Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Korea:Ga0059261_2542 Length = 258 Score = 110 bits (276), Expect = 2e-29 Identities = 69/214 (32%), Positives = 122/214 (57%), Gaps = 8/214 (3%) Query: 46 VGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALR 105 V ++D+SLS+G GE+ ++G +G+GK+T L+ P +G I++DG DI L M Sbjct: 35 VVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKPDAGRIMLDGVDITPLPM---- 90 Query: 106 EFRRHKISMVF--QSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYEN 163 +RR + + + Q + +V N++ L++ K A R + GL + Sbjct: 91 -YRRAILGLGYLPQETSIFRGLTVAKNISAVLELSEPDKSARAARLDQLLEEFGLTRLRD 149 Query: 164 KYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIV 223 LSGG R+R +ARALAAD I+L+DE F+ +DP+ A+++D + EL KT + ++ Sbjct: 150 APAMALSGGERRRAEIARALAADPSIMLLDEPFAGIDPISIADIRDLVKEL-KTRNIGVL 208 Query: 224 FITHDLDEAVRIGNRIAILKDGKLIQVGTPREIL 257 H++ E + I +R +I+ DG+++ G+P +++ Sbjct: 209 ITDHNVRETLDIVDRASIIYDGRVLFAGSPEDLV 242 Lambda K H 0.321 0.138 0.387 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: 144 Number of extensions: 7 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: 276 Length of database: 258 Length adjustment: 25 Effective length of query: 251 Effective length of database: 233 Effective search space: 58483 Effective search space used: 58483 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 (21.9 bits) S2: 47 (22.7 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