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 5210162 Shew_2606 ABC transporter-related protein (RefSeq)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__PV4:5210162 Length = 272 Score = 202 bits (513), Expect = 7e-57 Identities = 110/240 (45%), Positives = 158/240 (65%), Gaps = 8/240 (3%) Query: 1 MLSFDKVSTYYGK-IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCG-----SPQAA 54 +L+ + + Y IQ L VS+EV +GEIVTL+G NGAGKST L + G + + + Sbjct: 13 LLAINNIEVVYDDVIQVLRGVSIEVPQGEIVTLLGPNGAGKSTTLKAISGLLKTENGEVS 72 Query: 55 SGSIRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD 114 G I + GE + + ++R + V EGRR+ +TV ENL +G + ++ Sbjct: 73 RGDIHFMGERIDVKNADDVVRSGLFQVMEGRRIVEDMTVIENLKLGAYTRRDGQVNQDIE 132 Query: 115 KVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFE 174 V FPRLKER AG +SGGEQQMLAIGRALM++PK++ LDEPS+GL+P++++++F Sbjct: 133 MVFNYFPRLKER-TGLAGYLSGGEQQMLAIGRALMARPKMICLDEPSMGLSPLLVKEVFG 191 Query: 175 IIEQLRRE-GVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233 IIE++ RE G+T+ LVEQNAN ALK A+ Y++E+G+IV+ T A LL N V++ YLGG Sbjct: 192 IIEKINREQGITMLLVEQNANYALKAANYGYIMESGKIVLDGTKAQLLNNEDVKEFYLGG 251 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: 170 Number of extensions: 5 Number of successful extensions: 4 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: 272 Length adjustment: 24 Effective length of query: 209 Effective length of database: 248 Effective search space: 51832 Effective search space used: 51832 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