Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >FitnessBrowser__Cup4G11:RR42_RS16450 Length = 211 Score = 119 bits (297), Expect = 6e-32 Identities = 69/212 (32%), Positives = 116/212 (54%), Gaps = 9/212 (4%) Query: 1 MIFDYNVIWEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTY 60 M D+ + LP+ L + T+ L ++ G + L L L R S+ V+ +A+++ + Sbjct: 1 MNIDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIW 60 Query: 61 VIRGTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120 + RGTP+L+ LF +YY F E A A +A +++++AY AEII + Sbjct: 61 IFRGTPVLLHLFFVYYAAPMFGLRLE---------ALPAAIIALSMSSAAYNAEIIRAGI 111 Query: 121 RATPNGEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180 RA G+ EAA+A+GM+ ++ + ++LP A R LP Y I ++TSLAS++T+ ++ Sbjct: 112 RAVHRGQREAAQAVGMTNPRILRHVILPQATRIVLPPYMGNFISHTKSTSLASVITVPEL 171 Query: 181 TGAARTVNAQFYLPFEAYITAGVFYLCLTFIL 212 +A+T+ + Y E AG YL LT +L Sbjct: 172 MLSAQTIYSSTYRAVEVLTIAGAIYLALTTVL 203 Lambda K H 0.330 0.140 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: 104 Number of extensions: 5 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: 211 Length adjustment: 22 Effective length of query: 210 Effective length of database: 189 Effective search space: 39690 Effective search space used: 39690 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 (21.9 bits) S2: 45 (21.9 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