Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate GFF3696 Psest_3765 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__psRCH2:GFF3696 Length = 276 Score = 324 bits (831), Expect = 1e-93 Identities = 152/274 (55%), Positives = 196/274 (71%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHGLGNDFMV+D V+Q+ P+ ++ DRH GVGFDQLL+VEPP +P++DF Y Sbjct: 3 LRFTKMHGLGNDFMVIDLVSQHAHIQPKHAKQWGDRHTGVGFDQLLIVEPPQNPDVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFN+DGSEV QCGNGARCFARFV K LT KR I+V T G + L + D +RV+MG Sbjct: 63 RIFNSDGSEVEQCGNGARCFARFVVDKRLTVKRKIKVETKGGIIELDIRPDGQIRVDMGP 122 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P P+ +PF+A + Y + Q + VSMGNPH V++VD V+ A V LGP +E Sbjct: 123 PRLVPAEIPFQAEQEALCYPLEVDGQRVELAAVSMGNPHAVLRVDSVEQAPVHELGPKIE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H RFP+R N+GF+Q+V R RLRV+ERGAGETQACG+GACAA I+QG + V++ Sbjct: 183 HHPRFPQRVNVGFLQIVDRRQARLRVWERGAGETQACGTGACAAAVAAIRQGWMDSPVQI 242 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 +LPGGRL I W GPG P+ MTGPAV V++G + L Sbjct: 243 DLPGGRLSIEWAGPGQPVMMTGPAVRVFEGQVRL 276 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: 284 Number of extensions: 9 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: 276 Length adjustment: 25 Effective length of query: 249 Effective length of database: 251 Effective search space: 62499 Effective search space used: 62499 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 GFF3696 Psest_3765 (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.18872.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-99 316.3 0.0 9.6e-99 316.1 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3696 Psest_3765 diaminopimelate epime Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3696 Psest_3765 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.1 0.0 9.6e-99 9.6e-99 2 268 .. 4 274 .. 3 276 .] 0.94 Alignments for each domain: == domain 1 score: 316.1 bits; conditional E-value: 9.6e-99 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGN 75 +F+kmhGlgNdF+++d v ++ + ++ +++ drhtgvg+D++l+vep ++++ d+++rifNsDGSe+e+CGN lcl|FitnessBrowser__psRCH2:GFF3696 4 RFTKMHGLGNDFMVIDLVSQHAHIQ-PKHAKQWGDRHTGVGFDQLLIVEPpQNPDVDFRYRIFNSDGSEVEQCGN 77 8******************888888.9**********************98999********************* PP TIGR00652 76 giRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee....keellale 146 g+Rcfa+fv++k l++k++++vet+ g+i++ + ++ +++vdmg p++ ++eip+++e+e+ + + +++e lcl|FitnessBrowser__psRCH2:GFF3696 78 GARCFARFVVDKRLTVKRKIKVETKGGIIELDIRPDG-QIRVDMGPPRLVPAEIPFQAEQEALcyplEVDGQRVE 151 *************************************.*******************877665111134444445 PP TIGR00652 147 vlvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAs 221 + +v++GnPH+v+ v++ve+++++elg+++e+h++fp++vNv f++++++ + +lrv+ERGageT+aCGtGa+A+ lcl|FitnessBrowser__psRCH2:GFF3696 152 LAAVSMGNPHAVLRVDSVEQAPVHELGPKIEHHPRFPQRVNVGFLQIVDRRQARLRVWERGAGETQACGTGACAA 226 56************************************************************************* PP TIGR00652 222 avvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 av+a+++g +++ v++ l+gg+L ie+ g v++tGpav+v+eg++ lcl|FitnessBrowser__psRCH2:GFF3696 227 AVAAIRQGWMDSPVQIDLPGGRLSIEWAGPGqPVMMTGPAVRVFEGQV 274 *******************************99*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (276 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: 00:00:00.01 # Mc/sec: 7.04 // [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