Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate 207333 DVU1867 diaminopimelate epimerase
Query= curated2:O67693 (279 letters) >MicrobesOnline__882:207333 Length = 282 Score = 206 bits (523), Expect = 6e-58 Identities = 120/277 (43%), Positives = 155/277 (55%), Gaps = 11/277 (3%) Query: 3 FWKLQGSGNDFVVIDDRDEKLESFLKERGVSKEDFVRKVCAFHTGVGADGLILIKN-PDN 61 F KL G GNDFV ID+R KL + D+ R +C GVGADGL+ + P Sbjct: 10 FHKLHGCGNDFVFIDNRHLKLSV------EAMPDWARSICRRAFGVGADGLVFLDTAPQG 63 Query: 62 PENDFKWEFFNSDGSVAEMCGNGSRCAVRFAYERGIVGNKVRFETLAGVIKAEVYENGRK 121 E D+ W F+N+DGS AEMCGN SRCA A + G G + F T AG++ A Sbjct: 64 HEADYIWHFYNADGSRAEMCGNASRCAAVLAVDLGFAGPRHAFGTDAGIVHAVADVEAGY 123 Query: 122 VKVQLTPPSK-PEEKTLTVDGEEVIGVFINTGVPHFVVPVEDVEKVNVIKLGRAIRFHEE 180 KV+LT P TL ++G F+NTGVPH VV + V+ +++ +LG A+R+H Sbjct: 124 AKVELTRPRDLAAGTTLELEGTPFTVHFVNTGVPHAVVFSDSVDGLDLRRLGAALRYHPH 183 Query: 181 FQPKGTNVNFVQPVSEDTIKVRTYERGVESETLACGTGATACAIVSYLKGLVKKKPVNVL 240 F P GTN NF + TI +RTYERGVE ET ACGTGA A A +++ GL V V Sbjct: 184 FSPAGTNANFASIIDRRTIHLRTYERGVEDETYACGTGAAATAFIAHTLGLTDAS-VGVR 242 Query: 241 TRSGEVLTIDFSEDLKEVFLTGSVYKVFEGRLSEEVL 277 T GEVL ID + +FL+G +VF G + E L Sbjct: 243 TSGGEVLGIDIEDG--SIFLSGKAVRVFSGEMHPEGL 277 Lambda K H 0.317 0.138 0.399 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: 207 Number of extensions: 8 Number of successful extensions: 5 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: 279 Length of database: 282 Length adjustment: 26 Effective length of query: 253 Effective length of database: 256 Effective search space: 64768 Effective search space used: 64768 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate 207333 DVU1867 (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.3384.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-76 241.3 0.0 7.3e-76 241.1 0.0 1.0 1 lcl|MicrobesOnline__882:207333 DVU1867 diaminopimelate epimeras Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207333 DVU1867 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 241.1 0.0 7.3e-76 7.3e-76 3 268 .. 10 272 .. 8 274 .. 0.93 Alignments for each domain: == domain 1 score: 241.1 bits; conditional E-value: 7.3e-76 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkee.aelvrkvcdrhtgvgaDgvllvep..sseeadvklrifNsDGSeaemCGNgiR 78 F k+hG gNdFv +d+++ +l e ++ +r++c+r +gvgaDg++++ + + +ead+ ++++N+DGS+aemCGN++R lcl|MicrobesOnline__882:207333 10 FHKLHGCGNDFVFIDNRHLKLSVEAmPDWARSICRRAFGVGADGLVFLDTapQGHEADYIWHFYNADGSRAEMCGNASR 88 99****************77666666**********************9988899************************ PP TIGR00652 79 cfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalevlvvdvGnPHl 157 c+a +++ g + ++ + t+ag++++ e kv++++p+ ++ ++l+ e++ ++ + v++G+PH+ lcl|MicrobesOnline__882:207333 89 CAAVLAVDLGFAG-PRHAFGTDAGIVHAVADVEAGYAKVELTRPRDLAAGTTLELEGTPF--TVHF-----VNTGVPHA 159 ************7.9***********9999888889********9999999999866666..4444.....99****** PP TIGR00652 158 vvfvedvekldleelgklleaheef.pegvNvefvevkkedeiklrvyERG.ageTlaCGtGavAsavvalklgktkkk 234 vvf ++v++ldl +lg++l++h++f p+g+N +f+ + ++ +i+lr+yERG ++eT aCGtGa+A+a +a++lg+t+ + lcl|MicrobesOnline__882:207333 160 VVFSDSVDGLDLRRLGAALRYHPHFsPAGTNANFASIIDRRTIHLRTYERGvEDETYACGTGAAATAFIAHTLGLTDAS 238 ******************************************************************************* PP TIGR00652 235 vtvhlegge.LeievkedgkvyltGpavlvlegel 268 v v ++gge L i+++ dg+++l G+av+v++ge+ lcl|MicrobesOnline__882:207333 239 VGVRTSGGEvLGIDIE-DGSIFLSGKAVRVFSGEM 272 ********62567765.557*************97 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: 00:00:00.00 # Mc/sec: 10.47 // [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