Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate HSERO_RS05085 HSERO_RS05085 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__HerbieS:HSERO_RS05085 Length = 347 Score = 460 bits (1184), Expect = e-134 Identities = 229/331 (69%), Positives = 274/331 (82%) Query: 34 APSVEAPGLRTRLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFAL 93 AP P L L +NP FT+ LIV+ L V INP FFQ A LFD++ + TT+ LFAL Sbjct: 17 APVQRRPSLAALLKKNPSAFTLLLIVLVVLTVALINPAFFQLAVLFDIVRACTTLGLFAL 76 Query: 94 GTLVVLASGGIDVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLL 153 G ++VLA+GGIDVSF AIAALTMY ITK V W+P+ A+IL+ GA+GG LG++NGLL Sbjct: 77 GVMIVLAAGGIDVSFAAIAALTMYSITKVVMTWFPETHIAVILLAGAVGGAGLGVLNGLL 136 Query: 154 VHRLKAPSLIVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVL 213 V LKAPSLIVTIGTQYLYRG+LLTF+GT FFMNIPH+MD FG++ L + TA+GL AVL Sbjct: 137 VDWLKAPSLIVTIGTQYLYRGILLTFVGTVFFMNIPHAMDSFGKLTLARHDTANGLHAVL 196 Query: 214 PVSVLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAG 273 P +VL LV A+V+TWWLLNRT+MGRAVYA+GGSLAIAERLGY LR++HLFVFGY G L+G Sbjct: 197 PATVLVLVLASVLTWWLLNRTLMGRAVYAVGGSLAIAERLGYKLRSVHLFVFGYAGFLSG 256 Query: 274 IAGILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVL 333 +AGI+HVS+ RLANPFDLVGSELDVIAAV+LGGARITGG G+V+GTLLGV+LVTLI +VL Sbjct: 257 LAGIVHVSSTRLANPFDLVGSELDVIAAVVLGGARITGGHGSVMGTLLGVLLVTLINNVL 316 Query: 334 ILVGVPSTWQKVIIGAFILLAGTLFALQRKR 364 IL GVPSTWQK IIG FI+LAG +FAL+R++ Sbjct: 317 ILAGVPSTWQKAIIGGFIVLAGAVFALRREK 347 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: 415 Number of extensions: 9 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: 347 Length adjustment: 29 Effective length of query: 335 Effective length of database: 318 Effective search space: 106530 Effective search space used: 106530 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