Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 207079 DVU1627 ABC transporter, ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >MicrobesOnline__882:207079 Length = 241 Score = 145 bits (367), Expect = 6e-40 Identities = 83/252 (32%), Positives = 142/252 (56%), Gaps = 21/252 (8%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +L+ D+ KRFG + + GV +++++G+I GL+GPNGAGKTT F ++TG+ +P G L Sbjct: 4 VLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGIVRL 63 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH---K 121 DG+ + HE A+ G++ Q +F +TV EN+ + + H Sbjct: 64 DGQDIADWPLHERARVGLSYLPQESSVFKRLTVRENLEI-------------ILEHTGLP 110 Query: 122 AAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPA 181 AAR+ +E+++ L+ GI A A HLS G++RRLEIAR + +P+ + LDEP Sbjct: 111 AARQ-----KERAEALMADFGIAHLASSRAMHLSGGERRRLEIARCMIREPKFVLLDEPF 165 Query: 182 AGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241 AG++ ++ L+ K++ G +L+ +H+V+ + +C+R ++ G+ I +G P + Sbjct: 166 AGIDPLAVGDIQGLIRKLRDRGIGVLISDHNVRETLTICDRAYLVHQGQVILDGTPEHIV 225 Query: 242 KNPAVIEAYLGA 253 + YLGA Sbjct: 226 GDEQARLVYLGA 237 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: 163 Number of extensions: 10 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: 241 Length adjustment: 24 Effective length of query: 231 Effective length of database: 217 Effective search space: 50127 Effective search space used: 50127 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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