Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T0611_Ad2.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1vi0a2 | Hypothetical transcriptional regulator YsiA | Tetracyclin repressor-like, C-terminal domain | Tetracyclin repressor-like, C-terminal domain | All α |
| Hit | d1pb6a2 | Hypothetical transcriptional regulator YcdC | Tetracyclin repressor-like, C-terminal domain | Tetracyclin repressor-like, C-terminal domain | All α |
Query <-- 1.004 --> IntermediateDALI alignment (Z-score: 8.6 Raw score:541.40) query 1 fqeyeklvdyyldipedrpITLEDMTFYLESVFDGLWS---YRFFH-RDLEylLDSDPrL 56 ::::::::::::::::::: ::::: :::: ::::: : d1vi0a2 1 -------------------TAKEKLALVISKHFSLLAGdhnLAIVTqLELR--QSNLE-L 38 query 57 RQDYREFTNRCLAAINRIFAKLADAGIIQPQPedLRSAMSLNVWLVITNWMAFLKTAH-l 115 :::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1vi0a2 39 RQKINEILKGYLNILDGILTEGIQSGEIKEGL--DVRLARQMIFGTIDETVTTWVMNDqk 96 query 116 TELK-QGIYQVLTLEVPyltpeyrervlalrekyrp 150 :::: :::::::::::: d1vi0a2 97 YDLVaLSNSVLELLVSG---------------ihnk 117 FAST alignment (Normalized score: 8.02 Raw score:1063.00) query 1 FQEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLWSYRFFHRD--LEYLLD--SDPRL 56 ::::::::::::::::::::::::: :::: ::::: d1vi0a2 1 -------------------TAKEKLALVISKHFSLLAGDHNLAI-VTQLEL--RQSNLEL 38 query 57 RQDYREFTNRCLAAINRIFAKLADAGIIQPQPED---LRSAMSLNVWLVITNWMAFLKTA 113 ::::::::::::::::::::::::::::: ::::::::::::::::::::::: d1vi0a2 39 RQKINEILKGYLNILDGILTEGIQSGEIK-----EGLDVRLARQMIFGTIDETVTTWVMN 93 query 114 HLT----ELKQG-IYQVLTLEVPYLTPEYRERVLALREKYRP------ 150 ::::: :::::::: d1vi0a2 94 ---DQKYDLVALSNSVLELLV---------------------SGIHNK 117 TMalign alignment (TM-score: 0.54 Raw score:80.72) query 1 FQEYEKLVDYYLDIPEDRPITLEDMTFYLESVFDGLW-S--YRFF-HRDLEYLLD-SDPR 55 :::::::::::::::::: : :::: :::::: :: :: d1vi0a2 1 -------------------TAKEKLALVISKHFSLLAGDHNLAIVTQLELRQ-SNL-EL- 38 query 56 LRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLVITNWMAFL--KT- 112 ::: ::::::::::::::::::::::::::::: :::::::::::::::::::: :: d1vi0a2 39 RQK-INEILKGYLNILDGILTEGIQSGEIKEGL--DVRLARQMIFGTIDETVTTWVMNDQ 95 query 113 AHLTELK-QGIYQVLTLEVP----YLTPEYRERVLALREKYRP 150 :: ::: :::::::::::: d1vi0a2 96 -KY-DLVALSNSVLELLVSGIHNK------------------- 117 HHsearch alignment (Probability: 0.79 E-value:0.00) query 23 EDMTFYLESVFDGLWSYRFFHRDL-EYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADA 81 :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1vi0a2 4 EKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQS 63 query 82 GIIQP--QPEDLRSAMSLNVWLVITNWMAFLKTAHLTELKQGIYQVL 126 ::::: :::::::::::::::::::::::::::::::::::::::: d1vi0a2 64 GEIKEGLDVRLARQMIFGTIDETVTTWVMNDQKYDLVALSNSVLELL 110
Intermediate <-- 1.459 --> HitDALI alignment (Z-score: 7.6 Raw score:454.00) d1vi0a2 1 --TAKEKLALVISKHFSLLAGDHNLAIVTqLELR-QSNLeLRQKINEI-LKGYLNILDGI 56 ::::::::::::::::::::::::::: :::: :::: :::::::: ::::::::::: d1pb6a2 1 dfAPLAAIKEYIRLKLEVSRDYPQASRLF-CMEMlAGAP-LLMDELTGdLKALIDEKSAL 58 d1vi0a2 57 LTEGIQSGEIKEgLDVRLARQMIFGTIDETVTTWvmNDQK----------yDLVALSNSV 106 :::::::::::: ::::::::::::::::::::: :::: ::::::::: d1pb6a2 59 IAGWVKSGKLAP-IDPQHLIFMIWASTQHYADFA--PQVEavtgatlrdevFFNQTVENV 115 d1vi0a2 107 LELLVSGihnk 117 ::::::: d1pb6a2 116 QRIIIEGirpr 126 FAST alignment (Normalized score: 7.53 Raw score:914.80) d1vi0a2 1 T---AKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQK-----INEIL-KGYLN 51 ::::::::::::::::::::::::::::::: ::::: ::::: d1pb6a2 1 -DFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEML---------AGAPLLMDELTGDLKA 50 d1vi0a2 52 ILDGILTEGIQ---SGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQKY----------- 97 ::::::::::: :::: ::::::::::::::::::::: d1pb6a2 51 LIDEKSALIAGWVKSGKL-APIDPQHLIFMIWASTQHYAD---------FAPQVEAVTGA 100 d1vi0a2 98 ------DLVALSNSVLELLVSGIHNK------ 117 :::::::::::::: d1pb6a2 101 TLRDEVFFNQTVENVQRIII------EGIRPR 126 TMalign alignment (TM-score: 0.65 Raw score:75.61) d1vi0a2 1 --TAKEKLALVISKHFSLLAGDHNLAIVTQLELR-QSNLELRQKINE-ILK-GYLNILDG 55 ::::::::::::::::::::::::::: :::: :::: ::::::: ::: :::::::: d1pb6a2 1 DFAPLAAIKEYIRLKLEVSRDYPQASRLF-CMEMLAGAP-LLMDELTGDLKALIDEKSAL 58 d1vi0a2 56 ILTEGIQSGEIKEGLDVRLARQMIFGTIDET-VTTWVMND-QK-----YD----LVA-LS 103 ::: :::::::: :: :::: :::::::: :::::::: :: :: ::: :: d1pb6a2 59 IAG-WVKSGKLA--PI--DPQH-LIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTV 112 d1vi0a2 104 NSVLELLVSG----IHNK 117 :::::::::: d1pb6a2 113 ENVQRIIIEGIRPR---- 126 HHsearch alignment (Probability: 1.00 E-value:0.00) d1vi0a2 1 TAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEG 60 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1pb6a2 3 APLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGW 62 d1vi0a2 61 IQSGEIKEGLDVRLARQMIFGTIDETV-----TTWVMND---QKYDLVALSNSVLELLVS 112 :::::::: :::::::::::::::::: ::::::: :::::::::::::::::: d1pb6a2 63 VKSGKLAP-IDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIE 121 d1vi0a2 113 GIHNK 117 ::::: d1pb6a2 122 GIRPR 126