Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__psRCH2:GFF18 Length = 219 Score = 114 bits (284), Expect = 2e-30 Identities = 70/216 (32%), Positives = 110/216 (50%), Gaps = 10/216 (4%) Query: 8 VILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67 ++L G W+T+++ +LAI LI RLSP+ L WL Y V RG LV + Sbjct: 7 LLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSLLVQLFW 66 Query: 68 IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127 +++ V PM ++ I+++ A + LG GAY +E RGA ++ +GQ EA Sbjct: 67 LYF--------VLPMPPFN--IEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEA 116 Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187 A M+ R+++PQ + AIP TN + L K T+L+S++ L D+ F+A+Q A Sbjct: 117 CQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQA 176 Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVG 223 T F +Y V+ +R LE+R + G Sbjct: 177 TLMTMEIFGLALVIYFVLAQTINFGMRQLERRLARG 212 Lambda K H 0.329 0.144 0.428 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: 158 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: 229 Length of database: 219 Length adjustment: 22 Effective length of query: 207 Effective length of database: 197 Effective search space: 40779 Effective search space used: 40779 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 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