Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS14605 BWI76_RS14605 ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Koxy:BWI76_RS14605 Length = 336 Score = 176 bits (446), Expect = 8e-49 Identities = 104/289 (35%), Positives = 166/289 (57%), Gaps = 14/289 (4%) Query: 52 VIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAPAVGAML 111 V+ + I+ +FLT N ++++ SA L +V A +L++ TG DLS+ ST+ + A+ A+ Sbjct: 39 VVFSLITSNFLTGTNWLNIIRQSAPLLIVATAMTLVITTGGIDLSVGSTLALVGALSAI- 97 Query: 112 VMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLV 171 A +G+ WP LL +++G ++G INGF + + AFIVTLA L V+RG+ + Sbjct: 98 ----ALNNWGLPWPVV--LLGGLLLGGIVGAINGFFIAYEGIPAFIVTLATLAVVRGIAL 151 Query: 172 GATKGGTLFDMPTSFFALATTI----VLGLPLSVWLAAAAFAIAAFMLRYHRLGRALYAI 227 T+G + +P +L T I V+G+P+ + I +L + R GR + AI Sbjct: 152 LVTQG---YSIPVPADSLFTFIGRAWVVGIPMPALIGIMILLIGHIVLNHMRFGRYVTAI 208 Query: 228 GGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTVFAAAV 287 G N E AR +GI + +T V+++ + A++ G+I+T +G+ ++NQG G V AA V Sbjct: 209 GANAEGARRSGINTKAVTMKVYIISGMAAALAGMIITARLGSGSSNQGEGFELQVIAAVV 268 Query: 288 IGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIIL 336 +G SL GG GT+ G L G L + V+QN L L+ + F+ Q G IIL Sbjct: 269 LGSTSLFGGFGTIIGTLLGALSIAVIQNGLILSHISPFYTQIATGTIIL 317 Lambda K H 0.326 0.140 0.397 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: 299 Number of extensions: 14 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: 351 Length of database: 336 Length adjustment: 29 Effective length of query: 322 Effective length of database: 307 Effective search space: 98854 Effective search space used: 98854 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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