Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 120 bits (301), Expect = 5e-32 Identities = 87/300 (29%), Positives = 147/300 (49%), Gaps = 13/300 (4%) Query: 54 TVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAA 113 +V ++++ L P F L ++ +T + L AL +++ + G+D+S A+ Sbjct: 21 SVWVLLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAV-- 78 Query: 114 LTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYR 173 LT+ G+ A+ ++ L L L G+ G++NG LV L+ P + T+GT + + Sbjct: 79 LTLCGVVLAMVMVATES-LPLALGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQ 137 Query: 174 GLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLNR 233 GL L I + IPL + L LP+ + A+ + WLL Sbjct: 138 GLALVATDGQSVTGIGEA------IPLIY--AGQLLGVPLPIWIAAVFYG--LFHWLLYH 187 Query: 234 TMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVG 293 T G V+A+GG+ + G + + V+ G++AG+A +L + +P +G Sbjct: 188 TRFGAYVFALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIG 247 Query: 294 SELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFILL 353 E D IAAV +GG G G + GT+LGV+ V ++++ L LVGVPS+ Q IG +L+ Sbjct: 248 LEFDAIAAVAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLV 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: 271 Number of extensions: 19 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: 318 Length adjustment: 28 Effective length of query: 336 Effective length of database: 290 Effective search space: 97440 Effective search space used: 97440 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