Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_012385173.1 BIND_RS11125 methylmalonyl-CoA mutase
Query= BRENDA::A4YIE3 (155 letters) >NCBI__GCF_000019845.1:WP_012385173.1 Length = 727 Score = 117 bits (292), Expect = 5e-31 Identities = 59/128 (46%), Positives = 81/128 (63%) Query: 23 VVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVRTAIQEDADVIGISILSG 82 V+VAK+G DGHDRG KV+A D G VV L TPE+ R AI+ED DVIG+S L+G Sbjct: 589 VLVAKMGQDGHDRGQKVVASGFADLGFRVVLGPLFATPEETARQAIEEDVDVIGVSSLAG 648 Query: 83 AHLELMPKIVEALKKAGLDDVGLVLGGVIPPEDIPKLKAMGVDDVFLPGTSLKEIAQRVS 142 HL L+P++ E L K G ++ +V+GGV+PP+D +L+ G +F PGT L A + Sbjct: 649 GHLSLVPELREELAKLGHPEIMIVVGGVVPPQDYAQLRDSGAAAIFPPGTPLFSAATELL 708 Query: 143 KLASTKRG 150 + S +G Sbjct: 709 ETLSAHQG 716 Lambda K H 0.319 0.140 0.382 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: 8 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: 155 Length of database: 727 Length adjustment: 28 Effective length of query: 127 Effective length of database: 699 Effective search space: 88773 Effective search space used: 88773 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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