Align ABC transporter permease (characterized, see rationale)
to candidate WP_041305224.1 BTUS_RS06865 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000092905.1:WP_041305224.1 Length = 319 Score = 251 bits (642), Expect = 1e-71 Identities = 133/310 (42%), Positives = 190/310 (61%), Gaps = 5/310 (1%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQ--GAM 61 L Q +++G+ LG++YA +ALGYTMVYGI++LINFAHGE+ M GA + + + G + Sbjct: 9 LPQVLVDGITLGAVYATVALGYTMVYGILELINFAHGEIFMTGAFIGTAVLMGLNAAGVL 68 Query: 62 PGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMI 121 P LL+A A V+ L IE+VAYRPLR +PRL PLI+AIG+S +LQ + Sbjct: 69 AAIPKGAALLVALAAAMVITGLLGVGIERVAYRPLRKAPRLIPLISAIGVSFVLQDVVRF 128 Query: 122 I--WKP-NYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 I W+ NY L S G + +++LG V +A L V T G AMR Sbjct: 129 IAEWRTGNYIVTGISLFDSEISFGPVTVKTNALIVLGAAIVMMAGLDLFVQRTKWGTAMR 188 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 A A++ A+LM + + VI+ TF +G+ L G+++A YGT +GF+ GLKAFTA Sbjct: 189 AVAQDKDTAALMSIDVNKVIALTFFVGSALGGATGVLFAQQYGTIDPYIGFILGLKAFTA 248 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 AV GGIGN+ GA+ GG +LG++E S + LTGG+L + Y D+FAF++LI +L +P Sbjct: 249 AVLGGIGNIRGAMFGGFVLGILEMFASAELSVLTGGVLRAEYKDVFAFLILIAVLLFKPE 308 Query: 299 GLLGERVADR 308 GL G+ V ++ Sbjct: 309 GLFGQVVKEK 318 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: 244 Number of extensions: 10 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: 319 Length adjustment: 27 Effective length of query: 282 Effective length of database: 292 Effective search space: 82344 Effective search space used: 82344 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