GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaH in Rhizobium etli CFN 42

Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate WP_011427914.1 RHE_RS24305 protocatechuate 3,4-dioxygenase subunit alpha

Query= BRENDA::A0A193DXA9
         (206 letters)



>NCBI__GCF_000092045.1:WP_011427914.1
          Length = 203

 Score =  270 bits (691), Expect = 1e-77
 Identities = 132/205 (64%), Positives = 156/205 (76%), Gaps = 2/205 (0%)

Query: 2   VQPLNYFKETASQTAGPYVHIGCTPNFVGIEGVFEKDLGSGPLYNDKARGERISVRGTVY 61
           +Q L Y KET SQTAGPYVHIG TPNF  I GV++ DLG+  + NDK  GERI+V G ++
Sbjct: 1   MQQLGYLKETPSQTAGPYVHIGLTPNFCDITGVYDSDLGT-QMVNDKTLGERITVTGRIF 59

Query: 62  DGAGMPLKDALIEIWQADTDGYYNSPSETRGKADPNFIGWGRSPGDMDTGEFVFETIKPG 121
           DGAG  ++DA+ EIWQAD+ G YNSPSE RG ADPNF GWGR P   + G + FETIKPG
Sbjct: 60  DGAGALVRDAVAEIWQADSAGLYNSPSELRGAADPNFAGWGRCPTRAEDGVYSFETIKPG 119

Query: 122 SVPFRDGRPMAPHITFWIVARGINIGLQTRMYFPEEQEANAADPVLARIEQKSRIATLVA 181
            VPF+DGR  APHIT WIVARGINIGL TRMYFPEE EANA+DP+L+RIE + R+AT++A
Sbjct: 120 RVPFKDGRRQAPHITVWIVARGINIGLHTRMYFPEETEANASDPLLSRIEHRERVATMIA 179

Query: 182 KKEEGNVYRFDIRLQGEGETVFFDI 206
            + +G    FDI LQG  ETVF DI
Sbjct: 180 TR-DGATCHFDIHLQGPHETVFLDI 203


Lambda     K      H
   0.318    0.139    0.426 

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: 210
Number of extensions: 7
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: 206
Length of database: 203
Length adjustment: 21
Effective length of query: 185
Effective length of database: 182
Effective search space:    33670
Effective search space used:    33670
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: 45 (21.9 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