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 <-- 1.613 --> Intermediate <-- 1.645 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1heta2) through the intermediate protein (d1ps9a3) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ps9a3 2,​4-​dienoyl-​CoA reductase,​ middle domainNucleotide-​binding domainNucleotide-​binding domainα/β
Hit d1heta2 Alcohol dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.613 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 1.645 --> Hit
DALI alignment (Z-score: 5.2 Raw score:469.60) d1ps9a3 1 intciGCNQAcldqifvgkvtSCLVNP--rachetkmpilpavQKKNLAVVGAGPAGLAF 58 ::::: :::::: ::::::::::::::::: d1heta2 1 -----SPLEK-----------VCLIGCgfstgygsavkvakvtQGSTCAVFGLGGVGLSV 44 d1ps9a3 59 AINAAARGH-QVTLFDAHSEIggqfniakqipgkeefyetlryyRRMIevtgVTLKLNHT 117 ::::::::: ::::::::::: :::: :::::::: d1heta2 45 IMGCKAAGAaRIIGVDINKDK-------------------fakaKEVG----ATECVNPQ 81 d1ps9a3 118 ----vTADQLQ-----AFDETILASGipNRALAQ----plidsGKTVHLIggCDVAME-- 162 :::::: :::::::::: :::::: ::::::: :::::: d1heta2 82 dykkpIQEVLTemsngGVDFSFEVIG--RLDTMVtalsccqeaYGVSVIV--GVPPDSqn 137 d1ps9a3 163 ----------------------ldarraiaqgtrlalei 179 d1heta2 138 lsmnpmlllsgrtwkgaifggfkskdsvpklvadfmakk 176 FAST alignment (Normalized score: 4.35 Raw score:772.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP--------------------- 39 d1heta2 1 ---------------------------------------SPLEKVCLIGCGFSTGYGSAV 21 d1ps9a3 40 ----AVQKKNLAVVGAGPAGLAFAINAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEF 94 ::::::::::::::::::::::::::: :::::::::: d1heta2 22 KVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINK------------------ 63 d1ps9a3 95 YETLRY-YRRMIEVTG-VTLKLNHTV--------TADQLQ-----AFDETILASGIPNRA 139 ::::::::: :::: :::::: :::::::: ::::: d1heta2 64 ------DKFAKAKEVGATECV-----NPQDYKKPIQEVLTEMSNGGVDFSFEV--IGRLD 110 d1ps9a3 140 LAQPLID-----SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI--------------- 179 :::::: :::::::: d1heta2 111 TMVTAL-SCCQEAYGVSVIV-------------------------GVPPDSQNLSMNPML 144 d1ps9a3 180 -------------------------------- 180 d1heta2 145 LLSGRTWKGAIFGGFKSKDSVPKLVADFMAKK 176 TMalign alignment (TM-score: 0.47 Raw score:83.87) d1ps9a3 1 -INTCIGCNQACLDQIFVGKVTSCLVNPR-----ACHETKMP---ILPAVQKKNLAVVGA 51 ::::: : : ::::::: :: :::::::::::: d1heta2 1 S-PLEKV-C-L-----------IGCGFSTGYGSA------VKVAK---VTQGSTCAVFGL 37 d1ps9a3 52 GPAGLAFAINAAARGH-QVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 :::::::::::::::: :::::::::::: :: ::: ::: d1heta2 38 GGVGLSVIMGCKAAGAARIIGVDINKDKF---------------------AK-AKE-VGA 74 d1ps9a3 111 TLKLNHT----VTADQLQ--A---FDETILASGIPNRALAQP-LID-SG--KTVHLIGGC 157 ::::::: ::::::: : ::::::: :: ::::::: ::: :: ::::::::: d1heta2 75 TECVNPQDYKKPIQEVLTEMSNGGVDFSFEV-IG-RLDTMVTALSCCQEAYGVSVIVGVP 132 d1ps9a3 158 DVAM-------------------ELDARRAIAQGTR-----------------LALEI 179 :: :::: :: d1heta2 133 --PDSQNLSMNPMLLLSGRTWKG------AIFG-GFKSKDSVPKLVADFMAKK----- 176 HHsearch alignment (Probability: 0.96 E-value:0.00) d1ps9a3 39 PAVQKKNLAVVGAGPAGLAFAINAAARGH-QVTLFDAHSE-------IGGQFNIAKQIPG 90 ::::::::::::::::::::::::::::: :::::::::: :::::: : : d1heta2 25 KVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATEC----V-N 79 d1ps9a3 91 KEEFYETLRYYRRMIEVTGVTLKLNHTVTADQ 122 :::::::::::::::::::::::::::::::: d1heta2 80 PQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDT 111