GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Dechlorosoma suillum PS

Align 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway) protein; EC 4.2.1.80 (characterized, see rationale)
to candidate Dsui_1428 Dsui_1428 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase

Query= uniprot:D8INW0
         (281 letters)



>FitnessBrowser__PS:Dsui_1428
          Length = 238

 Score =  118 bits (296), Expect = 1e-31
 Identities = 78/217 (35%), Positives = 110/217 (50%), Gaps = 23/217 (10%)

Query: 70  IGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVV----GPNDNVKIPRGSKKTDWEV 125
           + +  C+G NYADHA E        P  F+K   A+V    G    V  P  +     EV
Sbjct: 24  VRRVYCVGRNYADHAREMGADTREPPFFFSKPADALVPVADGSAATVAYPPATNNLQHEV 83

Query: 126 ELGVIIG-------KGGSYIDEKDAMSHVAGYCVVNDVSEREYQI---ERGGTWDKGKGC 175
           EL V +G       + G  +    A+  V GY V  D++ R+ Q    E+   WD GKG 
Sbjct: 84  ELVVALGPRIAELGQRGLNVPVAAALEGVFGYAVGFDLTRRDQQQKAKEKAHPWDMGKGF 143

Query: 176 DTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFNVAHIVSYLSRFMSLQP 235
           D  GPIG  +V   +   P    +WLEV+G+R Q+G+ + M +NVA +V+ LS F+ L P
Sbjct: 144 DQSGPIGA-IVPAAQAGHPASGAIWLEVNGERRQSGDLAQMSWNVAEVVANLSTFLRLAP 202

Query: 236 GDVISTGTPPGVGMGVKPEAVYLRAGQTIRLGIDGLG 272
           GD+I TGTP GV   V+        G T+  G++G+G
Sbjct: 203 GDLIFTGTPAGVSTVVR--------GDTLVGGVEGIG 231


Lambda     K      H
   0.316    0.139    0.421 

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: 211
Number of extensions: 15
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: 281
Length of database: 238
Length adjustment: 24
Effective length of query: 257
Effective length of database: 214
Effective search space:    54998
Effective search space used:    54998
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