Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate WP_023431720.1 N177_RS07670 ABC transporter permease subunit
Query= reanno::WCS417:GFF4244 (229 letters) >NCBI__GCF_000496075.1:WP_023431720.1 Length = 234 Score = 197 bits (502), Expect = 1e-55 Identities = 102/224 (45%), Positives = 147/224 (65%) Query: 4 GYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLV 63 G+G +L GA LTLQ+AL S A+ + LGL+G A +LS LA G++Y+T++R +P+L+ Sbjct: 11 GWGGALLRGALLTLQIALLSYAIGLALGLLGAAAKLSGSPVLAGAGEVYTTLVRAVPELL 70 Query: 64 LILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKG 123 LI+L+FYGG +L LG+ + ++ AA I LG + GAY +E RGA AIP G Sbjct: 71 LIILLFYGGSTMLEMALIALGFPGAVQVSGFAAAIAVLGVVQGAYQTEVIRGAIEAIPVG 130 Query: 124 QAEAGLAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQ 183 Q EA A+GMS R+++P ++ +A+PGF N WL+L K TALIS+VG+ ++++ KQ Sbjct: 131 QIEAARAFGMSPSLRLRRIVIPALLPIALPGFANLWLILLKDTALISIVGISELLYVGKQ 190 Query: 184 AADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAA 227 AA ATR F F+ V A+YL +T VS A R +E+R G+ AA Sbjct: 191 AAGATRHYFFFYCVVGAIYLAMTLVSNGAFRLIERRVRRGIPAA 234 Lambda K H 0.329 0.143 0.424 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: 183 Number of extensions: 10 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: 234 Length adjustment: 23 Effective length of query: 206 Effective length of database: 211 Effective search space: 43466 Effective search space used: 43466 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 24 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