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 | d1kjqa2 | Glycinamide ribonucleotide transformylase PurT, N-domain | PreATP-grasp domain | PreATP-grasp 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 <-- 1.135 --> HitDALI alignment (Z-score: 5.9 Raw score:422.80) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQK-----KNLAVVGAGPAG 55 :::: :::::::::::: d1kjqa2 1 -------------------------------------tlLGTAlrpaaTRVMLLGSGELG 23 d1ps9a3 56 LAFAINAAARGHQVTLFDAHSEIGgqfniakqipgkeefyetlryyrrmievtgVTLKlN 115 :::::::::::::::::::::::: :::: : d1kjqa2 24 KEVAIECQRLGVEVIAVDRYADAP-------------------------amhvaHRSH-V 57 d1ps9a3 116 HTV----TADQLQ---AFDETILASGIpnRALAQPLIDSGKTVH-liggCDVAmeldarr 167 ::: :::::: ::::::::::: ::::::::::::::: :::: d1kjqa2 58 INMldgdALRRVVeleKPHYIVPEIEAiaTDMLIQLEEEGLNVVpcaraTKLT------- 110 d1ps9a3 168 aiaqgtrlalei 179 d1kjqa2 111 -----------m 111 FAST alignment (Normalized score: 4.71 Raw score:663.60) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAV---------QKKNLAVVGA 51 :::::::::: d1kjqa2 1 -----------------------------------------TLLGTALRPAATRVMLLGS 19 d1ps9a3 52 GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLR-YYRRMIEVTG- 109 :::::::::::::::::::::::::: ::::: d1kjqa2 20 GELGKEVAIECQRLGVEVIAVDRYAD----------------------APAMHV-----A 52 d1ps9a3 110 VTLKLNHTVTADQL----------------QAFDETILASGIP-----NRALAQPLIDSG 148 :::: :::::::: :::::::::::: d1kjqa2 53 HRSH----------VINMLDGDALRRVVELEKPHYIVP-----EIEAIATDMLIQLEEEG 97 d1ps9a3 149 KTVHLIGGCDVAMELDARRAIAQGTRLALEI----------- 179 ::: d1kjqa2 98 LNV----------------------------VPCARATKLTM 111 TMalign alignment (TM-score: 0.41 Raw score:73.16) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK-------KNLAVVGAGP 53 :::: :::::::::: d1kjqa2 1 ---------------------------------------TLLGTALRPAATRVMLLGSGE 21 d1ps9a3 54 AGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLK 113 :::::::::::::::::::::::::: : :: : :::: d1kjqa2 22 LGKEVAIECQRLGVEVIAVDRYADAP------------------A--MH--V----AHRS 55 d1ps9a3 114 LNHT-V----TADQLQ---AFDETILASGIPNRALAQPLIDS--G-KTVHL---IGGCD- 158 : :: : :::::: ::::::::: ::::::::::: : ::::: :: d1kjqa2 56 H-VINMLDGDALRRVVELEKPHYIVPEI---EAIATDMLIQLEEEGLNVVPCAR---ATK 108 d1ps9a3 159 -VAMELDARRAIAQGTRLALEI 179 :: d1kjqa2 109 LTM------------------- 111 HHsearch alignment (Probability: 0.97 E-value:0.00) d1ps9a3 40 AVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEI 78 ::::::::::::::::::::::::::::::::::::::: d1kjqa2 8 RPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADA 46