GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Sinorhizobium meliloti 1021

Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate SMa0559 SMa0559 4-carboxymuconolactone decarboxylase

Query= curated2:P20370
         (134 letters)



>FitnessBrowser__Smeli:SMa0559
          Length = 247

 Score = 65.9 bits (159), Expect = 4e-16
 Identities = 28/83 (33%), Positives = 55/83 (66%)

Query: 40  FISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACFNNGVTKDELKELIL 99
           + + + + ++W RP L    RSLVTIA L+++G+ +++  HL    +NG+++++  E+I 
Sbjct: 161 YTTDYLFRDLWLRPDLAPRDRSLVTIAALISVGQVEQITFHLNKALDNGLSEEQAAEVIT 220

Query: 100 HCSLYAGLPASNAAMHMAEEVFK 122
           H + YAG P + +A+ +A+ VF+
Sbjct: 221 HLAFYAGWPNAMSALPVAKAVFE 243



 Score = 64.3 bits (155), Expect = 1e-15
 Identities = 33/94 (35%), Positives = 48/94 (51%)

Query: 38  QNFISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACFNNGVTKDELKEL 97
           + +  +  +G+VW RPGL R  RSLVTIA L+A G    L  +      NGV   E+ E 
Sbjct: 32  EQYTQQRLYGDVWQRPGLNRRDRSLVTIAALIARGEAPALTYYADQALENGVKPSEISET 91

Query: 98  ILHCSLYAGLPASNAAMHMAEEVFKDLGIAPEKV 131
           I H + Y+G   + A +    E F   GI  +++
Sbjct: 92  ITHLAYYSGWGKAMATVGPVSEAFAKRGIGQDQL 125


Lambda     K      H
   0.320    0.135    0.403 

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: 85
Number of extensions: 3
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 134
Length of database: 247
Length adjustment: 19
Effective length of query: 115
Effective length of database: 228
Effective search space:    26220
Effective search space used:    26220
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: 44 (21.6 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