Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__BFirm:BPHYT_RS21915 Length = 222 Score = 112 bits (281), Expect = 4e-30 Identities = 67/220 (30%), Positives = 119/220 (54%), Gaps = 9/220 (4%) Query: 3 EFDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAW-FAKAYVN 61 E D+S ++ LP +L G V+T+++T ++ + + G ++ + RL+ + + F AY+ Sbjct: 2 ELDFSPVIAGLPDILHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLT 61 Query: 62 VFRSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQ 121 FR PL++ L + +P F L P + M+ ++ AAY SEI+R IQ Sbjct: 62 FFRGTPLLVQLFLLFFGLPQFGI----LLPA----FVCGMLGLGLYSAAYVSEIVRGAIQ 113 Query: 122 SISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFF 181 S+ RGQ AA ++GM+ Q+M+ IILPQA M+P L + I L ++++LV +L++ D Sbjct: 114 SVDRGQMEAARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLM 173 Query: 182 RTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKR 221 I +E+ L VY V++ + + + ++R Sbjct: 174 HEGQKIISVSYRSLEVYLAIALVYLVLTQATNYALHRVER 213 Lambda K H 0.330 0.140 0.412 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: 134 Number of extensions: 8 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: 224 Length of database: 222 Length adjustment: 22 Effective length of query: 202 Effective length of database: 200 Effective search space: 40400 Effective search space used: 40400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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