Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 17516 b3455 leucine/isoleucine/valine transporter subunit (NCBI)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Keio:17516 Length = 255 Score = 125 bits (313), Expect = 1e-33 Identities = 79/251 (31%), Positives = 134/251 (53%), Gaps = 18/251 (7%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 LL V GL + +GG+ AV V+ E+ E+VSLIG NGAGKTT +TG G I Sbjct: 5 LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD------- 121 + ++G + + G+V + +F MT+ ENL + + ++ K G+ + Sbjct: 65 RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQH-QQLKTGLFSGLLKTPSF 123 Query: 122 -------IEKMFTIFPR--LRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMG 172 +++ T R L E ++ A ++ G+Q+ L + R +++QP++L+LDEP+ G Sbjct: 124 RRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAG 183 Query: 173 LSPIMVDKIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLN 231 L+P ++ E++ ++ TI+L+E + + I+DR YV+ G G +Q+ N Sbjct: 184 LNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRN 243 Query: 232 DPKVRAAYLGE 242 +P V AYLGE Sbjct: 244 NPDVIRAYLGE 254 Lambda K H 0.317 0.136 0.373 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: 144 Number of extensions: 8 Number of successful extensions: 3 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: 242 Length of database: 255 Length adjustment: 24 Effective length of query: 218 Effective length of database: 231 Effective search space: 50358 Effective search space used: 50358 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: 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