Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_026607777.1 METAC_RS0115680 diaminopimelate epimerase
Query= curated2:B8EM14 (290 letters) >NCBI__GCF_000427445.1:WP_026607777.1 Length = 288 Score = 406 bits (1043), Expect = e-118 Identities = 200/290 (68%), Positives = 233/290 (80%), Gaps = 2/290 (0%) Query: 1 MNPLANRLAVKMNGIGNEILIVDLRGAGAGVTGPQARAIARTKGLAFDQLMVLEDPRSKG 60 M+PLANRL KMNG+GNEIL++D+RG G V G +ARAIAR GL FDQLM L+DP S G Sbjct: 1 MSPLANRLVTKMNGLGNEILVLDVRGGGVAVRGAEARAIAR--GLGFDQLMALQDPVSAG 58 Query: 61 CAAFVTIFNADGSQSAACGNGTRCVAWTLLKDGARDEVLLETAAGRLACRRVSELVFSVE 120 AFVTIFN DGSQ+ ACGNG RCVAW L++DGARD + +ETAAGRL CRR+ EL FSVE Sbjct: 59 TEAFVTIFNNDGSQAGACGNGARCVAWFLMRDGARDVLAVETAAGRLECRRLGELRFSVE 118 Query: 121 MGRPRLKAAEIPLSRDAPDTSAVDLSFGPADSPILKNPAVVNMGNPHAIFFVEDIGAYDL 180 MGRPRL EIPL A DT A+ L GP +P+L P+VVNMGNPHAIF+V + YDL Sbjct: 119 MGRPRLAWNEIPLRDPAEDTRAIGLRIGPESAPVLSGPSVVNMGNPHAIFWVAALDVYDL 178 Query: 181 AAIGPVLEHDPLFPERANISLARIVSPERIELKVWERGVGLTLACGSAACAALVAAARRG 240 AAIGP++EHDP+FP+R N+SLA+ +SP I L+VWERG GLT ACGSAACAALVA AR+G Sbjct: 179 AAIGPLVEHDPMFPDRVNVSLAQALSPAHIALRVWERGAGLTKACGSAACAALVAGARKG 238 Query: 241 LTGRRATVALPGGELDIFWRESDDMVVMTGPVAFEFETRLDPAIFADAAA 290 LT R A V+LPGG+L+I WRESDD+VVMTGPV FEFETRLDPA+FAD AA Sbjct: 239 LTRREAVVSLPGGDLEIAWRESDDIVVMTGPVEFEFETRLDPALFADLAA 288 Lambda K H 0.321 0.137 0.406 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: 347 Number of extensions: 4 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: 290 Length of database: 288 Length adjustment: 26 Effective length of query: 264 Effective length of database: 262 Effective search space: 69168 Effective search space used: 69168 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: 48 (23.1 bits)
Align candidate WP_026607777.1 METAC_RS0115680 (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.32581.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-64 203.0 0.0 3.8e-64 202.7 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026607777.1 METAC_RS0115680 diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026607777.1 METAC_RS0115680 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.7 0.0 3.8e-64 3.8e-64 4 267 .. 10 277 .. 8 279 .. 0.89 Alignments for each domain: == domain 1 score: 202.7 bits; conditional E-value: 3.8e-64 TIGR00652 4 lkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeae 71 +km+GlgN+ +++d + + +++r++ g+g+D+++ ++ s +++ ++ifN+DGS+a lcl|NCBI__GCF_000427445.1:WP_026607777.1 10 TKMNGLGNEILVLDVRGGGVAVR-GAEARAI---ARGLGFDQLMALQDpVSAGTEAFVTIFNNDGSQAG 74 79*******99999988666666.4556655...57**********9878999999************* PP TIGR00652 72 mCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeeke 140 CGNg+Rc+a f++ +g + l vet ag++++ e + +v+mg+p++ +eipl+ e ++ lcl|NCBI__GCF_000427445.1:WP_026607777.1 75 ACGNGARCVAWFLMRDGAR--DVLAVETAAGRLECRRLGEL-RFSVEMGRPRLAWNEIPLRDPAEDTRA 140 ***************9988..8**********999988887.*******************65555544 PP TIGR00652 141 ellalev.....l....vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeik 200 l++ l vv++GnPH+++ v+ ++ dl +g+l+e+++ fp++vNv +++++++ +i lcl|NCBI__GCF_000427445.1:WP_026607777.1 141 IGLRIGPesapvLsgpsVVNMGNPHAIFWVAALDVYDLAAIGPLVEHDPMFPDRVNVSLAQALSPAHIA 209 44443325667526677**************************************************** PP TIGR00652 201 lrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlege 267 lrv+ERGag T+aCG+ a+A+ v+++++g+t +++ v l+gg+Lei ++e++ v +tGp+++ +e + lcl|NCBI__GCF_000427445.1:WP_026607777.1 210 LRVWERGAGLTKACGSAACAALVAGARKGLTRREAVVSLPGGDLEIAWRESDdIVVMTGPVEFEFETR 277 *************************************************999789******9888765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (288 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.01 // [ok]
This GapMind analysis is from Apr 10 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