Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate GFF249 HP15_248 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__Marino:GFF249 Length = 304 Score = 335 bits (858), Expect = 9e-97 Identities = 166/274 (60%), Positives = 203/274 (74%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHGLGNDFMVVDA++Q PE+IR LA+R+ G+GFDQLLVVEPP P++DF Y Sbjct: 12 LRFTKMHGLGNDFMVVDAISQPFRLRPEMIRELANRNFGIGFDQLLVVEPPGLPDVDFRY 71 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEV QCGNGARCFARFVR + LTNK+ IRV TA G + L V + +V VNMG Sbjct: 72 RIFNADGSEVEQCGNGARCFARFVRDQRLTNKKVIRVQTAKGVIELRVGREGMVMVNMGV 131 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P F P A+PF A++ + Y + QT+ +SMGNPH V+ V+DVD A VETLGP LE Sbjct: 132 PEFNPPAIPFAADRRKDVYTVDVDGQTVELSALSMGNPHGVLLVEDVDQAPVETLGPKLE 191 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H RFP RANIGF+Q++ R H+RLRV+ERG+GET ACGSGACAAV G +GLL V V Sbjct: 192 RHPRFPARANIGFLQILDRTHVRLRVFERGSGETLACGSGACAAVVAGCLRGLLDARVEV 251 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 EL GG L I W+G G P+ M GPA V++G + L Sbjct: 252 ELRGGPLVIEWQGEGTPVMMEGPATSVFEGQLRL 285 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: 300 Number of extensions: 8 Number of successful extensions: 2 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: 304 Length adjustment: 26 Effective length of query: 248 Effective length of database: 278 Effective search space: 68944 Effective search space used: 68944 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: 48 (23.1 bits)
Align candidate GFF249 HP15_248 (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.7432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-95 303.7 0.0 6.9e-95 303.5 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF249 HP15_248 diaminopimelate epimera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF249 HP15_248 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.5 0.0 6.9e-95 6.9e-95 2 269 .. 13 284 .. 12 285 .. 0.93 Alignments for each domain: == domain 1 score: 303.5 bits; conditional E-value: 6.9e-95 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGNg 76 +F+kmhGlgNdF++vd + + + ++e++r++++r++g+g+D++l+vep + ++ d+++rifN+DGSe+e+CGNg lcl|FitnessBrowser__Marino:GFF249 13 RFTKMHGLGNDFMVVDAISQPFRL-RPEMIRELANRNFGIGFDQLLVVEPpGLPDVDFRYRIFNADGSEVEQCGNG 87 8*****************965555.5***********************9899*********************** PP TIGR00652 77 iRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeell.alevl... 148 +Rcfa+fv+++ l++kk ++v+t +g+i++ v +e+ v v+mg p+f++ +ip+ ++ + +++ +++ lcl|FitnessBrowser__Marino:GFF249 88 ARCFARFVRDQRLTNKKVIRVQTAKGVIELRVGREG-MVMVNMGVPEFNPPAIPFAADRRKDVYTVDvDGQTVels 162 ************************************.******************965544433332022222345 PP TIGR00652 149 vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavv 224 ++++GnPH v+ vedv+++++e+lg++le h++fp++ N+ f++++++ +++lrv+ERG+geTlaCG+Ga+A++v+ lcl|FitnessBrowser__Marino:GFF249 163 ALSMGNPHGVLLVEDVDQAPVETLGPKLERHPRFPARANIGFLQILDRTHVRLRVFERGSGETLACGSGACAAVVA 238 **************************************************************************** PP TIGR00652 225 alklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269 + g+++ +v+v+l+gg L+ie++ +g v+++Gpa+ v+eg+l lcl|FitnessBrowser__Marino:GFF249 239 GCLRGLLDARVEVELRGGPLVIEWQGEGtPVMMEGPATSVFEGQLR 284 ****************************9**************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (304 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: 6.55 // [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