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 BWI76_RS05980 BWI76_RS05980 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Koxy:BWI76_RS05980 Length = 260 Score = 225 bits (574), Expect = 6e-64 Identities = 108/253 (42%), Positives = 167/253 (66%) Query: 2 SRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGL 61 ++ ILEV +TM+FGGL A++ V+ V+E ++ +IGPNGAGKTT+FN +T Y+PT G Sbjct: 4 NKVILEVQDVTMQFGGLRAIDSVSFHVDEAEIFGLIGPNGAGKTTMFNVITANYKPTSGS 63 Query: 62 IRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTP 121 + L G+ ++GL +++ G+ RTFQN+RLF MT +EN++V + L Sbjct: 64 VTLAGKSLKGLKPNRVVNAGIARTFQNIRLFNSMTVLENVMVGLDSASRYSLLEAALHIG 123 Query: 122 AFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 + +ER A A L+++ + FA+ A L+YG QR++EIAR + T P++L+LDEPA Sbjct: 124 RYFPAERAAKAKAMAILDDIGIAHFADVQATNLSYGNQRKVEIARALATSPKLLLLDEPA 183 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 AG+NPKET++L LI ++R+++ ++VLLIEHDM V + + ++V+ G PL G + Sbjct: 184 AGMNPKETEELADLIFRMRNDYRLSVLLIEHDMPFVNKLCERVMVLEYGKPLFSGLMSEA 243 Query: 242 RDNPDVIKAYLGE 254 +PDVI AYLG+ Sbjct: 244 IQDPDVISAYLGD 256 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: 160 Number of extensions: 2 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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