Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_086511730.1 BZY95_RS20450 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_002151265.1:WP_086511730.1 Length = 277 Score = 337 bits (865), Expect = 1e-97 Identities = 168/274 (61%), Positives = 196/274 (71%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 + F+KMHGLGNDFMV+D +TQ E IR+LADR G+GFDQLLVVEPP P++DF Y Sbjct: 3 LHFTKMHGLGNDFMVIDLITQRARLRDEQIRKLADRRFGIGFDQLLVVEPPRSPDMDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEV CGNGARCFARFVR + LT+KR+I V TA G + L V DDD V V+MG Sbjct: 63 RIFNADGSEVENCGNGARCFARFVRDQRLTHKREIHVETAGGPLTLVVNDDDQVTVDMGT 122 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P FEP+A+PF A + + + + G VSMGNPH V++VDDVDTA VE LGP++E Sbjct: 123 PRFEPAALPFDATEDRPLHALEVDGERYEIGAVSMGNPHAVLRVDDVDTAPVERLGPLIE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H RFP R N GFMQVV IRLRV+ERG GET ACG+GACAAVA GI+QGLL V V Sbjct: 183 RHPRFPRRVNAGFMQVVSPHEIRLRVFERGTGETLACGTGACAAVASGIRQGLLESPVTV 242 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 L GG L I W G PL MTGPA V++G I L Sbjct: 243 HLRGGDLRIEWSGDEAPLLMTGPAERVFEGRIAL 276 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: 292 Number of extensions: 9 Number of successful extensions: 1 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_086511730.1 BZY95_RS20450 (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.21460.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-98 314.2 0.0 4.2e-98 314.0 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511730.1 BZY95_RS20450 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511730.1 BZY95_RS20450 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.0 0.0 4.2e-98 4.2e-98 2 269 .. 4 275 .. 3 276 .. 0.94 Alignments for each domain: == domain 1 score: 314.0 bits; conditional E-value: 4.2e-98 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSe 69 +F+kmhGlgNdF+++d ++++ e++rk++dr++g+g+D++l+vep s++ d+++rifN+DGSe lcl|NCBI__GCF_002151265.1:WP_086511730.1 4 HFTKMHGLGNDFMVIDLITQRARLR-DEQIRKLADRRFGIGFDQLLVVEPpRSPDMDFRYRIFNADGSE 71 7******************887777.7**********************999***************** PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee 138 +e+CGNg+Rcfa+fv+++ l++k+e++vet g +++ v++++ +v+vdmg+p+f++++ p+++++++ lcl|NCBI__GCF_002151265.1:WP_086511730.1 72 VENCGNGARCFARFVRDQRLTHKREIHVETAGGPLTLVVNDDD-QVTVDMGTPRFEPAALPFDATEDRP 139 *******************************************.*******************866655 PP TIGR00652 139 keellalev....l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklr 202 + l+++ + +v++GnPH+v+ v+dv+++++e+lg+l+e h++fp +vN f++v++++ei+lr lcl|NCBI__GCF_002151265.1:WP_086511730.1 140 L-HALEVDGeryeIgAVSMGNPHAVLRVDDVDTAPVERLGPLIERHPRFPRRVNAGFMQVVSPHEIRLR 207 3.3333333454437****************************************************** PP TIGR00652 203 vyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269 v+ERG geTlaCGtGa+A+++ ++++g++++ vtvhl+gg+L ie++ d+ +++tGpa++v+eg++a lcl|NCBI__GCF_002151265.1:WP_086511730.1 208 VFERGTGETLACGTGACAAVASGIRQGLLESPVTVHLRGGDLRIEWSGDEaPLLMTGPAERVFEGRIA 275 ************************************************999**************975 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.44 // [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