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 | d1c0pa1 | D-aminoacid oxidase, N-terminal domain | Nucleotide-binding domain | Nucleotide-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 <-- 1.454 --> HitDALI alignment (Z-score: 4.1 Raw score:386.50) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVS-------- 52 :::::::::::::::::::::::::::::::::::: d1c0pa1 1 ------------lmmhSQKRVVVLGSGVIGLSSALILARKGYSVHILARDLPedvssqtf 48 d1nyta1 53 ------------------------------------------------------------ 53 d1c0pa1 49 aspwaganwtpfmtltdgprqakweestfkkwvelvptghamwlkgtrrfaqnedgllgh 108 d1nyta1 53 -----------------------------------raeELAKLFAHTgSIQALSM----d 73 ::::::::: ::::::: d1c0pa1 109 wykditpnyrplpssecppgaigvtydtlsvhapkycqYLARELQKL-GATFERRtvtsl 167 d1nyta1 74 elegHEFDLIINATS-SGISGD------------------------------ipaipssl 102 ::::::::::: :::::: d1c0pa1 168 eqafDGADLVVNATGlGAKSIAgiddqarggprveaerivlpldrtksplslgrgsaraa 227 d1nyta1 103 ihPGIYCYDMFYqkgktpflawceqrgskrnadglgmlvaqaahafllwhgvlpdvepvi 162 :::::::::: d1c0pa1 228 keKEVTLVHAYG---------------------------fssagyqqswgaaedvaqlvd 260 d1nyta1 163 kqlqeels 170 d1c0pa1 261 eafqryhg 268 FAST alignment (Normalized score: 3.59 Raw score:766.90) d1nyta1 1 DGVGLLSDLERLSFIRP-----GLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSR-- 53 ::::::::::::::::::::::::::::::::: d1c0pa1 1 -----------------LMMHSQKRVVVLGSGVIGLSSALILARKGYSVHILARD---LP 40 d1nyta1 54 ------------------------------------------------------------ 54 d1c0pa1 41 EDVSSQTFASPWAGANWTPFMTLTDGPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQ 100 d1nyta1 54 --------------------------------------------AEELAKLFAHTGSIQA 69 ::::::::::: :::: d1c0pa1 101 NEDGLLGHWYKDITPNYRPLPSSECPPGAIGVTYDTLSVHAPKYCQYLARELQKL-GATF 159 d1nyta1 70 LSMDELEG-----------HEFDLIINAT-SSGISGDIPAIPSSLIH------------- 104 : :::::::::: :::: d1c0pa1 160 E-------RRTVTSLEQAFDGADLVVNATGLGAK-------------SIAGIDDQARGGP 199 d1nyta1 105 ------------------------------PGIYCYDMFYQKGKTPFLAWCEQRGSKRNA 134 :::::::: d1c0pa1 200 RVEAERIVLPLDRTKSPLSLGRGSARAAKEKEVTLVHA---------------------- 237 d1nyta1 135 DGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------------------------ 170 d1c0pa1 238 ------------------------------------YGFSSAGYQQSWGAAEDVAQLVDE 261 d1nyta1 171 ------- 171 d1c0pa1 262 AFQRYHG 268 TMalign alignment (TM-score: 0.34 Raw score:58.31) d1nyta1 1 ---------------DG-VGL-LSDLERLSFIRPGLRILLIGA---------GGAS---- 30 :: ::: :: ::: :::: : :::::: :::: d1c0pa1 1 LMMHSQKRVVVLGSGVIGLSSALI-LAR-KGYS--V-HILARDLPEDVSSQTFASPWAGA 55 d1nyta1 31 ------------------------------------------------------------ 31 d1c0pa1 56 NWTPFMTLTDGPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITP 115 d1nyta1 31 --------------------------R--G--VLLPLLSLDCAVTITNRTVSRAEELAKL 60 : : ::::::::::::::::: d1c0pa1 116 NYRPLPSSECPPGAIGVTYDTLSVHAPKYCQYLARELQKLGATFERRTV----------- 164 d1nyta1 61 FAHTGSIQALSMD-ELE-GHEFD-LIINAT-SSGISGDIPA--------IPSSLIHPGIY 108 :: :: :::: :::::: ::: : :::: d1c0pa1 165 -----------TSL-EQA-FDGADLVVNATGLGA-K-SIAGIDDQARGG----------- 198 d1nyta1 109 CYDMFYQKGKTPFLAWCEQR---------------------GSKRNADGL-GM---L-VA 142 ::: :: :: ::: ::::::::: : : :: d1c0pa1 199 ----PRV-EA---ER--IVLPLDRTKSPLSLGRGSARAAKEKEVTLVHAYG-FSSAGYQQ 247 d1nyta1 143 QAAH-AFLLWHGVLPDVE--PVIK----------QLQEELS 170 :::: :: :: d1c0pa1 248 SWGAA-----------EDVA--QLVDEAFQRYHG------- 268 HHsearch alignment (Probability: 0.96 E-value:0.00) d1nyta1 15 IRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTV 51 ::::::::::::::::::::::::::::::::::::: d1c0pa1 3 MHSQKRVVVLGSGVIGLSSALILARKGYSVHILARDL 39