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 | d1bg6a2 | N-(1-D-carboxylethyl)-L-norvaline dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.775 --> HitDALI alignment (Z-score: 8.6 Raw score:685.30) d1nyta1 1 dgvgllsdlerlsfirpGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELA-K 59 ::::::::::::::::::::::::::::::::::::::::: : d1bg6a2 1 -----------------SKTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQdR 43 d1nyta1 60 LFA---------HTGSIQALSmdELEG--HEFDLIINATSSGisgDIPA-IPSSLIHPGI 107 ::: ::::::::: :::: ::::::::::::: :::: :::::::::: d1bg6a2 44 GAIiaegpglagTAHPDLLTS--DIGLavKDADVILIVVPAI-hhASIAaNIASYISEGQ 100 d1nyta1 108 YCYDMFYQkGKTPflAWCEQR-----GSKRNADGLGML--------------vAQAA--- 145 :::::::: :::: :::::: :::::::::::: :::: d1bg6a2 101 LIILNPGA-TGGA-lEFRKILrengaPEVTIGETSSMLftcrserpgqvtvnaIKGAmdf 158 d1nyta1 146 ---hafllwhgvlpdvepvikqLQEEls 170 :::: d1bg6a2 159 aclpaakagwaleqigsvlpqyVAVE-- 184 FAST alignment (Normalized score: 6.98 Raw score:1235.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::: d1bg6a2 1 -----------------SKTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQD- 42 d1nyta1 61 FAHTGS-----------------IQALSMDELEG--HEFDLIINATSSGISGDIPAI--- 98 :::: ::::: :::::::::: d1bg6a2 43 ------RGAIIAEGPGLAGTAHPDLLT--SDIGLAVKDADVILIVV-----------PAI 83 d1nyta1 99 --------PSSLIHPGIYCYDMFYQKGK---TPFLAWCEQRGS--KRNADGLGMLVAQAA 145 :::::::::::::::::: :::::::::::: ::::::: d1bg6a2 84 HHASIAANIASYISEGQLIILNPGAT--GGALEFRKILRENGAPEVTIGETS-------- 133 d1nyta1 146 HAFLLWHGVLPDVEPVIKQLQEELS----------------------------------- 170 d1bg6a2 134 -------------------------SMLFTCRSERPGQVTVNAIKGAMDFACLPAAKAGW 168 d1nyta1 171 ---------------- 171 d1bg6a2 169 ALEQIGSVLPQYVAVE 184 TMalign alignment (TM-score: 0.60 Raw score:102.34) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELA-- 58 : :::::::::::::::::::::::::::::::::::::::: d1bg6a2 1 ----------------S-KTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQDR 43 d1nyta1 59 KLFA--------HTGSIQALSMDELEGHEFDLIINATSSGISGDIP-AIPSSLIHPGIYC 109 :::: :::::::::::::::::::::::::: ::::::: ::::::::::::: d1bg6a2 44 GAIIAEGPGLAGTAHPDLLTSDIGLAVKDADVILIVVP-AIHHASIAANIASYISEGQLI 102 d1nyta1 110 YDMFYQKGKT-PFLAWCEQ--RGSKRNADGLGMLVAQA-----------AHAFLLWHGVL 155 :::::::::: :::::::: :::::::::: ::::: :::: : d1bg6a2 103 ILNPGATGGALEFRKILRENGAPEVTIGETS--SMLFTCRSERPGQVTV-NAIK-----G 154 d1nyta1 156 PDVEPVIK----------------------QLQEELS 170 :: ::: ::: d1bg6a2 155 --AM-DFACLPAAKAGWALEQIGSVLPQYV-AVE--- 184 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 18 GLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGS----------I 67 ::::::::::::::::::::::::::::::::::::::::::::::::: : d1bg6a2 1 SKTYAVLGLGNGGHAFAAYLALKGQSVLAWDIDAQRIKEIQDRGAIIAEGPGLAGTAHPD 60 d1nyta1 68 QALSMDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQK-GKTPFLAWCE 126 ::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::: d1bg6a2 61 LLTSDIGLAVKDADVILIVVPAIHHASIAANIASYISEGQLIILNPGATGGALEFRKILR 120 d1nyta1 127 QRGSKR 132 :::::: d1bg6a2 121 ENGAPE 126