Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate Dsui_0649 Dsui_0649 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__PS:Dsui_0649 Length = 276 Score = 309 bits (791), Expect = 5e-89 Identities = 154/274 (56%), Positives = 192/274 (70%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHGLGNDF+V+D V QN+ +P +R LADR+ GVG DQ+L+VE P +DF Y Sbjct: 3 LEFTKMHGLGNDFVVLDGVRQNITLTPAQLRFLADRNFGVGCDQILLVEKPGQAGVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADGSEV QCGNGARCF RFV +GLT+KR+I+V T +G + + D V V+MG+ Sbjct: 63 RIFNADGSEVEQCGNGARCFVRFVHEQGLTDKREIKVETKSGIISPRLEADGNVTVDMGK 122 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P F P +PF + ++ +Q + VSMGNPH V V+DVDTA V GP++E Sbjct: 123 PVFAPDRIPFVSPTDAVIQPLQVGDQEVAITAVSMGNPHAVQVVEDVDTAPVAIQGPMIE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 SH RFP+R N GF+QVV R +RLRVYERGAGET ACG+GACAAV GI + LL VRV Sbjct: 183 SHPRFPQRVNAGFLQVVDRHSVRLRVYERGAGETLACGTGACAAVVAGISRDLLDSPVRV 242 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 GG L IAW GPG P++MTGPAV V+ G I L Sbjct: 243 STRGGELSIAWNGPGTPVHMTGPAVTVFSGEIEL 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: 271 Number of extensions: 6 Number of successful extensions: 2 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: 276 Length adjustment: 25 Effective length of query: 249 Effective length of database: 251 Effective search space: 62499 Effective search space used: 62499 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 Dsui_0649 Dsui_0649 (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.32423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-97 309.7 0.0 1e-96 309.5 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0649 Dsui_0649 diaminopimelate epimer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0649 Dsui_0649 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.5 0.0 1e-96 1e-96 2 268 .. 4 274 .. 3 276 .] 0.96 Alignments for each domain: == domain 1 score: 309.5 bits; conditional E-value: 1e-96 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGNgi 77 eF+kmhGlgNdFv++d v +++ + ++++r ++dr++gvg+D++llve+ ++ d+++rifN+DGSe+e+CGNg+ lcl|FitnessBrowser__PS:Dsui_0649 4 EFTKMHGLGNDFVVLDGVRQNITLT-PAQLRFLADRNFGVGCDQILLVEKpGQAGVDFRYRIFNADGSEVEQCGNGA 79 8******************999999.9*********************9989999********************** PP TIGR00652 78 Rcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev...l.vv 150 Rcf++fv e+gl++k+e++vet++g+i+ +e+++ +v+vdmg+p f ++ ip+++ ++++ + l+ + + +v lcl|FitnessBrowser__PS:Dsui_0649 80 RCFVRFVHEQGLTDKREIKVETKSGIISPRLEADG-NVTVDMGKPVFAPDRIPFVSPTDAVIQPLQVGDQevaItAV 155 ***********************************.*******************87777776666555554536** PP TIGR00652 151 dvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalk 227 ++GnPH+v +vedv+++++ g+++e+h++fp++vN f++v+++++++lrvyERGageTlaCGtGa+A++v+++ lcl|FitnessBrowser__PS:Dsui_0649 156 SMGNPHAVQVVEDVDTAPVAIQGPMIESHPRFPQRVNAGFLQVVDRHSVRLRVYERGAGETLACGTGACAAVVAGIS 232 ***************************************************************************** PP TIGR00652 228 lgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 ++++ v+v ++ggeL i ++ g v +tGpav+v++ge+ lcl|FitnessBrowser__PS:Dsui_0649 233 RDLLDSPVRVSTRGGELSIAWNGPGtPVHMTGPAVTVFSGEI 274 *************************9**************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (276 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: 7.30 // [ok]
This GapMind analysis is from Apr 09 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