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 | d1c0pa1 | D-aminoacid oxidase, N-terminal domain | Nucleotide-binding domain | Nucleotide-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 <-- 2.141 --> HitDALI alignment (Z-score: 9.5 Raw score:836.20) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGAGPAGLAFAI 60 ::::::::::::::::::: d1c0pa1 1 -------------------------------------lmmhSQKRVVVLGSGVIGLSSAL 23 d1ps9a3 61 NAAARGHQVTLFDAHSE-----igGQFNIAK----------------------------- 86 ::::::::::::::::: ::::::: d1c0pa1 24 ILARKGYSVHILARDLPedvssqtFASPWAGanwtpfmtltdgprqakweestfkkwvel 83 d1ps9a3 87 --------------------------------------------------qipgKEEFYE 96 :::::: d1c0pa1 84 vptghamwlkgtrrfaqnedgllghwykditpnyrplpssecppgaigvtydtlSVHAPK 143 d1ps9a3 97 TLRYYRRMIEVTGVTLKLnHTVT-ADQLQA-FDETILASGIpNRALAQP----------- 143 :::::::::::::::::: :::: :::::: :::::::::: ::::::: d1c0pa1 144 YCQYLARELQKLGATFER-RTVTsLEQAFDgADLVVNATGL-GAKSIAGiddqarggprv 201 d1ps9a3 144 ---lIDSG----------------------KTVHLIggCDVAmELDARRAIAQGTRLALE 178 :::: :::::: :::: ::::::::::::::::: d1c0pa1 202 eaerIVLPldrtksplslgrgsaraakekeVTLVHA--YGFS-SAGYQQSWGAAEDVAQL 258 d1ps9a3 179 I--------- 179 : d1c0pa1 259 Vdeafqryhg 268 FAST alignment (Normalized score: 6.46 Raw score:1414.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK------KNLAVVGAGPA 54 ::::::::::: d1c0pa1 1 -------------------------------------------LMMHSQKRVVVLGSGVI 17 d1ps9a3 55 GLAFAINAAARGHQVTLFDAHSEIG---------GQFNIAKQIPGKE------------- 92 ::::::::::::::::::::: ::::: d1c0pa1 18 GLSSALILARKGYSVHILARD----LPEDVSSQTFASPW--------AGANWTPFMTLTD 65 d1ps9a3 93 ------------------------------------------------------------ 93 d1c0pa1 66 GPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITPNYRPLPSSEC 125 d1ps9a3 93 --------------EFYETLRYYRRMIEVTGVTLKLNHTV-TADQL-QAFDETILASGIP 136 :::::::::::::::::::: ::::: ::::: :::::::::: d1c0pa1 126 PPGAIGVTYDTLSVHAPKYCQYLARELQKLGATF-ERRTVTSLEQAFDGADLVVNAT--- 181 d1ps9a3 137 NR-ALAQPLID-------------------------------------------SGKTVH 152 :::: :::::: d1c0pa1 182 --GLGAK----SIAGIDDQARGGPRVEAERIVLPLDRTKSPLSLGRGSARAAKEKEVTLV 235 d1ps9a3 153 LIGGC-DVAMEL---DARRAIAQGTRLALEI------- 179 :: ::::: ::::::::::::::: d1c0pa1 236 HA---YGFSSA-GYQQSWGAAEDVAQLVDE-AFQRYHG 268 TMalign alignment (TM-score: 0.60 Raw score:106.97) d1ps9a3 1 ----INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGL 56 ::::::::::::::: d1c0pa1 1 LMMH-----------------------------------------SQKRVVVLGSGVIGL 19 d1ps9a3 57 AFAINAAARGHQVTLFDAHSEI-G-----GQFNIAKQ----------------------- 87 ::::::::::::::::::: :: : :::::::: d1c0pa1 20 SSALILARKGYSVHILARD-LPEDVSSQTFASPWAGANWTPFMTLTDGPRQAKWEESTFK 78 d1ps9a3 88 -----------------------------------------------------------I 88 d1c0pa1 79 KWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITPNYRPLPSSECPPGAIGVTYDTL- 137 d1ps9a3 89 PGKEEFYETLRYYRRMIEVTGVTLKLNHTV-TADQLQ-AFDETILASGIPNR-ALAQP-- 143 :::::::::::::::::::::::: ::: :::::: :::::::::::::: ::::: d1c0pa1 138 --SVHAPKYCQYLARELQKLGATFER-RTVTSLEQAFDGADLVVNATGLGAKSIAGIDDQ 194 d1ps9a3 144 ----------LIDS----------------------GKTVHLIGGCDVAMELDARRAIAQ 171 :::: ::::::::: :: :::::::::: d1c0pa1 195 ARGGPRVEAERIVLPLDRTKSPLSLGRGSARAAKEKEVTLVHAYG--FS-SAGYQQSWGA 251 d1ps9a3 172 GTRLALE-I-------- 179 ::::::: : d1c0pa1 252 AEDVAQLVDEAFQRYHG 268 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 39 PAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIG-------GQFNIAKQ---- 87 ::::::::::::::::::::::::::::::::::::::::: :::::::: d1c0pa1 2 MMHSQKRVVVLGSGVIGLSSALILARKGYSVHILARDLPEDVSSQTFASPWAGANWTPFM 61 d1ps9a3 88 ------------------------------------------------------------ 88 d1c0pa1 62 TLTDGPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITPNYRPLP 121 d1ps9a3 88 -------------IPGKEEFYETLRYYRRMIEVTGVTLKLNHTVTAD-QLQAFDETILAS 133 :::::::::::::::::::::::::::::::::: :::::::::::: d1c0pa1 122 SSECPPGAIGVTYDTLSVHAPKYCQYLARELQKLGATFERRTVTSLEQAFDGADLVVNAT 181 d1ps9a3 134 GIPNRAL 140 ::::::: d1c0pa1 182 GLGAKSI 188