HorA Server Transitive Detail

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


Query <-- 1.356 --> Intermediate <-- 1.841 --> Hit

SVM
score
SVM
score

The query (T0611_Ad2.pdb) is transitively linked to the hit (d1vi0a2) through the intermediate protein (d1t56a2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1t56a2 Ethr repressorTetracyclin repressor-​like,​ C-​terminal domainTetracyclin repressor-​like,​ C-​terminal domainAll α
Hit d1vi0a2 Hypothetical transcriptional regulator YsiATetracyclin repressor-​like,​ C-​terminal domainTetracyclin repressor-​like,​ C-​terminal domainAll α

Supporting Alignments

Query <-- 1.356 --> Intermediate
DALI alignment (Z-score: 9.2 Raw score:578.80) query 1 fqeyeklvdyyldipedrpiTLEDMTFYLESVFDGLWSYRFFHRDLEYLLDSDPRLRQDY 60 :::::::::::::::::::::::::::::::::::::::: d1t56a2 1 ----------------adtdRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELW 44 query 61 REFTNRCLAAINRIFAKLADAGIIQPQPedLRSAMSLNVWLVITNWMAFL--KTAH---L 115 :::::::::::::::::::::::::::: :::::::::::::::::::: :::: : d1t56a2 45 STFMQKWIAYTAAVIDAERDRGAAPRTL--PAHELATALNLMNERTLFASfaGEQPsvpE 102 query 116 TELK-QGIYQVLTLEVPYltpeyrervlalrekyrp 150 :::: ::::::::::::: d1t56a2 103 ARVLdTLVHIWVTSIYGE------------------ 120 FAST alignment (Normalized score: 8.62 Raw score:1156.00) query 1 FQEYEKLVDYYLDIPEDRPI----TLEDMTFYLESVFDGLWSYRFFHRDLEYLLDSDPRL 56 :::::::::::::::::::::::::::::::::::: d1t56a2 1 --------------------ADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEV 40 query 57 RQDYREFTNRCLAAINRIFAKLADAGIIQPQ--PEDLRSAMSLNVWLVITNWMAFLKTAH 114 ::::::::::::::::::::::::::::::: :::::::::::::::::::: d1t56a2 41 AELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASF------- 93 query 115 LTE--------LKQGIYQVLTLEVPYLTPEYRERVLALREKYRP----- 150 :::::::::::::: d1t56a2 94 ---AGEQPSVPEARVLDTLVHIWVT-------------------SIYGE 120 TMalign alignment (TM-score: 0.56 Raw score:84.62) query 1 FQEYEKLVDYYLDIPEDRPITL-EDMTFYLESVFDGLWSYRFFHRD-LEYLLDSDPRLRQ 58 ::::: ::::::::::::::::::::::: ::::::::: ::: d1t56a2 1 -----------------ADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVE-VAE 42 query 59 DYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLVITNW-MAFL-K-TAH- 114 :::::::::::::::::::::::::::::: :::::::::::::::: :::: : ::: d1t56a2 43 LWSTFMQKWIAYTAAVIDAERDRGAAPRTL--PAHELATALNLMNERTLFASFAGEQPSV 100 query 115 LTELKQGI-YQVLTLEVPYLTPEYRERVLALREKYRP 150 :::::: ::::::::::::: d1t56a2 101 --PEARVLDTLVHIWVTSIYGE--------------- 120 HHsearch alignment (Probability: 0.73 E-value:0.00) query 23 EDMTFYLESVFDGLWSYRFFHRDLEYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAG 82 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1t56a2 7 NMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRG 66 query 83 IIQPQPEDLRSAMSLNVWLVITNWMAFLKT----AHLTELKQGIYQVL 126 :::::::::::::: ::::::::::::::: :::::::::::::: d1t56a2 67 AAPRTLPAHELATA-LNLMNERTLFASFAGEQPSVPEARVLDTLVHIW 113
Intermediate <-- 1.841 --> Hit
DALI alignment (Z-score: 10.9 Raw score:597.80) d1t56a2 1 adtDRENMWRTGINVFFETFGSHKAVTRAG-QAARATSV-EVAELWSTFmQKWIAYTAAV 58 ::::::::::::::::::::::::::: :::::::: ::::::::: :::::::::: d1vi0a2 1 ---TAKEKLALVISKHFSLLAGDHNLAIVTqLELRQSNLeLRQKINEIL-KGYLNILDGI 56 d1t56a2 59 IDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEqpsVPEARVLDTLVHIWVTSiy 118 :::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1vi0a2 57 LTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWVMND-qkYDLVALSNSVLELLVSGih 115 d1t56a2 119 ge 120 d1vi0a2 116 nk 117 FAST alignment (Normalized score: 10.13 Raw score:1200.00) d1t56a2 1 ADTD-RENMWRTGINVFFETFGSHKAVTRAGQAARA--TSVEVAELWSTFMQKWIAYTAA 57 :::::::::::::::::::::::::::::: :::::::::::::::::::::: d1vi0a2 1 ----TAKEKLALVISKHFSLLAGDHNLAIVTQLEL-RQSNLELRQKINEILKGYLNILDG 55 d1t56a2 58 VIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPE--------ARVLDTL 109 :::::::::::::::::::::::::::::::::::: ::::::: d1vi0a2 56 ILTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWV---------MNDQKYDLVALSNSV 106 d1t56a2 110 VHIWVTSIYGE------ 120 ::::: d1vi0a2 107 LELLV------SGIHNK 117 TMalign alignment (TM-score: 0.70 Raw score:84.09) d1t56a2 1 ADTDRENMWRTGINVFFETFGSHKAVTRAGQAA-RATS-VEVA-ELWSTFMQKWIAYTAA 57 :::::::::::::::::::::::::::::: :::: :: : :: ::::::::::::: d1vi0a2 1 ---TAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLEL-RQKI-NEILKGYLNILDG 55 d1t56a2 58 VIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGE--QPSVPEARVLDTLVHIWVT 115 ::::::::::::::::::::::::::::::::::::::: :::::::::::::::: d1vi0a2 56 ILTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQK---YDLVALSNSVLELLVS 112 d1t56a2 116 S----IYGE 120 : d1vi0a2 113 GIHNK---- 117 HHsearch alignment (Probability: 1.00 E-value:0.00) d1t56a2 4 DRENMWRTGINVFFETFGSHKAVTRAG-QAARATSVEVAELWSTFMQKWIAYTAAVIDAE 62 ::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::: d1vi0a2 1 TAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEG 60 d1t56a2 63 RDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYG 119 :::::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1vi0a2 61 IQSGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQK-YDLVALSNSVLELLVSGIHN 116