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_087412571.1 BUB52_RS05180 phosphate ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_900129655.1:WP_087412571.1 Length = 250 Score = 98.6 bits (244), Expect = 1e-25 Identities = 77/251 (30%), Positives = 130/251 (51%), Gaps = 21/251 (8%) Query: 6 LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTT---VFNCLTGFYQPTG--G 60 +E + +G A+ G+++ + EK VV+ IGP+G GK+T + N + T G Sbjct: 4 IETRDVNFWYGDFHALKGISMDIAEKSVVAFIGPSGCGKSTFLRLLNRMNDLIPDTRLTG 63 Query: 61 LIRLDGEEI--QGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLF 118 I +DG++I +G+ ++ RK V FQ F + + EN VA +N G+ Sbjct: 64 EILIDGQDIYKKGVQVDEL-RKNVGMVFQRPNPFPK-SIFEN--VAYGLRVN-----GVT 114 Query: 119 KTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLD 178 RR E ++ AA W E + + SA L+ GQQ+RL IAR M P +L++D Sbjct: 115 DNAFIRRRVEETLKGAALWDE---VKDKLKVSAYALSGGQQQRLCIARAMAVSPSVLLMD 171 Query: 179 EPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTP 238 EPA+ L+P T ++ LI +L+ ++ T++++ H+M+ +SD G + G Sbjct: 172 EPASALDPISTAKVEELIHELKKQY--TIVIVTHNMQQAARVSDSTAFFYMGEMVEFGDT 229 Query: 239 EQIRDNPDVIK 249 ++I NPD ++ Sbjct: 230 KKIFTNPDKVE 240 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: 134 Number of extensions: 10 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: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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: 46 (22.3 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