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 | d1k6ja_ | Negative transcriptional regulator NmrA | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.213 --> HitDALI alignment (Z-score: 6.2 Raw score:559.00) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGA-GPAGLAFA 59 :::::::::: :::::::: d1k6ja_ 1 -----------------------------------------QKKTIAVVNAtGRQAASLI 19 d1ps9a3 60 INAAARGHQVTLFDAHSeiggqfniakqipgkeefyetlRYYRRMIEVTG-VTLKLNHT- 117 ::::::::::::::::: ::::::::::: :::::::: d1k6ja_ 20 RVAAAVGHHVRAQVHSL---------------------kGLIAEELQAIPnVTLFQGPLl 58 d1ps9a3 118 ---vTADQL-QAFDETILASGI-------pNRALAQPLIDSGK--TVHLiggcDVAM--- 161 ::::: :::::::::::: ::::::::::::: :::: :::: d1k6ja_ 59 nnvpLMDTLfEGAHLAFINTTSqagdeiaiGKDLADAAKRAGTiqHYIY----SSMPdhs 114 d1ps9a3 162 -------------------------------eLDAR------------------------ 166 :::: d1k6ja_ 115 lygpwpavpmwapkftvenyvrqlglpstfvyAGIYnnnftslpyplfqmelmpdgtfew 174 d1ps9a3 167 -------------RAIA-QGTRLALEI--------------------------------- 179 :::: ::::::::: d1k6ja_ 175 hapfdpdiplpwlDAEHdVGPALLQIFkdgpqkwnghrialtfetlspvqvcaafsraln 234 d1ps9a3 180 ------------------------------------------------------------ 180 d1k6ja_ 235 rrvtyvqvpkveikvnipvgyreqleaievvfgehkapyfplpefsrpaaqrvtdearkl 294 d1ps9a3 180 ---------------------------- 180 d1k6ja_ 295 wsgwrdmeeyarevfpieeeangldwml 322 FAST alignment (Normalized score: 4.17 Raw score:1001.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-AGPAGLAFA 59 ::::::::: ::::::::: d1k6ja_ 1 -----------------------------------------QKKTIAVVNATGRQAASLI 19 d1ps9a3 60 INAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETL---RYYRRMIEVT-GVTLKLN 115 ::::::::::::::: :::::::::: ::::::: d1k6ja_ 20 RVAAAVGHHVRAQVH------------------------SLKGLIAEELQAIPNVTLFQG 55 d1ps9a3 116 HTV-------TADQL-QAFDETILASGIP------NRALAQPLIDSG--------KTVHL 153 ::::: :::::::::: :::::::::: ::::: d1k6ja_ 56 ---PLLNNVPLMDTLFEGAHLAFINT---TSQAGDEIAIGKDLAD--AAKRAGTIQHYIY 107 d1ps9a3 154 IGGC-------------------------------------DVAMELDARRA-------- 168 :::: d1k6ja_ 108 ----SSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAG-------IYNNNFTS 156 d1ps9a3 169 ----------------------------------IAQGTRLALEI--------------- 179 :::::::::: d1k6ja_ 157 LPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQI-FKDGPQKWNGHRIAL 215 d1ps9a3 180 ------------------------------------------------------------ 180 d1k6ja_ 216 TFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFP 275 d1ps9a3 180 ----------------------------------------------- 180 d1k6ja_ 276 LPEFSRPAAQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 322 TMalign alignment (TM-score: 0.29 Raw score:52.61) d1ps9a3 1 -------------------------------------------------------INTCI 5 d1k6ja_ 1 QKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQG----- 55 d1ps9a3 6 GCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPA--------GLA 57 :::: ::: :::::::::: ::: :::: :: d1k6ja_ 56 --------------------PLLN-NVP-LMDTLFEGAH-LAF--INTTSQAGDEIA-IG 89 d1ps9a3 58 -FAI-NAAARG-HQVTLFDAHSEIGGQFNIAKQ----IPGKEEFYETLRYYRRMIEVTGV 110 ::: :::::: :::::: :: ::: :: ::::::::::::::::::::::: d1k6ja_ 90 KDLADAAKRAGTIQHYIY-----SS--MPD-HSLYGPWPAVPMWAPKFTVENYVRQLGLP 141 d1ps9a3 111 TLKLN----------------------------------------HTVTADQLQAFDETI 130 ::::: d1k6ja_ 142 STFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPW--------------- 186 d1ps9a3 131 LASGIPNRALAQPLI---DSGK-------------------------------------- 149 :::::::::::: : d1k6ja_ 187 ---LDAEHDVGPALLQIF---KDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYV 240 d1ps9a3 150 ----------TVHLIGGCDVAME--LDA-------------------------------- 165 : : d1k6ja_ 241 QVPKVEIKVN------------IPV--GYREQLEAIEVVFGEHKAPYFPLPEFSRPAAQR 286 d1ps9a3 166 ------------------------------------RRAIAQGTRLALEI 179 d1k6ja_ 287 VTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML-------------- 322 HHsearch alignment (Probability: 0.93 E-value:0.00) d1ps9a3 42 QKKNLAVVG-AGPAGLAFAINAAARGHQVTLFDAHSE 77 ::::::::: ::::::::::::::::::::::::::: d1k6ja_ 1 QKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLK 37