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 | d1v7ca_ | 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 <-- 1.685 --> HitDALI alignment (Z-score: 26.7 Raw score:2889.40) d1j0aa_ 1 ---mhpkiFALLAKF----PRVELIPWETPIQYLPNIsREIG---ADVYIKRDDLTGlgI 50 ::::::: :::::::::::::::::: :::: :::::::::::: : d1v7ca_ 1 mrpplierYRNLLPVsektPVISLLEGSTPLIPLKGP-EEARkkgIRLYAKYEGLNP--T 57 d1j0aa_ 51 GGNKIRKLEYLLGDALSKGADVVITVGAvhSNHAFVTGLAAKKLGLDAILVLRGKeelKG 110 :::::::::::::::::::::::::::: ::::::::::::::::::::::::: :: d1v7ca_ 58 GSFKDRGMTLAVSKAVEGGAQAVACAST--GNTAASAAAYAARAGILAIVVLPAGyvaLG 115 d1j0aa_ 111 NYLLDKIMGIETRVYDAkDSFELMKYAEEIAEELkregrKPYVIPpgGASPIGTLGYVRA 170 ::::::::::::::::: :::::::::::::::: :::::: ::::::::::::: d1v7ca_ 116 KVAQSLVHGARIVQVEG-NFDDALRLTQKLTEAF-----PVALVN--SVNPHRLEGQKTL 167 d1j0aa_ 171 VGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILN------EDIRPVGIAV-GRFG--- 220 :::::::::::::::::::::::::::::::::::: :::::::::: :::: d1v7ca_ 168 AFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHalgkakRLPRMLGFQAaGAAPlvl 227 d1j0aa_ 221 EVMT--------------sKLDNLikeaaellgvkveVRPE------LYDYSFgeygkit 260 :::: ::::: :::: :::::: d1v7ca_ 228 GRPVerpetlatairignpASWQG------------aVRAKeesggvIEAVTD------- 268 d1j0aa_ 261 GEVAQIIRKVGTREGIILDPvYTGKAFYGLVDLARKGELG--EKILFIHTGGI-SGTFhY 317 :::::::::::::::::::: ::::::::::::::::::: ::::::::::: :::: : d1v7ca_ 269 EEILFAYRYLAREEGIFCEP-ASAAAMAGVFKLLREGRLEpeSTVVLTLTGHGlKDPA-T 326 d1j0aa_ 318 GDKLLS-----------------ll 325 :::::: d1v7ca_ 327 AERVAElpppvparleavaaaagll 351 FAST alignment (Normalized score: 15.90 Raw score:5371.00) d1j0aa_ 1 MHPK--------IFAL---LAKFPRVELIP---WETPIQYLPNISR------EIGADVYI 40 :::: :::::::: ::::::::: :::::::: d1v7ca_ 1 ----MRPPLIERYRNLLPVSEKTPVIS---LLEGSTPLIPLK----GPEEARKKGIRLYA 49 d1j0aa_ 41 KRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAIL 100 ::::: ::: :::::::::::::::::::::::::::: :::::::::::::::::::: d1v7ca_ 50 KYEGL-NPT-GSFKDRGMTLAVSKAVEGGAQAVACAST--GNTAASAAAYAARAGILAIV 105 d1j0aa_ 101 VLRGKEEL-----KGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIP 155 ::: :::::::::::::::::: :::::::::::::::: :::::: d1v7ca_ 106 VLP-----AGYVALGKVAQSLVHGARIVQVE-GNFDDALRLTQKLTEA-----FPVALV- 153 d1j0aa_ 156 PG-GASPIGTLGYVRAVGEIATQSEV-KFDSIVVAAGSGGTLAGLSLGLSILNE------ 207 :::::::::::::::::::::: :::::::::::::::::::::::: d1v7ca_ 154 --NSVNPHRLEGQKTLAFEVVDELG-DAPHYHALPVGNAGNITAHWMGYKA---YHALGK 207 d1j0aa_ 208 ---DIRPVGIAVGRFGEV-----------------------------MTSKLDNLIKEAA 235 :::::::: :::::: d1v7ca_ 208 AKRLPRMLGFQ-------AAGAAPLVLGRPVERPETLATAIRIGNPASWQGAV------- 253 d1j0aa_ 236 ELLGVKVEV------RPELYDYSFGEYGKI--TGEVAQIIRKVGTREGIILDPVYTGKAF 287 :::::: ::::::::::::::::::::: :::::: d1v7ca_ 254 ---------RAKEESGGVIEA---------VTDEEILFAYRYLAREEGIFCEP-ASAAAM 294 d1j0aa_ 288 YGLVDLARKGELG--EKILFIHTGGIS-GTFHYGDKLLSLL------------------- 325 ::::::::::::: ::::::::::: ::::::::: d1v7ca_ 295 AGVFKLLREGRLEPESTVVLTLTGHG-LKDPATAERV----AELPPPVPARLEAVAAAAG 349 d1j0aa_ 326 -- 326 d1v7ca_ 350 LL 351 TMalign alignment (TM-score: 0.77 Raw score:251.65) d1j0aa_ 1 ----M---HPKIFALLAKF--P-RVELIPWETPIQYLPNISREIG---ADVYIKRDDLTG 47 : :::::::: : ::::::::::::::::: :::: ::::::::::: d1v7ca_ 1 MRPPLIER---YRNLLPVSEKTPVISLLEGSTPLIPLKGP-EEARKKGIRLYAKYEGLN- 55 d1j0aa_ 48 LGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEE 107 :: :::::::::::::::::::::::::::: ::::::::::::::::::::::::::: d1v7ca_ 56 PT-GSFKDRGMTLAVSKAVEGGAQAVACAST--GNTAASAAAYAARAGILAIVVLPAGYV 112 d1j0aa_ 108 LKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGY 167 ::::::::::::::::::::: :::::::::::::: : :::::: :::::::::: d1v7ca_ 113 ALGKVAQSLVHGARIVQVEGN-FDDALRLTQKLTEA-F----PVALVN--SVNPHRLEGQ 164 d1j0aa_ 168 VRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILN------EDIRPVGIAV--GRF 219 ::::::::::::::::::::::::::::::::::::::: :::::::::: ::: d1v7ca_ 165 KTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAP 224 d1j0aa_ 220 G---EV--------------MTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGKITGE 262 : :: :::::::::: : :::::::::::: ::: d1v7ca_ 225 LVLGRPVERPETLATAIRIGNPASWQGAVR--A------KEESGGVIEAVT------DEE 270 d1j0aa_ 263 VAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGELG--EKILFIHTGGISGTFHYGDK 320 :::::::::::::::::: ::::::::::::::::::: :::::::::::::::::::: d1v7ca_ 271 ILFAYRYLAREEGIFCEP-ASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAER 329 d1j0aa_ 321 LLS-------------------LL 325 ::: d1v7ca_ 330 VAELPPPVPARLEAVAAAAGLL-- 351 HHsearch alignment (Probability: 1.00 E-value:0.00) d1j0aa_ 2 HPKIFALLAKFPRVELIPWETPIQYLPNISR--EIGADVYIKRDDLTGLGIGGNKIRKLE 59 ::::::::::::::::::::::::::::::: ::::::::::::::: :::::::::: d1v7ca_ 9 YRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNP--TGSFKDRGMT 66 d1j0aa_ 60 YLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMG 119 :::::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d1v7ca_ 67 LAVSKAVEGGAQAVAC--ASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHG 124 d1j0aa_ 120 IETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE 179 :::::::::: :::::::::::::::::::: :::::::::::::::::::::: d1v7ca_ 125 ARIVQVEGNF-----DDALRLTQKLTEAFPVALVN---SVNPHRLEGQKTLAFEVVDELG 176 d1j0aa_ 180 VKFDSIVVAAGSGGTLAGLSLGLSIL------NEDIRPVGIAVGRFGEVMTSKLDNLIKE 233 :::::::::::::::::::::::::: :::::::::::::::::::::::::::: d1v7ca_ 177 DAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPET 236 d1j0aa_ 234 AAELLGVKVE-----VRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFY 288 :::::::::: :::::::::::::::::::::::::::::::::::::: :::::: d1v7ca_ 237 LATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPA-SAAAMA 295 d1j0aa_ 289 GLVDLARKG--ELGEKILFIHTG-GISGTFHYGDKL 321 ::::::::: :::::::::::: :::::::::::: d1v7ca_ 296 GVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVA 331