Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 152 bits (384), Expect = 1e-41 Identities = 96/300 (32%), Positives = 155/300 (51%), Gaps = 8/300 (2%) Query: 46 ALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAP 105 AL LL ++ A S +FLT N+++VL ++ L L+ +L++LTG DLS+ + V ++ Sbjct: 23 ALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVAMSA 82 Query: 106 AVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIV 165 V A ++ S G+ AGL GA+IG NG LV LR+ FI T ML V Sbjct: 83 CVAATVMKATGSTMLGV----GAGL----GTGALIGLANGLLVAMLRIPPFIATYGMLWV 134 Query: 166 LRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALY 225 L G+ G T+ P +F A+ + + G+P+ V+L M + G+ +Y Sbjct: 135 LHGVTYWFMAGETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEIY 194 Query: 226 AIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTVFAA 285 AIG NP AAR +G+ V R V+++ +A + L+ + + + G + AA Sbjct: 195 AIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIAA 254 Query: 286 AVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMVARLA 345 +IGG SL GG G + G L G ++L +V N + L V + W + G I++ ++ + L+ Sbjct: 255 VLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLDTLS 314 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: 257 Number of extensions: 17 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 323 Effective length of database: 294 Effective search space: 94962 Effective search space used: 94962 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