Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 187 bits (476), Expect = 2e-52 Identities = 96/306 (31%), Positives = 171/306 (55%) Query: 31 QQITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDL 90 + I E L+V+ +++ SL F S+ N + + + IG+ + M + S + D+ Sbjct: 22 RHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDV 81 Query: 91 SVGSTVAFAGVLCAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATM 150 SVG VAF V A +L +A + + G ++G + G + + + + TL Sbjct: 82 SVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLW 141 Query: 151 EIVRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRN 210 +RG+G +++ V + + + G F GV + + ++ F +F + +T +GR+ Sbjct: 142 SALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAFGRS 201 Query: 211 TLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVI 270 A+GGN A++L GINV R R+ IF + G + A+ G++LA+R+ SG AA G E +VI Sbjct: 202 VFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVI 261 Query: 271 SACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQ 330 +A V+GG +L GGR ++ G ++GVL++ + N + L+ I++F+Q +VRG I++ AVL + Sbjct: 262 AAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANI 321 Query: 331 LKNRGS 336 L + S Sbjct: 322 LLTQRS 327 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: 293 Number of extensions: 15 Number of successful extensions: 1 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: 332 Length adjustment: 28 Effective length of query: 310 Effective length of database: 304 Effective search space: 94240 Effective search space used: 94240 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