GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Rhizobium freirei PRF 81

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate WP_004117116.1 RHSP_RS12195 4-hydroxy-2-oxovalerate aldolase

Query= SwissProt::P23522
         (256 letters)



>NCBI__GCF_000359745.1:WP_004117116.1
          Length = 260

 Score =  129 bits (323), Expect = 8e-35
 Identities = 74/230 (32%), Positives = 120/230 (52%)

Query: 10  FKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSA 69
           F+     +++ +G ++A+ +P++ EV   AG D+L +D EH+          + A     
Sbjct: 4   FRRNCIERRLIVGTFAAIPHPVAIEVTAAAGVDFLCIDWEHSQIGRERIEDLIRAADLHR 63

Query: 70  SAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRA 129
              +VRVP +    I  +LD G    L+P + T E+A  AV +TRYPP G RGV     A
Sbjct: 64  VPAMVRVPGHAAEDIAAVLDAGAAGVLVPRISTAEQARAAVQATRYPPLGARGVGPGRAA 123

Query: 130 NMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGN 189
                + DY A++N  + + +Q+E+ +G+ NV  IAA +GVD IF+GP DL+ ++  +G 
Sbjct: 124 AYGYRIPDYLAKANAELVLAIQVETAEGLANVADIAAVDGVDLIFIGPGDLSVSIDAIGP 183

Query: 190 ASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSD 239
           A    +  AI+ I   A +  +  GI  P   D   + + G +F  + SD
Sbjct: 184 AGKEKLDAAIRTITETALSADRAVGIFRPSPDDVGAWSQAGISFFLLASD 233


Lambda     K      H
   0.318    0.134    0.392 

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: 169
Number of extensions: 11
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: 256
Length of database: 260
Length adjustment: 24
Effective length of query: 232
Effective length of database: 236
Effective search space:    54752
Effective search space used:    54752
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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