cols=51  Identities=18%  Similarity=0.277  Sum_probs=46.9

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++..|..||..+.+++..+..+|++.+|++...+.++|..|.+.|++.+.
T Consensus       140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~  190 (203)
T TIGR01884       140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQK  190 (203)
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            467889999999988788999999999999999999999999999999875

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.

>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=85.20  E-value=2.4  Score=32.52  Aligned_cols=35  Identities=23%  Similarity=0.367  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        459 DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       459 ~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..+|..+|++.+|++...+.+.|..|.+.|+|...
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~   58 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR   58 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            56999999999999999999999999999999865

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=85.09  E-value=1.7  Score=43.91  Aligned_cols=54  Identities=20%  Similarity=0.342  Sum_probs=44.3

Q ss_pred             HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234        449 MAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN  506 (609)
Q Consensus       449 ~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN  506 (609)
                      +.||.+|.+++ .+|..||++.+|++...+.+.|..|...|+|.+++    .++.|.+-
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~----~~~~Y~Lg   68 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA----SDDSFRLT   68 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec----CCCcEEEc
Confidence            45788887654 59999999999999999999999999999998763    23456664

>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=85.06  E-value=2  Score=32.81  Aligned_cols=44  Identities=23%  Similarity=0.251  Sum_probs=37.4

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      |..+-.+...++..+|++.+|++...+...+..|.+.|++...+
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            44444577899999999999999999999999999999998764

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=84.78  E-value=2.2  Score=33.16  Aligned_cols=48  Identities=29%  Similarity=0.453  Sum_probs=41.2

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..+..|+..+.+.+ ++..+|++.+|++...+.+.|..|...|++...
T Consensus         6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~   53 (78)
T cd00090           6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESR   53 (78)
T ss_pred             ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence            345777887777766 999999999999999999999999999998754

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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=84.40  E-value=2.4  Score=37.74  Aligned_cols=45  Identities=13%  Similarity=0.253  Sum_probs=36.9

Q ss_pred             HHHHHhhc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        449 MAILLLFE--KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       449 ~~iLllFn--~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..+|..+.  ..+.+|..+|++.+|+|...+.+.|..|.+.|++...
T Consensus        12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            34454554  3457999999999999999999999999999999643

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

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=84.12  E-value=2  Score=37.68  Aligned_cols=62  Identities=19%  Similarity=0.287  Sum_probs=52.7

Q ss_pred             hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      ..++.|++||=+++..+.++++.++...   +.++...|+--|..|..||.|.|.-+ ...|.|-|
T Consensus         6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~---~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p   67 (123)
T COG3682           6 AAEWEVMEILWSRGPATVREIIEELPAD---REWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP   67 (123)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHhhc---ccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence            4578899999999999999888777665   67889999999999999999999875 47777754

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=84.10  E-value=2.2  Score=38.20  Aligned_cols=60  Identities=18%  Similarity=0.250  Sum_probs=45.0

Q ss_pred             hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +..|++++-..+.++..+++....+.   ..+....+...|+.|.+||+|+|..+ ...|.|-|
T Consensus         6 E~~VM~vlW~~~~~t~~eI~~~l~~~---~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p   65 (130)
T TIGR02698         6 EWEVMRVVWTLGETTSRDIIRILAEK---KDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA   65 (130)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHhhc---cCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence            45677888777788777666443322   56788999999999999999999854 35788854

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.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=83.53  E-value=2.5  Score=39.88  Aligned_cols=51  Identities=14%  Similarity=0.203  Sum_probs=44.1

Q ss_pred             ecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|..|..||.....  ..++|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~  105 (176)
T PRK10870         53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE  105 (176)
T ss_pred             CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            55678888877764  4679999999999999999999999999999998763

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=83.40  E-value=1.2  Score=35.25  Aligned_cols=41  Identities=15%  Similarity=0.193  Sum_probs=33.3

Q ss_pred             HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        452 LLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       452 LllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      +.++.....+|+.||++.+|+|...++..+..+.+.|+|.+
T Consensus        24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~~   64 (73)
T TIGR03879        24 AALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLVK   64 (73)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHHH
Confidence            33333346789999999999999999999999888887754

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>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=82.03  E-value=2.6  Score=35.82  Aligned_cols=49  Identities=12%  Similarity=0.281  Sum_probs=41.6

Q ss_pred             EecHHHHHHHHhhcC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234        443 TMQTFQMAILLLFEK----NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~----~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      .++..|-.||-.+.+    .+.+++++|++.++++..+++.+|..|+..|.+-
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            578899999988887    4679999999999999999999999999988774

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.

>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=81.73  E-value=1.4  Score=38.36  Aligned_cols=60  Identities=13%  Similarity=0.263  Sum_probs=45.5

Q ss_pred             hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +..|++++=..+.++..+++..+.+.   ..+....|...+..|.+||||.|... ...|.|-|
T Consensus         5 E~~IM~~lW~~~~~t~~eI~~~l~~~---~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p   64 (115)
T PF03965_consen    5 ELEIMEILWESGEATVREIHEALPEE---RSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP   64 (115)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHCTT---SS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhc---cccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence            56678888888888888776554333   56889999999999999999999865 46888864

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 ....

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=81.68  E-value=3  Score=31.25  Aligned_cols=36  Identities=25%  Similarity=0.457  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        458 NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++.|..+|++.+|++...+.+.|..|.+.|++...
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~   43 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESR   43 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence            567899999999999999999999999999998644

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=81.33  E-value=2.4  Score=41.27  Aligned_cols=44  Identities=23%  Similarity=0.348  Sum_probs=39.6

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ..||.+.+..++.|.+||++.+|++..-+++||+.|...|++..
T Consensus        14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~   57 (218)
T COG2345          14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEV   57 (218)
T ss_pred             HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceee
Confidence            34777888889999999999999999999999999999998864

>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=81.15  E-value=1.1  Score=35.01  Aligned_cols=56  Identities=21%  Similarity=0.260  Sum_probs=41.3

Q ss_pred             hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q psy16234        546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  608 (609)
Q Consensus       546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yi  608 (609)
                      ++.|-+.|-.++.++..+|...    +   ..+...+-+.++.|.++|+++|.++++..|..+
T Consensus        10 E~~vy~~Ll~~~~~t~~eIa~~----l---~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~   65 (68)
T PF01978_consen   10 EAKVYLALLKNGPATAEEIAEE----L---GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV   65 (68)
T ss_dssp             HHHHHHHHHHHCHEEHHHHHHH----H---TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence            4455555556777777766533    3   467899999999999999999999876555544

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

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=80.86  E-value=3.3  Score=35.78  Aligned_cols=51  Identities=18%  Similarity=0.290  Sum_probs=45.5

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +++.|..+|......+..+..+|++.++++...+.+.+..|.+.|++...+
T Consensus        20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~   70 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLR   70 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence            678999999888887776669999999999999999999999999998763

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

Probab=80.83  E-value=1.9  Score=33.76  Aligned_cols=43  Identities=7%  Similarity=0.186  Sum_probs=34.1

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      |.-...++..+|+++|+..++++.+.+...|..|+..|-+.+.
T Consensus         5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~   47 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV   47 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            3344556788999999999999999999999999999988754

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

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

Probab=80.52  E-value=3  Score=27.42  Aligned_cols=31  Identities=29%  Similarity=0.428  Sum_probs=25.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234        460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLL  490 (609)
Q Consensus       460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL  490 (609)
                      .+|-+||++.+|++.+.+-+.|..|-+.|++
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            3678999999999999999999999988875

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=80.50  E-value=5.1  Score=36.28  Aligned_cols=49  Identities=16%  Similarity=0.318  Sum_probs=38.8

Q ss_pred             hcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234        455 FEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN  506 (609)
Q Consensus       455 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN  506 (609)
                      +..+..+|.++|++..|+|...+.++|..|.+.|++...+   ..++.|.+.
T Consensus        20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~---G~~GG~~l~   68 (141)
T PRK11014         20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR---GKNGGIRLG   68 (141)
T ss_pred             CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec---CCCCCeeec
Confidence            4445578999999999999999999999999999997653   123445554

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=80.34  E-value=2.8  Score=32.21  Aligned_cols=35  Identities=20%  Similarity=0.324  Sum_probs=29.3

Q ss_pred             CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234        457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      .++.+|+.+|.+.|++|.+.++..|..|++.+++.
T Consensus        24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~   58 (62)
T PF08221_consen   24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ   58 (62)
T ss_dssp             HC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred             HcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence            45688999999999999999999999999999874

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	609
1ldj_A	760	Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiqu		1e-117
1u6g_A	776	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		1e-116
1ldk_B	366	Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiqu		1e-85
3rtr_A	368	A Ring E3-Substrate Complex Poised For Ubiquitin-Li		2e-83
4a0c_C	741	Structure Of The Cand1-Cul4b-Rbx1 Complex Length =		2e-68
4a0l_E	726	Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp		2e-68
4a0k_A	742	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		7e-65
2hye_C	759	Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Compl		8e-65
4f52_A	282	Structure Of A Glomulin-Rbx1-Cul1 Complex Length =		4e-58
3dpl_C	382	Structural Insights Into Nedd8 Activation Of Cullin		9e-32
3dqv_C	382	Structural Insights Into Nedd8 Activation Of Cullin		2e-27
1ldk_A	396	Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiqu		5e-25
3tdu_C	77	N-Terminal Acetylation Acts As An Avidity Enhancer		6e-17
1iuy_A	92	Solution Structure Of The Cullin-3 Homologue Length		2e-14
2wzk_A	391	Structure Of The Cul5 N-Terminal Domain At 2.05a Re		3e-13
2do7_A	101	Solution Structure Of The Winged Helix-Turn-Helix M		4e-13
4a64_A	354	Crystal Structure Of The N-Terminal Domain Of Human		4e-12
4ap2_B	410	Crystal Structure Of The Human Klhl11-cul3 Complex		7e-11
4apf_B	388	Crystal Structure Of The Human Klhl11-cul3 Complex		8e-11
3o2p_E	88	A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn		1e-10
3o6b_B	76	A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn		3e-10
4eoz_B	364	Crystal Structure Of The Spop Btb Domain Complexed		2e-05

>pdb|1LDJ|A Chain A, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin Ligase Complex Length = 760

Iteration: 1
 Score =  417 bits (1072), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 232/554 (41%), Positives = 328/554 (59%), Gaps = 17/554 (3%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 211 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 270
Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 271 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 330
Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 331 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 390
Query: 247 FDPKMP---SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFY 303
              KM    SKSPE LA+YCD           E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 391 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 450
Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 451 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 510
Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +DL   FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 511 NSEPLDLD--FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWL 566
Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 567 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 626
Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 627 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 686
Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+
Sbjct: 687 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 746
Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 747 ERVDGEKDTYSYLA 760

>pdb|1U6G|A Chain A, Crystal Structure Of The Cand1-Cul1-Roc1 Complex Length = 776

Iteration: 1
 Score =  417 bits (1071), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 232/554 (41%), Positives = 328/554 (59%), Gaps = 17/554 (3%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 227 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 286
Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 287 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 346
Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 347 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 406
Query: 247 FDPKMP---SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFY 303
              KM    SKSPE LA+YCD           E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 407 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 466
Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 467 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 526
Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +DL   FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 527 NSEPLDLD--FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWL 582
Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 583 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 642
Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 643 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 702
Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+
Sbjct: 703 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 762
Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 763 ERVDGEKDTYSYLA 776

>pdb|1LDK|B Chain B, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin Ligase Complex Length = 366

Iteration: 1
 Score =  313 bits (803), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 167/365 (45%), Positives = 228/365 (62%), Gaps = 12/365 (3%)
Query: 253 SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLI 312
           SKSPE LA+YCD           E+E++D L+Q + VFKYI+DKDVF KFYAKMLAKRL+
Sbjct: 6   SKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLV 65
Query: 313 HQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGI 372
           HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F      +  +DL  
Sbjct: 66  HQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLD- 124
Query: 373 HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELK 432
            FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL+ +S+ EL 
Sbjct: 125 -FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELV 181
Query: 433 LSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492
            +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  L++ KLL  
Sbjct: 182 TNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVL 241
Query: 493 NKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +
Sbjct: 242 EDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLI 301
Query: 546 QAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDE 604
           QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D 
Sbjct: 302 QAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDT 361
Query: 605 YSYVA 609
           YSY+A
Sbjct: 362 YSYLA 366

>pdb|3RTR|A Chain A, A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases Length = 368

Iteration: 1
 Score =  306 bits (784), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 165/365 (45%), Positives = 226/365 (61%), Gaps = 12/365 (3%)
Query: 253 SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLI 312
           SKSPE LA+YCD           E+E++D L+Q +  FK I+DKDVF KFYAKMLAKRL+
Sbjct: 8   SKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAKMLAKRLV 67
Query: 313 HQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGI 372
           HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F      +  +DL  
Sbjct: 68  HQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLD- 126
Query: 373 HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELK 432
            FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL+ +S+ EL 
Sbjct: 127 -FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELV 183
Query: 433 LSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492
            +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  L++ KLL  
Sbjct: 184 TNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVL 243
Query: 493 NKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 545
             E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +
Sbjct: 244 EDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLI 303
Query: 546 QAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDE 604
           QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D 
Sbjct: 304 QAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDT 363
Query: 605 YSYVA 609
           YSY+A
Sbjct: 364 YSYLA 368

>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex Length = 741

Iteration: 1
 Score =  256 bits (655), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 166/547 (30%), Positives = 285/547 (52%), Gaps = 17/547 (3%)
Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
            +Y D FE +FLE +   Y +E  KL+Q   V +Y+  V + L EE +R + +L  ++  
Sbjct: 207 QIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQK 266
Query: 128 KVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHI 186
            + A  E+ ++ +HL   LQ     ++ E R  DL+ +Y L   VR G+ +L+    ++I
Sbjct: 267 SLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYI 326
Query: 187 CKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
              G   +     D      V+ +L    K    +   F  ++ F+ A+ +A  + IN  
Sbjct: 327 KAFGSTIVINPEKDKT---MVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFIN-- 381
Query: 247 FDPKMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKM 306
              K P+K  E +AKY D           + E++  L + + +F++I  KDVF  FY K 
Sbjct: 382 ---KRPNKPAELIAKYVDSKLRAGNKEATDEELEKMLDKIMIIFRFIYGKDVFEAFYKKD 438
Query: 307 LAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN 366
           LAKRL+  +S S+D E++M++KLK  CG  FT+K   M  D+++S  +  +F  ++++  
Sbjct: 439 LAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMIQF-KQYMQNQ 497
Query: 367 EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNI 426
            +   I  ++NIL  G WP    V     +P E+ K   +F+ FY G+ +GRKL W   +
Sbjct: 498 NVPGNIELTVNILTMGYWP--TYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRKLQWQSTL 555
Query: 427 SQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV- 485
               LK  + +    + +  FQ  +LL+F + +  +  +I+    +   ++ R + SL  
Sbjct: 556 GHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQSLAC 615
Query: 486 -ECKLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRK 542
            + ++L  N   +++ +  +   N  + +K  ++KI+    KET +E   T   V +DR+
Sbjct: 616 GKARVLAKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQ 675
Query: 543 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANST 602
             + AAIVRIMK RK + HN L+ EV +Q K F    + +KK IESLID++Y+ER   + 
Sbjct: 676 YQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVKPADLKKRIESLIDRDYMERDKENP 734
Query: 603 DEYSYVA 609
           ++Y+Y+A
Sbjct: 735 NQYNYIA 741

>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 726

Iteration: 1
 Score =  256 bits (654), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 166/547 (30%), Positives = 285/547 (52%), Gaps = 17/547 (3%)
Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
            +Y D FE +FLE +   Y +E  KL+Q   V +Y+  V + L EE +R + +L  ++  
Sbjct: 192 QIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQK 251
Query: 128 KVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHI 186
            + A  E+ ++ +HL   LQ     ++ E R  DL+ +Y L   VR G+ +L+    ++I
Sbjct: 252 SLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYI 311
Query: 187 CKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
              G   +     D      V+ +L    K    +   F  ++ F+ A+ +A  + IN  
Sbjct: 312 KAFGSTIVINPEKDKT---MVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFIN-- 366
Query: 247 FDPKMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKM 306
              K P+K  E +AKY D           + E++  L + + +F++I  KDVF  FY K 
Sbjct: 367 ---KRPNKPAELIAKYVDSKLRAGNKEATDEELEKMLDKIMIIFRFIYGKDVFEAFYKKD 423
Query: 307 LAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN 366
           LAKRL+  +S S+D E++M++KLK  CG  FT+K   M  D+++S  +  +F  ++++  
Sbjct: 424 LAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMIQF-KQYMQNQ 482
Query: 367 EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNI 426
            +   I  ++NIL  G WP    V     +P E+ K   +F+ FY G+ +GRKL W   +
Sbjct: 483 NVPGNIELTVNILTMGYWP--TYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRKLQWQSTL 540
Query: 427 SQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV- 485
               LK  + +    + +  FQ  +LL+F + +  +  +I+    +   ++ R + SL  
Sbjct: 541 GHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQSLAC 600
Query: 486 -ECKLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRK 542
            + ++L  N   +++ +  +   N  + +K  ++KI+    KET +E   T   V +DR+
Sbjct: 601 GKARVLAKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQ 660
Query: 543 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANST 602
             + AAIVRIMK RK + HN L+ EV +Q K F    + +KK IESLID++Y+ER   + 
Sbjct: 661 YQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVKPADLKKRIESLIDRDYMERDKENP 719
Query: 603 DEYSYVA 609
           ++Y+Y+A
Sbjct: 720 NQYNYIA 726

>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 742

Iteration: 1
 Score =  244 bits (624), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 174/550 (31%), Positives = 280/550 (50%), Gaps = 19/550 (3%)
Query: 66  DQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSS 125
           D  +Y D FE +FLE +   Y +E  +L+Q   V +Y+  V + L EE +R + +L  S+
Sbjct: 206 DLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHST 265
Query: 126 YPKVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184
              + A  E+ ++ +HL   LQ     ++ E R  DLA MY L   VR G   L+    +
Sbjct: 266 QKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSE 325
Query: 185 HICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVIN 244
           +I   G   +     D      V+++L    K    ++  F  ++ F+  + ++  + IN
Sbjct: 326 YIKTFGTAIVINPEKDK---DMVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFIN 382
Query: 245 HKFDPKMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYA 304
                K P+K  E +AK+ D           + E++  L + + +F++I  KDVF  FY 
Sbjct: 383 -----KRPNKPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYK 437
Query: 305 KMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVK 364
           K LAKRL+  +S S+D E++M++KLK  CG  FT+K   M  D+++S  +   F      
Sbjct: 438 KDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQHM-- 495
Query: 365 TNEIDLG-IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            N+ D G I  ++NIL  G WP   T +     P E+ K   +F+ FY G+ +GRKL W 
Sbjct: 496 QNQSDSGPIDLTVNILTMGYWP-TYTPMEVHLTP-EMIKLQEVFKAFYLGKHSGRKLQWQ 553
Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
             +    LK  + +      +  FQ  +LL+F + D  +  +I+    +   ++ R + S
Sbjct: 554 TTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQS 613
Query: 484 LVECK---LLTSNKEELTEDTE-IRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDE 539
           L   K   L+ S K +  ED +    N  + +K  ++KI+    KET +E   T   V +
Sbjct: 614 LACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQ 673
Query: 540 DRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599
           DR+  + AAIVRIMK RK + HN L+ E+ +Q K F      +KK IESLID++Y+ER  
Sbjct: 674 DRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDK 732
Query: 600 NSTDEYSYVA 609
           ++ ++Y YVA
Sbjct: 733 DNPNQYHYVA 742

>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex Length = 759

Iteration: 1
 Score =  244 bits (624), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 174/550 (31%), Positives = 280/550 (50%), Gaps = 19/550 (3%)
Query: 66  DQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSS 125
           D  +Y D FE +FLE +   Y +E  +L+Q   V +Y+  V + L EE +R + +L  S+
Sbjct: 223 DLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHST 282
Query: 126 YPKVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184
              + A  E+ ++ +HL   LQ     ++ E R  DLA MY L   VR G   L+    +
Sbjct: 283 QKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSE 342
Query: 185 HICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVIN 244
           +I   G   +     D      V+++L    K    ++  F  ++ F+  + ++  + IN
Sbjct: 343 YIKTFGTAIVINPEKDK---DMVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFIN 399
Query: 245 HKFDPKMPSKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYA 304
                K P+K  E +AK+ D           + E++  L + + +F++I  KDVF  FY 
Sbjct: 400 -----KRPNKPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYK 454
Query: 305 KMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVK 364
           K LAKRL+  +S S+D E++M++KLK  CG  FT+K   M  D+++S  +   F      
Sbjct: 455 KDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQHM-- 512
Query: 365 TNEIDLG-IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            N+ D G I  ++NIL  G WP   T +     P E+ K   +F+ FY G+ +GRKL W 
Sbjct: 513 QNQSDSGPIDLTVNILTMGYWP-TYTPMEVHLTP-EMIKLQEVFKAFYLGKHSGRKLQWQ 570
Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
             +    LK  + +      +  FQ  +LL+F + D  +  +I+    +   ++ R + S
Sbjct: 571 TTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQS 630
Query: 484 LVECK---LLTSNKEELTEDTE-IRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDE 539
           L   K   L+ S K +  ED +    N  + +K  ++KI+    KET +E   T   V +
Sbjct: 631 LACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQ 690
Query: 540 DRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599
           DR+  + AAIVRIMK RK + HN L+ E+ +Q K F      +KK IESLID++Y+ER  
Sbjct: 691 DRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDK 749
Query: 600 NSTDEYSYVA 609
           ++ ++Y YVA
Sbjct: 750 DNPNQYHYVA 759

>pdb|4F52|A Chain A, Structure Of A Glomulin-Rbx1-Cul1 Complex Length = 282

Iteration: 1
 Score =  222 bits (566), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 119/274 (43%), Positives = 164/274 (59%), Gaps = 11/274 (4%)
Query: 253 SKSPEYLAKYCDMXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLI 312
           SKSPE LA+YCD           E+E++D L+Q +  FK I+DKDVF KFYAKMLAKRL+
Sbjct: 8   SKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAKMLAKRLV 67
Query: 313 HQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGI 372
           HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F      +  +DL  
Sbjct: 68  HQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLD- 126
Query: 373 HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELK 432
            FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL+ +S+ EL 
Sbjct: 127 -FSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELV 183
Query: 433 LSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492
            +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  L++ KLL  
Sbjct: 184 TNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVL 243
Query: 493 NKE-------ELTEDTEIRLNLGYNNKRTKLKIS 519
             E       EL  DT I+L LGY NK+ ++ I+
Sbjct: 244 EDENANVDEVELKPDTLIKLYLGYKNKKLRVNIN 277

>pdb|3DPL|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 382

Iteration: 1
 Score =  135 bits (339), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 115/381 (30%), Positives = 185/381 (48%), Gaps = 26/381 (6%)
Query: 253 SKSPEYLAKYCDMXXXXX--XXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKR 310
           SK PE LA YCDM              E++ KL + +   KY+ +KDVF +++   L +R
Sbjct: 4   SKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRR 63
Query: 311 LIHQQSTSMDGEEAMINKLKQ-ACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEID 369
           LI   S   + EE M+  L++     ++ NK  RM  DIK+S  LN+ F  E  K N++ 
Sbjct: 64  LILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAF-KEMHKNNKLA 122
Query: 370 LGI-HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
           L     +I IL AG+W      +   S+P ELE  I   E+FY    +GRKL W H +S 
Sbjct: 123 LPADSVNIKILNAGAWSRSSEKVF-VSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSN 181
Query: 429 VELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVE 486
             +        Y + + TFQ+A+L  + +   + ++  +++    L   ++ R + SLV 
Sbjct: 182 GIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVA 241
Query: 487 CKLL----------TSNKEELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQE 529
              L           ++ ++ TE T   +N  ++        KR K+ + G +Q  T + 
Sbjct: 242 FPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERM 301
Query: 530 IERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIES 588
            E     + + R L  Q AI++IMK RK+I +  L  E++   K+ F P   MIK+ IE 
Sbjct: 302 REEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEW 361
Query: 589 LIDKNYVERTANSTDEYSYVA 609
           LI+  Y+ R  +  + + Y+A
Sbjct: 362 LIEHKYIRRDESDINTFIYMA 382

>pdb|3DQV|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 382

Iteration: 1
 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 110/381 (28%), Positives = 179/381 (46%), Gaps = 26/381 (6%)
Query: 253 SKSPEYLAKYCD--MXXXXXXXXXXESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKR 310
           SK PE LA YCD  +            E++ KL + +   KY+ +KDVF +++   L +R
Sbjct: 4   SKCPEELANYCDXLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFXRYHKAHLTRR 63
Query: 311 LIHQQSTSMDGEEAMINKLKQ-ACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEID 369
           LI   S   + EE  +  L++     ++ NK  R   DIK+S  LN+ F  E  K N++ 
Sbjct: 64  LILDISADSEIEENXVEWLREVGXPADYVNKLARXFQDIKVSEDLNQAF-KEXHKNNKLA 122
Query: 370 LGI-HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQ 428
           L     +I IL AG+W      +   S+P ELE  I   E+FY    +GRKL W H  S 
Sbjct: 123 LPADSVNIKILNAGAWSRSSEKVF-VSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLXSN 181
Query: 429 VELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVE 486
             +        Y + + TFQ+A+L  + +   + ++  +++    L   ++ R + SLV 
Sbjct: 182 GIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVA 241
Query: 487 CKLL----------TSNKEELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQE 529
              L           ++ ++ TE T   +N  ++        KR K+ + G +Q  T + 
Sbjct: 242 FPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERX 301
Query: 530 IERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIES 588
            E     + + R L  Q AI++I K RK+I +  L  E++   K+ F P    IK+ IE 
Sbjct: 302 REEENEGIVQLRILRTQEAIIQIXKXRKKISNAQLQTELVEILKNXFLPQKKXIKEQIEW 361
Query: 589 LIDKNYVERTANSTDEYSYVA 609
           LI+  Y+ R  +  + + Y A
Sbjct: 362 LIEHKYIRRDESDINTFIYXA 382

>pdb|1LDK|A Chain A, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin Ligase Complex Length = 396

Iteration: 1
 Score =  112 bits (280), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 63/179 (35%), Positives = 98/179 (54%), Gaps = 2/179 (1%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 213 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 272
Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 273 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 332
Query: 189 QGLEAIS--GLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINH 245
           QGL AI   G +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+
Sbjct: 333 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINN 391

>pdb|3TDU|C Chain C, N-Terminal Acetylation Acts As An Avidity Enhancer Within An Interconnected Multiprotein Complex: Structure Of A Human Cul1whb- Dcn1p-Acetylated Ubc12n Complex Length = 77

Iteration: 1
 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 56/76 (73%), Gaps = 1/76 (1%)
Query: 535 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKN 593
           S+++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K 
Sbjct: 2   SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKE 61
Query: 594 YVERTANSTDEYSYVA 609
           Y+ER     D YSY+A
Sbjct: 62  YLERVDGEKDTYSYLA 77

>pdb|1IUY|A Chain A, Solution Structure Of The Cullin-3 Homologue Length = 92

Iteration: 1
 Score = 77.8 bits (190), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)
Query: 520 GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 578
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61
Query: 579 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>pdb|2WZK|A Chain A, Structure Of The Cul5 N-Terminal Domain At 2.05a Resolution Length = 391

Iteration: 1
 Score = 73.9 bits (180), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/184 (26%), Positives = 85/184 (46%), Gaps = 8/184 (4%)
Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHV---- 123
            +Y D FE  +L+ +  +Y+++A   LQ   V  YM+     L EE  R++R+L      
Sbjct: 196 QIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRREC 255
Query: 124 SSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVR 183
           +S   +   C   +V      +  EC  M+       L  M+ L+  V  GI  ++  + 
Sbjct: 256 NSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLE 315
Query: 184 DHICKQGLEAISGLSGDNIST---QFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACS 240
           +HI   GL  +   + + I+T   ++ E +  +  ++   VKE F  D  F+ A DKA  
Sbjct: 316 EHIISAGLADMVA-AAETITTDSEKYREQLDTLFNRFSKLVKEAFQDDPRFLTARDKAYK 374
Query: 241 SVIN 244
           +V+N
Sbjct: 375 AVVN 378

>pdb|2DO7|A Chain A, Solution Structure Of The Winged Helix-Turn-Helix Motif Of Human Cul-4b Length = 101

Iteration: 1
 Score = 73.2 bits (178), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)
Query: 519 SGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS 578
           SG   KET +E   T   V +DR+  + AAIVRIMK RK + HN L+ EV +Q K F   
Sbjct: 6   SGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVK 64
Query: 579 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
            + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 65  PADLKKRIESLIDRDYMERDKENPNQYNYIA 95

>pdb|4A64|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Cul4b At 2.57a Resolution Length = 354

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 86/180 (47%), Gaps = 4/180 (2%)
Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
            +Y D FE +FLE +   Y +E  KL+Q   V +Y+  V + L EE +R + +L  ++  
Sbjct: 176 QIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQK 235
Query: 128 KVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHI 186
            + A  E+ ++ +HL   LQ     ++ E R  DL+ +Y L   VR G+ +L+    ++I
Sbjct: 236 SLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYI 295
Query: 187 CKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
              G   +     D    Q +++      K    +   F  ++ F+ A+ +A  + IN +
Sbjct: 296 KAFGSTIVINPEKDKTMRQELDDF---KDKVDHIIDICFLKNEKFINAMKEAFETFINKR 352

>pdb|4AP2|B Chain B, Crystal Structure Of The Human Klhl11-cul3 Complex At 2.8a Resolution Length = 410

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 92/197 (46%), Gaps = 10/197 (5%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE  FLEMS E+++ E+ K L   + S Y+++V   ++EE  R +  L  S+   
Sbjct: 200 VYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEP 259
Query: 129 VKAKCEQHMVADHLNFL----QGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184
           +    E+ +++ H+  +        V M+   +  DL  MY L   V  G+  + + +  
Sbjct: 260 IVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSS 319
Query: 185 HICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVIN 244
           ++ +QG   +S          + + +  +  ++  F+ E F+ D+ F   +       +N
Sbjct: 320 YLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLN 379
Query: 245 HKFDPKMPSKSPEYLAK 261
                 + S+SPEYLA+
Sbjct: 380 ------LNSRSPEYLAE 390

>pdb|4APF|B Chain B, Crystal Structure Of The Human Klhl11-cul3 Complex At 3.1a Resolution Length = 388

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 92/197 (46%), Gaps = 10/197 (5%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE  FLEMS E+++ E+ K L   + S Y+++V   ++EE  R +  L  S+   
Sbjct: 178 VYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEP 237
Query: 129 VKAKCEQHMVADHLNFL----QGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184
           +    E+ +++ H+  +        V M+   +  DL  MY L   V  G+  + + +  
Sbjct: 238 IVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSS 297
Query: 185 HICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVIN 244
           ++ +QG   +S          + + +  +  ++  F+ E F+ D+ F   +       +N
Sbjct: 298 YLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLN 357
Query: 245 HKFDPKMPSKSPEYLAK 261
                 + S+SPEYLA+
Sbjct: 358 ------LNSRSPEYLAE 368

>pdb|3O2P|E Chain E, A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn1(P)-Cdc53(Whb) Length = 88

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 56/82 (68%), Gaps = 2/82 (2%)
Query: 529 EIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQS-KSFAPSISMIKKCIE 587
           E ER    ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS + F   +SM+K+ I+
Sbjct: 8   EDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAID 67
Query: 588 SLIDKNYVERTANSTDEYSYVA 609
           SLI K Y++R  +  + Y+Y+A
Sbjct: 68  SLIQKGYLQR-GDDGESYAYLA 88

>pdb|3O6B|B Chain B, A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn1(P)-Cdc53(Whb) Low Resolution Length = 76

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 54/76 (71%), Gaps = 2/76 (2%)
Query: 535 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQS-KSFAPSISMIKKCIESLIDKN 593
           S ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS + F   +SM+K+ I+SLI K 
Sbjct: 2   SELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKG 61
Query: 594 YVERTANSTDEYSYVA 609
           Y++R  +  + Y+Y+A
Sbjct: 62  YLQR-GDDGESYAYLA 76

>pdb|4EOZ|B Chain B, Crystal Structure Of The Spop Btb Domain Complexed With The Cul3 N- Terminal Domain Length = 364

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/167 (21%), Positives = 72/167 (43%), Gaps = 4/167 (2%)
Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE  FLE S E+++ E+ K L   + S Y+++V   ++EE  R    L  S+   
Sbjct: 183 VYEEDFEAPFLEXSAEFFQXESQKFLAENSASVYIKKVEARINEEIERVXHCLDKSTEEP 242
Query: 129 VKAKCEQHMVADHLNFL----QGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184
           +    E+ +++ H   +        V  +   +  DL   Y L   V  G+    +    
Sbjct: 243 IVKVVERELISKHXKTIVEXENSGLVHXLKNGKTEDLGCXYKLFSRVPNGLKTXCECXSS 302
Query: 185 HICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSF 231
           ++ +QG   +S          + + +  +  ++  F+ E F+ D+ F
Sbjct: 303 YLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLF 349

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	609
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	1e-166
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	3e-04
2hye_C	759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	1e-154
2hye_C	759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	9e-05
3dpl_C	382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	1e-107
4ap2_B	410	Cullin-3, CUL-3; ubiquitination, E3 ligase, cell c	5e-44
4ap2_B	410	Cullin-3, CUL-3; ubiquitination, E3 ligase, cell c	1e-05
2wzk_A	391	Cullin-5, CUL-5; UBL conjugation pathway, HIV, pho	1e-35
2wzk_A	391	Cullin-5, CUL-5; UBL conjugation pathway, HIV, pho	1e-10
4eoz_B	364	Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, pro	2e-35
4eoz_B	364	Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, pro	1e-04
4a64_A	354	Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo	2e-33
4a64_A	354	Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo	7e-05
1iuy_A	92	Cullin-3 homologue; winged helix, structural genom	9e-32
2do7_A	101	Cullin-4B, CUL-4B; helix-turn-helix motif, structu	4e-30
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	5e-28
3o2p_E	88	Cell division control protein 53; ligase, cell cyc	5e-27
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	7e-04

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A Length = 760

 Score =  491 bits (1264), Expect = e-166
 Identities = 234/554 (42%), Positives = 331/554 (59%), Gaps = 17/554 (3%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 211 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 270

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 271 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 330

Query: 189 QGLEAISGLS--GDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK 246
           QGL AI        N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN+ 
Sbjct: 331 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN 390

Query: 247 FD---PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFY 303
                 +  SKSPE LA+YCD LLKKSSK   E+E++D L+Q + VFKYI+DKDVF KFY
Sbjct: 391 AVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFY 450

Query: 304 AKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFV 363
           AKMLAKRL+HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F     
Sbjct: 451 AKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLT 510

Query: 364 KTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWL 423
            +  +   + FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL
Sbjct: 511 NSEPL--DLDFSIQVLSSGSWPFQQS--CTFALPSELERSYQRFTAFYASRHSGRKLTWL 566

Query: 424 HNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483
           + +S+ EL  +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  
Sbjct: 567 YQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQI 626

Query: 484 LVECKLLTSNKE-------ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSS 536
           L++ KLL    E       EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +
Sbjct: 627 LLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKN 686

Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 595
           ++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q  S F P + +IKKCI+ LI+K Y+
Sbjct: 687 IEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYL 746

Query: 596 ERTANSTDEYSYVA 609
           ER     D YSY+A
Sbjct: 747 ERVDGEKDTYSYLA 760

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A Length = 760

 Score = 42.9 bits (100), Expect = 3e-04
 Identities = 32/215 (14%), Positives = 72/215 (33%), Gaps = 46/215 (21%)

Query: 10  FNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVA--------------------- 48
            ++ W  L+  IQ V T  ++ ++ + + ++ +Y+ C +                     
Sbjct: 1   LDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQ 60

Query: 49  ---YPEPLADRLYQETKLFLDQHL------YVDIFETQFL-EMSGEWYK-SEASKLLQTC 97
                + +   LY+  K FL  +L        D+ +   L   + +W     +SK+L   
Sbjct: 61  TPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLN-- 118

Query: 98  NVSQYMERVLQVLHEETNR----SVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMV 153
            +  Y+ R       +  R     +  L + ++          +       +    + ++
Sbjct: 119 GICAYLNRHWVRRECDEGRKGIYEIYSLALVTW-------RDCLFRPLNKQVTNAVLKLI 171

Query: 154 AEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
            +ER  +  N   L+  V +    L     D   K
Sbjct: 172 EKERNGETINT-RLISGVVQSYVELGLNEDDAFAK 205

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E* Length = 759

 Score =  460 bits (1185), Expect = e-154
 Identities = 169/558 (30%), Positives = 281/558 (50%), Gaps = 17/558 (3%)

Query: 57  LYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNR 116
           L     +  D  +Y D FE +FLE +   Y +E  +L+Q   V +Y+  V + L EE +R
Sbjct: 214 LRSLLGMLSDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDR 273

Query: 117 SVRFLHVSSYPKVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGI 175
            + +L  S+   + A  E+ ++ +HL   LQ     ++ E R  DLA MY L   VR G 
Sbjct: 274 VITYLDHSTQKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQ 333

Query: 176 NILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGAL 235
             L+    ++I   G   +     D      V+++L    K    ++  F  ++ F+  +
Sbjct: 334 QALLQHWSEYIKTFGTAIVINPEKDK---DMVQDLLDFKDKVDHVIEVCFQKNERFVNLM 390

Query: 236 DKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDD 295
            ++  + IN     K P+K  E +AK+ D  L+  +K  ++ E++  L + + +F++I  
Sbjct: 391 KESFETFIN-----KRPNKPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHG 445

Query: 296 KDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLN 355
           KDVF  FY K LAKRL+  +S S+D E++M++KLK  CG  FT+K   M  D+++S  + 
Sbjct: 446 KDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIM 505

Query: 356 EKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQF 415
             F  + ++       I  ++NIL  G WP          +  E+ K   +F+ FY G+ 
Sbjct: 506 VHFK-QHMQNQSDSGPIDLTVNILTMGYWPTYTP--MEVHLTPEMIKLQEVFKAFYLGKH 562

Query: 416 NGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQD 475
           +GRKL W   +    LK  + +      +  FQ  +LL+F + D  +  +I+    +   
Sbjct: 563 SGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDS 622

Query: 476 QIGRHIASLVECKLLTSNKE----ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIE 531
           ++ R + SL   K     K     E+ +  +   N  + +K  ++KI+    KET +E  
Sbjct: 623 ELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQV 682

Query: 532 RTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLID 591
            T   V +DR+  + AAIVRIMK RK + HN L+ E+ +Q K F      +KK IESLID
Sbjct: 683 STTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLID 741

Query: 592 KNYVERTANSTDEYSYVA 609
           ++Y+ER  ++ ++Y YVA
Sbjct: 742 RDYMERDKDNPNQYHYVA 759

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E* Length = 759

 Score = 44.4 bits (104), Expect = 9e-05
 Identities = 23/144 (15%), Positives = 53/144 (36%), Gaps = 20/144 (13%)

Query: 9   DFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH 68
               TW  L E ++ V +     R    + +  + +LC       +  LY++ +   + H
Sbjct: 58  YTQDTWRKLHEAVRAVQS-STSIRYNLEELYQAVENLCSHKV---SPMLYKQLRQACEDH 113

Query: 69  LYVDIF--------ETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRF 120
           +   I            FL+     ++    +++   ++  +++R   VL   T  S+  
Sbjct: 114 VQAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTY-VLQNSTLPSIWD 172

Query: 121 L-------HVSSYPKVKAKCEQHM 137
           +       H+ S   V++K    +
Sbjct: 173 MGLELFRTHIISDKMVQSKTIDGI 196

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C Length = 382

 Score =  328 bits (841), Expect = e-107
 Identities = 117/380 (30%), Positives = 187/380 (49%), Gaps = 24/380 (6%)

Query: 253 SKSPEYLAKYCDMLLKKS--SKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKR 310
           SK PE LA YCDMLL+K+  SK L+  E++ KL + +   KY+ +KDVF +++   L +R
Sbjct: 4   SKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRR 63

Query: 311 LIHQQSTSMDGEEAMINKLKQ-ACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEID 369
           LI   S   + EE M+  L++     ++ NK  RM  DIK+S  LN+ F           
Sbjct: 64  LILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLAL 123

Query: 370 LGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQV 429
                +I IL AG+W          S+P ELE  I   E+FY    +GRKL W H +S  
Sbjct: 124 PADSVNIKILNAGAWSRSSEK-VFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNG 182

Query: 430 ELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
            +        Y + + TFQ+A+L  + +   + ++  +++    L   ++ R + SLV  
Sbjct: 183 IITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAF 242

Query: 488 KLL----------TSNKEELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEI 530
             L           ++ ++ TE T   +N  ++        KR K+ + G +Q  T +  
Sbjct: 243 PKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMR 302

Query: 531 ERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESL 589
           E     + + R L  Q AI++IMK RK+I +  L  E++   K+ F P   MIK+ IE L
Sbjct: 303 EEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWL 362

Query: 590 IDKNYVERTANSTDEYSYVA 609
           I+  Y+ R  +  + + Y+A
Sbjct: 363 IEHKYIRRDESDINTFIYMA 382

>4ap2_B Cullin-3, CUL-3; ubiquitination, E3 ligase, cell cycle; HET: EDO; 2.80A {Homo sapiens} PDB: 4apf_B Length = 410

 Score =  161 bits (407), Expect = 5e-44
 Identities = 47/219 (21%), Positives = 94/219 (42%), Gaps = 12/219 (5%)

Query: 66  DQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSS 125
            + +Y + FE  FLEMS E+++ E+ K L   + S Y+++V   ++EE  R +  L  S+
Sbjct: 197 GRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKST 256

Query: 126 YPKVKAKCEQHMVADHLNFL----QGECVPMVAEERRHDLANMYPLLRSVREGINILIDA 181
              +    E+ +++ H+  +        V M+   +  DL  MY L   V  G+  + + 
Sbjct: 257 EEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCEC 316

Query: 182 VRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSS 241
           +  ++ +QG   +S          + + +  +  ++  F+ E F+ D+ F   +      
Sbjct: 317 MSSYLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEY 376

Query: 242 VINHKFDPKMPSKSPEYLAKYC--DMLLKKSSKGLSESE 278
            +N        S+SPEYLA+                + +
Sbjct: 377 FLNLN------SRSPEYLAENLYFQSHHHHHHDYKDDDD 409

>4ap2_B Cullin-3, CUL-3; ubiquitination, E3 ligase, cell cycle; HET: EDO; 2.80A {Homo sapiens} PDB: 4apf_B Length = 410

 Score = 46.8 bits (110), Expect = 1e-05
 Identities = 21/173 (12%), Positives = 63/173 (36%), Gaps = 5/173 (2%)

Query: 1   MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQE 60
             +   +   N  W  L+  IQ  I   N    ++ + + + Y++ +       ++LY  
Sbjct: 21  FPMTMDEKYVNSIWDLLKNAIQE-IQRKNNSGLSFEELYRNAYTMVLH---KHGEKLYTG 76

Query: 61  TKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRF 120
            +  + +HL   + E     ++  + ++              +  +L  +     +    
Sbjct: 77  LREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNV 136

Query: 121 LHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVRE 173
            +V +   +  + +        + L+   + M+A ER+ ++ +    +R+  +
Sbjct: 137 ENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR-GAIRNACQ 188

>2wzk_A Cullin-5, CUL-5; UBL conjugation pathway, HIV, phosphoprotein, isopeptide bond, protein binding; 2.05A {Mus musculus} Length = 391

 Score =  137 bits (345), Expect = 1e-35
 Identities = 48/196 (24%), Positives = 82/196 (41%), Gaps = 6/196 (3%)

Query: 68  HLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYP 127
            +Y D FE  +L+ +  +Y+++A   LQ   V  YM+     L EE  R++R+L      
Sbjct: 196 QIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRREC 255

Query: 128 KVKAK----CEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVR 183
                    C   +V      +  EC  M+       L  M+ L+  V  GI  ++  + 
Sbjct: 256 NSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLE 315

Query: 184 DHICKQGLEAISGLSGDNI--STQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSS 241
           +HI   GL  +   +      S ++ E +  +  ++   VKE F  D  F+ A DKA  +
Sbjct: 316 EHIISAGLADMVAAAETITTDSEKYREQLDTLFNRFSKLVKEAFQDDPRFLTARDKAYKA 375

Query: 242 VINHKFDPKMPSKSPE 257
           V+N     K  +   +
Sbjct: 376 VVNDATIFKAENLYFQ 391

>2wzk_A Cullin-5, CUL-5; UBL conjugation pathway, HIV, phosphoprotein, isopeptide bond, protein binding; 2.05A {Mus musculus} Length = 391

 Score = 63.0 bits (152), Expect = 1e-10
 Identities = 28/194 (14%), Positives = 68/194 (35%), Gaps = 14/194 (7%)

Query: 1   MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQE 60
           +      + F   W  +   +  ++   +V +  W D FSD++++C+ + +  + +++Q 
Sbjct: 6   LLKNKGSLQFEDKWDFMHPIVLKLLRQESVTKQQWFDLFSDVHAVCL-WDDKGSSKIHQA 64

Query: 61  TKLFLDQHLYVDIFETQFLEMSGEWYKSEA---------SKLLQTCNVSQYMERVLQVLH 111
            K  + + +     + + L    +    +A         ++          +E  L    
Sbjct: 65  LKEDILEFI--KQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEVTLLGKQ 122

Query: 112 EETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSV 171
               +S           +     + + ++  N LQ   + +V  ER  +  +   L+  V
Sbjct: 123 SSNKKSNMED-SIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDS-QLVIGV 180

Query: 172 REGINILIDAVRDH 185
           RE    L     D 
Sbjct: 181 RESYVNLCSNPEDK 194

>4eoz_B Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, protein binding; 2.40A {Homo sapiens} PDB: 4apf_B Length = 364

 Score =  135 bits (341), Expect = 2e-35
 Identities = 40/183 (21%), Positives = 83/183 (45%), Gaps = 4/183 (2%)

Query: 66  DQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSS 125
            + +Y + FE  FLEMS E+++ E+ K L   + S Y+++V   ++EE  R +  L  S+
Sbjct: 180 GRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKST 239

Query: 126 YPKVKAKCEQHMVADHLNFL----QGECVPMVAEERRHDLANMYPLLRSVREGINILIDA 181
              +    E+ +++ H+  +        V M+   +  DL  MY L   V  G+  + + 
Sbjct: 240 EEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCEC 299

Query: 182 VRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSS 241
           +  ++ +QG   +S          + + +  +  ++  F+ E F+ D+ F   +      
Sbjct: 300 MSSYLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEY 359

Query: 242 VIN 244
            +N
Sbjct: 360 FLN 362

>4eoz_B Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, protein binding; 2.40A {Homo sapiens} PDB: 4apf_B Length = 364

 Score = 43.7 bits (102), Expect = 1e-04
 Identities = 21/169 (12%), Positives = 62/169 (36%), Gaps = 5/169 (2%)

Query: 5   PKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLF 64
             +   N  W  L+  IQ  I   N    ++ + + + Y++ +       ++LY   +  
Sbjct: 8   MDEKYVNSIWDLLKNAIQE-IQRKNNSGLSFEELYRNAYTMVL---HKHGEKLYTGLREV 63

Query: 65  LDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVS 124
           + +HL   + E     ++  + ++              +  +L  +     +     +V 
Sbjct: 64  VTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVY 123

Query: 125 SYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVRE 173
           +   +  + +        + L+   + M+A ER+ ++ +    +R+  +
Sbjct: 124 NLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR-GAIRNACQ 171

>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens} Length = 354

 Score =  130 bits (327), Expect = 2e-33
 Identities = 47/187 (25%), Positives = 86/187 (45%), Gaps = 4/187 (2%)

Query: 61  TKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRF 120
             +  D  +Y D FE +FLE +   Y +E  KL+Q   V +Y+  V + L EE +R + +
Sbjct: 169 LSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITY 228

Query: 121 LHVSSYPKVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGINILI 179
           L  ++   + A  E+ ++ +HL   LQ     ++ E R  DL+ +Y L   VR G+ +L+
Sbjct: 229 LDQTTQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLL 288

Query: 180 DAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKAC 239
               ++I   G   +     D       + +     K    +   F  ++ F+ A+ +A 
Sbjct: 289 QQWIEYIKAFGSTIVINPEKDK---TMRQELDDFKDKVDHIIDICFLKNEKFINAMKEAF 345

Query: 240 SSVINHK 246
            + IN +
Sbjct: 346 ETFINKR 352

>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens} Length = 354

 Score = 44.5 bits (104), Expect = 7e-05
 Identities = 38/364 (10%), Positives = 119/364 (32%), Gaps = 43/364 (11%)

Query: 4   KPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKL 63
           K  +   ++TW  L+E ++ +       +    + +  + +LC      ++  LY++ + 
Sbjct: 4   KLPENYTDETWQKLKEAVEAIQN-STSIKYNLEELYQAVENLCSY---KISANLYKQLRQ 59

Query: 64  FLDQHLY--------VDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETN 115
             + H+           +    FL+     +++   +++   ++  +++R     +   N
Sbjct: 60  ICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRT----YVLQN 115

Query: 116 RSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERR---------HDLANMYP 166
             +  +        +A           N      + ++  ER            L +M  
Sbjct: 116 SMLPSIWDMGLELFRAHIISDQ--KVQNKTIDGILLLIERERNGEAIDRSLLRSLLSMLS 173

Query: 167 LLRSVREGI-NILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELF 225
            L+  ++      ++        +G + +             + +     +   ++ +  
Sbjct: 174 DLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQ-- 231

Query: 226 SGDQSFMGALDKAC-----SSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMD 280
           +  +S +  ++K       ++++    +  +     + L+     L  +   G+    + 
Sbjct: 232 TTQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQ-LFSRVRGGV--QVLL 288

Query: 281 DKLSQSITVF--KYIDDKDVFHKFYAKMLA--KRLIHQQSTSMDGEEAMINKLKQACGYE 336
            +  + I  F    + + +       ++     ++ H         E  IN +K+A    
Sbjct: 289 QQWIEYIKAFGSTIVINPEKDKTMRQELDDFKDKVDHIIDICFLKNEKFINAMKEAFET- 347

Query: 337 FTNK 340
           F NK
Sbjct: 348 FINK 351

>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.34 Length = 92

 Score =  117 bits (294), Expect = 9e-32
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)

Query: 520 GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 578
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61

Query: 579 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score =  113 bits (283), Expect = 4e-30
 Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)

Query: 519 SGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS 578
           SG   KET +E   T   V +DR+  + AAIVRIMK RK + HN L+ EV +Q K F   
Sbjct: 6   SGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVK 64

Query: 579 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
            + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 65  PADLKKRIESLIDRDYMERDKENPNQYNYIA 95

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C Length = 77

 Score =  106 bits (266), Expect = 5e-28
 Identities = 42/76 (55%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 535 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKN 593
           S+++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q  S F P + +IKKCI+ LI+K 
Sbjct: 2   SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKE 61

Query: 594 YVERTANSTDEYSYVA 609
           Y+ER     D YSY+A
Sbjct: 62  YLERVDGEKDTYSYLA 77

>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A {Saccharomyces cerevisiae} PDB: 3o6b_B Length = 88

 Score =  103 bits (259), Expect = 5e-27
 Identities = 31/87 (35%), Positives = 56/87 (64%), Gaps = 2/87 (2%)

Query: 524 KETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMI 582
            +   E ER    ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS   F   +SM+
Sbjct: 3   NKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMV 62

Query: 583 KKCIESLIDKNYVERTANSTDEYSYVA 609
           K+ I+SLI K Y++R  +  + Y+Y+A
Sbjct: 63  KRAIDSLIQKGYLQRGDDG-ESYAYLA 88

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 55.6 bits (133), Expect = 4e-08
 Identities = 77/534 (14%), Positives = 164/534 (30%), Gaps = 180/534 (33%)

Query: 136 HMVADHLNFLQGE-------CVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           H    H++F  GE        + +  +    +  +   +    +   +IL     DHI  
Sbjct: 1   HHHHHHMDFETGEHQYQYKDILSVFEDAFVDNF-DCKDVQDMPK---SILSKEEIDHIIM 56

Query: 189 QGLEAISGL---------SGDNISTQFVENMLAVHKKYKAFVKELFSGD--------QSF 231
              +A+SG            + +  +FVE +L     YK F+      +        + +
Sbjct: 57  SK-DAVSGTLRLFWTLLSKQEEMVQKFVEEVLR--INYK-FLMSPIKTEQRQPSMMTRMY 112

Query: 232 MGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFK 291
           +   D+  +   N  F  K      +   K     L+++   L  +             K
Sbjct: 113 IEQRDRLYND--NQVF-AKYNVSRLQPYLK-----LRQALLELRPA-------------K 151

Query: 292 YIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKIS 351
            +                 LI      + G            G     K     T + + 
Sbjct: 152 NV-----------------LID----GVLG-----------SG-----K-----TWVALD 169

Query: 352 GGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFY 411
             L+ K   +       D  I           W      ++        E  + M +K  
Sbjct: 170 VCLSYKVQCKM------DFKIF----------W------LN-LKNCNSPETVLEMLQKLL 206

Query: 412 HGQFNGRKLSWLHNISQVELKL----SYLKRPYFVTMQTFQMAILLL---FEKN--DAMT 462
           + Q +    S   + S ++L++    + L+R   +  + ++  +L+L         +A  
Sbjct: 207 Y-QIDPNWTSRSDHSSNIKLRIHSIQAELRR--LLKSKPYENCLLVLLNVQNAKAWNAF- 262

Query: 463 CGDIQ-TVLSLSQD-QIGRHIASLVECKL-LTSNKEELTEDTEIRLNLGYNNKRTK---- 515
             ++   +L  ++  Q+   +++     + L  +   LT D    L L Y + R +    
Sbjct: 263 --NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320

Query: 516 -------LKIS--GAVQKETP-----------QEIERTV-SSVD-----EDRKLYLQAAI 549
                   ++S      ++              ++   + SS++     E RK++ + ++
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 550 VRIMKSRKQIRHNALI-QEVLS----QSKSFAPSISMIKKCIESLIDKNYVERT 598
                       +A I   +LS            + + K    SL++K   E T
Sbjct: 381 ---------FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST 425

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.8 bits (123), Expect = 5e-07
 Identities = 68/512 (13%), Positives = 139/512 (27%), Gaps = 168/512 (32%)

Query: 7   QVDFNKTWGSLQ-ETIQ---GVITLGNVRRATWND--RFSDIYSLCVAYPEP---LADRL 57
           ++++      ++ E  Q           R   +ND   F+  Y+  V+  +P   L   L
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK-YN--VSRLQPYLKLRQAL 144

Query: 58  YQETKLFLDQHLYVDIF-----------------ETQFLEMSGE--W-----YKSEASKL 93
            +     L     V I                       +M  +  W       S  + L
Sbjct: 145 LE-----LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 94  --LQT---------CNVSQYMERVLQVLHEETNRSVRFLHVSSYPK-------------V 129
             LQ           + S +   +   +H       R L    Y                
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259

Query: 130 KA---KC-------------------EQHMVADHLN--FLQGE-------CVPMVAEERR 158
            A    C                     H+  DH +      E        +    ++  
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319

Query: 159 HDLANMYPLL-----RSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAV 213
            ++    P        S+R+G+    D  +   C + L  I   S + +       M   
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLA-TWDNWKHVNCDK-LTTIIESSLNVLEPAEYRKM--- 374

Query: 214 HKKYKAFVKELFSGD--------QSFMGALDKACSSVINHKFDPK-MPSKSP-EYLAKYC 263
              +      +F                 + K+   V+ +K     +  K P E      
Sbjct: 375 ---FDRLS--VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429

Query: 264 DMLLKKSSKGLSESEMDDKLSQSITV------------------FKYI----------DD 295
            + L+   K  +E  +   +     +                  + +I          + 
Sbjct: 430 SIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER 489

Query: 296 KDVFHKFYA--KMLAKRLIHQQSTSMDGEEAMINKLKQACGYE--FT---NKFHRMLTDI 348
             +F   +   + L +++ H  ST+ +   +++N L+Q   Y+        K+ R++  I
Sbjct: 490 MTLFRMVFLDFRFLEQKIRH-DSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI 548

Query: 349 KISGGLNEKFHSEFVKTNEIDLGIHFSINILQ 380
                       +F+   E +L      ++L+
Sbjct: 549 L-----------DFLPKIEENLICSKYTDLLR 569

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae} Length = 583

 Score = 41.5 bits (97), Expect = 7e-04
 Identities = 17/180 (9%), Positives = 46/180 (25%), Gaps = 19/180 (10%)

Query: 422 WLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHI 481
                    L+L     P           +L L  +   +T   +   L   ++     +
Sbjct: 406 VGGRPVLPVLELVSSIVPEARQDDYRIAIVLYLLFQRPFITIDVVARGLQSGKEAARNAL 465

Query: 482 ASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDR 541
            +  +  +               L + ++     L  +        +    +        
Sbjct: 466 EAARQTTVA-----------GAPLIIAHDGVWL-LGNACREILRKVEPSPFSPVRYLSTD 513

Query: 542 KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 601
           +  L  A +  +     +  +  +  +   S+         K C++ L+D+  V      
Sbjct: 514 QAELTNAAMLWLSEVGDLATSD-LMAMCGVSR------GTAKACVDGLVDEERVVAVGGG 566

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	609
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	100.0
2hye_C	759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	100.0
3dpl_C	382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	100.0
4ap2_B	410	Cullin-3, CUL-3; ubiquitination, E3 ligase, cell c	100.0
2wzk_A	391	Cullin-5, CUL-5; UBL conjugation pathway, HIV, pho	100.0
4a64_A	354	Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo	100.0
4eoz_B	364	Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, pro	100.0
2do7_A	101	Cullin-4B, CUL-4B; helix-turn-helix motif, structu	99.94
3o2p_E	88	Cell division control protein 53; ligase, cell cyc	99.93
1iuy_A	92	Cullin-3 homologue; winged helix, structural genom	99.93
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	99.93
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	94.21
1sfx_A	109	Conserved hypothetical protein AF2008; structural	92.83
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	92.45
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	92.22
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	92.06
3r0a_A	123	Putative transcriptional regulator; structural gen	91.95
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	91.83
1y0u_A	96	Arsenical resistance operon repressor, putative; s	91.78
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	91.56
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	91.54
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	91.52
3jth_A	98	Transcription activator HLYU; transcription factor	91.39
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	91.34
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	91.19
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	91.16
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	91.05
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	91.03
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	90.85
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	90.83
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	90.79
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	90.78
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	90.69
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	90.42
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.41
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	90.4
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	90.24
1bja_A	95	Transcription regulatory protein MOTA; activation	90.11
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	90.04
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	89.89
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	89.7
2gxg_A	146	146AA long hypothetical transcriptional regulator;	89.59
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	89.48
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	89.44
2nnn_A	140	Probable transcriptional regulator; structural gen	89.42
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	89.41
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	89.28
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	89.11
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	89.0
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	88.91
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	88.86
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	88.81
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	88.8
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	88.6
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	88.6
2pex_A	153	Transcriptional regulator OHRR; transcription regu	88.6
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	88.58
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	88.57
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	88.57
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	88.55
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	88.49
1p6r_A	82	Penicillinase repressor; transcription regulation,	88.42
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	88.19
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	88.09
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	88.07
2eth_A	154	Transcriptional regulator, putative, MAR family; M	88.02
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	87.95
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	87.89
2obp_A	96	Putative DNA-binding protein; structural genomics,	87.78
1ku9_A	152	Hypothetical protein MJ223; putative transcription	87.7
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	87.6
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	87.58
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	87.54
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	87.54
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	87.49
2w25_A	150	Probable transcriptional regulatory protein; trans	87.46
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	87.46
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	87.36
3bja_A	139	Transcriptional regulator, MARR family, putative;	87.23
3f3x_A	144	Transcriptional regulator, MARR family, putative;	87.15
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	87.15
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	87.06
2vn2_A	128	DNAD, chromosome replication initiation protein; D	86.9
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	86.89
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	86.82
3s2w_A	159	Transcriptional regulator, MARR family; structural	86.81
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	86.67
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	86.63
1z91_A	147	Organic hydroperoxide resistance transcriptional;	86.41
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	86.3
3k69_A	162	Putative transcription regulator; putative transcr	86.2
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	86.14
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	86.05
1ylf_A	149	RRF2 family protein; structural genomics, transcri	86.04
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	86.04
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	85.81
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	85.37
1xd7_A	145	YWNA; structural genomics, protein structure initi	85.33
3nqo_A	189	MARR-family transcriptional regulator; structural	85.31
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	85.29
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	85.27
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	84.77
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	84.75
2fxa_A	207	Protease production regulatory protein HPR; protea	84.53
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	84.26
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	84.23
2pg4_A	95	Uncharacterized protein; structural genomics, join	84.1
2kko_A	108	Possible transcriptional regulatory protein (possi	83.99
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	83.64
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	83.62
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	83.58
1okr_A	123	MECI, methicillin resistance regulatory protein ME	83.4
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	83.39
1mkm_A	249	ICLR transcriptional regulator; structural genomic	83.29
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	83.04
4fx0_A	148	Probable transcriptional repressor protein; helix-	83.03
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	82.99
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	82.75
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	81.95
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	81.87
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	81.69
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	81.37
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	81.15
2xub_A	534	DNA-directed RNA polymerase III subunit RPC3; tran	81.13
2g7u_A	257	Transcriptional regulator; ICLR family, structural	80.91
1p6r_A	82	Penicillinase repressor; transcription regulation,	80.87
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	80.83
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	80.79
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	80.68
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	80.6

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A

Probab=100.00  E-value=2.9e-122  Score=1055.18  Aligned_cols=596  Identities=42%  Similarity=0.706  Sum_probs=559.2

Q ss_pred             hHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccC------------------------CcccHHHHHHHHHhhh
Q psy16234         10 FNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAY------------------------PEPLADRLYQETKLFL   65 (609)
Q Consensus        10 fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~------------------------~~~~~~~Ly~~~~~~l   65 (609)
                      ||++|..|++||..|++.++++...||++|++||++|++.                        |.++|++||+++++++
T Consensus         1 f~~~W~~L~~ai~~I~~~~~~s~~~~~~LY~~vYn~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LY~~l~~~l   80 (760)
T 1ldj_A            1 LDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFL   80 (760)
T ss_dssp             CHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHTCCC----------------------------TTHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhcCCcccCCCcccccccccccccccccCcchhHHHHHHHHHHHH
Confidence            7999999999999999977999999999999999999986                        5569999999999887


Q ss_pred             hhh-----------------------------------------------------------------------------
Q psy16234         66 DQH-----------------------------------------------------------------------------   68 (609)
Q Consensus        66 ~~~-----------------------------------------------------------------------------   68 (609)
                      .+|                                                                             
T Consensus        81 ~~~l~~~~~~~~~~~~e~lL~~~~~~W~~~~~~~~~i~~if~YLdR~yv~~~~~~g~~~~~~I~~lgL~~fr~~vf~~l~  160 (760)
T 1ldj_A           81 KNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLN  160 (760)
T ss_dssp             HHHHHHHHHTTCSCTTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSSCCC-------CCHHHHHHHTTHHHHTTTTT
T ss_pred             HHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHcccccccCCCcccHHHHHHHHHHHHHHHHHH
Confidence            766                                                                             


Q ss_pred             ----------------------------------c----------------cHHhhHHHHHHHHHHHHHHHHHHHHhcCC
Q psy16234         69 ----------------------------------L----------------YVDIFETQFLEMSGEWYKSEASKLLQTCN   98 (609)
Q Consensus        69 ----------------------------------~----------------Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s   98 (609)
                                                        +                |.+.||++||++|..||+.+|++|+++++
T Consensus       161 ~~l~~~lL~lI~~eR~Ge~id~~lik~vi~ml~~Lg~~~~~~~~~~~~l~vY~~~FE~~fL~~t~~fY~~es~~~l~~~~  240 (760)
T 1ldj_A          161 KQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNP  240 (760)
T ss_dssp             THHHHHHHHHHTTTSCCTTCCTHHHHHHHHHHHHTSCCSSSSSCSSCCCHHHHHHTHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCcccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence                                              1                78999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHH
Q psy16234         99 VSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINIL  178 (609)
Q Consensus        99 ~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l  178 (609)
                      +++||++|+.++++|.+||..||+++|.++|.++|+++||.+|++.|.+||..||++++.+||++||+||+|+++|+++|
T Consensus       241 ~~~Yl~~~e~~l~eE~~R~~~yL~~~t~~~l~~~~~~~Li~~~~~~l~~~~~~ll~~~~~~dL~~my~L~~rv~~gl~~l  320 (760)
T 1ldj_A          241 VTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGEL  320 (760)
T ss_dssp             TTSSHHHHHHHHHHHHHTTTTTTCSSSSHHHHHHHHHHHSSSSSHHHHHHHHHHHHSCCTTHHHHHHHHHHHSTTCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCcCcchHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcccC--CCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCC---CCCC
Q psy16234        179 IDAVRDHICKQGLEAISGLSG--DNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP---KMPS  253 (609)
Q Consensus       179 ~~~~~~~i~~~g~~~~~~~~~--~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~---~~~~  253 (609)
                      +..|++||++.|.+++.....  ...|..||+.||++|++|+.++..||++|+.|..++++||+.|+|.+...   ....
T Consensus       321 ~~~~~~~i~~~G~~~v~~~~~~~~~~~~~~V~~ll~l~~k~~~lv~~~F~~d~~f~~al~~af~~~iN~~~~~~~~~~~~  400 (760)
T 1ldj_A          321 KKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSS  400 (760)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSGGGCHHHHHHHHHHHHHHHHHHHHTTTTTCHHHHHHHHHHHHHHHHSSHHHHHHTSTT
T ss_pred             HHHHHHHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhcCCcccccccccc
Confidence            999999999999999987532  25789999999999999999999999999999999999999999976321   2347


Q ss_pred             CchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHh
Q psy16234        254 KSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQAC  333 (609)
Q Consensus       254 ~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~  333 (609)
                      ++||+||+|||.+||+|.++.+++|++..|++++.||+|+++||+|+.+|+++||+|||+++|++.|+|+.||++||.+|
T Consensus       401 ~~~E~la~y~D~~Lkk~~k~~~e~e~e~~L~~i~~lf~~i~~KDvF~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~  480 (760)
T 1ldj_A          401 KSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQAC  480 (760)
T ss_dssp             HHHHHHHHHHHHHHBCCSSCCCHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHTTCBSCHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHhHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHh
Confidence            89999999999999999999899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhh
Q psy16234        334 GYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHG  413 (609)
Q Consensus       334 G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~  413 (609)
                      |.+||+||++||+||..|++++..| ++++.+ +...+++|+|.|||+|+||..+.  .++.+|++|..+++.|++||.+
T Consensus       481 G~~~t~kle~M~~Di~~S~~l~~~f-~~~~~~-~~~~~~~~~v~VLs~~~WP~~~~--~~~~lP~~l~~~~~~F~~fY~~  556 (760)
T 1ldj_A          481 GFEYTSKLQRMFQDIGVSKDLNEQF-KKHLTN-SEPLDLDFSIQVLSSGSWPFQQS--CTFALPSELERSYQRFTAFYAS  556 (760)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHTT-TCCCSSEEEEEEEETTTSCCCCC--SCCCCCGGGHHHHHHHHHHTTT
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHH-HHHHhc-ccCCCCCeeEEecCCCCCCCCCC--CCCcCCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999 777654 12257999999999999999854  5899999999999999999999


Q ss_pred             cCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        414 QFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       414 k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|+||+|+|+|++|+|+|+++|+++.++++||++||+||++||+.+++|+++|++.||+++++++++|++|++.|||.+.
T Consensus       557 ~~~~RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Qa~iLllFn~~~~~t~~ei~~~t~i~~~~l~r~L~~l~k~~iL~~~  636 (760)
T 1ldj_A          557 RHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLE  636 (760)
T ss_dssp             TCTTCCEEECGGGCCCEEEESSSSSCCEEECCHHHHHHHHGGGSSSEEEHHHHHHHTCCCHHHHHHHHHHHHHTTTEECS
T ss_pred             hCCCCeEEEecccccEEEEEEECCceEEEEEcHHHHHHHHHhcCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcceeC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999843


Q ss_pred             -------CCCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHH
Q psy16234        494 -------KEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQ  566 (609)
Q Consensus       494 -------~~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~  566 (609)
                             ++++.+++.|++|.+|++++.||+|+.+.++++++|.+.+++.+++||+..|+||||||||+||+|+|++|+.
T Consensus       637 ~~~~~~~~~~~~~~~~f~lN~~F~~k~~ri~i~~~~~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~  716 (760)
T 1ldj_A          637 DENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLG  716 (760)
T ss_dssp             CTTCCTTTCCCCTTCEEEECSSCCCSSSSBCCCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHH
T ss_pred             CCccccccCCCCCCCEEEeeccccCCceEEEecCccccccchhhhhHHHHHHHHHHhHheeeehhhhhccCCCcHHHHHH
Confidence                   2567889999999999999999999877677777778888899999999999999999999999999999999


Q ss_pred             HHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        567 EVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       567 ~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +|++++++ |+|++.+||+|||+|||||||+|+++|+++|+|+|
T Consensus       717 ev~~ql~~rF~p~~~~IKk~Ie~LIereYl~R~~~~~~~y~YlA  760 (760)
T 1ldj_A          717 EVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA  760 (760)
T ss_dssp             HHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSSTTEEEECC
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHhhccceeeCCCCCcceeeCC
Confidence            99999998 99999999999999999999999999999999998

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*

Probab=100.00  E-value=3.2e-118  Score=1021.69  Aligned_cols=586  Identities=30%  Similarity=0.512  Sum_probs=552.2

Q ss_pred             cChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-------------------
Q psy16234          8 VDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-------------------   68 (609)
Q Consensus         8 ~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-------------------   68 (609)
                      ..||++|..|++||+.|++.++.+ ..|+++|+.||++|++.+   |++||+++++++++|                   
T Consensus        57 ~~~e~~W~~L~~ai~~I~~~~~~~-~s~e~LY~~vy~lc~~k~---~~~LY~~l~~~~~~~l~~~~~~l~~~~~~~~~~L  132 (759)
T 2hye_C           57 NYTQDTWRKLHEAVRAVQSSTSIR-YNLEELYQAVENLCSHKV---SPMLYKQLRQACEDHVQAQILPFREDSLDSVLFL  132 (759)
T ss_dssp             CTTTTHHHHHHHHHHTTSTTCCCS-SCHHHHHHHHHHHCCTTT---HHHHHHHHHHHHHHHHHHHHHHHTSCCCCTTHHH
T ss_pred             chHHHHHHHHHHHHHHHHhCCCCC-CCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHH
Confidence            457999999999999999876543 349999999999999874   899999998776554                   


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus       133 ~~~~~~W~~~~~~~~~i~~if~YLDR~yv~~~~~~~~I~~lgL~lfr~~v~~~~~i~~~l~~~lL~lI~~eR~Ge~id~~  212 (759)
T 2hye_C          133 KKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRS  212 (759)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTHHHHTTTTTSCSSSCCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHTTTTTCCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcHHhhCCCCCCcHHHHHHHHHHHHHhcCHhHHHHHHHHHHHHHHHHhcCCCCcHH
Confidence                                                                                            


Q ss_pred             -------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHH
Q psy16234         69 -------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQ  135 (609)
Q Consensus        69 -------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~  135 (609)
                                   +|.+.||++||++|.+||+.++++|++++++++||++|+.++++|.+||..||+++|.++|.++|++
T Consensus       213 llk~vi~ml~~L~vY~~~FE~~fL~~T~~fY~~e~~~~l~~~~~~~Yl~~~e~rl~eE~~r~~~yL~~~t~~~l~~~~~~  292 (759)
T 2hye_C          213 LLRSLLGMLSDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEK  292 (759)
T ss_dssp             HHHHHHHHHHHTTCHHHHTHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTHHHHTTTSCTTTHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHH
Confidence                         8999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh-hhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHH
Q psy16234        136 HMVADHLNFLQG-ECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVH  214 (609)
Q Consensus       136 ~LI~~~~~~l~~-~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~  214 (609)
                      +||.+|++.|.+ ||..||++++.+||++||+|++++++|++.++..|++||++.|.+++....   .+..||+.|+++|
T Consensus       293 ~Li~~~~~~ll~~~~~~lL~~~~~~dL~~mY~L~~rv~~~l~~l~~~~~~~I~~~g~~iv~~~~---~~~~~V~~ll~~~  369 (759)
T 2hye_C          293 QLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPE---KDKDMVQDLLDFK  369 (759)
T ss_dssp             HHTTTCSHHHHHTTHHHHHTTTCHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHSCGG---GTTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHhcCCHHHHHHHHHHHccCcchHHHHHHHHHHHHHHHhHHHhcCcc---cHHHHHHHHHHHH
Confidence            999999999885 999999999999999999999999999999999999999999999996543   2457999999999


Q ss_pred             HHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccC
Q psy16234        215 KKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYID  294 (609)
Q Consensus       215 ~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~  294 (609)
                      ++|+.++..||++|+.|..++++||+.|+|.+     ..++||+||+|||.+||+|.|+.+++|++..|++++.||+|++
T Consensus       370 ~k~~~lv~~~F~~d~~f~~al~~af~~fiN~~-----~~~~~E~la~y~D~~Lk~~~k~~~e~e~e~~L~~i~~lf~~i~  444 (759)
T 2hye_C          370 DKVDHVIEVCFQKNERFVNLMKESFETFINKR-----PNKPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIH  444 (759)
T ss_dssp             HHHHHHHHTTTTTCHHHHHHHHHHHHHHHTTS-----CSHHHHHHHHHHHHHHSSCGGGCCSTTHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHHCCC-----CCchHHHHHHHHHHHhccCCCCCCHHHHHHHHHHhhhhhhhcC
Confidence            99999999999999999999999999999975     2689999999999999999988888999999999999999999


Q ss_pred             ChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcce
Q psy16234        295 DKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHF  374 (609)
Q Consensus       295 ~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f  374 (609)
                      +||+|+.+|+++||+|||+++|++.|+|+.||++||.+||.+||+||++||+||..|++++..| ++++...+...+++|
T Consensus       445 ~KDvF~~~Y~~~LakRLL~~~s~s~d~E~~~i~~Lk~~~G~~~t~kle~M~~Di~~S~~l~~~f-~~~~~~~~~~~~~~~  523 (759)
T 2hye_C          445 GKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHF-KQHMQNQSDSGPIDL  523 (759)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHTTTCTTTTHHHHHHHHHHHHHHHHHHHH-HHHHHTTCCCCCCEE
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHH-HHHHhcccCCCCCce
Confidence            9999999999999999999999999999999999999999999999999999999999999999 777654433357899


Q ss_pred             EEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHh
Q psy16234        375 SINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLL  454 (609)
Q Consensus       375 ~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLll  454 (609)
                      +|.|||+|+||..+.  .++.+|++|..+++.|++||.++|+||+|+|+|++|+|+|+++|+++.++++||++||+||++
T Consensus       524 ~v~VLs~~~WP~~~~--~~~~lP~~l~~~~~~F~~fY~~~~~gRkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Qa~iLll  601 (759)
T 2hye_C          524 TVNILTMGYWPTYTP--MEVHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLLM  601 (759)
T ss_dssp             EEEEEETTTSCCCCC--CCCCCCHHHHHHHHHHHHHHHTTSCSEECCBCGGGCEEEEECCCSSCCCEEEEEHHHHHHHHH
T ss_pred             EEEEeCCCCCCCCCC--CCCcCCHHHHHHHHHHHHHHHhhCCCCEEEeccccCcEEEEEEeCCceEEEEEcHHHHHHHHH
Confidence            999999999999865  589999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hcCccccCC--CCCCCCCEEEEecCCCCCcceEEeccccccCChhHH
Q psy16234        455 FEKNDAMTCGDIQTVLSLSQDQIGRHIASLV--ECKLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEI  530 (609)
Q Consensus       455 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~--~~~iL~~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~  530 (609)
                      ||+.+++|+++|++.||+++++|+++|++|+  +.+||.+.|  +++.+++.|.+|.+|++++.||+|+.+..+++.+|.
T Consensus       602 Fn~~~~lt~~ei~~~t~i~~~~l~r~L~sL~~~k~~vL~~~p~~~~v~~~d~f~lN~~f~~~~~riki~~i~~~e~~~e~  681 (759)
T 2hye_C          602 FNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQ  681 (759)
T ss_dssp             TTSCCCEEHHHHHHHTCCCHHHHHHHHHTTTTTTTCSEEETTCSSSCCSSCEEEECCCCCCSCSSEECGGGGGCCCHHHH
T ss_pred             hcCCCCcCHHHHHHHHCcCHHHHHHHHHHHHccCCceeecCCCCCCCCCCCEEEeeccccCCceEEEeccccccccchhh
Confidence            9999999999999999999999999999999  678998876  678899999999999999999999977667788888


Q ss_pred             hhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        531 ERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       531 ~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +.+++.+++||+..||||||||||+||+|+|++|+.+|+++++ |+|++.+||+|||+|||||||+|+++|+++|+|+|
T Consensus       682 ~~t~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~-F~p~~~~IKk~Ie~LIereYleR~~~~~~~y~YlA  759 (759)
T 2hye_C          682 VSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA  759 (759)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSSEEETHHHHHHHHHHSS-SCCCHHHHHHHHHHHHHTTSCBCCSSCTTEEECCC
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhcccceecCCCCCCeeEecC
Confidence            8899999999999999999999999999999999999999999 99999999999999999999999999999999998

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C

Probab=100.00  E-value=2.4e-83  Score=677.20  Aligned_cols=354  Identities=34%  Similarity=0.524  Sum_probs=323.8

Q ss_pred             CCchhHhHHHHHHHHhcc--CCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Q psy16234        253 SKSPEYLAKYCDMLLKKS--SKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLK  330 (609)
Q Consensus       253 ~~~~e~La~y~D~~lkk~--~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk  330 (609)
                      .++||+||+|||.+||+|  +++.+++|++..|++++.||+|+++||+|+.+|+++||+|||+++|++.|+|+.||++||
T Consensus         4 ~~~~E~la~y~D~~lkk~~~~k~~~~~e~e~~L~~v~~lf~~l~~KDvF~~~Y~~~LakRLL~~~s~s~d~E~~~i~kLK   83 (382)
T 3dpl_C            4 SKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLR   83 (382)
T ss_dssp             CCSHHHHHHHHHHHHBSSHHHHTSCHHHHHHHHHHHHGGGGGCSCHHHHHHHHHHHHHHHHHTTCBSCHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            689999999999999997  477789999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCc--hhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCC-CCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHH
Q psy16234        331 QACGY--EFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEI-DLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMF  407 (609)
Q Consensus       331 ~~~G~--~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~-~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F  407 (609)
                       +||.  +||++|++||+||..|++++..| ++++.+.+. ..+++|+|.|||+|+||..+. ..++.+|++|+.+++.|
T Consensus        84 -~cG~~~~ft~kle~M~kDi~~S~~l~~~f-~~~~~~~~~~~~~~~~~v~VLs~~~WP~~~~-~~~~~lP~~l~~~~~~F  160 (382)
T 3dpl_C           84 -EVGMPADYVNKLARMFQDIKVSEDLNQAF-KEMHKNNKLALPADSVNIKILNAGAWSRSSE-KVFVSLPTELEDLIPEV  160 (382)
T ss_dssp             -HTTCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHTCCC--CCCGGGEEEEEEEHHHHCCCSC-CCCCCCCHHHHTTHHHH
T ss_pred             -HcCCchhHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcCCCCCCCceEEEEccCCcCCCCCC-CCCccCCHHHHHHHHHH
Confidence             9996  99999999999999999999999 776654331 136899999999999999853 25899999999999999


Q ss_pred             HHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234        408 EKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKN--DAMTCGDIQTVLSLSQDQIGRHIASLV  485 (609)
Q Consensus       408 ~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~~L~  485 (609)
                      ++||..+|+||+|+|+|++|+|+|+++++++.|+++||++||+||++||+.  +++|+++|++.|||++++|+++|++|+
T Consensus       161 ~~fY~~~~~gRkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Qa~ILllFn~~~~~~lt~~ei~~~t~i~~~~L~r~L~sL~  240 (382)
T 3dpl_C          161 EEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLV  240 (382)
T ss_dssp             HHHHHTTSSSEEEEECGGGCEEEEEEECSSCEEEEEEEHHHHHHHGGGTTCTTCCEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCEEEEecCcccEEEEEEeCCceEEEEEcHHHHHHHHHhccCCCCcCcHHHHHHHHCcCHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999985  899999999999999999999999997


Q ss_pred             h-----cCccccCC-----CCCCCCCEEEEecCCCCC-----cceEEecccc--ccCChhHHhhhhhhHHHHhhhhhhhh
Q psy16234        486 E-----CKLLTSNK-----EELTEDTEIRLNLGYNNK-----RTKLKISGAV--QKETPQEIERTVSSVDEDRKLYLQAA  548 (609)
Q Consensus       486 ~-----~~iL~~~~-----~~~~~~~~f~lN~~F~~~-----~~ki~i~~~~--~~~~~~e~~~~~~~v~~~R~~~i~A~  548 (609)
                      .     .|||.+.|     +++.+++.|.+|.+|++.     .++++|+.+.  +.++..+.+++++.+++||+..||||
T Consensus       241 ~~~k~k~~iL~~~~~~~~~~~~~~~d~f~~N~~F~~~k~~k~~~r~ki~~~~~~q~~~~~e~~~~~~~v~edR~~~i~Aa  320 (382)
T 3dpl_C          241 AFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEA  320 (382)
T ss_dssp             CCTTCSSCSEEESSCCSSGGGCCTTCEEEECTTCCEESSSSEESEEEEECCTTTTSCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhcceeeecCCccccCcCCCCCEEEEcCCCcCCcccccceeEEEecccccccccchhhhhhHHHHHHHhhheeeEE
Confidence            5     46888765     357789999999999861     2556665432  44566677788899999999999999


Q ss_pred             hhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        549 IVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       549 IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      ||||||+||+|+|++|+.+|++|+++ |.|++.+||+|||+|||||||+|+++|+++|+|+|
T Consensus       321 IVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~Ie~LIereYleR~~~d~~~y~YlA  382 (382)
T 3dpl_C          321 IIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA  382 (382)
T ss_dssp             HHHHHTTSSEECHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEECC
T ss_pred             EehhhhccCcccHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhhhhhccCCCCCCeEEEcC
Confidence            99999999999999999999999998 99999999999999999999999999999999998

>4ap2_B Cullin-3, CUL-3; ubiquitination, E3 ligase, cell cycle; HET: EDO; 2.80A {Homo sapiens}

Probab=100.00  E-value=8.8e-46  Score=395.14  Aligned_cols=250  Identities=23%  Similarity=0.426  Sum_probs=218.4

Q ss_pred             cChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-------------------
Q psy16234          8 VDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-------------------   68 (609)
Q Consensus         8 ~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-------------------   68 (609)
                      .+||++|+.|++||..|++.++. ...|+++|+.||++|++.   .|++||+++++++.+|                   
T Consensus        28 ~~~~~~W~~L~~ai~~I~~~~~~-~~s~eeLY~~vy~lc~~k---~g~~LY~~l~~~~~~~l~~~v~~~l~~~~~~~~L~  103 (410)
T 4ap2_B           28 KYVNSIWDLLKNAIQEIQRKNNS-GLSFEELYRNAYTMVLHK---HGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQ  103 (410)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCT-TCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHTHHHHHHTTTTSSHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhhc---cHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            56999999999999999987543 567999999999999975   7999999998877765                   


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus       104 ~~~~~W~~~~~~~~~i~~if~YLDR~yv~~~~~~~I~~lgL~lfr~~v~~~~~i~~~l~~~lL~lI~~eR~Ge~id~~li  183 (410)
T 4ap2_B          104 TLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDRGAI  183 (410)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTHHHHHTHHHHTTCCCHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHhhHHHHhcCCCCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHcCCCCCCHHHH
Confidence                                                                                            


Q ss_pred             ----------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHH
Q psy16234         69 ----------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAK  132 (609)
Q Consensus        69 ----------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~  132 (609)
                                      +|.+.||++||++|.+||+.+|++|++++++++||++|+.++++|.+||..||+++|.++|.++
T Consensus       184 k~vi~ml~~Lg~~~~~vY~~~FE~~fL~~T~~fY~~es~~~l~~~~~~~Yl~~ve~rL~eE~~R~~~yL~~sT~~kL~~~  263 (410)
T 4ap2_B          184 RNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEPIVKV  263 (410)
T ss_dssp             HHHHHHHHHTTSSSSHHHHHHTHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTSCGGGHHHHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHH
Confidence                            3999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH----hhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHH
Q psy16234        133 CEQHMVADHLNFLQ----GECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVE  208 (609)
Q Consensus       133 l~~~LI~~~~~~l~----~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~  208 (609)
                      |+++||.+|++.|.    +||..||++++.+||++||+|++|+++|+++|+.+|++||++.|.+++........|..||+
T Consensus       264 ~e~~LI~~h~~~ll~~e~~g~~~lL~~~~~~dL~~mY~L~~rv~~gl~~L~~~~~~~I~~~G~~iv~~~~~~~~~~~~V~  343 (410)
T 4ap2_B          264 VERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYRQ  343 (410)
T ss_dssp             HHHHHTGGGHHHHHTCTTTSHHHHHHTTCHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHC------CHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhhhHHHHHhCCCHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHhccccccChHHHHH
Confidence            99999999999996    59999999999999999999999999999999999999999999999998776667899999


Q ss_pred             HHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHH
Q psy16234        209 NMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLL  267 (609)
Q Consensus       209 ~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~l  267 (609)
                      .||++|++|+.++..||++|+.|..++++||+.|+|.+      .+.||+||+|||.--
T Consensus       344 ~LL~l~~k~~~iv~~~F~~d~~f~~al~~AF~~fiN~~------~~spElla~y~D~~~  396 (410)
T 4ap2_B          344 GLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLNLN------SRSPEYLAENLYFQS  396 (410)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHC---------------------
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCC------CCCHHHHHHHccCcc
Confidence            99999999999999999999999999999999999987      578899999999854

>2wzk_A Cullin-5, CUL-5; UBL conjugation pathway, HIV, phosphoprotein, isopeptide bond, protein binding; 2.05A {Mus musculus}

Probab=100.00  E-value=4.7e-43  Score=372.68  Aligned_cols=242  Identities=24%  Similarity=0.457  Sum_probs=226.3

Q ss_pred             CCccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh----------------
Q psy16234          5 PKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH----------------   68 (609)
Q Consensus         5 ~~~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~----------------   68 (609)
                      +++++||++|+.|++||.+|+..+++++..||++|++||++|++.+. .|++||+++++++++|                
T Consensus        10 ~~~~~~e~~W~~L~~ai~~I~~~~~~~~~s~e~LY~~vy~lc~~~~~-~~~~LY~~l~~~~~~~l~~~~~~~~~~~~~e~   88 (391)
T 2wzk_A           10 KGSLQFEDKWDFMHPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDK-GSSKIHQALKEDILEFIKQAQARVLSHQDDTA   88 (391)
T ss_dssp             --CCSHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHTCCSHHH
T ss_pred             CccccHHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHHHHHHHHHhccCHHH
Confidence            35689999999999999999998899999999999999999998654 7999999998777655                


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        89 ~L~~~~~~W~~~~~~~~~i~~if~YLdR~yv~~~~~~~~~~~~~~~I~~lgL~~fr~~v~~~i~~~l~~~ll~lI~~eR~  168 (391)
T 2wzk_A           89 LLKAYIVEWRKFFTQCDILPKPFCQLEVTLLGKQSSNKKSNMEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERL  168 (391)
T ss_dssp             HHHHHHHHHHHHHHHTTTTTGGGHHHHTTSTTC--------CTTCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence                                                                                            


Q ss_pred             ----------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhh
Q psy16234         69 ----------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRF  120 (609)
Q Consensus        69 ----------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~y  120 (609)
                                                  +|.+.||++||++|.+||+.+|++|++++++++||++|+.+|++|.+||..|
T Consensus       169 Ge~id~~llk~vi~~l~~L~~~~~~~l~vY~~~FE~~fL~~T~~fY~~es~~~l~~~~~~~Yl~~ve~rL~eE~~R~~~y  248 (391)
T 2wzk_A          169 GEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRY  248 (391)
T ss_dssp             TCCCCTHHHHHHHHHHHHSCCCSSCTTHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHccCccccHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence                                        5889999999999999999999999999999999999999999999999999


Q ss_pred             cC----CCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhc
Q psy16234        121 LH----VSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISG  196 (609)
Q Consensus       121 L~----~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~  196 (609)
                      ||    ++|.++|.++|+++||.+|++.|.++|..||++++.+||++||+|++|+|+|+++|+.+|++||++.|.+++..
T Consensus       249 L~~~~~~sT~~kl~~~~e~~LI~~h~~~ll~~~~~lL~~~~~~dL~~mY~L~~rv~~gl~~l~~~~~~~I~~~G~~~v~~  328 (391)
T 2wzk_A          249 LETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEHIISAGLADMVA  328 (391)
T ss_dssp             SCCTTCCSHHHHHHHHHHHHHTGGGHHHHHTTHHHHHHTTCHHHHHHHHHHHTTSTTCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCcCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHHHHHh
Confidence            99    99999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             cc--CCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCC
Q psy16234        197 LS--GDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKF  247 (609)
Q Consensus       197 ~~--~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~  247 (609)
                      ..  ...+|..||+.||++|++|+.++..||++|+.|.+++++||+.|+|.+.
T Consensus       329 ~~~~~~~~~~~~V~~LL~l~~k~~~lv~~~F~~d~~f~~al~~af~~fiN~~~  381 (391)
T 2wzk_A          329 AAETITTDSEKYREQLDTLFNRFSKLVKEAFQDDPRFLTARDKAYKAVVNDAT  381 (391)
T ss_dssp             HGGGTTTCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhCCch
Confidence            42  2357899999999999999999999999999999999999999999764

>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens}

Probab=100.00  E-value=7.7e-42  Score=358.83  Aligned_cols=234  Identities=23%  Similarity=0.443  Sum_probs=215.8

Q ss_pred             CccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-----------------
Q psy16234          6 KQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-----------------   68 (609)
Q Consensus         6 ~~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-----------------   68 (609)
                      ...+||++|+.|++||..|++.++. ...|+++|++||++|++.   .|++||+++++++.+|                 
T Consensus         6 ~~~~~~~~W~~L~~ai~~I~~~~~~-~~s~eeLY~~vy~lc~~~---~g~~LY~~l~~~~~~~l~~~~~~~~~~~~~~~~   81 (354)
T 4a64_A            6 PENYTDETWQKLKEAVEAIQNSTSI-KYNLEELYQAVENLCSYK---ISANLYKQLRQICEDHIKAQIHQFREDSLDSVL   81 (354)
T ss_dssp             CSSSTTHHHHHHHHHHHHHHTTCCC-CSCHHHHHHHHHHHHHHS---CHHHHHHHHHHHHHHHHHHTTGGGGCCSCCHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCCC-CCCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHHHHHHHHHHHHHHccccHHH
Confidence            3468999999999999999987653 457999999999999985   8999999998777655                 


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        82 ~L~~~~~~W~~~~~~~~~i~~if~YLdR~yv~~~~~~~~I~~lgL~lfr~~v~~~~~i~~~l~~~ll~lI~~eR~Ge~id  161 (354)
T 4a64_A           82 FLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAID  161 (354)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTHHHHHCSTTTSCCSCCHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHhcCCCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence                                                                                            


Q ss_pred             ---------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHH
Q psy16234         69 ---------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKC  133 (609)
Q Consensus        69 ---------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l  133 (609)
                                     +|.+.||++||++|.+||+.+|++|++++++++||++|+.++++|.+||..||+++|.++|.++|
T Consensus       162 ~~lik~~i~ml~~L~vY~~~FE~~fL~~t~~fY~~e~~~~l~~~~~~~Yl~~ve~rl~eE~~R~~~yL~~~T~~~l~~~~  241 (354)
T 4a64_A          162 RSLLRSLLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQKSLIATV  241 (354)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHTHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHH
Confidence                           89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH-HhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHH
Q psy16234        134 EQHMVADHLNFL-QGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLA  212 (609)
Q Consensus       134 ~~~LI~~~~~~l-~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~  212 (609)
                      +++||.+|++.| .+||..||++++.+||++||+|++|+|+|+++|+.+|++||++.|.+++.+..   .|..||+.||+
T Consensus       242 e~~LI~~h~~~ll~~~~~~lL~~~~~~dL~~mY~L~~rv~~gl~~l~~~~~~~I~~~G~~iv~~~~---~~~~~V~~LL~  318 (354)
T 4a64_A          242 EKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIKAFGSTIVINPE---KDKTMRQELDD  318 (354)
T ss_dssp             HHHHTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHSCC---SSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcCcc---chHHHHHHHHH
Confidence            999999999976 48999999999999999999999999999999999999999999999997643   35679999999


Q ss_pred             HHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCC
Q psy16234        213 VHKKYKAFVKELFSGDQSFMGALDKACSSVINHK  246 (609)
Q Consensus       213 ~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~  246 (609)
                      +|++|+.++..||++|+.|..++++||+.|+|.+
T Consensus       319 l~~k~~~iv~~~F~~d~~f~~al~~af~~fiN~~  352 (354)
T 4a64_A          319 FKDKVDHIIDICFLKNEKFINAMKEAFETFINKR  352 (354)
T ss_dssp             HHHHHHHHHHHHSTTCHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence            9999999999999999999999999999999976

>4eoz_B Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, protein binding; 2.40A {Homo sapiens} PDB: 4apf_B

Probab=100.00  E-value=9.6e-43  Score=367.06  Aligned_cols=237  Identities=21%  Similarity=0.416  Sum_probs=170.8

Q ss_pred             CccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-----------------
Q psy16234          6 KQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-----------------   68 (609)
Q Consensus         6 ~~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-----------------   68 (609)
                      ...+||++|+.|++||..|++.++. ...|+++|++||++|++.   .|++||+++++++.+|                 
T Consensus         9 ~~~~~~~~W~~L~~ai~~I~~~~~~-~~s~e~LY~~vy~lc~~k---~g~~LY~~l~~~~~~~l~~~v~~~~~~~~~~~~   84 (364)
T 4eoz_B            9 DEKYVNSIWDLLKNAIQEIQRKNNS-GLSFEELYRNAYTMVLHK---HGEKLYTGLREVVTEHLINKVREDVLNSLNNNF   84 (364)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCGG-GCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHTHHHHHHTTTTSSH
T ss_pred             ChhhHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHhhh---CHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHH
Confidence            3468999999999999999987543 567999999999999975   7999999998887765                 


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        85 L~~~~~~W~~~~~~~~~i~~if~YLdR~yv~~~~~~~I~~lgl~~fr~~v~~~~~i~~~l~~~ll~lI~~eR~Ge~id~~  164 (364)
T 4eoz_B           85 LQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDRG  164 (364)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTHHHHHHTTGGGTCCCHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHhcCCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhCCCCCCHH
Confidence                                                                                            


Q ss_pred             ------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHH
Q psy16234         69 ------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVK  130 (609)
Q Consensus        69 ------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~  130 (609)
                                        +|.+.||++||++|.+||+.+|++|++++++++||++|+.++++|.+||..||+++|.++|.
T Consensus       165 lik~~i~ml~~L~~~~~~~Y~~~FE~~fL~~t~~fY~~es~~~l~~~~~~~Yl~~ve~rl~eE~~R~~~yL~~~T~~~l~  244 (364)
T 4eoz_B          165 AIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEPIV  244 (364)
T ss_dssp             HHHHHHHHHHHTTSSSSHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHSCGGGHHHHH
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHH
Confidence                              39999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH----hhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHH
Q psy16234        131 AKCEQHMVADHLNFLQ----GECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQF  206 (609)
Q Consensus       131 ~~l~~~LI~~~~~~l~----~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~  206 (609)
                      ++|+++||.+|++.|.    +||..||++++.+||++||+|++|+|+|+++|+.+|++||++.|.+++........|..|
T Consensus       245 ~~~e~~LI~~h~~~ll~~e~~g~~~lL~~~~~~dL~~mY~L~~rv~~gl~~l~~~~~~~I~~~G~~iv~~~~~~~~~~~~  324 (364)
T 4eoz_B          245 KVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDY  324 (364)
T ss_dssp             HHHHHHHTTTTHHHHHTCTTTSHHHHTTTTCHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHTC----------------
T ss_pred             HHHHHHHHHHHHHHHHhhcchhHHHHHhCCCHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHhCccccCChHHH
Confidence            9999999999999996    599999999999999999999999999999999999999999999999887666678999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCC
Q psy16234        207 VENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK  246 (609)
Q Consensus       207 V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~  246 (609)
                      |+.||++|++|+.++..||++|+.|..++++||+.|+|.+
T Consensus       325 V~~LL~l~~k~~~iv~~~F~~d~~f~~al~~af~~fiN~n  364 (364)
T 4eoz_B          325 RQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLNLN  364 (364)
T ss_dssp             ----------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcCc
Confidence            9999999999999999999999999999999999999964

>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.94  E-value=3.2e-28  Score=202.78  Aligned_cols=93  Identities=45%  Similarity=0.620  Sum_probs=87.2

Q ss_pred             EEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccc
Q psy16234        516 LKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV  595 (609)
Q Consensus       516 i~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl  595 (609)
                      ++|+.++.+++++|.+.+++.+++||++.||||||||||+||+|+|++|+.+|+++++ |.|++.+||+|||.|||||||
T Consensus         3 ~ki~~i~~ke~~~e~~~t~~~v~~dR~~~iqAaIVRIMK~rK~l~h~~Lv~eV~~ql~-F~p~~~~IKk~IE~LIereYl   81 (101)
T 2do7_A            3 SGSSGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVKPADLKKRIESLIDRDYM   81 (101)
T ss_dssp             CSSCSCCCCCCCCCCSSCCSHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHCS-SCCCHHHHHHHHHHHHHTTSE
T ss_pred             eeecccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhhhhHH
Confidence            5566666677777888889999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             cccCCCCCceeecC
Q psy16234        596 ERTANSTDEYSYVA  609 (609)
Q Consensus       596 ~r~~~~~~~y~Yia  609 (609)
                      +|+++|++.|+|+|
T Consensus        82 eR~~~d~~~y~YlA   95 (101)
T 2do7_A           82 ERDKENPNQYNYIA   95 (101)
T ss_dssp             EECSSCTTEEEECC
T ss_pred             hcCCCCCCeEEEec
Confidence            99999999999998

>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A {Saccharomyces cerevisiae} PDB: 3o6b_B

Probab=99.93  E-value=5.2e-27  Score=190.71  Aligned_cols=80  Identities=39%  Similarity=0.769  Sum_probs=77.8

Q ss_pred             HHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234        529 EIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSY  607 (609)
Q Consensus       529 e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y  607 (609)
                      |.++|++.+++||+..||||||||||+||+|+|++|+.+|++++++ |+|++.+||+|||.|||||||+|+++| ++|+|
T Consensus         8 e~~~t~~~v~~dR~~~iqAaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIekeYleR~~~~-~~y~Y   86 (88)
T 3o2p_E            8 EDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDG-ESYAY   86 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEECTTS-SEEEE
T ss_pred             hHHHHHHHHHHHhhhhhheeeehhhcccccccHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhHHhcCCCC-CeEEe
Confidence            6778899999999999999999999999999999999999999998 999999999999999999999999999 99999


Q ss_pred             cC
Q psy16234        608 VA  609 (609)
Q Consensus       608 ia  609 (609)
                      +|
T Consensus        87 lA   88 (88)
T 3o2p_E           87 LA   88 (88)
T ss_dssp             CC
T ss_pred             eC
Confidence            98

>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.34

Probab=99.93  E-value=9e-28  Score=197.43  Aligned_cols=87  Identities=51%  Similarity=0.721  Sum_probs=81.7

Q ss_pred             ccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCC
Q psy16234        523 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  601 (609)
Q Consensus       523 ~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~  601 (609)
                      .+++++|.+.+++.+++||++.||||||||||+||+|+|++|+.+|++++++ |.|++.+||+|||.|||||||+|+++|
T Consensus         5 ~~e~~~e~~~t~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIereYleR~~~d   84 (92)
T 1iuy_A            5 QGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPED   84 (92)
T ss_dssp             CCCCCCCCCCCCSCSCCCTTTHHHHHHHHHHHHHCEEEHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSC
T ss_pred             ccccHHHHHHHHHHHHHHHHHHeeeeeeehhhccccccHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhhhhhhcCCCC
Confidence            4566667778889999999999999999999999999999999999999998 999999999999999999999999999


Q ss_pred             CCceeecC
Q psy16234        602 TDEYSYVA  609 (609)
Q Consensus       602 ~~~y~Yia  609 (609)
                      ++.|+|+|
T Consensus        85 ~~~y~Y~A   92 (92)
T 1iuy_A           85 RKVYTYVA   92 (92)
T ss_dssp             SSEEEEC-
T ss_pred             CCeeEecC
Confidence            99999998

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C

Probab=99.93  E-value=3.8e-27  Score=187.03  Aligned_cols=75  Identities=56%  Similarity=0.919  Sum_probs=72.5

Q ss_pred             hhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        535 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       535 ~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +.+++||+..||||||||||+||+|+|++|+.+|++++++ |+|++.+||+|||+|||||||+|+++|+++|+|+|
T Consensus         2 k~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIereYl~R~~~~~~~y~Y~A   77 (77)
T 3tdu_C            2 SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA   77 (77)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEECC
T ss_pred             cchhhhhhheEeeEEeeeecccceeeHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhHhhcCCCCCceEEEeC
Confidence            3578999999999999999999999999999999999998 99999999999999999999999999999999998

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

Probab=94.21  E-value=0.099  Score=41.26  Aligned_cols=59  Identities=14%  Similarity=0.095  Sum_probs=43.9

Q ss_pred             HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .||..+.+...+|..||++.+|++...+.+.|..|.+.|++...+..-..+..|.++.+
T Consensus         4 ~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~l~~~   62 (81)
T 2htj_A            4 EILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFLKGE   62 (81)
T ss_dssp             HHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEESSC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEEEChh
Confidence            45666666678999999999999999999999999999999743211122345565543

>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=92.83  E-value=0.11  Score=42.97  Aligned_cols=50  Identities=16%  Similarity=0.254  Sum_probs=45.2

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus        18 l~~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~   67 (109)
T 1sfx_A           18 FKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            57788999988877778999999999999999999999999999999754

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

Probab=92.45  E-value=0.18  Score=41.00  Aligned_cols=49  Identities=18%  Similarity=0.378  Sum_probs=44.0

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..|..||..+.+++.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus        23 ~~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~   71 (99)
T 3cuo_A           23 HPKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQ   71 (99)
T ss_dssp             SHHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ChHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4678888888888778999999999999999999999999999999754

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=92.22  E-value=0.14  Score=39.11  Aligned_cols=56  Identities=11%  Similarity=0.220  Sum_probs=49.0

Q ss_pred             hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      ...|...|.+|.+..++|-.+       |..+.+++-.+|+.|.+.|-|.-.-+|+..|+||+
T Consensus        10 ~~Fi~yIk~~Kvv~LedLA~~-------F~l~t~~~i~RI~~Le~~g~ltGViDDRGKfIyIs   65 (72)
T 1wi9_A           10 TEFINYIKKSKVVLLEDLAFQ-------MGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             HHHHHHHHHCSEECHHHHHHH-------HCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHHHcCeeeHHHHHHH-------hCCChHHHHHHHHHHHHCCCeEEEEeCCCCEEEec
Confidence            344677899999999887754       88999999999999999999999888999999985

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

Probab=92.06  E-value=0.23  Score=43.43  Aligned_cols=50  Identities=26%  Similarity=0.418  Sum_probs=46.0

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|+.|..||.....++ +|..+|++.+|++...+.++|..|.+.|++...
T Consensus        35 ~lt~~~~~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~   84 (146)
T 3tgn_A           35 ALTNTQEHILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETS   84 (146)
T ss_dssp             CCCHHHHHHHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEec
Confidence            46889999999998888 999999999999999999999999999999765

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

Probab=91.95  E-value=0.15  Score=43.79  Aligned_cols=52  Identities=13%  Similarity=0.292  Sum_probs=45.5

Q ss_pred             EEecHHHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        442 VTMQTFQMAILLLFEKNDA--MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +.++..|..||..+.+.+.  +|..+|++.+|++...+.++|..|.+.|++.+.
T Consensus        22 ~gLt~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           22 LNLTKADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HTCCHHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            3467889999988776655  999999999999999999999999999999764

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

Probab=91.83  E-value=0.19  Score=39.64  Aligned_cols=51  Identities=12%  Similarity=0.244  Sum_probs=45.1

Q ss_pred             EecHHHHHHHHhhcCC--CCCCHHHHHHHh-----CCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKN--DAMTCGDIQTVL-----SLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~--~~lt~~ei~~~t-----~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++.-+..||..+.+.  ..+|.+||++.+     +++...+.++|..|.+.|++...
T Consensus        14 ~~t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~   71 (83)
T 2fu4_A           14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH   71 (83)
T ss_dssp             CCCHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CcCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEE
Confidence            4567788899888775  589999999999     99999999999999999999764

>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=91.78  E-value=0.34  Score=39.41  Aligned_cols=56  Identities=18%  Similarity=0.188  Sum_probs=45.8

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      +..+..||.++  ...+|+.+|++.+|++...+.++|..|.+.|++....      +.|.++..
T Consensus        30 ~~~r~~Il~~L--~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~------g~y~l~~~   85 (96)
T 1y0u_A           30 NPVRRKILRML--DKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG------ERWVVTDA   85 (96)
T ss_dssp             CHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET------TEEEECTT
T ss_pred             CHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC------CEEEECCC
Confidence            34566777777  3569999999999999999999999999999997652      37777764

>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=91.56  E-value=0.22  Score=39.03  Aligned_cols=56  Identities=21%  Similarity=0.242  Sum_probs=42.7

Q ss_pred             HHHHHHhhcCCC---CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234        448 QMAILLLFEKND---AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN  506 (609)
Q Consensus       448 Q~~iLllFn~~~---~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN  506 (609)
                      +..||.++.+..   .+|..||++.+|++...+.++|..|.+.|++...+.   ....+.++
T Consensus        16 ~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~---~~~~W~i~   74 (77)
T 1qgp_A           16 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG---TPPLWKIA   74 (77)
T ss_dssp             HHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEECS---SSCEEEEC
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC---CCCceEec
Confidence            355665555444   899999999999999999999999999999876531   12455554

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=91.54  E-value=0.074  Score=58.57  Aligned_cols=133  Identities=14%  Similarity=0.130  Sum_probs=51.1

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----cCccccCCCCCCCCCEEEEecCCCCCcceEEec
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVE-----CKLLTSNKEELTEDTEIRLNLGYNNKRTKLKIS  519 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~-----~~iL~~~~~~~~~~~~f~lN~~F~~~~~ki~i~  519 (609)
                      +..+..||....++..+|..+|++.+|++...+++.|..|++     .|++...      ++.|.++..........   
T Consensus       429 ~~~~~~iL~~l~~~~~it~~~la~~l~~s~~~~~~~L~~L~~~~~~~~glie~~------g~~y~L~~~~~~~~~~~---  499 (583)
T 3lmm_A          429 DYRIAIVLYLLFQRPFITIDVVARGLQSGKEAARNALEAARQTTVAGAPLIIAH------DGVWLLGNACREILRKV---  499 (583)
T ss_dssp             CHHHHHHHHHHHHSSSBCHHHHHHHHTSCHHHHHHHHHHHHTCEETTEESEEEE------TTEEEECHHHHHHHTSC---
T ss_pred             chhHHHHHHHHHHCCCcCHHHHHHHhCcCHHHHHHHHHHHHhhhccccceEEEe------CCEEEECHHHHHHhccc---
Confidence            456778888778888999999999999999999999999998     6788765      36788887642111100   


Q ss_pred             cccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234        520 GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  599 (609)
Q Consensus       520 ~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~  599 (609)
                       . ...   ..-.....+.   ....+..|+..++.++.++-.++.+.       +..+.....+.|..|+++|-|++.+
T Consensus       500 -~-~~~---~~~~~~~~~~---~~~~~~~I~~~l~~~g~it~~di~~l-------~~ls~~qa~~~L~~Lv~~G~l~~~G  564 (583)
T 3lmm_A          500 -E-PSP---FSPVRYLSTD---QAELTNAAMLWLSEVGDLATSDLMAM-------CGVSRGTAKACVDGLVDEERVVAVG  564 (583)
T ss_dssp             -C------------------------------------------------------------------------------
T ss_pred             -c-ccc---ccccccccCC---hhHHHHHHHHHHHHcCCcCHHHHHHH-------HCCCHHHHHHHHHHHHHCCcEEEeC
Confidence             0 000   0000000111   23456679999999999888876632       3356778899999999999999876


Q ss_pred             CC
Q psy16234        600 NS  601 (609)
Q Consensus       600 ~~  601 (609)
                      ..
T Consensus       565 ~g  566 (583)
T 3lmm_A          565 GG  566 (583)
T ss_dssp             --
T ss_pred             CC
Confidence            54

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

Probab=91.52  E-value=0.16  Score=38.61  Aligned_cols=46  Identities=9%  Similarity=0.166  Sum_probs=38.6

Q ss_pred             HHHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        447 FQMAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       447 ~Q~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ..-.||.++.+. ..+|..+|++.+|++...+.++|..|.+.|++..
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            344577777654 5799999999999999999999999999999754

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

Probab=91.39  E-value=0.45  Score=38.70  Aligned_cols=48  Identities=25%  Similarity=0.432  Sum_probs=41.7

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..+..||..+.+ +.+|+.+|++.+|++...+.++|..|.+.|++...
T Consensus        22 ~~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~   69 (98)
T 3jth_A           22 NERRLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTR   69 (98)
T ss_dssp             SHHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3456677777776 78999999999999999999999999999999754

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

Probab=91.34  E-value=0.19  Score=39.44  Aligned_cols=43  Identities=16%  Similarity=0.120  Sum_probs=39.4

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      |+...+++..+|++||++.+++++..+++-|..|.+.|+|.+.
T Consensus         7 Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            7 VRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            6667788899999999999999999999999999999988765

>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=91.19  E-value=0.21  Score=43.58  Aligned_cols=50  Identities=8%  Similarity=0.168  Sum_probs=46.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        34 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   83 (140)
T 3hsr_A           34 LTYTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRT   83 (140)
T ss_dssp             CCHHHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEec
Confidence            56789999999988899999999999999999999999999999999765

>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=91.16  E-value=0.32  Score=39.41  Aligned_cols=52  Identities=15%  Similarity=0.205  Sum_probs=45.7

Q ss_pred             EEecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        442 VTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..++..|..||....+  ++.++..+|++.++++...+.++|..|.+.|++...
T Consensus        16 ~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~   69 (91)
T 2dk5_A           16 KGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   69 (91)
T ss_dssp             CCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3567789999988776  568999999999999999999999999999998743

>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=91.05  E-value=0.19  Score=43.95  Aligned_cols=51  Identities=16%  Similarity=0.263  Sum_probs=43.6

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        34 ~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           34 DLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             CCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-
T ss_pred             CCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeec
Confidence            367889999999988889999999999999999999999999999999875

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

Probab=91.03  E-value=0.23  Score=43.49  Aligned_cols=50  Identities=16%  Similarity=0.152  Sum_probs=46.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        29 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   78 (145)
T 3g3z_A           29 LNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQ   78 (145)
T ss_dssp             CCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            47789999998887778999999999999999999999999999999865

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

Probab=90.85  E-value=0.37  Score=42.63  Aligned_cols=50  Identities=18%  Similarity=0.236  Sum_probs=46.2

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        41 lt~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~   90 (155)
T 3cdh_A           41 LRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRV   90 (155)
T ss_dssp             CCHHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            47789999999988889999999999999999999999999999999765

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

Probab=90.79  E-value=0.38  Score=37.66  Aligned_cols=45  Identities=18%  Similarity=0.234  Sum_probs=38.3

Q ss_pred             HHHHhhcCC------CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        450 AILLLFEKN------DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       450 ~iLllFn~~------~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .||....+.      .+.|+.||++.+|++...+.+.|..|.+.|+|...+
T Consensus         8 ~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A            8 KIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             HHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence            355555443      789999999999999999999999999999998765

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

Probab=90.78  E-value=0.21  Score=40.05  Aligned_cols=43  Identities=9%  Similarity=0.080  Sum_probs=39.4

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      |+...++.+.+|++||++.+++++..+++-|..|.+.|+|.+.
T Consensus         7 Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            7 VRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            6677788899999999999999999999999999999988765

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

Probab=90.69  E-value=0.31  Score=42.73  Aligned_cols=51  Identities=18%  Similarity=0.302  Sum_probs=46.4

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        37 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             TCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            467889999999888889999999999999999999999999999999765

>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=90.42  E-value=0.26  Score=40.26  Aligned_cols=50  Identities=10%  Similarity=0.125  Sum_probs=45.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHH----HHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDI----QTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei----~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+.+.+.+|..+|    ++.++++...+.+.|..|.+.|++.+.
T Consensus         6 lt~~q~~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~   59 (99)
T 1tbx_A            6 FFYPEAIVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKER   59 (99)
T ss_dssp             SBCHHHHHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEE
Confidence            56789999988888889999999    899999999999999999999999764

>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=90.41  E-value=0.29  Score=40.31  Aligned_cols=50  Identities=18%  Similarity=0.391  Sum_probs=41.9

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..+|+.+-. .+.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus        19 l~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~   69 (109)
T 2d1h_A           19 ITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             CCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence            35567766655543 678999999999999999999999999999999765

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

Probab=90.40  E-value=0.32  Score=41.94  Aligned_cols=50  Identities=18%  Similarity=0.345  Sum_probs=45.8

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+..++.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        27 l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~   76 (138)
T 3bpv_A           27 LTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIERE   76 (138)
T ss_dssp             CCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            46789999988888889999999999999999999999999999999764

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

Probab=90.24  E-value=0.25  Score=43.54  Aligned_cols=50  Identities=16%  Similarity=0.210  Sum_probs=45.8

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||.....++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        39 lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           39 ITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             CCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeC
Confidence            56789999998888889999999999999999999999999999999875

>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=90.11  E-value=0.34  Score=39.44  Aligned_cols=50  Identities=18%  Similarity=0.300  Sum_probs=46.1

Q ss_pred             EEecHHHHHHHHhhcCCCCCCHHHHHH-HhCCCHHHHHHHHHHHHhcCccc
Q psy16234        442 VTMQTFQMAILLLFEKNDAMTCGDIQT-VLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~lt~~ei~~-~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      ..++..|..||......+..|..+|++ ..+++...+-+++.+|.+.|++.
T Consensus        12 ~~L~~~QfsiL~~L~~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           12 DVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             TSSCHHHHHHHHHHHHSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee
Confidence            346788999999998888999999999 99999999999999999999997

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

Probab=90.04  E-value=0.21  Score=43.60  Aligned_cols=50  Identities=16%  Similarity=0.209  Sum_probs=45.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        35 lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   84 (143)
T 3oop_A           35 VTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVRE   84 (143)
T ss_dssp             SCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeecc
Confidence            57789999988887789999999999999999999999999999999765

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

Probab=89.89  E-value=0.39  Score=42.79  Aligned_cols=50  Identities=10%  Similarity=0.242  Sum_probs=45.5

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||......+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        47 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~   96 (162)
T 2fa5_A           47 MAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRE   96 (162)
T ss_dssp             CCHHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeee
Confidence            57789999988887889999999999999999999999999999999765

>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=89.70  E-value=0.27  Score=42.31  Aligned_cols=52  Identities=17%  Similarity=0.239  Sum_probs=45.7

Q ss_pred             EecHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFEKN--DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .+|..|..||......  +.+|..+|++.++++...+.+.|..|.+.|++.+.+
T Consensus        34 ~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   87 (127)
T 2frh_A           34 SISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   87 (127)
T ss_dssp             CCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             CCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            3567888888877666  789999999999999999999999999999998753

>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=89.59  E-value=0.49  Score=41.19  Aligned_cols=49  Identities=14%  Similarity=0.160  Sum_probs=44.6

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||..+. .+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        35 l~~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   83 (146)
T 2gxg_A           35 LSYLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRV   83 (146)
T ss_dssp             CCHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEee
Confidence            4678999998888 788999999999999999999999999999999764

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

Probab=89.48  E-value=0.36  Score=38.14  Aligned_cols=44  Identities=9%  Similarity=0.219  Sum_probs=36.5

Q ss_pred             HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .||.++.+.. .|+.+|++.+|++...+.++|..|.+.|++...+
T Consensus        21 ~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~   64 (82)
T 1oyi_A           21 EAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSD   64 (82)
T ss_dssp             HHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECS
T ss_pred             HHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence            3444444444 9999999999999999999999999999997653

>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=89.44  E-value=0.38  Score=38.03  Aligned_cols=57  Identities=21%  Similarity=0.248  Sum_probs=43.3

Q ss_pred             HHHHHHhhcCCC---CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        448 QMAILLLFEKND---AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       448 Q~~iLllFn~~~---~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      +..||.++.+..   .+|..+|++.+|++...+.++|..|.+.|+|...++   ....|.+..
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~---~~~~W~i~~   71 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG---TPPLWKIAV   71 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESS---SSCEEEEC-
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC---CCCeeEEeC
Confidence            455666665545   899999999999999999999999999999876531   124565553

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

Probab=89.42  E-value=0.35  Score=41.80  Aligned_cols=50  Identities=12%  Similarity=0.164  Sum_probs=45.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        36 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~   85 (140)
T 2nnn_A           36 LTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRS   85 (140)
T ss_dssp             CCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            56789999988877779999999999999999999999999999999754

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

Probab=89.41  E-value=0.34  Score=42.77  Aligned_cols=49  Identities=12%  Similarity=0.278  Sum_probs=45.6

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      +|..|..||..+...+.+|..+|++.++++...+.+.+..|.+.|++..
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            5788999998888888899999999999999999999999999999977

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

Probab=89.28  E-value=0.34  Score=42.20  Aligned_cols=50  Identities=14%  Similarity=0.215  Sum_probs=44.7

Q ss_pred             ecHHHHHHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLF-EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+ ...+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        35 l~~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~   85 (146)
T 2fbh_A           35 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRL   85 (146)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeec
Confidence            456788888888 67788999999999999999999999999999999765

>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=89.11  E-value=0.31  Score=39.54  Aligned_cols=48  Identities=21%  Similarity=0.378  Sum_probs=42.3

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++.+..||..+...+.+|..+|++.+|++...+.++|..|.+.|++..
T Consensus        15 ~~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~   62 (100)
T 1ub9_A           15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKT   62 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ChHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            567788887776566899999999999999999999999999999864

>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=89.00  E-value=0.39  Score=41.53  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=44.6

Q ss_pred             ecHHHHHHHHhhcCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKND--AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~--~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+  .+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        29 lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   80 (139)
T 3eco_A           29 ITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRY   80 (139)
T ss_dssp             CCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            5678889998877654  8999999999999999999999999999999765

>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=88.91  E-value=0.39  Score=41.78  Aligned_cols=50  Identities=16%  Similarity=0.200  Sum_probs=45.6

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|+.||..+...+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~   80 (145)
T 2a61_A           31 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   80 (145)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            57789999988887778999999999999999999999999999999764

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=88.86  E-value=0.4  Score=41.98  Aligned_cols=53  Identities=13%  Similarity=0.171  Sum_probs=44.9

Q ss_pred             EEEecHHHHHHHHhhcC-----CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        441 FVTMQTFQMAILLLFEK-----NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       441 ~l~~s~~Q~~iLllFn~-----~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+-+|.-++.+|+++-.     ....|.++|++.+|++..++.+.|+.|++.|+|...
T Consensus        27 ~LgLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           27 QLGLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             HHTCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             HhCCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            45677888888877554     456899999999999999999999999999999763

>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=88.81  E-value=0.51  Score=40.81  Aligned_cols=50  Identities=18%  Similarity=0.232  Sum_probs=44.6

Q ss_pred             ecHHHHHHHHhhcCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKND--AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~--~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+  .+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   83 (141)
T 3bro_A           32 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   83 (141)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEee
Confidence            5678888888877666  8999999999999999999999999999999764

>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=88.80  E-value=0.71  Score=40.78  Aligned_cols=49  Identities=12%  Similarity=0.260  Sum_probs=43.6

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..+..||..+.++..+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus         2 d~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            2 DEIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             CHHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             ChHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            3457778888888889999999999999999999999999999999753

>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=88.60  E-value=0.41  Score=41.32  Aligned_cols=50  Identities=18%  Similarity=0.191  Sum_probs=45.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|+.||......+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~   81 (138)
T 1jgs_A           32 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             SCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            46789999988887778999999999999999999999999999999764

>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=88.60  E-value=0.42  Score=42.00  Aligned_cols=50  Identities=18%  Similarity=0.199  Sum_probs=45.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        38 lt~~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~   87 (152)
T 3bj6_A           38 VTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERR   87 (152)
T ss_dssp             CCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence            57789999988888789999999999999999999999999999999765

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

Probab=88.60  E-value=0.43  Score=42.09  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||......+.+|..+|++.++++...+.+.|..|.+.|++...
T Consensus        45 l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   94 (153)
T 2pex_A           45 LTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRT   94 (153)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            46789999988887788999999999999999999999999999999764

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

Probab=88.58  E-value=0.42  Score=41.40  Aligned_cols=51  Identities=18%  Similarity=0.250  Sum_probs=46.0

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++..|..||.....++.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        28 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~   78 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEESGYIIRK   78 (142)
T ss_dssp             SSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            357789999988887778999999999999999999999999999998754

>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=88.57  E-value=0.34  Score=43.36  Aligned_cols=50  Identities=6%  Similarity=0.120  Sum_probs=46.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        44 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   93 (162)
T 3k0l_A           44 ISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLANGWIEKA   93 (162)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEec
Confidence            56789999988888889999999999999999999999999999999765

>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=88.57  E-value=0.43  Score=43.03  Aligned_cols=50  Identities=10%  Similarity=0.151  Sum_probs=45.0

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..... .+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        51 lt~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~  101 (166)
T 3deu_A           51 LTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ  101 (166)
T ss_dssp             CCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEee
Confidence            46789999988876 677999999999999999999999999999999875

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

Probab=88.55  E-value=0.33  Score=43.43  Aligned_cols=50  Identities=20%  Similarity=0.308  Sum_probs=46.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        51 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~  100 (161)
T 3e6m_A           51 LPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARS  100 (161)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            56789999988887789999999999999999999999999999999875

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

Probab=88.49  E-value=0.44  Score=42.52  Aligned_cols=50  Identities=18%  Similarity=0.323  Sum_probs=45.8

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        50 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   99 (162)
T 3cjn_A           50 LSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRRE   99 (162)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            57789999988888888999999999999999999999999999999764

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

Probab=88.42  E-value=0.49  Score=37.14  Aligned_cols=51  Identities=14%  Similarity=0.249  Sum_probs=44.9

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhC----CCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLS----LSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~----i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|..||..+-+.+.+|..||++.++    ++...+.+.|..|.+.|++...
T Consensus         6 ~lt~~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~   60 (82)
T 1p6r_A            6 QISDAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHH   60 (82)
T ss_dssp             CCCHHHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEE
Confidence            36788999998887778899999999996    7899999999999999999765

>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=88.19  E-value=0.46  Score=41.52  Aligned_cols=50  Identities=12%  Similarity=0.214  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..... .+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        33 l~~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~   83 (147)
T 2hr3_A           33 VQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH   83 (147)
T ss_dssp             HHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeC
Confidence            57789999988887 788999999999999999999999999999999765

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

Probab=88.09  E-value=0.46  Score=41.66  Aligned_cols=50  Identities=12%  Similarity=0.181  Sum_probs=45.4

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        40 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   89 (150)
T 2rdp_A           40 ITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARV   89 (150)
T ss_dssp             SCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            56789999988887788999999999999999999999999999999754

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

Probab=88.07  E-value=0.4  Score=41.53  Aligned_cols=50  Identities=8%  Similarity=0.122  Sum_probs=45.5

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        34 lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~   83 (142)
T 2fbi_A           34 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRW   83 (142)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            57789999988887778999999999999999999999999999999764

>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=88.02  E-value=0.46  Score=42.06  Aligned_cols=50  Identities=18%  Similarity=0.222  Sum_probs=45.4

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+.+.+.+|..+|++.++++...+.+.+..|.+.|++...
T Consensus        42 lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   91 (154)
T 2eth_A           42 MKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   91 (154)
T ss_dssp             SBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            57789999988877778999999999999999999999999999999764

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=87.95  E-value=1.3  Score=39.86  Aligned_cols=58  Identities=16%  Similarity=0.149  Sum_probs=43.2

Q ss_pred             HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .+.+.+.-+. ...+|.++|++.+++|...+.+.|..|.++|++....   ..++.|.+..+
T Consensus        31 r~L~~LA~~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~r---G~~GGy~Lar~   89 (159)
T 3lwf_A           31 TITLELAKRIGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIR---GAHGGYVLNGD   89 (159)
T ss_dssp             HHHHHHHHTTTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC---STTCEEEECSC
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEec---CCCCceEecCC
Confidence            3344444443 3579999999999999999999999999999987542   12456777653

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

Probab=87.89  E-value=0.39  Score=43.36  Aligned_cols=51  Identities=18%  Similarity=0.356  Sum_probs=46.1

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .++..|..||..+...+.+|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        42 ~lt~~~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   92 (168)
T 2nyx_A           42 NITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRL   92 (168)
T ss_dssp             SCCHHHHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            357789999988887778999999999999999999999999999999764

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=87.78  E-value=0.63  Score=38.00  Aligned_cols=50  Identities=14%  Similarity=0.210  Sum_probs=43.8

Q ss_pred             ecHHHHHHHHhhcCC------CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKN------DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~------~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +++.|..+|..+.+.      ..+++.+|++.++++...+.++|..|.+.|++...
T Consensus        14 l~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~   69 (96)
T 2obp_A           14 IDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVS   69 (96)
T ss_dssp             CCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEee
Confidence            678899998866543      67999999999999999999999999999998653

>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=87.70  E-value=0.61  Score=40.68  Aligned_cols=50  Identities=16%  Similarity=0.240  Sum_probs=40.4

Q ss_pred             ecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..+|..+. ..+.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus        24 l~~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           24 LNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             CCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CChhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3456666654432 3467999999999999999999999999999999764

>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=87.60  E-value=1.1  Score=36.57  Aligned_cols=60  Identities=10%  Similarity=0.320  Sum_probs=44.5

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      ++....||....+ +..|+.+|++.+|++...+.++|..|.+.|++.....  .....|+++.
T Consensus        22 ~~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~--g~~~~y~l~~   81 (102)
T 3pqk_A           22 HPVRLMLVCTLVE-GEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRN--IKQIFYRLTE   81 (102)
T ss_dssp             SHHHHHHHHHHHT-CCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECS--SSCCEEEECS
T ss_pred             CHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe--CCEEEEEECc
Confidence            3445566666655 5699999999999999999999999999999975420  1123455554

>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=87.58  E-value=0.61  Score=39.82  Aligned_cols=49  Identities=12%  Similarity=0.245  Sum_probs=41.6

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.+..||..+.+.+.+|+.+|++.+|++...+.++|..|...|++...
T Consensus        41 ~~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~   89 (122)
T 1u2w_A           41 DENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR   89 (122)
T ss_dssp             SHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3456667777765577999999999999999999999999999999754

>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=87.54  E-value=0.32  Score=42.78  Aligned_cols=50  Identities=10%  Similarity=0.119  Sum_probs=39.0

Q ss_pred             ecHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKN--DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......  +.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        39 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           39 LNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             CCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC
T ss_pred             CCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEee
Confidence            567888898877765  78999999999999999999999999999999875

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=87.54  E-value=1.3  Score=38.95  Aligned_cols=55  Identities=16%  Similarity=0.176  Sum_probs=41.2

Q ss_pred             HHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        450 AILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       450 ~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      .+.+.-+.. ..+|.++|++.+|+|...+.+.|..|.++|++....   ..++.|.+..
T Consensus        17 L~~La~~~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~r---G~~GGy~Lar   72 (143)
T 3t8r_A           17 MISLAKKEGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVR---GAKGGYQLRV   72 (143)
T ss_dssp             HHHHHTTTTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECS---SSSSEEEESS
T ss_pred             HHHHHhCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecC---CCCCCeeecC
Confidence            333443333 469999999999999999999999999999986442   1245677754

>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=87.49  E-value=0.71  Score=38.24  Aligned_cols=48  Identities=21%  Similarity=0.345  Sum_probs=40.1

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.+..||..+. ...+|+.+|++.+|++...+.++|..|.+.|++...
T Consensus        25 ~~~r~~IL~~L~-~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~   72 (106)
T 1r1u_A           25 DYNRIRIMELLS-VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAK   72 (106)
T ss_dssp             SHHHHHHHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            345666776665 456899999999999999999999999999999654

>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=87.46  E-value=0.69  Score=40.92  Aligned_cols=49  Identities=10%  Similarity=0.169  Sum_probs=44.2

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++..+..||..+.+...+|+.+|++.+|++...+.+.|..|.+.|++..
T Consensus         5 ld~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   53 (150)
T 2w25_A            5 LDDIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESRGVVQG   53 (150)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5667888888888778899999999999999999999999999999964

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

Probab=87.46  E-value=0.59  Score=38.99  Aligned_cols=48  Identities=23%  Similarity=0.380  Sum_probs=41.0

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.+..||..+ ..+.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus        20 ~~~r~~IL~~L-~~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~   67 (114)
T 2oqg_A           20 DETRWEILTEL-GRADQSASSLATRLPVSRQAIAKHLNALQACGLVESV   67 (114)
T ss_dssp             CHHHHHHHHHH-HHSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ChHHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEE
Confidence            45667777777 4466999999999999999999999999999999754

>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=87.36  E-value=0.37  Score=42.46  Aligned_cols=49  Identities=18%  Similarity=0.351  Sum_probs=44.9

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .+|..|..||... ..+.+|..+|++.+|++...+.+.+..|.+.|++..
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            3578899999888 778999999999999999999999999999999976

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

Probab=87.23  E-value=0.3  Score=42.12  Aligned_cols=50  Identities=6%  Similarity=0.171  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||......+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   80 (139)
T 3bja_A           31 ISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTE   80 (139)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeec
Confidence            57789999988888888999999999999999999999999999999764

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=87.15  E-value=0.58  Score=40.75  Aligned_cols=50  Identities=12%  Similarity=0.102  Sum_probs=45.1

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|+.|..||......+. |..+|++.+|++...+.+.+..|.+.|++...
T Consensus        34 ~lt~~~~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~   83 (144)
T 3f3x_A           34 NLSYLDFSILKATSEEPR-SMVYLANRYFVTQSAITAAVDKLEAKGLVRRI   83 (144)
T ss_dssp             SCCHHHHHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            357789999988888777 99999999999999999999999999999764

>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=87.15  E-value=0.61  Score=40.99  Aligned_cols=50  Identities=16%  Similarity=0.243  Sum_probs=43.2

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||..... .+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        37 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~   87 (150)
T 3fm5_A           37 LRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRT   87 (150)
T ss_dssp             CCHHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-
T ss_pred             CCHHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            46788889987754 457899999999999999999999999999999765

>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=87.06  E-value=0.42  Score=41.57  Aligned_cols=50  Identities=16%  Similarity=0.185  Sum_probs=45.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|+.||......+.+|..+|++.++++...+.+.+..|.+.|++...
T Consensus        27 lt~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~   76 (144)
T 1lj9_A           27 LTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             CTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            46678888888877788999999999999999999999999999999764

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=86.90  E-value=0.81  Score=39.49  Aligned_cols=53  Identities=9%  Similarity=0.152  Sum_probs=42.5

Q ss_pred             EEecHHHHHHHHhhc---C--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        442 VTMQTFQMAILLLFE---K--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       442 l~~s~~Q~~iLllFn---~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +-++.-|+.||+.+-   +  ....|.++|++.+|++...+.+.|..|.+.|+|....
T Consensus        28 lgLt~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~   85 (128)
T 2vn2_A           28 LGLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEE   85 (128)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC
T ss_pred             cCCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            345667777765543   2  2348999999999999999999999999999998753

>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=86.89  E-value=0.43  Score=42.09  Aligned_cols=50  Identities=12%  Similarity=0.232  Sum_probs=45.6

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        35 l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   84 (155)
T 1s3j_A           35 VTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   84 (155)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            57789999988887778999999999999999999999999999999764

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=86.82  E-value=0.67  Score=45.31  Aligned_cols=57  Identities=14%  Similarity=0.255  Sum_probs=48.1

Q ss_pred             HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234        449 MAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY  509 (609)
Q Consensus       449 ~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F  509 (609)
                      ..||.+|.+ ...+|+.||++.+|++...+.+.|..|...|+|.+++    .+..|.+...+
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~----~~~~Y~lG~~~   66 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVE----GARSYRLGPQV   66 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECS----SSSEEEECTTH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEEcCHHH
Confidence            357888886 4689999999999999999999999999999998874    23678887654

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

Probab=86.81  E-value=0.37  Score=42.91  Aligned_cols=50  Identities=16%  Similarity=0.276  Sum_probs=44.6

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        48 lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   97 (159)
T 3s2w_A           48 IGSGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQ   97 (159)
T ss_dssp             CCTTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            35578888888877788999999999999999999999999999999765

>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=86.67  E-value=0.35  Score=42.06  Aligned_cols=50  Identities=12%  Similarity=0.240  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||......+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        35 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   84 (142)
T 2bv6_A           35 LTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRE   84 (142)
T ss_dssp             CCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            57789999988887788999999999999999999999999999999764

>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=86.63  E-value=1.5  Score=33.83  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=38.5

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      ++..+.+++..|..+|+..+|++...+.++|-+|.+.|.+...+
T Consensus        20 ~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~   63 (75)
T 1sfu_A           20 EVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVP   63 (75)
T ss_dssp             HHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCC
Confidence            35567777889999999999999999999999999999886654

>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=86.41  E-value=0.44  Score=41.65  Aligned_cols=50  Identities=18%  Similarity=0.234  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+...+.+|..+|++.++++...+.+.+..|.+.|++...
T Consensus        38 l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~   87 (147)
T 1z91_A           38 ITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   87 (147)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEec
Confidence            57789999988887778999999999999999999999999999999765

>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=86.30  E-value=0.9  Score=39.90  Aligned_cols=49  Identities=10%  Similarity=0.295  Sum_probs=43.4

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++..+-.||..+.++..+|..+|++.+|++...+.+.|..|.+.|++..
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            3556777888888778899999999999999999999999999999864

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=86.20  E-value=0.85  Score=41.16  Aligned_cols=57  Identities=16%  Similarity=0.218  Sum_probs=43.0

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      .+.+.+.-+....+|.++|++.+++|...+.+.|..|.+.|++....   ..++-|.+..
T Consensus        16 r~l~~La~~~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~r---G~~GGy~Lar   72 (162)
T 3k69_A           16 HSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTV---GKNGGYQLDL   72 (162)
T ss_dssp             HHHHHHHTTTTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEEC---STTCEEECCS
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec---CCCCCeEecC
Confidence            44444555555679999999999999999999999999999986432   1244576654

>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=86.14  E-value=0.72  Score=40.19  Aligned_cols=49  Identities=18%  Similarity=0.296  Sum_probs=42.8

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..+..||..+..+..+|+.+|++.+|++...+.+.|..|.+.|++...
T Consensus         3 d~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            3 DERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             CSHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            3456778888877778999999999999999999999999999998654

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=86.05  E-value=1.7  Score=37.30  Aligned_cols=48  Identities=15%  Similarity=0.126  Sum_probs=37.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        458 NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      ...+|..+|++.+|+|...+.+.|..|.+.|++....   ..++.|.+..+
T Consensus        24 ~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~---g~~ggy~L~~~   71 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIR---GAYGGYVLGSE   71 (129)
T ss_dssp             SCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC-------CCEEESSC
T ss_pred             CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecC---CCCCceEeCCC
Confidence            4579999999999999999999999999999987542   12355776654

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=86.04  E-value=1.3  Score=39.33  Aligned_cols=57  Identities=11%  Similarity=0.064  Sum_probs=42.0

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .+.+.+.-+....+|.++|++.+++|...+.+.|..|.+.|++....+    ++.|.+..+
T Consensus        18 ~~L~~La~~~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG----~GGy~L~~~   74 (149)
T 1ylf_A           18 HILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG----PGGAGLLKD   74 (149)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-------CCEEESSC
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC----CCceEeCCC
Confidence            333444443445799999999999999999999999999999875421    355776554

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=86.04  E-value=0.65  Score=44.99  Aligned_cols=50  Identities=18%  Similarity=0.246  Sum_probs=44.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||..+.+.+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus       150 L~~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          150 YSREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             CCHHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            56788899988777778999999999999999999999999999999764

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=85.81  E-value=0.63  Score=45.95  Aligned_cols=54  Identities=22%  Similarity=0.331  Sum_probs=44.2

Q ss_pred             HHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        450 AILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       450 ~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .||.+|.+. ..+|+.||++.+|+|...+.+.|..|...|+|.+++     +..|.+-..
T Consensus        34 ~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~-----~~~Y~LG~~   88 (275)
T 3mq0_A           34 RILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA-----DGTLRIGPH   88 (275)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT-----TSEEEECTH
T ss_pred             HHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC-----CCcEEehHH
Confidence            588888865 469999999999999999999999999999998874     457877554

>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=85.37  E-value=1  Score=39.80  Aligned_cols=50  Identities=14%  Similarity=0.298  Sum_probs=44.4

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..+..||.++.++...|+.+|++.+|++...+.+.|..|.+.|++...
T Consensus         5 ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            5 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            45677788888888788999999999999999999999999999998653

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=85.33  E-value=1.6  Score=38.37  Aligned_cols=55  Identities=16%  Similarity=0.192  Sum_probs=40.9

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .+.+.+.-+.. . |.++|++.+++|...+.+.|..|.++||+....   . ++-|.+..+
T Consensus        13 ~~L~~La~~~~-~-s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~r---G-~GGy~Lar~   67 (145)
T 1xd7_A           13 HILSLISMDEK-T-SSEIIADSVNTNPVVVRRMISLLKKADILTSRA---G-VPGASLKKD   67 (145)
T ss_dssp             HHHHHHHTCSC-C-CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCS---S-SSSCEESSC
T ss_pred             HHHHHHHhCCC-C-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeec---C-CCCceecCC
Confidence            33444444443 5 999999999999999999999999999997542   1 345666553

>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=85.31  E-value=0.73  Score=42.51  Aligned_cols=50  Identities=18%  Similarity=0.225  Sum_probs=45.0

Q ss_pred             ecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||.....  .+.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   90 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVI   90 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            67889999987765  468999999999999999999999999999999765

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=85.29  E-value=0.74  Score=40.57  Aligned_cols=50  Identities=16%  Similarity=0.276  Sum_probs=42.6

Q ss_pred             ecHHHHHHHHhh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLF--EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllF--n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||...  ++.+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        33 Lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~   84 (147)
T 4b8x_A           33 LTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKR   84 (147)
T ss_dssp             CCHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEe
Confidence            456777777555  45567999999999999999999999999999999765

>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=85.27  E-value=0.6  Score=36.66  Aligned_cols=48  Identities=6%  Similarity=0.027  Sum_probs=41.7

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHH-HHHHHHHHHHhcCccccC
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQD-QIGRHIASLVECKLLTSN  493 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~-~l~~~L~~L~~~~iL~~~  493 (609)
                      ..+--||.+.......|..+|++.+|++.. .+.++|..|.+.|++.+.
T Consensus        11 ~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           11 EIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            456667777777788999999999999998 999999999999998754

>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=84.77  E-value=1  Score=39.82  Aligned_cols=49  Identities=12%  Similarity=0.269  Sum_probs=44.1

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++..+..||.++.++..+|+.+|++.+|++...+.+.|..|.+.|++..
T Consensus         6 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A            6 IDNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             CCHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcce
Confidence            4567778888888888999999999999999999999999999999864

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=84.75  E-value=1  Score=43.38  Aligned_cols=55  Identities=18%  Similarity=0.251  Sum_probs=45.7

Q ss_pred             HHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        450 AILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       450 ~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .||.+|.+.+ .+|+.||++.+|++...+.+.|..|.+.|++..++    .+..|.+...
T Consensus        10 ~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~----~~~~Y~lg~~   65 (241)
T 2xrn_A           10 SIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALG----PAGGFRLGPA   65 (241)
T ss_dssp             HHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECG----GGCEEEECSH
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC----CCCeEEECHH
Confidence            5777787654 79999999999999999999999999999998763    1357877654

>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=84.53  E-value=0.61  Score=43.90  Aligned_cols=50  Identities=12%  Similarity=0.036  Sum_probs=45.7

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||......+.+|..+|++.++++...+.+.|..|.+.|++.+.
T Consensus        46 Lt~~q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~   95 (207)
T 2fxa_A           46 LNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFS   95 (207)
T ss_dssp             CCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            47789999988877788999999999999999999999999999999765

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

Probab=84.26  E-value=0.47  Score=42.15  Aligned_cols=50  Identities=8%  Similarity=0.281  Sum_probs=45.4

Q ss_pred             ecHHHHHHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLF-EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||... ...+.+|..+|++.+|++...+.+.+..|.+.|++...
T Consensus        45 l~~~~~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~   95 (160)
T 3boq_A           45 LSLAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKA   95 (160)
T ss_dssp             CCHHHHHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            577899999888 56778999999999999999999999999999999765

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

Probab=84.23  E-value=1.1  Score=39.49  Aligned_cols=49  Identities=16%  Similarity=0.424  Sum_probs=44.2

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++..+-.||.++.++..+|..+|++.+|++...+.+.+..|.+.|++..
T Consensus         7 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   55 (151)
T 2dbb_A            7 LDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK   55 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4567778888888888999999999999999999999999999999864

>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=84.10  E-value=0.95  Score=36.53  Aligned_cols=44  Identities=20%  Similarity=0.254  Sum_probs=38.4

Q ss_pred             HHHHHHhhcCCC-CCCHHHHHHHhCCCHHH-HHHHHHHHHhcCccc
Q psy16234        448 QMAILLLFEKND-AMTCGDIQTVLSLSQDQ-IGRHIASLVECKLLT  491 (609)
Q Consensus       448 Q~~iLllFn~~~-~lt~~ei~~~t~i~~~~-l~~~L~~L~~~~iL~  491 (609)
                      +..+|..+...+ .+|..+|++.+|++... +.+.|..|.+.|++.
T Consensus        17 ~l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           17 ILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCee
Confidence            445666666665 89999999999999999 999999999999986

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

Probab=83.99  E-value=0.66  Score=38.63  Aligned_cols=45  Identities=16%  Similarity=0.235  Sum_probs=38.0

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +..||..+.+ +.+|+.+|++.+|++...+.++|..|.+.|++...
T Consensus        27 r~~IL~~L~~-~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~   71 (108)
T 2kko_A           27 RLQILDLLAQ-GERAVEAIATATGMNLTTASANLQALKSGGLVEAR   71 (108)
T ss_dssp             THHHHHHHTT-CCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3456655554 67899999999999999999999999999999754

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

Probab=83.64  E-value=1.3  Score=40.30  Aligned_cols=51  Identities=20%  Similarity=0.322  Sum_probs=45.2

Q ss_pred             EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ..++..+..||....++..+|+.+|++.+|++...+.+.|..|.+.|++..
T Consensus        13 ~~ld~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~   63 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQERGVIER   63 (171)
T ss_dssp             -CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            346678888998888888899999999999999999999999999999864

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

Probab=83.62  E-value=1.4  Score=39.01  Aligned_cols=50  Identities=14%  Similarity=0.193  Sum_probs=43.9

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|+.||..... .+..+..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        29 Lt~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~   79 (151)
T 4aik_A           29 LTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRH   79 (151)
T ss_dssp             CCHHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEee
Confidence            56789999987764 566888999999999999999999999999999765

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

Probab=83.58  E-value=1.4  Score=39.48  Aligned_cols=49  Identities=16%  Similarity=0.309  Sum_probs=43.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ++..+..||..+.++..+|+.+|++.+|++...+.+.|..|.+.|++..
T Consensus         8 ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   56 (162)
T 2p5v_A            8 LDKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQ   56 (162)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEee
Confidence            4567778888888878899999999999999999999999999999864

>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=83.40  E-value=0.65  Score=39.36  Aligned_cols=51  Identities=10%  Similarity=0.148  Sum_probs=45.4

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhC----CCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLS----LSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~----i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|..||....+.+.+|..+|++.++    ++...+.+.|..|.+.|++...
T Consensus         7 ~lt~~~~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~   61 (123)
T 1okr_A            7 EISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK   61 (123)
T ss_dssp             CCCHHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             cCCHHHHHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEE
Confidence            36788999998887778899999999999    7899999999999999999764

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

Probab=83.39  E-value=1.3  Score=37.33  Aligned_cols=46  Identities=13%  Similarity=0.298  Sum_probs=40.6

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ..|..||..+.+ ...|+.+|++.+|++...+.++|..|.+.|++..
T Consensus        32 ~~~~~il~~L~~-~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~   77 (119)
T 2lkp_A           32 PSRLMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVG   77 (119)
T ss_dssp             HHHHHHHHHHHH-CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEE
T ss_pred             HHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            567778877776 6799999999999999999999999999998864

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=83.29  E-value=1.6  Score=42.30  Aligned_cols=55  Identities=18%  Similarity=0.204  Sum_probs=45.2

Q ss_pred             HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        449 MAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       449 ~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      ..||.+|.+.+ .+|+.||++.+|++...+.+.|..|.+.|++....     +..|.+...
T Consensus        11 l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~-----~~~Y~lg~~   66 (249)
T 1mkm_A           11 FEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK-----DKRYVPGYK   66 (249)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECT-----TSCEEECTH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEECC-----CCcEEECHH
Confidence            35777787654 79999999999999999999999999999997652     456777554

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

Probab=83.04  E-value=1.3  Score=34.64  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=38.8

Q ss_pred             hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc
Q psy16234        548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  598 (609)
Q Consensus       548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~  598 (609)
                      .|...++.++.++.++|...       |.++...|.+-|+.|.++|+|+|.
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~-------l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQT-------LNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHH-------TTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEe
Confidence            47777888899998877744       889999999999999999999997

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=83.03  E-value=1.7  Score=38.33  Aligned_cols=48  Identities=10%  Similarity=0.236  Sum_probs=39.5

Q ss_pred             ecHHHHHHHHhhcCC-----CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234        444 MQTFQMAILLLFEKN-----DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~-----~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      +|..|..||......     +.+|..+|++.++++...+.+.+..|.+.|++.
T Consensus        31 Lt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr   83 (148)
T 4fx0_A           31 LTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLVR   83 (148)
T ss_dssp             CCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC
T ss_pred             CCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEE
Confidence            567899888777653     359999999999999999999999999999884

>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=82.99  E-value=0.99  Score=38.35  Aligned_cols=51  Identities=10%  Similarity=0.218  Sum_probs=45.6

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhC----CCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLS----LSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~----i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|..||..+-+.+.+|..+|++.++    ++...+.+.|..|.+.|++...
T Consensus         7 ~Lt~~q~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~   61 (126)
T 1sd4_A            7 EISMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRY   61 (126)
T ss_dssp             CCCHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEE
Confidence            46789999998888788899999999997    5899999999999999999765

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=82.75  E-value=1.6  Score=42.60  Aligned_cols=54  Identities=20%  Similarity=0.282  Sum_probs=45.1

Q ss_pred             HHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        450 AILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       450 ~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .||.+|.+ ...+|+.||++.+|++...+.+.|..|.+.|++..++     ++.|.+...
T Consensus        27 ~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~-----~~~Y~lg~~   81 (260)
T 2o0y_A           27 DLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRA-----DGSYSLGPE   81 (260)
T ss_dssp             HHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECT-----TSCEEECHH
T ss_pred             HHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC-----CCeEEecHH
Confidence            57777864 4689999999999999999999999999999998764     237877554

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=81.95  E-value=1.7  Score=36.47  Aligned_cols=50  Identities=16%  Similarity=0.272  Sum_probs=44.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVL--SLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t--~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +....-.||.+..+...+|..+|++.+  |++...+.++|..|.+.|++...
T Consensus        11 md~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           11 MTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CCHHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            456677788888776789999999999  99999999999999999999764

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=81.87  E-value=2.1  Score=37.01  Aligned_cols=45  Identities=7%  Similarity=0.145  Sum_probs=38.2

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHh-CCCHHHHHHHHHHHHhcCccccC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVL-SLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t-~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+.||.... .+..++.||++.+ |++...|.+.|..|.+.|++.+.
T Consensus        28 ~l~IL~~L~-~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~   73 (131)
T 4a5n_A           28 KGILFYHMI-DGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHRE   73 (131)
T ss_dssp             HHHHHHHHT-TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHh-cCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEE
Confidence            445665554 5689999999999 99999999999999999999765

>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=81.69  E-value=2.5  Score=35.98  Aligned_cols=47  Identities=17%  Similarity=0.424  Sum_probs=39.5

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +.+..||..+.+ +..++.+|++.+|++...+.++|..|.+.|++...
T Consensus        46 ~~rl~IL~~L~~-~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~   92 (122)
T 1r1t_A           46 PNRLRLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYR   92 (122)
T ss_dssp             HHHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            355667766654 57899999999999999999999999999998653

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

Probab=81.37  E-value=1.8  Score=37.62  Aligned_cols=50  Identities=14%  Similarity=0.185  Sum_probs=45.0

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhC----CCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLS----LSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~----i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||..+-+ .+.+|..+|++.++    ++...+.+.|..|.+.|++...
T Consensus         7 lt~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~   61 (138)
T 2g9w_A            7 LGDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI   61 (138)
T ss_dssp             CCHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEE
Confidence            57889999988877 58899999999997    8999999999999999999765

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

Probab=81.15  E-value=2.7  Score=37.64  Aligned_cols=46  Identities=17%  Similarity=0.320  Sum_probs=41.1

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      ....||.+..++..+|+.+|++.+|++...+.+.+..|.+.|++..
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            3456788888888999999999999999999999999999999874

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S

Probab=81.13  E-value=1.5  Score=47.62  Aligned_cols=129  Identities=13%  Similarity=0.122  Sum_probs=86.3

Q ss_pred             cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhhhh
Q psy16234        456 EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVS  535 (609)
Q Consensus       456 n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~~~  535 (609)
                      ..++.+|+.+|...|+++...++..|..|++.+++...+.+ .+...|.+|.+=  --.+++.|-            ...
T Consensus        29 l~~G~ltL~~I~~~t~L~~~~Vk~~L~vLIQh~lV~~~~~~-~~~~~Y~~~~~~--il~~lR~pk------------~l~   93 (534)
T 2xub_A           29 IRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHNLVSYQVHK-RGVVEYEAQCSR--VLRMLRYPR------------YIY   93 (534)
T ss_dssp             HHHCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET-TTEEEEEECHHH--HHGGGGHHH------------HHH
T ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhcCCeeEEeCC-CCcEEEEEChhh--HHHHHhhHH------------HHH
Confidence            34578999999999999999999999999999998653200 011344444320  000111110            000


Q ss_pred             hHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-----CCCChHHHHHHHHHhhhhccccccCC
Q psy16234        536 SVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-----FAPSISMIKKCIESLIDKNYVERTAN  600 (609)
Q Consensus       536 ~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-----F~~~~~~ik~~Ie~LIekeyl~r~~~  600 (609)
                       .-+.+---.-|.|+-..=..+.++.++|+..+...+..     =.++...+...+..|++.+||.|.+.
T Consensus        94 -~i~~~~G~~a~~I~~~ll~~G~~t~~~ll~~~~~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fI~rv~~  162 (534)
T 2xub_A           94 -TTKTLYSDTGELIVEELLLNGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQRCPS  162 (534)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHCCBCHHHHHHHHHHHHHHTSSSSCCCCHHHHHHHHHHHHHTTSEEECCC
T ss_pred             -HHHHHhcHHHHHHHHHHHHcCCccHHHHHHHHHhhcccccccccccCHHHHHHHHHHHHhCCCEEeCCC
Confidence             11122223346777777788999999999888776431     12678999999999999999999874

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=80.91  E-value=2.1  Score=41.60  Aligned_cols=55  Identities=20%  Similarity=0.265  Sum_probs=46.3

Q ss_pred             HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234        449 MAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY  509 (609)
Q Consensus       449 ~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F  509 (609)
                      ..||.+|.+ ...+|+.||++.+|++...+.+.|..|.+.|++..+      +..|.+...+
T Consensus        17 l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~------~~~Y~Lg~~~   72 (257)
T 2g7u_A           17 FAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS------GGRWSLTPRV   72 (257)
T ss_dssp             HHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE------TTEEEECGGG
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC------CCEEEEcHHH
Confidence            357888875 467999999999999999999999999999999875      3678876553

>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=80.87  E-value=1.5  Score=34.17  Aligned_cols=59  Identities=17%  Similarity=0.272  Sum_probs=44.8

Q ss_pred             hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q psy16234        546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  608 (609)
Q Consensus       546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yi  608 (609)
                      +..|.+++-....++..+|...+-..   -.++.+.+...|+.|.++|||+|..+ ...+.|-
T Consensus        11 e~~vL~~L~~~~~~t~~ei~~~l~~~---~~~s~~Tv~~~l~rL~~kGlv~r~~~-gr~~~y~   69 (82)
T 1p6r_A           11 ELEVMKVIWKHSSINTNEVIKELSKT---STWSPKTIQTMLLRLIKKGALNHHKE-GRVFVYT   69 (82)
T ss_dssp             HHHHHHHHHTSSSEEHHHHHHHHHHH---SCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHhhc---CCccHHHHHHHHHHHHHCCCeEEEec-CCEEEEE
Confidence            44556666557788999888776543   23678999999999999999999875 3577774

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=80.83  E-value=0.86  Score=40.94  Aligned_cols=50  Identities=22%  Similarity=0.204  Sum_probs=41.4

Q ss_pred             ecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++..|..||.....  .+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        44 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   95 (168)
T 3u2r_A           44 LSAQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRT   95 (168)
T ss_dssp             CCHHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeec
Confidence            46788888887776  468999999999999999999999999999999765

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=80.79  E-value=1.8  Score=42.35  Aligned_cols=55  Identities=20%  Similarity=0.343  Sum_probs=46.5

Q ss_pred             HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234        449 MAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY  509 (609)
Q Consensus       449 ~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F  509 (609)
                      ..||.+|.+ ...+|+.||++.+|++...+.+.|..|...|++..+      +..|.+...+
T Consensus        24 l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~------~~~Y~Lg~~~   79 (265)
T 2ia2_A           24 LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD------GSAFWLTPRV   79 (265)
T ss_dssp             HHHHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES------SSEEEECGGG
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec------CCEEEEcHHH
Confidence            357888875 468999999999999999999999999999999875      3678886554

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

Probab=80.68  E-value=0.99  Score=37.08  Aligned_cols=61  Identities=13%  Similarity=0.296  Sum_probs=46.0

Q ss_pred             hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      -|..|.+++-....++..+|.+.+...   -.++...+...|+.|.++|+|+|..+ ...|.|-|
T Consensus        36 ~e~~VL~~L~~~~~~t~~eL~~~l~~~---~~~s~sTVt~~L~rLe~KGlV~R~~~-gR~~~Y~p   96 (99)
T 2k4b_A           36 AELIVMRVIWSLGEARVDEIYAQIPQE---LEWSLATVKTLLGRLVKKEMLSTEKE-GRKFVYRP   96 (99)
T ss_dssp             SCSHHHHHHHHHSCEEHHHHHHTCCGG---GCCCHHHHHHHHHHHHHTTSCEEEEE-TTEEEEEC
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHhcc---cCCCHhhHHHHHHHHHHCCCEEEEeC-CCEEEEEE
Confidence            456677777667778888777554322   24678999999999999999999875 47888865

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

Probab=80.60  E-value=1.5  Score=35.13  Aligned_cols=45  Identities=11%  Similarity=0.202  Sum_probs=38.9

Q ss_pred             hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234        548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  599 (609)
Q Consensus       548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~  599 (609)
                      .|...++.++.++.++|...       |.++...|.+-|+.|.++|+|.|..
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~-------l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSAR-------LQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHH-------TTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            46777788888888877744       8899999999999999999999974

---

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	609
d1ldja3	276	e.40.1.1 (A:411-686) Cullin homolog 1, cul-1 {Huma	4e-84
d2hyec3	273	e.40.1.1 (C:403-675) Cullin-4A {Human (Homo sapien	3e-82
d1ldja2	394	a.118.17.1 (A:17-410) Cullin homolog 1, Cul-1 {Hum	7e-40
d1ldja2	394	a.118.17.1 (A:17-410) Cullin homolog 1, Cul-1 {Hum	8e-05
d2hyec2	347	a.118.17.1 (C:55-401) Cullin-4A {Human (Homo sapie	5e-39
d2hyec2	347	a.118.17.1 (C:55-401) Cullin-4A {Human (Homo sapie	7e-06
d1iuya_	92	a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus muscu	1e-31
d1ldja1	90	a.4.5.34 (A:687-776) Anaphase promoting complex (A	4e-31
d2hyec1	84	a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapien	1e-30
d2p4wa1	194	a.4.5.64 (A:1-194) Transcriptional regulatory prot	0.001
d1u2wa1	108	a.4.5.5 (A:12-119) Cadmium efflux system accessory	0.002

>d1ldja3 e.40.1.1 (A:411-686) Cullin homolog 1, cul-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 276

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin homolog 1, cul-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  262 bits (671), Expect = 4e-84
 Identities = 129/275 (46%), Positives = 173/275 (62%), Gaps = 11/275 (4%)

Query: 252 PSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRL 311
            SKSPE LA+YCD LLKKSSK   E+E++D L+Q + VFKYI+DKDVF KFYAKMLAKRL
Sbjct: 5   SSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRL 64

Query: 312 IHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLG 371
           +HQ S S D E +MI+KLKQACG+E+T+K  RM  DI +S  LNE+F      TN   L 
Sbjct: 65  VHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKH--LTNSEPLD 122

Query: 372 IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVEL 431
           + FSI +L +GSWP   +   +F++P ELE+    F  FY  + +GRKL+WL+ +S+ EL
Sbjct: 123 LDFSIQVLSSGSWPFQQSC--TFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGEL 180

Query: 432 KLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491
             +  K  Y +   TFQMAILL +   DA T   +     +  D + + +  L++ KLL 
Sbjct: 181 VTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLV 240

Query: 492 SNKE-------ELTEDTEIRLNLGYNNKRTKLKIS 519
              E       EL  DT I+L LGY NK+ ++ I+
Sbjct: 241 LEDENANVDEVELKPDTLIKLYLGYKNKKLRVNIN 275

>d2hyec3 e.40.1.1 (C:403-675) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]} Length = 273

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  257 bits (658), Expect = 3e-82
 Identities = 77/276 (27%), Positives = 139/276 (50%), Gaps = 7/276 (2%)

Query: 253 SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLI 312
           +K  E +AK+ D  L+  +K  ++ E++  L + + +F++I  KDVF  FY K LAKRL+
Sbjct: 1   NKPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLL 60

Query: 313 HQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGI 372
             +S S+D E++M++KLK  CG  FT+K   M  D+++S  +   F  + ++       I
Sbjct: 61  VGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFK-QHMQNQSDSGPI 119

Query: 373 HFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELK 432
             ++NIL  G WP    +     +  E+ K   +F+ FY G+ +GRKL W   +    LK
Sbjct: 120 DLTVNILTMGYWPTYTPM--EVHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLK 177

Query: 433 LSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLL-- 490
             + +      +  FQ  +LL+F + D  +  +I+    +   ++ R + SL   K    
Sbjct: 178 AEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVL 237

Query: 491 --TSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQK 524
             +   +E+ +  +   N  + +K  ++KI+    K
Sbjct: 238 IKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMK 273

>d1ldja2 a.118.17.1 (A:17-410) Cullin homolog 1, Cul-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 394

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin homolog 1, Cul-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  147 bits (373), Expect = 7e-40
 Identities = 62/178 (34%), Positives = 96/178 (53%), Gaps = 2/178 (1%)

Query: 69  LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
           +Y + FE+QFL  +  +Y  E+++ LQ   V++YM++    L EE  R   +LH S+  +
Sbjct: 211 VYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDE 270

Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
           +  KCEQ ++  HL     E   ++  ++  DL  MY L+  +++G+  L   +  HI  
Sbjct: 271 LARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHN 330

Query: 189 QGLEAISGL--SGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVIN 244
           QGL AI     +  N    +V+ +L VHKKY A V   F+ D  F+ ALDKAC   IN
Sbjct: 331 QGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFIN 388

>d1ldja2 a.118.17.1 (A:17-410) Cullin homolog 1, Cul-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 394

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin homolog 1, Cul-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 8e-05
 Identities = 25/193 (12%), Positives = 62/193 (32%), Gaps = 34/193 (17%)

Query: 11  NKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEP------------------ 52
           ++ W  L+  IQ V T  ++ ++ + + ++ +Y+ C +  +                   
Sbjct: 2   DQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQT 61

Query: 53  ------LADRLYQETKLFLDQHL------YVDIFETQFLEMSGEWYKSEASKLLQTCNVS 100
                 +   LY+  K FL  +L        D+ +   L+   + ++           + 
Sbjct: 62  PGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGIC 121

Query: 101 QYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHD 160
            Y+ R       +  R   +     Y          +       +    + ++ +ER  +
Sbjct: 122 AYLNRHWVRRECDEGRKGIY---EIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGE 178

Query: 161 LANMYPLLRSVRE 173
             N   L+  V +
Sbjct: 179 TINT-RLISGVVQ 190

>d2hyec2 a.118.17.1 (C:55-401) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]} Length = 347

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  144 bits (364), Expect = 5e-39
 Identities = 50/191 (26%), Positives = 88/191 (46%), Gaps = 4/191 (2%)

Query: 57  LYQETKLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNR 116
           L     +  D  +Y D FE +FLE +   Y +E  +L+Q   V +Y+  V + L EE +R
Sbjct: 160 LRSLLGMLSDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDR 219

Query: 117 SVRFLHVSSYPKVKAKCEQHMVADHLN-FLQGECVPMVAEERRHDLANMYPLLRSVREGI 175
            + +L  S+   + A  E+ ++ +HL   LQ     ++ E R  DLA MY L   VR G 
Sbjct: 220 VITYLDHSTQKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQ 279

Query: 176 NILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGAL 235
             L+    ++I   G   +     D      V+++L    K    ++  F  ++ F+  +
Sbjct: 280 QALLQHWSEYIKTFGTAIVINPEKDK---DMVQDLLDFKDKVDHVIEVCFQKNERFVNLM 336

Query: 236 DKACSSVINHK 246
            ++  + IN +
Sbjct: 337 KESFETFINKR 347

>d2hyec2 a.118.17.1 (C:55-401) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]} Length = 347

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 7e-06
 Identities = 43/366 (11%), Positives = 112/366 (30%), Gaps = 74/366 (20%)

Query: 10  FNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHL 69
              TW  L E ++ V +     R    + +  + +LC       +  LY++ +   + H+
Sbjct: 5   TQDTWRKLHEAVRAVQS-STSIRYNLEELYQAVENLCSHKV---SPMLYKQLRQACEDHV 60

Query: 70  YVDIFETQ--------FLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLH------EETN 115
              I   +        FL+     ++    +++   ++  +++R   + +       +  
Sbjct: 61  QAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMG 120

Query: 116 RSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGI 175
             +   H+ S   V++K    ++             ++  ER  +  +   LLRS+   +
Sbjct: 121 LELFRTHIISDKMVQSKTIDGILL------------LIERERSGEAVDR-SLLRSLLGML 167

Query: 176 NIL-----------IDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKEL 224
           + L           ++        +G   +            V   L             
Sbjct: 168 SDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPE-YLNHVSKRLEEEGDRVITYL-- 224

Query: 225 FSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLS 284
              D S    L                     + L ++   +L+K    L +      L+
Sbjct: 225 ---DHSTQKPLIACVEK---------------QLLGEHLTAILQKGLDHLLDENRVPDLA 266

Query: 285 QSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSM---DGEEAMINKLKQACGYEFTNKF 341
           Q   +F  +       +   +  ++ +    +  +   + ++ M+  L      +F +K 
Sbjct: 267 QMYQLFSRVRGGQ---QALLQHWSEYIKTFGTAIVINPEKDKDMVQDL-----LDFKDKV 318

Query: 342 HRMLTD 347
             ++  
Sbjct: 319 DHVIEV 324

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  115 bits (290), Expect = 1e-31
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)

Query: 520 GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 578
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61

Query: 579 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 609
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  114 bits (286), Expect = 4e-31
 Identities = 46/89 (51%), Positives = 62/89 (69%), Gaps = 1/89 (1%)

Query: 522 VQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSIS 580
           ++ E  QE E T  +++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q  S F P + 
Sbjct: 2   MKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVP 61

Query: 581 MIKKCIESLIDKNYVERTANSTDEYSYVA 609
           +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 62  VIKKCIDILIEKEYLERVDGEKDTYSYLA 90

>d2hyec1 a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  112 bits (282), Expect = 1e-30
 Identities = 39/85 (45%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 525 ETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKK 584
           ET +E   T   V +DR+  + AAIVRIMK RK + HN L+ E+ +Q K F      +KK
Sbjct: 1   ETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKK 59

Query: 585 CIESLIDKNYVERTANSTDEYSYVA 609
            IESLID++Y+ER  ++ ++Y YVA
Sbjct: 60  RIESLIDRDYMERDKDNPNQYHYVA 84

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]} Length = 194

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 21/164 (12%), Positives = 59/164 (35%), Gaps = 17/164 (10%)

Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEE-----------L 497
             IL L  K       ++   L + Q  +  H+  L E  L+ S  E+           +
Sbjct: 18  RRILFLLTKRP-YFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMI 76

Query: 498 TEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRK 557
            +   + + L      +++  +  V+K    E  + +    E   + ++     + +  +
Sbjct: 77  KKGLRLEILLTPTLFGSEMYEAKGVRKSPEYEQAKELIKSQEPINVKMRELAEFLHELNE 136

Query: 558 QIRHNALIQEVLSQSKS-----FAPSISMIKKCIESLIDKNYVE 596
           +IR     +  L +++         ++  + +    +I++ + +
Sbjct: 137 RIREIIEEKRELEEARILIETYIENTMRRLAEENRQIIEEIFRD 180

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]} Length = 108

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]

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 8/47 (17%), Positives = 20/47 (42%)

Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKE 495
             I     +++ +   DI  +L ++      H+ +L +  ++   KE
Sbjct: 34  AKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKE 80

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	609
d1ldja3	276	Cullin homolog 1, cul-1 {Human (Homo sapiens) [Tax	100.0
d2hyec3	273	Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1ldja2	394	Cullin homolog 1, Cul-1 {Human (Homo sapiens) [Tax	100.0
d2hyec2	347	Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}	100.0
d2hyec1	84	Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}	99.93
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	99.93
d1iuya_	92	Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 1	99.91
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	94.88
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	93.9
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	93.57
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	93.05
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.67
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	92.66
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.46
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.16
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	92.14
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	91.9
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	91.83
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	91.58
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	91.26
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	91.24
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	90.85
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	90.79
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	90.61
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	89.55
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	89.43
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	89.25
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	89.12
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	89.05
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	88.78
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	88.75
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	88.74
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	88.5
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	88.46
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	88.41
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	88.39
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	88.14
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	87.49
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	87.14
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	87.11
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	86.9
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	86.79
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	86.69
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	86.02
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	85.64
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	84.13
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	83.86
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	82.52
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	82.33
d1okra_	120	Methicillin resistance regulatory protein MecI {St	82.17
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	81.43
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	80.97
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	80.78

>d1ldja3 e.40.1.1 (A:411-686) Cullin homolog 1, cul-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin homolog 1, cul-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-56  Score=452.01  Aligned_cols=264  Identities=48%  Similarity=0.810  Sum_probs=248.4

Q ss_pred             CCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHH
Q psy16234        252 PSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQ  331 (609)
Q Consensus       252 ~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~  331 (609)
                      +.++||+||+|||.++|++.++.++++++..++.++.||+|+++||+|+.+|+++||+|||.+++.+.+.|+.+|+.|+.
T Consensus         5 ~~~~~e~La~y~D~~lk~~~k~~~~~~~~~~l~~i~~if~~l~~KD~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~   84 (276)
T d1ldja3           5 SSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQ   84 (276)
T ss_dssp             TTHHHHHHHHHHHHHHBCCSSCCCHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHTTCBSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            47899999999999999999888888999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHH
Q psy16234        332 ACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFY  411 (609)
Q Consensus       332 ~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y  411 (609)
                      +||.+++.+|++|++|+..|++++.+| ++++.... ..+++|+|.||++++||..+.  .++.+|++|+++++.|++||
T Consensus        85 ~~g~~~~~kl~~Ml~D~~~S~~~~~~f-~~~~~~~~-~~~~~~~v~Vlt~~~WP~~~~--~~~~lP~~l~~~~~~f~~~Y  160 (276)
T d1ldja3          85 ACGFEYTSKLQRMFQDIGVSKDLNEQF-KKHLTNSE-PLDLDFSIQVLSSGSWPFQQS--CTFALPSELERSYQRFTAFY  160 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHTTTC-CCSSEEEEEEEETTTSCCCCC--SCCCCCGGGHHHHHHHHHHT
T ss_pred             HhChHHHHHHHHHHHHHHHHHHHHHHH-HHHHhccC-CcCceEEEEEeeCCccCcCCC--CCccCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999 77765443 257899999999999998765  58999999999999999999


Q ss_pred             hhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234        412 HGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT  491 (609)
Q Consensus       412 ~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~  491 (609)
                      +++|+||+|.|.|++|+|+|+++|+++.|+|+||++||+||++||+++++|+++|++.||++.++++++|.+|++.|+|.
T Consensus       161 ~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~l~vs~~Qa~ILllFN~~~~~t~~ei~~~~~i~~~~l~~~L~~L~~~kll~  240 (276)
T d1ldja3         161 ASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLV  240 (276)
T ss_dssp             TTTCTTCCEEECGGGCCCEEEESSSSSCCEEECCHHHHHHHHGGGSSSEEEHHHHHHHTCCCHHHHHHHHHHHHHTTTEE
T ss_pred             HHhCCCCeEEEecCCCcEEEEEEECCCcEEEEECHHHHHHHHhhcCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC-------CCCCCCCEEEEecCCCCCcceEEec
Q psy16234        492 SNK-------EELTEDTEIRLNLGYNNKRTKLKIS  519 (609)
Q Consensus       492 ~~~-------~~~~~~~~f~lN~~F~~~~~ki~i~  519 (609)
                      ..+       ..+.+++.|.+|.+|+++++||+|+
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~N~~f~~~~~ki~vn  275 (276)
T d1ldja3         241 LEDENANVDEVELKPDTLIKLYLGYKNKKLRVNIN  275 (276)
T ss_dssp             CSCTTCCTTTCCCCTTCEEEECSSCCCSSSSBCCC
T ss_pred             ecCCCCCccccccCCCCEEEEecCCCCCCeEEEeC
Confidence            543       3467899999999999999999885

>d2hyec3 e.40.1.1 (C:403-675) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.1e-56  Score=446.84  Aligned_cols=266  Identities=29%  Similarity=0.528  Sum_probs=250.4

Q ss_pred             CchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHh
Q psy16234        254 KSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQAC  333 (609)
Q Consensus       254 ~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~  333 (609)
                      ++||+||+|||.++|++.++.++++++..+++++.+|+|++|||+|+.+|+++||+|||.+.+.+.+.|+.+|++|+.+|
T Consensus         2 ~~~e~la~y~D~~lr~~~k~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~L~~~~   81 (273)
T d2hyec3           2 KPAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHEC   81 (273)
T ss_dssp             HHHHHHHHHHHHHHSSCGGGCCSTTHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHTTT
T ss_pred             CcHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence            46899999999999998888888899999999999999999999999999999999999999989999999999999999


Q ss_pred             CchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhh
Q psy16234        334 GYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHG  413 (609)
Q Consensus       334 G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~  413 (609)
                      |.++|.+|++|++|+..|++++.+| ++++.......+++|+|.||+++.||..+.  .++.+|++|..+++.|++||.+
T Consensus        82 g~~~~~kl~~Ml~D~~~S~~l~~~f-~~~~~~~~~~~~~~~~v~vLs~~~WP~~~~--~~~~lP~~l~~~~~~F~~~Y~~  158 (273)
T d2hyec3          82 GAAFTSKLEGMFKDMELSKDIMVHF-KQHMQNQSDSGPIDLTVNILTMGYWPTYTP--MEVHLTPEMIKLQEVFKAFYLG  158 (273)
T ss_dssp             CTTTTHHHHHHHHHHHHHHHHHHHH-HHHHHTTCCCCCCEEEEEEEETTTSCCCCC--CCCCCCHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHH-HHHHhccccCCCCceEEEEeeCCCCCCCCC--CCCcCCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999 777776665578999999999999998875  5899999999999999999999


Q ss_pred             cCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHh--cCccc
Q psy16234        414 QFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVE--CKLLT  491 (609)
Q Consensus       414 k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~--~~iL~  491 (609)
                      +|+||+|.|++++|+|+|+++|+++.++++||++||+||++||+.+++|+++|++.||++.+.++++|.+|+.  .+||.
T Consensus       159 ~~~~RkL~w~~~ls~~~l~~~~~~~~~~l~~s~~Qa~ILl~fn~~~~~t~~~i~~~~~i~~~~l~~~L~~L~~~k~~iL~  238 (273)
T d2hyec3         159 KHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLI  238 (273)
T ss_dssp             TSCSEECCBCGGGCEEEEECCCSSCCCEEEEEHHHHHHHHHTTSCCCEEHHHHHHHTCCCHHHHHHHHHTTTTTTTCSEE
T ss_pred             hCCCCEEEEecCCccEEEEEEECCCcEEEEEcHHHHHHHHHhcCCCCCcHHHHHHHHCcCHHHHHHHHHHHHhcccceee
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999995  45777


Q ss_pred             cCC--CCCCCCCEEEEecCCCCCcceEEecccc
Q psy16234        492 SNK--EELTEDTEIRLNLGYNNKRTKLKISGAV  522 (609)
Q Consensus       492 ~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~  522 (609)
                      +.+  +.+.+++.|.+|.+|+++++||+|++++
T Consensus       239 ~~~~~~~~~~~~~~~~N~~F~~k~~kiki~~~~  271 (273)
T d2hyec3         239 KSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQ  271 (273)
T ss_dssp             ETTCSSSCCSSCEEEECCCCCCSCSSEECGGGG
T ss_pred             ecCCCCcCCCCCEEEEeccCCCCCeEEeecccc
Confidence            665  5678899999999999999999998764

>d1ldja2 a.118.17.1 (A:17-410) Cullin homolog 1, Cul-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin homolog 1, Cul-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.8e-40  Score=351.90  Aligned_cols=237  Identities=32%  Similarity=0.586  Sum_probs=222.3

Q ss_pred             hHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcc------------------------cHHHHHHHHHhhh
Q psy16234         10 FNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEP------------------------LADRLYQETKLFL   65 (609)
Q Consensus        10 fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~------------------------~~~~Ly~~~~~~l   65 (609)
                      .|++|+.|++||+.|++.+++++..||++|++||++|++.+.+                        +|++||+++++++
T Consensus         1 ~d~~W~~L~~ai~~I~~~~~~~~~~~~~lY~~vy~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LY~~l~~~l   80 (394)
T d1ldja2           1 LDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFL   80 (394)
T ss_dssp             CHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHTCCC----------------------------TTHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhcCCccccccccccchhhhhhccccchhhhHHHHHHHHHHHHH
Confidence            4899999999999999988999999999999999999976432                        6889999998888


Q ss_pred             hhh-----------------------------------------------------------------------------
Q psy16234         66 DQH-----------------------------------------------------------------------------   68 (609)
Q Consensus        66 ~~~-----------------------------------------------------------------------------   68 (609)
                      ..|                                                                             
T Consensus        81 ~~~l~~i~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~~~~~~~~~~I~~~~l~~fr~~v~~~~~  160 (394)
T d1ldja2          81 KNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLN  160 (394)
T ss_dssp             HHHHHHHHHTTCSCTTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSSCCC-------CCHHHHHHHTTHHHHTTTTT
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHhcccccccccchHHHHHHHHHHHHHHHHHH
Confidence            765                                                                             


Q ss_pred             --------------------------------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCC
Q psy16234         69 --------------------------------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCN   98 (609)
Q Consensus        69 --------------------------------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s   98 (609)
                                                                        +|.+.||++||++|.+||++++..|+++++
T Consensus       161 ~~l~~~il~~I~~~R~g~~i~~~li~~~i~~l~~l~~~~~~~~~~~~~~~~Y~~~FE~~~L~~t~~~Y~~~~~~~l~~~~  240 (394)
T d1ldja2         161 KQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNP  240 (394)
T ss_dssp             THHHHHHHHHHTTTSCCTTCCTHHHHHHHHHHHHTSCCSSSSSCSSCCCHHHHHHTHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhCcchhhhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence                                                              499999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHH
Q psy16234         99 VSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINIL  178 (609)
Q Consensus        99 ~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l  178 (609)
                      +++||++|+.++++|.+||..||+++|.+++.++|+++||.+|++.|.+||..||++++.++|++||+|++++++|++.|
T Consensus       241 ~~eYl~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~lY~L~~rv~~~~~~l  320 (394)
T d1ldja2         241 VTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGEL  320 (394)
T ss_dssp             TTSSHHHHHHHHHHHHHTTTTTTCSSSSHHHHHHHHHHHSSSSSHHHHHHHHHHHHSCCTTHHHHHHHHHHHSTTCHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhhccchHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcccC--CCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCC
Q psy16234        179 IDAVRDHICKQGLEAISGLSG--DNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHK  246 (609)
Q Consensus       179 ~~~~~~~i~~~g~~~~~~~~~--~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~  246 (609)
                      +.+|++||++.|.+++.....  .++|..||+.|+++|++|+.++..||++|+.|..++++||+.|+|++
T Consensus       321 ~~~~~~~I~~~G~~~i~~~~~~~~~~~~~~V~~ll~l~~~~~~ii~~~F~~d~~f~~~l~~af~~fiN~n  390 (394)
T d1ldja2         321 KKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNN  390 (394)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSGGGCHHHHHHHHHHHHHHHHHHHHTTTTTCHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHhhhhcccCChHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhCcc
Confidence            999999999999999986533  34689999999999999999999999999999999999999999987

>d2hyec2 a.118.17.1 (C:55-401) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cullin repeat-like
family: Cullin repeat
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.5e-37  Score=323.89  Aligned_cols=231  Identities=25%  Similarity=0.430  Sum_probs=216.6

Q ss_pred             cChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-------------------
Q psy16234          8 VDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH-------------------   68 (609)
Q Consensus         8 ~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~-------------------   68 (609)
                      ..||++|..|++||+.|+..++ ++..|+++|++||++|++.   .|++||++++.++.+|                   
T Consensus         3 ~~~e~~W~~L~~ai~~I~~~~~-~~~s~e~lY~~vy~lc~~~---~~~~LY~~l~~~l~~~~~~~~~~~~~~~~~~~~~L   78 (347)
T d2hyec2           3 NYTQDTWRKLHEAVRAVQSSTS-IRYNLEELYQAVENLCSHK---VSPMLYKQLRQACEDHVQAQILPFREDSLDSVLFL   78 (347)
T ss_dssp             CTTTTHHHHHHHHHHTTSTTCC-CSSCHHHHHHHHHHHCCTT---THHHHHHHHHHHHHHHHHHHHHHHTSCCCCTTHHH
T ss_pred             chHHHHHHHHHHHHHHHHhCCC-CCCCHHHHHHHHHHHHccC---cHHHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHH
Confidence            5799999999999999988654 4567999999999999986   6899999998887766                   


Q ss_pred             --------------------------------------------------------------------------------
Q psy16234         69 --------------------------------------------------------------------------------   68 (609)
Q Consensus        69 --------------------------------------------------------------------------------   68 (609)
                                                                                                      
T Consensus        79 ~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~~~~~i~~~~l~lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~~~  158 (347)
T d2hyec2          79 KKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRS  158 (347)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTHHHHTTTTTSCSSSCCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHTTTTTCCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcchhhhhcCCCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHcCCCCcHH
Confidence                                                                                            


Q ss_pred             -------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHH
Q psy16234         69 -------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQ  135 (609)
Q Consensus        69 -------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~  135 (609)
                                   +|.+.||++||++|.+||++++..|++++++++|+.+|+.++++|.+||..||+++|.++|.++|++
T Consensus       159 ll~~~~~~~~~l~~Y~~~fE~~~l~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~~l~~~l~~  238 (347)
T d2hyec2         159 LLRSLLGMLSDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEK  238 (347)
T ss_dssp             HHHHHHHHHHHTTCHHHHTHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTHHHHTTTSCTTTHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhccHhHHHHHHHHHHH
Confidence                         8999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH-HhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHH
Q psy16234        136 HMVADHLNFL-QGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVH  214 (609)
Q Consensus       136 ~LI~~~~~~l-~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~  214 (609)
                      +||.+|.+.+ .+++..||++++.++|++||+|++++++|++.++++|++||++.|.+++....   .+..||+.|+++|
T Consensus       239 ~Li~~~~~~il~~~~~~ll~~~~~~~L~~ly~L~~r~~~~~~~l~~~f~~~i~~~G~~~v~~~~---~~~~~V~~ll~l~  315 (347)
T d2hyec2         239 QLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPE---KDKDMVQDLLDFK  315 (347)
T ss_dssp             HHTTTCSHHHHHTTHHHHHTTTCHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHSCGG---GTTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHhCcc---cchHHHHHHHHHH
Confidence            9999999876 57899999999999999999999999999999999999999999999997544   3457999999999


Q ss_pred             HHHHHHHHHhcCCChhHHHHHHHHHHHhhcC
Q psy16234        215 KKYKAFVKELFSGDQSFMGALDKACSSVINH  245 (609)
Q Consensus       215 ~k~~~li~~~F~~~~~f~~~l~~af~~~~N~  245 (609)
                      ++|+.++..||++|+.|.+++++||+.|+|+
T Consensus       316 ~k~~~li~~~F~~d~~f~~~l~~af~~~iNk  346 (347)
T d2hyec2         316 DKVDHVIEVCFQKNERFVNLMKESFETFINK  346 (347)
T ss_dssp             HHHHHHHHTTTTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHccC
Confidence            9999999999999999999999999999996

>d2hyec1 a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=1.1e-26  Score=185.80  Aligned_cols=83  Identities=46%  Similarity=0.647  Sum_probs=79.8

Q ss_pred             ChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCce
Q psy16234        526 TPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY  605 (609)
Q Consensus       526 ~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y  605 (609)
                      +++|.+.+.+.+.++|...|+||||||||++|+|+|++|+.+|.++++ |+|++++||+|||.||+||||+|+++|+++|
T Consensus         2 ~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~k~l~h~eL~~~v~~~l~-f~~~~~~iK~~Ie~LIereYi~R~~~~~~~y   80 (84)
T d2hyec1           2 TVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQY   80 (84)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEETHHHHHHHHHHSS-SCCCHHHHHHHHHHHHHTTSCBCCSSCTTEE
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCcHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHhhhHhhcCCCCCcee
Confidence            556788888999999999999999999999999999999999999997 9999999999999999999999999999999


Q ss_pred             eecC
Q psy16234        606 SYVA  609 (609)
Q Consensus       606 ~Yia  609 (609)
                      +|+|
T Consensus        81 ~Y~A   84 (84)
T d2hyec1          81 HYVA   84 (84)
T ss_dssp             ECCC
T ss_pred             eeeC
Confidence            9998

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=8.7e-27  Score=189.27  Aligned_cols=87  Identities=53%  Similarity=0.833  Sum_probs=82.3

Q ss_pred             ccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCC
Q psy16234        523 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  601 (609)
Q Consensus       523 ~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~  601 (609)
                      ++++++|.+.+.+.++++|...|+||||||||++|+|+|++|+.+|.+++++ |+|++.+||+|||.||+||||+|+++|
T Consensus         3 ~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~k~l~h~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereYi~R~~~~   82 (90)
T d1ldja1           3 KTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGE   82 (90)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSS
T ss_pred             CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhHHHhcCCCC
Confidence            3445567888899999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCceeecC
Q psy16234        602 TDEYSYVA  609 (609)
Q Consensus       602 ~~~y~Yia  609 (609)
                      +++|+|+|
T Consensus        83 ~~~y~YvA   90 (90)
T d1ldja1          83 KDTYSYLA   90 (90)
T ss_dssp             TTEEEECC
T ss_pred             CceeeeeC
Confidence            99999998

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=4.2e-26  Score=186.65  Aligned_cols=87  Identities=51%  Similarity=0.721  Sum_probs=80.5

Q ss_pred             ccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCC
Q psy16234        523 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  601 (609)
Q Consensus       523 ~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~  601 (609)
                      ++++++|.+.+.+.++++|...|+|+||||||++|+|+|++|+.+|.+++++ |+|++.+||+|||.||+||||+|+++|
T Consensus         5 ~~e~~~e~~~~~~~i~~dR~~~i~AaIVRIMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIekeYi~R~~~d   84 (92)
T d1iuya_           5 QGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPED   84 (92)
T ss_dssp             CCCCCCCCCCCCSCSCCCTTTHHHHHHHHHHHHHCEEEHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSC
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhhhhcCCCC
Confidence            4455556677788899999999999999999999999999999999999998 999999999999999999999999999


Q ss_pred             CCceeecC
Q psy16234        602 TDEYSYVA  609 (609)
Q Consensus       602 ~~~y~Yia  609 (609)
                      +++|+|+|
T Consensus        85 ~~~y~Y~A   92 (92)
T d1iuya_          85 RKVYTYVA   92 (92)
T ss_dssp             SSEEEEC-
T ss_pred             CCeeeeeC
Confidence            99999998

>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=94.88  E-value=0.023  Score=42.60  Aligned_cols=52  Identities=19%  Similarity=0.218  Sum_probs=43.6

Q ss_pred             HHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234        450 AILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN  506 (609)
Q Consensus       450 ~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN  506 (609)
                      .||..|.+. .++|+.||++.+|+|...+.+.|..|.+.|++.+++     ++.|.+-
T Consensus         9 ~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~-----~g~y~lG   61 (75)
T d1mkma1           9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK-----DKRYVPG   61 (75)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECT-----TSCEEEC
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC-----CCCEeec
Confidence            477777754 579999999999999999999999999999998764     4456553

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=93.90  E-value=0.03  Score=41.35  Aligned_cols=46  Identities=13%  Similarity=0.246  Sum_probs=40.1

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+.||-++-.+..+|..||++.+|++...+.+++..|++.|++...
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3457766667789999999999999999999999999999998754

>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=93.57  E-value=0.033  Score=44.91  Aligned_cols=52  Identities=15%  Similarity=0.265  Sum_probs=47.1

Q ss_pred             EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +-+|..|+.|+...-+.+..|..+|++.+|++...+.+.|..|.+.|++.+.
T Consensus        16 lGlt~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          16 LSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             TCCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEE
Confidence            3467899999988888899999999999999999999999999999999653

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=93.05  E-value=0.072  Score=44.76  Aligned_cols=58  Identities=10%  Similarity=0.067  Sum_probs=46.3

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      .+++.+.+..+....+|.++|++.+++|...+.+.|..|.++|+|....+   + +-|.+..
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG---~-GG~~L~~   66 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG---P-GGAGLLK   66 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-------CCEEESS
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecC---C-CCceecC
Confidence            35667777777777899999999999999999999999999999975531   2 4466765

>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=92.67  E-value=0.064  Score=38.07  Aligned_cols=44  Identities=20%  Similarity=0.351  Sum_probs=39.2

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .-||.++.++..+|+.+|++.+|++...+...++.|.+.|++..
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            34677777778999999999999999999999999999999864

>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=92.66  E-value=0.051  Score=45.70  Aligned_cols=50  Identities=16%  Similarity=0.200  Sum_probs=46.4

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|+.|+.||......+++|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        28 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~   77 (139)
T d2a61a1          28 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   77 (139)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeee
Confidence            57899999999888889999999999999999999999999999999765

>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=92.46  E-value=0.071  Score=38.22  Aligned_cols=48  Identities=13%  Similarity=0.257  Sum_probs=42.4

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .-.-..||..+.++...|+.+|++.+|+|...+...+..|.+.|++..
T Consensus         4 D~~D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~   51 (63)
T d2cg4a1           4 DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG   51 (63)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            344566888888889999999999999999999999999999999863

>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=92.16  E-value=0.096  Score=37.52  Aligned_cols=48  Identities=10%  Similarity=0.282  Sum_probs=42.1

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      +-.-.-||..+.++..+|+.+|++.+|++...+.+.++.|.+.|++..
T Consensus         4 D~~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1           4 DQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             CHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            344556888888888999999999999999999999999999999863

>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=92.14  E-value=0.095  Score=44.08  Aligned_cols=51  Identities=16%  Similarity=0.263  Sum_probs=47.2

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|+.||..+.+.+.+|..+|++.++++...+.+.++.|++.|++.+.
T Consensus        33 ~lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~   83 (141)
T d1lnwa_          33 DLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   83 (141)
T ss_dssp             CCCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeee
Confidence            357899999999988888999999999999999999999999999999765

>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=91.90  E-value=0.057  Score=42.57  Aligned_cols=49  Identities=20%  Similarity=0.361  Sum_probs=44.6

Q ss_pred             cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ++.|..||.....++.+|+.+|++.+|++...+.++|..|.+.|++...
T Consensus        15 ~p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~   63 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEE
Confidence            6788999988877788999999999999999999999999999999653

>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=91.83  E-value=0.13  Score=36.36  Aligned_cols=46  Identities=15%  Similarity=0.320  Sum_probs=40.9

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .-.-||..+.++...|+.+|++.+|++...+...+..|.+.|++..
T Consensus         4 ~D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~   49 (60)
T d2cyya1           4 IDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKK   49 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            3456788888888999999999999999999999999999999864

>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=91.58  E-value=0.047  Score=46.26  Aligned_cols=50  Identities=16%  Similarity=0.185  Sum_probs=46.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|+.+|....+++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        27 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~   76 (144)
T d1lj9a_          27 LTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             CTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHHHHHhhhccccc
Confidence            56789999998888888999999999999999999999999999999765

>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=91.26  E-value=0.1  Score=41.80  Aligned_cols=51  Identities=20%  Similarity=0.398  Sum_probs=43.8

Q ss_pred             EecHHHHHHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLF-EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      -+|..|..||... ...+.+|..+|++.+|++...+.++|..|...|++.+.
T Consensus        18 gLs~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~   69 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEe
Confidence            3577888888655 44567999999999999999999999999999999765

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.24  E-value=0.11  Score=37.53  Aligned_cols=56  Identities=11%  Similarity=0.220  Sum_probs=48.7

Q ss_pred             hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +..|+..|.+|.+..++|-.+       |....++...+|..|.+.|-|.-.-+|+..|.||.
T Consensus        10 ~~FI~~Ik~~Kvv~LedLAa~-------F~lktqd~i~RIq~Le~~g~ltGViDDRGKfIyIS   65 (72)
T d1wi9a_          10 TEFINYIKKSKVVLLEDLAFQ-------MGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             HHHHHHHHHCSEECHHHHHHH-------HCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHHHCCEeeHHHHHHH-------cCCcHHHHHHHHHHHHHCCCeeeEEcCCCCEEEEc
Confidence            345677799999999887744       88999999999999999999999888999999984

>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=90.85  E-value=0.1  Score=43.76  Aligned_cols=51  Identities=18%  Similarity=0.217  Sum_probs=47.1

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|+.||.....++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        29 ~lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~   79 (140)
T d2etha1          29 DMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   79 (140)
T ss_dssp             HSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            357889999999988889999999999999999999999999999999865

>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=90.79  E-value=0.081  Score=44.25  Aligned_cols=51  Identities=18%  Similarity=0.247  Sum_probs=47.0

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|+.|..||......+.+|..+|++.++++...+.+.+..|.+.|++...+
T Consensus        31 Lt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~   81 (137)
T d1z91a1          31 ITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKR   81 (137)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCB
T ss_pred             cCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEee
Confidence            578899999988888899999999999999999999999999999998764

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.61  E-value=0.12  Score=41.75  Aligned_cols=52  Identities=15%  Similarity=0.220  Sum_probs=45.0

Q ss_pred             EecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      .+|..|..||..+..  .+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~   83 (115)
T d2frha1          30 SISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   83 (115)
T ss_dssp             CCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             CCCHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeee
Confidence            357789999977744  4569999999999999999999999999999998764

>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=89.55  E-value=0.4  Score=34.06  Aligned_cols=46  Identities=15%  Similarity=0.296  Sum_probs=39.7

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .+.-||.+++++..+|.++|++.+|++...+.+.+..|-+.|+.+.
T Consensus         6 ~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~   51 (63)
T d1biaa1           6 VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF   51 (63)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCE
T ss_pred             HHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEE
Confidence            3445777778888999999999999999999999999999997543

>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=89.43  E-value=0.27  Score=35.80  Aligned_cols=45  Identities=16%  Similarity=0.254  Sum_probs=40.6

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..||-+.-.+..+|-.||++.||++...+.+++..|++.|++...
T Consensus         8 ~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           8 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            457777778899999999999999999999999999999998754

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=89.25  E-value=0.12  Score=43.43  Aligned_cols=50  Identities=12%  Similarity=0.232  Sum_probs=45.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|+.|..||......+..|..+|++.++++...+.+.+..|.+.|++.+.
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            46789999988888888999999999999999999999999999999764

>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=89.12  E-value=0.11  Score=42.85  Aligned_cols=51  Identities=18%  Similarity=0.311  Sum_probs=44.6

Q ss_pred             EecHHHHHHHHhh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLF--EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllF--n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|+.||..+  ++.+++|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        31 ~Lt~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~   83 (125)
T d1p4xa1          31 DMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKV   83 (125)
T ss_dssp             SSCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEE
T ss_pred             CCCHHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceee
Confidence            3678899999776  34457999999999999999999999999999999765

>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=89.05  E-value=0.2  Score=41.15  Aligned_cols=51  Identities=16%  Similarity=0.217  Sum_probs=44.6

Q ss_pred             EecHHHHHHHHhhc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFE--KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn--~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|..||..+.  +.+.+|..+|++.+|++...+.+.+..|.+.|++.+.
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~   82 (125)
T d1p4xa2          30 TLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE   82 (125)
T ss_dssp             SSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             CCCHHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeee
Confidence            46778999997774  4567999999999999999999999999999999765

>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=88.78  E-value=0.15  Score=42.50  Aligned_cols=50  Identities=18%  Similarity=0.191  Sum_probs=45.8

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..+|..+..++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        32 Lt~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~   81 (138)
T d1jgsa_          32 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             SCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEe
Confidence            46789999988888789999999999999999999999999999999765

>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=88.75  E-value=0.16  Score=42.22  Aligned_cols=50  Identities=8%  Similarity=0.122  Sum_probs=46.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|..|..||.....++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        28 lt~~q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~   77 (136)
T d2fbia1          28 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRW   77 (136)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            67789999988888889999999999999999999999999999999765

>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=88.74  E-value=0.13  Score=44.45  Aligned_cols=51  Identities=12%  Similarity=0.036  Sum_probs=46.9

Q ss_pred             EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|..|+.||.....++++|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus        38 ~Lt~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~   88 (162)
T d2fxaa1          38 DLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFS   88 (162)
T ss_dssp             TCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCCHHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceee
Confidence            357789999999988889999999999999999999999999999999765

>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=88.50  E-value=0.41  Score=40.16  Aligned_cols=47  Identities=19%  Similarity=0.267  Sum_probs=38.3

Q ss_pred             HHHHHHH--HhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        446 TFQMAIL--LLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       446 ~~Q~~iL--llFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      ..++-|+  +.++ .+++|..||++.+|++...+.+.|..|.+.|++.+.
T Consensus        26 ~~~~~i~~~L~~~-~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~   74 (151)
T d1ku9a_          26 KSVGAVYAILYLS-DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (151)
T ss_dssp             HHHHHHHHHHHHC-SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhC-CCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEE
Confidence            4455555  3344 456999999999999999999999999999999754

>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=88.46  E-value=0.26  Score=40.67  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=44.0

Q ss_pred             EecHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        443 TMQTFQMAILLLFEKN--DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      -+|..|+.||..+..+  ..+|..+|++.++++...+.+.++.|.+.|++.+.
T Consensus        26 glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~   78 (135)
T d3broa1          26 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   78 (135)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHH
Confidence            3678899988766654  45999999999999999999999999999999754

>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=88.41  E-value=0.23  Score=40.05  Aligned_cols=51  Identities=14%  Similarity=0.260  Sum_probs=43.9

Q ss_pred             ecHHHHHHHHhh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLF--EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllF--n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|..|..||..+  ++.+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus        30 Lt~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~   82 (115)
T d1hsja1          30 LNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKR   82 (115)
T ss_dssp             CCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEE
T ss_pred             CCHHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEe
Confidence            667888888544  456789999999999999999999999999999998753

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=88.39  E-value=0.54  Score=38.40  Aligned_cols=56  Identities=16%  Similarity=0.204  Sum_probs=41.9

Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234        447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG  508 (609)
Q Consensus       447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~  508 (609)
                      .++.+.+.-  +..+|.++|++.+|+|...+++.|..|.++||+.... +.  ++.| ++.+
T Consensus         7 v~~L~~la~--~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~r-G~--~GGy-Lar~   62 (127)
T d1xd7a_           7 IHILSLISM--DEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRA-GV--PGAS-LKKD   62 (127)
T ss_dssp             HHHHHHHHT--CSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCS-SS--SSCE-ESSC
T ss_pred             HHHHHHHhc--CCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccC-CC--CCcc-ccCC
Confidence            455445544  4569999999999999999999999999999987542 22  2336 7653

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=88.14  E-value=0.31  Score=36.96  Aligned_cols=45  Identities=20%  Similarity=0.139  Sum_probs=38.6

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        458 NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      ..+.|++||++.+|++++.+.+.|..|+..|++...+     ++.|..+.
T Consensus        32 ~gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~-----~~~y~lt~   76 (85)
T d1tw3a1          32 AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDA-----PGEFVPTE   76 (85)
T ss_dssp             TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE-----TTEEEECT
T ss_pred             cCCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecC-----CCeEecCH
Confidence            4679999999999999999999999999999997653     46777653

>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=87.49  E-value=0.42  Score=34.62  Aligned_cols=49  Identities=18%  Similarity=0.240  Sum_probs=42.2

Q ss_pred             ecHHHHHHHHhhcC---CCCCCHHHHHHHh-CCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEK---NDAMTCGDIQTVL-SLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~---~~~lt~~ei~~~t-~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      +|+.|..|+-++..   ...+++++|+..+ |+|...++.++..|+..|.+-.
T Consensus         4 Ls~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_           4 LTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             SCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCceec
Confidence            47889999988874   3569999999988 8999999999999999998753

>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=87.14  E-value=0.15  Score=42.43  Aligned_cols=50  Identities=12%  Similarity=0.240  Sum_probs=46.3

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      +|+.|..||.....++.+|..+|++.++++...+.+.+..|++.|++.+.
T Consensus        32 lt~~q~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~   81 (136)
T d2bv6a1          32 LTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRE   81 (136)
T ss_dssp             CCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEe
Confidence            57899999988888889999999999999999999999999999999765

>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=87.11  E-value=0.32  Score=40.75  Aligned_cols=52  Identities=12%  Similarity=0.204  Sum_probs=44.2

Q ss_pred             EecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        443 TMQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       443 ~~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      -+|..|+.||..+.. .+.+|..+|++.+|++...+.+.+..|.+.|++.+.+
T Consensus        31 glt~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~   83 (145)
T d2hr3a1          31 PVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA   83 (145)
T ss_dssp             HHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeee
Confidence            356788888877743 3579999999999999999999999999999997653

>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=86.90  E-value=0.3  Score=36.76  Aligned_cols=61  Identities=16%  Similarity=0.258  Sum_probs=48.2

Q ss_pred             hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      .+..|++++=.++.++..+++..+.+.   .......|..-|..|.+||||.|... ...|.|-|
T Consensus        10 ~E~~IM~~lW~~~~~t~~ei~~~l~~~---~~~~~tTv~T~L~rL~~KG~l~~~k~-gr~~~Y~p   70 (82)
T d1p6ra_          10 AELEVMKVIWKHSSINTNEVIKELSKT---STWSPKTIQTMLLRLIKKGALNHHKE-GRVFVYTP   70 (82)
T ss_dssp             HHHHHHHHHHTSSSEEHHHHHHHHHHH---SCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhccc---cCCcHhHHHHHHHHHHHCCCeEEEec-CCeEEEEe
Confidence            356788888888889888877666443   55678999999999999999998765 46788854

>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=86.79  E-value=0.32  Score=40.43  Aligned_cols=51  Identities=10%  Similarity=0.149  Sum_probs=44.8

Q ss_pred             ecHHHHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|..|..+|....+ ++.+|..+|++.++++...+.+.+..|.+.|++...+
T Consensus        29 lt~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~   80 (140)
T d3deua1          29 LTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQT   80 (140)
T ss_dssp             CCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCHHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecc
Confidence            56789999988765 5679999999999999999999999999999997653

>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=86.69  E-value=0.49  Score=37.57  Aligned_cols=60  Identities=13%  Similarity=0.161  Sum_probs=43.7

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234        446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL  507 (609)
Q Consensus       446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~  507 (609)
                      +.-..||......+.+++.+|++.+|++...+-.+|..|..+||+....  -+..-.|++|.
T Consensus        31 p~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r--~G~~~~Y~l~~   90 (108)
T d1u2wa1          31 ENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK--EGKLALYSLGD   90 (108)
T ss_dssp             HHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC------CCEEEESC
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEE--ECCEEEEEECH
Confidence            3445566555445679999999999999999999999999999997542  01123566654

>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=86.02  E-value=0.36  Score=34.18  Aligned_cols=34  Identities=12%  Similarity=0.263  Sum_probs=32.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .+|-.||++.+|++...+.+++..|++.|++...
T Consensus        12 pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~   45 (62)
T d2hoea1          12 PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEE   45 (62)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            5899999999999999999999999999999754

>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=85.64  E-value=0.31  Score=40.28  Aligned_cols=51  Identities=14%  Similarity=0.206  Sum_probs=43.2

Q ss_pred             ecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|..|..||.... ..+.+|..+|++.++++...+.+.+..|++.|++.+.+
T Consensus        26 lt~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~   77 (137)
T d2fbha1          26 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLA   77 (137)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccC
Confidence            4567888886665 34579999999999999999999999999999998653

>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=84.13  E-value=0.6  Score=32.88  Aligned_cols=44  Identities=20%  Similarity=0.326  Sum_probs=36.2

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      |..+-.++...+..+|++.+|++...+...+..|.+.|++...+
T Consensus        12 I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~~   55 (61)
T d2ev0a1          12 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK   55 (61)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEcc
Confidence            33333456789999999999999999999999999999998765

>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=83.86  E-value=0.92  Score=32.18  Aligned_cols=45  Identities=9%  Similarity=0.118  Sum_probs=38.4

Q ss_pred             HHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234        449 MAILLLFEKN--DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN  493 (609)
Q Consensus       449 ~~iLllFn~~--~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~  493 (609)
                      .-|.-.|.++  .+.++.||++.+|++++.+...|.-|++.|.|++.
T Consensus        10 ~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI   56 (64)
T d1lvaa3          10 KDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKI   56 (64)
T ss_dssp             HHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3456667653  67899999999999999999999999999998875

>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=82.52  E-value=1.1  Score=31.55  Aligned_cols=44  Identities=18%  Similarity=0.104  Sum_probs=37.6

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      |..+-.+++..+..+|++.+|++...+..++..|.+.|++...+
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            33344456789999999999999999999999999999998764

>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=82.33  E-value=0.86  Score=32.38  Aligned_cols=42  Identities=21%  Similarity=0.299  Sum_probs=34.9

Q ss_pred             HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234        448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKL  489 (609)
Q Consensus       448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~i  489 (609)
                      +..||.++.+ ...+|.++|++.+|++...+.+.|..|-..|+
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            3456655544 45799999999999999999999999988886

>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=82.17  E-value=0.5  Score=38.19  Aligned_cols=60  Identities=22%  Similarity=0.342  Sum_probs=47.2

Q ss_pred             hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234        546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  609 (609)
Q Consensus       546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia  609 (609)
                      +..|++++=..+.++-.+++..+...   ..++...+...+..|.+||||.|..+ ...|.|.|
T Consensus         9 E~~VM~~lW~~~~~t~~ei~~~l~~~---~~~~~sTv~t~L~rL~~Kg~l~r~~~-gr~~~Y~~   68 (120)
T d1okra_           9 EWEVMNIIWMKKYASANNIIEEIQMQ---KDWSPKTIRTLITRLYKKGFIDRKKD-NKIFQYYS   68 (120)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHhcc---cCccHHhHHHHHHHHHHCCCeEEEec-CCceEEee
Confidence            34566666677888888888666543   56889999999999999999999875 47888865

>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=81.43  E-value=0.87  Score=32.63  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=38.8

Q ss_pred             HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234        451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      ++.....++..|..+|+..+|++..++.++|-+|.+.|.+.+.+
T Consensus        15 ~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~   58 (70)
T d1sfua_          15 EVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVP   58 (70)
T ss_dssp             HHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCC
Confidence            45566678899999999999999999999999999999887764

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.97  E-value=1.1  Score=39.04  Aligned_cols=48  Identities=27%  Similarity=0.394  Sum_probs=40.9

Q ss_pred             ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234        444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS  492 (609)
Q Consensus       444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~  492 (609)
                      .++.-.-||.++. ..++|+.+|++.+|++...+.+||..|.+.|++..
T Consensus        17 ~~p~R~~Il~~L~-~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~   64 (190)
T d1ulya_          17 LEDTRRKILKLLR-NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   64 (190)
T ss_dssp             HSHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            3555667787775 46799999999999999999999999999999854

>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=80.78  E-value=1.4  Score=31.82  Aligned_cols=51  Identities=16%  Similarity=0.194  Sum_probs=40.8

Q ss_pred             ecHHHHHHHHhhcC-----CCCCCHHHHHHHhCC-CHHHHHHHHHHHHhcCccccCC
Q psy16234        444 MQTFQMAILLLFEK-----NDAMTCGDIQTVLSL-SQDQIGRHIASLVECKLLTSNK  494 (609)
Q Consensus       444 ~s~~Q~~iLllFn~-----~~~lt~~ei~~~t~i-~~~~l~~~L~~L~~~~iL~~~~  494 (609)
                      +|.-|.-||....+     +-+-|+.||++.+|+ +...+..+|..|.+.|.|.+.+
T Consensus         3 LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1           3 LTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCC
Confidence            34556666655442     456899999999999 6899999999999999998864