Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_061534737.1 CAter10_RS19525 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_001584165.1:WP_061534737.1 Length = 601 Score = 205 bits (522), Expect = 2e-57 Identities = 111/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 +VVL++ K FGGL A++D+ ++ GQ+ GLIGPNGAGK+T FN++TG+ +GT Sbjct: 342 DVVLEIENARKEFGGLVAVNDISFNVRAGQIVGLIGPNGAGKSTMFNLVTGVLPLTSGTI 401 Query: 67 ---------ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTG--- 114 +++G P ++ GIARTFQ++RL MT LENV +G H+R Sbjct: 402 RFRAQRELQQISGLPSR-----QIVARGIARTFQHVRLMPAMTVLENVAIGAHLRGSHND 456 Query: 115 -SGLFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALA 173 +G+ ++ R + EE A+ A++ L+ VG+G +A +L+ G QR LEIARAL Sbjct: 457 VNGIAVSLLRLN--RNEERALLFEAKQQLERVGLGHLLYEEAGSLALGQQRILEIARALC 514 Query: 174 TDPQLIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYG 233 DP L+ LDEPAAG+ EK L EL+ +++ + +ILL+EHD+ VM L D++ V+++G Sbjct: 515 CDPTLLLLDEPAAGLRYQEKQALAELLRKLKAEGMSILLVEHDMDFVMNLTDQLVVMEFG 574 Query: 234 KQIAEGNPAEVQKNEKVIEAYLG 256 +IA+G PAE+Q++ V+EAYLG Sbjct: 575 TKIAQGLPAEIQQDPAVLEAYLG 597 Lambda K H 0.319 0.137 0.384 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: 377 Number of extensions: 19 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: 260 Length of database: 601 Length adjustment: 31 Effective length of query: 229 Effective length of database: 570 Effective search space: 130530 Effective search space used: 130530 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 (21.7 bits) S2: 50 (23.9 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