Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate CA265_RS23025 CA265_RS23025 diaminopimelate epimerase
Query= curated2:A6GYX5 (256 letters) >FitnessBrowser__Pedo557:CA265_RS23025 Length = 260 Score = 245 bits (625), Expect = 8e-70 Identities = 122/255 (47%), Positives = 167/255 (65%), Gaps = 3/255 (1%) Query: 1 MKLYKYQGTGNDFIMIDNRLQIFPKQNTALIQKLCDRRFGIGADGLILLENDQSTDFKMV 60 + +KYQG GNDFI+ID+ + + L+++LC RRFGIGADGL+ + + DF+M Sbjct: 3 INFFKYQGAGNDFILIDHTMSPLKNIDNQLVEQLCHRRFGIGADGLMFITKHEDYDFEMH 62 Query: 61 YYNSDGNQSTMCGNGGRCLVAFAKKLNIIKNKTTFIAIDGLHHATINEN-DIISLQMKNV 119 Y+N+DG +MCGNGGRC+VAFAK+L II +T F+A+DG H+A I+EN + + LQM +V Sbjct: 63 YFNADGKLGSMCGNGGRCIVAFAKQLGIIDRETNFLAVDGPHYARISENGEWVDLQMIDV 122 Query: 120 EEVNIHDNYVFLNTGSPHHVQFADNLSNFDVKNEGAKIRYSDLYGQAGSNINFVHQTSPT 179 + + LNTGSPH+V +L +FDV G IRY+ Y + G N+NFV Sbjct: 123 DTITKDGEAYILNTGSPHYVALQSDLKDFDVFTAGKNIRYNATYAEKGINVNFVEDKGDH 182 Query: 180 QFSIRTYERGVEDETLSCGTGATATAIAM-KATGKTNSNNITINVQGGKLEVSFNQENSI 238 F +RTYERGVEDET +CGTG TA A+AM K +T I V GG +++ F+ + Sbjct: 183 LF-VRTYERGVEDETYACGTGVTAVAMAMAKHKNQTGHIKTAIKVLGGDIKIEFDYDGKE 241 Query: 239 FTNIFLKGPAEFVFE 253 FTN+FL GPA+ VFE Sbjct: 242 FTNVFLCGPAKLVFE 256 Lambda K H 0.318 0.135 0.386 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: 251 Number of extensions: 9 Number of successful extensions: 4 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: 256 Length of database: 260 Length adjustment: 24 Effective length of query: 232 Effective length of database: 236 Effective search space: 54752 Effective search space used: 54752 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 CA265_RS23025 CA265_RS23025 (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.17275.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-66 211.0 1.8 2.2e-65 206.7 1.8 1.9 1 lcl|FitnessBrowser__Pedo557:CA265_RS23025 CA265_RS23025 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS23025 CA265_RS23025 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.7 1.8 2.2e-65 2.2e-65 1 268 [. 3 259 .. 3 260 .] 0.90 Alignments for each domain: == domain 1 score: 206.7 bits; conditional E-value: 2.2e-65 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGS 68 ++F+k++G+gNdF+l+d+ + l + +++lv+++c+r++g+gaDg++++++ +e++d+++++fN+DG lcl|FitnessBrowser__Pedo557:CA265_RS23025 3 INFFKYQGAGNDFILIDHTMSPLKNIDNQLVEQLCHRRFGIGADGLMFITK-HEDYDFEMHYFNADGK 69 68*****************988888889**********************6.**************** PP TIGR00652 69 eaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltveke 136 +mCGNg Rc+++f+++ g+ + +e ++ + g + + e++++v +m ++ +t++ lcl|FitnessBrowser__Pedo557:CA265_RS23025 70 LGSMCGNGGRCIVAFAKQLGIID-RETNFLAVDGPHYARISENGEWVDLQMIDVDT------ITKD-- 128 **********************6.999*****************999999988732......2221.. PP TIGR00652 137 eekeellalevlvvdvGnPHlvvfvedvekldleelgklleaheef.pegvNvefvevkkedeiklrv 203 e +++++G PH v +d++++d+ + gk ++++ ++ +g+Nv+fve k+ d++++r+ lcl|FitnessBrowser__Pedo557:CA265_RS23025 129 G--------EAYILNTGSPHYVALQSDLKDFDVFTAGKNIRYNATYaEKGINVNFVEDKG-DHLFVRT 187 1........124589*******************************899**********9.9****** PP TIGR00652 204 yERG.ageTlaCGtGavAsavvalklgktkkk..vtvhleggeLeievkedg....kvyltGpavlvl 264 yERG ++eT aCGtG +A+a++ +k +++ + ++++ gg+++ie+ dg +v+l Gpa+lv+ lcl|FitnessBrowser__Pedo557:CA265_RS23025 188 YERGvEDETYACGTGVTAVAMAMAKHKNQTGHikTAIKVLGGDIKIEFDYDGkeftNVFLCGPAKLVF 255 ****************9999887775554443238999**********988877889*********** PP TIGR00652 265 egel 268 ege+ lcl|FitnessBrowser__Pedo557:CA265_RS23025 256 EGEV 259 *986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (260 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2.74 // [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