Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_029329001.1 ON01_RS05555 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >NCBI__GCF_000224785.1:WP_029329001.1 Length = 287 Score = 288 bits (738), Expect = 7e-83 Identities = 137/284 (48%), Positives = 194/284 (68%), Gaps = 4/284 (1%) Query: 1 MSQFSFTKMHGLGNSYIYVNMFEEQ---IPEEDLALVAEKVSNINTGIGADGMILICPSD 57 M + FTKM GLGN+Y+ + +PE D +A +VS+++ GIG+DG+ILI S+ Sbjct: 1 MGELMFTKMQGLGNNYVVFDQLGHSANILPENDYPELARRVSDMSFGIGSDGIILIGASE 60 Query: 58 VAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEE-G 116 A KMR+FN DGSE K+CGNGLRCVAK+ Y+++ +D F+IETL G+VT +VTV Sbjct: 61 QADFKMRIFNKDGSEAKNCGNGLRCVAKFLYDNQYPKDPRFSIETLGGVVTVDVTVNHHN 120 Query: 117 KVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDV 176 + +DMG PRL + IPM G+ + ++E + + + Y T +SMGNPHA+IFVDDV Sbjct: 121 QAAYVTVDMGKPRLAKKMIPMQGDPDETAVKEVYTFGDKSYQLTCLSMGNPHAIIFVDDV 180 Query: 177 EQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVA 236 ++ PL T+GP++E +FPERVN+ + + N++E+N+RVWERGSG+T ACGTGACA+V A Sbjct: 181 DKVPLETIGPIIEHSSLFPERVNIGVVHVKNQQEINYRVWERGSGITMACGTGACASVAA 240 Query: 237 SILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRG 280 + LN + + VHL GGDL I + G++LM+G A IC G Sbjct: 241 AALNNLLNTTQPTLVHLPGGDLTIELADNGHILMQGKACYICHG 284 Lambda K H 0.318 0.136 0.398 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: 269 Number of extensions: 10 Number of successful extensions: 3 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: 288 Length of database: 287 Length adjustment: 26 Effective length of query: 262 Effective length of database: 261 Effective search space: 68382 Effective search space used: 68382 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: 47 (22.7 bits)
Align candidate WP_029329001.1 ON01_RS05555 (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.983538.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-93 299.0 0.0 1.8e-93 298.9 0.0 1.0 1 NCBI__GCF_000224785.1:WP_029329001.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_029329001.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.9 0.0 1.8e-93 1.8e-93 2 268 .. 5 286 .. 4 287 .] 0.90 Alignments for each domain: == domain 1 score: 298.9 bits; conditional E-value: 1.8e-93 TIGR00652 2 eFlkmhGlgNdFvlvdevd..eelvkee..aelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSea 70 F+km+GlgN++v+ d++ ++++ e+ +el+r+v+d+ +g+g+Dg++l+ + se+ad+k+rifN DGSea NCBI__GCF_000224785.1:WP_029329001.1 5 MFTKMQGLGNNYVVFDQLGhsANILPENdyPELARRVSDMSFGIGSDGIILIGA-SEQADFKMRIFNKDGSEA 76 6****************9865666666679***********************5.****************** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeen....kkvkvdmgepkfkkeeipltvekee.. 137 ++CGNg+Rc+akf+y++++ + ++s+etl g+++v v+ + + v+vdmg+p++ k+ ip++++++e NCBI__GCF_000224785.1:WP_029329001.1 77 KNCGNGLRCVAKFLYDNQYPKDPRFSIETLGGVVTVDVTVNHhnqaAYVTVDMGKPRLAKKMIPMQGDPDEta 149 *********************9***********998776555558999******************6655511 PP TIGR00652 138 ekeellalev...l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyER 206 +ke+ ++ + l ++++GnPH+++fv+dv+k++le++g+ +e++ fpe+vN+ +v+vk+++ei rv+ER NCBI__GCF_000224785.1:WP_029329001.1 150 VKEVYTFGDKsyqLtCLSMGNPHAIIFVDDVDKVPLETIGPIIEHSSLFPERVNIGVVHVKNQQEINYRVWER 222 445555555465527********************************************************** PP TIGR00652 207 GageTlaCGtGavAsavvalk..lgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 G+g+T+aCGtGa+As+++a+ l +t + vhl+gg+L+ie+ ++g+++++G+a ++++gel NCBI__GCF_000224785.1:WP_029329001.1 223 GSGITMACGTGACASVAAAALnnLLNTTQPTLVHLPGGDLTIELADNGHILMQGKACYICHGEL 286 ****************99987445555666*******************************997 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 13.54 // [ok]
This GapMind analysis is from Jul 26 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