Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS25825 BPHYT_RS25825 ABC transporter permease
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS25825 Length = 333 Score = 197 bits (501), Expect = 3e-55 Identities = 102/293 (34%), Positives = 172/293 (58%), Gaps = 2/293 (0%) Query: 36 YSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGST 95 Y+L F ++ S F SI+N L + + + +++ M F + +R DLSVGST Sbjct: 36 YALYAAFAILLVVFSFASPWFLSIDNFLNIGRQTALVSIIAIGMTFVIIARQIDLSVGST 95 Query: 96 VAFAGVLCAMVLNATGNTF-IAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVR 154 +A +G+ A+ + GN + I +A + G ++G +NG V + I + + TL T+ R Sbjct: 96 LALSGMSAALAMAYVGNNWVIGAIAGIGTGAIVGAINGIVTTRVNIPSFLVTLGTLSAAR 155 Query: 155 GLGFIVSHGQAVGVSSDTFIALGGLS-FFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLA 213 GL +V+ + V + +D+FI++ G FGV +PI TLL I ++L+ +V+GR A Sbjct: 156 GLALMVTTTKPVIIDNDSFISIFGEGDIFGVPVPIIWTLLAVIAGILLLHYSVFGRQIYA 215 Query: 214 IGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISAC 273 GGNP A+ +GIN R F++ G + LA ++L++R + +P+ QG EL+VI++ Sbjct: 216 AGGNPTAALYSGINTRRVTTLAFILTGMLAGLAALVLSARSHAARPDVVQGMELDVIASV 275 Query: 274 VLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAV 326 LGG SL GGR + G ++G LI+GT+ N + L+ + + Q +++G I++AAV Sbjct: 276 TLGGCSLFGGRGFVLGTLLGSLIIGTLNNGLVLLGVSSSLQLVIKGVIIVAAV 328 Lambda K H 0.326 0.139 0.396 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: 292 Number of extensions: 21 Number of successful extensions: 5 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: 338 Length of database: 333 Length adjustment: 28 Effective length of query: 310 Effective length of database: 305 Effective search space: 94550 Effective search space used: 94550 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 (21.7 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