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 | d1kyqa1 | Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain | 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 <-- 1.568 --> HitDALI alignment (Z-score: 7.6 Raw score:523.00) d1nyta1 1 dgvgllsdlERLSfIRPG-LRILLIGAGGASRGVLLPLLSLDCAVTITNrTVSRaeELAK 59 :::: :::: :::::::::::::::::::::::::::::: :::: :::: d1kyqa1 1 -----mvksLQLA-HQLKdKRILLIGGGEVGLTRLYKLMPTGCKLTLVS-PDLH-kSIIP 52 d1nyta1 60 LFAH--------------TGSI-QALS---MDELEG-----hEFDLIINATSSgisGDIP 96 :::: :::: :::: :::::: ::::::::::: :::: d1kyqa1 53 KFGKfiqkrfinpnwdptKNEIyEYIRsdfKDEYLDlenendAWYIIMTCIPD---HPES 109 d1nyta1 97 -aipSSLI---HPGIYCYDMFYqkgkTPFLawceqrgskrNADGlgmlvaqaahafllwh 152 :::: ::::::::::: :::: :::: d1kyqa1 110 ariyHLCKerfGKQQLVNVADK----PDLC----------DFYF---------------- 139 d1nyta1 153 gvlpdvepvikqlqeels 170 d1kyqa1 140 ------------------ 140 FAST alignment (Normalized score: 4.76 Raw score:731.10) d1nyta1 1 DGVGLLSDLERLSFI----------RPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRT 50 ::::::::::::::::::::::::::::::::::: d1kyqa1 1 ---------------MVKSLQLAHQLKDKRILLIGGGEVGLTRLYKLMPTGCKLTLVSPD 45 d1nyta1 51 -VSRAEELAKLFAHTGS----------------------IQALSMDEL------------ 75 :::::: :::: d1kyqa1 46 LHKSIIP----------KFGKFIQKRFINPNWDPTKNEIYEYI-----RSDFKDEYLDLE 90 d1nyta1 76 -EGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGK-----TPFLAWCEQRG 129 ::::::::::::: ::::::::: d1kyqa1 91 NENDAWYIIMTCIP------------------------------DHPESARIYHLCKE-- 118 d1nyta1 130 S-----KRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS----------- 170 ::::: d1kyqa1 119 -RFGKQQLVNV-----------------------------------ADKPDLCDFYF 139 TMalign alignment (TM-score: 0.47 Raw score:79.74) d1nyta1 1 ---DGVGLLSDLERLSFIRPG-LRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEE 56 : :::: :::: :::::::::::::::::::::::::::::: : ::::: d1kyqa1 1 MVK-------S-LQLA-HQLKDKRILLIGGGEVGLTRLYKLMPTGCKLTLVS-P-DLHKS 49 d1nyta1 57 LAKLFAH-------------TG-SI-QALS--MD-EL-EGH---E-FDLIINATSSGISG 93 ::::::: :: :: :::: :: :: ::: : ::::::::::: : d1kyqa1 50 IIPKFGKFIQKRFINPNWDPTKNEIYEYIRSDFKDEYLDLENENDAWYIIMTCIPDH--P 107 d1nyta1 94 DIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKR-NAD---GL----GMLVAQAA 145 :: :::::::::::::: ::: :: :: : d1kyqa1 108 ES-----------------------ARIYHLCKERFGKQQLVNVADKPDLCDFY--F--- 139 d1nyta1 146 HAFLLWHGVLPDVEPVIKQLQEELS 170 d1kyqa1 140 ------------------------- 140 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSR 53 ::::::::::::::::::::::::::::::::::::::::: d1kyqa1 8 AHQLKDKRILLIGGGEVGLTRLYKLMPTGCKLTLVSPDLHK 48