GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Azohydromonas australica DSM 1124

Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate WP_028999516.1 H537_RS0121640 2-hydroxyacid dehydrogenase

Query= SwissProt::P53839
         (350 letters)



>NCBI__GCF_000430725.1:WP_028999516.1
          Length = 325

 Score =  137 bits (345), Expect = 4e-37
 Identities = 86/256 (33%), Positives = 138/256 (53%), Gaps = 18/256 (7%)

Query: 72  DEELALALPSSVVAVCHTGAGYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGAL 131
           D  +  ALP   V +   G G D+ID+   ++R IQV   P ++ +  ADT + L++ A 
Sbjct: 66  DAAMMAALPGLQV-ISSFGVGLDRIDLAAARERGIQVGYTPHVLDDCVADTAMGLVIDAA 124

Query: 132 RNFGIGNRRLIEGNWPEAGPACGSPFGY--DPEGKTVGILGLGRIGRCILERLKPFGFEN 189
           R     +R +  G WP      G PF       G  +GI+G+GRIG+ I  R + F  E 
Sbjct: 125 RGLSAADRYVRAGRWP------GGPFATMRKVSGARMGIVGMGRIGQQIAARAEGFRME- 177

Query: 190 FIYHNRH---QLPSEEEHGCEYVGFEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDG 246
             YH R    +LP   E     +      + +D + + +P    T H+++A  ++ +   
Sbjct: 178 VRYHARQPVSRLPQAHEPSLHALA-----RWADFLVLALPGGAATRHIVDAAVLDALGPE 232

Query: 247 VVIVNTARGAVIDEQAMTDALRSGKIRSAGLDVFEYEPKISKELLSMSQVLGLPHMGTHS 306
             +VN ARG+V+DE A+ +AL  G+I  AGLDV++ EP++ + LL +  V+ LPH+G+++
Sbjct: 233 GFLVNIARGSVVDEDALVEALAEGRIAGAGLDVYQNEPRVPERLLQLDNVVLLPHVGSNT 292

Query: 307 VETRKKMEELVVENAK 322
            ETR  M +LVV+N +
Sbjct: 293 RETRAAMADLVVDNLR 308


Lambda     K      H
   0.317    0.136    0.396 

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: 244
Number of extensions: 6
Number of successful extensions: 2
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: 350
Length of database: 325
Length adjustment: 28
Effective length of query: 322
Effective length of database: 297
Effective search space:    95634
Effective search space used:    95634
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.

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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