Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >NCBI__GCF_000017845.1:WP_009545830.1 Length = 238 Score = 117 bits (294), Expect = 2e-31 Identities = 72/236 (30%), Positives = 126/236 (53%), Gaps = 7/236 (2%) Query: 2 LKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFE 61 L + +H YG + + V++++ GEIV L+G NGAGK+T G + GR+ Sbjct: 3 LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62 Query: 62 GQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLFP 121 Q++T++P + RLGI + IF +SV EN+Q+ ++ F +R+ TL Sbjct: 63 QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQV-ALEQTNVPFRQRPQRLHTLLK 121 Query: 122 RLK-ERISQRAGT-MSGGEQQMLAIGRAL---MSQPRLLLLDEPSLGLAPLVVKQIFQAV 176 + E+I+ G+ +SGGE++ + R+L P LLLDEP G+ P+ V +I + Sbjct: 122 EFRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMI 181 Query: 177 KDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 + +++M + + + N L + +R Y+M +G++ +G+ E+ N VR YL Sbjct: 182 AQL-CDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYL 236 Lambda K H 0.320 0.136 0.377 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: 135 Number of extensions: 4 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: 236 Length of database: 238 Length adjustment: 23 Effective length of query: 213 Effective length of database: 215 Effective search space: 45795 Effective search space used: 45795 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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