Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate 5207806 Shew_0323 diaminopimelate epimerase (RefSeq)
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__PV4:5207806 Length = 279 Score = 394 bits (1012), Expect = e-114 Identities = 192/276 (69%), Positives = 221/276 (80%), Gaps = 4/276 (1%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 + F+KMHGLGNDFMVVD VTQNV+FSPE I+RLADR+ G+GFDQLL+VEPPYDP+LDFHY Sbjct: 2 IHFTKMHGLGNDFMVVDGVTQNVYFSPEQIKRLADRNFGIGFDQLLLVEPPYDPDLDFHY 61 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEV QCGNGARCFARFV+ KGL NK+ I+VST++G+M L + D V VNMG Sbjct: 62 RIFNADGSEVEQCGNGARCFARFVKSKGLINKQKIKVSTSSGKMTLRLERDGSVTVNMGI 121 Query: 121 PNFEPSAVPFRANKAEKTYIMRA----AEQTILCGVVSMGNPHCVIQVDDVDTAAVETLG 176 P EPS +PF A KAEKTY+++A QT LCG VSMGNPHCV++VDDV A VE +G Sbjct: 122 PVLEPSRIPFNAKKAEKTYLLQADMPEGMQTFLCGAVSMGNPHCVLEVDDVANADVERIG 181 Query: 177 PVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAE 236 +L HERFP+ N+GFMQVV HI+LRVYERGA ET ACGSGACAAVAVG QG LA Sbjct: 182 SLLTKHERFPKGVNVGFMQVVDANHIKLRVYERGAAETLACGSGACAAVAVGQLQGKLAR 241 Query: 237 EVRVELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFI 272 VRV+LPGG L I W+G G PL+MTGPA HVYDG I Sbjct: 242 RVRVDLPGGSLTINWEGEGKPLWMTGPAEHVYDGQI 277 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: 279 Number of extensions: 7 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: 274 Length of database: 279 Length adjustment: 25 Effective length of query: 249 Effective length of database: 254 Effective search space: 63246 Effective search space used: 63246 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 5207806 Shew_0323 (diaminopimelate epimerase (RefSeq))
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.5011.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-101 325.4 0.0 1.7e-101 325.2 0.0 1.0 1 lcl|FitnessBrowser__PV4:5207806 Shew_0323 diaminopimelate epimer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207806 Shew_0323 diaminopimelate epimerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 325.2 0.0 1.7e-101 1.7e-101 1 269 [. 2 278 .. 2 279 .] 0.97 Alignments for each domain: == domain 1 score: 325.2 bits; conditional E-value: 1.7e-101 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGNgi 77 ++F+kmhGlgNdF++vd v+++++++ +e++++++dr++g+g+D++llvep ++++ d+++rifN+DGSe+e+CGNg+ lcl|FitnessBrowser__PV4:5207806 2 IHFTKMHGLGNDFMVVDGVTQNVYFS-PEQIKRLADRNFGIGFDQLLLVEPpYDPDLDFHYRIFNADGSEVEQCGNGA 78 58***********************9.9**********************999************************* PP TIGR00652 78 Rcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev......l. 148 Rcfa+fv++kgl +k++++v+t +g++++ +e+++ +v+v+mg p ++++ ip++++k+e+ ++ll++++ + lcl|FitnessBrowser__PV4:5207806 79 RCFARFVKSKGLINKQKIKVSTSSGKMTLRLERDG-SVTVNMGIPVLEPSRIPFNAKKAEK-TYLLQADMpegmqtFl 154 ***********************************.********************88888.7788888888877625 PP TIGR00652 149 ..vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavv 224 +v++GnPH+v+ v+dv ++d+e++g+ll +he+fp+gvNv f++v++ ++iklrvyERGa eTlaCG+Ga+A+++v lcl|FitnessBrowser__PV4:5207806 155 cgAVSMGNPHCVLEVDDVANADVERIGSLLTKHERFPKGVNVGFMQVVDANHIKLRVYERGAAETLACGSGACAAVAV 232 79**************************************************************************** PP TIGR00652 225 alklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269 + +gk+ ++v+v l+gg+L+i+++ +g +++tGpa++v++g+++ lcl|FitnessBrowser__PV4:5207806 233 GQLQGKLARRVRVDLPGGSLTINWEGEGkPLWMTGPAEHVYDGQIQ 278 ****************************99*************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5.77 // [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