Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate BWI76_RS01200 BWI76_RS01200 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__Koxy:BWI76_RS01200 Length = 274 Score = 535 bits (1378), Expect = e-157 Identities = 258/274 (94%), Positives = 266/274 (97%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY Sbjct: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVST+NGRMVL+VT+DDLVRVNMGE Sbjct: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTSNGRMVLSVTEDDLVRVNMGE 120 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 PNFEPS VPFRANKAEKTYIMRAAEQT+LCGVVSMGNPHCVIQVDDV+TA VETLGPV+E Sbjct: 121 PNFEPSQVPFRANKAEKTYIMRAAEQTVLCGVVSMGNPHCVIQVDDVETATVETLGPVME 180 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 +HERFPERANIGFMQV+ R HIRLRVYERGAGETQACGSGACAA AVGIQQGLL EEVRV Sbjct: 181 NHERFPERANIGFMQVISRSHIRLRVYERGAGETQACGSGACAAAAVGIQQGLLGEEVRV 240 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 ELPGGRLDIAWKGPG PLYMTGPA HVYDGFIHL Sbjct: 241 ELPGGRLDIAWKGPGQPLYMTGPAAHVYDGFIHL 274 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: 376 Number of extensions: 6 Number of successful extensions: 1 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: 274 Length adjustment: 25 Effective length of query: 249 Effective length of database: 249 Effective search space: 62001 Effective search space used: 62001 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 BWI76_RS01200 BWI76_RS01200 (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.31823.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-107 344.5 0.0 2.3e-107 344.4 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS01200 BWI76_RS01200 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS01200 BWI76_RS01200 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 344.4 0.0 2.3e-107 2.3e-107 1 269 [. 1 273 [. 1 274 [] 0.97 Alignments for each domain: == domain 1 score: 344.4 bits; conditional E-value: 2.3e-107 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSea 70 m+F+kmhGlgNdF++vd v+++++++ +el+r+++drh gvg+D++l+vep +++e d+++rifN+DGSe+ lcl|FitnessBrowser__Koxy:BWI76_RS01200 1 MQFSKMHGLGNDFMVVDAVTQNVFFS-PELIRRLADRHLGVGFDQLLVVEPpYDPELDFHYRIFNADGSEV 70 89***********************9.***********************999****************** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekee 141 ++CGNg+Rcfa+fv+ kgl++k++++v+t +g++++ v+e++ v+v+mgep+f+++++p++++k+e+++ lcl|FitnessBrowser__Koxy:BWI76_RS01200 71 AQCGNGARCFARFVRLKGLTNKRDIRVSTSNGRMVLSVTEDD-LVRVNMGEPNFEPSQVPFRANKAEKTYI 140 ******************************************.********************99999888 PP TIGR00652 142 llalev.l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGa 208 + a+e + vv++GnPH+v++v+dve++ +e+lg+++e+he+fpe+ N+ f++v ++++i+lrvyERGa lcl|FitnessBrowser__Koxy:BWI76_RS01200 141 MRAAEQtVlcgVVSMGNPHCVIQVDDVETATVETLGPVMENHERFPERANIGFMQVISRSHIRLRVYERGA 211 87777762579************************************************************ PP TIGR00652 209 geTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269 geT+aCG+Ga+A+a+v++++g++ ++v+v+l+gg+L i +k g +y+tGpa +v++g ++ lcl|FitnessBrowser__Koxy:BWI76_RS01200 212 GETQACGSGACAAAAVGIQQGLLGEEVRVELPGGRLDIAWKGPGqPLYMTGPAAHVYDGFIH 273 ********************************************99*************875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (274 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.59 // [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