Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_041550214.1 SARO_RS07030 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >NCBI__GCF_000013325.1:WP_041550214.1 Length = 269 Score = 195 bits (495), Expect = 1e-54 Identities = 115/281 (40%), Positives = 163/281 (58%), Gaps = 25/281 (8%) Query: 6 FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRM 65 F KMHGLGN ++ ++ E + A A +++ TGIG D +I++ PSDVA V+MR+ Sbjct: 5 FRKMHGLGNDFVVIDAREAAVSMT--AARAAALADRRTGIGCDQLIVLEPSDVADVRMRI 62 Query: 66 FNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDM 125 FNNDGSE ++CGN R V L+ T F IETL G++ +E + +DM Sbjct: 63 FNNDGSEVEACGNASRAVGL------LLGGTQF-IETLGGLIRSEARPDG-----VSVDM 110 Query: 126 GAPRLTRAEIPM---LGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLT 182 GAPRL EIP+ + E P E+ L N V++GNPH + FVDD + L Sbjct: 111 GAPRLRWDEIPVSYAMDTLEMPVGWED-LENP-----VGVNVGNPHVIFFVDDADAVDLA 164 Query: 183 TLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGK 242 LGP++E +FPER+NV ++ + + RVWERG+G+T+ACGTGACA VA+I + Sbjct: 165 RLGPLIENDPLFPERINVNVASVVGPDHLKLRVWERGAGLTRACGTGACATAVAAI--RR 222 Query: 243 MERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYE 283 G+++ + L GG L I W E G + M GPA + G +E Sbjct: 223 KLTGRKVRIDLPGGPLTITWPEGGTIDMTGPATLSFEGAFE 263 Lambda K H 0.318 0.136 0.398 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: 220 Number of extensions: 17 Number of successful extensions: 6 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: 288 Length of database: 269 Length adjustment: 25 Effective length of query: 263 Effective length of database: 244 Effective search space: 64172 Effective search space used: 64172 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_041550214.1 SARO_RS07030 (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.5281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-82 260.7 0.0 9.3e-82 260.4 0.0 1.1 1 lcl|NCBI__GCF_000013325.1:WP_041550214.1 SARO_RS07030 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_041550214.1 SARO_RS07030 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.4 0.0 9.3e-82 9.3e-82 2 268 .. 4 262 .. 3 264 .. 0.92 Alignments for each domain: == domain 1 score: 260.4 bits; conditional E-value: 9.3e-82 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSea 70 F kmhGlgNdFv++d +++ + + a+++++++dr+tg+g+D+++++ep s+ adv++rifN+DGSe+ lcl|NCBI__GCF_000013325.1:WP_041550214.1 4 PFRKMHGLGNDFVVIDAREAAVSMT-AARAAALADRRTGIGCDQLIVLEP-SDVADVRMRIFNNDGSEV 70 599****************887777.9**********************8.****************** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt..vekee 137 e CGN++R + + ++ +etl gli +e ++ v+vdmg p+++ +eip+ +++ e lcl|NCBI__GCF_000013325.1:WP_041550214.1 71 EACGNASRAVGLLLGGTQ-------FIETLGGLIRSEARPDG--VSVDMGAPRLRWDEIPVSyaMDTLE 130 **********98875443.......579**********9999..******************4444444 PP TIGR00652 138 ekeellalev.lvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyE 205 ++ + le + v+vGnPH+++fv+d + +dl +lg+l+e+++ fpe++Nv+++ v+++d++klrv+E lcl|NCBI__GCF_000013325.1:WP_041550214.1 131 MPVGWEDLENpVGVNVGNPHVIFFVDDADAVDLARLGPLIENDPLFPERINVNVASVVGPDHLKLRVWE 199 4444444444679******************************************************** PP TIGR00652 206 RGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 RGag T+aCGtGa+A+av+a++ ++t +kv++ l+gg L+i++ e g++ +tGpa+l +eg lcl|NCBI__GCF_000013325.1:WP_041550214.1 200 RGAGLTRACGTGACATAVAAIRRKLTGRKVRIDLPGGPLTITWPEGGTIDMTGPATLSFEGAF 262 *********************************************************999975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (269 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.76 // [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