Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate BPHYT_RS25785 BPHYT_RS25785 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS25785 Length = 352 Score = 643 bits (1658), Expect = 0.0 Identities = 331/363 (91%), Positives = 341/363 (93%), Gaps = 12/363 (3%) Query: 1 MNSRIPSRTDPRTDPPSASPMKQTMTTPTVVEIAPSVEAPGLRTRLARNPEWFTVALIVV 60 MNSRI SR + QTMTTPTVVE+AP V+ P LRT+LARNPEWFT+ALI V Sbjct: 1 MNSRIDSR------------LNQTMTTPTVVEVAPEVKPPSLRTKLARNPEWFTLALIAV 48 Query: 61 TCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGIT 120 TCLIVGAINPRFFQ ATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGIT Sbjct: 49 TCLIVGAINPRFFQLATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGIT 108 Query: 121 KAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFI 180 KAVFAWWPDAPFALIL+TGALGGVVLG+VNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFI Sbjct: 109 KAVFAWWPDAPFALILITGALGGVVLGIVNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFI 168 Query: 181 GTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLNRTMMGRAV 240 GTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSV+ALVAAAVVTWWLLNRTMMGR V Sbjct: 169 GTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVVALVAAAVVTWWLLNRTMMGRGV 228 Query: 241 YAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVGSELDVIA 300 YAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVG+ELDVIA Sbjct: 229 YAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVGTELDVIA 288 Query: 301 AVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFILLAGTLFAL 360 AVILGGARITGGTGTV GTLLGVVLVTLI SVLILVGVPSTWQKVIIGAFIL+AGTLFAL Sbjct: 289 AVILGGARITGGTGTVAGTLLGVVLVTLINSVLILVGVPSTWQKVIIGAFILIAGTLFAL 348 Query: 361 QRK 363 QRK Sbjct: 349 QRK 351 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: 533 Number of extensions: 10 Number of successful extensions: 1 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: 352 Length adjustment: 29 Effective length of query: 335 Effective length of database: 323 Effective search space: 108205 Effective search space used: 108205 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