GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Acidovorax caeni R-24608

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_001298675.1:WP_054255950.1
          Length = 376

 Score =  189 bits (479), Expect = 1e-52
 Identities = 114/372 (30%), Positives = 190/372 (51%), Gaps = 5/372 (1%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           LT+++ MVRD+   F ++++ P      +       + + + ++G  G  +PEQYGG+GL
Sbjct: 3   LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
           +YV   L+  E+   D G  + +SV +  V   +  +G+EAQKQ++L  LA GE +G F 
Sbjct: 63  DYVTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGSEAQKQQWLAPLARGEMLGAFC 122

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGF 194
           LTEP+ GSD  ++ T A +    Y + G K +IT+     V +V A  D       +  F
Sbjct: 123 LTEPHVGSDASALRTTATREGDDYVINGVKQFITSGKNGHVAIVIAVTDKAAGKKGMSAF 182

Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARY 253
           ++     G     +  K+G  +S T +I  DN  +P  N+   +  G K   + L   R 
Sbjct: 183 LVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIALSALEGGRI 242

Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313
           GI+  ++G A A +  A QY+ +R+ FG+P+  +Q +  +LAD  T++  A Q       
Sbjct: 243 GIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAARQLIWHAAS 302

Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373
           ++D G   ++  ++ K  +   A  +   A   LGG G+ ++F V R   ++ V   YEG
Sbjct: 303 LRDAGQPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRDVRVCQIYEG 362

Query: 374 THDVHALILGRA 385
           T DV  +I+ RA
Sbjct: 363 TSDVQKIIIQRA 374


Lambda     K      H
   0.320    0.137    0.413 

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: 335
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: 393
Length of database: 376
Length adjustment: 30
Effective length of query: 363
Effective length of database: 346
Effective search space:   125598
Effective search space used:   125598
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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