Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BWI76_RS15325 BWI76_RS15325 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Koxy:BWI76_RS15325 Length = 265 Score = 124 bits (311), Expect = 2e-33 Identities = 87/261 (33%), Positives = 135/261 (51%), Gaps = 19/261 (7%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 D +L++E +++ F G A+ + S + G++ +IGPNGAGKTT+ + ITG +P G Sbjct: 22 DPVLQLEEINVNFDGFQALTNLSLQIGVGELRCVIGPNGAGKTTLMDVITGKTRPQSGRA 81 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKLMKASGY 130 ++Q L L I ++ + R FQ +F LTV ENL L + +K + AS Sbjct: 82 LYDQSVD----LTTLDPIAIARQG-IGRKFQKPTVFEALTVAENLELAMKGDKSVWASLR 136 Query: 131 TILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190 L +E + L R E+ PAG L +G ++ LEI + P Sbjct: 137 ARLN----SEQADRISETLRLLRLEGERY-------RPAGLLSHGQKQFLEIGMLLVQEP 185 Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250 LL LDEPAAG+ E+ L +++ + S++++EHDM V I+D V VL GQ Sbjct: 186 HLLLLDEPAAGMTDAETEYTAELFRTLAGQ--HSLMVVEHDMGFVETIADRVTVLHQGQV 243 Query: 251 ISDGTPDHVKNDPRVIAAYLG 271 +++G+ VK + +VI YLG Sbjct: 244 LAEGSLREVKANEQVIEVYLG 264 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: 164 Number of extensions: 7 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: 265 Length adjustment: 25 Effective length of query: 267 Effective length of database: 240 Effective search space: 64080 Effective search space used: 64080 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: 47 (22.7 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