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 | d1ep3b2 | Dihydroorotate dehydrogenase B, PyrK subunit | Ferredoxin reductase-like, C-terminal NADP-linked domain | Ferredoxin reductase-like, C-terminal NADP-linked 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 <-- 1.489 --> HitDALI alignment (Z-score: 5.2 Raw score:393.80) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQK--KNLAVVG---aGPAG 55 :::: ::::::: :::: d1ep3b2 1 -------------------------------------pvAEVTstDKILIIGggigVPPL 23 d1ps9a3 56 LAFAINAAARGHQVTLFDAH----SEIGgqfniakqipgkeefyetlrYYRRMIevTGVT 111 :::::::::::::::::::: :::: :::::: :::: d1ep3b2 24 YELAKQLEKTGCQMTILLGFasenVKIL-------------------eNEFSNL--KNVT 62 d1ps9a3 112 LKLN----------HTVT-aDQLQ-AFDETILaSGIPN--RALAQPLIdSGKTVH----- 152 :::: :::: :::: ::::::: ::::: :::::::: :::::: d1ep3b2 63 LKIAtddgsygtkgHVGMlmNEIDfEVDALYT-CGAPAmlKAVAKKYD-QLERLYismes 120 d1ps9a3 153 -------------liggcdvameldarraiaqgtrlalei 179 d1ep3b2 121 rmacgigacyacvehdkedeshalkvcedgpvflgkqlsl 160 FAST alignment (Normalized score: 2.78 Raw score:470.70) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP------AVQKKNLAVVGA--- 51 ::::::::: d1ep3b2 1 ---------------------------------------PVAEVTSTDKILIIG---GGI 18 d1ps9a3 52 -GPAGLAFAINAAARG--HQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRY------YR 102 ::::::::::::::: :::::::: :: d1ep3b2 19 GVPPLYELAKQLEKTGCQMTILLGFA--------------------------SENVKILE 52 d1ps9a3 103 RMIEV---TGVTLKLNHTVTADQLQ---------------------AFDETILASGIPNR 138 ::::: :::::: ::::::::: :: d1ep3b2 53 NEFSNLKNVTLKIA-----------TDDGSYGTKGHVGMLMNEIDFEVDALYTCG---AP 98 d1ps9a3 139 ALAQPLIDSG-----KTVHLIGGCDVAMELDARRAIAQGTRLALEI-------------- 179 :::::::: :::::: d1ep3b2 99 AMLKAVAK--KYDQLERLYIS-------------------------MESRMACGIGACYA 131 d1ps9a3 180 ----------------------------- 180 d1ep3b2 132 CVEHDKEDESHALKVCEDGPVFLGKQLSL 160 TMalign alignment (TM-score: 0.44 Raw score:79.48) d1ps9a3 1 -INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK-KNLAVVGA---GPAG 55 :: :::: :::::::: :::: d1ep3b2 1 P------------------------------------VA-EVTSTDKILIIGGGIGVPPL 23 d1ps9a3 56 LAFAINAAARGHQVTLFDAH--S-EIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTL 112 :::::::::::::::::::: : ::: : :::::::::::: d1ep3b2 24 YELAKQLEKTGCQMTILLGFASENVKI------------------L--ENEFSNLKNVTL 63 d1ps9a3 113 KLN-------H---TVTADQ-L-QAFDETILASGIPN-RA-LAQPLIDSGKT-VHLIGGC 157 ::: : :::::: : ::::::::: :::: :: :::::: ::: :::: d1ep3b2 64 KIATDDGSYGTKGHVGMLMNEIDFEVDALYTC-GAPAMLKAVAKKYD--QLERLYIS--- 117 d1ps9a3 158 DVAME--L---------------------DARR---AIAQG--------TRLALEI 179 ::::: : : :: d1ep3b2 118 MESRMACGIGACYACVEHDKEDESHALKV---CEDG---PVFLGKQLSL------- 160 HHsearch alignment (Probability: 0.66 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPA---GLAFAINAAARGHQVTLFDAHSEI 78 :::::::::::::::::: :::::::::::::::::::::::: d1ep3b2 2 VAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASE 46