GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Pseudomonas fluorescens FW300-N2E3

Align Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; EC 4.1.3.17; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.1.112; Regulator of ribonuclease activity homolog; RraA-like protein (uncharacterized)
to candidate AO353_07830 AO353_07830 dimethylmenaquinone methyltransferase

Query= curated2:Q9KBI9
         (210 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07830
          Length = 231

 Score =  125 bits (313), Expect = 8e-34
 Identities = 71/185 (38%), Positives = 100/185 (54%), Gaps = 1/185 (0%)

Query: 8   FITQFRTIPTTCISDALDGLTNLTSTIKPLNENDQVVGPARTVQVASGDNLAVLKAMYEA 67
           ++ +F  IP   +SD L G       +K  + N  ++G A TV+V  GDNL +LKAM  A
Sbjct: 27  WLKEFSKIPAAAVSDCL-GRNVGGLGLKAFHGNAPMLGSALTVRVRPGDNLMILKAMQMA 85

Query: 68  SPGDVIVIDAKGDCTRAIAGDFVLGMAKTLGIAGFVVDGAIRDIRASKALNFPIFCRGTT 127
            PGDV+VID   D TRA+ G  +  MA   GI G V++GA+RD+   +    P +  G  
Sbjct: 86  RPGDVLVIDGSADLTRAVFGGIMRAMALKAGIVGVVINGALRDLDEWQTGELPAYAIGGV 145

Query: 128 IAASKKTGIGNINVPISCGGVPIRPGDLIVGDADGVTVIPKGQEENVLQKAKKKQADDEA 187
                  G G INVPISC G+ + PGDL++GD DGV    + +   +L +     A ++A
Sbjct: 146 HRGPSTDGGGEINVPISCAGMLVAPGDLMIGDGDGVVAASRSELPELLVRCHDLLAREQA 205

Query: 188 RERAI 192
              AI
Sbjct: 206 TLAAI 210


Lambda     K      H
   0.318    0.136    0.384 

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: 155
Number of extensions: 8
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: 210
Length of database: 231
Length adjustment: 22
Effective length of query: 188
Effective length of database: 209
Effective search space:    39292
Effective search space used:    39292
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 (21.7 bits)
S2: 45 (21.9 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:

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