Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_038211696.1 Q392_RS20540 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_000745855.1:WP_038211696.1 Length = 292 Score = 263 bits (673), Expect = 2e-75 Identities = 144/284 (50%), Positives = 178/284 (62%), Gaps = 12/284 (4%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KM G GNDF+V+D + SP R LADRH GVG DQ+L V P +DF Y Sbjct: 3 IRFTKMQGAGNDFVVLDETKGPLGLSPGQYRFLADRHFGVGADQILSVRPATAEGIDFQY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 I NADG EV QCGNGARCF RFVR +GLT+K +RV T +G + + D V V+MG Sbjct: 63 VIHNADGGEVEQCGNGARCFLRFVREQGLTDKDVVRVQTLSGVIAPRMNADGRVTVDMGA 122 Query: 121 PNFEPSAVPF-------RANKAEKTYIMRAAEQT----ILCGVVSMGNPHCVIQVDDVDT 169 P FEP+ VPF R +T+ + + + + V+SMGNPH V VDD++T Sbjct: 123 PVFEPARVPFDTAGLDPRPEGGWQTWHLALSTEAEGAIVAVAVLSMGNPHAVQVVDDIET 182 Query: 170 AAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGI 229 A V GP++E H RFP+R N GF+QVV R H RLRVYERGAGET ACG+GACAAV GI Sbjct: 183 APVAEQGPLIEHHPRFPQRVNAGFLQVVDRSHARLRVYERGAGETLACGTGACAAVVAGI 242 Query: 230 QQGLLAEEVRVELPGGRLDIAWK-GPGHPLYMTGPAVHVYDGFI 272 + G V VE GG L I W G P++MTGPAV V+ G I Sbjct: 243 RLGRFDRRVDVETRGGILTIEWAGGASDPVFMTGPAVTVFSGEI 286 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: 282 Number of extensions: 9 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: 292 Length adjustment: 26 Effective length of query: 248 Effective length of database: 266 Effective search space: 65968 Effective search space used: 65968 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 WP_038211696.1 Q392_RS20540 (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.1778.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-87 279.3 0.0 2.2e-87 278.9 0.0 1.1 1 lcl|NCBI__GCF_000745855.1:WP_038211696.1 Q392_RS20540 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038211696.1 Q392_RS20540 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.9 0.0 2.2e-87 2.2e-87 1 268 [. 3 286 .. 3 288 .. 0.91 Alignments for each domain: == domain 1 score: 278.9 bits; conditional E-value: 2.2e-87 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGS 68 ++F+km+G+gNdFv++de + l + + + r ++drh+gvgaD++l v+p + e d+++ i N+DG lcl|NCBI__GCF_000745855.1:WP_038211696.1 3 IRFTKMQGAGNDFVVLDETKGPLGLS-PGQYRFLADRHFGVGADQILSVRPaTAEGIDFQYVIHNADGG 70 68******************888777.9***********************788899************ PP TIGR00652 69 eaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekee 137 e+e+CGNg+Rcf +fv+e+gl++k+ ++v+tl+g+i +++++ +v+vdmg p f+++ +p+++++ lcl|NCBI__GCF_000745855.1:WP_038211696.1 71 EVEQCGNGARCFLRFVREQGLTDKDVVRVQTLSGVIAPRMNADG-RVTVDMGAPVFEPARVPFDTAGLD 138 ********************************************.******************944333 PP TIGR00652 138 ekeellalev............l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefv 191 + e + + v+++GnPH+v +v+d+e++++ e g+l+e+h++fp++vN f+ lcl|NCBI__GCF_000745855.1:WP_038211696.1 139 PRPEGGWQTWhlalsteaegaiVavaVLSMGNPHAVQVVDDIETAPVAEQGPLIEHHPRFPQRVNAGFL 207 2222221111234455677776255799***************************************** PP TIGR00652 192 evkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg..kvyltG 258 +v+++++ +lrvyERGageTlaCGtGa+A++v++++lg+ +++v+v+++gg L+ie+ v++tG lcl|NCBI__GCF_000745855.1:WP_038211696.1 208 QVVDRSHARLRVYERGAGETLACGTGACAAVVAGIRLGRFDRRVDVETRGGILTIEWAGGAsdPVFMTG 276 *********************************************************9876679***** PP TIGR00652 259 pavlvlegel 268 pav+v++ge+ lcl|NCBI__GCF_000745855.1:WP_038211696.1 277 PAVTVFSGEI 286 *******986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (292 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: 8.56 // [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