Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AZOBR_RS08245 AZOBR_RS08245 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__azobra:AZOBR_RS08245 Length = 294 Score = 272 bits (696), Expect = 5e-78 Identities = 139/260 (53%), Positives = 190/260 (73%), Gaps = 9/260 (3%) Query: 4 PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63 P+L V LTMRFGGL+AVN V+ ++ ++IGPNGAGKTT+FNC+TGFY PT G + Sbjct: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 Query: 64 L---DGEE--IQGLPGHKIARKG-VVRTFQNVRLFKEMTAVENLLVAQHRHL---NTNFL 114 L DG+E ++ +PG++I++K V RTFQN+RLF M+ +ENL+VAQH L + + Sbjct: 70 LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129 Query: 115 AGLFKTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRI 174 AGL P++ R+EREA++ A +WL+ V L EFA+ AG L YG QRRLEIAR M T P + Sbjct: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 Query: 175 LMLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLA 234 L LDEPAAGLNP+E+ +L L+ +R EH + VLLIEHDM +VM+ISDH+VV++ G ++ Sbjct: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249 Query: 235 DGTPEQIRDNPDVIKAYLGE 254 DG P ++++P VI+AYLGE Sbjct: 250 DGDPAFVKNDPAVIRAYLGE 269 Lambda K H 0.320 0.137 0.391 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: 240 Number of extensions: 7 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: 255 Length of database: 294 Length adjustment: 25 Effective length of query: 230 Effective length of database: 269 Effective search space: 61870 Effective search space used: 61870 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 (21.8 bits) S2: 47 (22.7 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