Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate PP_0226 PP_0226 sulfur compound ABC transporter - permease subunit
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Putida:PP_0226 Length = 222 Score = 144 bits (362), Expect = 2e-39 Identities = 81/203 (39%), Positives = 116/203 (57%), Gaps = 4/203 (1%) Query: 17 LLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLILLI 76 LL G G + L++ + G V+G A+A LSK L LA VYV+ R TP+LV + +I Sbjct: 16 LLKGAGYTVLLSVGGMFFGLVLGFALALMRLSKILPLNWLARVYVSFFRGTPLLVQLFVI 75 Query: 77 YFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGEWQVKA 136 YF +P +GI LD +P+ +I LSL AY+ E+ R + SI +GQ EA +IG+ Q Sbjct: 76 YFGMPQIGIELDPIPASLIGLSLNMAAYICEILRAAISSIDRGQWEAAASIGMTRVQAMR 135 Query: 137 YVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTA 196 +P LR LP L N+FISL KDT+LAA I VPEL A+ I ++ V ++ Sbjct: 136 RAILPQALRTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEVFTMYVAVAV 195 Query: 197 LYVAACYLIAMVLRYFEQRLAIR 219 +Y C ++A +F+ R+ R Sbjct: 196 IYWVLCSILA----HFQNRMEAR 214 Lambda K H 0.329 0.142 0.414 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: 112 Number of extensions: 6 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: 220 Length of database: 222 Length adjustment: 22 Effective length of query: 198 Effective length of database: 200 Effective search space: 39600 Effective search space used: 39600 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 (21.8 bits) S2: 45 (21.9 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