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 RR42_RS20240 RR42_RS20240 hypothetical protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS20240 Length = 595 Score = 199 bits (507), Expect = 8e-56 Identities = 113/253 (44%), Positives = 156/253 (61%), Gaps = 7/253 (2%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 IL+V FGGL+AVN V+ +V +++ +IGPNGAGK+T FN +TG T G + Sbjct: 343 ILDVKAARKEFGGLVAVNDVSFQVRAGEIIGLIGPNGAGKSTTFNLVTGVLPATRGEVLY 402 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 GE+I GLP +I ++G+ RTFQ+V L MT +EN VA HL +F T A Sbjct: 403 RGEQISGLPSREIVKRGIGRTFQHVHLLPTMTVLEN--VAIGAHLRGDFAPQGGVTAAIL 460 Query: 125 R----SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 R E + + AA LE V L + AG+LA GQQR LEIAR + P +L+LDEP Sbjct: 461 RMNKNEEAKLLHEAARQLERVGLADCMYMEAGSLALGQQRILEIARALCCDPALLLLDEP 520 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 AAGL KE L L+ KL+ E ++VLL+EHDM VM+++D +VV+ G +A+G PE Sbjct: 521 AAGLRYKEKQALAELLKKLKGE-GMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEGVPED 579 Query: 241 IRDNPDVIKAYLG 253 ++ +P V++AYLG Sbjct: 580 VQKDPAVLEAYLG 592 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: 361 Number of extensions: 14 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: 595 Length adjustment: 30 Effective length of query: 225 Effective length of database: 565 Effective search space: 127125 Effective search space used: 127125 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: 50 (23.9 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