GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Phaeobacter inhibens BS107

Align Probable lactoylglutathione lyase; EC 4.4.1.5; Aldoketomutase; Glyoxalase I; Glx I; Ketone-aldehyde mutase; Methylglyoxalase; S-D-lactoylglutathione methylglyoxal lyase (uncharacterized)
to candidate GFF2088 PGA1_c21210 putative lactoylglutathione lyase

Query= curated2:Q9KT93
         (138 letters)



>FitnessBrowser__Phaeo:GFF2088
          Length = 142

 Score = 89.0 bits (219), Expect = 3e-23
 Identities = 51/130 (39%), Positives = 79/130 (60%), Gaps = 9/130 (6%)

Query: 5   RILHTMLRVGDLDKSIEFYTQVMGMSLLRKNENTEYKYTLAFLGYGDESQGAVIELTYNW 64
           + LHTM+RV DL+KS+ FY  ++G+   ++ ++ + +++L F+   +  +   IELTYNW
Sbjct: 4   KYLHTMVRVKDLEKSMAFYA-LLGLKETKRYDSEKGRFSLIFMA-AEGQEDTPIELTYNW 61

Query: 65  GVADYEKGNA--YGHIAIGVDDIYATCDTIKAAGGIVTREPGPVKGGTTHIAFVKDPDGY 122
              D    ++  +GH+A GVDDIYATC  +   G  + R P   + G  H+AFV+ PD  
Sbjct: 62  DGDDALPSDSRHFGHLAYGVDDIYATCQHLMDNGVTINRPP---RDG--HMAFVRSPDNI 116

Query: 123 MIELIQNKQA 132
            IEL+QN  A
Sbjct: 117 SIELLQNGDA 126


Lambda     K      H
   0.317    0.138    0.408 

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: 87
Number of extensions: 8
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: 138
Length of database: 142
Length adjustment: 15
Effective length of query: 123
Effective length of database: 127
Effective search space:    15621
Effective search space used:    15621
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: 42 (20.8 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