Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate SM_b20318 SM_b20318 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Smeli:SM_b20318 Length = 343 Score = 399 bits (1025), Expect = e-116 Identities = 206/342 (60%), Positives = 254/342 (74%), Gaps = 3/342 (0%) Query: 25 MTTPTVVEIAPSVEAPG-LRTR--LARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDL 81 M ++ S E P +RT R+P T L+V+ C++VG INP F+Q + LFD+ Sbjct: 1 MADVAATPVSGSEEVPAAIRTMRWFIRHPPAVTFLLVVIVCIVVGTINPDFWQVSNLFDM 60 Query: 82 LHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGAL 141 S LFALG LVVLASGG+DVSFTAIAAL MY IT V + PD IL A Sbjct: 61 ARSTVVRGLFALGVLVVLASGGLDVSFTAIAALVMYVITMLVTNYVPDLSIWPILGIAAA 120 Query: 142 GGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLF 201 GG +LG+ NGLLVH L+APSLIVTIGTQY RG LLTFIGT FMNIP SMD FG++ LF Sbjct: 121 GGAILGICNGLLVHALQAPSLIVTIGTQYAIRGFLLTFIGTALFMNIPESMDAFGKLALF 180 Query: 202 FYHTADGLRAVLPVSVLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIH 261 Y A+G + LP L LV AA+ TW++L RT++GRA+YA+GG+ +IA RLGYNLR +H Sbjct: 181 RYEGANGAVSTLPAYFLVLVVAALATWYILKRTLIGRAIYAVGGNASIASRLGYNLRTVH 240 Query: 262 LFVFGYTGMLAGIAGILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLL 321 +FVF Y G+LAGIAGI+HVS+NRLANPFDL GSELDVIAAV+LGGARITGG+GTV+GTLL Sbjct: 241 VFVFAYAGLLAGIAGIMHVSSNRLANPFDLAGSELDVIAAVVLGGARITGGSGTVLGTLL 300 Query: 322 GVVLVTLIKSVLILVGVPSTWQKVIIGAFILLAGTLFALQRK 363 GV+L+TL+ +VLILVG+PST Q IIG FI++AG +F+++ K Sbjct: 301 GVLLITLVNNVLILVGIPSTLQLAIIGLFIVVAGAMFSIRPK 342 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: 416 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: 343 Length adjustment: 29 Effective length of query: 335 Effective length of database: 314 Effective search space: 105190 Effective search space used: 105190 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