Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_057508273.1 ABB28_RS08815 lipid A export permease/ATP-binding protein MsbA
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_001431535.1:WP_057508273.1 Length = 582 Score = 80.5 bits (197), Expect = 9e-20 Identities = 72/249 (28%), Positives = 112/249 (44%), Gaps = 35/249 (14%) Query: 12 LTVEHLTMRF--GGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 L EH+ +R+ A++D+SF A G +TA++G +G+GKT+L + FY P+ GR+T Sbjct: 341 LAFEHVMLRYREDAGTALDDISFVARPGTVTAVVGRSGSGKTSLIRLVPRFYEPSGGRIT 400 Query: 70 LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129 L ++ L + + VA Q + LF G +I Sbjct: 401 LDGVALDDYPLADL-------RRQVAMVGQKVMLFDD-----------------TIGSNI 436 Query: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGN----LPYGAQRRLEIARAMCT 185 A G+ + R A + A W RL + D G L G ++RL IARA+ Sbjct: 437 A--YGMQASQEQIRAAAEAANAWEFIARLPQQLDTPVGENGALLSGGQRQRLAIARAILR 494 Query: 186 EPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYG 245 + +L LDE A L+ + D L + E L+I H +S + +D V+V+D G Sbjct: 495 DAPILILDEATAALDNESERLVQDALQRLMPERT--TLVIAHRLSTI-EHADQVLVMDQG 551 Query: 246 RKISDGDPA 254 R + G A Sbjct: 552 RIVERGTHA 560 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: 317 Number of extensions: 11 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: 294 Length of database: 582 Length adjustment: 31 Effective length of query: 263 Effective length of database: 551 Effective search space: 144913 Effective search space used: 144913 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: 50 (23.9 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