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 <-- 1.552 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1pl7a2) 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 d1pl7a2 Ketose reductase (sorbitol dehydrogenase)NAD(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 <-- 1.552 --> Hit
DALI alignment (Z-score: 5.6 Raw score:481.10) d1ps9a3 1 intciGCNQAcldqifvgkvtSCLVNPrachetkmpilpavQKKNLAVVGAGPAGLAFAI 60 ::::: :::::: ::::::::::::::::::: d1pl7a2 1 -----VTFEE-----------GALIEPlsvgihacrrggvtLGHKVLVCGAGPIGMVTLL 44 d1ps9a3 61 NAAARGH-QVTLFDAHSEIggqfniakqipgkeefyetlryyRRMIevtgVTLKLNHT-- 117 ::::::: ::::::::::: :::: :::::::: d1pl7a2 45 VAKAMGAaQVVVTDLSATR-------------------lskaKEIG----ADLVLQISke 81 d1ps9a3 118 ---vTADQLQ-----AFDETILASGipNRALAQPLI---dsGKTVHLIggCDVAM----- 161 :::::: :::::::::: ::::::::: ::::::: ::::: d1pl7a2 82 spqeIARKVEgqlgcKPEVTIECTG--AEASIQAGIyatrsGGTLVLV--GLGSEmttvp 137 d1ps9a3 162 ----------------eldarraiaqgtrlalei 179 d1pl7a2 138 llhaairevdikgvfrycntwpvaismlasksvn 171 FAST alignment (Normalized score: 4.40 Raw score:769.60) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPA-------------------- 40 d1pl7a2 1 ----------------------------------------VTFEEGALIEPLSVGIHACR 20 d1ps9a3 41 ----VQKKNLAVVGAGPAGLAFAINAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEFY 95 :::::::::::::::::::::::::: :::::::::: d1pl7a2 21 RGGVTLGHKVLVCGAGPIGMVTLLVAKAMGAAQVVVTDLSA------------------- 61 d1ps9a3 96 ET--LRYYRRMIEVTG---VTLKLNHTV---------TADQLQ-------AFDETILASG 134 :::::: :::: :::: ::::::: d1pl7a2 62 --TRLSKAKE------IGADLVL-----QISKESPQEIARK--VEGQLGCKPEVTIE--- 103 d1ps9a3 135 -IPNRALAQPLID---SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI----------- 179 :::::::::::: :::::::: d1pl7a2 104 CTGAEASIQAGIYATRSGGTLVLV-------------------------GLGSEMTTVPL 138 d1ps9a3 180 --------------------------------- 180 d1pl7a2 139 LHAAIREVDIKGVFRYCNTWPVAISMLASKSVN 171 TMalign alignment (TM-score: 0.46 Raw score:81.97) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACH---ETKM--PIL---PAVQKKNLAVVGAG 52 ::::: :: ::::: : : : ::::::::::::: d1pl7a2 1 VTFEE----------------GA-LIEPL-SVGI---HAC--RRGG-VTLGHKVLVCGAG 36 d1ps9a3 53 PAGLAFAINAAARGH-QVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVT 111 ::::::::::::::: :::::::::::: ::: ::: ::: d1pl7a2 37 PIGMVTLLVAKAMGAAQVVVTDLSATRL---------------------SKA-KEI-GAD 73 d1ps9a3 112 LKLNHT-VTAD-Q---LQ-----AFDETILASGIPNRALAQPLIDSGK----TVHLIGGC 157 :::::: :::: : :: ::::::::: :::::::::: ::: :::::::: d1pl7a2 74 LVLQISKESPQEIARKVEGQLGCKPEVTIECT--GAEASIQAGI-YATRSGGTLVLVGLG 130 d1ps9a3 158 DV------------------AMELDARRA-IAQ--GTR---LAL----------EI 179 :: : :: : : d1pl7a2 131 SEMTTVPLLHAAIREVDIKG--------VF-RYCN--TWPV--AISMLASKSVN-- 171 HHsearch alignment (Probability: 0.97 E-value:0.00) d1ps9a3 27 PRACHETKMPILPAVQKKNLAVVGAGPAGLAFAINAAARGH-QVTLFDAHSEI 78 ::::::::::::::::::::::::::::::::::::::::: ::::::::::: d1pl7a2 11 PLSVGIHACRRGGVTLGHKVLVCGAGPIGMVTLLVAKAMGAAQVVVTDLSATR 63