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_RS26485 AZOBR_RS26485 enoyl-CoA hydratase

Query= reanno::psRCH2:GFF2391
         (364 letters)



>FitnessBrowser__azobra:AZOBR_RS26485
          Length = 262

 Score =  105 bits (261), Expect = 2e-27
 Identities = 63/184 (34%), Positives = 101/184 (54%), Gaps = 3/184 (1%)

Query: 5   ERPVLAAVRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAF 64
           ERP+L +    VG +T+NRP  LNA+ +  +  L++ L    +D  +H +V+   GE+AF
Sbjct: 4   ERPILTSRDGAVGLITINRPTTLNALDVPTLLELERALGELESDDGVHVIVVTGAGERAF 63

Query: 65  CAGGDIRSLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGA 124
            AGGDI  L DS ++G   +  F E  + + +      KP +A ++G+ LGGG  LV   
Sbjct: 64  VAGGDIADL-DS-RQGLAHYLDFAEVVHRVFRRFETCDKPTIAAVNGWALGGGTELVLSL 121

Query: 125 SLRVVTERVRMGMPEVGIGYFPDVGGSY-FLSRLPGELGTYMGVTGLQIRAADALHVGLA 183
            +R+  +  + G+PE+ +G FP  GG+   L ++P      +  TG Q  AA+A+  GL 
Sbjct: 122 DIRIAADTAKFGLPEINLGLFPGAGGTQRILRQIPPCRARELVFTGDQFTAAEAVAWGLV 181

Query: 184 DWCV 187
           +  V
Sbjct: 182 NRAV 185


Lambda     K      H
   0.321    0.136    0.412 

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: 226
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 364
Length of database: 262
Length adjustment: 27
Effective length of query: 337
Effective length of database: 235
Effective search space:    79195
Effective search space used:    79195
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