GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catA in Rhizobium etli CFN 42

Align catechol 1,2-dioxygenase 1; EC 1.13.11.1 (characterized)
to candidate WP_011427915.1 RHE_RS24310 protocatechuate 3,4-dioxygenase subunit beta

Query= CharProtDB::CH_014952
         (311 letters)



>NCBI__GCF_000092045.1:WP_011427915.1
          Length = 249

 Score = 79.7 bits (195), Expect = 6e-20
 Identities = 56/164 (34%), Positives = 76/164 (46%), Gaps = 29/164 (17%)

Query: 100 GTPRTIEGPLYVAGATVHDGVSKID-------INPDEDA--GPLVIHGTVTGPDGKPVAG 150
           GT   I GP++      H  + ++D         P E A    +++HG V     KPVAG
Sbjct: 47  GTISEITGPVFG-----HSMIGELDNDLILNYARPGESAIGERIIVHGRVLDERAKPVAG 101

Query: 151 AVVECWHANSKGFYSHFDPT---GAQSDFNLRGAVKTGADGKYEFRTLMPVGYGCPPQGA 207
           A+VE W AN+ G Y H   T       +F   G   T  +G+Y FRT+ P  Y  P    
Sbjct: 102 ALVEFWQANAGGRYRHKKETYLAAIDPNFGGCGRAITDEEGRYHFRTVRPGAYPWPN--- 158

Query: 208 TQQLLNVLGRHGNRPAHVHFFVSSDS-ARKLTTQFNIEGDPLIW 250
                   G +  RPAH+HF +     A++L TQ   EGDP+IW
Sbjct: 159 --------GVNDWRPAHIHFSIFGHGFAQRLITQMYFEGDPMIW 194


Lambda     K      H
   0.316    0.136    0.404 

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: 211
Number of extensions: 12
Number of successful extensions: 4
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: 311
Length of database: 249
Length adjustment: 25
Effective length of query: 286
Effective length of database: 224
Effective search space:    64064
Effective search space used:    64064
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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