GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Caulobacter crescentus NA1000

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate CCNA_01375 CCNA_01375 lactoylglutathione lyase

Query= BRENDA::P0A0T3
         (138 letters)



>FitnessBrowser__Caulo:CCNA_01375
          Length = 145

 Score = 96.7 bits (239), Expect = 1e-25
 Identities = 53/131 (40%), Positives = 77/131 (58%), Gaps = 11/131 (8%)

Query: 1   MRLLHTMLRVGNLEKSLDFYQNVLGMKLLRRKDYPEGRFTLAFVGYGDETD------STV 54
           MR LHTM+RV +L+ SL FY   LG++ + R +  +GRFTL F+   ++ +      + +
Sbjct: 1   MRYLHTMIRVRDLDASLRFYCKGLGLQEMYRTENEKGRFTLVFLAAPEDVELAKARKAPL 60

Query: 55  LELTHNWDTERYDLGNAYGHIAVEVDDAYEACERVKRQGGNVVREAGPMKHGTTVIAFVE 114
           +ELT+NWD E Y  G  +GH+A  VDD YE C+R+   G  + R   P + G   +AFV 
Sbjct: 61  VELTYNWDDEEYGGGRNFGHLAYRVDDIYETCQRLMDMGVTINR---PPRDGH--MAFVR 115

Query: 115 DPDGYKIEFIQ 125
            PD   IE +Q
Sbjct: 116 SPDNISIELLQ 126


Lambda     K      H
   0.318    0.137    0.405 

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: 77
Number of extensions: 4
Number of successful extensions: 3
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: 138
Length of database: 145
Length adjustment: 16
Effective length of query: 122
Effective length of database: 129
Effective search space:    15738
Effective search space used:    15738
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 (21.7 bits)
S2: 42 (20.8 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