GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Echinicola vietnamensis KMM 6221, DSM 17526

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Echvi_2939 Echvi_2939 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__Cola:Echvi_2939
          Length = 285

 Score =  149 bits (375), Expect = 1e-40
 Identities = 79/189 (41%), Positives = 116/189 (61%), Gaps = 9/189 (4%)

Query: 98  PPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157
           P    +F K++ +L+GP DDI++PR    EK D+EVEL V++GK A  VD+++AM +V G
Sbjct: 95  PKQPIIFMKSTTSLSGPNDDIIIPR--NSEKTDWEVELAVMIGKKASYVDKENAMDYVAG 152

Query: 158 YCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLA 216
           YC++NDVS R    + GGQW  GKS DT+ P GP LV+   +  DP  L +    NGK+ 
Sbjct: 153 YCLLNDVSERDFQLSHGGQWVKGKSNDTFSPLGPYLVTKDEI-KDPQHLRLWLKHNGKML 211

Query: 217 QKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEI 276
           Q  NT+D+V  IP L++ LS+  TL  G +I TG+P  +G       +    ++K+GD +
Sbjct: 212 QDSNTSDMVFDIPTLVSHLSNYMTLLPGDIISTGTPSGVGM-----GLTPPTYLKEGDVV 266

Query: 277 RCFVEGCGT 285
              ++G GT
Sbjct: 267 ELGIDGLGT 275


Lambda     K      H
   0.316    0.135    0.411 

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: 275
Number of extensions: 20
Number of successful extensions: 5
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: 308
Length of database: 285
Length adjustment: 26
Effective length of query: 282
Effective length of database: 259
Effective search space:    73038
Effective search space used:    73038
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: 48 (23.1 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