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_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jfla2 | Aspartate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
| Hit | d1tjya_ | AI-2 receptor LsrB | Periplasmic binding protein-like I | Periplasmic binding protein-like I | α/β |
Query <-- 0.802 --> IntermediateDALI alignment (Z-score: 1.0 Raw score:191.90) query 1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE 23 ::::::: :::: ::::::::: d1jfla2 1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE 58 query 24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg 82 ::::::::::::::::::: :::: :::: d1jfla2 59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l 91 query 83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv 142 ::::: d1jfla2 92 KVPLI------------------------------------------------------- 96 query 143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel 202 d1jfla2 97 ------------------------------------------------------------ 97 query 203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa 262 d1jfla2 97 ------------------------------------------------------------ 97 query 263 eaepptgvvddglridrlviseeplpayeaelaggyadrl 302 d1jfla2 97 -----------------------dpmdviaevavkvalek 113 FAST alignment (Normalized score: 1.26 Raw score:232.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAI---------------LRWTRHSAEQGAHLVAFPEM 45 :::::::::::: d1jfla2 1 -------------------------FKKAGLLATTGTIVSGVYEKEFSKYGV-------- 27 query 46 ALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPA 105 d1jfla2 28 ------------------------------------------------------------ 28 query 106 GAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDL 165 d1jfla2 28 ------------------------------------------------------------ 28 query 166 WQDG----------------------------------GRVPAARSAGAGLLLSVNASPY 191 :::::::::::::::: d1jfla2 28 ----EIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIA------ 77 query 192 ERDKD--DTRLELVRK-RAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQF 248 :::::: ::::::::::: d1jfla2 78 -----GCTEVSVV---LKQDDLKVPLID-------------------------------- 97 query 249 SEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL------ 302 d1jfla2 98 ------------------------------------------------------PMDVIA 103 query 303 ---------- 303 d1jfla2 104 EVAVKVALEK 113 TMalign alignment (TM-score: 0.20 Raw score:60.72) query 1 -SLQLR-LA-LN-QIDSTV-GDIAGN--AEAI--LRWT-RHSAEQGAHLV-AF-----PE 44 : : : :::: : : :: :: :::::: : d1jfla2 1 F----KK-AG-LL--ATTGT-----IVS---GVY--EKE-FS--KYGVEIM-TPTEDE-- 36 query 45 MA-LTG-YPV---EDLALRSSFVEASRTALRELAARLAEEGFGELPVLVG-Y--LDRSES 96 : ::: ::: :: :::::::::::::::::::: : : ::::: : :: d1jfla2 37 -QKDVMRGIYEGVKA-GNLKLGRELLLKTAKILEER-G----A--ECIIAGCTEVS---- 83 query 97 AQPKYGQPAGAPRNAAA--VLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHG 154 ::::: :::::::: d1jfla2 84 ------------VVLKQDD-----LKVPLIDP---------------------------- 98 query 155 VDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTT 214 :::: : : : : :::::: d1jfla2 99 ----MDVI--A------E----------V-------------------A--VKVALE--- 112 query 215 AYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDG 274 : d1jfla2 113 -----------------------K------------------------------------ 113 query 275 LRIDRLVISEEPLPAYEAELAGGYADRL 302 d1jfla2 114 ---------------------------- 114 HHsearch alignment (Probability: 0.06 E-value:0.03) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.189 --> HitDALI alignment (Z-score: 5.6 Raw score:399.80) d1jfla2 1 --fKKAGLLA----ttGTIV-sGVYEKEFSKYGVEIMTPtedeqkdVMRGiyegvkagnl 53 ::::::: :::: ::::::::::::::::: :::: d1tjya_ 1 gsaERIAFIPklvgvgFFTSggNGAQEAGKALGIDVTYD------gPTEP---------- 44 d1jfla2 54 klGRELLLKTAKILEERGAECIIAGCTEvsVVLK--QDDLK---VPLIDPM--------- 99 :::::::::::::::::::::::::: :::: ::::: ::::::: d1tjya_ 45 --SVSGQVQLVNNFVNQGYDAIIVSAVS-pDGLCpaLKRAMqrgVKILTWDsdtkpecrs 101 d1jfla2 100 -DVIA------------------------------------------------------- 103 :::: d1tjya_ 102 yYINQgtpkqlgsmlvemaahqvdkekakvaffyssptvtdqnqwvkeakakisqehpgw 161 d1jfla2 104 ------------------------------------------------------------ 104 d1tjya_ 162 eivttqfgyndatkslqtaegiikaypdldaiiapdanalpaaaqaaenlkrnnlaivgf 221 d1jfla2 104 ------------------------------------------------------------ 104 d1tjya_ 222 stpnvmrpyvqrgtvkefglwdvvqqgkisvyvanallknmpmnvgdsldipgigkvtvs 281 d1jfla2 104 ----------------EVAVKV---------alek 113 :::::: d1tjya_ 282 pnseqgyhyeakgngiVLLPERvifnkdnidkydf 316 FAST alignment (Normalized score: 3.14 Raw score:592.90) d1jfla2 1 ------------------------------------------------------------ 1 d1tjya_ 1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQG 60 d1jfla2 1 ------------------------------------------------------------ 1 d1tjya_ 61 YDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYINQGTPKQLGSMLVEMA 120 d1jfla2 1 -------FKKAGLLA-------TTGTIVSGVYEKEFSK--YGVEIMTPTEDEQKDVMRGI 44 :::::::: ::::: ::::::::: ::::: d1tjya_ 121 AHQVDKEKAKVAFFYSSPTVTDQNQWV--KEAKAKISQEHPGWEI--------------- 163 d1jfla2 45 YEGVKAGNLKL--------GRELLLKTAKILEE--RGAECIIAGCTEVSVVLKQDD---- 90 :::::::::::::: :::::::::::::::: d1tjya_ 164 -----------VTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPA-----AAQA 207 d1jfla2 91 ------LKVPLIDPMDVIAEVAVKVALEK------------------------------- 113 :::::::: d1tjya_ 208 AENLKRNNLAIVGF---------------STPNVMRPYVQRGTVKEFGLWDVVQQGKISV 252 d1jfla2 114 ------------------------------------------------------------ 114 d1tjya_ 253 YVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKDNID 312 d1jfla2 114 ---- 114 d1tjya_ 313 KYDF 316 TMalign alignment (TM-score: 0.58 Raw score:65.21) d1jfla2 1 --FKKAGLLA-TT--G-TIV-SGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNL 53 :::::::: :: : ::: :::::::::::::::::: : ::: : : d1tjya_ 1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYD----G--PTE-P--S------ 45 d1jfla2 54 KLGRELLLKTAKILEERGAECIIAGCTEVSV-VLK--QDDL--K-VPLIDPM-------- 99 : :::::::::::::::::::: :::: : ::: :::: : ::::::: d1tjya_ 46 --V-SGQVQLVNNFVNQGYDAIIV-SAVS-PDGLCPALKRAMQRGVKILTWDSDTKPECR 100 d1jfla2 100 --DVI-A----------------------------------------------------- 103 ::: : d1tjya_ 101 SYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPG 160 d1jfla2 104 ------------------------------------------------------------ 104 d1tjya_ 161 WEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVG 220 d1jfla2 104 ---------------------------------------------------------EVA 106 ::: d1tjya_ 221 FSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPGIGKVTV 280 d1jfla2 107 V----------------KV-A---------------LEK 113 : :: : d1tjya_ 281 SPNSEQGYHYEAKGNGIVLLPERVIFNKDNIDKYDF--- 316 HHsearch alignment (Probability: 0.25 E-value:0.01) d1jfla2 19 EKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIAG 78 :::::::::::::::: :::::::::::::::::::::::::: d1tjya_ 26 QEAGKALGIDVTYDGP------------------TEPSVSGQVQLVNNFVNQGYDAIIVS 67 d1jfla2 79 CTEVSV----VLKQDDLKVPLI 96 :::::: :::::::::::: d1tjya_ 68 AVSPDGLCPALKRAMQRGVKIL 89