Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_011610919.1 TERY_RS05480 diaminopimelate epimerase
Query= SwissProt::P44859 (274 letters) >NCBI__GCF_000014265.1:WP_011610919.1 Length = 278 Score = 212 bits (539), Expect = 8e-60 Identities = 112/274 (40%), Positives = 166/274 (60%), Gaps = 5/274 (1%) Query: 3 FSKMHGLGNDFVVVDGVTQ-NVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHYR 61 F+K HGLGNDF+++D Q TPE L +R+ GIG D ++ P + D+ R Sbjct: 5 FTKYHGLGNDFILIDNRHQLQPILTPEQAIELCDRNFGIGADGVIFA-LPGVKQTDYTMR 63 Query: 62 IFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGEP 121 IFN+DGSE CGNG RC A+F+ NK ++ T G +V ++ D Q+ V+MG+P Sbjct: 64 IFNSDGSEPEMCGNGIRCLAKFIAELENNNKTKYNIHTGAGIIVPELQGDGQVTVDMGQP 123 Query: 122 IWEPAKIPFT-ANKFEK--NYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPL 178 ++IP T AN +K + +L ++ VSMGNPHC+ V+D+ ++ ++GP Sbjct: 124 RLLASEIPTTLANADDKVVDQLLEVGGKSWFVTCVSMGNPHCITFVEDVTAIDLAKIGPK 183 Query: 179 LESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNV 238 E + FPER N F+Q+I+ +++K+RV+ERGAG T ACG+GACA+V G++ V Sbjct: 184 FEHNPVFPERTNTEFIQVISPKYVKMRVWERGAGATLACGTGACASVVAGVLTQNNERLV 243 Query: 239 QVDLPGGSLMIEWNGVGHPLYMTGEATHIYDGFI 272 V+LPGG L IEW+ + +YMTG A ++ G I Sbjct: 244 TVELPGGCLEIEWSTIDQKIYMTGPAEKVFTGII 277 Lambda K H 0.321 0.139 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: 235 Number of extensions: 8 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: 278 Length adjustment: 25 Effective length of query: 249 Effective length of database: 253 Effective search space: 62997 Effective search space used: 62997 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_011610919.1 TERY_RS05480 (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.28168.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-101 324.8 0.0 2.4e-101 324.7 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011610919.1 TERY_RS05480 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011610919.1 TERY_RS05480 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 324.7 0.0 2.4e-101 2.4e-101 2 268 .. 4 277 .. 3 278 .] 0.95 Alignments for each domain: == domain 1 score: 324.7 bits; conditional E-value: 2.4e-101 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSea 70 +F+k+hGlgNdF+l+d++++ ++ ++e++ ++cdr++g+gaDgv++ p+ +++d+++rifNsDGSe+ lcl|NCBI__GCF_000014265.1:WP_011610919.1 4 SFTKYHGLGNDFILIDNRHQLQPILTPEQAIELCDRNFGIGADGVIFALPGVKQTDYTMRIFNSDGSEP 72 6******************9999999******************************************* PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeek 139 emCGNgiRc+akf++e + ++k++++++t ag+i+ e++ ++ +v+vdmg+p++ ++eip+t +++ k lcl|NCBI__GCF_000014265.1:WP_011610919.1 73 EMCGNGIRCLAKFIAELENNNKTKYNIHTGAGIIVPELQGDG-QVTVDMGQPRLLASEIPTTLANADDK 140 ******************************************.*******************7777776 PP TIGR00652 140 eellalev.....l..vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeikl 201 + + lev + +v++GnPH+++fvedv +dl ++g+++e+++ fpe++N+ef++v +++ +k+ lcl|NCBI__GCF_000014265.1:WP_011610919.1 141 VVDQLLEVggkswFvtCVSMGNPHCITFVEDVTAIDLAKIGPKFEHNPVFPERTNTEFIQVISPKYVKM 209 6666666777886257***************************************************** PP TIGR00652 202 rvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 rv+ERGag TlaCGtGa+As+v+++ +++ ++ vtv+l+gg Leie++ + k+y+tGpa++v+ g + lcl|NCBI__GCF_000014265.1:WP_011610919.1 210 RVWERGAGATLACGTGACASVVAGVLTQNNERLVTVELPGGCLEIEWSTIDqKIYMTGPAEKVFTGII 277 *****************************9999**************997779***********9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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: 7.28 // [ok]
This GapMind analysis is from Apr 10 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