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: T0582_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.971 --> Intermediate <-- 0.996 --> Hit

HHsearch
probability
HHsearch
probability

The query (T0582_Ad1.pdb) is transitively linked to the hit (d1dgwa_) through the intermediate protein (d1lrha_) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1lrha_ Auxin binding proteinRmlC-​like cupinsDouble-​stranded beta-​helixAll β
Hit d1dgwa_ Seed storage 7S proteinRmlC-​like cupinsDouble-​stranded beta-​helixAll β

Supporting Alignments

Query <-- 0.971 --> Intermediate
DALI alignment (Z-score: 9.7 Raw score:629.00) query 1 meinadftKPVVIDTDQLEWRPSPMKGVERRMLDRIG--gevARATSIVRYAPGSRFSAH 58 ::::::::::::::::::::::::::::: :::::::::::::::::: d1lrha_ 1 ---scvrdNSLVRDISQMPQSSYGIEGLSHITVAGALnhgmkEVEVWLQTISPGQRTPIH 57 query 59 THDGGEEFIVLDGVFQDE-------------HGDYPAGTYVRNPPTTSHVPGSAE---GC 102 :::::::::::::::::: :::::::::::::::::::::::: :: d1lrha_ 58 RHSCEEVFTVLKGKGTLLmgssslkypgqpqEIPFFQNTTFSIPVNDPHQVWNSDeheDL 117 query 103 TIFVKLWQ----------------------fdpadrtqfsknm 123 :::::::: d1lrha_ 118 QVLVIISRppakiflyddwsmphtaavlkfpfvwdedcfeaak 160 FAST alignment (Normalized score: 7.67 Raw score:1076.00) query 1 MEINADFTKP-------VVIDTDQLEWRPSPMKGVERRMLDRIGGEVA--------RATS 45 ::::::::::::::::::::::::: :::: d1lrha_ 1 ----------SCVRDNSLVRDISQMPQSSYGIEGLSHITVAG------ALNHGMKEVEVW 44 query 46 IVRYAPGSRFSAHTHDGGEEFIVLDGVFQDE--------------HGDYPAGTYVRNPPT 91 :::::::::::::::::::::::::::::: ::::::::::::::: d1lrha_ 45 LQTISPGQRTPIHRHSCEEVFTVLKGKGTL-LMGSSSLKYPGQPQEIPFFQNTTFSIPVN 103 query 92 TSHVPGSA----EGCTIFVKLWQFDPADRTQFSKNM------------------------ 123 ::::::: :::::::: d1lrha_ 104 DPHQVWN-SDEHEDLQVLVI----------------ISRPPAKIFLYDDWSMPHTAAVLK 146 query 124 -------------- 124 d1lrha_ 147 FPFVWDEDCFEAAK 160 TMalign alignment (TM-score: 0.67 Raw score:82.39) query 1 -MEINADFTKPVVIDTDQLEWRPSPMKGVERRMLDRIGG---EVA-RATSIVRYAPGSRF 55 :::: : : :::::::::::::::::::::::::::: : :::::::::::::: d1lrha_ 1 SCVRD-N--S-LVRDISQMPQSSYGIEGLSHITVAGALNHGM--KEVEVWLQTISPGQRT 54 query 56 SAHTHDGGEEFIVLDGVFQDE-------------HGDYPAGTYVRNPPTTSHVPGSAE-- 100 ::::::::::::::::::::: :::::::::::::::::::::::: d1lrha_ 55 PIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEH 114 query 101 -GCTIFVKLWQF----------------------------------DPADRTQFSKNM 123 ::::::::::: d1lrha_ 115 EDLQVLVIISRPPAKIFLYDDWSMPHTAAVLKFPFVWDEDCFEAAK------------ 160 HHsearch alignment (Probability: 0.97 E-value:0.00) query 10 PVVIDTDQLEWRPSPMKGVERRML--DRIGGEVARATSIVRYAPGSRFSAHTHDGGEEFI 67 :::::::::::::::::::::::: :::::::::::::::::::::::::::::::::: d1lrha_ 7 SLVRDISQMPQSSYGIEGLSHITVAGALNHGMKEVEVWLQTISPGQRTPIHRHSCEEVFT 66 query 68 VLDGVFQDEHGD-------------YPAGTYVRNPPTTSHVP--GSA-EGCTIFV 106 :::::::::::: ::::::::::::::::: ::: ::::::: d1lrha_ 67 VLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLV 121
Intermediate <-- 0.996 --> Hit
DALI alignment (Z-score: 12.7 Raw score:863.00) d1lrha_ 1 scvrdnSLVRDISQMPQSSYgIEGLSHITVAgaLNHG-------MKEVEVWLQTISPGQR 53 :::::::::::::: :::::::::: :::: :::::::::::::::: d1dgwa_ 1 ----nnPYLFRSNKFLTLFK-NQHGSLRLLQ--RFNEdteklenLRDYRVLEYCSKPNTL 53 d1lrha_ 54 TPIHRHSCEEVFTVLKGKGTLLMGSSSlkypgQPQEIPFFQNTTFSIPVNDPHQVWNSDE 113 ::::::::::::::::::::::::::: :::::::::::::::::::::::::::: d1dgwa_ 54 LLPHHSDSDLLVLVLEGQAILVLVNPD-----GRDTYKLDQGDAIKIQAGTPFYLINPDN 108 d1lrha_ 114 HEDLQVLVIISR----PPAKIFLYDdwsmphTAAV---------------------lkfp 148 :::::::::::: ::::::::: :::: d1dgwa_ 109 NQNLRILKFAITfrrpGTVEDFFLS--stkrLPSYlsafsknfleasydspydeieqtll 166 d1lrha_ 149 fvwdedcfeaak 160 d1dgwa_ 167 qeeqegvivkmp 178 FAST alignment (Normalized score: 9.99 Raw score:1686.00) d1lrha_ 1 SCVRDN--SLVRDISQMPQSSYG---IEGLSHITVAGALNH-----------GMKEVEVW 44 ::::::::::: ::::::::: :::::::: d1dgwa_ 1 ------NNPYLFRSNKFLT----LFKNQHGSLRLL------QRFNEDTEKLENLRDYRVL 44 d1lrha_ 45 LQTISPGQRTPIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVND 104 :::::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1dgwa_ 45 EYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVN-----PDGRDTYKLDQGDAIKIQAGT 99 d1lrha_ 105 PHQVWNSDEHEDLQVLVIIS-----RPPAKIFLYDDWSMPHTAAVLKFPFVWDEDCFEAA 159 ::::::::::::::::::: :::::::: d1dgwa_ 100 PFYLINPDNNQNLRILKFA-ITFRRPGTVEDFF--------------------------- 131 d1lrha_ 160 K----------------------------------------------- 160 d1dgwa_ 132 -LSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 178 TMalign alignment (TM-score: 0.65 Raw score:104.46) d1lrha_ 1 -SCVRDNSLVRDISQMPQSSYGIEGLSHITVAGALNHG------MKEVEVWLQTISPGQR 53 ::::::: :::::::::::::::::::: ::: :::::::::::::::: d1dgwa_ 1 N-----NPYLFRS-NKFLTLFKNQHGSLRLLQRF-NEDTEKLENLRDYRVLEYCSKPNTL 53 d1lrha_ 54 TPIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDE 113 ::::::::::::::::::::::::: :: : ::::::::::::::::::::::::::: d1dgwa_ 54 LLPHHSDSDLLVLVLEGQAILVLVN-PD---G-RDTYKLDQGDAIKIQAGTPFYLINPDN 108 d1lrha_ 114 HEDLQVLVIISR----PPAKIFLYDD-----WSMPHTAAVL------------------- 145 :::::::::::: :::::::::: ::: d1dgwa_ 109 NQNLRILKFAITFRRPGTVEDFFLSSTKRLP-------SYLSAFSKNFLEASYDSPYDEI 161 d1lrha_ 146 ----------KFPFV------WDEDCFEAAK 160 : d1dgwa_ 162 EQTLLQEEQE----GVIVKMP---------- 178 HHsearch alignment (Probability: 1.00 E-value:0.00) d1lrha_ 34 LNHGMKEVEVWLQTISPGQRTPIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFF 93 ::::::::::::::::::::::::::::::::::::::::::::: :::::::::: d1dgwa_ 34 KLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVN-----PDGRDTYKLD 88 d1lrha_ 94 QNTTFSIPVNDPHQVWNSDEHEDLQVLVIIS 124 ::::::::::::::::::::::::::::::: d1dgwa_ 89 QGDAIKIQAGTPFYLINPDNNQNLRILKFAI 119