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 | d1w4xa2 | Phenylacetone monooxygenase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 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 <-- 1.365 --> HitDALI alignment (Z-score: 4.5 Raw score:369.20) d1nyta1 1 --------------dgvgllsdlERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTI 46 ::::::::::::::::::::::::::::::::::::: d1w4xa2 1 vpqlpnfpglkdfagnlyhtgnwPHEPVDFSGQRVGVIGTGSSGIQVSPQIAKQAAELFV 60 d1nyta1 47 TNRTVS------------------------------------------------------ 52 :::::: d1w4xa2 61 FQRTPHfavparnapldpefladlkkryaefreesrntpggthryqgpksalevsdeelv 120 d1nyta1 53 ------------------------------------------------------------ 53 d1w4xa2 121 etlerywqeggpdilaayrdilrdrdanervaefirnkirntvrdpevaerlvpkgypfg 180 d1nyta1 53 ----raeelaKLFAHTGSIQALSM--DELE------------GHEFDLIINATSSgisgd 94 :::::::::::::: :::: ::::::::::::: d1w4xa2 181 tkrlileidyYEMFNRDNVHLVDTlsAPIEtitprgvrtserEYELDSLVLATGF----- 235 d1nyta1 95 ipaipsslihpgiycydmfyqkgktpflawceqrgskrnadglgmlvaqaahafllwhgv 154 d1w4xa2 236 ------------------------------------------------------------ 236 d1nyta1 155 lpdvepvikqlqeels 170 d1w4xa2 236 ---------------- 236 FAST alignment (Normalized score: 3.26 Raw score:651.90) d1nyta1 1 DGVGLLS---------------------DLERLSFI--RPGLRILLIGAGGASRGVLLPL 37 :::::: :::::::::::::::::::::: d1w4xa2 1 -------VPQLPNFPGLKDFAGNLYHTGNWPHEP--VDFSGQRVGVIGTGSSGIQVSPQI 51 d1nyta1 38 LSLD--CAVTITNRTVSRAEEL-------------------------------------- 57 :: ::::::::: d1w4xa2 52 AK--QAAELFVFQRT-------PHFAVPARNAPLDPEFLADLKKRYAEFREESRNTPGGT 102 d1nyta1 58 ------------------------------------------------------------ 58 d1w4xa2 103 HRYQGPKSALEVSDEELVETLERYWQEGGPDILAAYRDILRDRDANERVAEFIRNKIRNT 162 d1nyta1 58 ---------------------------AKLFAHTGSIQALSMDEL--------------- 75 :::::::::::::::: d1w4xa2 163 VRDPEVAERLVPKGYPFGTKRLILEIDYYEMFNRDNVHLVDTL--SAPIETITPRGVRTS 220 d1nyta1 76 -EGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNA 134 ::::::::::: d1w4xa2 221 EREYELDSLVLA------------------------------------------------ 232 d1nyta1 135 DGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS--- 170 d1w4xa2 233 ------------------------------------TGF 235 TMalign alignment (TM-score: 0.38 Raw score:65.14) d1nyta1 1 -------------------DGVGL--LSDLERLSFIRPGLRILLIGAGGASRGVLLPLLS 39 : ::::: :::::::::::::::::::::::::: d1w4xa2 1 VPQLPNFPGLKDFAGNLYH----TGN--WPHEP-VDFSGQRVGVIGTGSSGIQVSPQIAK 53 d1nyta1 40 LDCAVTITNRTVSR---------------------------------------------- 53 ::::::::::: :: d1w4xa2 54 QAAELFVFQRT-PHFAVPARNAPLDPEFLADLKKRYAEFREESRNTPGGTHRYQGPKSAL 112 d1nyta1 54 -------------------------------------------------------A--EE 56 : :: d1w4xa2 113 EVSDEELVETLERYWQEGGPDILAAYRDILRDRDANERVAEFIRNKIRNTVRDPEVAERL 172 d1nyta1 57 L----------------AKLFAHTGSIQAL-S----M---------DELEGHEFDLIINA 86 : ::::::::::::: : : :::::::::::::: d1w4xa2 173 VPKGYPFGTKRLILEIDYYEMFNRDNVHLVDTLSAPIETITPRGVRTSEREYELDSLVLA 232 d1nyta1 87 TSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAH 146 :: : d1w4xa2 233 TG--F------------------------------------------------------- 235 d1nyta1 147 AFLLWHGVLPDVEPVIKQLQEELS 170 d1w4xa2 236 ------------------------ 236 HHsearch alignment (Probability: 0.96 E-value:0.00) d1nyta1 12 LSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVS 52 ::::::::::::::::::::::::::::::::::::::::: d1w4xa2 26 EPVDFSGQRVGVIGTGSSGIQVSPQIAKQAAELFVFQRTPH 66