GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Cupriavidus basilensis 4G11

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate RR42_RS19805 RR42_RS19805 enoyl-CoA hydratase

Query= reanno::Cup4G11:RR42_RS28545
         (384 letters)



>FitnessBrowser__Cup4G11:RR42_RS19805
          Length = 258

 Score = 74.3 bits (181), Expect = 3e-18
 Identities = 51/153 (33%), Positives = 78/153 (50%), Gaps = 12/153 (7%)

Query: 23  VRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAG 82
           V +    G+  ITLNRP  LNAL+  ++  L A +   AA+D+    V+  A  + FCAG
Sbjct: 5   VLYHAAEGVATITLNRPDVLNALNSALLLELRAAVER-AAQDEAVRAVVLSANGRGFCAG 63

Query: 83  GDIRA----LYDSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQA 138
            D+      L DS   GT L  ++    + +   L   PKPV+  ++G+  G GM LA A
Sbjct: 64  ADLAGRGTGLQDS---GTLLRERY----HPIILALRNMPKPVITSVNGVAAGAGMSLALA 116

Query: 139 AHLRVLTERSRVAMPETGIGLVPDVGASHFLSK 171
             + +    +      + IGLVPD G+++FL +
Sbjct: 117 GDVVLAGRSASFLQAFSKIGLVPDAGSTYFLPR 149


Lambda     K      H
   0.322    0.137    0.405 

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: 228
Number of extensions: 10
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: 384
Length of database: 258
Length adjustment: 27
Effective length of query: 357
Effective length of database: 231
Effective search space:    82467
Effective search space used:    82467
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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