Align Sugar ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_03745 H281DRAFT_03745 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Burk376:H281DRAFT_03745 Length = 283 Score = 162 bits (410), Expect = 8e-45 Identities = 97/284 (34%), Positives = 156/284 (54%), Gaps = 8/284 (2%) Query: 3 LRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEV-SYWIE-NPDFSNYA 60 + L KA L W + L++ +FPF + T+LKP+S +F + W+ + +SN+ Sbjct: 1 MTLSAKAKRSLWCWLALSPLVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFV 60 Query: 61 AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ 120 + A+F A+ NS V++L LAL +SL AAYAL R FRGRGT +L M Sbjct: 61 DMWQAANFGVALRNSTVISLLSTLLALAVSLPAAYALARFPFRGRGTYRQFLLVTQMLSP 120 Query: 121 VAVLSGLFEVIRAL-----GLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAI 175 + ++ GLF + + L ++ +I+SY F + F VW+L+++ +P +LEE+A Sbjct: 121 ILLVVGLFRLAAMIPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAW 180 Query: 176 MDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALIS 235 ++G + +V LPL PA+V T + FI AWNEF T + +T+ V + + Sbjct: 181 LEGCGRTKAVFKVFLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMV 240 Query: 236 GGSPHELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALK 279 G + + W L+MAA++ T+P+ I+ QR +V GL GA+K Sbjct: 241 AGK-YVVEWHLVMAATLCATLPVSIVFAWLQRYLVKGLALGAVK 283 Lambda K H 0.329 0.141 0.433 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: 207 Number of extensions: 15 Number of successful extensions: 4 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: 280 Length of database: 283 Length adjustment: 26 Effective length of query: 254 Effective length of database: 257 Effective search space: 65278 Effective search space used: 65278 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 (21.8 bits) S2: 47 (22.7 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