Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate CCNA_03714 CCNA_03714 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Caulo:CCNA_03714 Length = 252 Score = 143 bits (360), Expect = 4e-39 Identities = 84/247 (34%), Positives = 136/247 (55%), Gaps = 15/247 (6%) Query: 6 LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65 L + V K FG + V + ++RG++ GL+GPNGAGKTT F ++TGL D G LD Sbjct: 11 LFVDSVGKSFGDRPVVKNVSLRLKRGEVAGLLGPNGAGKTTCFYMVTGLIAADYGAIYLD 70 Query: 66 GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125 G+ + + A+ G+ Q +F MTV +NVM +R + + ARE Sbjct: 71 GENITAQPMFQRARLGVGYLPQEASIFRGMTVEQNVMAVVEMRERDP--------RKARE 122 Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185 + +I E+ + I K A LS G++RR+EIARALA++P + LDEP AG++ Sbjct: 123 QVTSILEELR-------ITHIRKSPAVALSGGERRRVEIARALASEPSFMLLDEPFAGID 175 Query: 186 ATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNPA 245 +RE++ ++ G IL+ +H+V+ + + +R +++ G+ + EG P ++ +NP Sbjct: 176 PLAIADIREVIGYLKGRGIGILITDHNVRETLDIIDRASIIHAGEVLFEGSPREIVENPE 235 Query: 246 VIEAYLG 252 V YLG Sbjct: 236 VKRVYLG 242 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: 179 Number of extensions: 11 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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