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 WP_011384430.1 AMB_RS10235 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000009985.1:WP_011384430.1 Length = 245 Score = 185 bits (469), Expect = 9e-52 Identities = 104/251 (41%), Positives = 150/251 (59%), Gaps = 14/251 (5%) Query: 4 PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63 P+L V L F GL AVN V +V +V++IGPNGAGKTT FN + G P+ G + Sbjct: 6 PMLSVENLGKSFRGLRAVNQVAFEVPRGDIVALIGPNGAGKTTTFNLIAGALPPSDGKVV 65 Query: 64 LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAF 123 LDG +I GL I R GV RTFQ V+ F ++ EN++V RH N + + K A Sbjct: 66 LDGHDITGLGQAAICRAGVGRTFQIVKPFAGLSVEENVMVGALRHDNGD----VDKARAA 121 Query: 124 RRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183 R+ + +E L + A A TL ++RLE+A+ + TRP++L+LDE AG Sbjct: 122 SRATLDLLE----------LGDKARDPAQTLTLPDRKRLEVAKALATRPKLLLLDEVMAG 171 Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243 L P E D + A++ L E +T+LLIEH M+ VM++SDH+VV++ G +A+GTP ++ Sbjct: 172 LRPVECDRMVAILTGLNKETGLTILLIEHVMRAVMALSDHVVVLHHGEKIAEGTPAEVTS 231 Query: 244 NPDVIKAYLGE 254 +P V++ YLGE Sbjct: 232 HPKVLECYLGE 242 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: 163 Number of extensions: 6 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: 255 Length of database: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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: 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