Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::BFirm:BPHYT_RS07675 (229 letters) >FitnessBrowser__Dino:3608832 Length = 268 Score = 79.7 bits (195), Expect = 5e-20 Identities = 67/218 (30%), Positives = 93/218 (42%), Gaps = 18/218 (8%) Query: 12 AGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPDLVLMLLLFY 71 +G I + +L L A A K S LR A + + R P L + L Y Sbjct: 38 SGLIWNVYFGAFALLFGFFLATAVALGKASDRAVLRVPADWFIFVFRGSP-LFIQFFLAY 96 Query: 72 SIQIAVNNLTDALNLPQFDIDPFV---AGVLTLGFIY-GAYFTETFRGAFLAVPRGQLEA 127 + I + ++ A DPF AG L + F+ AY E F GA +VP+G LEA Sbjct: 97 FLFIQLKAVSPAF-------DPFTSAWAGALVVLFLNTSAYAGEIFYGALRSVPKGDLEA 149 Query: 128 GSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGL------ADVVKAA 181 AYG++G F R+ +P M+R A P N L AT LV G D + A Sbjct: 150 ADAYGLAGWTKFRRVTWPTMLRLAWPSYTNEAIFLFHATTLVFFAGFPAFQQRGDALYYA 209 Query: 182 QDAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKR 219 Q TFN F + A ++ +T A V + +R Sbjct: 210 QYFADKTFNPFIPYPIVAFYFILLTLAVIFVFSLINRR 247 Lambda K H 0.329 0.142 0.411 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: 181 Number of extensions: 8 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: 229 Length of database: 268 Length adjustment: 24 Effective length of query: 205 Effective length of database: 244 Effective search space: 50020 Effective search space used: 50020 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: 46 (22.3 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