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 | d1mo9a2 | NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase | 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 <-- 1.973 --> HitDALI alignment (Z-score: 6.0 Raw score:462.40) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqKKNLAVVGAGPAGLAFAI 60 :::::::::::::::::: d1mo9a2 1 ---------------------gvnakgvfdhatlveeldyepGSTVVVVGGSKTAVEYGC 39 d1ps9a3 61 NAAARGHQVTLFDAhSEIGgQFNIakqipgkeeFYETLRYYRRMIEVTGVTLKLNHTVTA 120 :::::::::::::: :::: :::: ::::::::::::::::::::::::::: d1mo9a2 40 FFNATGRRTVMLVR-TEPL-KLIK---------DNETRAYVLDRMKEQGMEIISGSNVTR 88 d1ps9a3 121 D-------------------QLQAFDETILASGipnralaqplidsgktvhliggcdvam 161 : ::::::::::::: d1mo9a2 89 IeedangrvqavvamtpngeMRIETDFVFLGLG--------------------------- 121 d1ps9a3 162 eldarraiaqgtrlalei 179 d1mo9a2 122 ------------------ 122 FAST alignment (Normalized score: 6.32 Raw score:930.60) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP----------------AVQK- 43 :::: d1mo9a2 1 ---------------------------------------GVNAKGVFDHATLVEELDYEP 21 d1ps9a3 44 -KNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEE--FYETLRY 100 ::::::::::::::::::::::::::::::: :::::: ::::::: d1mo9a2 22 GSTVVVVGGSKTAVEYGCFFNATGRRTVMLVR-TEPLKL------------IKDNETRAY 68 d1ps9a3 101 YRRMIEVTGVTLKLNHTVTAD----------------------QLQAFDETILASGIPNR 138 :::::::::::::::::: :::::::::::: d1mo9a2 69 VLDRMKEQGMEIISGSNV---TRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGL----- 120 d1ps9a3 139 ALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI- 179 d1mo9a2 121 -----------------------------------------G 121 TMalign alignment (TM-score: 0.39 Raw score:69.62) d1ps9a3 1 -------------------INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAV 41 : d1mo9a2 1 GVNAKGVFDHATLVEELDY----------------------------------------E 20 d1ps9a3 42 QKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYY 101 :::::::::::::::::::::::::::::::::: :::: :: : : ::: :::: d1mo9a2 21 PGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRT-EPLK-LI--K-----D-NET-RAYV 69 d1ps9a3 102 RRMIEVTGVTLKLNHTVTAD-----------Q--------LQAFDETILASGIPNRALAQ 142 :::::::::::::::::::: : :::::::::::: d1mo9a2 70 LDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRIETDFVFLGLG-------- 121 d1ps9a3 143 PLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 d1mo9a2 122 ------------------------------------- 122 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 39 PAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETL 98 :::::::::::::::::::::::::::::::::::::::::::: ::::: d1mo9a2 18 DYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKLIK-----------DNETR 66 d1ps9a3 99 RYYRRMIEVTGVTLKLNHTVTAD 121 ::::::::::::::::::::::: d1mo9a2 67 AYVLDRMKEQGMEIISGSNVTRI 89