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_111608864.1 DK187_RS18825 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::P21629 (255 letters) >NCBI__GCF_003259225.1:WP_111608864.1 Length = 288 Score = 146 bits (368), Expect = 5e-40 Identities = 91/254 (35%), Positives = 139/254 (54%), Gaps = 16/254 (6%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 IL V GL + F G A+N +NL V + ++ +IG NGAGKTT+ + +TG Q G + Sbjct: 39 ILYVEGLNLSFDGFKALNNLNLYVNDGELRCLIGANGAGKTTLMDVITGKTQCDSGTVFF 98 Query: 65 -DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL---LVAQHRHLNTNFLAGLFKT 120 + +IA+ G+ R FQ +F+E T +NL L R L T Sbjct: 99 GQNHNLLNKDEAEIAQLGIGRKFQKPTVFEEQTVFDNLELSLKTDKRVLPT--------- 149 Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 F R ++ L+ + L + AG L++GQ++ LEI ++ PR+L++DEP Sbjct: 150 -LFSRLTPTQIDRIDEVLKTIGLAKHRFMLAGALSHGQKQWLEIGMLLVAEPRLLLIDEP 208 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 AG+ +ET+ L+ L E TV+++EHDM+ V SI+ + V++QG+ LA+GT Q Sbjct: 209 VAGMTAQETERTAELLTSLAGER--TVIVVEHDMEFVRSIARTVTVLHQGSVLAEGTMNQ 266 Query: 241 IRDNPDVIKAYLGE 254 I+ N DVI+ YLGE Sbjct: 267 IQSNKDVIEVYLGE 280 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: 177 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: 288 Length adjustment: 25 Effective length of query: 230 Effective length of database: 263 Effective search space: 60490 Effective search space used: 60490 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