GapMind for catabolism of small carbon sources

 

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

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Pf6N2E2_2401 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2401
          Length = 270

 Score =  101 bits (252), Expect = 2e-26
 Identities = 85/249 (34%), Positives = 125/249 (50%), Gaps = 22/249 (8%)

Query: 20  PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGES-PAPDGPYSVRDLSEDVLAL 78
           PVV+L GS   + +MW PQI  LS   RV+A D  GHG+S   P+G  S+ DL+  ++ L
Sbjct: 20  PVVLLGGSYLWDHAMWAPQIEVLSRHYRVIAPDLWGHGQSGQMPEGMSSLNDLARQMMEL 79

Query: 79  LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQ-------AWIER 131
           LD L +D  H VGLS+GG     L   AP R+ SL L+ T     EP+       +  ++
Sbjct: 80  LDYLSIDCFHLVGLSVGGMWGTRLALAAPTRIQSLVLMDTYVGV-EPEQTRQYYFSLFDK 138

Query: 132 AAASRTDGPESLADAVVARWFSEGLAKRDPE--FVRHYREMIASTSPEGYAACCDALADW 189
             AS +  PE L D +V  +F  G+   DP+    + +R  +A+   +   A    L   
Sbjct: 139 IEASGSI-PEPLLDIIVPIFFRPGI---DPQSALYQQFRATLAALPSDRLRASIVPLGRI 194

Query: 190 DFTAD--LSRISA----PTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLE 243
            F  D  L R+ A     T+V+ G++D   PPS  + +A+ +      V+  A H++NLE
Sbjct: 195 IFGRDDILPRLHALDAKGTVVMCGDQDKPRPPSESREMAE-LIGCPHVVIPDAGHISNLE 253

Query: 244 QAGAVTALL 252
               VT  L
Sbjct: 254 NPEFVTGAL 262


Lambda     K      H
   0.318    0.132    0.392 

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: 239
Number of extensions: 13
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: 400
Length of database: 270
Length adjustment: 28
Effective length of query: 372
Effective length of database: 242
Effective search space:    90024
Effective search space used:    90024
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: 49 (23.5 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