Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_001484605.1:WP_058929663.1 Length = 345 Score = 167 bits (422), Expect = 4e-46 Identities = 91/253 (35%), Positives = 147/253 (58%), Gaps = 1/253 (0%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 K + ++ +++ FGG+ A+ + I R ++ LIGPNGAGKTT FN++TG P++ Sbjct: 33 KKRDPIVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNS 92 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123 G ++ G + ++VA+ G+ RTFQ ++ ++T +EN+ +G + G L A+F+ Sbjct: 93 GKWQFEGNSLAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKALFK 152 Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183 + E I +A LL+ + D A +LS G ++ LE+AR+L P+L+ LDE Sbjct: 153 GL-WGGREKEITAQANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDE 211 Query: 184 PAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243 P AG+N L + I ++ + T+L +EHD+ +V + D V V+ GK +AEG P E Sbjct: 212 PMAGVNPALTQSLLDHIKNLKAEGMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGE 271 Query: 244 VQKNEKVIEAYLG 256 V KN VI+AYLG Sbjct: 272 VMKNPAVIDAYLG 284 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: 241 Number of extensions: 16 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: 345 Length adjustment: 27 Effective length of query: 233 Effective length of database: 318 Effective search space: 74094 Effective search space used: 74094 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: 48 (23.1 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