Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate WP_023431213.1 N177_RS05250 amino acid ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771 (248 letters) >NCBI__GCF_000496075.1:WP_023431213.1 Length = 281 Score = 84.3 bits (207), Expect = 2e-21 Identities = 64/221 (28%), Positives = 99/221 (44%), Gaps = 17/221 (7%) Query: 26 VTGLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85 ++G + I I++ A + +G LG+M V ++ + FRN P LV LF Sbjct: 69 LSGFVFNIAISLMAMTLGTVVGLALGLMAVSETMPVRKVSWAVTQFFRNSPWLVLLFFAM 128 Query: 86 FLVPDLLPADLQEWYKQDLNPTTSAF---LSVVVCLGLFTTARVCEQVRTGIQALPKGQE 142 FLVP Y+ L T F + V+ L A V E VR I+++P GQ Sbjct: 129 FLVP----------YEFRLLGVTVPFPDWIKAVIGFSLPVMANVSEIVRGAIRSIPDGQW 178 Query: 143 SAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQTA 202 +A A+ F Q W ++LPQ R ++PP + + V T +AS++G+ E+L T Q Sbjct: 179 ESAEALAFSRRQTMWMIILPQCLRRMLPPWMNLYSLVTMATVLASVVGVSEMLTLTSQVH 238 Query: 203 EFSAN----LFEAFTLATLIYFTLNMSLMLLMRVVEKKVAV 239 L + A L +F + L R +E + V Sbjct: 239 AAEGGRPELLAPLYGFALLCFFVYCYPIDRLTRRLEHRFQV 279 Lambda K H 0.326 0.139 0.432 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: 164 Number of extensions: 10 Number of successful extensions: 2 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: 248 Length of database: 281 Length adjustment: 25 Effective length of query: 223 Effective length of database: 256 Effective search space: 57088 Effective search space used: 57088 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: 47 (22.7 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