Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_041575065.1 XAUT_RS02085 diaminopimelate epimerase
Query= curated2:Q8YJF0 (303 letters) >NCBI__GCF_000017645.1:WP_041575065.1 Length = 285 Score = 285 bits (728), Expect = 1e-81 Identities = 148/276 (53%), Positives = 185/276 (67%), Gaps = 6/276 (2%) Query: 7 FARMNGLGNQIIVADMRGRADSITSAAAIRLASDSETAFDQIMAIHDPRTPGTDYYIAII 66 F +MNGLGN+I+V D+R + +AAA LA S FDQ M ++ PR GT ++ I+ Sbjct: 9 FVKMNGLGNEILVLDLRADPVEVPAAAARALARPSVLPFDQAMVLYPPRREGTAAFVRIL 68 Query: 67 NCDGTQAQACGNGTRCVVQALAAETGRHAFTFETRAGILTATEHDDGLISVDMGTPRFDW 126 N DG+ + ACGNGTRC+ A TG FE+ AG+L DG + VDMG PRFDW Sbjct: 69 NSDGSFSAACGNGTRCIAALEAERTGAPHALFESEAGLLDCLVRPDGQVEVDMGAPRFDW 128 Query: 127 QDIPLAQAVADTRKIELQVDPADAPVLHSPSIASMGNPHAVFWVDKDVWSYELDKFGPLL 186 +DIPLA+ VA+T ++ + A P S+ SMGNPHAVF+V D + +++K G L Sbjct: 129 RDIPLARDVAETAQVIVPGFEALGPT----SLVSMGNPHAVFFV-PDANAVDVEKLGAAL 183 Query: 187 ENHPIFPERANISIAHVTSSDTIDLRTWERGAGLTRACGSAACAAAVSAARTGRTGRKVT 246 E+HP+FPERANIS A +T+ D I L WERGAG TRACG+AACA VSAARTGRTGR VT Sbjct: 184 EHHPLFPERANISFASLTAPDRILLHVWERGAGRTRACGTAACATGVSAARTGRTGRSVT 243 Query: 247 VNVPGGPLLIEWRD-DDHVMMTGPAEWEFSGTFDPA 281 V +PGG L I WR+ D HV+MTGP E EFSGT PA Sbjct: 244 VTLPGGDLEISWREADGHVLMTGPVEHEFSGTLSPA 279 Lambda K H 0.318 0.132 0.408 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: 297 Number of extensions: 12 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: 303 Length of database: 285 Length adjustment: 26 Effective length of query: 277 Effective length of database: 259 Effective search space: 71743 Effective search space used: 71743 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: 48 (23.1 bits)
Align candidate WP_041575065.1 XAUT_RS02085 (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.15205.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-68 216.9 0.0 2e-68 216.7 0.0 1.0 1 lcl|NCBI__GCF_000017645.1:WP_041575065.1 XAUT_RS02085 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_041575065.1 XAUT_RS02085 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.7 0.0 2e-68 2e-68 3 268 .. 9 276 .. 7 278 .. 0.92 Alignments for each domain: == domain 1 score: 216.7 bits; conditional E-value: 2e-68 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSea 70 F+km+GlgN+ +++d + + v+ ++ +++ +r + +D+ +++ p e + + +ri NsDGS lcl|NCBI__GCF_000017645.1:WP_041575065.1 9 FVKMNGLGNEILVLDLRA-DPVEV-PAAAARALARPSVLPFDQAMVLYPpRREGTAAFVRILNSDGSFS 75 9*********99999887.44444.7788888889999*****9999984566677778********** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeek 139 + CGNg Rc+a+ +e++++ + +e++agl+ + v ++ +v+vdmg p+f +ipl + +e+ lcl|NCBI__GCF_000017645.1:WP_041575065.1 76 AACGNGTRCIAALEAERTGA--PHALFESEAGLLDCLVRPDG-QVEVDMGAPRFDWRDIPLARDVAETA 141 ********************..7999****************.*******************9999998 PP TIGR00652 140 eellalev.l....vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrv 203 ++++ l +v++GnPH+v+fv d + +d+e+lg++le+h+ fpe+ N+ f+ + +d+i l+v lcl|NCBI__GCF_000017645.1:WP_041575065.1 142 QVIVPGFEaLgptsLVSMGNPHAVFFVPDANAVDVEKLGAALEHHPLFPERANISFASLTAPDRILLHV 210 88887544435567******************************************************* PP TIGR00652 204 yERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 +ERGag T+aCGt a+A+ v a+++g+t ++vtv+l+gg+Lei+++e++ +v++tGp+++ ++g+l lcl|NCBI__GCF_000017645.1:WP_041575065.1 211 WERGAGRTRACGTAACATGVSAARTGRTGRSVTVTLPGGDLEISWREADgHVLMTGPVEHEFSGTL 276 *********************************************99888**********999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (285 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.08 // [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