Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate GFF3002 PS417_15365 diaminopimelate epimerase
Query= curated2:Q3IZB6 (279 letters) >FitnessBrowser__WCS417:GFF3002 Length = 267 Score = 244 bits (624), Expect = 1e-69 Identities = 126/261 (48%), Positives = 165/261 (63%), Gaps = 2/261 (0%) Query: 10 LGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQEGADCALD 69 L F+KMH G+DF++ID RG +TA +AR LG+RH G+GF+QLA + D + A + Sbjct: 3 LPFVKMHAHGDDFIIIDRRGLHDP-ITAKVARQLGNRHTGIGFNQLAVLLDCDDAAARIK 61 Query: 70 FWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVAVNMGAPQL 129 FWN +G+ TCG+ATR V+D LM + G D V L T RG L R ++VNMG P L Sbjct: 62 FWNPNGTLLATCGSATRGVADRLMHEAGTDSVVLRTDRGLLTCARAAGRQISVNMGEPSL 121 Query: 130 LWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVETDPLFPER 189 WS +PLA AM+T +LP++G P+A MGNPHC +FVED AVD+A G A+E PLFP + Sbjct: 122 DWSAVPLAEAMDTLTLPIDGNPAACSMGNPHCTFFVEDLTAVDVATVGPALEIHPLFPAK 181 Query: 190 TNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRLEMDGGVLE 249 TNV F ++ +RLR+WERG G+ L GS C V RRGL V++ DGG + Sbjct: 182 TNVHFVQVLDRGHIRLRIWERGGGVPLGSGSCCCGAVVNGIRRGLLDATVQVHCDGGTVT 241 Query: 250 VDWRDEG-VWLSGPVARVFEG 269 V W EG V L+G V V +G Sbjct: 242 VHWAGEGAVVLTGSVEPVMQG 262 Lambda K H 0.321 0.138 0.423 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: 280 Number of extensions: 5 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: 279 Length of database: 267 Length adjustment: 25 Effective length of query: 254 Effective length of database: 242 Effective search space: 61468 Effective search space used: 61468 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate GFF3002 PS417_15365 (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.15859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-58 184.2 0.0 1.9e-58 184.0 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF3002 PS417_15365 diaminopimelate epim Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF3002 PS417_15365 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 184.0 0.0 1.9e-58 1.9e-58 3 268 .. 5 264 .. 3 266 .. 0.94 Alignments for each domain: == domain 1 score: 184.0 bits; conditional E-value: 1.9e-58 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemCGNgi 77 F+kmh+ g dF+++d + + + + a+++r++ +rhtg+g+ ++ ++ + ++a ++++++N G + CG + lcl|FitnessBrowser__WCS417:GFF3002 5 FVKMHAHGDDFIIIDRRGLHDPIT-AKVARQLGNRHTGIGFNQLAVLL-DCDDAAARIKFWNPNGTLLATCGSAT 77 9*****************999999.8******************9999.59999********************* PP TIGR00652 78 Rcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev..lvv 150 R +a +++++++ +++++ t++gl+++ + +++v+mgep++ +++pl ++ ++ l ++ + lcl|FitnessBrowser__WCS417:GFF3002 78 RGVADRLMHEAGT--DSVVLRTDRGLLTCARAAGR-QISVNMGEPSLDWSAVPLAEAMDTL---TLPIDGnpAAC 146 ************9..8**********998766555.*****************99866666...4444443369* PP TIGR00652 151 dvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavva 225 ++GnPH+ +fved+ +d+ ++g++le h+ fp+++Nv+fv+v+++ +i+lr++ERG g l G+ + ++v + lcl|FitnessBrowser__WCS417:GFF3002 147 SMGNPHCTFFVEDLTAVDVATVGPALEIHPLFPAKTNVHFVQVLDRGHIRLRIWERGGGVPLGSGSCCCGAVVNG 221 *************************************************************************** PP TIGR00652 226 lklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 ++ g+++ v+vh +gg +++++ +g v ltG+++ v++g + lcl|FitnessBrowser__WCS417:GFF3002 222 IRRGLLDATVQVHCDGGTVTVHWAGEGAVVLTGSVEPVMQGSA 264 ***************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (267 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: 9.62 // [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