Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_092482542.1 BM299_RS05955 cobalamin B12-binding domain-containing protein
Query= BRENDA::O58013 (147 letters) >NCBI__GCF_900115975.1:WP_092482542.1 Length = 133 Score = 159 bits (401), Expect = 2e-44 Identities = 79/130 (60%), Positives = 103/130 (79%), Gaps = 4/130 (3%) Query: 9 KVRVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLGISI 68 K+RVLVAKPGLDGHDRGA+V+ARALRDAG EV+YTG+ QTPEQIVEA I+EDVDV+G+SI Sbjct: 4 KIRVLVAKPGLDGHDRGARVIARALRDAGMEVVYTGLHQTPEQIVEAAIQEDVDVVGLSI 63 Query: 69 LSGAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMG-VAEVFGPGTPLR 127 LSGAHM L P++ +LL+E D++V+ GG IP D + LK+ G A++F PGT + Sbjct: 64 LSGAHMTLFPRVCELLKENDA---GDIVVIGGGTIPEADVKTLKEGGWAAQLFTPGTTIE 120 Query: 128 EIIEFIDKNV 137 I+++I+ NV Sbjct: 121 TIVDWINANV 130 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: 68 Number of extensions: 1 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: 147 Length of database: 133 Length adjustment: 15 Effective length of query: 132 Effective length of database: 118 Effective search space: 15576 Effective search space used: 15576 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: 42 (20.8 bits)
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