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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1nyta1 | Shikimate 5-dehydrogenase AroE | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1m2ka_ | AF1676, Sir2 homolog (Sir2-AF1?) | DHS-like NAD/FAD-binding domain | DHS-like NAD/FAD-binding domain | α/β |
Query <-- 0.853 --> IntermediateDALI alignment (Z-score: 3.8 Raw score:453.70) query 1 dadeevYSALVVGL--rAYVAkngfRSVLIGLSgGIDSALVAAIACDALGaqNVYGVSMp 58 :::::::: :::: :::::::: :::::::::::::::: ::::::: d1nyta1 1 -----dGVGLLSDLerlSFIR--pgLRILLIGA-GGASRGVLLPLLSLDC--AVTITNR- 49 query 59 skyssdhSKGDAAELARRTG----LNFRTVSiepmfdaymaslgltglaeenlqsrlrgt 114 ::::::::::::: ::::::: d1nyta1 50 -------TVSRAEELAKLFAhtgsIQALSMD----------------------------- 73 query 115 tlmaisNQEGH-IVLAPgnkselavGYSTLY-------gdsvgAYGPikdvyktsifrla 166 ::::: ::::: :::::: :::: d1nyta1 74 ----elEGHEFdLIINA----tssgISGDIPaipsslihpgiyCYDM------------- 112 query 167 ewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktl 226 d1nyta1 113 ------------------------------------------------------------ 113 query 227 rmvdtaeyKRRQY-------------PPGTK-------------------iSAKGFG-KD 253 ::::: ::::: :::::: :: d1nyta1 113 ------fyQKGKTpflawceqrgskrNADGLgmlvaqaahafllwhgvlpdVEPVIKqLQ 166 query 254 RRlpitnrwregh 266 :: d1nyta1 167 EE---------ls 170 FAST alignment (Normalized score: 2.78 Raw score:591.60) query 1 DADEEV-YSALVVGLRAYVAKNGF-------RSVLIGLSGGIDSALVAAIACDALGAQ-N 51 :::::::::: ::::: :::::::::::::::: : d1nyta1 1 ------DGVGLLSDLER-------LSFIRPGLRILL-IGAGGASRGVLLPLLS-----LD 41 query 52 VYGVSMPSKYSSDH--SKGDAAELARRTG----LNFRTVSIEPMFDAYMASLGLTGLAEE 105 :::::: ::::::::::: :::::: d1nyta1 42 CAVTIT--------NRTVSRAEELAKL--FAHTGSIQAL--------------------- 70 query 106 NLQSRLRGTTLMAISNQEG---HIVLAPGNK-SELAVGYSTLYGDSVGAYGPIKDVYKTS 161 ::::::: :::::: :::::::::: d1nyta1 71 ------SMDELEG------HEFDLIINA---TSSGISGDIPA------------------ 97 query 162 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 221 d1nyta1 98 ------------------------------------------------------------ 98 query 222 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 266 d1nyta1 98 ---------------------------------------------IPSSLIHPGIYCYDM 112 query 267 ---------------------------------------------------------- 267 d1nyta1 113 FYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 TMalign alignment (TM-score: 0.35 Raw score:94.08) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :: :::::::::::::: :::::::::::::::::::::::: : :::::::: d1nyta1 1 --DG-VGLLSDLERLSFIR---PGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNR-- 49 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE-PM-------------FDAYMASLGLTGL-AEE 105 ::: :::::::::::::::::::::: : : :: d1nyta1 50 -TVS-RAEELAKLFAHTGSIQALSMDEL-EGHEFDLIINATSS------------GI-SG 93 query 106 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS--V----G-AYGPIKDVY 158 : :: :::::::: : : :::::: :::::::: : : : : ::::::::: d1nyta1 94 D-IP-AIPSSLIH--P--G-IYCYDM---FYQKGKTP--F-LAWCEQRGSKRNADGLGML 140 query 159 KTSI-FRL--AEW------RNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 :::: :: : d1nyta1 141 VAQAA-HAFL--LWHGVLP----------------------------------------- 156 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 :::::::::::::: d1nyta1 157 -----------------------------------DVEPVIKQLQEELS-------- 170 HHsearch alignment (Probability: 0.04 E-value:0.17) query 7 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 66 ::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1nyta1 2 GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--SLDCAVTIT---------NRT 50 query 67 KGDAAELARRTGLNFRTVSIE 87 ::::::::::::::::::::: d1nyta1 51 VSRAEELAKLFAHTGSIQALS 71
Intermediate <-- 1.097 --> HitDALI alignment (Z-score: 5.9 Raw score:473.20) d1nyta1 1 dgvgllsDLERLS-FIRPGLRILLIG---------------------------------- 25 :::::: :::::::::::: d1m2ka_ 1 -------MDEKLLkTIAESKYLVALTgagvsaesgiptfrgkdglwnryrpeelanpqaf 53 d1nyta1 26 ---------------------agGASRGVLLPLLSLDCAVTITNRTVSraEELAKLFaht 64 ::::::::::::::::::::::::: ::::::: d1m2ka_ 54 akdpekvwkwyawrmekvfnaqpNKAHQAFAELERLGVLKCLITQNVD--DLHERAG--- 108 d1nyta1 65 gsIQALSM---------------------------------------------------- 72 :::::: d1m2ka_ 109 -sRNVIHLhgslrvvrctscnnsfevesapkipplpkcdkcgsllrpgvvwagemlppdv 167 d1nyta1 73 -DELEGH--EFDLIINATSSGisgdiPAIP-SSLIHPGIYCYDMFYQkgKTPFLAWCeqr 128 :::::: :::::::::::: :::: :::::::::::::::: :::::::: d1m2ka_ 168 lDRAMREveRADVIIVAGTSA-vvqpAASLpLIVKQRGGAIIEINPD--ETPLTPIA--- 221 d1nyta1 129 gskrNADGLgmlvaqaahafllwhgvlpdvepvikqlqeels 170 ::::: d1m2ka_ 222 ----DYSLR----------gkagevmdelvrhvrkalslkln 249 FAST alignment (Normalized score: 2.46 Raw score:506.50) d1nyta1 1 DGVGLLSDLER-----LSFI--RPGLRILLIGA--------------------------- 26 :::: :::::::: d1m2ka_ 1 -----------MDEKLLKTIAESKYLVALT---GAGVSAESGIPTFRGKDGLWNRYRPEE 46 d1nyta1 27 -----------------------------GGASRGVLLPLLSLD--CAVTITNRTVSRAE 55 ::::::::::::::: :::::::: ::::: d1m2ka_ 47 LANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNV-DDLHE 105 d1nyta1 56 ELAKLFAH--TGSIQAL------------------------------------------- 70 : :::::: d1m2ka_ 106 R-------AGSRNVIH-LHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVV 157 d1nyta1 71 ---------SMDELEG--HEFDLIINATSSGISGDIPAI---------PSSLIH------ 104 ::::::: :::::::: :::: d1m2ka_ 158 WAGEMLPPDVLDRAMREVERADVIIV-------------AGTSAVVQPAASL--PLIVKQ 202 d1nyta1 105 PGIYCYDMFYQKG---KTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPV 161 :::::::: :::::: :::::: d1m2ka_ 203 RGGAIIEI-----NPDETPLTP-----IADYSL--------------------------- 225 d1nyta1 162 IKQLQEELS------------------------ 170 d1m2ka_ 226 ---------RGKAGEVMDELVRHVRKALSLKLN 249 TMalign alignment (TM-score: 0.39 Raw score:66.63) d1nyta1 1 -------------------------D---------------------------------- 1 : d1m2ka_ 1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKV 60 d1nyta1 2 ---------------GVGLLSDLERLSFIRPG--LRILLIGAGGASRGVLLPLLSLDCAV 44 ::::::::: :::::: :::::::: : ::::::::::: d1m2ka_ 61 WKWYAWRMEKVFNAQPNKAHQAFA--ELERLGVLKCLITQNV----D--DLHERAGSRNV 112 d1nyta1 45 TITNRTVSRAEELA----------KLFA-------------------HTGSIQAL----- 70 :::: ::::: :::: ::: d1m2ka_ 113 IHLH-----GSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRP-----GVVWAGEM 162 d1nyta1 71 SMDELEGHEFDLIINATSSGISGDIPAIPSSLI-HPGIYCYDMFYQKGKTP----F-LAW 124 :::::::: : : ::: ::::::::::: :: : ::: d1m2ka_ 163 LPPDVLDR-A------------------M-REVERADVIIVAGTS----AVVQPAASLPL 198 d1nyta1 125 -CEQRGSKRNADG---------------LGMLVAQAAHAFLLWHGVLPDVE--------- 159 :::::::::::: ::::::: :: d1m2ka_ 199 IVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVM--------------DELVRHVRKAL 244 d1nyta1 160 -----PVIKQLQEELS 170 d1m2ka_ 245 SLKLN----------- 249 HHsearch alignment (Probability: 0.31 E-value:0.00) d1nyta1 20 RILLIGAGGASRG 32 ::::::::::::: d1m2ka_ 15 LVALTGAGVSAES 27