GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaG in Pseudomonas fluorescens FW300-N2E3

Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate AO353_17210 AO353_17210 protocatechuate 3,4-dioxygenase

Query= BRENDA::Q0SH27
         (237 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17210
          Length = 234

 Score =  271 bits (692), Expect = 1e-77
 Identities = 124/215 (57%), Positives = 155/215 (72%), Gaps = 1/215 (0%)

Query: 19  LFPEYKTTRLRSPKNDLILIPQRLGEITGPVFGDADVAKGENDMTHANGGEAQGQRIIVH 78
           L P Y++T  RSP   L+ +P  L EITGP  G   + + +ND+T  + G   G+RII+H
Sbjct: 19  LHPAYQSTNRRSPSKPLVFLPHSLSEITGPTIGAESLQERDNDLTAQHQGAPLGERIIIH 78

Query: 79  GRVLDSAGKPIPDTLIEVWQANAGGRYRHKMDSWPAPLDPHFNGVARCLTDKQGHYEFTT 138
           GRVLD  G P+P  L+E+WQANA GRY H  D   APLDP+F G  R +TD  G Y+F T
Sbjct: 79  GRVLDENGLPVPGILVEIWQANAAGRYNHDRDLHDAPLDPNFTGTGRTVTDADGWYQFQT 138

Query: 139 IKPGAYPWGNHHNAWRPAHIHFSLFGQAFTQRLVTQMYFPDDPFFFQDPIYNSVPE-AAR 197
           IKPGAYPWGNHHNAWRPAHIHFSLFG +   RLVTQMYFP DP    DPIYN VP+ +A+
Sbjct: 139 IKPGAYPWGNHHNAWRPAHIHFSLFGPSILTRLVTQMYFPGDPLLAYDPIYNCVPDTSAK 198

Query: 198 ERMISTFDYDHTRDNWAVGFKFDIVLRGRDATPFE 232
           ER+I++FD + T  ++A+G+++DIVLRGRDATP E
Sbjct: 199 ERLIASFDLEKTIPSYALGYRWDIVLRGRDATPME 233


Lambda     K      H
   0.322    0.140    0.458 

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: 232
Number of extensions: 5
Number of successful extensions: 2
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: 237
Length of database: 234
Length adjustment: 23
Effective length of query: 214
Effective length of database: 211
Effective search space:    45154
Effective search space used:    45154
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 (21.9 bits)
S2: 46 (22.3 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