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 | d2cmda1 | Malate 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 <-- 2.102 --> HitDALI alignment (Z-score: 10.5 Raw score:642.40) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIG-AGGASRGVLLPLLSLD---CAVTITNRTvSRAEE 56 ::::::: :::::::::::::::: ::::::::: ::::: d2cmda1 1 ------------------MKVAVLGaAGGIGQALALLLKTQLpsgSELSLYDIA-PVTPG 41 d1nyta1 57 LAKLFAHT---GSIQALS-mDELE-gHEFDLIINATSS------------gISGDI---P 96 :::::::: ::::::: :::: :::::::::::: ::::: : d2cmda1 42 VAVDLSHIptaVKIKGFSgeDATPalEGADVVLISAGVrrkpgmdrsdlfnVNAGIvknL 101 d1nyta1 97 AIP-SSLIHpGIYCYDMFYQkGKTPflAWCEQ------RGSK-RNADglgmlvaqaahaf 148 ::: ::::: :::::::::: :::: ::::: :::: :::: d2cmda1 102 VQQvAKTCP-KACIGIITNPvNTTV--AIAAEvlkkagVYDKnKLFG------------- 145 d1nyta1 149 llwhgvlpdvepvikqlqeels 170 d2cmda1 146 ---------------------- 146 FAST alignment (Normalized score: 6.55 Raw score:1028.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLI-GAGGASRGVLLPLLS---LDCAVTITNRTVSRAEE 56 :::::: ::::::::::::::: :::::::::: :::::: d2cmda1 1 ------------------MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDI-APVTPG 41 d1nyta1 57 LAKLFA--HTG-SIQALS-MDELEG--HEFDLIINATSSGISGDIPAIPSSLI------- 103 :::::: ::: ::::: :::::: ::::::::: d2cmda1 42 VAVDLSHIPTAVKIKGF-SGEDATPALEGADVVLIS-----------------AGVRRKP 83 d1nyta1 104 -------------------------HPGIYCYDMFYQKGK---TPFLAWCEQRG------ 129 :::::::::: ::::::::: d2cmda1 84 GMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIIT-----NPVNTTVAIAAE--VLKKAG 136 d1nyta1 130 ---SKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS- 170 ::::: d2cmda1 137 VYDKNKLF------------------------------------G 145 TMalign alignment (TM-score: 0.57 Raw score:96.08) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLL-SLD--CAVTITNRTVSRAEE 56 ::::::: ::::::::::::: ::: ::::::::: ::::: d2cmda1 1 ------------------MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIA-PVTPG 41 d1nyta1 57 LAKLFAHT---GSIQALS-MDELE-GHEFDLIINATSS----------GI-S-GDIP-AI 98 :::::::: ::::::: ::::: ::::::::::::: :: : :::: :: d2cmda1 42 VAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVRRKPGMDRSDLFNVNAGIVKNL 101 d1nyta1 99 --P-SSLIHPGIYCYDMF--YQKGKTPFLAWCEQR-GSK--RNADGLGMLVAQAAHAFLL 150 : ::::: :::::::: ::::::::::::::: ::: :::: d2cmda1 102 VQQVAKTCP-KACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFG--------------- 145 d1nyta1 151 WHGVLPDVEPVIKQLQEELS 170 d2cmda1 146 -------------------- 146 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 20 RILLIGA-GGASRGVLLPLLSLD--CAVTITNRTVSRAEELAKLFAHTGS-----IQALS 71 ::::::: ::::::::::::::: ::::::::::::::::::::::::: ::::: d2cmda1 2 KVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61 d1nyta1 72 MDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSK 131 ::::::::::::::::::::: ::::::::::::::: :::::::::::::: d2cmda1 62 DATPALEGADVVLISAGVRRK--PGMDRSDLFNVNAGI--------VKNLVQQVAKTCPK 111 d1nyta1 132 R----NADGLGMLVAQAAHAFLLWHGVLPD 157 : ::::::::::::::::::::::::: d2cmda1 112 ACIGIITNPVNTTVAIAAEVLKKAGVYDKN 141