Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Pf1N1B4_1346 Urea ABC transporter, ATPase protein UrtD
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1346 Length = 289 Score = 135 bits (339), Expect = 1e-36 Identities = 91/259 (35%), Positives = 139/259 (53%), Gaps = 19/259 (7%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +LT+E +++ F G A+ND++ GE+ IIGPNGAGKTTL + ITG P+ G+ Sbjct: 48 ILTLEDISVSFDGFKALNDLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 107 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQH-NKLIRASGFSI 129 G+ L +M +I+Q A + R FQ +F +SV ENL +AQ +K + AS Sbjct: 108 ----GETLDLTQMSEVQIAQ-AGIGRKFQKPTVFEALSVFENLELAQKTDKSVWAS---- 158 Query: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 R E D L+ +RL + AG L +G ++ LEI + +P + Sbjct: 159 -------LRARLSGEQKDRISEVLETIRLTASVNRPAGMLSHGQKQFLEIGMLLMQDPQL 211 Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249 L LDEP AG+ E+ A+L + +H + +++EHDM V +I+DHV VL G ++ Sbjct: 212 LLLDEPVAGMTDAETEFTAELFKSLAGKHSL--MVVEHDMGFVGSIADHVTVLHQGSVLA 269 Query: 250 DGDPAFVKNDPAVIRAYLG 268 +G V+++ VI YLG Sbjct: 270 EGSLEQVQDNERVIEVYLG 288 Lambda K H 0.319 0.137 0.397 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: 188 Number of extensions: 9 Number of successful extensions: 4 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: 294 Length of database: 289 Length adjustment: 26 Effective length of query: 268 Effective length of database: 263 Effective search space: 70484 Effective search space used: 70484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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