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 | d1iuka_ | Hypothetical protein TT1466 | 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 <-- 1.507 --> HitDALI alignment (Z-score: 8.7 Raw score:565.70) d1nyta1 1 dgvgllsdlERLS-FIRPGLRILLIGAG----GASRGVLLPLLSLDCAVTITNRTVSraE 55 :::: :::::::::::::: ::::::::::::::::::::::::: : d1iuka_ 1 ------mndQELRaYLSQAKTIAVLGAHkdpsRPAHYVPRYLREQGYRVLPVNPRFQ--G 52 d1nyta1 56 ELAklfahtgSIQALSM-DELEgHEFDLIINATSsGISGDIP-aIPSSLIhpgIYCYDM- 112 ::: ::::::: :::: ::::::::::: ::::::: :::::: :::::: d1iuka_ 53 EEL------fGEEAVASlLDLK-EPVDILDVFRP-PSALMDHlpEVLALR--pGLVWLQs 102 d1nyta1 113 -FYQKgktPFLAWCEQRGSkRNADGLgmlvaqaahafllwhgvlpdvepvikqlqeels 170 :::: ::::::::::: :::::: d1iuka_ 103 gIRHP---EFEKALKEAGI-PVVADR---------------------clmvehkrlfrg 136 FAST alignment (Normalized score: 5.11 Raw score:777.40) d1nyta1 1 DGVGLLSDLER------LSFIRPG---LRILLIGAG-----GASRGVLLPLLSLDCAVTI 46 :::: :::::::: ::::::::::::::::::: d1iuka_ 1 -----------MNDQELRAYL---SQAKTIAVLGA-HKDPSRPAHYVPRYLREQGYRVLP 45 d1nyta1 47 TNRTVSRAEELAKLFAHTG--------SIQAL-SMDELEGHEFDLIINATSSGISGDIPA 97 ::: ::::: ::::: ::::::::::: d1iuka_ 46 VNP----------------RFQGEELFGEEAVASLLDL-KEPVDILDVFR---------- 78 d1nyta1 98 IPSSLIHPG-----------------IYCYDMFYQKGK-----TPFLAWCEQRGSKRNAD 135 :::::: ::::::::::: :::: d1iuka_ 79 ---------PPSALMDHLPEVLALRPGLVWLQ------SGIRHPEFEKALKEAG-IPVV- 121 d1nyta1 136 GLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS--------------- 170 d1iuka_ 122 -----------------------------------ADRCLMVEHKRLFRG 136 TMalign alignment (TM-score: 0.54 Raw score:92.12) d1nyta1 1 --DGVGLLSDLERLS-FIRPGLRILLIGAG----GASRGVLLPLLSLDCAVTITNRTVSR 53 ::::: :::::::::::::: ::::::::::::::::::::::: : d1iuka_ 1 MN--------DQELRAYLSQAKTIAVLGAHKDPSRPAHYVPRYLREQGYRVLPVNPR--F 50 d1nyta1 54 AEELAKLFAHTGSIQALSM-DELEGHEFDLIINATSSGISGDIPA--IPSSLIHPGIYCY 110 ::::: :: :::::: ::: :::::::::::: : :::::: ::::::: :::: d1iuka_ 51 QGEEL--FG----EEAVASLLDL-KEPVDILDVFRP-P-SALMDHLPEVLALRP--GLVW 99 d1nyta1 111 DM-FYQKGKTPFLAWCEQRGSKRNADGLGML-VAQ-------AAHAFLLWHGVLPDVEPV 161 :: ::: :::: ::::::::: ::::: ::: :: d1iuka_ 100 LQSGIR-HPEF-EKALKEAGI-PVVAD-RCLM-VEHKRLFRG------------------ 136 d1nyta1 162 IKQLQEELS 170 d1iuka_ 137 --------- 137 HHsearch alignment (Probability: 0.93 E-value:0.00) d1nyta1 17 PGLRILLIGAG----GASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 ::::::::::: ::::::::::::::::::::::::::: : : :::::::: d1iuka_ 12 QAKTIAVLGAHKDPSRPAHYVPRYLREQGYRVLPVNPRFQGE-E----L---FGEEAVAS 63 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKR 132 :::::::::::::::::: :::::::::::::::::::::::::::::::::::::: d1iuka_ 64 LLDLKEPVDILDVFRPPS---ALMDHLPEVLALRPGLVWLQSGIRHPEFEKALKEAGIP- 119 d1nyta1 133 NADGLGMLV-AQ 143 ::::::::: :: d1iuka_ 120 VVADRCLMVEHK 131