GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Paraburkholderia bryophila 376MFSha3.1

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate H281DRAFT_01137 H281DRAFT_01137 2-oxoglutaroyl-CoA hydrolase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__Burk376:H281DRAFT_01137
          Length = 268

 Score =  118 bits (296), Expect = 1e-31
 Identities = 82/250 (32%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 6   IKVEKDERVARIKIANPPVNVLDM---ETMKEIISAIDEVEGVDVIVFSGEGKSFSAGAE 62
           I+++ +   A I +  PP NV+ M   + ++    A+DE E V VIV   +G+ FS+G +
Sbjct: 20  IEIDAERERADIVLHRPPFNVISMHARDQLRAAFEALDEDERVRVIVVRAKGEHFSSGGD 79

Query: 63  IKEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKL 122
           IK  F + +PE +      I    RC    +AA +GF  G GFEL++ACDF +A+     
Sbjct: 80  IKG-FLEASPEHVSKLAWNIAAPARCSKPVIAANRGFCFGVGFELSLACDFRIATDTTFY 138

Query: 123 GVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEE 181
            +PE  L   P     A L +M+G     ++++    I  ++A+E G+  +   D   E 
Sbjct: 139 ALPEQKLGQIPGSGGSARLQQMVGIGRTKDIVMRSRRIPGKQAYEWGIAVECVADAQLEA 198

Query: 182 SVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAF 241
           + +  V+ L   S +A R  KK LL  TE   LS+   +     S+L  S+D  EG++AF
Sbjct: 199 ATDALVDELRAFSPLAQRTAKK-LLNDTEDAPLSIAIELEGHCYSRLRTSDDFREGVEAF 257

Query: 242 LEKRKPEWKG 251
             KRKP ++G
Sbjct: 258 HGKRKPVFRG 267


Lambda     K      H
   0.318    0.136    0.382 

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: 153
Number of extensions: 11
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: 252
Length of database: 268
Length adjustment: 24
Effective length of query: 228
Effective length of database: 244
Effective search space:    55632
Effective search space used:    55632
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: 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