Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 117 bits (292), Expect = 6e-31 Identities = 94/309 (30%), Positives = 150/309 (48%), Gaps = 31/309 (10%) Query: 57 LIVVTCLIVG--AINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVS------F 108 LI I+G NP+F +++ S+ + + ALG V+ SG +D+S F Sbjct: 19 LIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMMSF 78 Query: 109 TAIAALTMY---GITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVT 165 + I L ++ G T A+ A FA+ L GAL G ++G LK SLIVT Sbjct: 79 STIVVLDLHDKLGPTLAI-----PAMFAMTLCLGALIGFLVGY--------LKLNSLIVT 125 Query: 166 IGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAV 225 +G GL LT+ G +MD + +F G + +L +A A Sbjct: 126 LGMLSAIHGLTLTYSGGK-------NMDIADKEGTWFAIFGQGNILGIQTPILIFIALAA 178 Query: 226 VTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRL 285 + +L +T GR VYA+GG+ A G + + + + AG++ S + Sbjct: 179 LLGIILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMG 238 Query: 286 ANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKV 345 + G EL+V+AAVILGGA + GG+GT+ T++GV+++ I++ L+LVG+ + Q V Sbjct: 239 SQNTVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYV 298 Query: 346 IIGAFILLA 354 + I+LA Sbjct: 299 VTWIIIILA 307 Lambda K H 0.328 0.141 0.426 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: 267 Number of extensions: 16 Number of successful extensions: 5 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: 364 Length of database: 324 Length adjustment: 29 Effective length of query: 335 Effective length of database: 295 Effective search space: 98825 Effective search space used: 98825 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: 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