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 | d1t2da1 | Lactate dehydrogenase | 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 <-- 1.719 --> HitDALI alignment (Z-score: 5.2 Raw score:451.80) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpaVQKKNLAVVGAGPAGLAFAI 60 :::::::::::::::::::: d1t2da1 1 ----------------------------------------APKAKIVLVGSGMIGGVMAT 20 d1ps9a3 61 NAAARG-HQVTLFDAHSEIggqfniakqipgkeefyetlryYRRMIEVT--------GVT 111 :::::: :::::::::::: :::::::: ::: d1t2da1 21 LIVQKNlGDVVLFDIVKNM-------------------phgKALDTSHTnvmaysncKVS 61 d1ps9a3 112 LKlnHTVTadqLQAFDETILASGI---------------------PNRA-LAQPLID--S 147 :: :::: ::::::::::::: :::: ::::::: : d1t2da1 62 GS--NTYD--dLAGADVVIVTAGFtkapgksdkewnrddllplnnKIMIeIGGHIKKncP 117 d1ps9a3 148 GKTVHLIggCDVAM---eldarraiaqgtrlalei 179 ::::::: ::::: d1t2da1 118 NAFIIVV--TNPVDvmvqllhqhsgvpknkiiglg 150 FAST alignment (Normalized score: 4.53 Raw score:742.50) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAV-QKKNLAVVGAGPAGLAFA 59 :::::::::::::::::: d1t2da1 1 -----------------------------------------APKAKIVLVGSGMIGGVMA 19 d1ps9a3 60 INAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEFYET------LRYYRRMIEV----T 108 ::::::: :::::::::: :::::::::: : d1t2da1 20 TLIVQKNLGDVVLFDIVK---------------------NMPHGKALDTSHTNVMAYSNC 58 d1ps9a3 109 GVTLKLNHTVTADQL-------QAFDETILASGI-------------------PNRALAQ 142 :::: ::::::::::: ::::::: d1t2da1 59 KVSG-----------SNTYDDLAGADVVIVTAG-FTKAPGKSDKEWNRDDLLPLNNKIMI 106 d1ps9a3 143 PLID------SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI----------------- 179 :::: ::::::: d1t2da1 107 EIGGHIKKNCPNAFIIV--------------------------VTNPVDVMVQLLHQHSG 140 d1ps9a3 180 ---------- 180 d1t2da1 141 VPKNKIIGLG 150 TMalign alignment (TM-score: 0.42 Raw score:74.47) d1ps9a3 1 --INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAF 58 :::::::::::::::: d1t2da1 1 AP------------------------------------------KAKIVLVGSGMIGGVM 18 d1ps9a3 59 AINAAARGH-QVTLFDAHSEIG-GQFNIAKQIPGKEEFYETLRYYRRMIEVT------GV 110 ::::::::: :::::::::::: :: :::::::: :: d1t2da1 19 ATLIVQKNLGDVVLFDIVKNMPH------------------GK-ALDTSHTNVMAYSNCK 59 d1ps9a3 111 TLKLNHTVTADQL-QAFDETILASGI-------------------P--NR-ALAQPLID- 146 :::: ::: :: :::::::::::: : :: :::::::: d1t2da1 60 VSGS-NTY---DDLAGADVVIVTAGFTKAPGKSDKEWNRDDLLPLNNKIMIEIGGHIKKN 115 d1ps9a3 147 -SGKTVHLIGGCDVA--------------------MELDARRAIAQGTRL-ALEI 179 :::::::: :::: : d1t2da1 116 CPNAFIIVV--TNPVDVMVQLLHQHSGVPKNKIIG--------------LG---- 150 HHsearch alignment (Probability: 0.98 E-value:0.00) d1ps9a3 41 VQKKNLAVVGAGPAGLAFAINAAARG-HQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLR 99 :::::::::::::::::::::::::: :::::::::::: ::: ::: d1t2da1 1 APKAKIVLVGSGMIGGVMATLIVQKNLGDVVLFDIVKNM---------PHG------KAL 45 d1ps9a3 100 YYRRMIEVTGVTLKLNHTVTADQLQAFDETILASGIPNRALAQ 142 ::::::::::::::::::::::::::::::::::::: ::::: d1t2da1 46 DTSHTNVMAYSNCKVSGSNTYDDLAGADVVIVTAGFT-KAPGK 87