Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate GFF340 PS417_01730 histidine ABC transporter substrate-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09620 (322 letters) >FitnessBrowser__WCS417:GFF340 Length = 321 Score = 617 bits (1590), Expect = 0.0 Identities = 302/322 (93%), Positives = 313/322 (97%), Gaps = 1/322 (0%) Query: 1 MKSNKTLLTTLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKGY 60 MK +KTL+ TLLS G+LASAGA QAAGWCESGKPVKFAGLNWESGMLLTD+LQ VLEKGY Sbjct: 1 MKMHKTLMATLLSAGVLASAGA-QAAGWCESGKPVKFAGLNWESGMLLTDILQTVLEKGY 59 Query: 61 DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW 120 DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW Sbjct: 60 DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW 119 Query: 121 YVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDNS 180 YVPRYV+EGDAKRKLEAKAP LKNIADL +YA+VFKD EEPSKGRFYNCPAGWTCELDNS Sbjct: 120 YVPRYVIEGDAKRKLEAKAPDLKNIADLAKYASVFKDQEEPSKGRFYNCPAGWTCELDNS 179 Query: 181 EMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP 240 EMLKSYGLE TYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP Sbjct: 180 EMLKSYGLESTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP 239 Query: 241 GVDKSVSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLK 300 GVDKSVSIKVGLSKTFH++APELVAVLEKVNLPID+LNQNLGRMAKERIESPKLAKIFLK Sbjct: 240 GVDKSVSIKVGLSKTFHEQAPELVAVLEKVNLPIDLLNQNLGRMAKERIESPKLAKIFLK 299 Query: 301 EHPEVWHAWVSEDAAKKIDAAL 322 EHPEVWHAWVS+DAAKKIDAAL Sbjct: 300 EHPEVWHAWVSDDAAKKIDAAL 321 Lambda K H 0.314 0.133 0.398 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: 466 Number of extensions: 16 Number of successful extensions: 1 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: 322 Length of database: 321 Length adjustment: 28 Effective length of query: 294 Effective length of database: 293 Effective search space: 86142 Effective search space used: 86142 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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