Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 15431 b1311 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__Keio:15431 Length = 293 Score = 147 bits (372), Expect = 2e-40 Identities = 90/287 (31%), Positives = 146/287 (50%), Gaps = 19/287 (6%) Query: 30 FAYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYYEILFDEKS 89 FA +L P+ + + + PM+ I +S L +L + + + F+G+ NY IL D Sbjct: 13 FALLLLAPSLLLLGGLVAWPMVSNIEISFL---RLPLNPNIESTFVGVSNYVRILSDP-- 67 Query: 90 LIRRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVPSYVV 149 GFW +L T YT +V + LG+ +AM NREF+ R R+ +++ +V PS + Sbjct: 68 ----GFWHSLWMTVWYTALVVAGSTVLGLAVAMFFNREFRLRKTARSLVILSYVTPSISL 123 Query: 150 GMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQIWAIIIP-TIWRGLPLSMILML 208 W +++ G++N + D+LH+ + P W + +++ IWR P + I L Sbjct: 124 VFAWKYMFNNGYGIVNYLGVDLLHLYEQAPLWFDNPGSSFVLVVLFAIWRYFPYAFISFL 183 Query: 209 AGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSMMFG 268 A LQ+I YEAA++DGAN WQ+F +TLP + P+LA V I Y F V ++ Sbjct: 184 AILQTIDKSLYEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLLTT 243 Query: 269 NGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVAL 315 D+L Y+ + F G AAA+ +V+F ++ V L Sbjct: 244 K--------VDILGVYLYKTAFAFNDLGK-AAAISVVLFIIIFAVIL 281 Lambda K H 0.330 0.145 0.468 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: 26 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: 327 Length of database: 293 Length adjustment: 27 Effective length of query: 300 Effective length of database: 266 Effective search space: 79800 Effective search space used: 79800 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: 48 (23.1 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