Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001484605.1:WP_058929663.1 Length = 345 Score = 155 bits (393), Expect = 9e-43 Identities = 106/282 (37%), Positives = 159/282 (56%), Gaps = 20/282 (7%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 D ++ E+++ FGG+ A++ E R ITALIGPNGAGKTT+FN +TGF P G Sbjct: 36 DPIVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKW 95 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKLMKASGY 130 F S L + +++ + V RTFQ ++ LTV+EN+ L + S Sbjct: 96 QFEGNS-----LAGISPYKVARMGMV-RTFQLTKVMGKLTVMENMRLGGSEQPGERLSKA 149 Query: 131 TILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190 GL G G K A+A L LEK L + DD A L G ++ LE+AR++ P Sbjct: 150 LFKGLWG-GREKEITAQANVL----LEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRP 204 Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250 +L+ LDEP AG+NP + +L +K+++AE G ++L +EHDM++V I+D VVV+ G+ Sbjct: 205 KLVMLDEPMAGVNPALTQSLLDHIKNLKAE-GMTVLFVEHDMNMVRHIADWVVVMAEGKI 263 Query: 251 ISDGTPDHVKNDPRVIAAYLGV-------EDEEVEEVIAAVE 285 +++G P V +P VI AYLG + E ++E+ A +E Sbjct: 264 VAEGPPGEVMKNPAVIDAYLGAHHDVDLGDTEGIKELAAELE 305 Lambda K H 0.318 0.136 0.386 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: 249 Number of extensions: 15 Number of successful extensions: 4 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: 292 Length of database: 345 Length adjustment: 27 Effective length of query: 265 Effective length of database: 318 Effective search space: 84270 Effective search space used: 84270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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