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 | d1uira_ | Spermidine synthase | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 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 <-- 1.520 --> HitDALI alignment (Z-score: 4.1 Raw score:463.00) d1ps9a3 1 ---------------------------------intCIGCNQAC--ldqifvgkvtsCLV 25 :::::::: ::: d1uira_ 1 mdygmyffehvtpyetlvrrmerviasgktpfqdyfLFESKGFGkvlildkdvqsteRDE 60 d1ps9a3 26 NPrachetkmpilpaVQKKNLAVVGAGPagLAFAINAAARG--HQVTLFDAHSEIGgqfn 83 :: ::::::::::::: ::::::::::: ::::::::::::: d1uira_ 61 YIyhetlvhpamlthPEPKRVLIVGGGE--GATLREVLKHPtvEKAVMVDIDGELV---- 114 d1ps9a3 84 iakqipgkeefYETLRYYRRMIEVTGVTLKLnHTVT--ADQLQ-AFDETILASGIP---- 136 :::::::::::::::::::: :::: ::::: :::::::::::: d1uira_ 115 -------evakRHMPEWHQGAFDDPRAVLVI-DDARayLERTEeRYDVVIIDLTDPvged 166 d1ps9a3 137 --NRALAQ-PLIDSGK-------TVHLIggcDVAM-----------------------el 163 :::::: ::::::: ::::: :::: d1uira_ 167 npARLLYTvEFYRLVKahlnpggVMGMQ---TGMIllrvhpvvhrtvreafryvrsyknh 223 d1ps9a3 164 DARR-------------------------------------------------------- 167 :::: d1uira_ 224 IPGFflnfgfllasdafdpaafsegviearirernlalrhltapyleamfvlpkdlleal 283 d1ps9a3 168 --------------aiaqgtrlalei 179 d1uira_ 284 eketmvstdqnpfyvtpegearqapy 309 FAST alignment (Normalized score: 2.23 Raw score:523.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK----------------- 43 d1uira_ 1 -------------------------------------------MDYGMYFFEHVTPYETL 17 d1ps9a3 44 ------------------------------------------------------------ 44 d1uira_ 18 VRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPE 77 d1ps9a3 44 -KNLAVVGAGPAG--LAFAINAAARG---HQVTLFDAHSEIGGQFNIAKQIPGK------ 91 :::::::: :::::::::: :::::::: d1uira_ 78 PKRVLIVGG----GEGATLREVLKH-PTVEKAVMVDI-----------------DGELVE 115 d1ps9a3 92 ---EEFYETLRYYRRMIEV--TGVTLKLNHTV------TADQLQ---AFDETILASGIPN 137 ::::::::::: :::::: :::: :::::::::: d1uira_ 116 VAKRHMPEWHQGAF-----DDPRAVLV-----IDDARAYLER--TEERYDVVIIDLT--- 160 d1ps9a3 138 RA----------------LAQPLID---SGKTVHLIGGCDVAMELDARRAIAQGTRLALE 178 ::::::: :::::: d1uira_ 161 --DPVGEDNPARLLYTVEFYRLVKAHLNPGGVMG-------------------------- 192 d1ps9a3 179 I----------------------------------------------------------- 179 d1uira_ 193 -MQTGMILLRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIE 251 d1ps9a3 180 ---------------------------------------------------------- 180 d1uira_ 252 ARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 309 TMalign alignment (TM-score: 0.51 Raw score:91.58) d1ps9a3 1 --------------------------------------INTCIGCNQA------------ 10 :::::: d1uira_ 1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLF----ESKGFGKVLILDKDVQST 56 d1ps9a3 11 CLDQIFVGKVTSCLVNPR---------ACHETKMPIL-PAVQKKNLAVVGAGPAGLAFAI 60 ::::::: : :::::::::::::: ::::: d1uira_ 57 -----------ERDEYIYHETLVHPAM---------LT-HPEPKRVLIVGGGE--GATLR 93 d1ps9a3 61 NAAARG-H-QVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLKLNHTV 118 :::::: : ::::::::::::: : : ::::::::::::::::::::: ::: d1uira_ 94 EVLKHPTVEKAVMVDIDGELVE--V--A-------KRHMPEWHQGAFDDPRAVLVI-DDA 141 d1ps9a3 119 T--ADQLQ-AFDETILASGIP------NRALA-QPLIDSGK-------TVHLIGGCDVAM 161 : ::::: :::::::::::: ::::: :::::::: ::::: :::: d1uira_ 142 RAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQ---TGMI 198 d1ps9a3 162 E-----------------------LDARR-A-IA-Q------------------------ 171 : ::::: : : : d1uira_ 199 LLRVHPVVHRTVREAFRYVRSYKNHIPGFFLN-FGFLLASDAFDPAAFSEGVIEARIRER 257 d1ps9a3 172 ---GT-RL-AL--E----------------------------------------I 179 : :: : : d1uira_ 258 NLA-LRHLT-APYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY- 309 HHsearch alignment (Probability: 0.93 E-value:0.00) d1ps9a3 17 VGKVTSCLVNPR-ACHE--TKMPILPAVQKKNLAVVGAGPAGLAFAINAAARG-HQVTLF 72 :::::::::::: :::: :::::::::::::::::::::::::: ::::::: :::::: d1uira_ 49 LDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLR-EVLKHPTVEKAVMV 107 d1ps9a3 73 DAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLKLNHTV--TADQLQAFDETI 130 :::::::::: :: ::::: :::::::::::::::::: :::::::::::: d1uira_ 108 DIDGELVEVA---KR--HMPEW------HQGAFDDPRAVLVIDDARAYLERTEERYDVVI 156 d1ps9a3 131 LAS 133 ::: d1uira_ 157 IDL 159