GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catA in Burkholderia phytofirmans PsJN

Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate BPHYT_RS33455 BPHYT_RS33455 protocatechuate 3,4-dioxygenase subunit beta

Query= BRENDA::Q8GAZ6
         (300 letters)



>FitnessBrowser__BFirm:BPHYT_RS33455
          Length = 234

 Score = 65.1 bits (157), Expect = 1e-15
 Identities = 49/135 (36%), Positives = 63/135 (46%), Gaps = 19/135 (14%)

Query: 120 NGNEPGETLVMRGRVLAENGEPVRDALVEVWHANHLGNYSH-FDKSQAEFN-----LRRS 173
           NG   GE +++ GRVL E   PVR+ LVE+W AN  G Y H  D+  A  +       R 
Sbjct: 68  NGEPLGERIIVTGRVLDEGNRPVRNTLVEIWQANAAGRYVHKADQHDAPLDPNFLGAGRC 127

Query: 174 IRTDENGTYSFRSVVPIGYSVPPQGKTQQLLDLLGRHGHRPAHIHFFVSAPGY-RKLTTQ 232
           I TD  G Y F ++ P  Y   P G           +  RP HIHF +    +  +L TQ
Sbjct: 128 I-TDNEGRYRFLTIKPGAY---PWGNHP--------NAWRPNHIHFSLFGDHFGSRLVTQ 175

Query: 233 INIEGDPYLWDDFAF 247
           +   GDP L  D  F
Sbjct: 176 MYFPGDPLLAFDPIF 190


Lambda     K      H
   0.317    0.137    0.407 

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: 239
Number of extensions: 16
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: 300
Length of database: 234
Length adjustment: 25
Effective length of query: 275
Effective length of database: 209
Effective search space:    57475
Effective search space used:    57475
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 (21.6 bits)
S2: 47 (22.7 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