Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 199 bits (506), Expect = 1e-55 Identities = 115/260 (44%), Positives = 156/260 (60%), Gaps = 12/260 (4%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 + LL V+ +FGGL+A+ND SFE K G I LIGPNGAGK+T FN +TG + T G I Sbjct: 344 EPLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAI 403 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 TF + ++ L I K + RTFQ+++L G+TVLEN+ + H + + Sbjct: 404 TFRGER-----IDALNSREIVKRG-IGRTFQHVKLLPGMTVLENVAIGGHLRGRAGVWRS 457 Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191 + L G + A A ++ R LE + D AG L G QR LEIARA+C P Sbjct: 458 VARLNGAEEGRLMAEAARQIRRVGLE-----EHMYDEAGSLALGKQRILEIARALCCDPT 512 Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251 LL LDEPAAGL +E L LL+ +R E G S+LL+EHDM VM ++D +VV+E+G +I Sbjct: 513 LLLLDEPAAGLRYQEKQQLATLLRKLR-EEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRI 571 Query: 252 SDGTPDHVKNDPRVIAAYLG 271 ++G P V+NDP V+ AYLG Sbjct: 572 AEGLPQDVQNDPAVLEAYLG 591 Lambda K H 0.318 0.136 0.386 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: 402 Number of extensions: 24 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: 292 Length of database: 594 Length adjustment: 31 Effective length of query: 261 Effective length of database: 563 Effective search space: 146943 Effective search space used: 146943 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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