Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_028990196.1 G579_RS0110750 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_000423825.1:WP_028990196.1 Length = 282 Score = 312 bits (800), Expect = 5e-90 Identities = 158/270 (58%), Positives = 188/270 (69%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++FSKMHGLGNDF+V+D V Q V S +RRLADR GVG DQ+L+VE DP DF Y Sbjct: 6 LRFSKMHGLGNDFVVIDGVRQTVRLSAAEVRRLADRRFGVGCDQVLLVEASTDPRADFRY 65 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADG EV QCGNGARCFARFVR +GLT+K I V T GR+ L + V+V+MG Sbjct: 66 RIFNADGGEVQQCGNGARCFARFVREQGLTDKDVIPVETLAGRITLAIQPSGEVQVDMGV 125 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P EP+ +PFRA Y + A QT G VSMGNPH ++ V V A V+TLGP +E Sbjct: 126 PILEPARIPFRAPAQALRYPLPVAGQTYEIGAVSMGNPHAILPVASVAQAPVDTLGPAIE 185 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H FPER N+GFM+ V +HIRLRV+ERGAGET ACG+ ACAAV G LL E VRV Sbjct: 186 RHPDFPERVNVGFMERVGPDHIRLRVWERGAGETLACGTNACAAVVAGRLWNLLDETVRV 245 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDG 270 LPGG L I+W+GPG P++MTGPAV V+ G Sbjct: 246 SLPGGDLRISWRGPGEPVFMTGPAVTVFQG 275 Lambda K H 0.323 0.140 0.425 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: 262 Number of extensions: 6 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: 274 Length of database: 282 Length adjustment: 25 Effective length of query: 249 Effective length of database: 257 Effective search space: 63993 Effective search space used: 63993 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 bits)
Align candidate WP_028990196.1 G579_RS0110750 (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.17829.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-95 304.5 0.0 3.9e-95 304.3 0.0 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028990196.1 G579_RS0110750 diaminopimelate e Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028990196.1 G579_RS0110750 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 304.3 0.0 3.9e-95 3.9e-95 2 268 .. 7 277 .. 6 279 .. 0.94 Alignments for each domain: == domain 1 score: 304.3 bits; conditional E-value: 3.9e-95 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSe 69 +F+kmhGlgNdFv++d v +++ + a++vr+++dr++gvg+D+vllve+ ++++ad+++rifN+DG e lcl|NCBI__GCF_000423825.1:WP_028990196.1 7 RFSKMHGLGNDFVVIDGVRQTVRLS-AAEVRRLADRRFGVGCDQVLLVEAsTDPRADFRYRIFNADGGE 74 8******************777776.9**********************98899*************** PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee 138 +++CGNg+Rcfa+fv+e+gl++k+ + vetlag+i++ ++ + +v+vdmg p ++++ ip+++ ++ lcl|NCBI__GCF_000423825.1:WP_028990196.1 75 VQQCGNGARCFARFVREQGLTDKDVIPVETLAGRITLAIQPSG-EVQVDMGVPILEPARIPFRAPAQAL 142 *******************************************.*******************766665 PP TIGR00652 139 keellalev..l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklr 202 ++ l + + +v++GnPH++++v++v ++++++lg+++e h++fpe+vNv f+e++++d+i+lr lcl|NCBI__GCF_000423825.1:WP_028990196.1 143 RYPLPV-AGqtYeigAVSMGNPHAILPVASVAQAPVDTLGPAIERHPDFPERVNVGFMERVGPDHIRLR 210 444322.22232447****************************************************** PP TIGR00652 203 vyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 v+ERGageTlaCGt a+A++v+++ ++++ v+v l+gg+L i+++ g v++tGpav+v++ge lcl|NCBI__GCF_000423825.1:WP_028990196.1 211 VWERGAGETLACGTNACAAVVAGRLWNLLDETVRVSLPGGDLRISWRGPGePVFMTGPAVTVFQGEW 277 **************************************************99************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (282 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: 00:00:00.01 # Mc/sec: 6.56 // [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