Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate PP_5228 PP_5228 diaminopimelate epimerase
Query= SwissProt::P44859 (274 letters) >FitnessBrowser__Putida:PP_5228 Length = 287 Score = 328 bits (841), Expect = 8e-95 Identities = 160/274 (58%), Positives = 204/274 (74%) Query: 1 MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHY 60 ++F+KMHGLGNDF+V+D V+Q+ P+ ++ +RH G+GFDQLLIVEAP +PE+DF Y Sbjct: 14 LRFTKMHGLGNDFMVLDLVSQHAHIQPKHAKQWGDRHTGVGFDQLLIVEAPNNPEVDFRY 73 Query: 61 RIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGE 120 RIFNADGSEV QCGNGARCFARFV K LT KK I V T+ G +VL V++D Q+ V+MG Sbjct: 74 RIFNADGSEVEQCGNGARCFARFVLDKRLTAKKRIRVETKSGIIVLDVQNDGQVSVDMGP 133 Query: 121 PIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLE 180 P + PA+IPF A+ NY L D Q AVSMGNPH V++VDD+QTA V +LGP +E Sbjct: 134 PRFIPAEIPFVADAQALNYPLEVDGQLHSIAAVSMGNPHAVLRVDDVQTAPVHELGPKIE 193 Query: 181 SHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQV 240 +H RFP+RVNAGF+Q+I++ LRV+ERGAGETQACG+GACAA I QG +++ V + Sbjct: 194 NHPRFPQRVNAGFIQVIDRHRANLRVWERGAGETQACGTGACAAAVAAISQGWMDSPVSL 253 Query: 241 DLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL 274 DLPGG L IEW G G P+ MTG A +Y+G + L Sbjct: 254 DLPGGRLHIEWAGPGKPVMMTGPAVRVYEGQVRL 287 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: 270 Number of extensions: 5 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: 287 Length adjustment: 26 Effective length of query: 248 Effective length of database: 261 Effective search space: 64728 Effective search space used: 64728 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 PP_5228 PP_5228 (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.6747.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-97 312.6 0.0 1.3e-97 312.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_5228 PP_5228 diaminopimelate epimeras Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_5228 PP_5228 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 312.4 0.0 1.3e-97 1.3e-97 2 268 .. 15 285 .. 14 287 .] 0.95 Alignments for each domain: == domain 1 score: 312.4 bits; conditional E-value: 1.3e-97 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGN 75 +F+kmhGlgNdF+++d v ++ + ++ +++ drhtgvg+D++l+ve+ +++e d+++rifN+DGSe+e+CGN lcl|FitnessBrowser__Putida:PP_5228 15 RFTKMHGLGNDFMVLDLVSQHAHIQ-PKHAKQWGDRHTGVGFDQLLIVEApNNPEVDFRYRIFNADGSEVEQCGN 88 8******************888888.9*********************987999********************* PP TIGR00652 76 giRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev... 147 g+Rcfa+fv +k l+ kk+++vet++g+i++ v++++ +v+vdmg p+f ++eip++++ ++ ++ l+ lcl|FitnessBrowser__Putida:PP_5228 89 GARCFARFVLDKRLTAKKRIRVETKSGIIVLDVQNDG-QVSVDMGPPRFIPAEIPFVADAQALNYPLEVDGQlhs 162 *************************************.*******************988888665544333444 PP TIGR00652 148 l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAs 221 + +v++GnPH+v+ v+dv++++++elg+++e+h++fp++vN f++v ++++ lrv+ERGageT+aCGtGa+A+ lcl|FitnessBrowser__Putida:PP_5228 163 IaAVSMGNPHAVLRVDDVQTAPVHELGPKIENHPRFPQRVNAGFIQVIDRHRANLRVWERGAGETQACGTGACAA 237 36************************************************************************* PP TIGR00652 222 avvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 av+a+ +g +++ v l+gg+L+ie+ g v++tGpav+v+eg++ lcl|FitnessBrowser__Putida:PP_5228 238 AVAAISQGWMDSPVSLDLPGGRLHIEWAGPGkPVMMTGPAVRVYEGQV 285 *******************************99*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (287 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.06 // [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