Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_052892752.1 PATSB16_RS19085 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_001931675.1:WP_052892752.1 Length = 598 Score = 217 bits (552), Expect = 5e-61 Identities = 115/258 (44%), Positives = 164/258 (63%), Gaps = 10/258 (3%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 EV+L V K FGGL A++DV +K G++ GLIGPNGAGK+T FN++TG+ +G Sbjct: 340 EVILDVRAARKEFGGLVAVNDVSFQVKAGEIVGLIGPNGAGKSTTFNLVTGVLQATSGEI 399 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGL--------F 118 G+ + A E+ K GI RTFQ++RL M+ LENV +G H+R GL + Sbjct: 400 TFHGERIDKLASREIVKRGIGRTFQHVRLLPTMSVLENVAIGAHLRDRQGLRRRPQGGVW 459 Query: 119 GAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQL 178 +V R +AEEA + A ++ VG+G+ +A +L+ G QR LEIARALA DP L Sbjct: 460 SSVLRLD--RAEEAMLMHEAARQIERVGLGEHMYEEAGSLALGQQRILEIARALACDPTL 517 Query: 179 IALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAE 238 + LDEPAAG+ EK L EL+ ++ ++ ++LL+EHD+ VM L D + V+++G +IAE Sbjct: 518 LLLDEPAAGLRYKEKQALAELLRKLSDEGMSVLLVEHDMDFVMNLTDHLVVMEFGTKIAE 577 Query: 239 GNPAEVQKNEKVIEAYLG 256 G P +VQK+ V+EAYLG Sbjct: 578 GLPEDVQKDPAVLEAYLG 595 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: 401 Number of extensions: 19 Number of successful extensions: 2 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: 598 Length adjustment: 31 Effective length of query: 229 Effective length of database: 567 Effective search space: 129843 Effective search space used: 129843 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