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 <-- 1.074 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1iowa1) 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 d1iowa1 D-​Ala-​D-​Ala ligase,​ N-​domainPreATP-​grasp domainPreATP-​grasp domainα/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 <-- 1.074 --> Hit
DALI alignment (Z-score: 4.9 Raw score:348.20) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGA--------- 51 :::::::::: d1iowa1 1 -----------------------------------------MTDKIAVLLGgtsaerevs 19 d1ps9a3 52 GPAGLAFAINAAARGHQVTLFDAHseiggqfniakqipgkeefyetlryyrrmievtgvt 111 :::::::::::::::::::::::: d1iowa1 20 LNSGAAVLAGLREGGIDAYPVDPK------------------------------------ 43 d1ps9a3 112 lklNHTVtaDQLQ--AFDETILASGIPNR---ALAQPLIDSGKTVHL--iggcdVAMEld 164 :::: :::: :::::::::::::: ::::::::::::::: :::: d1iowa1 44 ---EVDV--TQLKsmGFQKVFIALHGRGGedgTLQGMLELMGLPYTGsgvmasaLSMD-- 96 d1ps9a3 165 arraiaqgtrlalei 179 d1iowa1 97 --------------- 97 FAST alignment (Normalized score: 4.31 Raw score:565.60) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQ-KKNLAVVGA-------- 51 :::::: d1iowa1 1 ------------------------------------------MTDKIAV---LLGGTSAE 15 d1ps9a3 52 ----GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEV 107 :::::::::::::::::::::::: d1iowa1 16 REVSLNSGAAVLAGLREGGIDAYPVDPK-------------------------------- 43 d1ps9a3 108 TGVTLKLNHTVTADQL---------QAFDETILASGIP---NRALAQPLIDSGKTVHLIG 155 ::::::::::::: ::::::::::::::: d1iowa1 44 ----------------EVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPY---- 83 d1ps9a3 156 GCDVAMELDARRAIAQGTRLALEI------------- 179 d1iowa1 84 ------------------------TGSGVMASALSMD 96 TMalign alignment (TM-score: 0.28 Raw score:50.38) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAI 60 : : d1iowa1 1 ------------------------------------------M-T--------------- 2 d1ps9a3 61 NAAARGHQVTLFDAH------S--EIGG-QFNIAKQIPGKEEFYETLRYYRRMIEV-TGV 110 :::::::: : :::: : ::::::: ::: d1iowa1 3 -------DKIAVLLGGTSAEREVSLNSGA-----------------A--VLAGLREGGID 36 d1ps9a3 111 TLKLNHT---VTADQLQA-FDETILA-S----GIPNRALAQPLIDSGKTVHLIGGCD--V 159 :::: :: ::: :::: ::::::: : :::::::::::: :::::::: : : d1iowa1 37 AYPV-DPKEVDVT-QLKSMGFQKVFIALHGRGGEDGTLQGMLEL---MGLPYTGS-GVMA 90 d1ps9a3 160 A-MEL-DARRAIAQGTRLALEI 179 : ::: d1iowa1 91 SALSMD---------------- 96 HHsearch alignment (Probability: 0.65 E-value:0.00) d1ps9a3 43 KKNLAVVGAGPA---------GLAFAINAAARGHQVTLFDAHSEIG 79 :::::::::::: ::::::::::::::::::::::::: d1iowa1 2 TDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDV 47