GapMind for catabolism of small carbon sources

 

Alignments for a candidate for had in Pseudomonas fluorescens FW300-N2E3

Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate AO353_19865 AO353_19865 alcohol dehydrogenase

Query= SwissProt::O87871
         (368 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19865
          Length = 327

 Score = 87.4 bits (215), Expect = 5e-22
 Identities = 59/195 (30%), Positives = 84/195 (43%), Gaps = 11/195 (5%)

Query: 22  MMTSPGAPMVRAEFEIGELSADQVVVAVAGCGVCHTDLGYYYDSVRTNHALPLALGHEIS 81
           ++ +PG P+ R E  I    A Q+++ V  CGVC TDL +  D       LP   GHEI 
Sbjct: 5   VLQTPGQPLQREERAIPTPDAQQLLIKVLACGVCRTDL-HLVDGELPQATLPRVPGHEIV 63

Query: 82  GRVVQAGANAA-QWLGRAVIVPAV-MPCGTCELCTSGHGTICRDQVMPGNDIQGGFASHV 139
           G V   GA+ A  W+G+ V VP +   CG CE C SG   +C      G ++ GG+A + 
Sbjct: 64  GEVTAVGADVAPDWIGQRVGVPWLGSTCGRCEFCRSGRENLCDQAQFTGCNLDGGYADYT 123

Query: 140 VVPARGLCPVDEARLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIGVGGVGG 199
           V  AR    + +   A     L    ++        +     G        + G G    
Sbjct: 124 VADARFCFRLPDTLSATEAAPLLCAGLIGFRALQMAKTARHLG--------LYGFGAAAH 175

Query: 200 YAVQIANAFGASVVA 214
            A+Q+A   G  V A
Sbjct: 176 LAIQVALGRGQQVYA 190


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: 244
Number of extensions: 13
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: 368
Length of database: 327
Length adjustment: 29
Effective length of query: 339
Effective length of database: 298
Effective search space:   101022
Effective search space used:   101022
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: 49 (23.5 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