GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Azospirillum brasilense Sp245

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AZOBR_RS01260 AZOBR_RS01260 enoyl-CoA hydratase

Query= reanno::WCS417:GFF2712
         (367 letters)



>FitnessBrowser__azobra:AZOBR_RS01260
          Length = 258

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 63/190 (33%), Positives = 97/190 (51%), Gaps = 6/190 (3%)

Query: 17  DEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFC 76
           + +L E R  +G +TLNRP  LNA++  +V  L   L A   D  V A+V+ G+ EKAF 
Sbjct: 4   ETILVETRGPVGLVTLNRPKALNALSDLLVTELGQALDALEADDSVGAIVVTGS-EKAFA 62

Query: 77  AGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGAD 136
           AG DI+ +  +F   D    +F   ++     +   RKP +A + G+ LGGG  L   AD
Sbjct: 63  AGADIKEM-QNFSYMDVYKANFITAKWE---RLAKCRKPTIAAVAGYALGGGCELAMMAD 118

Query: 137 LRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGE-LGIYLGVTGVQIRAADALYCGLAD 195
             +  + ++   PE+ IG  P  GG+  L R  G+   + + +TG  + AA+A   GL  
Sbjct: 119 FILAADTAKFGQPEITIGTIPGAGGTQRLTRFVGKSKAMEMCLTGRLMDAAEAERAGLVS 178

Query: 196 WYLESSKLAD 205
             + +  L D
Sbjct: 179 RVVPAVDLVD 188


Lambda     K      H
   0.322    0.138    0.419 

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: 196
Number of extensions: 9
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: 367
Length of database: 258
Length adjustment: 27
Effective length of query: 340
Effective length of database: 231
Effective search space:    78540
Effective search space used:    78540
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