Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_026329672.1 F612_RS0106660 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_000381085.1:WP_026329672.1 Length = 277 Score = 325 bits (832), Expect = 9e-94 Identities = 160/275 (58%), Positives = 201/275 (73%), Gaps = 1/275 (0%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 + F+KMHGLGNDFMV+DA+ Q + FS + IR+ +DRH G+GFDQLLVVE +DF Y Sbjct: 3 LNFTKMHGLGNDFMVIDAIGQKIEFSADKIRQWSDRHFGIGFDQLLVVEQAMQMGVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEV QCGNGARCFARFV KGLT+K +I+V TA+G +VL + DD LVRVNMG Sbjct: 63 RIFNADGSEVQQCGNGARCFARFVHDKGLTDKTEIQVETASGVIVLYIEDDGLVRVNMGA 122 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 PNF P+++PF + + Y + Q I G VSMGNPH ++ V+D+ +A VE LG LE Sbjct: 123 PNFNPASLPFSQTEQQDHYSVDVGGQKISLGAVSMGNPHALVLVNDIQSAPVEALGEALE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 SH FPER N+GF Q++ HI+LRVYERGA ET ACG+GACAAVAV + GLLA++V V Sbjct: 183 SHALFPERVNVGFAQIIDPTHIKLRVYERGAAETLACGTGACAAVAVLKKWGLLADQVNV 242 Query: 241 ELPGGRLDIAWKGP-GHPLYMTGPAVHVYDGFIHL 274 LPGG L I W G PL+M+GP V V++G + + Sbjct: 243 SLPGGDLVIRWSGDMDSPLWMSGPTVTVFEGSLEV 277 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: 249 Number of extensions: 6 Number of successful extensions: 3 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: 277 Length adjustment: 25 Effective length of query: 249 Effective length of database: 252 Effective search space: 62748 Effective search space used: 62748 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_026329672.1 F612_RS0106660 (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.20921.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-95 303.0 0.0 1.1e-94 302.8 0.0 1.0 1 lcl|NCBI__GCF_000381085.1:WP_026329672.1 F612_RS0106660 diaminopimelate e Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_026329672.1 F612_RS0106660 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.8 0.0 1.1e-94 1.1e-94 2 268 .. 4 275 .. 3 277 .] 0.94 Alignments for each domain: == domain 1 score: 302.8 bits; conditional E-value: 1.1e-94 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSe 69 +F+kmhGlgNdF+++d + +++ ++ a+ +r+ +drh+g+g+D++l+ve+ + d+++rifN+DGSe lcl|NCBI__GCF_000381085.1:WP_026329672.1 4 NFTKMHGLGNDFMVIDAIGQKIEFS-ADKIRQWSDRHFGIGFDQLLVVEQaMQMGVDFRYRIFNADGSE 71 8******************887777.9**********************9778899************* PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee 138 +++CGNg+Rcfa+fv +kgl++k+e++vet +g+i++++e+++ v+v+mg p+f+++ p+ +++++ lcl|NCBI__GCF_000381085.1:WP_026329672.1 72 VQQCGNGARCFARFVHDKGLTDKTEIQVETASGVIVLYIEDDG-LVRVNMGAPNFNPASLPFSQTEQQD 139 *******************************************.*******************776666 PP TIGR00652 139 keellalev.l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrv 203 ++ + + +v++GnPH++v v+d++++++e lg++le+h fpe+vNv f+++ ++ +iklrv lcl|NCBI__GCF_000381085.1:WP_026329672.1 140 HYSVDVGGQkIslgAVSMGNPHALVLVNDIQSAPVEALGEALESHALFPERVNVGFAQIIDPTHIKLRV 208 55555543343458******************************************************* PP TIGR00652 204 yERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg..kvyltGpavlvlegel 268 yERGa eTlaCGtGa+A+++v k g++ ++v+v l+gg+L+i+++ d +++ Gp v+v+eg l lcl|NCBI__GCF_000381085.1:WP_026329672.1 209 YERGAAETLACGTGACAAVAVLKKWGLLADQVNVSLPGGDLVIRWSGDMdsPLWMSGPTVTVFEGSL 275 **********************************************998889*************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (277 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: 00:00:00.01 # Mc/sec: 7.26 // [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