Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_089136613.1 CES79_RS06000 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_002217945.1:WP_089136613.1 Length = 229 Score = 95.9 bits (237), Expect = 6e-25 Identities = 63/206 (30%), Positives = 112/206 (54%), Gaps = 14/206 (6%) Query: 6 NVIWEALPLY--FGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIR 63 NV++E L FGGL TT+++ A++L+ GL+ + LG++R ++ + LY R Sbjct: 7 NVLFEGRNLIRLFGGLWTTVEIAAVALVLGLILGVILGVLRTFPNRLLRLVLRLYLEFFR 66 Query: 64 GTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRAT 123 P +V LFL YY L + V A A L FA+ T+A ++I+ G+L + Sbjct: 67 IVPTVVLLFLFYYILPKQLGVN--------LPANQVATLVFALWTAAEMSDIVRGALISV 118 Query: 124 PNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGA 183 P + E+ A+G++R ++Y+ +L+P A+ LP N V +++TTSL +++++D+ Sbjct: 119 PKHQRESGMAIGLNRLQLYRYVLIPQAVSLELPATINLVTRVIKTTSLLMLISVMDVINV 178 Query: 184 ARTV---NAQYYLPFEAYITAGVFYL 206 + V N Q Y P + G+ ++ Sbjct: 179 GQQVVEANNQKY-PTGVFWVYGIIFV 203 Lambda K H 0.329 0.139 0.427 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: 108 Number of extensions: 7 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: 232 Length of database: 229 Length adjustment: 23 Effective length of query: 209 Effective length of database: 206 Effective search space: 43054 Effective search space used: 43054 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