Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085771912.1 B1812_RS12645 LPS export ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002117405.1:WP_085771912.1 Length = 288 Score = 140 bits (352), Expect = 4e-38 Identities = 85/251 (33%), Positives = 135/251 (53%), Gaps = 15/251 (5%) Query: 2 SQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGT 61 S+ +L I +++K + + + V + + RG+ GL+GPNGAGKTT F +ITGL +PD+G Sbjct: 48 SEGVLAIHNLAKSYKTRRVVEDVSLHVRRGEAVGLLGPNGAGKTTVFYMITGLVKPDSGR 107 Query: 62 FELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHK 121 LDG +P + A+ GI Q + +F +TV EN++ V V K Sbjct: 108 ITLDGYDVTPLPMYRRARLGIGYLPQEMSVFRGLTVEENILA---------VLEIVEPDK 158 Query: 122 AAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPA 181 R E+ LL+ + K A +S G++RR EIARA+A P + LDEP Sbjct: 159 KKRAEQL------DGLLEEFRLAHLRKTPAIAVSGGERRRCEIARAIAGRPSFMLLDEPF 212 Query: 182 AGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241 AG++ G+++L+ ++ G +L+ +H V+ +GL +R ++ G + EG PA++ Sbjct: 213 AGIDPIAIGGIQDLVRHLKQRGIGVLITDHSVRETLGLTDRAYIIYNGHVLTEGAPAEIV 272 Query: 242 KNPAVIEAYLG 252 NP V YLG Sbjct: 273 ANPDVRRIYLG 283 Lambda K H 0.320 0.138 0.394 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: 194 Number of extensions: 13 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: 255 Length of database: 288 Length adjustment: 25 Effective length of query: 230 Effective length of database: 263 Effective search space: 60490 Effective search space used: 60490 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: 47 (22.7 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