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 <-- 1.741 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1d5ta1) 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 d1d5ta1 Guanine nucleotide dissociation inhibitor,​ GDIFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding 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 <-- 1.741 --> Hit
DALI alignment (Z-score: 7.2 Raw score:636.00) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkkNLAVVGAGPAGLAFAI 60 :::::::::::::::: d1d5ta1 1 -------------------------------------hhmdeeyDVIVLGTGLTECILSG 23 d1ps9a3 61 NAAARGHQVTLFDAHSEIGGQFNIA---------------------kqIPGK-------- 91 ::::::::::::::::::::::::: :::: d1d5ta1 24 IMSVNGKKVLHMDRNPYYGGESSSItpleelykrfqllegppetmgrgRDWNvdlipkfl 83 d1ps9a3 92 ------------------------------------------------------------ 92 d1d5ta1 84 mangqlvkmllytevtryldfkvvegsfvykggkiykvpstetealasnlmgmfekrrfr 143 d1ps9a3 92 ------------------------------------------------------------ 92 d1d5ta1 144 kflvfvanfdendpktfegvdpqntsmrdvyrkfdlgqdvidftghalalyrtddyldqp 203 d1ps9a3 92 ---------------------------EEFYETLRYYRRMIEVTGVTLKLNHTV-TADQ- 122 ::::::::::::::::::::::::::: :::: d1d5ta1 204 cletinriklyseslarygkspylyplYGLGELPQGFARLSAIYGGTYMLNKPVdDIIMe 263 d1ps9a3 123 ------------LQAFDETILAsgipNRALAQP---lidsGKTVHLIGGcdVAMElDARR 167 :::::::::: ::::::: ::::::::: :::: :::: d1d5ta1 264 ngkvvgvksegeVARCKQLICD----PSYVPDRvpiddgsESQVFCSCS--YDATtHFET 317 d1ps9a3 168 AIAQGTRLALEI------- 179 :::::::::::: d1d5ta1 318 TCNDIKDIYKRMagsafdf 336 FAST alignment (Normalized score: 5.32 Raw score:1305.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKK-------NLAVVGAGP 53 ::::::::: d1d5ta1 1 --------------------------------------------HHMDEEYDVIVLGTGL 16 d1ps9a3 54 AGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPG----------------------- 90 ::::::::::::::::::::::::::::: d1d5ta1 17 TECILSGIMSVNGKKVLHMDRNPYYGGES--------SSITPLEELYKRFQLLEGPPETM 68 d1ps9a3 91 ------------------------------------------------------------ 91 d1d5ta1 69 GRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEA 128 d1ps9a3 91 ------------------------------------------------------------ 91 d1d5ta1 129 LASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQDVIDFTG 188 d1ps9a3 91 -----------------------------------------KEEFYETLRYYRRMIEVTG 109 ::::::::::::::::::: d1d5ta1 189 HALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYG 248 d1ps9a3 110 VTLKLNHTVTAD-----------------QLQAFDETILASGIPNRALAQPLIDS----- 147 ::::::::: ::::::::: d1d5ta1 249 GTYMLNKPV---DDIIMENGKVVGVKSEGEVARCKQLI-----------------CDPSY 288 d1ps9a3 148 -----------GKTVHLIGGCDVAME------LDARRAIAQGTRLALEI-------- 179 ::::::: :::::::::::::::: d1d5ta1 289 VPDRVPIDDGSESQVFCS--------CSYDATTHFETTCNDIKDIYKR-MAGSAFDF 336 TMalign alignment (TM-score: 0.28 Raw score:50.47) d1ps9a3 1 ------------INTCIGCNQACLD----------------QIF----VGKVTSCLVNPR 28 ::::::: :: ::::: : : d1d5ta1 1 HHMDEEYDVIVL------GTGLTECILSGIMSVNGKKVLHM-DRNPYY---GGESS-S-I 48 d1ps9a3 29 A---CH--ETK--------------------MPILPAVQKKNLAVVGAGPAGLAFAINAA 63 : :: ::: :: :: d1d5ta1 49 TPLEELYKRFQLLEGPPETMGRGRDWNVDLI------------------PK-FL------ 83 d1ps9a3 64 ARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTL----------- 112 : ::::::::::: ::::::: :::: : ::: d1d5ta1 84 ---------M----ANGQLVKMLLY--TEVTRYL-DFKV--V----EGSFVYKGGKIYKV 121 d1ps9a3 113 KLNHTVTADQLQ-AFDE----------------------------------TILASGIPN 137 :::::::: :::: d1d5ta1 122 ----PSTETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNT--------- 168 d1ps9a3 138 RAL-AQP---LIDSGK-TV-HLI-GGCDV------------------------------- 159 ::: :: :::::: :: ::: ::::: d1d5ta1 169 SMRD-VYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYL 227 d1ps9a3 160 ------------------------------------------------------------ 160 d1d5ta1 228 YPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPS 287 d1ps9a3 160 ------------------AMELDARRAIAQGT----------------------RLALEI 179 ::::: :::: d1d5ta1 288 YVPDRVPIDDGSESQVFC----SCSYD-ATTHFETTCNDIKDIYKRMAGSAFDF------ 336 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 40 AVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQF 82 ::::::::::::::::::::::::::::::::::::::::::: d1d5ta1 3 MDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGES 45