Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate 3608606 Dshi_1999 inner-membrane translocator (RefSeq)
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Dino:3608606 Length = 435 Score = 107 bits (267), Expect = 6e-28 Identities = 54/155 (34%), Positives = 94/155 (60%) Query: 177 GGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIF 236 G +G+ + + + + V+ +T +GR A GGNP+A+ L+GIN V +F Sbjct: 272 GYTEVYGIPYSVLLLIAVAVAMTVIAKKTRFGRYIFATGGNPDAAELSGINTRMLTVKVF 331 Query: 237 LIQGAVTALAGVILASRITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLI 296 + GA+ A++ ++ ++R+T+ + EL VI+A V+GG +L GG TI G ++G LI Sbjct: 332 ALMGALCAISAIVASARLTNHSNDIGTLDELRVIAAAVIGGTALAGGIGTIYGAILGALI 391 Query: 297 MGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQL 331 M ++++ M ++ +DA Q +V G +L+AAVL+D L Sbjct: 392 MQSLQSGMAMVGVDAPLQNIVVGTVLVAAVLIDIL 426 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: 338 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 338 Length of database: 435 Length adjustment: 30 Effective length of query: 308 Effective length of database: 405 Effective search space: 124740 Effective search space used: 124740 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: 50 (23.9 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