GapMind for catabolism of small carbon sources

 

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

Align 4a-hydroxytetrahydrobiopterin dehydratase (EC 4.2.1.96) (characterized)
to candidate AO353_18580 AO353_18580 pterin-4-alpha-carbinolamine dehydratase

Query= BRENDA::Q48G05
         (118 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_18580
          Length = 118

 Score =  228 bits (581), Expect = 2e-65
 Identities = 108/118 (91%), Positives = 112/118 (94%)

Query: 1   MSTLNQAHCEACRADAPQVSEAELPELLKQIPDWNIEVRDGVMQLEKVFLFKNFKFALAF 60
           M+ LNQAHCEACRADAPQVS+ ELP L+KQIPDWNIEVRDGVMQLEKVFLFKNFKFALAF
Sbjct: 1   MNALNQAHCEACRADAPQVSDEELPVLIKQIPDWNIEVRDGVMQLEKVFLFKNFKFALAF 60

Query: 61  TNAVGEIAEAEGHHPGLLTEWGKVTVTWWSHSIKGLHRNDFIMAARTDGVASGAEGRK 118
           TNAVGEI+EAEGHHPGLLTEWGKVTVTWWSHSIKGLHRNDFIMAARTD VA  AEGRK
Sbjct: 61  TNAVGEISEAEGHHPGLLTEWGKVTVTWWSHSIKGLHRNDFIMAARTDEVAKDAEGRK 118


Lambda     K      H
   0.319    0.133    0.415 

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: 109
Number of extensions: 3
Number of successful extensions: 1
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: 118
Length of database: 118
Length adjustment: 13
Effective length of query: 105
Effective length of database: 105
Effective search space:    11025
Effective search space used:    11025
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: 41 (20.4 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