Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate GFF5388 PS417_27585 diaminopimelate epimerase
Query= SwissProt::P44859 (274 letters) >FitnessBrowser__WCS417:GFF5388 Length = 276 Score = 322 bits (824), Expect = 7e-93 Identities = 157/274 (57%), Positives = 200/274 (72%) Query: 1 MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHY 60 ++F+KMHGLGNDF+V+D V+Q+ P+ ++ +RH GIGFDQLLIVEAP +PE+DF Y Sbjct: 3 LRFTKMHGLGNDFMVLDLVSQHAHILPKHAKQWGDRHTGIGFDQLLIVEAPSNPEVDFRY 62 Query: 61 RIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGE 120 RIFNADGSEV QCGNGARCFARFV K LT K+ I V T+ G + L ++ D QI VNMG Sbjct: 63 RIFNADGSEVEQCGNGARCFARFVLDKRLTAKRQIRVETKSGVIELDIRSDGQISVNMGA 122 Query: 121 PIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLE 180 P PA IPF A + +Y L D +TV AVSMGNPH V++V+DI A V +LGP +E Sbjct: 123 PRLVPADIPFQAPEQAASYALDVDGKTVEIAAVSMGNPHAVLRVNDINNAPVHELGPKIE 182 Query: 181 SHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQV 240 H RFP RVN GF+Q+I++ +LRV+ERGAGETQACG+GACAA I QG +++ + + Sbjct: 183 HHPRFPARVNVGFLQVIDRTRAQLRVWERGAGETQACGTGACAAAVAAISQGWMDSPLLI 242 Query: 241 DLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL 274 DLPGG L IEW G GHP+ MTG A+ +Y+G + L Sbjct: 243 DLPGGRLSIEWAGPGHPVMMTGPASRVYEGQVRL 276 Lambda K H 0.321 0.139 0.423 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 259 Number of extensions: 6 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 274 Length of database: 276 Length adjustment: 25 Effective length of query: 249 Effective length of database: 251 Effective search space: 62499 Effective search space used: 62499 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate GFF5388 PS417_27585 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00652.hmm # target sequence database: /tmp/gapView.24132.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00652 [M=270] Accession: TIGR00652 Description: DapF: diaminopimelate epimerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-96 308.8 0.0 1.9e-96 308.6 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF5388 PS417_27585 diaminopimelate epim Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF5388 PS417_27585 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.6 0.0 1.9e-96 1.9e-96 2 268 .. 4 274 .. 3 276 .] 0.94 Alignments for each domain: == domain 1 score: 308.6 bits; conditional E-value: 1.9e-96 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGN 75 +F+kmhGlgNdF+++d v ++ ++ +++ drhtg+g+D++l+ve+ s++e d+++rifN+DGSe+e+CGN lcl|FitnessBrowser__WCS417:GFF5388 4 RFTKMHGLGNDFMVLDLVSQHAHIL-PKHAKQWGDRHTGIGFDQLLIVEApSNPEVDFRYRIFNADGSEVEQCGN 77 8******************999988.9*********************987999********************* PP TIGR00652 76 giRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt....vekeeekeellale 146 g+Rcfa+fv +k l+ k++++vet++g+i++ + +++ +++v+mg p++ +++ip++ ++ ++ + + ++e lcl|FitnessBrowser__WCS417:GFF5388 78 GARCFARFVLDKRLTAKRQIRVETKSGVIELDIRSDG-QISVNMGAPRLVPADIPFQapeqAASYALDVDGKTVE 151 *************************************.*******************443333344444444555 PP TIGR00652 147 vlvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAs 221 + +v++GnPH+v+ v+d+++++++elg+++e+h++fp++vNv f++v ++ + +lrv+ERGageT+aCGtGa+A+ lcl|FitnessBrowser__WCS417:GFF5388 152 IAAVSMGNPHAVLRVNDINNAPVHELGPKIEHHPRFPARVNVGFLQVIDRTRAQLRVWERGAGETQACGTGACAA 226 56************************************************************************* PP TIGR00652 222 avvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 av+a+ +g +++ + + l+gg+L ie+ g v++tGpa++v+eg++ lcl|FitnessBrowser__WCS417:GFF5388 227 AVAAISQGWMDSPLLIDLPGGRLSIEWAGPGhPVMMTGPASRVYEGQV 274 *******************************99*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (276 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.72 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory