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 | d1e5xa_ | Threonine synthase | Tryptophan synthase beta subunit-like PLP-dependent enzymes | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 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 <-- 1.943 --> HitDALI alignment (Z-score: 22.7 Raw score:2581.50) d1j0aa_ 1 ------------------------------------------------------------ 1 d1e5xa_ 1 ietavkpphrtednirdenavnpfsakyvpfnaapgstesysldeivyrglldvehdmea 60 d1j0aa_ 1 --------------------------mhpkIFALLAKFP----RVELIPWETPIQYLPNI 30 ::::::::: ::::::::::::::::: d1e5xa_ 61 lkrfdgaywrdlfdsrvgkstwpygsgvwsKKEWVLPEIddddIVSAFEGNSNLFWAERF 120 d1j0aa_ 31 SR-EIGA-DVYIKRDDLTGLgiGGNKIRKLEYLLGDALSKG-----ADVVITVGavHSNH 83 :: :::: :::::::::::: ::::::::::::::::::: :::::::: :::: d1e5xa_ 121 GKqFLGMnDLWVKHCGISHT--GSFKDLGMTVLVSQVNRLRkmkrpVVGVGCAS--TGDT 176 d1j0aa_ 84 AFVTGLAAKKLGLDAILVLR-GKEELKgNYLLDKIMGIETRVYDAKDsfELMKYAEEIAE 142 :::::::::::::::::::: :::::: ::::::::::::::::::: ::::::::::: d1e5xa_ 177 SAALSAYCASAGIPSIVFLPaNKISMA-QLVQPIANGAFVLSIDTDF-dGCMKLIREITA 234 d1j0aa_ 143 ELkregrKPYVIPpggaSPIGTLGYVRAVGEIATQSE-VKFDSIVVAAGSGGTLAGLSLG 201 :: :::::: :::::::::::::::::::: :::::::::::::::::::::: d1e5xa_ 235 EL-----PIYLAN--slNSLRLEGQKTAAIEILQQFDwQVPDWVIVPGGNLGNIYAFYKG 287 d1j0aa_ 202 LSILN------EDIRPVGIAV--GRFG------------eVMTSKLDNlikeaaellgvk 241 ::::: :::::::::: :::: :::::::: d1e5xa_ 288 FKXCQelglvdRIPRMVCAQAanANPLylhyksgwkdfkpVSIDRAVY-----------a 336 d1j0aa_ 242 veVRPELYDYSFgeygkiTGEVAQIIRKVGTReGIILDPvYTGKAFYGLVDLARKGELG- 300 :::::::::: :::::::::::::: :::::: ::::::::::::::::::: d1e5xa_ 337 lkKCNGIVEEAT------EEELMDAMAQADST-GMFICP-HTGVALTALFKLRNQGVIAp 388 d1j0aa_ 301 -EKILFIHTGGISGTFHYGDKLLSL----------------------------------- 324 :::::::::::::::::::::::: d1e5xa_ 389 tDRTVVVSTAHGLKFTQSKIDYHSNaipdmacrfsnppvdvkadfgavmdvlksylgsnt 448 d1j0aa_ 325 --l 325 d1e5xa_ 449 lts 451 FAST alignment (Normalized score: 13.04 Raw score:4994.00) d1j0aa_ 1 MHPK-------------------------------------------------------- 4 d1e5xa_ 1 ----IETAVKPPHRTEDNIRDENAVNPFSAKYVPFNAAPGSTESYSLDEIVYRGLLDVEH 56 d1j0aa_ 5 ----------------------------------IFAL-LAKF---PRVELI--PWETPI 24 :::: :::: :::: :::::: d1e5xa_ 57 DMEALKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVS--AFEGNSNL 114 d1j0aa_ 25 QYLPNIS-REIG-ADVYIKRDDLTGLGI--GGNKIRKLEYLLGDALS-----KGADVVIT 75 ::::::: :::: ::::::::::: ::::::::::::::::: :::::::: d1e5xa_ 115 FWAERFGKQFLGMNDLWVKHCGIS----HTGSFKDLGMTVLVSQVNRLRKMKRPVVGVGC 170 d1j0aa_ 76 VGAVH--SNHAFVTGLAAKKLGLDAILVLRG--KEELKGNYLLDKIMGIETRVYDAKDSF 131 : ::::::::::::::::::::::: ::::: ::::::::::::::::: ::: d1e5xa_ 171 A----STGDTSAALSAYCASAGIPSIVFLP-ANKISMA-QLVQPIANGAFVLSIDT-DFD 223 d1j0aa_ 132 ELMKYAEEIAEELKREGRKPYVIPPGGA----SPIGTLGYVRAVGEIATQS-EVKFDSIV 186 ::::::::::: :::::: ::::::::::::::::::: :::::::: d1e5xa_ 224 GCMKLIREITA-----ELPIYL------ANSLNSLRLEGQKTAAIEILQQFDWQVPDWVI 272 d1j0aa_ 187 VAAGSGGTLAGLSLGLSILNE---------DIRPVGIAVGRFGEV--------------- 222 :::::::::::::::::: ::::::::: d1e5xa_ 273 VPGGNLGNIYAFYKGFKA---CQELGLVDRIPRMVCAQA------ANANPLYLHYKSGWK 323 d1j0aa_ 223 -----MTSKLDNLIKEAAELLGVKVEV------RPELYDYSFGEYGKI--TGEVAQIIRK 269 :::::: :::::: :::::::::: d1e5xa_ 324 DFKPVSIDRAV----------------YALKKCNGIVEE---------ATEEELMDAMAQ 358 d1j0aa_ 270 VGTREGIILDPVYTGKAFYGLVDLARKGELG--EKILFIHTGGIS-GTFHYGDKLLSLL- 325 ::: :::::: :::::::::::::::::::: :::::::: ::::::::::: d1e5xa_ 359 ADS-TGMFIC-PHTGVALTALFKLRNQGVIAPTDRTVVVST----AHGLKFTQSKID--Y 410 d1j0aa_ 326 ----------------------------------------- 326 d1e5xa_ 411 HSNAIPDMACRFSNPPVDVKADFGAVMDVLKSYLGSNTLTS 451 TMalign alignment (TM-score: 0.76 Raw score:246.85) d1j0aa_ 1 ------------------------------------------------------------ 1 d1e5xa_ 1 IETAVKPPHRTEDNIRDENAVNPFSAKYVPFNAAPGSTESYSLDEIVYRGLLDVEHDMEA 60 d1j0aa_ 1 --------MH-PK-----------------IFALLAKFP----RVELIPWETPIQYLPNI 30 :: :: ::::::::: ::::::::::::::::: d1e5xa_ 61 LKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVSAFEGNSNLFWAERF 120 d1j0aa_ 31 SR-EIGA-DVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKG-----ADVVITVGAVHSNH 83 :: :::: :::::::::: ::: :::::::::::::::::: :::::::: : ::: d1e5xa_ 121 GKQFLGMNDLWVKHCGIS-HTG-SFKDLGMTVLVSQVNRLRKMKRPVVGVGCAS-T-GDT 176 d1j0aa_ 84 AFVTGLAAKKLGLDAILVLR-GKEELKGNYLLDKIMGIETRV--YDAKDSFELMKYAEEI 140 :::::::::::::::::::: :::::: :::::::::::::: :::: ::::::::: d1e5xa_ 177 SAALSAYCASAGIPSIVFLPANKISMA-QLVQPIANGAFVLSIDTDFD---GCMKLIREI 232 d1j0aa_ 141 AEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-VKFDSIVVAAGSGGTLAGLS 199 ::: : ::::::: : :::::::::::::::::::: :::::::::::::::::::: d1e5xa_ 233 TAE-L----PIYLANS-L-NSLRLEGQKTAAIEILQQFDWQVPDWVIVPGGNLGNIYAFY 285 d1j0aa_ 200 LGLSILN------EDIRPVGIAV--GRFG----------E--VMTSKLDNLIKEAAELLG 239 ::::::: :::::::::: :::: : :::::::: : d1e5xa_ 286 KGFKACQELGLVDRIPRMVCAQAANANPLYLHYKSGWKDFKPVSIDRAVY-A-------- 336 d1j0aa_ 240 VKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGEL 299 :::::::::::: :::::::::::::: :::::: :::::::::::::::::: d1e5xa_ 337 --LKKCNGIVEEAT------EEELMDAMAQADST-GMFICP-HTGVALTALFKLRNQGVI 386 d1j0aa_ 300 G--EKILFIHTGGISGTFHYGDKL-L-SL----L-------------------------- 325 : ::::::::::::::::::::: : :: : d1e5xa_ 387 APTDRTVVVSTAHGLKFTQSKIDYHSNAIPDMACRFSNPPVDVKADFGAVMDVLKSYLGS 446 d1j0aa_ 326 ----- 326 d1e5xa_ 447 NTLTS 451 HHsearch alignment (Probability: 1.00 E-value:0.00) d1j0aa_ 8 LLAKFPRVELIPWETPIQYLPNISRE-IGA-DVYIKRDDLTGLGIGGNKIRKLEYLLGDA 65 :::::::::::::::::::::::::: ::: ::::::::::: :::::::::::::::: d1e5xa_ 98 EIDDDDIVSAFEGNSNLFWAERFGKQFLGMNDLWVKHCGISH--TGSFKDLGMTVLVSQV 155 d1j0aa_ 66 LS---KGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIET 122 :: ::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1e5xa_ 156 NRLRKMKRPVVGVGCASTGDTSAALSAYCASAGIPSIVFLPANKISMAQLVQPIANGAFV 215 d1j0aa_ 123 RVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-VK 181 ::::: :::::::::::::::::::: :::::::::::::::::::::::: :: d1e5xa_ 216 LSIDT-----DFDGCMKLIREITAELPIYL---ANSLNSLRLEGQKTAAIEILQQFDWQV 267 d1j0aa_ 182 FDSIVVAAGSGGTLAGLSLGLSILN------EDIRPVGIAVGRFGEVMTSKLDNLIKEAA 235 ::::::::::::::::::::::::: :::::::::::::::::::::::::: d1e5xa_ 268 PDWVIVPGGNLGNIYAFYKGFKXCQELGLVDRIPRMVCAQAANANPLYLHYKSGWKD--- 324 d1j0aa_ 236 ELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLAR 295 ::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::: d1e5xa_ 325 -FKPVSIDRAVYALKKCNGIVEEATEEELMDAMAQADSTGMFICPH-TGVALTALFKLRN 382 d1j0aa_ 296 KG--ELGEKILFIHTGGIS 312 :: ::::::::::::::: d1e5xa_ 383 QGVIAPTDRTVVVSTAHGL 401