Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate Pf1N1B4_917 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917 Length = 343 Score = 289 bits (739), Expect = 9e-83 Identities = 146/345 (42%), Positives = 219/345 (63%), Gaps = 5/345 (1%) Query: 17 RFLLVLLCFLPLAACRSLGGNETESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSG 76 + L L + AA + G ++ + L+ VQ +G + CGV LPGFS DS G G Sbjct: 2 KMLKSTLAIVTAAAVLGVSGF-AQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVG 60 Query: 77 LDVDICKAIAAALFNDPKAIEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNL 136 +D D C+A+AAA+F D +++ L++ ERF AL SGE+D+LSRN+T T SRDA G L Sbjct: 61 IDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDVLSRNSTMTSSRDA--GMGL 118 Query: 137 EFAP-TTFYDGQGLMVRRNSGIQSLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIK 195 +F T+YDG G + G++S ++ G +IC++ GTT+ELN++D R G++Y I Sbjct: 119 KFPGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPIT 178 Query: 196 FPNSDANYAAYAQGRCEGVTSDRSQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDS 255 F SD + + GRC+ +TSD+SQL A+R+ L+ + +L ISKEPL P N D Sbjct: 179 FDTSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDD 238 Query: 256 PWFDVVKWVVNATIQAEEFGITQANID-QFKTSKNPEIRRFLGLEGELGQQLGLSNDFAY 314 W +V+W A + AEE G+T N++ + K++KNP++ R LG +GE G+ L L D+ Sbjct: 239 EWLAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVV 298 Query: 315 RAIKAVGNYGEIYERNVGQQSPLKLNRGLNQLYKNGGLLYSPPFR 359 + +K VGNYGE++ERN+G+ +PL+++RGLN L+ GG+ Y+PP R Sbjct: 299 KIVKQVGNYGEMFERNLGKDTPLQIDRGLNALWNAGGIQYAPPVR 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: 285 Number of extensions: 10 Number of successful extensions: 3 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 Apr 09 2024. 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