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 SM_b20785 SM_b20785 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Smeli:SM_b20785 Length = 254 Score = 160 bits (406), Expect = 2e-44 Identities = 95/251 (37%), Positives = 137/251 (54%), Gaps = 11/251 (4%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 I EV L FGGL N V+L + V++IGPNGAGKTT N +TG +P G +R+ Sbjct: 4 IFEVRNLKRSFGGLAVTNDVSLSMAPGDRVALIGPNGAGKTTFVNLVTGNLKPDAGEVRI 63 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVEN--LLVAQHRHLNTNFLAGLFKTPA 122 GE + + R+G+VR+FQ RLF++MT E+ L V Q P Sbjct: 64 GGETVTNVDAIGRVRRGLVRSFQVTRLFQDMTPAEHVALAVLQRDGRAGRMFGNFLAMPG 123 Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 M A L ++ L + A+R +AYGQQR LEIA + +PR+L+LDEPAA Sbjct: 124 -------VMAEAGSLLGKLGLRDLAHRPVREIAYGQQRLLEIAVALALKPRVLLLDEPAA 176 Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242 G+ +T ++ +A L + + VL+IEHDM LV + ++V+ G + DG+P + Sbjct: 177 GVPQSDTGRIEQALADLPDD--LAVLMIEHDMDLVFRFAKRVIVLAAGTVIFDGSPADVT 234 Query: 243 DNPDVIKAYLG 253 +P V +AYLG Sbjct: 235 KDPRVREAYLG 245 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: 165 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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 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