Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= reanno::BFirm:BPHYT_RS07675 (229 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 127 bits (320), Expect = 2e-34 Identities = 63/206 (30%), Positives = 120/206 (58%), Gaps = 3/206 (1%) Query: 17 TIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPDLVLMLLLFYSIQIA 76 T+ ++V+S ++LG+ GA +LS N LR +AT Y ++R +P LV ++ +++ + Sbjct: 63 TVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVI 122 Query: 77 VNNLTDALN---LPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPRGQLEAGSAYGM 133 + ++ LN + + +P V + + F YGAY +E +R ++P+GQ+EA + GM Sbjct: 123 IQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEAARSLGM 182 Query: 134 SGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQDAGKSTFNMFF 193 S + ++ PQ +R LP +GN + L+K T+LVS + +AD+V+ ++ + FN Sbjct: 183 SHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNPIE 242 Query: 194 FILVAALIYLAITTASNLVLIWLEKR 219 + L+YL +T S+ ++ ++EK+ Sbjct: 243 VWTMIGLLYLILTLLSSRLINYIEKK 268 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: 155 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: 229 Length of database: 273 Length adjustment: 24 Effective length of query: 205 Effective length of database: 249 Effective search space: 51045 Effective search space used: 51045 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 Apr 09 2024. 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