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 | d1teaa2 | Hydroxyisobutyrate 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 <-- 2.156 --> HitDALI alignment (Z-score: 10.5 Raw score:631.00) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::: d1teaa2 1 ------------------MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAA 42 d1nyta1 61 FahtgsIQALSmdELEG--HEFDLIINATSSGIsgDIPA----IPSSLIHPGIYCYDMF- 113 : ::::: :::: :::::::::::::: :::: :::::::::::::::: d1teaa2 43 G-----AETAS--TAKAiaEQCDVIITMLPNSPhvKEVAlgenGIIEGAKPGTVLIDMSs 95 d1nyta1 114 YQKGKT-PFLAWCEQRGSkRNADGlgMLVAQ---------------aahafllwhgvlpd 157 :::::: ::::::::::: ::::: ::::: d1teaa2 96 IAPLASrEISDALKAKGV-EMLDA--PVSGGepkaidgtlsvmvggdkaifdkyydlmka 152 d1nyta1 158 vepviKQLQeels 170 :::: d1teaa2 153 magsvVHTG---- 161 FAST alignment (Normalized score: 6.42 Raw score:1062.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 ::::::::::::::::::::::::::::::::::::::::: d1teaa2 1 ------------------MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIA- 41 d1nyta1 61 FAHTG-SIQAL-SMDELEGH---EFDLIINATSSGISGDIPAI--------------PSS 101 ::::: :::: :::::::::: ::: d1teaa2 42 -----AGAETASTAKA----IAEQCDVIITMLP----------NSPHVKEVALGENGIIE 82 d1nyta1 102 LIHPGIYCYDMFYQKGK-----TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLP 156 :::::::::::::: ::::::::::: :::: d1teaa2 83 GAKPGTVLIDMSSI---APLASREISDALKAKG-VEML---------------------- 116 d1nyta1 157 DVEPVIKQLQEELS--------------------------------------------- 170 d1teaa2 117 --------------DAPVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTG 161 TMalign alignment (TM-score: 0.57 Raw score:97.38) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 ::::::::::::::::::::::::::::::::::::::::: d1teaa2 1 ------------------MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIA- 41 d1nyta1 61 FAHTGSIQALSMDELEGHEFDLIINATSSGISGDIP----AIPSSLIHPGIYCYDMF-YQ 115 :: :::::::::::::::::::::::::::::: ::::::::::::::::: :: d1teaa2 42 AG----AETASTAKAIAEQCDVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIA 97 d1nyta1 116 KGKT-PFLAWCEQRGSKRNADGLGMLV--------AQAA--------------------H 146 :::: ::::::::::: :::::: ::: :::: d1teaa2 98 PLASREISDALKAKGV-EMLDAP-VSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMA- 154 d1nyta1 147 AFLLWHGVLPDVEPVIKQLQEELS 170 :::: :: : d1teaa2 155 ---------GSVV--HT--G---- 161 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 20 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 79 :::::::::::::::::::::::::::::::::::::::::: ::::::::::::: d1teaa2 2 KVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAG-----AETASTAKAIAEQ 56 d1nyta1 80 FDLIINATSSGISGDIPAIP----SSLIHPGIYCYDMFYQKGKT--PFLAWCEQRGSKRN 133 :::::::::::::::::::: :::::::::::::::::::: :::::::::::: : d1teaa2 57 CDVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVE-M 115 d1nyta1 134 ADGLGML--VAQAAH-AFLLWHGVLPDVEPVIKQLQE 167 ::: ::: :::::: ::::::::::::::::::::: d1teaa2 116 LDA-PVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMK 151