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_084935580.1 HA51_RS15830 ATP-binding cassette domain-containing protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_002095475.1:WP_084935580.1 Length = 291 Score = 288 bits (738), Expect = 7e-83 Identities = 153/283 (54%), Positives = 191/283 (67%), Gaps = 30/283 (10%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 MS IL+V+ L MRFGG+ A+N V+L VE V S+IGPNGAGKTTVFNCLTGFY+ TGG Sbjct: 1 MSDAILQVNNLMMRFGGIKALNDVSLSVERGSVTSLIGPNGAGKTTVFNCLTGFYRATGG 60 Query: 61 LIRLDGEE-----IQGL-------------------------PGHKIARKGVVRTFQNVR 90 I L+ + IQ L H + R G+ RTFQN+R Sbjct: 61 RIMLNANQRHTDVIQVLGQKIHPQDWLNPARLGSRIWYKMFGGAHLVNRAGLARTFQNIR 120 Query: 91 LFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLEEVNLTEFANRS 150 LF+EM+ VENLLVAQH +N LAG+ T +R +E A++ A +WLE V+L ANR Sbjct: 121 LFREMSVVENLLVAQHMLVNRQLLAGVMNTRGYREAENRALDRAFYWLENVDLVSSANRL 180 Query: 151 AGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLI 210 AGTL+YGQQRRLEIAR M TRP ++ LDEPAAGLNP ETD L ++ +LR++H ++VLLI Sbjct: 181 AGTLSYGQQRRLEIARAMCTRPELICLDEPAAGLNPVETDTLSQILHRLRADHRISVLLI 240 Query: 211 EHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNPDVIKAYLG 253 EHDM +VM ISDHIVV++ G +A GTP+QIR +P VI AYLG Sbjct: 241 EHDMPMVMRISDHIVVLDHGDVIAQGTPQQIRHDPKVIAAYLG 283 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: 220 Number of extensions: 5 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: 255 Length of database: 291 Length adjustment: 25 Effective length of query: 230 Effective length of database: 266 Effective search space: 61180 Effective search space used: 61180 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 24 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