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 | d1jsxa_ | Glucose-inhibited division protein B (GidB) | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 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 <-- 1.290 --> HitDALI alignment (Z-score: 4.2 Raw score:421.90) d1ps9a3 1 intcigcnqacldqifvgkVTSClvnpRACHETKMPIL---------------------- 38 :::: ::::::::::: d1jsxa_ 1 -------------------MLNK--lsLLLKDAGISLTdhqknqliayvnmlhkwnemlv 39 d1ps9a3 39 ----------pavqkKNLAVVGAGPagLAFAINAAARG--HQVTLFDAHSEIggqfniak 86 :::::::::: ::::::::::: :::::::::::: d1jsxa_ 40 rhildsivvapylqgERFIDVGTGP--GLPGIPLSIVRpeAHFTLLDSLGKR-------- 89 d1ps9a3 87 qipgkeefyetlryYRRMI--EVTG-VTLKLnHTVTadQLQA-FDETILASgIPNR-ALA 141 ::::: :::: ::::: :::: :::: :::::::: :::: ::: d1jsxa_ 90 -----------vrfLRQVQheLKLEnIEPVQ-SRVEefPSEPpFDGVISRA-FASLnDMV 136 d1ps9a3 142 QPL---idSGKTVHLiggcDVAME--------------------ldarraiaqgtrlale 178 ::: ::::::: ::::: d1jsxa_ 137 SWChhlpgEQGRFYA----LKGQMpedeiallpeeyqvesvvklqvpdgerhlvvikank 192 d1ps9a3 179 i 179 d1jsxa_ 193 i 193 FAST alignment (Normalized score: 3.17 Raw score:590.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNP------RACHETKMPILPAVQK----------- 43 :::::::::: d1jsxa_ 1 ---------------------------MLNKLSLLLKDAGISL------TDHQKNQLIAY 27 d1ps9a3 44 ---------------------------KNLAVVGAGPAG-LAFAINAAA--RGHQVTLFD 73 ::::::::: ::::::::: ::::::::: d1jsxa_ 28 VNMLHKWNEMLVRHILDSIVVAPYLQGERFIDVGTG---PGLPGIPLSIVRPEAHFTLLD 84 d1ps9a3 74 AHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVT---GVTLKLNHTVTADQLQ------ 124 :: :::::::::::::: :::::: d1jsxa_ 85 SL-------------------GKRVRFLRQVQHELKLENIEPVQ----------SRVEEF 115 d1ps9a3 125 ----AFDETILASGIPNR---ALAQPLID--------SGKTVHLIGGCDVAMELDARRAI 169 ::::::: ::::::: ::::::: d1jsxa_ 116 PSEPPFDGVIS-------RAFASLNDMV-SWCHHLPGEQGRFYA---------------- 151 d1ps9a3 170 AQGTRLALEI------------------------------------------ 179 d1jsxa_ 152 ----------LKGQMPEDEIALLPEEYQVESVVKLQVPDGERHLVVIKANKI 193 TMalign alignment (TM-score: 0.45 Raw score:80.69) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPIL--P------------------- 39 : : : ::: : :::::::::: : d1jsxa_ 1 ---M-L----N---------KLS--L--LLKDAGISLTDHQKNQLIAYVNMLHKWNEMLV 39 d1ps9a3 40 ---------AV--QKKNLAVVGAG--PAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAK 86 :: ::::::::::: :::::::::: ::::::::::::::: d1jsxa_ 40 RHILDSIVVAPYLQGERFIDVGTGPGLPGIPLSIVR--PEAHFTLLDSLGKRV------- 90 d1ps9a3 87 QIPGKEEFYETLRYYRRMIE--VTG-VTLKLNHTVTADQLQAFDETILASGIPNR-ALAQ 142 :: :::::: ::: ::::: ::::::::::::::::::::::: :::: d1jsxa_ 91 -----------RF-LRQVQHELKLENIEPVQ-SRVEEFPSEPPFDGVISRAFASLNDMVS 137 d1ps9a3 143 --PLIDSG-KTVHLIGG-CDV---------------------AMELDARR---AIAQ-GT 173 :::::: :::::::: :: : : d1jsxa_ 138 WCHHLPGEQGRFYALKGQ-MPEDEIALLPEEYQVESVVKLQV-------PDGE---RH-- 184 d1ps9a3 174 R--------LALEI 179 : d1jsxa_ 185 LVVIKANKI----- 193 HHsearch alignment (Probability: 0.71 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 :::::::::::::::::::::::::::::::::::::::::: :: d1jsxa_ 48 VAPYLQGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKR----------------VR 91 d1ps9a3 97 TLRYYRRMIEVTGVTLKLNHTVTADQLQAFDETIL 131 ::::::::::::::::::::::::::::::::::: d1jsxa_ 92 FLRQVQHELKLENIEPVQSRVEEFPSEPPFDGVIS 126