Align ABC transporter permease (characterized, see rationale)
to candidate WP_073040673.1 BUB04_RS14300 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_900129305.1:WP_073040673.1 Length = 291 Score = 198 bits (504), Expect = 1e-55 Identities = 114/308 (37%), Positives = 176/308 (57%), Gaps = 18/308 (5%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M +LQ +++G+ G++YA+IALG+TM+Y +L+NFA GE +M+G+L +S + + Sbjct: 1 MSEILQYLLSGITAGAIYAVIALGFTMLYNATELVNFAQGEFVMLGSLGLFSLLSAL--- 57 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G P W T++ L V+E++A RP++ +A +I +G SI L+ LAM Sbjct: 58 --GWPLWAAFPAVTLLV----GLLGVVLERLAIRPVKKPEPIALIIITVGASIFLRGLAM 111 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 ++W + P +P IGGA I P + IL V A+ +A L T G+AM A Sbjct: 112 LVWGKDPHSVPGFGAGAPIRIGGAAIMPQSLWILAVVALLMAGLHLFTKRTLTGKAMEAC 171 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 A N A ++G+ D ++ F + A L I GI+ S A + MG + GLK F AA+ Sbjct: 172 AINRNGAWILGIPSDRMVLLAFAMSAALGGIGGII-ISPITMAAYDMGTMLGLKGFCAAM 230 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GG+G+ GA VGG+LLG++E++G GL+ S D AF++L++IL RPSG+ Sbjct: 231 LGGLGSHWGAAVGGLLLGVLESLGV--------GLVSSGIKDAIAFLILLVILMARPSGI 282 Query: 301 LGERVADR 308 LG++ A R Sbjct: 283 LGQKAATR 290 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: 225 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: 291 Length adjustment: 27 Effective length of query: 282 Effective length of database: 264 Effective search space: 74448 Effective search space used: 74448 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