GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudomonas fluorescens FW300-N2C3

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AO356_14000 AO356_14000 aldehyde dismutase

Query= BRENDA::P35497
         (357 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14000
          Length = 399

 Score = 98.6 bits (244), Expect = 3e-25
 Identities = 91/273 (33%), Positives = 123/273 (45%), Gaps = 32/273 (11%)

Query: 4   NSNPAVVLEKVGDIAIEQRPIPTIKDP------HYVKLAIKATGICGSDIHYYRSGGIGK 57
           + N  VV    G + +++   P ++DP      H V L + +T ICGSD H  R    G+
Sbjct: 2   SGNRGVVYLGNGKVEVQKIDYPKMQDPRGRKIEHGVILRVVSTNICGSDQHMVR----GR 57

Query: 58  YILKAPMVLGHESSGQVVEVGDAVTRVKVGDRVAIEPGVPSRYSDETKEGRYNLC----P 113
              +  +VLGHE +G+V+E G  V  +K+GD V++   V        KE    +C    P
Sbjct: 58  TTAQTGLVLGHEITGEVIEKGSDVENLKIGDLVSVPFNVACGRCRSCKEQHTGVCLTVNP 117

Query: 114 HMAFAATPPID-----GTLVKYYLSP-EDF-LVKLPEGVSYEEG----ACVEP-LSVGVH 161
             A  A   +D     G   +Y L P  DF L+KLP+     E      C+   L  G H
Sbjct: 118 ARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYH 177

Query: 162 SNKLAGVRFGTKVVVFGAGPVGLLTGAVARAFGATDVIFVDVFDNKLQRAKDFGATNTFN 221
               AGV  G+ V + GAGPVGL   A AR  GA  VI  DV   +L  AK  G    F 
Sbjct: 178 GAVTAGVGPGSTVYIAGAGPVGLAAAASARLLGAAVVIIGDVNPVRLAHAKAQG----FE 233

Query: 222 SSQFSTDKAQDLADGVQKLLGGNHADVVFECSG 254
            +  STD    L + +  LLG    D   +  G
Sbjct: 234 IADLSTD--TPLHEQIAALLGEPEVDCAVDAVG 264


Lambda     K      H
   0.318    0.137    0.403 

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: 371
Number of extensions: 21
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: 357
Length of database: 399
Length adjustment: 30
Effective length of query: 327
Effective length of database: 369
Effective search space:   120663
Effective search space used:   120663
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: 50 (23.9 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