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 <-- 1.478 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1kola2) 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 d1kola2 Formaldehyde 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 <-- 1.478 --> Hit
DALI alignment (Z-score: 4.6 Raw score:456.10) d1ps9a3 1 -INTCigcnqacldqifvgkvtsclVNPR--achetkmpilpavQKKNLAVVGAGPAGLA 57 :::: :::: :::::::::::::::: d1kola2 1 iRDLT--------------------CLSDilptgyhgavtagvgPGSTVYVAGAGPVGLA 40 d1ps9a3 58 FAINAAARGH-QVTLFDAHSEIggqfniakqipgkeefyetlryyrrmIEVTgVTLKLN- 115 :::::::::: ::::::::::: :::: :::::: d1kola2 41 AAASARLLGAaVVIVGDLNPAR----------------------lahaKAQG-FEIADLs 77 d1ps9a3 116 htvTADQL-------QAFDETILASGIPN-------------RALAQPLI---dsGKTVH 152 ::::: :::::::::::::: :::::::: ::::: d1kola2 78 ldtPLHEQiaallgePEVDCAVDAVGFEArghghegakheapATVLNSLMqvtrvAGKIG 137 d1ps9a3 153 LIGGcdVAME---------------------------------ldarraiaqgtrlalei 179 :::: :::: d1kola2 138 IPGL--YVTEdpgavdaaakigslsirfglgwakshsfhtgqtpvmkynralmqaimwdr 195 FAST alignment (Normalized score: 4.01 Raw score:749.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPA-------------------- 40 d1kola2 1 ----------------------------------------IRDLTCLSDILPTGYHGAVT 20 d1ps9a3 41 ---VQKKNLAVVGAGPAGLAFAINAAARGH-QVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 ::::::::::::::::::::::::::: ::::::::: d1kola2 21 AGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNP-------------------- 60 d1ps9a3 97 T--LRYYRRMIEVTGVTLKLNHTVTADQLQ-------------------AFDETILASGI 135 :::::: :::::: ::::::::: d1kola2 61 -ARLAHAKA----QGFEIA-----------DLSLDTPLHEQIAALLGEPEVDCAVDAV-- 102 d1ps9a3 136 ---------------PNRALAQPLID---SGKTVHLIGGCDVAMELDARRAIAQGTRLAL 177 ::::::::::: :::::::: d1kola2 103 GFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIP----------------------- 139 d1ps9a3 178 EI-------------------------------------------------------- 179 d1kola2 140 --GLYVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAIMWDR 195 TMalign alignment (TM-score: 0.46 Raw score:81.48) d1ps9a3 1 -INTCIGCNQACLDQIFVGKVTSCLVNPR---------ACHETKMPILPAVQKKNLAVVG 50 ::::: ::::::: ::::::::::: d1kola2 1 IRDLTC----------------LSDILPTGYHGAVTAG-----------VGPGSTVYVAG 33 d1ps9a3 51 AGPAGLAFAINAAARGH-QVTLFDAHSEIG-GQFNIAKQIPGKEEFYETLRYYRRMIEVT 108 ::::::::::::::::: :::::::::::: ::::: d1kola2 34 AGPVGLAAAASARLLGAAVVIVGDLNPARLA----------------------HAKAQ-- 69 d1ps9a3 109 GVTLKLNHTV---TADQ-L------QAFDETILASG-IP------------NRALAQPLI 145 ::: :: ::: :::: : ::::::::::: :: ::::::::: d1kola2 70 GFE-IA-DLSLDTPLHEQIAALLGEPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLM 127 d1ps9a3 146 DSGK--T-VHLIGGCDVAME-------------------------------LDARRAIA- 170 :::: : :::::: :::: :::: d1kola2 128 QVTRVAGKIGIPGL--YVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTG----QTPVM 181 d1ps9a3 171 -QGTR--LAL--------EI 179 :: : d1kola2 182 K--YNRA--LMQAIMWDR-- 195 HHsearch alignment (Probability: 0.96 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINAAARGH-QVTLFDAHSE 77 ::::::::::::::::::::::::::::::: :::::::::: d1kola2 20 TAGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNPA 61