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 | d1vlla_ | Archaeal alanine 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 <-- 2.315 --> HitDALI alignment (Z-score: 9.8 Raw score:816.90) d1nyta1 1 ------------------------------------------------------------ 1 d1vlla_ 1 metliltqeeveslismdeamnaveeafrlyalgkaqmppkvylefekgdlrampahlmg 60 d1nyta1 1 ------------------------------------------------DGVGLLSDLErL 12 :::::::::: : d1vlla_ 61 yaglkwvnshpgnpdkglptvmalmilnspetgfplavmdatyttslrTGAAGGIAAK-Y 119 d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLL-SLDC-AVTITNRTVSRAEELAKLFAHTGS-IQA 69 :::::::::::::::::::::::::: :::: :::::::::::::::::::::::: ::: d1vlla_ 120 LARKNSSVFGFIGCGTQAYFQLEALRrVFDIgEVKAYDVREKAAKKFVSYCEDRGIsASV 179 d1nyta1 70 LSMDEleghEFDLIINATSSgisGDIPaIPSSLIHPGIYCYDM-FYQKGkTPFL-AWCEq 127 ::::: ::::::::::: :::: ::::::::::::::: ::::: :::: :::: d1vlla_ 180 QPAEE--asRCDVLVTTTPS---RKPV-VKAEWVEEGTHINAIgADGPG-KQELdVEIL- 231 d1nyta1 128 RGSK--------------------------------------------------RNADGL 137 :::: :::::: d1vlla_ 232 KKAKivvddleqakhggeinvavskgvigvedvhatigeviaglkdgresdeeiTIFDST 291 d1nyta1 138 gmLVAQAAHAFLLWHGVlpdvepvikqlqeels 170 ::::::::::::::: d1vlla_ 292 --GLAIQDVAVAKVVYE-nalsknvgskikffr 321 FAST alignment (Normalized score: 6.12 Raw score:1429.00) d1nyta1 1 D----------------------------------------------------------- 1 d1vlla_ 1 -METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLM 59 d1nyta1 2 ----------------------------------------------GVGLLSDLERL--- 12 :::::::::: d1vlla_ 60 GYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGI-AAK 118 d1nyta1 13 SFIRPG-LRILLIGAGGASRGVLLPLLSLD----CAVTITNRTVSRAEELAKLFAHTG-S 66 :::::: ::::::::::::::::::::: :::::::::::::::::::::::: : d1vlla_ 119 YLARKNSSVFGFIGCGTQAYFQLEALRR--VFDIGEVKAYDVREKAAKKFVSYCEDRGIS 176 d1nyta1 67 IQALSMDELEG--HEFDLIINATSSGISGDIP----AIPSSLIHPGIYCYDMFYQKGKTP 120 ::::::: ::::::::::: :::::::::::::::::::::: d1vlla_ 177 ASVQPAE----EASRCDVLVTTTP--------SRKPVVKAEWVEEGTHINAIGADGPG-- 222 d1nyta1 121 F----LAWCEQRGS---------------------------------------------- 130 :::::: d1vlla_ 223 -KQELDVEILK---KAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDG 278 d1nyta1 131 ------KRNADGL----GMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---------- 170 :::::: ::::::::::::::: d1vlla_ 279 RESDEEITIFDS-TGLAIQDVAVAKVVYENAL------------------SKNVGSKIKF 319 d1nyta1 171 -- 171 d1vlla_ 320 FR 321 TMalign alignment (TM-score: 0.65 Raw score:111.10) d1nyta1 1 ------------------------------------------------------------ 1 d1vlla_ 1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMG 60 d1nyta1 1 ----------------------------------------------D--GVGLLSDLERL 12 : ::::::::: : d1vlla_ 61 YAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGIAAK-Y 119 d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLS-LDC-AVTITNRTVSRAEELAKLFAH-TGSIQA 69 ::::::::::::::::::::::::::: ::: ::::::::::::::::::::: :::::: d1vlla_ 120 LARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASV 179 d1nyta1 70 LSMDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFL-AWCEQR 128 :::: :: :::::::::::: :::: ::::::::::::::::::::::::: ::::: d1vlla_ 180 QPAE-EA-SRCDVLVTTTPS---RKPV-VKAEWVEEGTHINAIGADGPGKQELDVEILK- 232 d1nyta1 129 GSK--------------------------------------------------RNADGLG 138 ::: :::::: d1vlla_ 233 KAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDST- 291 d1nyta1 139 MLV-AQA-AHAFLLWHG--------------VLPDVEPVIKQLQEELS 170 :: ::: ::::::::: d1vlla_ 292 -GLAIQDVAVAKVVYENALSKNVGSKIKFFR----------------- 321 HHsearch alignment (Probability: 0.99 E-value:0.00) d1nyta1 15 IRPGLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 ::::::::::::::::::::::::: :::::::::::::::::::::::::::::::: d1vlla_ 122 RKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASVQ- 180 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMF-YQKGKTPFLAWCEQRGSK 131 ::::::::::::::::: :::::::::::::::::::: ::::::::::::::: :: d1vlla_ 181 PAEEASRCDVLVTTTPS----RKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKK-AK 235 d1nyta1 132 RNADGLGMLVAQA 144 ::::::::::::: d1vlla_ 236 IVVDDLEQAKHGG 248