Align BadK (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 109 bits (273), Expect = 1e-28 Identities = 69/196 (35%), Positives = 109/196 (55%), Gaps = 10/196 (5%) Query: 7 LTETQGRVGIITLNRP-DVLNALNDALMDALGGALLAFDADDGI-GAIVIAGNTRAFAAG 64 L+ + ++T++ P + +N L + L AD I G ++I+G +F AG Sbjct: 7 LSRRDDGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAG 66 Query: 65 ADIASMAAWSYSDVYGSNFITRN----WETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 ADI+ + A ++ + ++R + + + PV+AA+ G GGG ELALAC Sbjct: 67 ADISMLDACETAE--DARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALACHQR 124 Query: 121 IAGRSAKFAL--PEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVS 178 + S+K L PE++LGLLPG GGTQRLPR IG AKA+D+ L+ + + ++A + GLV Sbjct: 125 VCSDSSKTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVD 184 Query: 179 RVVDDDRLRDETVALA 194 VV + L D + +A Sbjct: 185 DVVPESILLDTAIEMA 200 Lambda K H 0.321 0.135 0.389 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: 270 Number of extensions: 11 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: 258 Length of database: 706 Length adjustment: 32 Effective length of query: 226 Effective length of database: 674 Effective search space: 152324 Effective search space used: 152324 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 (21.9 bits) S2: 50 (23.9 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