Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate CCNA_02006 CCNA_02006 lipoprotein releasing system ATP-binding protein lolD
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Caulo:CCNA_02006 Length = 228 Score = 101 bits (252), Expect = 1e-26 Identities = 69/201 (34%), Positives = 106/201 (52%), Gaps = 8/201 (3%) Query: 1 MLKVSGVHTFY----GAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMG 56 +L + G+ Y G + L+GVD+++ GE+V LIG +G+GKS+LL + R G Sbjct: 5 VLALRGLERVYKTEAGDLPVLRGVDLDVYPGEVVGLIGPSGSGKSSLLHSAGLLERPDAG 64 Query: 57 RITFEGQDITQMP--TYELVRLG-IAQSPEGRRIFPRMSVLENLQMG-SITAKPGSFANE 112 + EG+D +++ +RLG + + + P S LEN+ M +I K A Sbjct: 65 LVALEGRDCSKLSERARTRIRLGTVGFVYQFHHLLPEFSALENVAMPLTIAGKSRREAEA 124 Query: 113 LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQI 172 R L L R++ + MSGGEQQ +AI RAL ++P+LLL DEP+ L P + Sbjct: 125 RARELLESLGLGHRLNHQPAQMSGGEQQRVAIARALANRPKLLLADEPTGNLDPATSTAV 184 Query: 173 FQAVKDINREQKMTVFMVEQN 193 FQA+ + REQ + + N Sbjct: 185 FQALYQVCREQGVAAVIATHN 205 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: 119 Number of extensions: 3 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: 228 Length adjustment: 23 Effective length of query: 213 Effective length of database: 205 Effective search space: 43665 Effective search space used: 43665 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 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