Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS20010 CA265_RS20010 methylmalonyl-CoA mutase
Query= BRENDA::A4YIE3 (155 letters) >FitnessBrowser__Pedo557:CA265_RS20010 Length = 139 Score = 157 bits (396), Expect = 8e-44 Identities = 77/137 (56%), Positives = 102/137 (74%) Query: 13 MILLMDKRIKVVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVRTAIQEDA 72 M ++++ I+V+VAK+GLDGHDRGAKVIA +L+DAGMEV+YTGLRQTPE +V TA+QED Sbjct: 1 MSKVLNRPIRVLVAKVGLDGHDRGAKVIATSLRDAGMEVIYTGLRQTPEMVVNTALQEDV 60 Query: 73 DVIGISILSGAHLELMPKIVEALKKAGLDDVGLVLGGVIPPEDIPKLKAMGVDDVFLPGT 132 D IGISILSGAH+ + PKI+ +K+ LDDV L GG+IP D KL MGV ++F PGT Sbjct: 61 DAIGISILSGAHMTVFPKIIHFMKEKQLDDVLLTGGGIIPEADRLKLAGMGVGELFPPGT 120 Query: 133 SLKEIAQRVSKLASTKR 149 ++ I + + + R Sbjct: 121 TMASIVEYIQNWVTENR 137 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: 94 Number of extensions: 2 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: 139 Length adjustment: 16 Effective length of query: 139 Effective length of database: 123 Effective search space: 17097 Effective search space used: 17097 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: 42 (20.8 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