Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Marino:GFF4159 Length = 269 Score = 197 bits (501), Expect = 2e-55 Identities = 108/243 (44%), Positives = 156/243 (64%), Gaps = 8/243 (3%) Query: 1 MLKVSGVHTFYG-AIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRIT 59 +L++ + Y +++ L+G+ + + G IV+L+G+NGAGKST L ++ G G +T Sbjct: 4 LLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGEVT 63 Query: 60 -----FEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGS--ITAKPGSFANE 112 F G+D+ +P LVR G+ EGRR+F ++V ENL + ++ S ++ Sbjct: 64 AGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLSDS 123 Query: 113 LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQI 172 E V FPRLKER Q AG +SGGEQQMLA+GRAL++QP L++LDEPSLGLAPL+V++I Sbjct: 124 YELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVEEI 183 Query: 173 FQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 F V INREQ + +VEQNA +L +A GY+M NGK+ + G +L ANE+V+ YL Sbjct: 184 FTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEFYL 243 Query: 233 EGG 235 G Sbjct: 244 GVG 246 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: 200 Number of extensions: 9 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: 269 Length adjustment: 24 Effective length of query: 212 Effective length of database: 245 Effective search space: 51940 Effective search space used: 51940 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