Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_008507473.1 BIBO1_RS12225 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000182725.1:WP_008507473.1 Length = 371 Score = 303 bits (775), Expect = 7e-87 Identities = 156/359 (43%), Positives = 231/359 (64%), Gaps = 3/359 (0%) Query: 11 LFAAMAIAGFASYSMAA-DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69 LF+ +A+A ++ +A + + + PVTGP A YG + GA AI+++N AGG+NG Sbjct: 5 LFSGVALAAMIAFGGSAWADVLVGIGIPVTGPNAVYGAQIQKGAEAAIKEVNDAGGINGE 64 Query: 70 QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129 ++ I DD DPKQ ++VANK DGVKFV+GH S T PA+ +Y + G+L I+P AT Sbjct: 65 KIAITIGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVTIPASQVYAENGILEISPGAT 124 Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189 P+ T +G FRT G D+ QG VAG++I + +KD IAV+HDK YG+G+A E KK + Sbjct: 125 NPQYTEQGLWNTFRTCGRDDQQGTVAGQYIFDHFKDAKIAVIHDKTPYGQGLADETKKKL 184 Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249 + G K ++EG+N G+KDF+ALI+KLK+AGV VY+GG HPE GL++RQ GL A+F Sbjct: 185 NELGTKEVLYEGVNVGEKDFSALIAKLKQAGVNVVYWGGLHPEAGLIIRQMADQGLKAQF 244 Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYS 309 + +G+ ++E+ +IAG A EG L T +P N L+ F+ +P + L +Y+ Sbjct: 245 ISGDGIVSNELASIAGPAVEGTLNTFGPDPRNNPDNAELVKKFRDAGFEPEA-YTLYSYA 303 Query: 310 AVTVIAKGIEKAGEADPEKVAEALR-ANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDA 367 AV +A+ + AG DP++VA+A++ F+T G+L +DEKGD K + +Y+W K A Sbjct: 304 AVQSLAQAAKAAGSNDPQEVAKAMKEKGPFKTVLGDLSYDEKGDPKLPGYVMYKWEKGA 362 Lambda K H 0.316 0.133 0.377 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: 432 Number of extensions: 16 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: 373 Length of database: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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