GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PCBD in Sinorhizobium meliloti 1021

Align Pterin-4-alpha-carbinolamine dehydratase; PHS; 4-alpha-hydroxy-tetrahydropterin dehydratase; Overlapping meiotic transcript 2; Pterin carbinolamine dehydratase; PCD; EC 4.2.1.96 (characterized)
to candidate SMc03834 SMc03834 pterin-4-alpha-carbinolamine dehydratase

Query= SwissProt::O42658
         (96 letters)



>FitnessBrowser__Smeli:SMc03834
          Length = 104

 Score = 95.5 bits (236), Expect = 1e-25
 Identities = 43/77 (55%), Positives = 56/77 (72%)

Query: 18 WILQQGDTKLFKSFRFKNFIEAWGFMSCVALRAQQLNHHPEWTNVYNKVDITLTTHDTKG 77
          W+L +    ++K+FRFK F EA+ FM+  A  A++LNHHPEW NVYNKVD+TL+THD  G
Sbjct: 21 WVLAEDGGSIWKTFRFKTFAEAFTFMTQCAFAAEKLNHHPEWFNVYNKVDVTLSTHDADG 80

Query: 78 LTEKDLKLAEFIDTLAK 94
          LTE D KLA  +D  A+
Sbjct: 81 LTELDFKLAAKMDQAAE 97


Lambda     K      H
   0.319    0.131    0.396 

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: 45
Number of extensions: 1
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: 96
Length of database: 104
Length adjustment: 11
Effective length of query: 85
Effective length of database: 93
Effective search space:     7905
Effective search space used:     7905
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: 39 (20.9 bits)
S2: 39 (19.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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