Align Sugar ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS17835 BWI76_RS17835 sugar ABC transporter permease
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Koxy:BWI76_RS17835 Length = 279 Score = 133 bits (334), Expect = 5e-36 Identities = 87/287 (30%), Positives = 142/287 (49%), Gaps = 19/287 (6%) Query: 5 LLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTS-----LKPSSALFEVSYWIENPDFSNY 59 +L K G WC+ +LL+ V PF+ + T+ +KP E+ W F N+ Sbjct: 1 MLSKRWDTAGRWCIYALLLIVFVGPFWGIVATAFSGAPVKPG----ELLAWPNQFSFENF 56 Query: 60 AAVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFP 119 + + NS++V L + +S AAYAL R KFRG V +++L M P Sbjct: 57 IFAWMDIGVWQYLLNSILVVFFGTVLQVSVSALAAYALARKKFRGVALVSLVILSTMMLP 116 Query: 120 QVAVLSGLFEVIR------ALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEA 173 + + L+ +I LYN+ +IL + F+++VLT FM +P ELEEA Sbjct: 117 EEVIAIPLYMIINWRLPFIDASLYNSYLGMILP--VVGWAFSIFVLTEFMSAIPKELEEA 174 Query: 174 AIMDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIAL 233 A +DGA+ W V+LPL+ PAL T FI W+++L L D+ T+PV + Sbjct: 175 ARIDGANEWQIFFHVILPLVKPALGTVVTFGFIMIWDQYLLPLIVVNQDSLNTIPVILGT 234 Query: 234 ISGGSPHELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG 280 + + + + +A +++ +P +I+ L Q+ G+ +GA+KG Sbjct: 235 LR--TDESITPNIFIAITLLAMLPSIIVYLGLQKHFNRGIMSGAVKG 279 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: 204 Number of extensions: 12 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: 279 Length adjustment: 26 Effective length of query: 254 Effective length of database: 253 Effective search space: 64262 Effective search space used: 64262 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