Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_011764329.1 AZO_RS02990 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_000061505.1:WP_011764329.1 Length = 277 Score = 315 bits (807), Expect = 7e-91 Identities = 159/274 (58%), Positives = 190/274 (69%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHGLGNDF+V+DA V +P ++ +ADRH GVG DQLLVVEPP E+DF Y Sbjct: 3 IRFTKMHGLGNDFVVIDATRTPVDLTPARVKAIADRHFGVGCDQLLVVEPPGSDEVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFNADG EV QCGNGARCF RFV KGLT+KR+IRV T G + + D LV V+MG Sbjct: 63 RIFNADGGEVEQCGNGARCFVRFVHDKGLTDKREIRVETRAGVIAPALRPDGLVSVDMGV 122 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P P+ +PF ++ ++ AE T+ VSMGNPH V V DVDTA V G +E Sbjct: 123 PELSPARIPFVSDSDAWVQPLQLAEDTVAITAVSMGNPHAVQVVADVDTAPVARQGAEIE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H RFP R N GFMQVV HIRLRV+ERGAGET ACG+GACAAV GI +GLL VRV Sbjct: 183 CHPRFPARVNAGFMQVVDAGHIRLRVFERGAGETLACGTGACAAVVAGIGRGLLVSPVRV 242 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274 E GG L+IAW GPG P+ MTGPAV V++G + L Sbjct: 243 ETRGGELEIAWAGPGTPVVMTGPAVTVFEGELEL 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: 286 Number of extensions: 7 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: 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_011764329.1 AZO_RS02990 (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.13103.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-95 304.3 0.0 4.5e-95 304.1 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764329.1 AZO_RS02990 diaminopimelate epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764329.1 AZO_RS02990 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 304.1 0.0 4.5e-95 4.5e-95 1 269 [. 3 275 .. 3 276 .. 0.94 Alignments for each domain: == domain 1 score: 304.1 bits; conditional E-value: 4.5e-95 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGS 68 ++F+kmhGlgNdFv++d + v ++++v++++drh+gvg+D++l+vep +s+e d+++rifN+DG lcl|NCBI__GCF_000061505.1:WP_011764329.1 3 IRFTKMHGLGNDFVVIDATR-TPVDLTPARVKAIADRHFGVGCDQLLVVEPpGSDEVDFRYRIFNADGG 70 68***************999.556666***********************999**************** PP TIGR00652 69 eaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekee 137 e+e+CGNg+Rcf++fv +kgl++k+e++vet ag+i + ++ v+vdmg p++ ++ ip++++ ++ lcl|NCBI__GCF_000061505.1:WP_011764329.1 71 EVEQCGNGARCFVRFVHDKGLTDKREIRVETRAGVIAPALRPDG-LVSVDMGVPELSPARIPFVSDSDA 138 ********************************************.*******************87777 PP TIGR00652 138 ekeellalev.l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklr 202 + l+ +e + +v++GnPH+v +v+dv+++++ + g+++e h++fp++vN f++v++ +i+lr lcl|NCBI__GCF_000061505.1:WP_011764329.1 139 WVQPLQLAEDtVaitAVSMGNPHAVQVVADVDTAPVARQGAEIECHPRFPARVNAGFMQVVDAGHIRLR 207 655555444442346****************************************************** PP TIGR00652 203 vyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269 v+ERGageTlaCGtGa+A++v+++ g++ + v+v+++ggeLei + g v +tGpav+v+egel+ lcl|NCBI__GCF_000061505.1:WP_011764329.1 208 VFERGAGETLACGTGACAAVVAGIGRGLLVSPVRVETRGGELEIAWAGPGtPVVMTGPAVTVFEGELE 275 **************************************************9**************985 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: 8.97 // [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