Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_018233195.1 THITHI_RS0111255 diaminopimelate epimerase
Query= SwissProt::P44859 (274 letters) >NCBI__GCF_000378965.1:WP_018233195.1 Length = 278 Score = 312 bits (800), Expect = 4e-90 Identities = 157/276 (56%), Positives = 198/276 (71%), Gaps = 2/276 (0%) Query: 1 MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPEL-DFH 59 +QFSKMHGLGNDFVV+D ++Q V TP+ +R LA+R G+G DQ+L+VE P DP L DF Sbjct: 3 LQFSKMHGLGNDFVVIDAISQPVELTPDQVRLLAHRRFGVGCDQVLLVEKPTDPALADFR 62 Query: 60 YRIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMG 119 YR+FNADG+EV QCGNGARCFA FV +GLT+K I V T G + L ++ D Q+ V+MG Sbjct: 63 YRVFNADGNEVEQCGNGARCFAVFVRERGLTHKDRIPVETAAGLIQLEIQQDGQVTVDMG 122 Query: 120 EPIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLL 179 P P +IPF A Y L D +T GAVSMGNPH V++VD++QTA V +LGP + Sbjct: 123 PPKLAPWQIPFEAEAAMPAYPLEVDGETWEIGAVSMGNPHAVLRVDNVQTAPVARLGPAI 182 Query: 180 ESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQ 239 ESHERFP VN GFM++++ I+LRVYERG GET ACG+GACAAV VG +QGLL++ V Sbjct: 183 ESHERFPRHVNVGFMEVVSSGEIRLRVYERGVGETLACGTGACAAVVVGRIQGLLDDTVA 242 Query: 240 VDLPGGSLMIEWNGVGH-PLYMTGEATHIYDGFITL 274 VDLPGG L+I W G P+ MTG AT ++ G + L Sbjct: 243 VDLPGGRLVINWPGTDQVPVMMTGPATQVFTGSMDL 278 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: 257 Number of extensions: 10 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: 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_018233195.1 THITHI_RS0111255 (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.12897.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-95 305.5 0.0 1.9e-95 305.3 0.0 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018233195.1 THITHI_RS0111255 diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018233195.1 THITHI_RS0111255 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.3 0.0 1.9e-95 1.9e-95 2 268 .. 4 276 .. 3 278 .] 0.92 Alignments for each domain: == domain 1 score: 305.3 bits; conditional E-value: 1.9e-95 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep..sseeadvklrifNsDGS 68 +F+kmhGlgNdFv++d + + + + +++vr +++r++gvg+D+vllve+ + ad+++r+fN+DG lcl|NCBI__GCF_000378965.1:WP_018233195.1 4 QFSKMHGLGNDFVVIDAISQPVELT-PDQVRLLAHRRFGVGCDQVLLVEKptDPALADFRYRVFNADGN 71 8******************665555.***********************97666789************ PP TIGR00652 69 eaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekee 137 e+e+CGNg+Rcfa fv+e+gl++k+++ vet agli++e+++++ +v+vdmg pk+ + +ip+++e + lcl|NCBI__GCF_000378965.1:WP_018233195.1 72 EVEQCGNGARCFAVFVRERGLTHKDRIPVETAAGLIQLEIQQDG-QVTVDMGPPKLAPWQIPFEAEAAM 139 ********************************************.*******************75443 PP TIGR00652 138 ekeellalev..l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeikl 201 + l+++ + +v++GnPH+v+ v++v+++++ +lg+++e+he+fp vNv f+ev+++ ei+l lcl|NCBI__GCF_000378965.1:WP_018233195.1 140 P-AYPLEVDGetWeigAVSMGNPHAVLRVDNVQTAPVARLGPAIESHERFPRHVNVGFMEVVSSGEIRL 207 3.33333333333457***************************************************** PP TIGR00652 202 rvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg..kvyltGpavlvlegel 268 rvyERG+geTlaCGtGa+A++vv++ +g++++ v+v l+gg+L+i++ + v++tGpa++v+ g + lcl|NCBI__GCF_000378965.1:WP_018233195.1 208 RVYERGVGETLACGTGACAAVVVGRIQGLLDDTVAVDLPGGRLVINWPGTDqvPVMMTGPATQVFTGSM 276 ***********************************************7766569***********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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.03 // [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