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 | d1hnja2 | 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 <-- 1.501 --> HitDALI alignment (Z-score: 4.0 Raw score:393.00) d1j0aa_ 1 mhpkifallakfprvelipwETPIqylpnisreigadvyikrddLTGLGI---------- 50 :::: :::::: d1hnja2 1 -------------------iSTHL--------------------HADGSYgelltlpnad 21 d1j0aa_ 51 --------------ggnKIRKleyllgdalskgadvvitvgavhsnhafvtglaakklgl 96 :::: d1hnja2 22 rvnpensihltmagnevFKVA--------------------------------------- 42 d1j0aa_ 97 dailvlrgkeelkgnylldkimgietrvydakdsfelmkyaeeiaeelkregrkpyvipp 156 d1hnja2 43 ------------------------------------------------------------ 43 d1j0aa_ 157 ggaspigTLGYVRAVGEIATQSEV---KFDSIVVAAGSGGTLAGLSLGLSilnediRPVG 213 ::::::::::::::::: ::::::::::::::::::::::: :::: d1hnja2 43 -------VTELAHIVDETLAANNLdrsQLDWLVPHQANLRIISATAKKLG--msmdNVVV 93 d1j0aa_ 214 IAvgrfgevmtskldnlikeaaellgvkvevrpelYDYSfgeygkitgevaqiirkvgtr 273 :: :::: d1hnja2 94 TL---------------------------------DRHG--------------------- 99 d1j0aa_ 274 egiildpVYTGKAFYGLVDLARKGELG--EKILFIHTGGisgtfhygdkllsll 325 :::::::::::::::::::: :::::::::: d1hnja2 100 ------nTSAASVPCALDEAVRDGRIKpgQLVLLEAFGG----gftwgsalvrf 143 FAST alignment (Normalized score: 2.76 Raw score:595.10) d1j0aa_ 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEY 60 d1hnja2 1 ------------------------------------------------------------ 1 d1j0aa_ 61 LLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGI 120 d1hnja2 1 ------------------------------------------------------------ 1 d1j0aa_ 121 ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGA--------------------- 159 d1hnja2 1 ---------------------------------------ISTHLHADGSYGELLTLPNAD 21 d1j0aa_ 160 -----------------SPIGTLGYVRAVGEIATQSEV---KFDSIVVAAGSGGTLAGLS 199 ::::::::::::::::::::: ::::::::::::::::::: d1hnja2 22 RVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATA 81 d1j0aa_ 200 LGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRP------ELYDYSF 253 :: ::::: d1hnja2 82 KK---------------------------------------------LGMSMDNVVVT-- 94 d1j0aa_ 254 GEYGKITGEVAQIIRKVGTREGIILDP------VYTGKAFYGLVDLARKGELG--EKILF 305 :::::::::::::::::::: ::::: d1hnja2 95 ---------------------------LDRHGNTSAASVPCALDEAVRDGRIKPGQLVLL 127 d1j0aa_ 306 IHTGGISGTFHYGDKLLSLL------------ 325 :::: d1hnja2 128 EAFG----------------GGFTWGSALVRF 143 TMalign alignment (TM-score: 0.29 Raw score:95.36) d1j0aa_ 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEY 60 :: :: :: : : d1hnja2 1 ----------------------IS-----------------TH-LH-A------D----- 8 d1j0aa_ 61 LLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKI--- 117 :::: :::: ::: ::: d1hnja2 9 ----------------------------GSYG-----ELLT---------LPN-ADRVNP 25 d1j0aa_ 118 -MGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIAT 176 :::: : :: ::::::: ::::::::::::::: d1hnja2 26 E----NSIH----L--TM-------------------AGNEVFK-VAVTELAHIVDETLA 55 d1j0aa_ 177 QSEV---KFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKE 233 :::: ::::::::::::::::::::::: :::::::::: : d1hnja2 56 ANNLDRSQLDWLVPHQANLRIISATAKKLG---MSMDNVVVTL--D-------------- 96 d1j0aa_ 234 AAELLGVKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDL 293 : : ::: ::: :::::::::::: d1hnja2 97 ----------------R-H--GNT--------------------SAA-SVPCALDEAVRD 116 d1j0aa_ 294 ARKGELG-EKILFIHTGG------------ISGTFHYGDKLLSLL 325 : ::: :::::::::: d1hnja2 117 --G-RIKPGQLVLLEAFGGGFTWGSALVRF--------------- 143 HHsearch alignment (Probability: 0.03 E-value:0.07) d1j0aa_ 100 LVLRG 104 ::::: d1hnja2 66 WLVPH 70