Align ABC transporter permease (characterized, see rationale)
to candidate WP_011159555.1 TX73_RS20500 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000195775.1:WP_011159555.1 Length = 290 Score = 190 bits (483), Expect = 3e-53 Identities = 113/308 (36%), Positives = 177/308 (57%), Gaps = 19/308 (6%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M LLQ +I+GL +G++YAL+ALG+T+VY ++NFA GE +M+G + + + Sbjct: 1 MSELLQFLISGLTVGAVYALVALGFTLVYHASDVVNFAQGEFVMLGGMVT------VFAY 54 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G P L LA ++A +VA + ++ +A P R + ++ +I IG SILL+ A Sbjct: 55 AAGLP----LPLAALLAVIVAVVVGLLLYWLAIAPARGASAVSLIIITIGASILLRGAAQ 110 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 I++ + P +P + GA I P + +LG A+ + +L Y++ T +G+A+ AT Sbjct: 111 IVFDKQFHKLPAFSGDAPIHLLGAVIQPQSLWVLGGAALVVLTLYYVMERTLIGKAVVAT 170 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 A N A L+GV V++ F A + AIAGI+ T+ + +G L LK F AA+ Sbjct: 171 AANRLAARLVGVNVATVMALAFGGSAAIGAIAGILITPITLTS-YDVGTLLALKGFAAAM 229 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GG+GN GAV+GG+LLGL+E+ G+GY+ S Y D AFIV++ +L + P GL Sbjct: 230 LGGMGNPLGAVIGGLLLGLLESFGAGYV--------SSTYKDAIAFIVILAVLFVAPQGL 281 Query: 301 LGERVADR 308 +G R +R Sbjct: 282 VGRRTVER 289 Lambda K H 0.327 0.142 0.419 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: 208 Number of extensions: 16 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: 309 Length of database: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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