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 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Keio:17272 Length = 241 Score = 130 bits (326), Expect = 3e-35 Identities = 75/225 (33%), Positives = 122/225 (54%), Gaps = 3/225 (1%) Query: 10 YYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLP 69 Y G+ + + DVS+ V GEIV L+G NGAGK+T + G +G+I + +++ LP Sbjct: 13 YKGR-RVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIIDDDDISLLP 71 Query: 70 SSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPR--LKERY 127 R+ I +P+ +F RL+V +NL D + + D+ EL ++ Sbjct: 72 LHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRANELMEEFHIEHLR 131 Query: 128 EQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVF 187 + ++SGGE++ + I RAL + PK +LLDEP G+ PI + I IIE LR G+ V Sbjct: 132 DSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKRIIEHLRDSGLGVL 191 Query: 188 LVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 + + N + L + +RAY++ G ++ H T +L + V+ YLG Sbjct: 192 ITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYLG 236 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: 133 Number of extensions: 4 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 241 Length adjustment: 23 Effective length of query: 210 Effective length of database: 218 Effective search space: 45780 Effective search space used: 45780 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