Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate BWI76_RS00655 BWI76_RS00655 inner-membrane translocator
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Koxy:BWI76_RS00655 Length = 334 Score = 152 bits (384), Expect = 1e-41 Identities = 100/312 (32%), Positives = 158/312 (50%), Gaps = 13/312 (4%) Query: 45 RLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGI 104 +L ++ E A+I++ +G+ P F L ++ + + + ALG ++VL + GI Sbjct: 4 QLLKHREALLAAVIILMIGAIGSRAPSFVSPGNLVEMFNDTAILIILALGQMMVLLTKGI 63 Query: 105 DVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIV 164 D+S A ALT I + A +P P A +L L G+++GM+NGLLV RL P+++V Sbjct: 64 DLSMAANLALTGM-IVALLNAHYPGIPVAALLALATLLGLLMGMINGLLVWRLGIPAIVV 122 Query: 165 TIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFG--RIPLFFYHTADGLRAVLPVSVLALVA 222 T+GT +YRG++ + + S D G R L LP+ +A Sbjct: 123 TLGTMSIYRGIIFLLSDGGWVNSHQMSADFLGLPRASLLG----------LPLLSWCAIA 172 Query: 223 AAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSN 282 A ++ + L + GRA+Y GG+ A G N + F +G LAG G L +S Sbjct: 173 ALLLVGYFLRYSRTGRALYTAGGNATAAYYTGINAGKMQFVSFCLSGALAGFCGYLWISR 232 Query: 283 NRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTW 342 +A G EL V+AA ++GG GGTG V+G L G + + +I + L ++G+ W Sbjct: 233 FAVAYVDVANGFELQVVAACVIGGISTMGGTGRVLGCLCGALFLGVINNALPVIGISPFW 292 Query: 343 QKVIIGAFILLA 354 Q I GA I++A Sbjct: 293 QMAISGAVIVIA 304 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: 268 Number of extensions: 18 Number of successful extensions: 3 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: 334 Length adjustment: 29 Effective length of query: 335 Effective length of database: 305 Effective search space: 102175 Effective search space used: 102175 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