Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_193377911.1 NGR_RS27260 diaminopimelate epimerase
Query= curated2:Q8YJF0 (303 letters) >NCBI__GCF_000018545.1:WP_193377911.1 Length = 301 Score = 454 bits (1167), Expect = e-132 Identities = 220/297 (74%), Positives = 244/297 (82%), Gaps = 1/297 (0%) Query: 1 MATKAAFARMNGLGNQIIVADMRGRADSITSAAAIRLASDSETAFDQIMAIHDPRTPGTD 60 MA FARMNGLGN+I+V DMRGR D +T AAI L +D T FDQIMAIHDPR PGTD Sbjct: 1 MADHVQFARMNGLGNKILVVDMRGRKDRVTPGAAIALNADPATEFDQIMAIHDPRAPGTD 60 Query: 61 YYIAIINCDGTQAQACGNGTRCVVQALAAETGRHAFTFETRAGILTATEHDDGLISVDMG 120 +I I+N DG+ AQACGNGTRCVVQALAAETG+ AF F T AG+L A EHDDGLISVDMG Sbjct: 61 AWIDIVNSDGSMAQACGNGTRCVVQALAAETGKKAFLFHTVAGLLEAREHDDGLISVDMG 120 Query: 121 TPRFDWQDIPLAQAVADTRKIELQVDPADAPVLHSPSIASMGNPHAVFWVDKDVWSYELD 180 +PRF W +IPLA+ DTR+IELQ+ P D PVLHSPS+ASMGNPHA+FWV+ DVWSYELD Sbjct: 121 SPRFGWNEIPLAEEFHDTRRIELQIGPIDDPVLHSPSVASMGNPHAIFWVENDVWSYELD 180 Query: 181 KFGPLLENHPIFPERANISIAHVTSSDTIDLRTWERGAGLTRACGSAACAAAVSAARTGR 240 +FGPLLENHPIFPERANISIAHV S +DLRTWERGAGLT ACGSAACAAAVS ARTGR Sbjct: 181 RFGPLLENHPIFPERANISIAHVRSRQEMDLRTWERGAGLTLACGSAACAAAVSGARTGR 240 Query: 241 TGRKVTVNVPGGPLLIEWRD-DDHVMMTGPAEWEFSGTFDPATGEWSRDTQGLQGSG 296 T R VTVNVPGGPL IEWR+ DDHV+MTGPAEWE++GT DPATG + RD SG Sbjct: 241 TDRIVTVNVPGGPLKIEWRESDDHVIMTGPAEWEWTGTVDPATGAFERDAAATSESG 297 Lambda K H 0.318 0.132 0.408 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: 425 Number of extensions: 14 Number of successful extensions: 2 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: 303 Length of database: 301 Length adjustment: 27 Effective length of query: 276 Effective length of database: 274 Effective search space: 75624 Effective search space used: 75624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_193377911.1 NGR_RS27260 (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.1745118.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-64 203.0 0.0 3.5e-64 202.8 0.0 1.0 1 NCBI__GCF_000018545.1:WP_193377911.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_193377911.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.8 0.0 3.5e-64 3.5e-64 2 263 .. 6 274 .. 5 280 .. 0.90 Alignments for each domain: == domain 1 score: 202.8 bits; conditional E-value: 3.5e-64 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemC 73 +F++m+GlgN+ ++vd + ++ + + + ++ + + +D+++ ++ + +d+ ++i NsDGS a+ C NCBI__GCF_000018545.1:WP_193377911.1 6 QFARMNGLGNKILVVDMRGRKDRVT-PGAAIAL-NADPATEFDQIMAIHDpRAPGTDAWIDIVNSDGSMAQAC 76 8****************99888888.5555555.5667889******9976899******************* PP TIGR00652 74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellale 146 GNg Rc+++ ++++++k k + ++t agl+++ ++++ ++vdmg+p+f +eipl +e + +++ l+ NCBI__GCF_000018545.1:WP_193377911.1 77 GNGTRCVVQALAAETGK--KAFLFHTVAGLLEAREHDDG-LISVDMGSPRFGWNEIPLAEEFHDTRRIELQ-- 144 ***************99..8**************99999.*******************876666443333.. PP TIGR00652 147 v.......l....vvdvGnPHlvvfved.vekldleelgklleaheefpegvNvefvevkkedeiklrvyERG 207 + l v ++GnPH+++ ve+ v + +l++ g+lle+h+ fpe+ N+ +++v +++e+ lr++ERG NCBI__GCF_000018545.1:WP_193377911.1 145 IgpiddpvLhspsVASMGNPHAIFWVENdVWSYELDRFGPLLENHPIFPERANISIAHVRSRQEMDLRTWERG 217 2234777625677***********998769******************************************* PP TIGR00652 208 ageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlv 263 ag TlaCG+ a+A+av ++++g+t++ vtv+++gg L+ie++e++ +v++tGpa+ NCBI__GCF_000018545.1:WP_193377911.1 218 AGLTLACGSAACAAAVSGARTGRTDRIVTVNVPGGPLKIEWRESDdHVIMTGPAEWE 274 ******************************************9998*******9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (301 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: 14.64 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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