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 | d1sqga2 | Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), C-terminal domain | 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 <-- 1.614 --> HitDALI alignment (Z-score: 4.5 Raw score:498.90) d1ps9a3 1 -------------------intcigCNQAcldqifvgkvtsCLVN--------------- 26 :::: :::: d1sqga2 1 hpswllkrlqkaypeqwqsiveannQRPP------------MWLRinrthhsrdswlall 48 d1ps9a3 27 ----praCHETKMPI----------------------------------lpavQKKNLAV 48 :::::::: ::::::: d1sqga2 49 deagmkgFPHADYPDavrletpapvhalpgfedgwvtvqdasaqgcmtwlapqNGEHILD 108 d1ps9a3 49 VGAGPagLAFAINAAARG--HQVTLFDAHSEIggqfniakqipgkeefyetlryYRRMIE 106 ::::: ::::::::::: :::::::::::: :::::: d1sqga2 109 LCAAP--GGKTTHILEVApeAQVVAVDIDEQR-------------------lsrVYDNLK 147 d1ps9a3 107 --VTGVTLKLnHTVT-ADQL---QAFDETILASGIP------------------------ 136 :::::::: :::: :::: ::::::::::::: d1sqga2 148 rlGMKATVKQ-GDGRyPSQWcgeQQFDRILLDAPCSatgvirrhpdikwlrrdrdipela 206 d1ps9a3 137 --NRALAQPLID---sgKTVHLIGgcdVAME----------------------------- 162 :::::::::: ::::::: :::: d1sqga2 207 qlQSEILDAIWPhlktgGTLVYAT---CSVLpeenslqikaflqrtadaelcetgtpeqp 263 d1ps9a3 163 ----ldarraiaqgtrlalei 179 d1sqga2 264 gkqnlpgaeegdgffyaklik 284 FAST alignment (Normalized score: 3.65 Raw score:823.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRA------------------------------- 29 d1sqga2 1 -----------------------------HPSWLLKRLQKAYPEQWQSIVEANNQRPPMW 31 d1ps9a3 30 ------------------------CHETKMPILPAV------------------------ 41 :::::: d1sqga2 32 LRINRTHHSRDSWLALLDEAGMKGFPHADY------PDAVRLETPAPVHALPGFEDGWVT 85 d1ps9a3 42 ----------------QKKNLAVVGAGPAG-LAFAINAAA--RGHQVTLFDAHSEIGGQF 82 ::::::::::: ::::::::: :::::::::::: d1sqga2 86 VQDASAQGCMTWLAPQNGEHILDLCAA---PGGKTTHILEVAPEAQVVAVDIDE------ 136 d1ps9a3 83 NIAKQIPGKEEFYE-TLRYYRRMIE--VTGVTLKLNHTV--TADQLQ-----AFDETILA 132 :::::::::: :::::: :::: :::: :::::::: d1sqga2 137 --------------QRLSRVYDNLKRLGMKATV-KQGD-GRYPSQ--WCGEQQFDRILLD 178 d1ps9a3 133 SGIP-----------------------------NRALAQPLID---SGKTVHLIGGCDVA 160 : :::::::::: ::::::: d1sqga2 179 A---PCSATGVIRRHPDIKWLRRDRDIPELAQLQSEILDAIWPHLKTGGTLVY------- 228 d1ps9a3 161 MELDARRAIAQGTRLALEI----------------------------------------- 179 d1sqga2 229 -------------------ATCSVLPEENSLQIKAFLQRTADAELCETGTPEQPGKQNLP 269 d1ps9a3 180 --------------- 180 d1sqga2 270 GAEEGDGFFYAKLIK 284 TMalign alignment (TM-score: 0.51 Raw score:91.44) d1ps9a3 1 -------------------------INTCIGCNQACLDQIFVGKVTSCLVNPR------- 28 ::::: : ::: d1sqga2 1 HPSWLLKRLQKAYPEQWQSIVEANN------QRPPM-----------W--LRINRTHHSR 41 d1ps9a3 29 -------------ACHET-KMP-------------------------------I---LPA 40 ::::: ::: : : d1sqga2 42 DSWLALLDEAGMKGFPHADYPDAVRLETPAPVHALPGFEDGWVTVQDASAQGCMTWL--A 99 d1ps9a3 41 VQK-KNLAVVGAGPAGLAFAINAAA-RG-HQVTLFDAHSEIGGQFNIAKQIPGKEEFYET 97 ::: :::::::::: ::::::::: :: ::::::::::::: : d1sqga2 100 PQNGEHILDLCAAP--GGKTTHILEVAPEAQVVAVDIDEQRL---S-------------- 140 d1ps9a3 98 LRYYRRMIE--VTGVTLKLNHTVTADQ--L--QAFDETILASGI---------------- 135 : :::::: :::::::: ::::::: : :::::::::::: d1sqga2 141 R--VYDNLKRLGMKATVKQ-GDGRYPSQWCGEQQFDRILLDAPCSATGVIRRHPDIKWLR 197 d1ps9a3 136 -------P--NR-ALAQPLIDSGK----TVHLIGGCDVAM-------------------- 161 : :: ::::::: ::: ::::::: ::: d1sqga2 198 RDRDIPELAQLQSEILDAIW-PHLKTGGTLVYATC--SVLPEENSLQIKAFLQRTADAEL 254 d1ps9a3 162 -------------EL----DARRAIAQG-TRL---ALEI 179 :: ::: ::: : d1sqga2 255 CETGTPEQPGKQNLPGAEE--GDG-FFYA--KLIK---- 284 HHsearch alignment (Probability: 0.89 E-value:0.00) d1ps9a3 38 LPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYET 97 ::::::::::::::::::::::::::::::::::::::::: d1sqga2 98 LAPQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQR------------------- 138 d1ps9a3 98 LRYYRRMIEVTGVTLKLNHT-V----TADQLQAFDETIL-----ASGIPNRALAQPLIDS 147 :::::::::::::::::::: : ::::::::::::: :::::::::::::::: d1sqga2 139 LSRVYDNLKRLGMKATVKQGDGRYPSQWCGEQQFDRILLDAPCSATGVIRRHPDIKWLRR 198 d1ps9a3 148 GK 149 :: d1sqga2 199 DR 200