GapMind for catabolism of small carbon sources

 

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

Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate AO356_14000 AO356_14000 aldehyde dismutase

Query= SwissProt::O87871
         (368 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14000
          Length = 399

 Score = 79.0 bits (193), Expect = 2e-19
 Identities = 60/198 (30%), Positives = 88/198 (44%), Gaps = 16/198 (8%)

Query: 45  VVVAVAGCGVCHTDLGYYYDSVRTNHALPLALGHEISGRVVQAGANAAQW-LGRAVIVPA 103
           V++ V    +C +D   +    RT     L LGHEI+G V++ G++     +G  V VP 
Sbjct: 37  VILRVVSTNICGSD--QHMVRGRTTAQTGLVLGHEITGEVIEKGSDVENLKIGDLVSVPF 94

Query: 104 VMPCGTCELCTSGHGTICRDQVMPGN-----------DIQGGFASHVVVPARGLCPVDEA 152
            + CG C  C   H  +C   V P             D  GG A +V+VP      +   
Sbjct: 95  NVACGRCRSCKEQHTGVCLT-VNPARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKLP 153

Query: 153 RLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIGVGGVGGYAVQIANAFGASV 212
               A  ++ D++ ++D + T Y   + AGV PG    + G G VG  A   A   GA+V
Sbjct: 154 DRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYIAGAGPVGLAAAASARLLGAAV 213

Query: 213 VAI-DVDPAKLEMMSKHG 229
           V I DV+P +L      G
Sbjct: 214 VIIGDVNPVRLAHAKAQG 231


Lambda     K      H
   0.320    0.134    0.406 

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: 343
Number of extensions: 20
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: 368
Length of database: 399
Length adjustment: 30
Effective length of query: 338
Effective length of database: 369
Effective search space:   124722
Effective search space used:   124722
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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