GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Cupriavidus basilensis 4G11

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate RR42_RS10010 RR42_RS10010 3-oxoadipate CoA-transferase

Query= reanno::psRCH2:GFF1044
         (209 letters)



>FitnessBrowser__Cup4G11:RR42_RS10010
          Length = 220

 Score =  179 bits (455), Expect = 3e-50
 Identities = 90/200 (45%), Positives = 128/200 (64%), Gaps = 1/200 (0%)

Query: 5   REQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDP 64
           R  +A R A+++ +G YVNLGIGLPTLVAN++P   +V L SENG+LG        + D 
Sbjct: 6   RNLLAARVARDIPNGAYVNLGIGLPTLVANHLPRHREVILHSENGVLGQWSAAEPGQEDW 65

Query: 65  DLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG-KMV 123
           +LINAGK+ +    G++FF +A +F M+RGGH+++ +LGA QVSE+GDLANW       +
Sbjct: 66  ELINAGKEAIRLERGAAFFHHADAFGMMRGGHLDICVLGAFQVSERGDLANWHTGAPDAI 125

Query: 124 KGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTEQ 183
             +GGAMDL  G K+V V+M+H  K G  K+   C  PLTG+  V R+ T+LG   +  Q
Sbjct: 126 PAVGGAMDLAIGAKQVFVMMDHLTKDGTSKLRRQCSYPLTGMACVSRVYTELGTFAIGPQ 185

Query: 184 GLKLVELAEGVSFDELQEAT 203
           G+ ++E+   +S   LQ  T
Sbjct: 186 GVSVIEIVGDMSSQALQSVT 205


Lambda     K      H
   0.318    0.138    0.404 

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: 155
Number of extensions: 7
Number of successful extensions: 2
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: 209
Length of database: 220
Length adjustment: 22
Effective length of query: 187
Effective length of database: 198
Effective search space:    37026
Effective search space used:    37026
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: 45 (21.9 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