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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.466 --> Intermediate <-- 1.540 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1qora2) through the intermediate protein (d1q1ra2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1q1ra2 Putidaredoxin reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1qora2 Quinone oxidoreductaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.466 --> Intermediate
DALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.540 --> Hit
DALI alignment (Z-score: 4.3 Raw score:329.60) d1q1ra2 1 rplpvasgavgkannfrylrtLEDAECIR--RQLIADNRLVVIG-gGYIGLEVAATAIKA 57 :::::::: ::::::::::::: :::::::::::::: d1qora2 1 --------isfeqaaasflkgLTVYYLLRktYEIKPDEQFLFHAaaGGVGLIACQWAKAL 52 d1q1ra2 58 NMHVTLLDTaarvlervtappvSAFYEHLHREAGV-DIRTG--TQVCGfemstdqqkvta 114 ::::::::: ::::::::::::: ::::: ::::: d1qora2 53 GAKLIGTVG-------------TAQKAQSALKAGAwQVINYreEDLVE------------ 87 d1q1ra2 115 vlcedgTRLP----ADLVIAGIG------------------------------------- 133 :::: ::::::::: d1qora2 88 ----rlKEITggkkVRVVYDSVGrdtwersldclqrrglmvsfgnssgavtgvnlgilnq 143 d1q1ra2 134 ------------------------------------ 134 d1qora2 144 kgslyvtrpslqgyittreelteasnelfsliasgv 179 FAST alignment (Normalized score: 4.49 Raw score:692.50) d1q1ra2 1 RPLPVASGAVGKANNFRYLR--------TLEDAECIRR------QLIADNRLVVI-GGGY 45 :::::::::: ::::::::::: :::: d1qora2 1 --------------------ISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGG 40 d1q1ra2 46 IGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAG-VDIR--TGTQVCG 102 ::::::::::::::::::::: :::::::::::: :::: :::: d1qora2 41 VGLIACQWAKALGAKLIGTVG-------------TAQKAQSALKAGAWQVINYREED--- 84 d1q1ra2 103 FEMSTDQQKVTAVLCEDGTRL------------PADLVIAGIG----------------- 133 :::::::: d1qora2 85 ---------------------LVERLKEITGGKKVRVVYDS--VGRDTWERSLDCLQRRG 121 d1q1ra2 134 ---------------------------------------------------------- 134 d1qora2 122 LMVSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGV 179 TMalign alignment (TM-score: 0.48 Raw score:63.80) d1q1ra2 1 ----------RPLPVASGAVGKANNFRYLR-TLEDAECIRR--QLIADNRLVVIG-GGYI 46 :: ::::::::: :::::::::::: :::: d1qora2 1 ISFEQAAASF------------------LKG-LTVYYLLRKTYEIKPDEQFLFHAAAGGV 41 d1q1ra2 47 GLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMS 106 :::::::::::::::::::::::: :: ::::: ::::::: :::: d1qora2 42 GLIACQWAKALGAKLIGTVGTAQK---------AQ-SALKA--GAWQVIN-YREE----- 83 d1q1ra2 107 TDQQKVTAVLCEDGT-R--L---PADLVIAGI-----------------------G---- 133 ::: :: : : ::::::::: : d1qora2 84 ---------DLV-ERLKEITGGKKVRVVYDSVGRDTWERSLDCLQRRGLMVSFGNSSGAV 133 d1q1ra2 134 ---------------------------------------------- 134 d1qora2 134 TGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGV 179 HHsearch alignment (Probability: 0.88 E-value:0.00) d1q1ra2 26 ECIRR--QLIADNRLVVIGG-GYIGLEVAATAIKANMHVTLLDTAARVLE---------- 72 ::::: ::::::::::::: ::::::::::::::::::::::::::::: d1qora2 18 YLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTVGTAQKAQSALKAGAWQV 77 d1q1ra2 73 -RVTAPPVSAFYEHLHREAGVDIRTGT 98 :::::::::::::::::::::::::: d1qora2 78 INYREEDLVERLKEITGGKKVRVVYDS 104