Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 150 bits (380), Expect = 3e-41 Identities = 98/302 (32%), Positives = 161/302 (53%), Gaps = 14/302 (4%) Query: 55 VALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAAL 114 +AL+V+ IV ++P FF LF++L + ++ A+G +V+ + GID+S ++ AL Sbjct: 24 IALLVLIA-IVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 Query: 115 TMYGITKAVFAWWPDAPFALILVTGALG-GVVLGMVNGLLVHRLKAPSLIVTIGTQYLYR 173 T V AL+ V AL G +G V G++V + + + I T+ L R Sbjct: 83 TGAVAASIVGI----EVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLR 138 Query: 174 GLLLTFI-GTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLN 232 G+ + + G+ + D FG ++ L PV ++A+V A W++L+ Sbjct: 139 GVTMVYTNGSPVNTGFTDNADLFG-----WFGIGRPLGIPTPVWIMAIVFLAA--WYMLH 191 Query: 233 RTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLV 292 T +GR +YA+GG+ A G ++ + + V+ GMLA +AGI+ V+ A P Sbjct: 192 HTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGT 251 Query: 293 GSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFIL 352 G ELD IAAV+LGG + GG G +VGTL+G +++ + + L L+GV S +Q ++ IL Sbjct: 252 GYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVIL 311 Query: 353 LA 354 LA Sbjct: 312 LA 313 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: 276 Number of extensions: 12 Number of successful extensions: 2 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: 321 Length adjustment: 29 Effective length of query: 335 Effective length of database: 292 Effective search space: 97820 Effective search space used: 97820 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