GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catB in Pseudomonas simiae WCS417

Align Muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate GFF4626 PS417_23670 muconate cycloisomerase

Query= reanno::WCS417:GFF4626
         (375 letters)



>FitnessBrowser__WCS417:GFF4626
          Length = 375

 Score =  733 bits (1891), Expect = 0.0
 Identities = 375/375 (100%), Positives = 375/375 (100%)

Query: 1   MPICAIESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYG 60
           MPICAIESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYG
Sbjct: 1   MPICAIESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYG 60

Query: 61  NESPDSIKVNIDRHFAPLLIGQDASNINAAMLRLERSIRGNTFAKSGIESALLDALGKRL 120
           NESPDSIKVNIDRHFAPLLIGQDASNINAAMLRLERSIRGNTFAKSGIESALLDALGKRL
Sbjct: 61  NESPDSIKVNIDRHFAPLLIGQDASNINAAMLRLERSIRGNTFAKSGIESALLDALGKRL 120

Query: 121 NLPVSELLGGRVRDALPVAWTLASGNTEKDIAEAEKMLDLRRHRLFKLKIGAGEVSHDLA 180
           NLPVSELLGGRVRDALPVAWTLASGNTEKDIAEAEKMLDLRRHRLFKLKIGAGEVSHDLA
Sbjct: 121 NLPVSELLGGRVRDALPVAWTLASGNTEKDIAEAEKMLDLRRHRLFKLKIGAGEVSHDLA 180

Query: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNL 240
           HVIAIKKALGDRASVRVDVNQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNL
Sbjct: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNL 240

Query: 241 SSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGG 300
           SSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGG
Sbjct: 241 SSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGG 300

Query: 301 TMLEGGIGTLASAHAFLTLNKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGL 360
           TMLEGGIGTLASAHAFLTLNKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGL
Sbjct: 301 TMLEGGIGTLASAHAFLTLNKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGL 360

Query: 361 AIDEERLAFFRRDKH 375
           AIDEERLAFFRRDKH
Sbjct: 361 AIDEERLAFFRRDKH 375


Lambda     K      H
   0.320    0.137    0.394 

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: 622
Number of extensions: 14
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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