Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 147 bits (370), Expect = 5e-40 Identities = 101/320 (31%), Positives = 164/320 (51%), Gaps = 9/320 (2%) Query: 45 RLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGI 104 RL + E +A I++ ++ + P F + L + + + + L A+G ++V+ + I Sbjct: 4 RLIASRETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCI 63 Query: 105 DVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIV 164 D+S A ALT ++ A P P +IL G +LGM NGLLV +L+ P ++V Sbjct: 64 DLSVAANLALTGMVVSMVNVAA-PGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVV 122 Query: 165 TIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAA 224 T+GT ++RG++ I ++N F P GL + +++LA++ Sbjct: 123 TLGTMTIFRGIIF-LISDGKWVNSHEMSPAFKAFPRA---ELLGLPVLSWIAILAVILFT 178 Query: 225 VVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNR 284 +V + RT +GRA YA GG+ A G ++ + F +G LAG+ G L VS Sbjct: 179 IV----MTRTTLGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFA 234 Query: 285 LANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQK 344 ++ G ELDV+AA ++GG I GG GTV G LLG + + +IK+ L +V + WQ Sbjct: 235 VSYVDIAGGFELDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQL 294 Query: 345 VIIGAFILLAGTLFALQRKR 364 I G I++A L A ++ Sbjct: 295 AISGGAIIIAVALNAQANRK 314 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: 285 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: 364 Length of database: 327 Length adjustment: 29 Effective length of query: 335 Effective length of database: 298 Effective search space: 99830 Effective search space used: 99830 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