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 | d1j0aa_ | 1-aminocyclopropane-1-carboxylate deaminase | Tryptophan synthase beta subunit-like PLP-dependent enzymes | Tryptophan synthase beta subunit-like PLP-dependent enzymes | α/β |
| Hit | d1ub7a2 | Ketoacyl-ACP synthase III (FabH) | Thiolase-like | Thiolase-like | α/β |
Query <-- 0.705 --> IntermediateDALI alignment (Z-score: 6.6 Raw score:607.90) query 1 -----------------------------------------DADEEVY------salvVG 13 ::::::: :: d1j0aa_ 1 mhpkifallakfprvelipwetpiqylpnisreigadvyikRDDLTGLgiggnkirklEY 60 query 14 LRAYVAKNGFRSVLIGLS-GGIDSALVAAIACDALGaqNVYGVSMPskySSDHskGDAAE 72 :::::::::::::::::: ::::::::::::::::: :::::::: :::: ::::: d1j0aa_ 61 LLGDALSKGADVVITVGAvHSNHAFVTGLAAKKLGL--DAILVLRG---KEEL--KGNYL 113 query 73 LARRTGLNFRTVSIEpmfdaymaslgltglaeenlQSRLRGTTLMAISNQEG-----HIV 127 ::::::::::::::: ::::::::::::::::: ::: d1j0aa_ 114 LDKIMGIETRVYDAK--------------------DSFELMKYAEEIAEELKregrkPYV 153 query 128 LA-PGNKselavgystlygdsvgaygpIKDVYktsifrlaewrnraaaergqtppipeas 186 :: :::: ::::: d1j0aa_ 154 IPpGGAS------------------piGTLGY--------vravgeiatqsevkfdsivv 187 query 187 itkpdypvldailELYVdRDTGAdaivaagydrelvvkTLRM------vdtaEYKRRQYp 240 :::: ::::: :::: ::::::: d1j0aa_ 188 aagsggtlaglslGLSI-LNEDI---------------RPVGiavgrfgevmTSKLDNL- 230 query 241 pgtkisakGFGK-DRRL------------------------------------------- 256 :::: :::: d1j0aa_ 231 -----ikeAAELlGVKVevrpelydysfgeygkitgevaqiirkvgtregiildpvytgk 285 query 257 ------------------------------pitnrwregh 266 d1j0aa_ 286 afyglvdlarkgelgekilfihtggisgtfhygdkllsll 325 FAST alignment (Normalized score: 3.52 Raw score:1034.00) query 1 DADE---------------------------------------------------EVYSA 9 ::::: d1j0aa_ 1 ----MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIR 56 query 10 LVVGLRAYVAKNGFRSVLIGLSG--GIDSALVAAIACDALGAQ---NVYGVSMPSKYSSD 64 :::::::::::::::::::::: ::::::::::::: :::::: d1j0aa_ 57 KLEYLLGDALSKGADVVITVGA-VHSNHAFVTGLAAKK-----LGLDAILVL-------- 102 query 65 HS-----KGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENL--QSRLRGTTLM 117 ::::::::::::::::::: :::::::::: d1j0aa_ 103 --RGKEELKGNYLLDKIMGIETRVYD----------------------AKDSFELMKYAE 138 query 118 AISNQ-----EGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRA 172 ::::: :::::: d1j0aa_ 139 EIAEELKREGRKPYVI-------------------------------------------- 154 query 173 AAERGQTPPIPEASITKPDY---------------------------------------P 193 : d1j0aa_ 155 --------------------PPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGT 194 query 194 VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD 253 :::::::: ::::: d1j0aa_ 195 LAGLSLGL-SILNE---------------------------------------------- 207 query 254 RRLPITNRWREGH----------------------------------------------- 266 d1j0aa_ 208 -------------DIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFG 254 query 267 ------------------------------------------------------------ 267 d1j0aa_ 255 EYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELGEKILFIHTGGISGT 314 query 267 ----------- 267 d1j0aa_ 315 FHYGDKLLSLL 325 TMalign alignment (TM-score: 0.33 Raw score:88.80) query 1 ------DADEEV------------------------------------------------ 6 :::::: d1j0aa_ 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEY 60 query 7 ------------------------------------------------------------ 7 d1j0aa_ 61 LLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGI 120 query 7 --------------------------------------------Y--SALVVGLRAYVAK 20 : ::::::::::: : d1j0aa_ 121 ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQS-E 179 query 21 NGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELAR----- 75 :::::::::::::::::::::::::::: ::::::::::: :::::::::::::: d1j0aa_ 180 VKFDSIVVAAGSGGTLAGLSLGLSILNE-DIRPVGIAVGR-FGEVMTSKLDNLIKEAAEL 237 query 76 ----RTGLNFRTVSIEPM--FDAYM-ASL-------------GLTGLAEENLQS-RLRGT 114 :::::::::::::: ::::: :: :::: ::::: d1j0aa_ 238 LGVKVEVRPELYDYSFGEYGKITGEV-AQIIRKVGTREGIIL--------DPVYTGKAFY 288 query 115 TLMAISN-Q-EG--HIVLAPGNKSELAVGYST-----------LYGDSVGAYGPIKDVYK 159 ::::::: : :: ::::::: : :::: d1j0aa_ 289 GLVDLARKGELGEKILFIHTG---G---ISGTFHYGDKLLSLL----------------- 325 query 160 TSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDR 219 d1j0aa_ 326 ------------------------------------------------------------ 326 query 220 ELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1j0aa_ 326 ----------------------------------------------- 326 HHsearch alignment (Probability: 0.05 E-value:0.29) query 11 VVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDA 70 :::::::::::::::::::::::::::::::::::::::::: :::: :::::::::: d1j0aa_ 58 LEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAI--LVLR--GKEELKGNYL 113 query 71 AELARRTGLNFRTVS 85 ::::::::::::::: d1j0aa_ 114 LDKIMGIETRVYDAK 128
Intermediate <-- 1.440 --> HitDALI alignment (Z-score: 3.2 Raw score:357.50) d1j0aa_ 1 mhpkifallakfprvelipwetpiqylpnisreigadvyikrddLTGLGI---------- 50 :::::: d1ub7a2 1 ---------------------------------------rsfvlGADGTGakelyhacva 21 d1j0aa_ 51 ----------------ggnKIRKleyllgdalskgadvvitvgavhsnhafvtglaakkl 94 :::: d1ub7a2 22 prlpdgtsmknrlymngreVFKF------------------------------------- 44 d1j0aa_ 95 gldailvlrgkeelkgnylldkimgietrvydakdsfelmkyaeeiaeelkregrkpyvi 154 d1ub7a2 45 ------------------------------------------------------------ 45 d1j0aa_ 155 ppggaspigTLGYVRAVGEIATQSEV---KFDSIVVAAGSGGTLAGLSLGLSilnediRP 211 ::::::::::::::::: ::::::::::::::::::::::: :: d1ub7a2 45 --------aVRVMNTATLEAIEKAGLtpeDIRLFVPHQANLRIIDAARERLG--lpweRV 94 d1j0aa_ 212 VGIAvgrfgevmtskldnlikeaaellgvkvevrpelYDYSfgeygkitgevaqiirkvg 271 :::: :::: d1ub7a2 95 AVNV---------------------------------DRYG------------------- 102 d1j0aa_ 272 tregiildpVYTGKAFYGLVDLARKGELG--EKILFIHTGGisgtfhygdkllsll 325 :::::::::::::::::::: :::::::::: d1ub7a2 103 --------nTSTASIPLALKEAVDAGRIRegDHVLLVSFGA-gltwaaavltwgga 149 FAST alignment (Normalized score: 2.51 Raw score:552.70) d1j0aa_ 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEY 60 d1ub7a2 1 ------------------------------------------------------------ 1 d1j0aa_ 61 LLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGI 120 d1ub7a2 1 ------------------------------------------------------------ 1 d1j0aa_ 121 ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGA--------------------- 159 d1ub7a2 1 ---------------------------------------RSFVLGADGTGAKELYHACVA 21 d1j0aa_ 160 ----------------SPIGTLGYV-RAVGEIAT---QSEV---KFDSIVVAAGSGGTLA 196 ::::::::: :::::::: :::: :::::::::: ::: d1ub7a2 22 PRLPDGTSMKNRLYMNGREVFKFAVRVMNTATLEAIEKAGLTPEDIRLFVPHQA---NLR 78 d1j0aa_ 197 GLSLGLSILNEDI---RPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSF 253 ::::::::::: :::: d1ub7a2 79 IIDAARERLGL--PWERVAV---------------------------------------- 96 d1j0aa_ 254 GEYGKITGEVAQIIRKVGTREGIILDP----------VYTGKAFYGLVDLARKGELG--E 301 :::::::::::: ::::: : d1ub7a2 97 ---------------------------NVDRYGNTSTASIPLALKEAVD---AGRIREGD 126 d1j0aa_ 302 KILFIHTGGISGTFHYGDKLLSLL----------------- 325 :::::: d1ub7a2 127 HVLLVS------------------FGAGLTWAAAVLTWGGA 149 TMalign alignment (TM-score: 0.30 Raw score:97.53) d1j0aa_ 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEY 60 :: :: :: : : d1ub7a2 1 ----------------------RS-----------------FV-LG-A------D----- 8 d1j0aa_ 61 LLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGI 120 :::: ::::: :: ::::: d1ub7a2 9 ----------------------------GTGA-----KELYH---------AC--VAPRL 24 d1j0aa_ 121 ----ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIAT 176 ::::: : :: ::::::: ::::::::::::::: d1ub7a2 25 PDGTSMKNR----L--YM-------------------NGREVFK-FAVRVMNTATLEAIE 58 d1j0aa_ 177 QSEV---KFDSIVVAAGSG-GTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIK 232 :::: :::::::::::: ::::: ::::: :::::::::: : d1ub7a2 59 KAGLTPEDIRLFVPHQANLRIIDAA-RERLG---LPWERVAVNV--D------------- 99 d1j0aa_ 233 EAAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVD 292 : : ::: ::: ::::::::::: d1ub7a2 100 -----------------R-Y--GNT--------------------STA-SIPLALKEAVD 118 d1j0aa_ 293 LARKGELG-EKILFIHTGG---------------ISGTFHYGDKLLSLL 325 : :::: :::::::::: d1ub7a2 119 A---GRIREGDHVLLVSFGAGLTWAAAVLTWGGA--------------- 149 HHsearch alignment (Probability: 0.04 E-value:0.11) d1j0aa_ 100 LVLRGKEE 107 :::::::: d1ub7a2 69 LFVPHQAN 76