Align methylmalonyl CoA epimerase subunit (EC 5.1.99.1) (characterized)
to candidate WP_037579705.1 BS73_RS15090 methylmalonyl-CoA epimerase
Query= metacyc::MONOMER-13075 (148 letters) >NCBI__GCF_000744815.1:WP_037579705.1 Length = 147 Score = 110 bits (276), Expect = 7e-30 Identities = 56/133 (42%), Positives = 84/133 (63%), Gaps = 2/133 (1%) Query: 10 IDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAP 69 IDH+ AC D D+ ++Y+ T+G+ H E N EQGV E M+ + +Q++ P Sbjct: 5 IDHIGIACFDLDKTVEFYRATYGFEVFHTEVNEEQGVREAMLRINRTDDGGASYLQLLEP 64 Query: 70 LNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINF 129 + ++S V KWLAK NG G+HH+A+ D+D S +R +GV++LY+EP+ G+ +RI F Sbjct: 65 VREDSAVGKWLAK-NGE-GVHHIAFGTADVDGDSEAIRGKGVRVLYEEPRRGSMDSRITF 122 Query: 130 MHPKSGKGVLIEL 142 +HPK GVL EL Sbjct: 123 LHPKDCHGVLTEL 135 Lambda K H 0.317 0.133 0.408 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: 88 Number of extensions: 5 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: 148 Length of database: 147 Length adjustment: 16 Effective length of query: 132 Effective length of database: 131 Effective search space: 17292 Effective search space used: 17292 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 (21.7 bits) S2: 42 (20.8 bits)
Align candidate WP_037579705.1 BS73_RS15090 (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.2178477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-45 139.9 0.0 3.9e-45 139.7 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037579705.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037579705.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 139.7 0.0 3.9e-45 3.9e-45 1 128 [. 4 136 .. 4 137 .. 0.97 Alignments for each domain: == domain 1 score: 139.7 bits; conditional E-value: 3.9e-45 TIGR03081 1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelge......tklellepleedspiakfle 67 ++dh++ia+ dl++ +++yr+++G++v ++e ++eqgv++++l+++ ++l+llep+ eds++ k+l+ NCBI__GCF_000744815.1:WP_037579705.1 4 RIDHIGIACFDLDKTVEFYRATYGFEVFHTEVNEEQGVREAMLRINRtddggaSYLQLLEPVREDSAVGKWLA 76 79*****************************************99865678889******************* PP TIGR03081 68 kkkgeGlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLiele 128 k+ geG+hhia+ + d++ +e ++ kgvr+l+eepr G+ +++FlhPkd++GvL+el+ NCBI__GCF_000744815.1:WP_037579705.1 77 KN-GEGVHHIAFGTADVDGDSEAIRGKGVRVLYEEPRRGSMDSRITFLHPKDCHGVLTELV 136 **.********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (147 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: 8.32 // [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