Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 137 bits (344), Expect = 5e-37 Identities = 91/307 (29%), Positives = 154/307 (50%), Gaps = 14/307 (4%) Query: 48 RNPEWFTVALIVVTCLIVGA--INPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGID 105 R W T+ L+V + V +P F L D + T ++ A +++ SG ID Sbjct: 19 RLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEID 78 Query: 106 VSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVT 165 +S +I AL + AV P +++ G G++ G NG+LV R+ PS++VT Sbjct: 79 LSVASIIALASTAMGAAV-QMGVGTPGLVLIGLGV--GLLCGAFNGVLVTRMGLPSIVVT 135 Query: 166 IGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAV 225 IGT L+RG+ +G F P S FG+ +++ V+ ++ AV Sbjct: 136 IGTMSLFRGISYIVLGDQAFRGYPESFSWFGQGYVWW---------VISFELVLFAIIAV 186 Query: 226 VTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRL 285 + LL++T GRAVYA+G + A G ++ + +F TG+++G+A I + Sbjct: 187 IYAMLLHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGS 246 Query: 286 ANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKV 345 P +G EL+V+ V+LGG I GG+GT++G ++ ++ L+ L L+ VP + Sbjct: 247 TRPSIAMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSI 306 Query: 346 IIGAFIL 352 +IGA ++ Sbjct: 307 VIGALLI 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: 306 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 364 Length of database: 328 Length adjustment: 29 Effective length of query: 335 Effective length of database: 299 Effective search space: 100165 Effective search space used: 100165 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