Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate Ga0059261_2394 Ga0059261_2394 diaminopimelate epimerase (EC 5.1.1.7)
Query= curated2:Q97FV2 (333 letters) >FitnessBrowser__Korea:Ga0059261_2394 Length = 315 Score = 171 bits (433), Expect = 2e-47 Identities = 105/290 (36%), Positives = 158/290 (54%), Gaps = 6/290 (2%) Query: 12 VEINILKCHGTGNDFILIDEYNNNYNLDDETRRDIAIQACNRAKFIGGDGILFV-QKSDI 70 + + KCHG+GNDF+L+D + L D IA C R +G DG+L + + SD Sbjct: 4 MRLTFTKCHGSGNDFVLLDARGST--LSDSEWGRIARSLCERDGPVGADGLLLLGEGSDG 61 Query: 71 CDAKMRIFNADGSEAEMCGNGLRCVGRYVIEMLNKESVEIETLKSKYWVKLQEDIYEGVK 130 ++ NADGS E C NGLRC R E+L E+ ++ S V D+ GV Sbjct: 62 AQFAQKVVNADGSIPETCLNGLRCTARAGFELLGIEAATVQLKTSDAQVARDADLAPGVY 121 Query: 131 TVKIDIKSVSLDVKTLPLNYKKEKLIFDKIPELSDEFDFTAVSITNPHLIAIVNNIDSDK 190 TV+ + S D + +N +I +P L + +FTAV++ NPHLIA V+ +D + Sbjct: 122 TVRTTVGPASTDPQAAGVNLAAP-VIDAPVPGLPNGRNFTAVAMPNPHLIAFVDTVDVAE 180 Query: 191 LVEIGKKGNSTKSVLPQGVNVSFVKVIDSSNIYVKTYERGVGLTKSCGTAMTASSIVSCI 250 L +G + +L NVSFV + ++V+TYERGVGLT +CGTAM A++ V+ + Sbjct: 181 LTALGDWCEAGPDLLADRANVSFV-ALRPDGLFVQTYERGVGLTNACGTAMGAATHVAGL 239 Query: 251 GEKVQFDNAINVYNDGGAIKTIVHKDSNGNYSVDFIGNATFIFEGTMELD 300 ++ F I V+N GG +K + G+ +V GNATF ++G +E+D Sbjct: 240 TGRIPFGAWITVHNPGGRVKARAEGPAGGD-AVTIAGNATFEWDGEIEID 288 Lambda K H 0.317 0.136 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: 231 Number of extensions: 9 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: 333 Length of database: 315 Length adjustment: 28 Effective length of query: 305 Effective length of database: 287 Effective search space: 87535 Effective search space used: 87535 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: 48 (23.1 bits)
Align candidate Ga0059261_2394 Ga0059261_2394 (diaminopimelate epimerase (EC 5.1.1.7))
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.10947.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-48 150.1 0.0 4.8e-48 149.9 0.0 1.1 1 lcl|FitnessBrowser__Korea:Ga0059261_2394 Ga0059261_2394 diaminopimelate e Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2394 Ga0059261_2394 diaminopimelate epimerase (EC 5.1.1.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 149.9 0.0 4.8e-48 4.8e-48 2 268 .. 7 285 .. 6 287 .. 0.89 Alignments for each domain: == domain 1 score: 149.9 bits; conditional E-value: 4.8e-48 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkee.aelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSe 69 +F+k hG+gNdFvl+d + ++l +e +++r++c+r vgaDg+ll+ ++s+ a++ ++ N+DGS lcl|FitnessBrowser__Korea:Ga0059261_2394 7 TFTKCHGSGNDFVLLDARGSTLSDSEwGRIARSLCERDGPVGADGLLLLGEGSDGAQFAQKVVNADGSI 75 7******************999999999***************************************** PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeen..kkvkvdmgepkfkkeeipltveke 136 +e C Ng+Rc a+ e + e +++++t ++ + +v+ +g ++ +++ ++ + lcl|FitnessBrowser__Korea:Ga0059261_2394 76 PETCLNGLRCTARAGFELLGIEAATVQLKTSDAQVARDADLAPgvYTVRTTVGPASTDPQAAGVNLAAP 144 *************9999999988999999998888777766556899********99999888886555 PP TIGR00652 137 eekeellalev...l.vvdvGnPHlvvfvedvekldleelgklleaheef.pegvNvefvevkkedeik 200 + + l + +v + nPHl+ fv+ v+ ++l+ lg ea ++ +++ Nv fv d ++ lcl|FitnessBrowser__Korea:Ga0059261_2394 145 VIDAPVPGLPNgrnFtAVAMPNPHLIAFVDTVDVAELTALGDWCEAGPDLlADRANVSFVALRP-DGLF 212 5544443333344546*********************************99*********8776.99** PP TIGR00652 201 lrvyERGageTlaCGtGavAsavvalklgktkkk..vtvhleggeLeievkedg...kvyltGpavlvl 264 +++yERG+g T aCGt + A+ va +g+ + +tvh +gg+++ + + v + G+a++ lcl|FitnessBrowser__Korea:Ga0059261_2394 213 VQTYERGVGLTNACGTAMGAATHVAGLTGRIPFGawITVHNPGGRVKARAEGPAggdAVTIAGNATFEW 281 ******************************999888************999865566788999998888 PP TIGR00652 265 egel 268 +ge+ lcl|FitnessBrowser__Korea:Ga0059261_2394 282 DGEI 285 8876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (315 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: 11.90 // [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