GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Xanthobacter autotrophicus Py2

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate WP_012113724.1 XAUT_RS08530 acyl-CoA dehydrogenase family protein

Query= metacyc::MONOMER-20677
         (380 letters)



>NCBI__GCF_000017645.1:WP_012113724.1
          Length = 354

 Score =  150 bits (380), Expect = 4e-41
 Identities = 119/367 (32%), Positives = 162/367 (44%), Gaps = 27/367 (7%)

Query: 7   EEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEEDGGFGA 66
           EE  LL++S    L+ +Y       ++  +    +A W   AE G   L   E  GG G 
Sbjct: 9   EEDALLRDSARRFLEDTY------AWSPTRACDPKARWRAMAELGWFALGLPEALGGIGG 62

Query: 67  GAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAG-SAAQKAAHLPGIIDGSKTFAFAQ 125
            A + M+++E  G  L   P L ++++    L       AQ  A   G+  GS   A+  
Sbjct: 63  DAAQCMVILEEAGRVLDEAPLLASLLLAAPVLAALPLEVAQPLAD--GLQAGSVRLAYVP 120

Query: 126 LEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRTGVGVF 185
                  D G      +    G ++ G   + L  + A   IV      G     G  V 
Sbjct: 121 -------DAG-----LRLGEGGTLLSGRSRLALGIDLATHWIVPV----GSGSANGAAVL 164

Query: 186 LVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDARTALC 245
           L+PA A     +     DG  AA ++F  + V  DA +   E A EL   + D A     
Sbjct: 165 LLPASAAAALDRTL-LMDGRTAAVLSFANLPVAPDAIVARGEAAFELAALLADAAAVGAS 223

Query: 246 AEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFATMAAE 305
           AEA+G  D  L  TV Y+K R QFG P+ SFQ +QH  A+ F    Q RS+ M+A  A  
Sbjct: 224 AEALGAADAGLALTVSYLKDRTQFGAPLASFQAVQHMMAESFCEIAQMRSLLMWAADALA 283

Query: 306 FDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIEQTFGD 365
              A ERA A +A K   G  G     + IQ+ GGIG+T E +IGH +KRL      FG 
Sbjct: 284 -GPAGERARAASALKAYAGMQGLKAVARCIQVSGGIGVTQEYRIGHVYKRLQTHAALFGS 342

Query: 366 TDHHLAR 372
           T  HLAR
Sbjct: 343 TQEHLAR 349


Lambda     K      H
   0.318    0.135    0.388 

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: 279
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: 380
Length of database: 354
Length adjustment: 30
Effective length of query: 350
Effective length of database: 324
Effective search space:   113400
Effective search space used:   113400
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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