Align Trehalose transport system permease protein SugB (characterized)
to candidate BPHYT_RS33285 BPHYT_RS33285 sugar ABC transporter permease
Query= SwissProt::P9WG01 (274 letters) >FitnessBrowser__BFirm:BPHYT_RS33285 Length = 269 Score = 130 bits (327), Expect = 3e-35 Identities = 85/272 (31%), Positives = 139/272 (51%), Gaps = 8/272 (2%) Query: 5 RATYW---AVLDTLVVGYALLPVLWIFSLSLKPTS-TVKDGKLIPSTVTFDNYRGIFRGD 60 R+ W AVL T+ + +AL+P+ W+ S+SL+ T+ + P VTFDNY+ IF Sbjct: 2 RSNRWMRVAVL-TVYILFALIPLYWMLSISLRTNEETMSAFAIWPHHVTFDNYKVIFTDP 60 Query: 61 LFSSALINSIGIGLITTVIAVVLGAMAAYAVARLEFPGKRLLIGAALLITMFPSISLVTP 120 + INSI L+ TV++V++ AAYA +R F G + + L M P + P Sbjct: 61 SWYWGYINSIIYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLLP 120 Query: 121 LFNIERAIGLFDTWPGLILPYITFALPLAIYTLSAFFREIPWDLEKAAKMDGATPGQAFR 180 F + ++GL DT+ + L ++ F +PLA++ L F +P ++++ A +DG T F Sbjct: 121 FFQLYSSVGLMDTYIAVALAHMLFNVPLAVWILEGFMSGVPREIDETAYIDGYTFPAFFI 180 Query: 181 KVIVPLAAPGLVTAAILVFIFAWNDLLLALSLTATKAAITAPVAIANFTGSSQFEEPTGS 240 K+ +PL G+ A F+F+W +LLLA +LT A P+A S G Sbjct: 181 KIFLPLIKSGVGVTAFFCFMFSWVELLLARTLTTVNA---KPIAAVMTRTVSAAGMDWGV 237 Query: 241 IAAGAIVITIPIIVFVLIFQRRIVAGLTSGAV 272 ++A ++ +P + + + I G G V Sbjct: 238 LSAAGVLTIVPGALVIYFVRNYIAKGFAMGRV 269 Lambda K H 0.327 0.141 0.418 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: 219 Number of extensions: 14 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: 274 Length of database: 269 Length adjustment: 25 Effective length of query: 249 Effective length of database: 244 Effective search space: 60756 Effective search space used: 60756 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: 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