GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natF in Pseudomonas fluorescens FW300-N1B4

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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917 Glutamate Aspartate
           periplasmic binding protein precursor GltI (TC
           3.A.1.3.4)
          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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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