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 <-- 1.600 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1a9xa3) 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 d1a9xa3 Carbamoyl phosphate synthetase (CPS),​ large subunit PreATP-​grasp domainsPreATP-​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 <-- 1.600 --> Hit
DALI alignment (Z-score: 5.3 Raw score:428.20) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpiLPAVQ-kKNLAVVG--------- 50 ::::: ::::::: d1a9xa3 1 -------------------------------------MPKRTdiKSILILGagpivigqa 23 d1ps9a3 51 --aGPAGLAFAINAAARGHQVTLFDAHSEIGgqfniakqipgkeefyetlryyRRMIevt 108 :::::::::::::::::::::::::::: :::: d1a9xa3 24 cefDYSGAQACKALREEGYRVINVNSNPATI--------------------mtDPEM--- 60 d1ps9a3 109 gVTLKLnHTVTA---DQLQ---AFDETIL-ASGIpnRALAQPLI-DSGK-----TVHLig 155 ::::: ::::: :::: ::::::: :::: :::::::: :::: :::: d1a9xa3 61 aDATYI-EPIHWevvRKIIekeRPDAVLPtMGGQtaLNCALELErQGVLeefgvTMIG-- 117 d1ps9a3 156 gcdvameldarraiaqgtrlalei 179 d1a9xa3 118 --------------atadaidkae 127 FAST alignment (Normalized score: 4.15 Raw score:625.80) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPI-LPAVQK--KNLAVVGA------ 51 :::: ::::: d1a9xa3 1 -------------------------------------MPKRT--DIKSILI---LGAGPI 18 d1ps9a3 52 --------GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRY--- 100 :::::::::::::::::::::::::: d1a9xa3 19 VIGQACEFDYSGAQACKALREEGYRVINVNSNPA-----------------------TIM 55 d1ps9a3 101 -YRRMIEVTG-VTLKLNHTVTADQL-------QAFDETILASGIPN--------RALAQP 143 :::: :::: :::::::: ::::::: :::::: d1a9xa3 56 TDPEM-----ADATY-IEPIHWEV-VRKIIEKERPDAVL-------PTMGGQTALNCALE 101 d1ps9a3 144 LIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI--------------------- 179 ::::: d1a9xa3 102 LERQG-------------------------------VLEEFGVTMIGATADAIDKAE 127 TMalign alignment (TM-score: 0.41 Raw score:74.00) d1ps9a3 1 -INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQ-KKNLAVVG-------- 50 : ::: :::::::: d1a9xa3 1 M-------------------------------------P-KRTDIKSILILGAGPIVIGQ 22 d1ps9a3 51 ---AGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEV 107 ::::::::::::::::::::::::::::: : :: :: d1a9xa3 23 ACEFDYSGAQACKALREEGYRVINVNSNPATI------------------M--TD--PE- 59 d1ps9a3 108 TGVTLKLNHTVTA---DQLQ---AFDETIL-ASGIPN-RALAQPLID-S--G---KTVHL 153 :::::::::::: :::: ::::::: ::: :: ::::::::: : : ::::: d1a9xa3 60 -MADATYIEPIHWEVVRKIIEKERPDAVLPTMGG-QTALNCALELERQGVLEEFGVTMIG 117 d1ps9a3 154 I----GGCD----VAMELDARRAIAQGTRLALEI 179 : : d1a9xa3 118 ATADA---IDKAE--------------------- 127 HHsearch alignment (Probability: 0.95 E-value:0.00) d1ps9a3 39 PAVQKKNLAVVGAGP-----------AGLAFAINAAARGHQVTLFDAHSEI 78 ::::::::::::::: ::::::::::::::::::::::::: d1a9xa3 3 KRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVINVNSNPAT 53