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 | d2at2a2 | Aspartate carbamoyltransferase catalytic subunit | Aspartate/ornithine carbamoyltransferase | ATC-like | 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 <-- 1.275 --> HitDALI alignment (Z-score: 6.4 Raw score:521.20) d1nyta1 1 dgvgllsdlerlsfiRPGLRILLIGA---GGASRGVLLPLLSLDCAVTITNRTVSRAeeL 57 ::::::::::: :::::::::::::::::::::::::::: : d2at2a2 1 ---------------FKGLTVSIHGDikhSRVARSNAEVLTRLGARVLFSGPSEWQD--E 43 d1nyta1 58 AKLfahtgsIQALSMdeLEGH-EFDLIINATSS------------gisgdiPAIPSSL-I 103 ::: :::::: :::: ::::::::::: ::::::: : d2at2a2 44 ENT-----fGTYVSM--DEAVeSSDVVMLLRIQnerhqsavsqegylnkygLTVERAErM 96 d1nyta1 104 HPGIYCYDMFYqkgKTPF---lAWCEQrgSKRNAD--GLGMLVAQAAHAFLLWHGvlpdv 158 ::::::::::: :::: ::::: :::::: :::::::::::::::::: d2at2a2 97 KRHAIIMHPAP---VNRGveidDSLVE--SEKSRIfkQMKNGVFIRMAVIQCALQ----- 146 d1nyta1 159 epvikqlqeels 170 d2at2a2 147 -------tnvkr 151 FAST alignment (Normalized score: 4.43 Raw score:709.10) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGA-----GGASRGVLLPLLSL--DCAVTITNRTVSR 53 ::::::::: :::::::::::: ::::::::: d2at2a2 1 ---------------FKGLTVSIH--GDIKHSRVARSNAEVLT--RLGARVLFSGP---- 37 d1nyta1 54 AEELAKLFAH-------TGSIQAL-SMDELEGHEFDLIINATSSGISGDIPAIPSSL--- 102 ::::::: ::::: :::::::: d2at2a2 38 ----------SEWQDEENTFGTYVSMDEAV--ESSDVVML-----------------LRI 68 d1nyta1 103 ---------------------------IHPGIYCYDMFYQKGKTPFLAWCEQRG------ 129 :::::::::::: d2at2a2 69 QNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAP---------------VNRGVE 113 d1nyta1 130 -------SKRNADGLG---MLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------- 170 :::: :::: ::::::::::::: d2at2a2 114 IDDSLVESEKS-RIFKQMKNGVFIRMAVIQCA-------------------LQTNVKR 151 TMalign alignment (TM-score: 0.53 Raw score:89.55) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-A--GGASRGVLLPLL-SLDCAVTITNRTVSRAEE 56 :::::::::: : :::::::::::: :: ::::::::::::: d2at2a2 1 ---------------FKGLTVSIHGDIKHSRVARSNAEVLTRLG-ARVLFSGPSEWQD-- 42 d1nyta1 57 LAKLFAHTGSIQALSMDELEGHE-FDLIINATSS------------GISGD----IPAIP 99 :: :: :::::: : ::::: :::::::::: : ::::: d2at2a2 43 EE-NT----FGTYVS-M-DEAVESSDVVMLLRIQNERHQSAVSQEG----YLNKYGLTVE 91 d1nyta1 100 -SSLIHPGIYCYDMFYQKGKTP----FLAWCEQRGSKRNAD--GLGMLVAQAAHAFLLWH 152 ::::::::::::::: :: ::::::: :::::: ::::::::::::::::: d2at2a2 92 RAERMKRHAIIMHPAP----VNRGVEIDDSLVE--SEKSRIFKQMKNGVFIRMAVIQCAL 145 d1nyta1 153 GVLP--DVEPVIKQLQEELS 170 :::: d2at2a2 146 QTNVKR-------------- 151 HHsearch alignment (Probability: 0.90 E-value:0.00) d1nyta1 16 RPGLRILLIGA---GGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 ::::::::::: ::::::::::::::::::::::::::::: ::::::::: d2at2a2 1 FKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDE--------ENTFGTYVS 52 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPA 97 :::::::::::: :::::::::::: d2at2a2 53 MDEAVESSDVVM-LLRIQNERHQSA 76