Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_043745759.1 AMB_RS01095 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >NCBI__GCF_000009985.1:WP_043745759.1 Length = 284 Score = 177 bits (450), Expect = 2e-49 Identities = 111/273 (40%), Positives = 147/273 (53%), Gaps = 9/273 (3%) Query: 3 FSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRI 62 F KMHGLGNDF+V+DA + + +PE +R +A R GVG DQL+V+ DP D I Sbjct: 8 FLKMHGLGNDFVVLDARARALDLTPERVRAIASRGTGVGCDQLVVMTQATDPCADATMLI 67 Query: 63 FNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPN 122 +NADGSEVA CGN +RC A + + +K + T G + V V+MG Sbjct: 68 YNADGSEVAACGNASRCVAWLLMKEIAADK--VVFQTKAGLLDAESRGPHQVAVDMGPAR 125 Query: 123 FEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESH 182 + +P A + ++ +A VSMGNPH V VDD + + LG LE H Sbjct: 126 LDWREIPL-AEAVDTLHLGISAGPLADPVGVSMGNPHAVFFVDDAEAVNLAQLGRGLEHH 184 Query: 183 ERFPERANIGFMQVV-----KREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEE 237 FPERANI QV+ + IR+RV+ERGAG T ACG+GACA + ++GL + Sbjct: 185 ALFPERANIEVAQVLTPPDAEMGRIRMRVWERGAGITMACGTGACATLVAAARRGLSPRK 244 Query: 238 VRVELPGGRLDIAWKGPGHPLYMTGPAVHVYDG 270 + L GG L I W GH L MTGP + G Sbjct: 245 AEIILDGGTLTIEWLKDGHVL-MTGPVAVAFTG 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: 215 Number of extensions: 8 Number of successful extensions: 4 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: 284 Length adjustment: 26 Effective length of query: 248 Effective length of database: 258 Effective search space: 63984 Effective search space used: 63984 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_043745759.1 AMB_RS01095 (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.4552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-81 260.3 0.0 1.1e-81 260.1 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043745759.1 AMB_RS01095 diaminopimelate epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043745759.1 AMB_RS01095 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.1 0.0 1.1e-81 1.1e-81 3 268 .. 8 278 .. 6 280 .. 0.93 Alignments for each domain: == domain 1 score: 260.1 bits; conditional E-value: 1.1e-81 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSea 70 FlkmhGlgNdFv++d + + l + +e+vr++++r tgvg+D+++++++ ++++ad+++ i+N+DGSe+ lcl|NCBI__GCF_000009985.1:WP_043745759.1 8 FLKMHGLGNDFVVLDARARALDLT-PERVRAIASRGTGVGCDQLVVMTQaTDPCADATMLIYNADGSEV 75 9****************9666666.*******************99988799***************** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeek 139 + CGN++Rc+a ++++ + ++++++t+agl+ +e +v vdmg +++ eipl ++ ++ + lcl|NCBI__GCF_000009985.1:WP_043745759.1 76 AACGNASRCVAWLLMKEIAA--DKVVFQTKAGLLDAESRGPH-QVAVDMGPARLDWREIPLAEAVDTLH 141 ***********999999888..8**************99999.*******************9889887 PP TIGR00652 140 eellalev...lvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkke.....deik 200 + a + + v++GnPH+v+fv+d e ++l +lg+ le+h fpe+ N+e+++v+ + +i+ lcl|NCBI__GCF_000009985.1:WP_043745759.1 142 LGISAGPLadpVGVSMGNPHAVFFVDDAEAVNLAQLGRGLEHHALFPERANIEVAQVLTPpdaemGRIR 210 7787777765569*******************************************98642222279** PP TIGR00652 201 lrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 +rv+ERGag+T+aCGtGa+A+ v+a++ g++++k+++ l+gg L+ie+ +dg+v++tGp+ + + g+l lcl|NCBI__GCF_000009985.1:WP_043745759.1 211 MRVWERGAGITMACGTGACATLVAAARRGLSPRKAEIILDGGTLTIEWLKDGHVLMTGPVAVAFTGTL 278 *************************************************************9999976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (284 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: 00:00:00.01 # Mc/sec: 7.01 // [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