GapMind for catabolism of small carbon sources

 

Aligments for a candidate for catB in Pseudomonas fluorescens FW300-N2E3

Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate AO353_23515 AO353_23515 muconate cycloisomerase

Query= metacyc::MONOMER-14643
         (382 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23515 AO353_23515 muconate
           cycloisomerase
          Length = 382

 Score =  696 bits (1797), Expect = 0.0
 Identities = 354/382 (92%), Positives = 369/382 (96%)

Query: 1   MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 60
           ML++AIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG
Sbjct: 1   MLSSAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 60

Query: 61  NESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRL 120
           NESPDSIKTNIDKHFAPLL+GQD+ N+NAAMLRLERSIRGNTFAKSGIETALLDAHGKRL
Sbjct: 61  NESPDSIKTNIDKHFAPLLLGQDACNINAAMLRLERSIRGNTFAKSGIETALLDAHGKRL 120

Query: 121 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA 180
           GLPVSELLGGRVRD+LPVAWTLASGDT KDIAEAE+MLDLRRHRIFKLKIGAGEV+RDLA
Sbjct: 121 GLPVSELLGGRVRDSLPVAWTLASGDTAKDIAEAEQMLDLRRHRIFKLKIGAGEVDRDLA 180

Query: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNA 240
           HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILG NGIDL+EQPISRNNR GM RLNA
Sbjct: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGGNGIDLIEQPISRNNRAGMVRLNA 240

Query: 241 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG 300
           MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTA+IAEAAGI LYGG
Sbjct: 241 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGG 300

Query: 301 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL 360
           TMLEGG+GT+ASAHAF+TLN+L+WDTELFGPLLLTEDILSEP VY DF LHV   PGLGL
Sbjct: 301 TMLEGGIGTLASAHAFLTLNELSWDTELFGPLLLTEDILSEPPVYCDFHLHVSQAPGLGL 360

Query: 361 SLDEERLAFFRRDKTSTAIHQA 382
           SLDEERLAFFRRDKTSTAIH A
Sbjct: 361 SLDEERLAFFRRDKTSTAIHSA 382


Lambda     K      H
   0.319    0.136    0.386 

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: 545
Number of extensions: 12
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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