Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 157 bits (397), Expect = 4e-43 Identities = 96/300 (32%), Positives = 153/300 (51%), Gaps = 8/300 (2%) Query: 39 RELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLE 98 RE L+ A+ LL+ + A P+F+ +NL V ++ L L+ + + +++LT DLS+ Sbjct: 9 RETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVA 68 Query: 99 STVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIV 158 + + + V +M+ + A P L + +G ++G NG LV +L++ +V Sbjct: 69 ANLALTGMVVSMVNVAAPGL------PIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVV 122 Query: 159 TLAMLIVLRGM--LVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLR 216 TL + + RG+ L+ K +M +F A +LGLP+ W+A A + ++ Sbjct: 123 TLGTMTIFRGIIFLISDGKWVNSHEMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMT 182 Query: 217 YHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGN 276 LGRA YA GGNP AA AGI V + + F + LA + G + + Sbjct: 183 RTTLGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAG 242 Query: 277 GMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIIL 336 G V AA VIGG+S+ GG GT+ GAL G L LG+++N L + + FW AI G I+ Sbjct: 243 GFELDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAII 302 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: 263 Number of extensions: 19 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: 351 Length of database: 327 Length adjustment: 28 Effective length of query: 323 Effective length of database: 299 Effective search space: 96577 Effective search space used: 96577 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