GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cadA in Pseudomonas fluorescens FW300-N2E2

Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate Pf6N2E2_2991 decarboxylase

Query= BRENDA::A0A2Z4EVE5
         (218 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2991
          Length = 372

 Score = 60.8 bits (146), Expect = 3e-14
 Identities = 57/193 (29%), Positives = 93/193 (48%), Gaps = 15/193 (7%)

Query: 13  RRICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDG-GR-H 70
           R++ VF  +    +      A ELG  L   ++ ++ G G     G +  A H+G GR H
Sbjct: 85  RKVTVFGSARTPIEHPLYGLARELGAALARSDMMVITGAG-----GGIMAAAHEGAGRDH 139

Query: 71  VIGVIPKTLMPRELTGETVGEVKAVADMH---QRKAEMARHSDAFIALPGGYGTLEELLE 127
            +G    TL   +    TV     +   H    RK    + +DA +  PGG+GTL+E LE
Sbjct: 140 SLG-FNITLPFEQHANPTVEGTPNLLPFHFFFTRKLFFVKEADALVLCPGGFGTLDEALE 198

Query: 128 VITWAQLGIHD-KPVGLLNVDG--YYNSLLSFIDKAVEEG-FISPSARHIIVSAPTAKEL 183
           V+T  Q G     PV LL+V G  ++   L+FI + +EE  +I P+   ++     A+E 
Sbjct: 199 VLTLVQTGKSPLVPVVLLDVPGGKFWQGALNFIREQLEENRYILPTDMKLMRLVYNAEEA 258

Query: 184 VKKLEEYVPSHES 196
           V+++ ++  +  S
Sbjct: 259 VEEINQFYRNFHS 271


Lambda     K      H
   0.316    0.134    0.383 

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: 188
Number of extensions: 16
Number of successful extensions: 1
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: 218
Length of database: 372
Length adjustment: 26
Effective length of query: 192
Effective length of database: 346
Effective search space:    66432
Effective search space used:    66432
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 (21.6 bits)
S2: 47 (22.7 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