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 | d2naca1 | Formate 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 <-- 2.199 --> HitDALI alignment (Z-score: 9.4 Raw score:724.40) d1nyta1 1 --DGVGLLSDLERLS------------------------fiRPGLRILLIGAGGASRGVL 34 ::::::::::::: ::::::::::::::::::: d2naca1 1 isVAEHVVMMILSLVrnylpshewarkggwniadcvshaydLEAMHVGTVAAGRIGLAVL 60 d1nyta1 35 LPLLSLDCAVTITNRtvsRAEElaKLFAHTgSIQALS-MDELegHEFDLIINATSSgISG 93 ::::::::::::::: :::: :::::: :::::: :::: :::::::::::: ::: d2naca1 61 RRLAPFDVHLHYTDR---HRLP-eSVEKEL-NLTWHAtREDM-yPVCDVVTLNCPL-HPE 113 d1nyta1 94 DI---paiPSSLIHPGIYCYDMFYqkgkTPFLAW-cEQRG-----SKRNADGL------- 137 :: :::::::::::::::: :::::: :::: :::::::: d2naca1 114 TEhmindeTLKLFKRGAYIVNTAR----GKLCDRdaVARAlesgrLAGYAGDVwfpqpap 169 d1nyta1 138 -------------gmLVAQaahafllwhgvlpdvepvikqlqeels 170 :::: d2naca1 170 kdhpwrtmpyngmtpHISG--------------------------- 188 FAST alignment (Normalized score: 6.78 Raw score:1213.00) d1nyta1 1 D---GVGLLSDLERLSFI----------------------------RPGLRILLIGAGGA 29 :::::::::: :::::::::::::: d2naca1 1 -ISVAEHVVMMILS----LVRNYLPSHEWARKGGWNIADCVSHAYDLEAMHVGTVAAGRI 55 d1nyta1 30 SRGVLLPLLSLDCAVTITNRTVSR--AEELAKLFAHTG-SIQAL-SMDELEGH---EFDL 82 ::::::::::::::::::::: ::::::: ::::: :::: :::: d2naca1 56 GLAVLRRLAPFDVHLHYTDRH---RLPESVEKE-----LNLTWHATRED----MYPVCDV 103 d1nyta1 83 IINATSSGISGDIP--------AIPSSL---IHPGIYCYDMFYQKGKTP------FLAWC 125 ::::: :::::: :::::::::: ::::: d2naca1 104 VTLNC---------PLHPETEHMINDETLKLFKRGAYIVNT--------ARGKLCDRDAV 146 d1nyta1 126 EQR-----GSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---------- 170 :: :::::: d2naca1 147 AR-ALESGRLAGYA------------------------------------GDVWFPQPAP 169 d1nyta1 171 ------------------- 171 d2naca1 170 KDHPWRTMPYNGMTPHISG 188 TMalign alignment (TM-score: 0.60 Raw score:101.29) d1nyta1 1 D--GVGLLSDLERLSF------------------------IRPGLRILLIGAGGASRGVL 34 : ::::::::::::: :::::::::::::::::::: d2naca1 1 ISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVL 60 d1nyta1 35 LPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGISGD 94 :::::::::::::: : : :::::::::: ::::::::::::::::::::::::::::: d2naca1 61 RRLAPFDVHLHYTD-R-H--RLPESVEKEL-NLTWHATREDMYPVCDVVTLNCPLHPETE 115 d1nyta1 95 IPAI-PS-SLIHPGIYCYDMFYQKGKTPFLAW-CE-QR----GSKRNADGL--------- 137 :::: :: :::::::::::::: :::::: :: :: ::::::::: d2naca1 116 HMINDETLKLFKRGAYIVNTAR----GKLCDRDAVARALESGRLAGYAGDVWFPQPAPKD 171 d1nyta1 138 ---------GMLVAQAAHAFLLWHGVLPDVEPVIKQLQ---EELS 170 ::::: d2naca1 172 HPWRTMPYN------------------------GMTPHISG---- 188 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 ::::::::::::::::::::::::::::::::::::::::::::::: :::::::: d2naca1 39 AYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKE-----LNLTWHAT 93 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAIPSS---LIHPGIYCYDMFYQKG-KTPFLAWCEQR 128 :::::::::::::::::: :::::::::: :::::::::::::::: ::::::::::: d2naca1 94 REDMYPVCDVVTLNCPLH-PETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALES 152 d1nyta1 129 GSKRNADGLGML 140 ::: :::::::: d2naca1 153 GRL-AGYAGDVW 163