Align ABC transporter permease (characterized, see rationale)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein
Query= uniprot:A0A165KC95 (309 letters) >MicrobesOnline__882:208249 Length = 306 Score = 199 bits (507), Expect = 5e-56 Identities = 114/307 (37%), Positives = 175/307 (57%), Gaps = 13/307 (4%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+ +Q I N L GS YALIALGYT+VYG++ LINFAHG++ M+GA S+ ++ G Sbjct: 1 METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60 Query: 61 MPG---APGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILL 115 + G G + L L + V+ A + +E+VAYRPLR + RL +ITA+ I+L Sbjct: 61 IGGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIML 120 Query: 116 QTLAMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGR 175 + + + + K P M+ + IG +T +++++ + A L ++V T +G Sbjct: 121 ENGNLALLGASRKALPEMIDKVVYTIGTVSVTNLKLMVIVTAFLVFALLQFIVTRTRIGM 180 Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 AMRA A + LMG+ D +I TF++G+ A +AG+++A +Y MG + G KA Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240 Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 F AAV GGIG++ GA +GG LL IE + + S + D+FAF +L+ I+ Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIE--------IMVAAVFPSTFRDLFAFSILLFIMWQ 292 Query: 296 RPSGLLG 302 RP+GL G Sbjct: 293 RPTGLFG 299 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: 224 Number of extensions: 13 Number of successful extensions: 4 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: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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 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