Align methylmalonyl-CoA epimerase (EC 5.1.99.1) (characterized)
to candidate WP_045586149.1 AL072_RS14955 VOC family protein
Query= BRENDA::Q8RCQ6 (150 letters) >NCBI__GCF_001305595.1:WP_045586149.1 Length = 179 Score = 76.6 bits (187), Expect = 2e-19 Identities = 44/138 (31%), Positives = 72/138 (52%), Gaps = 4/138 (2%) Query: 13 QIGIVVRDIEESLQNYAEFFGVEKPQWFWTDDYSKAHTKFNGRPTKARAKLAFFELGPLQ 72 Q G VVRDIE ++ ++ G+ WF+ + + + G + +A GPLQ Sbjct: 10 QAGYVVRDIEAAMDYWSRTLGIGP--WFYNERVPIRNYSYRGESYEVHNSVALANSGPLQ 67 Query: 73 LELIEP-DENPSTWREFLDKNGEGIHHIAFVVKDMDRKVEELYRKGMKVIQKGDF-EGGR 130 +ELI+ ++ PS +R+FL G+ H+A+ +D D ++ L +G K + G+ E GR Sbjct: 68 MELIQTRNDAPSMYRDFLQAGNTGLQHVAYWTEDYDADLDRLLGQGFKPVMSGEVGEKGR 127 Query: 131 YAYIDTLRALKVMIELLE 148 + Y DT +IEL E Sbjct: 128 FIYFDTEYHPGTVIELSE 145 Lambda K H 0.320 0.139 0.415 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: 76 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: 150 Length of database: 179 Length adjustment: 18 Effective length of query: 132 Effective length of database: 161 Effective search space: 21252 Effective search space used: 21252 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 (21.8 bits) S2: 43 (21.2 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