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_011914281.1 PST_RS16095 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000013785.1:WP_011914281.1 Length = 258 Score = 170 bits (431), Expect = 2e-47 Identities = 100/249 (40%), Positives = 149/249 (59%), Gaps = 7/249 (2%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +LE GLT F G AV+ V+LKV + + ++IGPNGAGKTTVFN LT F PT G I Sbjct: 6 VLETRGLTKEFRGFTAVDSVDLKVRQGHIHALIGPNGAGKTTVFNLLTKFLTPTRGEILY 65 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 G+ I + ++IAR G+VR+FQ +F M+ +EN+ VA + + +F +K+ Sbjct: 66 RGKNITSMKTNEIARLGLVRSFQISAVFGHMSVLENVRVALQQKMGNSF--HFWKS---E 120 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 RS RE + L EV+L FA A L YG++R LE+A + P +L+LDEP G+ Sbjct: 121 RSLRELDDKVMQLLAEVDLQAFAQTLAVELPYGRKRALELATTLALDPIVLLLDEPTQGM 180 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 ++ D + L+ K + N TVL++EH++ +V + D I V+ +G+ LA+G + + N Sbjct: 181 GGEDVDMVVELVRKAAA--NRTVLMVEHNLSVVSRLCDRITVLARGSVLAEGDYDSVSAN 238 Query: 245 PDVIKAYLG 253 P V +AYLG Sbjct: 239 PQVREAYLG 247 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: 144 Number of extensions: 5 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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