Align ABC transporter permease (characterized, see rationale)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Marino:GFF3113 Length = 307 Score = 240 bits (613), Expect = 3e-68 Identities = 132/303 (43%), Positives = 197/303 (65%), Gaps = 15/303 (4%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCI-GMMQGAMPGA 64 QQ+INGL +GS YALIA+GYTMVYGII +INFAHGE+ MIGA T+ I G+ + Sbjct: 9 QQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGIAWL 68 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 P +IL++A + A +V++++ + +E+VAYRP+R RL PLI+AIGMSI LQ + Sbjct: 69 P--LILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHLAQG 126 Query: 125 PNYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 +P ++ F G F ++ QI I T + + +L ++ + GRA RA Sbjct: 127 SRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRACRAV 186 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 +++ +A+L+G+ + +ISATF+IGA LAA+AG++ YG+ GF+ GLKAFTAAV Sbjct: 187 SQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFTAAV 246 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GGIG++ GA++GG++LG+ E++ SGY L Y D+ +F +LI+IL +P+GL Sbjct: 247 LGGIGSIPGAMLGGLILGVAESMTSGY--------LSGEYKDVISFSLLILILLFKPTGL 298 Query: 301 LGE 303 LG+ Sbjct: 299 LGK 301 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: 263 Number of extensions: 10 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: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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