Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate GFF966 PS417_04900 amino acid ABC transporter substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__WCS417:GFF966 Length = 343 Score = 294 bits (752), Expect = 3e-84 Identities = 144/322 (44%), Positives = 214/322 (66%), Gaps = 4/322 (1%) Query: 40 ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYR 99 ++ + L+ VQ +G + CGV LPGFS D+ G G+D D+C+A+AAA+F D +++ Sbjct: 24 QAGATLDAVQKKGFVQCGVSDGLPGFSVPDASGKILGIDADVCRAVAAAVFGDATKVKFS 83 Query: 100 SLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAP-TTFYDGQGLMVRRNSGIQ 158 L++ ERF AL SGEVD+LSRNTT T SRDA G L+F T+YDG G +V G++ Sbjct: 84 QLNAKERFTALQSGEVDILSRNTTMTSSRDA--GMGLKFPGFITYYDGIGFLVNNKLGVK 141 Query: 159 SLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDR 218 S ++ G +IC++ GTT+ELN++D R ++Y I F SD + + GRC+ +TSD+ Sbjct: 142 SAKELDGATICIQAGTTTELNVSDYFRGNNLKYTPITFDTSDESAKSLESGRCDVLTSDK 201 Query: 219 SQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQ 278 SQL A+R+ L+ + +L ISKEPL P N D W +V+WV A + AEE GIT Sbjct: 202 SQLFAQRSKLAAPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWVGYAMLNAEEAGITS 261 Query: 279 ANID-QFKTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPL 337 N++ + K++KNP++ R LG +GE G+ L + D+ + +K VGNYGE++ERN+G+ +PL Sbjct: 262 KNVEAEAKSTKNPDVARLLGADGEYGKDLKVKKDWVVQIVKQVGNYGEVFERNLGKSTPL 321 Query: 338 KLNRGLNQLYKNGGLLYSPPFR 359 +++RGLN L+ NGG+ Y+PP R Sbjct: 322 EIDRGLNALWNNGGIQYAPPVR 343 Lambda K H 0.317 0.134 0.391 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: 290 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: 359 Length of database: 343 Length adjustment: 29 Effective length of query: 330 Effective length of database: 314 Effective search space: 103620 Effective search space used: 103620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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