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 | d1d7ya1 | NADH-dependent ferredoxin reductase, BphA4 | 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 <-- 1.410 --> HitDALI alignment (Z-score: 4.4 Raw score:369.80) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSR----- 53 ::::::::::::::::::::: :::::::::::::: d1d7ya1 1 ---------------alkAPVVVLGAGLASVSFVAELRQagYQGLITVVGDEAERpydrp 45 d1nyta1 54 -----------aeelakLFAHTGSIQAL--SMDE-------------lEGHEFDLIINAT 87 ::::::::::: :::: :::::::::::: d1d7ya1 46 plskdfmahgdaekirlDCKRAPEVEWLlgVTAQsfdpqahtvalsdgRTLPYGTLVLAT 105 d1nyta1 88 SS--giSGDIP--------------aipsslihpgIYCYDM---FYQK------GKTPfl 122 :: ::::: :::::: :::: :::: d1d7ya1 106 GAapraVLANDalaraaglacddgifvdaygrttcPDVYALgdvTRQRnplsgrFERI-- 163 d1nyta1 123 awceqrgskrnadglgmlvaqaahafllwhgvlpdvepvikqlqeels 170 d1d7ya1 164 ----------------------------etwsnaqnqgiavarhlvdp 183 FAST alignment (Normalized score: 3.31 Raw score:584.20) d1nyta1 1 DGVGLLSDLERLSFIRPG---LRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSRAE 55 ::::::::::::::::::::: :::::::::::: d1d7ya1 1 ------------------ALKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEA---- 38 d1nyta1 56 ELA-----------------------KLFAHTGSIQALSMDEL----------------- 75 :::::::::::: d1d7ya1 39 ---ERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWL-----LGVTAQSFDPQAHTVAL 90 d1nyta1 76 ---EGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGK----------TPFL 122 :::::::::::: :::: d1d7ya1 91 SDGRTLPYGTLVLAT-------------------------------GAAPRAVLANDALA 119 d1nyta1 123 AWCEQRG------------------SKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQ 164 :: ::::: d1d7ya1 120 RA-----AGLACDDGIFVDAYGRTTCPDVY------------------------------ 144 d1nyta1 165 LQEELS--------------------------------------- 170 d1d7ya1 145 ------ALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDP 183 TMalign alignment (TM-score: 0.43 Raw score:72.31) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL-S-LDCAVTITNRTVSRA---- 54 :: ::::::::::::::::::::: : ::::::::::::::: d1d7ya1 1 --------------AL-KAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRP 45 d1nyta1 55 ---------------EELAKLFAHTGSIQAL--SM-------------DELEGHEF-DLI 83 ::::::: :: :::: :: :::::::: ::: d1d7ya1 46 PLSKDFMAHGDAEKI-RLDCKRA-PE-VEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLV 102 d1nyta1 84 INATSSGI-SGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLA------WCEQRGSKR--N- 133 :::::::: :::::::::: : : :: :::: :: ::: : d1d7ya1 103 LATGAAPRAVLANDALARA-A-G---LA------CDDG-IFVDAYGR------TTCPDVY 144 d1nyta1 134 A----DGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEEL-------------------- 169 : :::: : :::::: :: d1d7ya1 145 ALGDVTRQR--N-------------------PLSGRF-ERIETWSNAQNQGIAVARHLVD 182 d1nyta1 170 -S 170 d1d7ya1 183 P- 183 HHsearch alignment (Probability: 0.95 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTV 51 ::::::::::::::::::::::::::::::::::: d1d7ya1 2 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGD 36