GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Thiothrix lacustris DSM 21227

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_028488570.1 Q394_RS0106530 fumarylacetoacetate hydrolase family protein

Query= reanno::Smeli:SM_b21112
         (281 letters)



>NCBI__GCF_000621325.1:WP_028488570.1
          Length = 294

 Score =  178 bits (452), Expect = 1e-49
 Identities = 93/226 (41%), Positives = 137/226 (60%), Gaps = 12/226 (5%)

Query: 63  LGPCVAGTGKFICIGLNYSDHAAETGATV------PPEPIIFMKATSAIVGPNDDLVLPR 116
           L P        +C+GLNY +HA ET   +      P  PI+F K  ++++G   D V+P 
Sbjct: 70  LAPIPRPRKNVMCLGLNYLEHAEETANQIGRTGKAPQYPIVFTKCPTSVIG--QDAVVPF 127

Query: 117 GSE---KTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGK 173
             +   + DWE ELG+V+GK  K ++ A ALD+V GY  ++D+S R  Q   H Q+  GK
Sbjct: 128 DPDTCSQLDWEAELGVVLGKGGKKIAAANALDHVFGYTVINDLSARDIQLS-HKQYFLGK 186

Query: 174 SCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSL 233
           S D   P GPW+VT D++ADPQ+LA+  +VNG T Q  +T+ M++  A ++ +LS+ M+L
Sbjct: 187 SLDGGCPMGPWIVTADDIADPQNLAIACRVNGVTKQASNTRNMIFNVASIIEWLSRGMTL 246

Query: 234 RPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRA 279
             GD+I+TGTP GVG   +PP +L  GDVVE  +E +G  +  + A
Sbjct: 247 EAGDVIATGTPSGVGFVREPPEFLLPGDVVECEVESVGVLRNSISA 292


Lambda     K      H
   0.315    0.136    0.408 

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: 243
Number of extensions: 16
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: 294
Length adjustment: 26
Effective length of query: 255
Effective length of database: 268
Effective search space:    68340
Effective search space used:    68340
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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