Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate HSERO_RS21455 HSERO_RS21455 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__HerbieS:HSERO_RS21455 Length = 287 Score = 291 bits (745), Expect = 1e-83 Identities = 152/281 (54%), Positives = 193/281 (68%), Gaps = 7/281 (2%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHG GNDF+V+DA+ Q++ SP + +ADR G+G DQ+LVVE +DF Y Sbjct: 3 IKFTKMHGAGNDFVVLDAINQSISLSPAQWQFIADRRFGIGADQMLVVEKARGEGVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RI+NADG EV QCGNGAR F +FV KGLT+KR IRV T +G + + DD + V+MG Sbjct: 63 RIYNADGGEVEQCGNGARAFVKFVTDKGLTSKRAIRVETMSGVIEPRLEDDGQITVDMGA 122 Query: 121 PNFEPSAVPFRA------NKAEKT-YIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVE 173 P P+ VPF + N+AE T + + A +T VVSMGNPH V V+D + A V Sbjct: 123 PILTPADVPFDSHGLQHRNEAEDTLWPLDVAGKTTWISVVSMGNPHAVQVVEDSEAAPVL 182 Query: 174 TLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGL 233 + GP++E HERFP+R N GFMQVV R H+ LRVYERGAGET ACG+GACAAV GI++GL Sbjct: 183 SEGPLIERHERFPKRVNAGFMQVVDRHHVNLRVYERGAGETLACGTGACAAVVAGIRRGL 242 Query: 234 LAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 L V V+ GG L+IAW GPG + MTGPAV VY+G I L Sbjct: 243 LDSPVAVQTHGGVLNIAWAGPGEAVMMTGPAVSVYEGEIEL 283 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: 255 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: 287 Length adjustment: 26 Effective length of query: 248 Effective length of database: 261 Effective search space: 64728 Effective search space used: 64728 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 HSERO_RS21455 HSERO_RS21455 (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.1560.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-91 291.8 0.0 2.8e-91 291.6 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS21455 HSERO_RS21455 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS21455 HSERO_RS21455 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.6 0.0 2.8e-91 2.8e-91 1 268 [. 3 281 .. 3 283 .. 0.92 Alignments for each domain: == domain 1 score: 291.6 bits; conditional E-value: 2.8e-91 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDG 67 ++F+kmhG+gNdFv++d +++++ + +++ + ++dr++g+gaD++l+ve+ e d+++ri+N+DG lcl|FitnessBrowser__HerbieS:HSERO_RS21455 3 IKFTKMHGAGNDFVVLDAINQSISLS-PAQWQFIADRRFGIGADQMLVVEKaRGEGVDFRYRIYNADG 69 68******************777766.***********************9666779*********** PP TIGR00652 68 SeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt... 132 e+e+CGNg+R f+kfv++kgl++k+ ++vet +g+i+ +e+++ +++vdmg p ++++++p++ lcl|FitnessBrowser__HerbieS:HSERO_RS21455 70 GEVEQCGNGARAFVKFVTDKGLTSKRAIRVETMSGVIEPRLEDDG-QITVDMGAPILTPADVPFDshg 136 *********************************************.*******************544 PP TIGR00652 133 .vekeeekeellalev.....l..vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefve 192 ++ +e +++l l+v + vv++GnPH+v +ved e +++ + g+l+e he+fp++vN f++ lcl|FitnessBrowser__HerbieS:HSERO_RS21455 137 lQHRNEAEDTLWPLDVagkttWisVVSMGNPHAVQVVEDSEAAPVLSEGPLIERHERFPKRVNAGFMQ 204 333333334444444477776268******************************************** PP TIGR00652 193 vkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGp 259 v++++++ lrvyERGageTlaCGtGa+A++v++++ g++++ v+v+++gg L+i + g v++tGp lcl|FitnessBrowser__HerbieS:HSERO_RS21455 205 VVDRHHVNLRVYERGAGETLACGTGACAAVVAGIRRGLLDSPVAVQTHGGVLNIAWAGPGeAVMMTGP 272 ************************************************************99****** PP TIGR00652 260 avlvlegel 268 av v+ege+ lcl|FitnessBrowser__HerbieS:HSERO_RS21455 273 AVSVYEGEI 281 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (287 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.15 // [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