Align ABC transporter permease (characterized, see rationale)
to candidate WP_028585879.1 G494_RS0119640 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000429965.1:WP_028585879.1 Length = 304 Score = 254 bits (649), Expect = 2e-72 Identities = 132/308 (42%), Positives = 201/308 (65%), Gaps = 8/308 (2%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 +DILLQQ+ NGL+LGS YAL+ALGYTMVYGII+L+NFAHG++ M GA + + ++ G Sbjct: 4 LDILLQQLANGLILGSFYALVALGYTMVYGIIKLLNFAHGDLYMCGAFIGFLFLSLVSGL 63 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 + W +L + I++ + L +I++VAY P+ ++PRL+ LITA+ +S++L M Sbjct: 64 L--GESWGGILCSMILSMITVGLLGVLIQRVAYLPMLAAPRLSILITALAVSMVLSNGVM 121 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 + Y+ + T L E+G F+T TQI ++ A+ + +L + +N T G+AMRA Sbjct: 122 ALTDGEYEAFSTDLGFEGLEMGNVFVTYTQIALVVSAALLMVTLFFFINRTMYGKAMRAI 181 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 A + LMG+ + VI+ TF IG+ LAA AG+M YG+ MGF+ GLKAFTAAV Sbjct: 182 AIDQDACRLMGINVNKVITLTFFIGSALAAAAGVMAGVYYGSVHFFMGFVIGLKAFTAAV 241 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GGIG++ GA++GG++LGL+EA G+ +GS + D+F+F +LI++L +P+GL Sbjct: 242 IGGIGSIRGAMLGGLVLGLLEAFGTQI------PFIGSEWKDVFSFGILILLLVFKPTGL 295 Query: 301 LGERVADR 308 LG+ +R Sbjct: 296 LGKTEIER 303 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: 259 Number of extensions: 11 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: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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