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 <-- 1.694 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1lssa_) 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 d1lssa_ Ktn Mja218NAD(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 <-- 1.694 --> Hit
DALI alignment (Z-score: 7.5 Raw score:543.60) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkKNLAVVGAGPAGLAFAI 60 ::::::::::::::::: d1lssa_ 1 -------------------------------------------MYIIIAGIGRVGYTLAK 17 d1ps9a3 61 NAAARGHQVTLFDAHSEIggqfniakqipgkeefyetlryYRRMIevtGVTLKLnHTVTa 120 :::::::::::::::::: ::::: :::::: :::: d1lssa_ 18 SLSEKGHDIVLIDIDKDI-------------------ckkASAEI---DALVIN-GDCTk 54 d1ps9a3 121 DQLQ------AFDETILASGIPN--RALAQPLIDSGK-TVHLiggCDVAME--------- 162 :::: ::::::::::::: :::::::::::: :::: :::::: d1lssa_ 55 IKTLedagieDADMYIAVTGKEEvnLMSSLLAKSYGInKTIA---RISEIEykdvferlg 111 d1ps9a3 163 -----LDARRaiaqgtrlalei 179 ::::: d1lssa_ 112 vdvvvSPELI-aanyieklier 132 FAST alignment (Normalized score: 5.80 Raw score:890.90) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 ::::::::::::::::: d1lssa_ 1 -------------------------------------------MYIIIAGIGRVGYTLAK 17 d1ps9a3 61 NAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYET--LRYYRRMIEVTGVTLKLNHTV 118 :::::::::::::::: :::::: ::::::: d1lssa_ 18 SLSEKGHDIVLIDIDK---------------------DICKKASA---EIDALVI----- 48 d1ps9a3 119 --------TADQL---QAFDETILASGIPN----RALAQPLIDSG-KTVHLIGGCDVAME 162 :::: :::::::::::: ::::::::::: ::::: d1lssa_ 49 NGDCTKIKTLED-AGIEDADMYIAVTGK--EEVNLMSSLLAKSYGINKTIA--------- 96 d1ps9a3 163 LDARRAIAQGTRLALEI------------------------------------ 179 d1lssa_ 97 -----------------RISEIEYKDVFERLGVDVVVSPELIAANYIEKLIER 132 TMalign alignment (TM-score: 0.44 Raw score:79.03) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 ::::::::::::::::: d1lssa_ 1 -------------------------------------------MYIIIAGIGRVGYTLAK 17 d1ps9a3 61 NAAARGHQVTLFDAHSEIG-GQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLKLNHTVT 119 ::::::::::::::::::: :: :::::::::: :::: d1lssa_ 18 SLSEKGHDIVLIDIDKDICK----------------------KA-SAEIDALVIN-GDCT 53 d1ps9a3 120 ADQ--L---Q-AFDETILASGIPN--RALAQPLIDSGK-TVHLIGGCDVAME-------- 162 ::: : : ::::::::::::: :::::::::::: :::: ::::: d1lssa_ 54 KIKTLEDAGIEDADMYIAVTGKEEVNLMSSLLAKSYGINKTIA----RISEIEYKDVFER 109 d1ps9a3 163 --------LDARRA-IAQ----------GTRLALEI 179 :: :: d1lssa_ 110 LGVDVVVS----PEL-IAANYIEKLIER-------- 132 HHsearch alignment (Probability: 0.96 E-value:0.00) d1ps9a3 44 KNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEI 78 ::::::::::::::::::::::::::::::::::: d1lssa_ 1 MYIIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDI 35