GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Lacinutrix algicola AKS293

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_055437597.1 ASC41_RS15620 acyl-CoA dehydrogenase

Query= reanno::acidovorax_3H11:Ac3H11_2991
         (396 letters)



>NCBI__GCF_001418085.1:WP_055437597.1
          Length = 600

 Score =  233 bits (594), Expect = 1e-65
 Identities = 136/389 (34%), Positives = 211/389 (54%), Gaps = 21/389 (5%)

Query: 16  EDIDALRDAVRDFAQAEIAPRAADIDKSDQ-FPMDLWRKMGDLGVLGITVPEQYGGAAMG 74
           E+ + +++AV +F   EI P     +  D     ++ RK G+LG LG+ VPE YGG  MG
Sbjct: 32  EEQNMMKEAVTEFNDREIIPHKPRFEAKDYALTEEVMRKAGELGFLGVAVPEAYGGLGMG 91

Query: 75  YLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAM 134
           +++ ++  + IS  + S   ++GAH+ +    I   G EAQK KY+ KL SGE  G+  +
Sbjct: 92  FVSTVLTCDYISSGTGSFSTAFGAHTGIGTMPITLYGTEAQKQKYVPKLASGEWFGSYCL 151

Query: 135 SEPGAGSDVISMKLKA--EDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTA 192
           +EPGAGSD  S K  A   + G  Y +NG KMWI+N      ++V+A+ E +   + +T 
Sbjct: 152 TEPGAGSDANSGKTTAVLSEDGKSYKINGQKMWISNAGFCTVMIVFARLEDD---KNITG 208

Query: 193 FLIEK-GMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYE 251
           F++E     G ++ ++  KLG+R S T ++ F D  VP EN+L G  +G K+ M+ L+  
Sbjct: 209 FIVENDAANGITMGEEEHKLGIRASSTRQVFFNDTVVPIENMLAGRGEGFKIAMNALNVG 268

Query: 252 RAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTV 311
           R  L    L   + ++ + + Y  +RKQF   I +F  I+ K+A+M T   AG S  Y  
Sbjct: 269 RIKLAAACLDSQRRIVTHGVKYAMERKQFKTPIADFGAIKMKLAEMATNAYAGESATYRA 328

Query: 312 AKNL-------DMLGTDH-------VRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGY 357
           AKN+       +  G  H       V +   +C+ + +  +E     A EG+QI+GG G+
Sbjct: 329 AKNIEDRIALREAAGNTHQEAELKGVEEYAIECSILKVAVSEDVQNCADEGIQIFGGMGF 388

Query: 358 INEYPLGRLWRDAKLYEIGAGTSEIRRML 386
             E P+   WRDA++  I  GT+EI RML
Sbjct: 389 SEETPMESAWRDARIARIYEGTNEINRML 417


Lambda     K      H
   0.318    0.136    0.400 

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: 550
Number of extensions: 25
Number of successful extensions: 4
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: 396
Length of database: 600
Length adjustment: 34
Effective length of query: 362
Effective length of database: 566
Effective search space:   204892
Effective search space used:   204892
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: 52 (24.6 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