Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_084037500.1 AMYHA_RS25265 methylmalonyl-CoA mutase
Query= BRENDA::O58013 (147 letters) >NCBI__GCF_000504245.1:WP_084037500.1 Length = 746 Score = 103 bits (258), Expect = 4e-27 Identities = 51/123 (41%), Positives = 74/123 (60%), Gaps = 3/123 (2%) Query: 6 ERSKVRVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLG 65 E + R+LVAK G DGHDRG KV+A A D G++V + TP ++ +E DV V+G Sbjct: 589 EGRRPRILVAKMGQDGHDRGQKVIATAFADIGFDVDVGPLFSTPAEVARQAVEADVHVIG 648 Query: 66 ISILSGAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMGVAEVFGPGTP 125 +S L+ H+ L+P + L E D++VV GG+IPP D + L++ G A +F PGT Sbjct: 649 VSSLAAGHLTLVPALRAELAELD---RSDIMVVVGGVIPPQDFDALREAGAAAIFPPGTV 705 Query: 126 LRE 128 + E Sbjct: 706 IAE 708 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: 225 Number of extensions: 10 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: 746 Length adjustment: 28 Effective length of query: 119 Effective length of database: 718 Effective search space: 85442 Effective search space used: 85442 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 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