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 | d1jwqa_ | N-acetylmuramoyl-L-alanine amidase CwlV | Zn-dependent exopeptidases | Phosphorylase/hydrolase-like | 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 <-- 0.963 --> HitDALI alignment (Z-score: 3.4 Raw score:275.10) d1jfla2 1 FKKAGLLA---------------------TTGTIvsGVYEKEFSKYG-VEIMTPtedeQK 38 :::::::: ::::: ::::::::::: :::::: :: d1jwqa_ 1 MKVVVIDAghgakdsgavgisrknyektfNLAMA--LKVESILKQNPkLEVVLT-rsdDT 57 d1jfla2 39 DVmrgiyegvkagnlklgreLLLKTAKILEERGAECIIAGCT------------------ 80 :: :::::::::::::::::::::: d1jwqa_ 58 FL------------------ELKQRVKVAENLKANVFVSIHAnssgssasngtetyyqrs 99 d1jfla2 81 ------------------------evsVVLKQDDLKVPLI-------------------- 96 ::::::::::::: d1jwqa_ 100 askafanvmhkyfapatgltdrgirygNFHVIRETTMPAVllevgylsnakeeatlfded 159 d1jfla2 97 ---dpmdviaevavkvalek 113 d1jwqa_ 160 fqnrvaqgiadgiteyldvk 179 FAST alignment (Normalized score: 3.48 Raw score:495.50) d1jfla2 1 FKKAGLLA-----------------------TTGTIVSGVYEKEFSK-YGVEIMTPTEDE 36 :::::: ::::: ::::::::: :::::::: d1jwqa_ 1 MKVVVI--DAGHGAKDSGAVGISRKNYEKTFNLAMA--LKVESILKQNPKLEVVLT---- 52 d1jfla2 37 QKDVMRGIYEGVKAGNLKL-------GRELLLKTAKILEERGAECIIAGCTEVSVVL--- 86 ::::::::::: ::::::::: d1jwqa_ 53 -------------------RSDDTFLELKQRVKVAEN---LKANVFVSI--------HAN 82 d1jfla2 87 -----------------------------------------------KQDDLKVPLIDPM 99 ::::::::::: d1jwqa_ 83 SSGSSASNGTETYYQRSASKAFANVMHKYFAPATGLTDRGIRYGNFHVIRETTMPAVL-- 140 d1jfla2 100 DVIAEVAVKVALEK--------------------------------------- 113 d1jwqa_ 141 --------------LEVGYLSNAKEEATLFDEDFQNRVAQGIADGITEYLDVK 179 TMalign alignment (TM-score: 0.49 Raw score:54.83) d1jfla2 1 FKKAGLLAT-T----------------G--TIVSGVYEKEFSKYG-VEIMTPTED-EQKD 39 ::::::::: : : ::::::::::::::: ::::::::: ::: d1jwqa_ 1 MKVVVIDAGHGAKDSGAVGISRKNYEKTFNLAMALKVESILKQNPKLEVVLTRSDD-TFL 59 d1jfla2 40 VMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIAGCTE------------VS---- 83 ::::::::::::::::::::::: : d1jwqa_ 60 -------------------ELKQRVKVAENLKANVFVSIHANSSGSSASNGTET-YYQRS 99 d1jfla2 84 --------------------------V-VLKQDDLKVPLIDPMD---------------- 100 : :::::::::::::::: d1jwqa_ 100 ASKAFANVMHKYFAPATGLTDRGIRYGNFHVIRETTMPAVLLEVGYLSNAKEEATLFDED 159 d1jfla2 101 ----V--I---AEV--------AVKVALEK 113 : : : d1jwqa_ 160 FQNRVAQGIAD--GITEYLDVK-------- 179 HHsearch alignment (Probability: 0.00 E-value:0.76) d1jfla2 76 IAGCTEVSV 84 ::::::::: d1jwqa_ 130 VIRETTMPA 138