Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 5209155 Shew_1633 lipoprotein releasing system, ATP-binding protein (RefSeq)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__PV4:5209155 Length = 233 Score = 100 bits (248), Expect = 3e-26 Identities = 70/220 (31%), Positives = 114/220 (51%), Gaps = 10/220 (4%) Query: 1 MLSFDKVSTYY--GKI--QALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASG 56 +L VS Y G I Q L V++ + KGE V +IG++G+GKSTLL + + +SG Sbjct: 9 LLQVSNVSKRYHEGSIDTQVLSGVNLSIAKGEQVAIIGSSGSGKSTLLHIMGTLDKPSSG 68 Query: 57 SIRYEGEELVGLPSS---TIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQM 113 + ++GE+L L S I + + + + + T EN+AM G + +V+ Sbjct: 69 QVMFDGEDLYQLSPSRQAAIRNQELGFIYQFHHLLPEFTALENVAMPGLIQKRPRQEVEQ 128 Query: 114 DKVLELFPR--LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQ 171 + EL R L R MSGGE+Q AI RAL+++PKL+L DEP+ L Sbjct: 129 E-AKELLSRVGLGHRLHHTPAEMSGGERQRTAIARALINRPKLVLADEPTGNLDAASGDS 187 Query: 172 IFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRI 211 ++E+I +L + T F+V + + DR +++G++ Sbjct: 188 VYELIRELGSQLGTAFVVVTHDPKLAARMDRQLKMQDGQL 227 Lambda K H 0.318 0.136 0.374 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: 126 Number of extensions: 2 Number of successful extensions: 2 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: 233 Length of database: 233 Length adjustment: 23 Effective length of query: 210 Effective length of database: 210 Effective search space: 44100 Effective search space used: 44100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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