Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_090271704.1 BLU11_RS01420 LPS export ABC transporter ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >NCBI__GCF_900105005.1:WP_090271704.1 Length = 241 Score = 117 bits (294), Expect = 2e-31 Identities = 73/231 (31%), Positives = 123/231 (53%), Gaps = 11/231 (4%) Query: 11 YGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFEGQDITQMPT 70 Y + ++ V + I +GEIV L+G NGAGK+T I G +A G I QD+T++P Sbjct: 13 YKSRRVVEDVSLSINSGEIVGLLGPNGAGKTTCFYMIVGLVKADQGNILINDQDVTRLPM 72 Query: 71 YELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKP---GSFANELERVLTLF--PRLKE 125 + R G+ P+ IF ++SV +N+ T K +L+ +L F L++ Sbjct: 73 HGRARQGLGYLPQEASIFRKLSVADNIMAILETRKELNRKGREGKLDSLLREFHIHHLRD 132 Query: 126 RISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDINREQKM 185 + ++SGGE++ I RAL + P+ +LLDEP G+ P+ V I Q ++ + +++ + Sbjct: 133 SLGM---SLSGGERRRAEIARALATDPQFILLDEPFAGVDPISVNDIKQIIQHL-KDKGI 188 Query: 186 TVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGGH 236 V + + N L + + Y++ +G + G E+LAN+ VR YL GH Sbjct: 189 GVLITDHNVRETLDICDKAYIVNDGHIIAEGGAEEVLANQLVRDVYL--GH 237 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: 120 Number of extensions: 10 Number of successful extensions: 3 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: 241 Length adjustment: 23 Effective length of query: 213 Effective length of database: 218 Effective search space: 46434 Effective search space used: 46434 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 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