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 | d1ff9a1 | Saccharopine reductase | 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 <-- 1.340 --> HitDALI alignment (Z-score: 9.0 Raw score:576.30) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::::: d1ff9a1 1 ----------------ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKLSAG 44 d1nyta1 61 FahtGSIQALSMD-----ELEGH--EFDLIINATSSGisgdipaipSSLIHPGIYCYDMF 113 : ::::::::: ::::: :::::::::::: :::::::::::::: d1ff9a1 45 V---QHSTPISLDvnddaALDAEvaKHDLVISLIPFH-----atviKSAIRQKKHVVTTS 96 d1nyta1 114 Y-QKGKtpflaWCEQRGSkRNAD---------------------------glgmlvaqaa 145 : :::: ::::::: :::: d1ff9a1 97 YvSPAMmeldqAAKDAGI-TVMNeigysamaklvgvpcavavkfvldgtisdrgvlapmn 155 d1nyta1 146 hafllwhgvlpdvepvikqlqeels 170 d1ff9a1 156 skindplmkelkekygieckekvva 180 FAST alignment (Normalized score: 6.78 Raw score:1186.00) d1nyta1 1 DGVGLLSDLERLSFIRP-GLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 :::::::::::::::::::::::::::::::::::::::: d1ff9a1 1 -----------------ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKL-- 41 d1nyta1 60 LFAHTGSIQALS------MDELEGH---EFDLIINATSSGISGDIPAIPSSLIH------ 104 :::::::::: :::::: :::::::::: d1ff9a1 42 -SAGVQHSTPI-SLDVNDDAALDA-EVAKHDLVISLIP----------------FHATVI 82 d1nyta1 105 -----PGIYCYDM-FYQKGKTP----FLAWCEQRGSKRNADGLG---------------- 138 :::::::: :::: ::::::::: :::: d1ff9a1 83 KSAIRQKKHVVTTSYVSP----AMMELDQAAKDAG-ITVM----NEIGYSAMAKLVGVPC 133 d1nyta1 139 ------------------------MLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---- 170 :::::::::: d1ff9a1 134 AVAVKFVLDGTISDRGVLAPMNSKINDPLMKELK----------------------EKYG 171 d1nyta1 171 --------- 171 d1ff9a1 172 IECKEKVVA 180 TMalign alignment (TM-score: 0.54 Raw score:91.90) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::::: d1ff9a1 1 ----------------ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKLSAG 44 d1nyta1 61 FAHTGSIQALSMD-----EL-EG-HEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMF 113 : : :::::::: :: :: ::::::::::::: ::: :::::::: ::::::: d1ff9a1 45 V--Q-HSTPISLDVNDDAALDAEVAKHDLVISLIPFH---ATV-IKSAIRQK-KHVVTTS 96 d1nyta1 114 YQKGKTPFLAW-CEQRGSKRNADGLG----------ML-------------------V-- 141 ::::::: ::: :::::::::::::: :: : d1ff9a1 97 YVSPAMM-ELDQAAKDAGITVMNEIGYSAMAKLVGVPCAVAVKFVLDGTISDRGVLAPMN 155 d1nyta1 142 ------AQ--AAH---AFLLWHGVLPD-----VEPVIKQLQEELS 170 :: :: :: ::: d1ff9a1 156 SKINDPLMKE-LKEKY--GI----ECKEKVVA------------- 180 HHsearch alignment (Probability: 1.00 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQAL----SM 72 :::::::::::::::::::::::::::::::::::::::::::::::::::::: :: d1ff9a1 1 ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKLSAGVQHSTPISLDVNDDAA 60 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTP-FLAWCEQRGSK 131 ::::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1ff9a1 61 LDAEVAKHDLVISLIPF-----HATVIKSAIRQKKHVVTTSYVSPAMMELDQAAKDAGIT 115 d1nyta1 132 RNAD-----------GLGMLVAQA--AHAFLLWHGVL-PDV----EPVIKQLQ 166 ::: ::::::::: ::::::::::: ::: :::::::: d1ff9a1 116 -VMNEIGYSAMAKLVGVPCAVAVKFVLDGTISDRGVLAPMNSKINDPLMKELK 167