Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate BPHYT_RS28205 BPHYT_RS28205 ATPase
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS28205 Length = 338 Score = 141 bits (355), Expect = 3e-38 Identities = 94/316 (29%), Positives = 162/316 (51%), Gaps = 18/316 (5%) Query: 42 LRTRLARNPEWFTVALIVVTCLIVGA---INPRFFQFATLFDLLHSATTMSLFALGTLVV 98 L TR P + V L++V L + ++P F A L ++L T ++L AL ++ Sbjct: 8 LLTRKRETPLQWEVLLVIVLILSLALGRLLSPVFLTGANLSNVLADLTEIALMALPMTLI 67 Query: 99 LASGGIDVSFTAI--AALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHR 156 + + ID+S ++ A+ + G+ W P L++V + G + G++NGL++ + Sbjct: 68 IVAAEIDLSVASVLGASSALMGVL-----WHMGLPMPLVIVLVLVAGALAGLLNGLVIVK 122 Query: 157 LKAPSLIVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVS 216 L PSL VTIGT L+RGL +G + P + FG T G + +P+ Sbjct: 123 LNLPSLAVTIGTLALFRGLAYVLLGDQAVADFPPAYTAFGM------DTLGG--SFIPLP 174 Query: 217 VLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAG 276 + ++ A+V LL T GR++YA+G + A G + I L +F +G ++ +AG Sbjct: 175 FVIVIVGAIVFTVLLQSTAFGRSLYAIGANPTAAAFSGIEVAKIRLRLFVLSGAMSALAG 234 Query: 277 ILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILV 336 +++ A + G EL VIAAV+ GG I GG G+++G LL ++++ ++K+ L L Sbjct: 235 VVYTLRFTSARGDNGEGFELSVIAAVLFGGVSIFGGRGSMIGVLLSLLIIGVLKNALTLD 294 Query: 337 GVPSTWQKVIIGAFIL 352 V S ++ G +L Sbjct: 295 DVSSETLTIVTGVLLL 310 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: 11 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: 338 Length adjustment: 29 Effective length of query: 335 Effective length of database: 309 Effective search space: 103515 Effective search space used: 103515 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