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_013134865.1 ARNIT_RS05295 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000092245.1:WP_013134865.1 Length = 262 Score = 134 bits (336), Expect = 2e-36 Identities = 81/252 (32%), Positives = 140/252 (55%), Gaps = 12/252 (4%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 IL V G+++ F G A+N ++ + ++ +IG NGAGK+T+ + +TG +P G + + Sbjct: 21 ILLVDGVSVSFDGFKALNNLSFSINYGELRCIIGANGAGKSTMMDVVTGKTRPDEGEV-I 79 Query: 65 DGEEIQ--GLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122 GE + L I+ G+ R FQ +F+ + ENL +A FKT Sbjct: 80 FGEAVNLLELDEPTISEIGIGRKFQKPTVFQNHSVFENLELAMKDDKR------FFKT-L 132 Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 F + E + ++ + L E N AG L++GQ++ LEI +M P++L++DEP A Sbjct: 133 FSKLRSEQKDRIEETMKLIGLKELYNLDAGILSHGQKQWLEIGMLIMQEPKLLLVDEPVA 192 Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242 G+ P+E + ++ L E+ V+++EHDM+ + SI+ + V+++G+ LA+G + I+ Sbjct: 193 GMTPQEVEKTAEILTSLSKEN--AVVVVEHDMEFIRSIASKVTVLHEGSVLAEGNMDAIQ 250 Query: 243 DNPDVIKAYLGE 254 +N V K YLGE Sbjct: 251 NNEKVRKVYLGE 262 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: 171 Number of extensions: 10 Number of successful extensions: 4 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: 262 Length adjustment: 24 Effective length of query: 231 Effective length of database: 238 Effective search space: 54978 Effective search space used: 54978 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 Apr 09 2024. 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