Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_076581962.1 BB347_RS05905 methylmalonyl-CoA epimerase
Query= SwissProt::O58010 (136 letters) >NCBI__GCF_001971705.1:WP_076581962.1 Length = 127 Score = 96.7 bits (239), Expect = 1e-25 Identities = 53/126 (42%), Positives = 77/126 (61%), Gaps = 4/126 (3%) Query: 9 DHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTEDSPI 67 +H GIA ++ +E +++ L G V EE ++V ++ G+ ELLE ED I Sbjct: 4 EHAGIATEDAQELAELYSDLFGLAVAHEEEFDG--MRVVFLECGDGYFELLEPF-EDGTI 60 Query: 68 AKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSVTGV 127 A+++E G GIHHLA+ E+IE+ LE ++ LIDE+PR GA G +AF+HPK G+ Sbjct: 61 AQYLEANGSGIHHLALATEDIEAALETAREHDVSLIDEEPRPGAWGHSVAFLHPKDTGGI 120 Query: 128 LLELCE 133 LLEL E Sbjct: 121 LLELVE 126 Lambda K H 0.317 0.138 0.389 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: 50 Number of extensions: 2 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: 136 Length of database: 127 Length adjustment: 14 Effective length of query: 122 Effective length of database: 113 Effective search space: 13786 Effective search space used: 13786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 41 (20.4 bits)
Align candidate WP_076581962.1 BB347_RS05905 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))
# 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.carbon/TIGR03081.hmm # target sequence database: /tmp/gapView.3084980.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03081 [M=129] Accession: TIGR03081 Description: metmalonyl_epim: methylmalonyl-CoA 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-49 151.8 0.1 7.9e-49 151.7 0.1 1.0 1 NCBI__GCF_001971705.1:WP_076581962.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001971705.1:WP_076581962.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 151.7 0.1 7.9e-49 7.9e-49 2 129 .] 3 126 .. 2 126 .. 0.98 Alignments for each domain: == domain 1 score: 151.7 bits; conditional E-value: 7.9e-49 TIGR03081 2 ldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeGl 74 ++h +ia++d++e+a+ly d++G++v++eee+ +g++vvfle g++++ellep ed++ia++le + g+G+ NCBI__GCF_001971705.1:WP_076581962.1 3 FEHAGIATEDAQELAELYSDLFGLAVAHEEEF--DGMRVVFLECGDGYFELLEP-FEDGTIAQYLEAN-GSGI 71 79******************************..89******************.689*********9.**** PP TIGR03081 75 hhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129 hh+al+++dieaalet++e++v l+deepr Ga+G++vaFlhPkdtgG+L+el+e NCBI__GCF_001971705.1:WP_076581962.1 72 HHLALATEDIEAALETAREHDVSLIDEEPRPGAWGHSVAFLHPKDTGGILLELVE 126 *****************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (127 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: 7.54 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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