Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase
Query= BRENDA::O58013 (147 letters) >FitnessBrowser__Burk376:H281DRAFT_01038 Length = 703 Score = 88.6 bits (218), Expect = 2e-22 Identities = 49/123 (39%), Positives = 73/123 (59%), Gaps = 4/123 (3%) Query: 11 RVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLGISILS 70 RVL+AK G DGHDRGA+++A AL DAG+ V + +P V+ E VDV+G+S L+ Sbjct: 563 RVLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERVDVIGVSSLA 622 Query: 71 GAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMGVAEVFGPGTPLREII 130 GA LI + L +G+++ +V GGII L++ GVA F GTP+++I+ Sbjct: 623 GAQNDLITALHDQLTVRGLRIP----IVVGGIIDQASQLVLRRSGVAACFPAGTPIKKIV 678 Query: 131 EFI 133 + Sbjct: 679 TLL 681 Lambda K H 0.318 0.140 0.383 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: 178 Number of extensions: 6 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: 147 Length of database: 703 Length adjustment: 27 Effective length of query: 120 Effective length of database: 676 Effective search space: 81120 Effective search space used: 81120 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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