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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ps9a3 | 2,4-dienoyl-CoA reductase, middle domain | Nucleotide-binding domain | Nucleotide-binding domain | α/β |
| Hit | d1ojta2 | Dihydrolipoamide dehydrogenase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
Query <-- 1.613 --> IntermediateDALI 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 <-- 1.849 --> HitDALI alignment (Z-score: 6.1 Raw score:456.90) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQK-KNLAVVGAGPAGLAFA 59 :::: :::::::::::::::: d1ojta2 1 ------------------vtklpfipedpriidssgalaLKEVpGKLLIIGGGIIGLEMG 42 d1ps9a3 60 INAAARGHQVTLFDAHSEIGGQFniakqipgkeeFYETLRYYRRMIEvTGVT-LKLNHTV 118 ::::::::::::::::::::::: ::::::::::::: :::: ::::::: d1ojta2 43 TVYSTLGSRLDVVEMMDGLMQGA-----------DRDLVKVWQKQNE-YRFDnIMVNTKT 90 d1ps9a3 119 TAD------------------qLQAFDETILASGIpnralaqplidsgktvhliggcdva 160 ::: ::::::::::::: d1ojta2 91 VAVepkedgvyvtfeganapkePQRYDAVLVAAGR------------------------- 125 d1ps9a3 161 meldarraiaqgtrlalei 179 d1ojta2 126 ------------------- 126 FAST alignment (Normalized score: 6.12 Raw score:914.90) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPIL--------------------PA 40 :: d1ojta2 1 --------------------------------------VTKLPFIPEDPRIIDSSGALAL 22 d1ps9a3 41 VQK-KNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEE-FYETL 98 ::: :::::::::::::::::::::::::::::::::::::: ::::: d1ojta2 23 KEVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQG------------ADRDLV 70 d1ps9a3 99 RYYRRMIEVTG--VTLKLNHTVTADQ----------------------LQAFDETILASG 134 ::::::::: ::::::::: ::::::::::: d1ojta2 71 KVWQKQNEY--RFDNIMVNTKT----VAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAA- 123 d1ps9a3 135 IPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI-- 179 d1ojta2 124 ---------------------------------------------GR 125 TMalign alignment (TM-score: 0.40 Raw score:70.87) d1ps9a3 1 -----------------------INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPI 37 d1ojta2 1 VTKLPFIPEDPRIIDSSGALALK------------------------------------- 23 d1ps9a3 38 LPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYET 97 :::::::::::::::::::::::::::::::::::::::: : : : ::: d1ojta2 24 ---EVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQ--G--A-----D-RDL- 69 d1ps9a3 98 LRYYRRMIEVTGVT-LKLNHTVTAD---------Q---------LQAFDETILASGIPNR 138 :::::::::: ::: :::::::::: : :::::::::::: d1ojta2 70 VKVWQKQNEY-RFDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAG---- 124 d1ps9a3 139 ALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 : d1ojta2 125 -----------------R----------------------- 125 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 36 PILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFY 95 :::::::::::::::::::::::::::::::::::::::::::: :: ::: d1ojta2 19 ALALKEVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLM---------QG--ADR 67 d1ps9a3 96 ETLRYYRRMIEVTGVTLKLNHTVTADQL------------------QAFDETILASG 134 :::::::::::::::::::::::::::: ::::::::::: d1ojta2 68 DLVKVWQKQNEYRFDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAG 124