GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Azospirillum brasilense Sp245

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase

Query= reanno::Pedo557:CA265_RS09125
         (258 letters)



>FitnessBrowser__azobra:AZOBR_RS18155
          Length = 248

 Score = 94.4 bits (233), Expect = 2e-24
 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 9/243 (3%)

Query: 13  IATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGD-AFSAGADLAYLQQ 71
           +ATIT++RP+K NA+ P++ A+L AA  + + DD ++ V+L   G  AF  G+D+  L  
Sbjct: 5   VATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIRELD- 63

Query: 72  LQYNTFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATICDIVFATPESNF 131
            +Y+T      +  + +     I  L K  IA V G+A  GG   A  CDI  A+  + F
Sbjct: 64  -RYDT----AWNFRNREDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENAQF 118

Query: 132 GYTEVKIGFV-PAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYNLINFVTNSSDIHQ 190
           G  E+K+G++    V+ FL   +  S A  ++LTG    A++AL + L++ V  +  +  
Sbjct: 119 GAPEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPADRLLA 178

Query: 191 IVREFALSLCSGSSGNSLMITKQLITQTTNPLLEKCLETAVQINARVRESEDFKKGISSF 250
             +E A  + S +   +      L    T P +EK +E    +      + D  +G ++F
Sbjct: 179 RAQEIAAIVASRAPIAAETAKLNLKAAHTMP-VEKAIEYERDLQTICFATADAAEGRAAF 237

Query: 251 LNK 253
             K
Sbjct: 238 KEK 240


Lambda     K      H
   0.318    0.133    0.367 

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: 122
Number of extensions: 4
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: 258
Length of database: 248
Length adjustment: 24
Effective length of query: 234
Effective length of database: 224
Effective search space:    52416
Effective search space used:    52416
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: 46 (22.3 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