Citrus Sinensis ID: 009896

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------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---
MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF
cccHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHcccEEcccccccccccccEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccEEEEEHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccHHHHHHHcccccccHHHHHHHHHHcccEEEEEEEcccccccEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHccEEEEEcccccccccEEEEEEcHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEcccccccccccHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHcccccEcccccEEEEcHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
MLTEYGTKHAVHVITNHFGDLVAKVCECllrkgpltrqnvKRYTELSDEQVKNALLVLIQQNCVQaftteqpdgpkantQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAkssekegnlvdlDSLRETLVKLVTAHyvercpasepllmpiseeegparkkgsksakkigepetIEQQVVEAALPMEAMRFSVVTNvesdvgekeknsnnvtpgekrkhdvleldecgvadeqsVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAekkvktknsvplsLSSIYEEVIKSEAGRNMTLDHVRASLVQLGelsfvdassdsysiDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKsgrlletdkisdttfvekkdapKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKEllnlpadkrtgplqdryNRIRKVRILLESSQMKLDDAILLFHDF
mlteygtkHAVHVITNHFGDLVAKVCECLLRkgpltrqnvkRYTELSDEQVKNALLVLIQQNCVQAFTteqpdgpkANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFdrakssekegnlvdldsLRETLVKLVTAHYVercpasepllmpiseeegparkkgsksakkigepetIEQQVVEAALPMEAMRFSVVtnvesdvgekeknsnnvtpgekrkhdVLELDEcgvadeqsvvYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATssaekkvktknsvplslsSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIeiaqneevesvvskrygrdaYRIFRllsksgrlletdkisdttfvekkdapkiLYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKEllnlpadkrtgplqdrynrIRKVRIllessqmklddailLFHDF
MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF
****YGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMF***********LVDLDSLRETLVKLVTAHYVERCP******************************************************************************VLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAM**********************SIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLP*******LQDRYNRIRKVRILLESSQMKLDDAILLF***
***EYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFD***************SLRETLVKLVTAHYVERCPA****************************************************************************************EQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSF*DASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV**ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKEL******************IRKVRILLESSQMKLDDAILLFHDF
MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEE***************GEPETIEQQVVEAALPMEAMRFSVVTNVE******************RKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQA**************PLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF
*LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMP****E**********AKKIGEPETIEQQVVEAALPMEAMRFSVVTNV*********************************DEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF
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MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query523 2.2.26 [Sep-21-2011]
Q7ZUX1539 DNA-directed RNA polymera yes no 0.848 0.823 0.247 2e-28
Q2TBL4533 DNA-directed RNA polymera yes no 0.854 0.838 0.240 4e-27
Q9D483533 DNA-directed RNA polymera yes no 0.833 0.818 0.221 6e-25
Q9BUI4534 DNA-directed RNA polymera yes no 0.854 0.837 0.234 1e-24
Q5XIL3533 DNA-directed RNA polymera yes no 0.833 0.818 0.217 7e-22
Q55FJ5 666 DNA-directed RNA polymera yes no 0.342 0.268 0.268 2e-11
A3LQX9599 DNA-directed RNA polymera yes no 0.256 0.223 0.256 8e-06
Q9C106591 DNA-directed RNA polymera yes no 0.560 0.495 0.192 5e-05
A1C4R7635 DNA-directed RNA polymera N/A no 0.242 0.2 0.230 0.0006
A2QUS7627 DNA-directed RNA polymera yes no 0.242 0.202 0.223 0.0007
>sp|Q7ZUX1|RPC3_DANRE DNA-directed RNA polymerase III subunit RPC3 OS=Danio rerio GN=polr3c PE=2 SV=1 Back     alignment and function desciption
 Score =  127 bits (320), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 119/480 (24%), Positives = 213/480 (44%), Gaps = 36/480 (7%)

Query: 13  VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQN-CVQAFTTEQ 71
           ++  HFGD+V  V   L+R G LT + +   T+L+ + VK +L VL+Q   C        
Sbjct: 12  LLQEHFGDVVENVGTHLIRNGVLTLRALAHETKLALDLVKKSLCVLVQHGMCTFGPGRRG 71

Query: 72  PDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTL----KQM 127
           P GP    +Y +  ++ILH +R+ +++      +      +V+ +L+ G++T+    K +
Sbjct: 72  PAGP---VEYHINCEHILHMLRYPRYIYTAKSLYGDTGELIVEEILQRGQMTMSSTVKTV 128

Query: 128 FDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGPARKKGSKSA 187
            DR   +  EG  +D + +     +LV  H+++RCP      M  +E  G      +++ 
Sbjct: 129 ADRLTHNMPEGQSMDYNEVVSAFSRLVETHFLQRCPP-----MASAESSGTG---SAETP 180

Query: 188 KKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDE 247
             + +P   E       LP  ++         S+ GE ++ +      +K K D     E
Sbjct: 181 PAVTQPSNPESHPDCYKLPYISLSGHGKRRRSSEDGEADQRA-----AKKAKTDS---SE 232

Query: 248 CGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTK 307
           CG   ++ + ++ NFE F    R +  I  V   LD  +  ++  ML+  S         
Sbjct: 233 CG---DEGIHWQVNFERFHLHFRDQAIISAVSCKLDQTSGEIVRTMLR-MSEVTTSANAA 288

Query: 308 NSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDS----YSIDFEKII 363
            +  LS + I+  +  +       LD     LV    + FV  + DS    + ++  + +
Sbjct: 289 FTQALSANEIFRALPSNYNIARPILDQYLTLLVD-DPMEFVGKAGDSGGGMFVVNLHRAL 347

Query: 364 EIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKD 423
                  +ESVV +R+G  + RIFRLL +  R LE  ++ D   +  K+A ++LY L  +
Sbjct: 348 ANLARATLESVVQERFGSRSARIFRLLLRK-RHLEQKQVEDFAMIPAKEAKEMLYTLLSE 406

Query: 424 GYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELL 481
             + ++++  T   A    F L+ VN+    + +L   +    NL  R  YE    K LL
Sbjct: 407 NLVQLQEIPKTPDHAPSRTFYLYAVNQLPTARLLLQHCYKTVGNLIERRLYETKENKRLL 466
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.
Danio rerio (taxid: 7955)
>sp|Q2TBL4|RPC3_BOVIN DNA-directed RNA polymerase III subunit RPC3 OS=Bos taurus GN=POLR3C PE=2 SV=1 Back     alignment and function description
>sp|Q9D483|RPC3_MOUSE DNA-directed RNA polymerase III subunit RPC3 OS=Mus musculus GN=Polr3c PE=2 SV=1 Back     alignment and function description
>sp|Q9BUI4|RPC3_HUMAN DNA-directed RNA polymerase III subunit RPC3 OS=Homo sapiens GN=POLR3C PE=1 SV=1 Back     alignment and function description
>sp|Q5XIL3|RPC3_RAT DNA-directed RNA polymerase III subunit RPC3 OS=Rattus norvegicus GN=Polr3c PE=2 SV=1 Back     alignment and function description
>sp|Q55FJ5|RPC3_DICDI DNA-directed RNA polymerase III subunit rpc3 OS=Dictyostelium discoideum GN=polr3c PE=3 SV=1 Back     alignment and function description
>sp|A3LQX9|RPC3_PICST DNA-directed RNA polymerase III subunit RPC3 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=RPC82 PE=3 SV=1 Back     alignment and function description
>sp|Q9C106|RPC3_SCHPO DNA-directed RNA polymerase III subunit rpc3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc82 PE=1 SV=1 Back     alignment and function description
>sp|A1C4R7|RPC3_ASPCL DNA-directed RNA polymerase III subunit rpc3 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=rpc82 PE=3 SV=1 Back     alignment and function description
>sp|A2QUS7|RPC3_ASPNC DNA-directed RNA polymerase III subunit rpc3 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=rpc82 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query523
302143859524 unnamed protein product [Vitis vinifera] 0.992 0.990 0.645 0.0
359490507511 PREDICTED: DNA-directed RNA polymerase I 0.975 0.998 0.635 0.0
224134849519 predicted protein [Populus trichocarpa] 0.977 0.984 0.569 1e-164
255539431485 DNA-directed RNA polymerase III 62 kDa p 0.871 0.940 0.616 1e-163
449446151518 PREDICTED: DNA-directed RNA polymerase I 0.980 0.990 0.544 1e-157
449522480518 PREDICTED: DNA-directed RNA polymerase I 0.980 0.990 0.542 1e-156
356534135510 PREDICTED: DNA-directed RNA polymerase I 0.965 0.990 0.547 1e-154
356574495518 PREDICTED: DNA-directed RNA polymerase I 0.973 0.982 0.541 1e-153
297737009517 unnamed protein product [Vitis vinifera] 0.975 0.986 0.545 1e-151
297809071521 RNA polymerase III subunit RPC82 family 0.973 0.976 0.498 1e-141
>gi|302143859|emb|CBI22720.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/528 (64%), Positives = 426/528 (80%), Gaps = 9/528 (1%)

Query: 1   MLTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQ 60
           M T+YG + AVH+I++HFG+LVAKVC+CLLRKG LT  +V R+TEL  +QVK+ +LVLIQ
Sbjct: 1   MATQYGVQLAVHLISSHFGNLVAKVCDCLLRKGTLTLASVIRFTELPPQQVKSCILVLIQ 60

Query: 61  QNCVQAFTTEQPDG----PKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGL 116
            NCVQAF  +Q  G    P+  TQY+ LF NILHR+RFAKFL I+S+E D++C E+++GL
Sbjct: 61  HNCVQAFAIQQEVGFGEAPRVVTQYMALFHNILHRMRFAKFLAIVSEELDKECEEILEGL 120

Query: 117 LEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEE 176
           L+HGRLTL+Q+ DRAKS++ EG  V  D+LRE+ +KLV AH+VERCPASEP L P SEEE
Sbjct: 121 LQHGRLTLEQILDRAKSNQSEGEPVVQDALRESFLKLVRAHFVERCPASEPFLAPPSEEE 180

Query: 177 GPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGE 236
            PARK+G+KSAK + EP+TIEQ+ + AA PM+A RFSV+ N  +DV     +S NVT GE
Sbjct: 181 TPARKRGAKSAKLVEEPQTIEQRAIAAAAPMDAKRFSVIINTGTDV----DDSPNVTAGE 236

Query: 237 KRKHDVLELD-ECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQ 295
           KRK D LELD E G + E+ V++RANFE F+R LRHK CI +V+  LDDGAA VLSAML+
Sbjct: 237 KRKQDALELDKETGASCEKDVLWRANFEEFVRCLRHKACIANVKTRLDDGAAIVLSAMLE 296

Query: 296 ATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSY 355
           AT S EKKVKT+NSVPLS+ +I+E V+KSEAGR+MTL+ VR SL+QLG    V  +++SY
Sbjct: 297 ATRSEEKKVKTENSVPLSMDTIFEGVMKSEAGRSMTLERVRGSLIQLGCAPCVRGAAESY 356

Query: 356 SIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPK 415
           S+D + IIE+AQN+EVES+  KRYGRDAYRIFRLLSKS RLLETDKISDTTFVEKKD  K
Sbjct: 357 SVDLKNIIELAQNDEVESITLKRYGRDAYRIFRLLSKSCRLLETDKISDTTFVEKKDTAK 416

Query: 416 ILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELD 475
           ILY+LWKD YL MEKL + G+RQSQFLLWKV +  LW HVL+EM+H+ALNLSLRV+YEL+
Sbjct: 417 ILYQLWKDEYLQMEKLNLHGSRQSQFLLWKVTKDTLWGHVLNEMYHSALNLSLRVAYELE 476

Query: 476 REKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF 523
           +E+E++ LP +KR G L +R+ R+RKVRILLESS MKLDDAI+LF+DF
Sbjct: 477 QEQEIIQLPREKRVGALGNRFERLRKVRILLESSLMKLDDAIMLFNDF 524

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359490507|ref|XP_002267664.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC3 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224134849|ref|XP_002321920.1| predicted protein [Populus trichocarpa] gi|222868916|gb|EEF06047.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255539431|ref|XP_002510780.1| DNA-directed RNA polymerase III 62 kDa polypeptide, putative [Ricinus communis] gi|223549895|gb|EEF51382.1| DNA-directed RNA polymerase III 62 kDa polypeptide, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449446151|ref|XP_004140835.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449522480|ref|XP_004168254.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356534135|ref|XP_003535613.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Glycine max] Back     alignment and taxonomy information
>gi|356574495|ref|XP_003555382.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC3-like [Glycine max] Back     alignment and taxonomy information
>gi|297737009|emb|CBI26210.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297809071|ref|XP_002872419.1| RNA polymerase III subunit RPC82 family protein [Arabidopsis lyrata subsp. lyrata] gi|297318256|gb|EFH48678.1| RNA polymerase III subunit RPC82 family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query523
TAIR|locus:2101268523 AT3G49000 [Arabidopsis thalian 0.977 0.977 0.501 6.7e-136
UNIPROTKB|F1SDD7508 POLR3C "Uncharacterized protei 0.543 0.559 0.233 3.3e-27
UNIPROTKB|Q2TBL4533 POLR3C "DNA-directed RNA polym 0.483 0.474 0.245 1.6e-26
UNIPROTKB|Q9BUI4534 POLR3C "DNA-directed RNA polym 0.483 0.473 0.241 1.9e-26
UNIPROTKB|F1MUY3533 POLR3C "DNA-directed RNA polym 0.483 0.474 0.245 2.6e-26
UNIPROTKB|E2R8J4511 POLR3C "Uncharacterized protei 0.483 0.495 0.241 4.2e-25
UNIPROTKB|E2R8N8534 POLR3C "Uncharacterized protei 0.483 0.473 0.241 5.1e-25
MGI|MGI:1921664533 Polr3c "polymerase (RNA) III ( 0.483 0.474 0.227 3.3e-24
DICTYBASE|DDB_G0268080 666 rpc3 "RNA polymerase III subun 0.346 0.271 0.280 5e-24
UNIPROTKB|E9PHH9411 POLR3C "DNA-directed RNA polym 0.384 0.489 0.237 1.7e-23
TAIR|locus:2101268 AT3G49000 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1331 (473.6 bits), Expect = 6.7e-136, P = 6.7e-136
 Identities = 267/532 (50%), Positives = 379/532 (71%)

Query:     2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTE--LSDEQVKNALLVLI 59
             ++E+G  +A+H+IT  FG +V+KVCECLLRKGPL+ +++ R  E  ++  +VK+ L +LI
Sbjct:     3 MSEFGIVYAIHIITVQFGSVVSKVCECLLRKGPLSSRDISRLAESDINHNKVKDILYLLI 62

Query:    60 QQNCVQAFTTEQPDGP--KANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLL 117
             Q NCVQAF+ E PDG   KA  QY+VLF+NILHRVR+ KF  I+++E D +C  ++ GLL
Sbjct:    63 QHNCVQAFSIEPPDGSESKAIVQYIVLFNNILHRVRYNKFSRIVNEELDSKCGAVLDGLL 122

Query:   118 EHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEG 177
              +GRLTL Q  +R + S   GN +  +++R++L KLV A +VER P+ EP+L   ++E+ 
Sbjct:   123 SNGRLTLGQFIERDRDS---GNTIGSEAIRDSLQKLVAARFVERIPSPEPVLG--NKEKE 177

Query:   178 PARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEK 237
             PA+++G+K+AK + EPET+E+QVVEAA P++A+RF ++   +S+    + NSN +T G++
Sbjct:   178 PAKRRGAKAAKILKEPETLEEQVVEAATPVDAIRFPLIFEEDSNSSLADDNSN-ITEGKR 236

Query:   238 RKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQAT 297
             ++ DV   D         V++R NFE FI RLRHK C++ V+   D+G A VL AML+  
Sbjct:   237 KQRDVDTSDS-----SSGVIWRPNFEEFIHRLRHKACVEIVKERRDEGCAIVLRAMLEVG 291

Query:   298 SSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELS-----FVDASS 352
              S EKKVKT NS P+S+ SIYEEVIK+EAGR M  + V A L QL   S     FV+  +
Sbjct:   292 RSQEKKVKTDNSAPMSVGSIYEEVIKTEAGRTMLQERVEACLDQLSATSSYLPAFVNEVN 351

Query:   353 DSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKD 412
             DSY +D++ II +AQ +E+E+VV +RYG++A+R+FR LS+ GR +ETDKI+D    EKKD
Sbjct:   352 DSYIVDYKSIISVAQKDEIEAVVMRRYGKEAFRMFRYLSQEGRFVETDKIADAALTEKKD 411

Query:   413 APKILYKLWKDGYLLMEKLVVTG-ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVS 471
              P+ L K+WKDGYL M+KL VT     + FLLWKVN+ I+   +LDEM+HA+LNLSLR++
Sbjct:   412 TPQFLLKMWKDGYLHMQKLAVTAPGMYTPFLLWKVNKLIVTTQMLDEMYHASLNLSLRLA 471

Query:   472 YELDREKELLNLPADKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF 523
             +EL+ EKELL LP DK  GPL++R  +++  R+LL S+  KLDDAI+LFHDF
Sbjct:   472 HELEAEKELLLLPLDKLEGPLKERLKKVKAKRLLLSSTMFKLDDAIMLFHDF 523
GO:0003677 "DNA binding" evidence=IEA
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006351 "transcription, DNA-dependent" evidence=IEA
UNIPROTKB|F1SDD7 POLR3C "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q2TBL4 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9BUI4 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1MUY3 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R8J4 POLR3C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E2R8N8 POLR3C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1921664 Polr3c "polymerase (RNA) III (DNA directed) polypeptide C" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0268080 rpc3 "RNA polymerase III subunit" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|E9PHH9 POLR3C "DNA-directed RNA polymerase III subunit RPC3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00009152001
SubName- Full=Chromosome undetermined scaffold_222, whole genome shotgun sequence; (510 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00038611001
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (573 aa)
     •  0.899
GSVIVG00036953001
SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (417 aa)
     •  0.899
GSVIVG00034786001
SubName- Full=Chromosome chr5 scaffold_72, whole genome shotgun sequence; (471 aa)
     •  0.899
GSVIVG00034055001
RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (159 aa)
     •  0.899
26N20_30
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (493 aa)
     •  0.899
GSVIVG00028076001
SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)
     •  0.899
GSVIVG00025495001
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (475 aa)
     •  0.899
GSVIVG00024850001
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (491 aa)
     •  0.899
GSVIVG00023818001
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (569 aa)
     •  0.899
GSVIVG00021710001
RecName- Full=Pyruvate kinase; EC=2.7.1.40; (264 aa)
     •  0.899

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query523
pfam05645215 pfam05645, RNA_pol_Rpc82, RNA polymerase III subun 3e-15
pfam0822162 pfam08221, HTH_9, RNA polymerase III subunit RPC82 5e-14
>gnl|CDD|191331 pfam05645, RNA_pol_Rpc82, RNA polymerase III subunit RPC82 Back     alignment and domain information 
 Score = 74.4 bits (183), Expect = 3e-15
 Identities = 42/228 (18%), Positives = 79/228 (34%), Gaps = 24/228 (10%)

Query: 148 ETLVKLVTAHYVERCPASE--PLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAAL 205
              VKLV A ++ R P+    P+    ++      +   +S+         E +V     
Sbjct: 1   SIFVKLVEAGFLIRVPSPHFRPIGDLWNQLYEEHLRSTPRSSTTSEIKRRAEAKVKAKTE 60

Query: 206 PMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGF 265
             +      +          +   N   P  K++  +L+           +V+R N E F
Sbjct: 61  LRDLRESPEILLKGLGRSLADDTDN---PTGKKRTKILDPG---------LVWRVNLERF 108

Query: 266 IRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKN----SVPLSLSSIYEEV 321
            + LR +  +D  ++ +    A V  A L+ + S             S+  + + I    
Sbjct: 109 HKHLRDEALVDLAKSRIGSTTAEVYRAALRLSESRTPPCSAPLSEDPSITFTANDIARA- 167

Query: 322 IKSEAGRNMTLDHVRASLVQLGELSFVDASSDS----YSIDFEKIIEI 365
           +      +M LD     L     L F+     S    Y++DF ++IE 
Sbjct: 168 LPKSLDLSMLLDQHLKLLAS-SPLPFLRKIGPSGGGQYTVDFSRLIEQ 214

This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. Length = 215
>gnl|CDD|191971 pfam08221, HTH_9, RNA polymerase III subunit RPC82 helix-turn-helix domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 523
KOG2587551 consensus RNA polymerase III (C) subunit [Transcri 100.0
PF05645258 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; I 99.92
PF0822162 HTH_9: RNA polymerase III subunit RPC82 helix-turn 99.78
PF02002105 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024 99.48
TIGR00373158 conserved hypothetical protein TIGR00373. This fam 98.89
PRK06266178 transcription initiation factor E subunit alpha; V 98.82
COG1675176 TFA1 Transcription initiation factor IIE, alpha su 98.6
smart00531147 TFIIE Transcription initiation factor IIE. 98.35
PF02002105 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024 98.15
TIGR00373158 conserved hypothetical protein TIGR00373. This fam 97.44
PF0822162 HTH_9: RNA polymerase III subunit RPC82 helix-turn 97.22
KOG2587 551 consensus RNA polymerase III (C) subunit [Transcri 97.16
PRK06266178 transcription initiation factor E subunit alpha; V 96.83
PF0197868 TrmB: Sugar-specific transcriptional regulator Trm 95.73
smart0055068 Zalpha Z-DNA-binding domain in adenosine deaminase 95.65
PHA02943165 hypothetical protein; Provisional 95.61
KOG2593 436 consensus Transcription initiation factor IIE, alp 95.34
smart00531147 TFIIE Transcription initiation factor IIE. 95.31
PF1360180 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9 95.05
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 94.89
smart0055068 Zalpha Z-DNA-binding domain in adenosine deaminase 94.33
PHA02943165 hypothetical protein; Provisional 94.02
PF0470362 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A. 93.42
PF0197868 TrmB: Sugar-specific transcriptional regulator Trm 93.19
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 92.82
TIGR02702203 SufR_cyano iron-sulfur cluster biosynthesis transc 92.76
PF0933952 HTH_IclR: IclR helix-turn-helix domain; InterPro: 92.51
COG3355126 Predicted transcriptional regulator [Transcription 92.01
PF04337148 DUF480: Protein of unknown function, DUF480; Inter 91.37
COG3355126 Predicted transcriptional regulator [Transcription 91.34
PRK10141117 DNA-binding transcriptional repressor ArsR; Provis 91.18
PF0933952 HTH_IclR: IclR helix-turn-helix domain; InterPro: 91.06
COG1675176 TFA1 Transcription initiation factor IIE, alpha su 90.99
smart0041866 HTH_ARSR helix_turn_helix, Arsenical Resistance Op 90.87
COG5647773 Cullin, a subunit of E3 ubiquitin ligase [Posttran 90.45
KOG2593436 consensus Transcription initiation factor IIE, alp 90.34
PF0901269 FeoC: FeoC like transcriptional regulator; InterPr 89.65
PF1077165 DUF2582: Protein of unknown function (DUF2582); In 89.48
smart0042053 HTH_DEOR helix_turn_helix, Deoxyribose operon repr 89.34
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 89.28
cd0009078 HTH_ARSR Arsenical Resistance Operon Repressor and 89.04
PF05645258 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; I 88.88
smart00347101 HTH_MARR helix_turn_helix multiple antibiotic resi 88.74
PF03965115 Penicillinase_R: Penicillinase repressor; InterPro 88.33
PRK11239215 hypothetical protein; Provisional 88.0
COG2345218 Predicted transcriptional regulator [Transcription 87.97
COG1378247 Predicted transcriptional regulators [Transcriptio 87.62
PF1284061 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_ 87.48
smart00344108 HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto 87.46
COG1510177 Predicted transcriptional regulators [Transcriptio 87.4
TIGR02698130 CopY_TcrY copper transport repressor, CopY/TcrY fa 86.95
PF1494777 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_ 86.72
smart0034691 HTH_ICLR helix_turn_helix isocitrate lyase regulat 86.66
PF1284061 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_ 86.49
PF03962188 Mnd1: Mnd1 family; InterPro: IPR005647 This family 86.45
PF0822057 HTH_DeoR: DeoR-like helix-turn-helix domain; Inter 86.26
COG3388101 Predicted transcriptional regulator [Transcription 85.61
COG3132215 Uncharacterized protein conserved in bacteria [Fun 85.13
PRK00135188 scpB segregation and condensation protein B; Revie 85.04
smart00344108 HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto 84.43
PF06163127 DUF977: Bacterial protein of unknown function (DUF 83.94
PRK00135188 scpB segregation and condensation protein B; Revie 83.83
PF1280262 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP 82.51
PF0208283 Rrf2: Transcriptional regulator; InterPro: IPR0009 82.45
PF0104759 MarR: MarR family; InterPro: IPR000835 The MarR-ty 82.4
PF1055768 Cullin_Nedd8: Cullin protein neddylation domain; I 82.35
PF09824160 ArsR: ArsR transcriptional regulator; InterPro: IP 82.25
PF0470362 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A. 81.71
PF0163890 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002 81.58
TIGR02702203 SufR_cyano iron-sulfur cluster biosynthesis transc 81.55
PHA02701183 ORF020 dsRNA-binding PKR inhibitor; Provisional 80.99
COG2345218 Predicted transcriptional regulator [Transcription 80.94
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 80.01
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=3e-81  Score=631.37  Aligned_cols=500  Identities=26%  Similarity=0.413  Sum_probs=386.0

Q ss_pred             ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCc-HHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceE
Q 009896            2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLT-RQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQ   80 (523)
Q Consensus         2 ~~~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~lt-l~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~   80 (523)
                      ||+|+++||.+||++|||++|++|+.+|++.|++| ..-+...++++..+||.+|++|||||||.|+......  +..++
T Consensus         1 msq~eielc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~--g~vt~   78 (551)
T KOG2587|consen    1 MSQYEIELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNS--GKVTT   78 (551)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCCC--CceEE
Confidence            79999999999999999999999999999999999 7777888999999999999999999999988776433  35799


Q ss_pred             EEechhhHHHHhchhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhcccCCCccC-----HHHHHHHHHHHHh
Q 009896           81 YVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVD-----LDSLRETLVKLVT  155 (523)
Q Consensus        81 Y~~~~~~il~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~-----~~~i~~~f~~Lv~  155 (523)
                      |++.+++|+++||||+|+..++++||+.|+.|+++|+.+|++|++++++++.++.......+     ...+.+.|..++.
T Consensus        79 Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~~~~~~ss~~~ql~~lv~q~F~~~~~  158 (551)
T KOG2587|consen   79 YEAQCSEILHILRYPRYIYITKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRLTTTMESSKTMQLCALVSQTFVELAD  158 (551)
T ss_pred             EEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999999999887643322111     1335666666666


Q ss_pred             c---ccceecCCCCCCCCCCCCCCCcccccCCCCccccCCchhhhHHHHHHhCccchhhhhhhhcccccccccccCCCCC
Q 009896          156 A---HYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNV  232 (523)
Q Consensus       156 ~---~fi~~v~~~~~~~~p~~~~~~~~~~~g~~~~k~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  232 (523)
                      .   ||..++|.+.+.             .+.+.++.+.++-+........++..+...++.+....+++.    ..+..
T Consensus       159 ~~ekH~~~r~~e~~~~-------------~~~~a~~~~~e~~~~~~~~~q~lt~~pkis~~~~~~~~s~s~----~~d~~  221 (551)
T KOG2587|consen  159 PLEKHFVNRCPESVPT-------------VENSAAGPPPEAPTLVINEKQILTLVPKISLPGKGKRRSSSD----EDDRG  221 (551)
T ss_pred             chhhHhhccCCCcccc-------------cccccCCCCcccccchhhhccccccccccccCCCCCcccccc----ccccc
Confidence            6   666666532211             112222222222222222222223333333333221111111    11112


Q ss_pred             CCCCccccccccccccCcCCCCceEEEeehhhHHHHhchhHHHHHHHhhcCccHHHHHHHHHhccch-hcc-ccc---c-
Q 009896          233 TPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSS-AEK-KVK---T-  306 (523)
Q Consensus       233 ~~~~krk~~~~~~d~~~~~~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~-~~~-~~~---~-  306 (523)
                      .++.++|.-  ..|......+.+++||+|+++|+.++||++|+++|.+|.+++++.++++||..... -++ .+.   . 
T Consensus       222 ~~~~~~k~l--~~D~~~~~~d~ga~wr~N~~rf~~~lRd~~~v~~v~~r~~e~ts~v~~a~Lt~~tie~~r~~~~~l~~e  299 (551)
T KOG2587|consen  222 EKKAKRKKL--TTDNKTPDPDDGAYWRINLDRFHQHLRDQAIVSAVANRMDEGTSEVLRAMLTRMTIELTRHSPAPLDTE  299 (551)
T ss_pred             Ccccccccc--ccccCCCCCCCceeEehhhHHhhHHhhhHHHHHHHHhcccchhHHHHHHHHHhhhhhhccCCchhhhch
Confidence            233333321  01111223467899999999999999999999999999999999999999944321 111 110   0 


Q ss_pred             ------cCCcc------ccHHHHHHHhhh-----hccCCCCCHHHHHHHHHHhccCC------CCCCCCCeEEEehHHHH
Q 009896          307 ------KNSVP------LSLSSIYEEVIK-----SEAGRNMTLDHVRASLVQLGELS------FVDASSDSYSIDFEKII  363 (523)
Q Consensus       307 ------~~s~~------~s~~~I~~~l~~-----~~~~~~~~~~~i~~~L~~La~~~------~~~~~~~~y~V~~~~i~  363 (523)
                            ..|.+      .+...+-+.+..     ++++.+...+.+..|+..|++++      +++.|||+|.|||++++
T Consensus       300 ~si~~~~~s~n~~s~~~~~~esl~~~~~l~Er~~~ee~~nl~~~~~~~ac~~l~d~slk~l~klges~~G~yiV~y~k~i  379 (551)
T KOG2587|consen  300 LSINEIFRSLNVGSNGSISMESLDQYLTLLERGDTEEEENLDADTEDPACASLADDSLKFLGKLGESGGGMYIVNYHKAI  379 (551)
T ss_pred             hhhhhhccCcccccchHHHHHhhhhHHHHHhhccchhhccccccchhhHHHHhhcchHHHHHHhccCCCCEEEEEHHHHH
Confidence                  01111      111111111111     12344556677889999999888      77999999999999999


Q ss_pred             HHHHHHHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCceEE
Q 009896          364 EIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQF  441 (523)
Q Consensus       364 ~~lr~~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~--~~~~t~  441 (523)
                      ..++...+|++|.++||..|.|+||+|..+|++ |||||++.|||+.||+|..||+|+++||+++||||||+  +|+|||
T Consensus       380 ~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~v-eekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~psrtF  458 (551)
T KOG2587|consen  380 AVLATATYESVIQERFGSRAIRLFRLLLQKKHV-EEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAPSRTF  458 (551)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-hHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCCcceE
Confidence            999999999999999999999999999999866 99999999999999999999999999999999999998  999999


Q ss_pred             EEEEEchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccCCC-----------hhhHHHHHHHHHHHHHHHHHH
Q 009896          442 LLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRT-----------GPLQDRYNRIRKVRILLESSQ  510 (523)
Q Consensus       442 ~lw~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~ll~k~~~~~~-----------~~e~~~l~~~~~~~~~L~~~~  510 (523)
                      |||+||+..+++++++++||++.||+.|++||+.+++.||+|.++.+.           +.+..+++++...+..++...
T Consensus       459 ~L~~v~~~~a~~~lld~ly~~iaNL~~R~~~eraEn~~LL~Ka~rve~~Ik~~e~~~~k~~qlael~~~~~~ql~lf~r~  538 (551)
T KOG2587|consen  459 YLYTVNILRAYRMLLDELYKSIANLIERLRHERAENKRLLEKAQRVEAIIKGREATGAKEAQLAELEEMYTAQLNLFKRA  538 (551)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHhhhhhHHhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999765551           778888899999999999999


Q ss_pred             hhhhhhhhcccCC
Q 009896          511 MKLDDAILLFHDF  523 (523)
Q Consensus       511 ~rlD~~l~ll~d~  523 (523)
                      .|+|+++++|++|
T Consensus       539 s~l~~~~~vf~~~  551 (551)
T KOG2587|consen  539 SQLDETILVFESY  551 (551)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999999987

>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors Back     alignment and domain information
>TIGR00373 conserved hypothetical protein TIGR00373 Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription] Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors Back     alignment and domain information
>TIGR00373 conserved hypothetical protein TIGR00373 Back     alignment and domain information
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2 Back     alignment and domain information
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription] Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>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 Back     alignment and domain information
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases Back     alignment and domain information
>PHA02943 hypothetical protein; Provisional Back     alignment and domain information
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription] Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A Back     alignment and domain information
>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 Back     alignment and domain information
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases Back     alignment and domain information
>PHA02943 hypothetical protein; Provisional Back     alignment and domain information
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR Back     alignment and domain information
>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 Back     alignment and domain information
>COG3355 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function Back     alignment and domain information
>COG3355 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription] Back     alignment and domain information
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor Back     alignment and domain information
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription] Back     alignment and domain information
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif Back     alignment and domain information
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea Back     alignment and domain information
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor Back     alignment and domain information
>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 Back     alignment and domain information
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors Back     alignment and domain information
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2 Back     alignment and domain information
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein Back     alignment and domain information
>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 Back     alignment and domain information
>PRK11239 hypothetical protein; Provisional Back     alignment and domain information
>COG2345 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG1378 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>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 Back     alignment and domain information
>smart00344 HTH_ASNC helix_turn_helix ASNC type Back     alignment and domain information
>COG1510 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family Back     alignment and domain information
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A Back     alignment and domain information
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation Back     alignment and domain information
>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 Back     alignment and domain information
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast) Back     alignment and domain information
>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 Back     alignment and domain information
>COG3388 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK00135 scpB segregation and condensation protein B; Reviewed Back     alignment and domain information
>smart00344 HTH_ASNC helix_turn_helix ASNC type Back     alignment and domain information
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function Back     alignment and domain information
>PRK00135 scpB segregation and condensation protein B; Reviewed Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family Back     alignment and domain information
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A Back     alignment and domain information
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure Back     alignment and domain information
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR Back     alignment and domain information
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional Back     alignment and domain information
>COG2345 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>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 Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query523
2xub_A534 Human Rpc62 Subunit Structure Length = 534 1e-25
>pdb|2XUB|A Chain A, Human Rpc62 Subunit Structure Length = 534 Back     alignment and structure 
Iteration: 1

 Score =  114 bits (286), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 116/494 (23%), Positives = 223/494 (45%), Gaps = 47/494 (9%)
Query: 2   LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQ 61
           +T+   K    ++  HFG++V K+   L+R G    + +   T  S +QVK AL VL+Q 
Sbjct: 1   MTQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQH 60
Query: 62  NCVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGR 121
           N V ++   +    +   +Y      +L  +R+ +++      +      +V+ LL +G+
Sbjct: 61  NLV-SYQVHK----RGVVEYEAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLLNGK 115
Query: 122 LTL----KQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEG 177
           LT+    K++ DR   + ++G  +D   +  T V+L   H+V+RCP+     +P +E   
Sbjct: 116 LTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQRCPS-----VPTTENSD 170
Query: 178 PARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGE- 236
           P     + +   I E +          +P    + S++       G++ ++S+    GE 
Sbjct: 171 PGPPPPAPTL-VINEKDMY-------LVP----KLSLIGK-----GKRRRSSDEDAAGEP 213
Query: 237 KRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQA 296
           K K      D      +  + ++AN + F +  R +  +  V   +D  ++ ++  ML+ 
Sbjct: 214 KAKRPKYTTDNKEPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRTMLRM 273
Query: 297 TSSAEKKVKTKNSVPLSLSSIYEEVIKS-EAGRNMTLDHVRASLVQLGE--LSFVDASSD 353
           +     ++ T +S P +      E+ +S   G N++   +   L  L +  L FV  S D
Sbjct: 274 S-----EITTSSSAPFTQPLSSNEIFRSLPVGYNISKQVLDQYLTLLADDPLEFVGKSGD 328
Query: 354 S----YSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVE 409
           S    Y I+  K +       +ESVV +R+G    RIFRL+ +  + +E  ++ D   + 
Sbjct: 329 SGGGMYVINLHKALASLATATLESVVQERFGSRCARIFRLVLQK-KHIEQKQVEDFAMIP 387
Query: 410 KKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAALNLS 467
            K+A  +LYK+  + ++ ++++  T   A    F L+ VN     + +L   + +  NL 
Sbjct: 388 AKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSIANLI 447
Query: 468 LRVSYELDREKELL 481
            R  +E    K LL
Sbjct: 448 ERRQFETKENKRLL 461

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query523
2xub_A534 DNA-directed RNA polymerase III subunit RPC3; tran 5e-93
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
1q1h_A110 TFE, transcription factor E, TFE; TFIIE, transcrip 2e-05
>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S Length = 534 Back     alignment and structure
 Score =  292 bits (749), Expect = 5e-93
 Identities = 113/556 (20%), Positives = 219/556 (39%), Gaps = 66/556 (11%)

Query: 3   TEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQN 62
           T+   K    ++  HFG++V K+   L+R G    + +   T  S +QVK AL VL+Q N
Sbjct: 2   TQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHN 61

Query: 63  CVQAFTTEQPDGPKANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRL 122
            V           +   +Y      +L  +R+ +++      +      +V+ LL +G+L
Sbjct: 62  LVSYQVH-----KRGVVEYEAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLLNGKL 116

Query: 123 T----LKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPASEPLLMPISEEEGP 178
           T    +K++ DR   + ++G  +D   +  T V+L   H+V+RCP+             P
Sbjct: 117 TMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQRCPSVPTTENSDPGPPPP 176

Query: 179 ARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKNSNNVTPGEKR 238
           A             P+                      ++      +  +  +     K 
Sbjct: 177 APTLVINEKDMYLVPK---------------------LSLIGKGKRRRSSDEDAAGEPKA 215

Query: 239 KHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATS 298
           K      D      +  + ++AN + F +  R +  +  V   +D  ++ ++  ML+ + 
Sbjct: 216 KRPKYTTDNKEPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRTMLRMSE 275

Query: 299 SAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGE--LSFVDASSDS-- 354
                     + PLS + I+  +     G N++   +   L  L +  L FV  S DS  
Sbjct: 276 ITTSSSAPF-TQPLSSNEIFRSL---PVGYNISKQVLDQYLTLLADDPLEFVGKSGDSGG 331

Query: 355 --YSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKD 412
             Y I+  K +       +ESVV +R+G    RIFRL+ +    +E  ++ D   +  K+
Sbjct: 332 GMYVINLHKALASLATATLESVVQERFGSRCARIFRLVLQKK-HIEQKQVEDFAMIPAKE 390

Query: 413 APKILYKLWKDGYLLMEKLVVTGAR--QSQFLLWKVNRQILWKHVLDEMFHAALNLSLRV 470
           A  +LYK+  + ++ ++++  T        F L+ VN     + +L   + +  NL  R 
Sbjct: 391 AKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSIANLIERR 450

Query: 471 SYELDREKELLNL-----------------------PADKRTGPLQDRYNRIRKVRILLE 507
            +E    K LL                           +  T P + +   +++    L+
Sbjct: 451 QFETKENKRLLEKSQRVEAIIASMQATGAEEAQLQEIEEMITAPERQQLETLKRNVNKLD 510

Query: 508 SSQMKLDDAILLFHDF 523
           +S++++D+ I L   +
Sbjct: 511 ASEIQVDETIFLLESY 526
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Length = 110 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query523
2xub_A534 DNA-directed RNA polymerase III subunit RPC3; tran 100.0
2xub_A534 DNA-directed RNA polymerase III subunit RPC3; tran 99.22
1q1h_A110 TFE, transcription factor E, TFE; TFIIE, transcrip 98.19
1q1h_A110 TFE, transcription factor E, TFE; TFIIE, transcrip 96.66
2qlz_A232 Transcription factor PF0095; 2.50A {Pyrococcus fur 96.23
1xmk_A79 Double-stranded RNA-specific adenosine deaminase; 95.16
2oqg_A114 Possible transcriptional regulator, ARSR family P; 94.92
1r1u_A106 CZRA, repressor protein; zinc, DNA binding, transc 94.79
3pqk_A102 Biofilm growth-associated repressor; helix-turn-he 94.19
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 93.91
3jth_A98 Transcription activator HLYU; transcription factor 93.67
3r0a_A123 Putative transcriptional regulator; structural gen 93.59
2d1h_A109 ST1889, 109AA long hypothetical transcriptional re 93.46
1qbj_A81 Protein (double-stranded RNA specific adenosine D 93.4
3cuo_A99 Uncharacterized HTH-type transcriptional regulato; 93.14
3r0a_A123 Putative transcriptional regulator; structural gen 93.1
2nr3_A183 Hypothetical protein; APC84902, conserved domain, 93.0
1u2w_A122 CADC repressor, cadmium efflux system accessory pr 92.8
2kko_A108 Possible transcriptional regulatory protein (possi 92.72
1ku9_A152 Hypothetical protein MJ223; putative transcription 92.72
1oyi_A82 Double-stranded RNA-binding protein; (alpha+beta) 92.52
2vxz_A165 Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py 91.98
1sfx_A109 Conserved hypothetical protein AF2008; structural 91.87
1ldj_A760 Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc 91.85
1qgp_A77 Protein (double stranded RNA adenosine deaminase); 91.84
1sfx_A109 Conserved hypothetical protein AF2008; structural 91.71
3bz6_A183 UPF0502 protein pspto_2686; APC84902, conserved do 91.59
2jsc_A118 Transcriptional regulator RV1994C/MT2050; cadmium, 91.52
1qgp_A77 Protein (double stranded RNA adenosine deaminase); 91.5
1r1t_A122 Transcriptional repressor SMTB; zinc, transcriptio 91.43
2lkp_A119 Transcriptional regulator, ARSR family; symmetric 91.32
3bdd_A142 Regulatory protein MARR; putative multiple antibio 91.2
2zkz_A99 Transcriptional repressor PAGR; protein-DNA, HTH m 91.1
1ub9_A100 Hypothetical protein PH1061; helix-turn-helix moti 90.96
1xmk_A79 Double-stranded RNA-specific adenosine deaminase; 90.81
3eyi_A72 Z-DNA-binding protein 1; alternative splicing, DNA 90.8
3f6o_A118 Probable transcriptional regulator, ARSR family pr 90.41
2fu4_A83 Ferric uptake regulation protein; DNA binding doma 90.02
2lnb_A80 Z-DNA-binding protein 1; structural genomics, nort 89.9
3boq_A160 Transcriptional regulator, MARR family; MARR famil 89.81
2l02_A82 Uncharacterized protein; structural genomics, nort 88.87
1sfu_A75 34L protein; protein/Z-DNA complex, DNA binding pr 88.82
1t6s_A162 Conserved hypothetical protein; A winged helix-tur 88.77
1oyi_A82 Double-stranded RNA-binding protein; (alpha+beta) 88.51
3f6v_A151 Possible transcriptional regulator, ARSR family pr 88.32
3tgn_A146 ADC operon repressor ADCR; helix-turn-helix, trans 88.12
2p4w_A202 Transcriptional regulatory protein ARSR family; ar 87.71
1z7u_A112 Hypothetical protein EF0647; winged-helix-turn-hel 87.67
2hr3_A147 Probable transcriptional regulator; MCSG, structur 87.53
1ku9_A152 Hypothetical protein MJ223; putative transcription 87.48
2d1h_A109 ST1889, 109AA long hypothetical transcriptional re 87.37
3lmm_A583 Uncharacterized protein; multi-domained alpha-beta 87.18
1xn7_A78 Hypothetical protein YHGG; alpha+beta, GFT structu 87.16
2xvc_A59 ESCRT-III, SSO0910; cell cycle, cell division, cyt 86.9
2l01_A77 Uncharacterized protein; structural genomics, nort 86.87
1qbj_A81 Protein (double-stranded RNA specific adenosine D 86.82
3bpv_A138 Transcriptional regulator; MARR, DNA binding, tran 86.81
2pex_A153 Transcriptional regulator OHRR; transcription regu 86.73
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 86.6
1y0u_A96 Arsenical resistance operon repressor, putative; s 86.39
2hzt_A107 Putative HTH-type transcriptional regulator YTCD; 86.07
1s3j_A155 YUSO protein; structural genomics, MARR transcript 86.04
3bj6_A152 Transcriptional regulator, MARR family; helix-turn 86.02
2oqg_A114 Possible transcriptional regulator, ARSR family P; 86.01
2nnn_A140 Probable transcriptional regulator; structural gen 85.83
1p4x_A250 Staphylococcal accessory regulator A homologue; wi 85.82
2cg4_A152 Regulatory protein ASNC; DNA binding, FFRP, LRP fa 85.75
2qww_A154 Transcriptional regulator, MARR family; YP_013417. 85.75
2eth_A154 Transcriptional regulator, putative, MAR family; M 85.57
2bv6_A142 MGRA, HTH-type transcriptional regulator MGRA; mul 85.4
1lj9_A144 Transcriptional regulator SLYA; HTH DNA binding pr 85.39
2l02_A82 Uncharacterized protein; structural genomics, nort 85.34
2fbh_A146 Transcriptional regulator PA3341; MARR, transcript 85.32
3bro_A141 Transcriptional regulator; helix_TURN_helix, multi 85.31
2a61_A145 Transcriptional regulator TM0710; APC4350, MCSG, m 85.31
2k02_A87 Ferrous iron transport protein C; FEOC, iron-sulfu 85.28
3bja_A139 Transcriptional regulator, MARR family, putative; 85.24
2fbi_A142 Probable transcriptional regulator; MARR, APC5816, 84.97
1z6r_A406 MLC protein; transcriptional repressor, ROK family 84.94
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 84.91
2fa5_A162 Transcriptional regulator MARR/EMRR family; multip 84.88
3bja_A139 Transcriptional regulator, MARR family, putative; 84.86
3bpv_A138 Transcriptional regulator; MARR, DNA binding, tran 84.84
2cfx_A144 HTH-type transcriptional regulator LRPC; transcrip 84.71
2bv6_A142 MGRA, HTH-type transcriptional regulator MGRA; mul 84.4
1yyv_A131 Putative transcriptional regulator; reductive meth 84.39
2fbi_A142 Probable transcriptional regulator; MARR, APC5816, 84.38
1jgs_A138 Multiple antibiotic resistance protein MARR; trans 84.34
2hoe_A380 N-acetylglucosamine kinase; TM1224, structural gen 84.21
3k0l_A162 Repressor protein; helix-turn-helix, structural ge 84.18
2rdp_A150 Putative transcriptional regulator MARR; PFAM PF01 84.17
3cjn_A162 Transcriptional regulator, MARR family; silicibact 84.15
2gxg_A146 146AA long hypothetical transcriptional regulator; 84.09
1sd4_A126 Penicillinase repressor; BLAI, MECI, methicillin, 84.01
3b73_A111 PHIH1 repressor-like protein; winged-helix-turn-he 83.88
3s2w_A159 Transcriptional regulator, MARR family; structural 83.79
2a61_A145 Transcriptional regulator TM0710; APC4350, MCSG, m 83.75
3eco_A139 MEPR; mutlidrug efflux pump regulator winged helix 83.59
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 83.56
2hye_C759 Cullin-4A, CUL-4A; beta propeller, ring finger, zi 83.5
2vxz_A165 Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py 83.24
2nnn_A140 Probable transcriptional regulator; structural gen 83.1
3dpl_C382 Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int 83.08
1ub9_A100 Hypothetical protein PH1061; helix-turn-helix moti 83.07
3nrv_A148 Putative transcriptional regulator (MARR/EMRR FAM; 82.71
2dk5_A91 DNA-directed RNA polymerase III 39 kDa polypeptide 82.62
3g3z_A145 NMB1585, transcriptional regulator, MARR family; t 82.52
3eco_A139 MEPR; mutlidrug efflux pump regulator winged helix 82.44
3oop_A143 LIN2960 protein; protein structure initiative, PSI 82.4
2ia0_A171 Putative HTH-type transcriptional regulator PF086; 81.91
1okr_A123 MECI, methicillin resistance regulatory protein ME 81.72
2l01_A77 Uncharacterized protein; structural genomics, nort 81.68
1xn7_A78 Hypothetical protein YHGG; alpha+beta, GFT structu 81.59
3bro_A141 Transcriptional regulator; helix_TURN_helix, multi 81.51
2nyx_A168 Probable transcriptional regulatory protein, RV14; 81.38
3cdh_A155 Transcriptional regulator, MARR family; helix-turn 81.3
2fsw_A107 PG_0823 protein; alpha-beta structure, helix-turn- 81.16
2p5v_A162 Transcriptional regulator, LRP/ASNC family; NMB057 81.15
3e6m_A161 MARR family transcriptional regulator; APC88769, s 81.1
3bj6_A152 Transcriptional regulator, MARR family; helix-turn 81.04
3ech_A142 MEXR, multidrug resistance operon repressor; winge 80.92
2h09_A155 Transcriptional regulator MNTR; transcription regu 80.73
4a5n_A131 Uncharacterized HTH-type transcriptional regulato; 80.68
1z91_A147 Organic hydroperoxide resistance transcriptional; 80.61
1s3j_A155 YUSO protein; structural genomics, MARR transcript 80.56
3ech_A142 MEXR, multidrug resistance operon repressor; winge 80.46
2jt1_A77 PEFI protein; solution structure, winged helix-tur 80.31
3s2w_A159 Transcriptional regulator, MARR family; structural 80.26
1z05_A429 Transcriptional regulator, ROK family; structural 80.25
3hsr_A140 HTH-type transcriptional regulator SARZ; helix-tur 80.13
1lj9_A144 Transcriptional regulator SLYA; HTH DNA binding pr 80.06
>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S Back     alignment and structure
Probab=100.00  E-value=8.1e-92  Score=759.74  Aligned_cols=489  Identities=21%  Similarity=0.376  Sum_probs=376.8

Q ss_pred             ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHhhcCCCHHHHHHHHHHHHhhcccccccccCCCCCCcceEE
Q 009896            2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGPKANTQY   81 (523)
Q Consensus         2 ~~~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~l~~~t~l~~~~vr~aL~vLiQhn~V~~~~~~~~~~~~~~~~Y   81 (523)
                      ||+++++||++||+++||++|++||++|+++|++||++|++.|++++++||+||++|||||||.|+..+.     ..++|
T Consensus         1 Ms~~~~~L~~~li~~~FG~~~~~V~~~Ll~~G~ltL~~I~~~t~L~~~~Vk~~L~vLIQh~lV~~~~~~~-----~~~~Y   75 (534)
T 2xub_A            1 MTQAEIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHNLVSYQVHKR-----GVVEY   75 (534)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT-----TEEEE
T ss_pred             CCHHHHHHHHHHHHHhcChHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhcCCeeEEeCCC-----CcEEE
Confidence            7899999999999999999999999999999999999999999999999999999999999999665532     25899


Q ss_pred             EechhhHHHHhchhhHHHHHHHHhhHHHHHHHHHHHHcCcCCHHHHHHHhhhccc----CCCccCHHHHHHHHHHHHhcc
Q 009896           82 VVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEK----EGNLVDLDSLRETLVKLVTAH  157 (523)
Q Consensus        82 ~~~~~~il~rlR~p~~i~~i~~~~G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~----~~~~~~~~~i~~~f~~Lv~~~  157 (523)
                      ++|+++||+|+|||+||.+|+++||++|+.|+++||.+|++|+++++..+.++.+    +++..+...++++|.+|+++|
T Consensus        76 ~~~~~~il~~lR~pk~l~~i~~~~G~~a~~I~~~ll~~G~~t~~~ll~~~~~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~  155 (534)
T 2xub_A           76 EAQCSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLLNGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTH  155 (534)
T ss_dssp             EECHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCBCHHHHHHHHHHHHHHTSSSSCCCCHHHHHHHHHHHHHTT
T ss_pred             EEChhhHHHHHhhHHHHHHHHHHhcHHHHHHHHHHHHcCCccHHHHHHHHHhhcccccccccccCHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999999999999876532    222347889999999999999


Q ss_pred             cceecCCCCCCCCCCCCCCCcccccCCCCccccCCchhhhHHHHHHhCccchhhhhhhh-ccccccccccc-CCCCCCCC
Q 009896          158 YVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVT-NVESDVGEKEK-NSNNVTPG  235 (523)
Q Consensus       158 fi~~v~~~~~~~~p~~~~~~~~~~~g~~~~k~~~~~~~~~~~~~~~~~~~~~~r~~~~~-~~~~~~~~~~~-~~~~~~~~  235 (523)
                      ||+|||+..+..+  +++..   ..|.+.   +..              .+.+.|..|. +.....+++.+ .+..+.++
T Consensus       156 fI~rv~~~~~~~~--~~~~~---~~~~~~---~~~--------------~~~~~~~~p~~~~~~~~k~~~~~~~~~~~~~  213 (534)
T 2xub_A          156 FVQRCPSVPTTEN--SDPGP---PPPAPT---LVI--------------NEKDMYLVPKLSLIGKGKRRRSSDEDAAGEP  213 (534)
T ss_dssp             SEEECCCC------------------------------------------------------------------------
T ss_pred             CEEeCCCCCcccc--ccccc---ccCCch---hhh--------------cchhhhccchhhhHHHhhhccccCCcccccc
Confidence            9999986432111  11100   011110   000              0001111111 00000111110 11111233


Q ss_pred             CccccccccccccCcCCCCceEEEeehhhHHHHhchhHHHHHHHhhcCccHHHHHHHHHhccchhcccccccCCccccHH
Q 009896          236 EKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLS  315 (523)
Q Consensus       236 ~krk~~~~~~d~~~~~~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~~s~~~s~~  315 (523)
                      +|++.+..++|+ +...+++++|||||++|+++||++.|+++|++|+|..||.||++||++.+..+ ++|.+.|.|++++
T Consensus       214 ~~k~~~~~~~~~-~~~~d~~~~wrvN~erf~~~lR~~~lv~~v~~r~~~~a~~V~~~lL~~~e~~~-~~~~~~s~~is~~  291 (534)
T 2xub_A          214 KAKRPKYTTDNK-EPIPDDGIYWQANLDRFHQHFRDQAIVSAVANRMDQTSSEIVRTMLRMSEITT-SSSAPFTQPLSSN  291 (534)
T ss_dssp             ------------------CTTSEEECHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTS-CTTCSBCCCEEHH
T ss_pred             ccccccCCCccc-cccCCCCceEEeeHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhhccC-CccccCCCcccHH
Confidence            444433222221 23457889999999999999999999999999999999999999999988766 5677889999999


Q ss_pred             HHHHHhhhhccCCCCCHHHHHHHHHHhccCC------CCCCCCCeEEEehHHHHHHHHHHHHHHHHHHHcCCchHHHHHH
Q 009896          316 SIYEEVIKSEAGRNMTLDHVRASLVQLGELS------FVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRL  389 (523)
Q Consensus       316 ~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~------~~~~~~~~y~V~~~~i~~~lr~~~le~~v~~~~G~~a~RI~r~  389 (523)
                      +|.+.++   .+.+++.+.+.+||.+|++++      ++++|+|+|+|||+++++.||+.+++++|.++||..|+||||+
T Consensus       292 ~I~~~l~---~~~~l~~~~l~~~L~lL~~~~~~fv~~~g~~g~g~y~V~~~~~~~~lr~~~ie~ii~~~~G~~a~RI~r~  368 (534)
T 2xub_A          292 EIFRSLP---VGYNISKQVLDQYLTLLADDPLEFVGKSGDSGGGMYVINLHKALASLATATLESVVQERFGSRCARIFRL  368 (534)
T ss_dssp             HHHHTSC---TTCCCCHHHHHHHHHHHHSCTTCCEEECCCCSSCEEEEBHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHHHcC---CcccccHHHHHHHHHHHhCCcHHhhhccccCCCceEEEeHHHHHHHHHHHHHHHHHHHHhChHHHHHHHH
Confidence            9999994   357788999999999999998      3467899999999999999999999999999999999999999


Q ss_pred             HHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCceEEEEEEEchHHHHHHHHHHHHHHHHHHH
Q 009896          390 LSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFHAALNLS  467 (523)
Q Consensus       390 L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~--~~~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~  467 (523)
                      |+.+|++ ||++|++.+|||.|++|++||+|+++|||++||+||++  +|+|+||||++|.+++..++++++||++.||+
T Consensus       369 L~~~~~l-~d~~ia~~a~i~~k~vR~~Ly~L~~~g~v~~qevp~~~d~~~~~~~ylW~~~~~~~~~~l~~~~~k~l~nl~  447 (534)
T 2xub_A          369 VLQKKHI-EQKQVEDFAMIPAKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTVNILSAARMLLHRCYKSIANLI  447 (534)
T ss_dssp             HHHC----CHHHHHHHHCSCHHHHHHHHHHHHHTTCC---------------------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEccCCCCCCCcceEEEEEEcHHHHHHHHHHHHHHHHHHHH
Confidence            9999998 99999999999999999999999999999999999986  89999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhhhccccc-----------------------cCCChhhHHHHHHHHHHHHHHHHHHhhhhhhhhcccCC
Q 009896          468 LRVSYELDREKELLNLPA-----------------------DKRTGPLQDRYNRIRKVRILLESSQMKLDDAILLFHDF  523 (523)
Q Consensus       468 ~R~~~e~~~~k~ll~k~~-----------------------~~~~~~e~~~l~~~~~~~~~L~~~~~rlD~~l~ll~d~  523 (523)
                      +|+++|+++++.||+|.+                       ++.+|+|+++|++|++++++|+++++|||++||+|+||
T Consensus       448 ~Rl~~E~~~~~~lL~k~eR~d~~~~~vk~~~~~~~~~~e~~e~lt~~e~~~l~~~~~~~~~L~~~~~~lD~~i~vl~dy  526 (534)
T 2xub_A          448 ERRQFETKENKRLLEKSQRVEAIIASMQATGAEEAQLQEIEEMITAPERQQLETLKRNVNKLDASEIQVDETIFLLESY  526 (534)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHHHHCCC--------CHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHhhhhHHHHhhccccchhhhHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHH
Confidence            999999999999999943                       35679999999999999999999999999999999997
>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S Back     alignment and structure
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Back     alignment and structure
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Back     alignment and structure
>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A Back     alignment and structure
>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 Back     alignment and structure
>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus} Back     alignment and structure
>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12} Back     alignment and structure
>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei} Back     alignment and structure
>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 Back     alignment and structure
>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A Back     alignment and structure
>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36 Back     alignment and structure
>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19 Back     alignment and structure
>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3bz6_A UPF0502 protein pspto_2686; APC84902, conserved domain, pseudomonas syringae PV. tomato DC3000, structural genomics, PSI-2; 2.21A {Pseudomonas syringae PV} SCOP: a.4.5.75 a.4.5.75 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis} Back     alignment and structure
>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis} Back     alignment and structure
>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis} Back     alignment and structure
>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28 Back     alignment and structure
>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 Back     alignment and structure
>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A Back     alignment and structure
>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP} Back     alignment and structure
>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli} Back     alignment and structure
>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens} Back     alignment and structure
>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3} Back     alignment and structure
>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron} Back     alignment and structure
>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19 Back     alignment and structure
>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60 Back     alignment and structure
>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19 Back     alignment and structure
>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP} Back     alignment and structure
>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae} Back     alignment and structure
>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64 Back     alignment and structure
>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69 Back     alignment and structure
>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 Back     alignment and structure
>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36 Back     alignment and structure
>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 Back     alignment and structure
>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae} Back     alignment and structure
>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62 Back     alignment and structure
>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus} Back     alignment and structure
>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus} Back     alignment and structure
>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 Back     alignment and structure
>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A* Back     alignment and structure
>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5 Back     alignment and structure
>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69 Back     alignment and structure
>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 Back     alignment and structure
>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3} Back     alignment and structure
>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP} Back     alignment and structure
>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa} Back     alignment and structure
>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28 Back     alignment and structure
>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 Back     alignment and structure
>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str} Back     alignment and structure
>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 Back     alignment and structure
>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28 Back     alignment and structure
>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28 Back     alignment and structure
>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron} Back     alignment and structure
>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp} Back     alignment and structure
>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus} Back     alignment and structure
>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28 Back     alignment and structure
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris} Back     alignment and structure
>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus} Back     alignment and structure
>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A* Back     alignment and structure
>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 Back     alignment and structure
>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28 Back     alignment and structure
>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69 Back     alignment and structure
>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28 Back     alignment and structure
>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28 Back     alignment and structure
>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Back     alignment and structure
>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP} Back     alignment and structure
>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus} Back     alignment and structure
>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3} Back     alignment and structure
>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 Back     alignment and structure
>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A Back     alignment and structure
>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049} Back     alignment and structure
>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>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* Back     alignment and structure
>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus} Back     alignment and structure
>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa} Back     alignment and structure
>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 Back     alignment and structure
>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28 Back     alignment and structure
>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP} Back     alignment and structure
>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85 Back     alignment and structure
>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B} Back     alignment and structure
>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 Back     alignment and structure
>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua} Back     alignment and structure
>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus} Back     alignment and structure
>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 Back     alignment and structure
>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus} Back     alignment and structure
>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62 Back     alignment and structure
>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 Back     alignment and structure
>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis} Back     alignment and structure
>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3} Back     alignment and structure
>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69 Back     alignment and structure
>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A Back     alignment and structure
>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi} Back     alignment and structure
>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3} Back     alignment and structure
>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 Back     alignment and structure
>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli} Back     alignment and structure
>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei} Back     alignment and structure
>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Back     alignment and structure
>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 Back     alignment and structure
>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query523
d1q1ha_88 Transcription factor E/IIe-alpha, N-terminal domai 98.73
d1q1ha_88 Transcription factor E/IIe-alpha, N-terminal domai 97.07
d1sfxa_109 Hypothetical protein AF2008 {Archaeoglobus fulgidu 96.78
d1sfxa_109 Hypothetical protein AF2008 {Archaeoglobus fulgidu 96.13
d1z05a171 Transcriptional regulator VC2007 N-terminal domain 95.18
d1ub9a_100 Hypothetical protein PH1061 {Archaeon Pyrococcus h 95.16
d2d1ha1109 Hypothetical transcriptional regulator ST1889 {Sul 94.74
d2hoea162 N-acetylglucosamine kinase {Thermotoga maritima [T 94.32
d2d1ha1109 Hypothetical transcriptional regulator ST1889 {Sul 94.12
d1u2wa1108 Cadmium efflux system accessory protein CadC {Stap 93.96
d1z6ra170 Mlc protein N-terminal domain {Escherichia coli [T 93.76
d1ku9a_151 DNA-binding protein Mj223 {Archaeon Methanococcus 93.63
d1ku9a_151 DNA-binding protein Mj223 {Archaeon Methanococcus 93.02
d1r1ta_98 SmtB repressor {Cyanobacteria (Synechococcus), pcc 92.12
d1z05a171 Transcriptional regulator VC2007 N-terminal domain 92.05
d1sd4a_122 Penicillinase repressor BlaI {Staphylococcus aureu 90.88
d1r1ua_94 Metal-sensing transcriptional repressor CzrA {Stap 90.72
d2cfxa163 Transcriptional regulator LrpC {Bacillus subtilis 89.98
d1s3ja_143 Putative transcriptional regulator YusO {Bacillus 89.36
d1okra_120 Methicillin resistance regulatory protein MecI {St 89.36
d1z6ra170 Mlc protein N-terminal domain {Escherichia coli [T 89.01
d2cg4a163 Regulatory protein AsnC {Escherichia coli [TaxId: 88.84
d1mkma175 Transcriptional regulator IclR, N-terminal domain 88.83
d1i1ga160 LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} 88.64
d2a61a1139 Transcriptional regulator TM0710 {Thermotoga marit 88.49
d1j75a_57 Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]} 87.33
d2cyya160 Putative transcriptional regulator PH1519 {Archaeo 87.09
d1i1ga160 LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} 87.07
d1mkma175 Transcriptional regulator IclR, N-terminal domain 86.92
d1lnwa_141 MexR repressor {Pseudomonas aeruginosa [TaxId: 287 86.7
d2hoea162 N-acetylglucosamine kinase {Thermotoga maritima [T 86.61
d1ulya_190 Hypothetical protein PH1932 {Pyrococcus horikoshii 85.93
d2p4wa1194 Transcriptional regulatory protein PF1790 {Pyrococ 85.68
d2cfxa163 Transcriptional regulator LrpC {Bacillus subtilis 84.98
d1ulya_190 Hypothetical protein PH1932 {Pyrococcus horikoshii 84.76
d1sd4a_122 Penicillinase repressor BlaI {Staphylococcus aureu 84.42
d1xmka173 Z-alpha domain of dsRNA-specific adenosine deamina 84.31
d2cg4a163 Regulatory protein AsnC {Escherichia coli [TaxId: 83.31
d1jgsa_138 Multiple antibiotic resistance repressor, MarR {Es 83.0
d2etha1140 Putative transcriptional regulator TM0816 {Thermot 82.35
d2p4wa1194 Transcriptional regulatory protein PF1790 {Pyrococ 82.3
d1lnwa_141 MexR repressor {Pseudomonas aeruginosa [TaxId: 287 81.43
d3broa1135 Transcriptional regulator OEOE1854 {Oenococcus oen 81.2
d2g9wa1122 Hypothetical protein Rv1846c {Mycobacterium tuberc 81.07
d1xmka173 Z-alpha domain of dsRNA-specific adenosine deamina 80.73
d2cyya160 Putative transcriptional regulator PH1519 {Archaeo 80.14
d1xd7a_127 Hypothetical protein ywnA {Bacillus subtilis [TaxI 80.12
>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.73  E-value=1.5e-08  Score=78.40  Aligned_cols=82  Identities=18%  Similarity=0.279  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHcCCchHHHHHHHHhhCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCceEEEEEEEch
Q 009896          369 EEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNR  448 (523)
Q Consensus       369 ~~le~~v~~~~G~~a~RI~r~L~~k~~l~eek~i~~~ami~~k~~R~~L~~L~~~g~v~lQEvpk~~~~~~t~~lw~v~~  448 (523)
                      ..+..++.+-.|..|.+|++.|.+++.-+++.+||+...+..+++|++||.|+..|++..-..... ..++..|+|+++.
T Consensus         6 ~ll~~~~~~i~Ge~~~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd~-~~gw~~Y~W~~~~   84 (88)
T d1q1ha_           6 DLFINLAKSLLGDDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDK-DSGWFIYYWKPNI   84 (88)
T ss_dssp             THHHHHHHTTSCSTTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC----CCCCEEEEECTH
T ss_pred             HHHHHHHHHHccHHHHHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeecC-CCCcEEEEEEech
Confidence            467889999999999999999987654339999999999999999999999999999977444333 6799999999998


Q ss_pred             HHH
Q 009896          449 QIL  451 (523)
Q Consensus       449 ~~~  451 (523)
                      +++
T Consensus        85 e~i   87 (88)
T d1q1ha_          85 DQI   87 (88)
T ss_dssp             HHH
T ss_pred             hcC
Confidence            865
>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]} Back     information, alignment and structure
>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]} Back     information, alignment and structure
>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]} Back     information, alignment and structure
>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]} Back     information, alignment and structure
>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure