GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF in Acidovorax sp. GW101-3H11

Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate Ac3H11_413 N-formylglutamate deformylase (EC 3.5.1.68)

Query= BRENDA::G3KFX4
         (282 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_413
          Length = 331

 Score = 83.6 bits (205), Expect = 5e-21
 Identities = 77/263 (29%), Positives = 121/263 (46%), Gaps = 20/263 (7%)

Query: 31  PVLLIHGSGPGVTAWANWRLVMPQLAQNRRVIAPDMLGFGYSDRPADGRYHQQRWVEHAI 90
           P++L+HG       W ++    P  AQ R V+APD  GFG S R  D  Y      +   
Sbjct: 74  PLVLLHGIFAEKDHWVDF--ARPLTAQYR-VVAPDFPGFGESTRLDDQPYDYAAHTQRLG 130

Query: 91  GVLDALGIQQADIVGNSFGGGLALALAIRHPERVRRLVLMGSV-GVSFPITPGLDAV--W 147
            +LDALGI++A + GNS GG +A   A++HPE V  +  +G+  G+  P    +D +   
Sbjct: 131 ALLDALGIEKAHLAGNSMGGTIAALFALQHPEHVASVAFIGAPHGIHSPKPSTMDRLIDA 190

Query: 148 GYEP----SFASMRRLMDVFAYDRSLVTNELAELRYQASIRPGFQESFAQMFPAPRQRWV 203
           G  P      A+   +MD+    R  +   +     QA++  G   S  +++ A  +   
Sbjct: 191 GQRPLVAHDAATFSAMMDLVFEKRPFLPYPILHATEQAAL--GNAASNTRLWDAQLK--- 245

Query: 204 DGLASDEADIRALPHETLVIHGREDQVIPLAASLTLAEWIARAQLHVFGHCGHWTQIE-- 261
           D    ++       H  L + G  D+V   +  L L + + +AQL      GH   +E  
Sbjct: 246 DRYLLEQRLGGLQQHPVLALWGDSDRVFDRSGLLPLQKLLPQAQLEALPGVGHLPMMEAP 305

Query: 262 --HAERFARLVENFLAEADALHS 282
              A+R+AR +E  LA + AL S
Sbjct: 306 ADTAQRYARFLEG-LAPSSALAS 327


Lambda     K      H
   0.323    0.138    0.432 

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: 279
Number of extensions: 15
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: 282
Length of database: 331
Length adjustment: 27
Effective length of query: 255
Effective length of database: 304
Effective search space:    77520
Effective search space used:    77520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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