Align Amino acid ABC transporter, periplasmic binding protein (characterized, see rationale)
to candidate GFF5094 PS417_26100 amino acid ABC transporter
Query= uniprot:Q88GX4 (250 letters) >FitnessBrowser__WCS417:GFF5094 Length = 253 Score = 336 bits (862), Expect = 2e-97 Identities = 166/235 (70%), Positives = 195/235 (82%) Query: 15 LAGAASAETLRFATEGAYPPFNYVDADNKLHGFDVDITHALCEQMKVECTLVAQDWEGII 74 +AGAA AETLR A+EGAYPPFNYVD++N+LHGFD+DI +ALCE+MKV CT V QDWEG+I Sbjct: 19 VAGAAHAETLRIASEGAYPPFNYVDSNNRLHGFDIDIANALCERMKVNCTFVTQDWEGMI 78 Query: 75 PALMARKYDAIVASMIDTEERRKKIAFTDHYYRTPLTVAVAKDSKIDSAQTDFVGYTVGA 134 PAL+A+KYDAIVASM TEER+KKIAFT+ YYRTPL+VAVA DS I AQT+F G TVGA Sbjct: 79 PALLAKKYDAIVASMNVTEERKKKIAFTNRYYRTPLSVAVAHDSGISDAQTNFKGLTVGA 138 Query: 135 QSSSTQAIYAEDVYGKAGADVKLYPTMDEANADLAAGRLDGVIADKFPLHEWMNKNGGDC 194 QS STQAIYAE+ Y +AGA VKLYP+ DEA +DLAAGRLDGVIADK+PL W+ G DC Sbjct: 139 QSYSTQAIYAEEHYAEAGATVKLYPSQDEAASDLAAGRLDGVIADKYPLLAWVAGAGKDC 198 Query: 195 CKILGDVADTKADAAIAVRKDDEALRQRLNTALQQIVANGTYQKIASKYFAFDIY 249 C LGD+ T DAAIAVR+ D LR+RLN AL +IVA+GTY+ I+ +YFAFDIY Sbjct: 199 CTFLGDIDGTNTDAAIAVRQGDVELRERLNKALDEIVADGTYKNISRRYFAFDIY 253 Lambda K H 0.319 0.132 0.385 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: 232 Number of extensions: 3 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: 250 Length of database: 253 Length adjustment: 24 Effective length of query: 226 Effective length of database: 229 Effective search space: 51754 Effective search space used: 51754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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