GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pseudomonas fluorescens FW300-N2C3

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate AO356_27315 AO356_27315 short-chain dehydrogenase

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27315
          Length = 249

 Score =  126 bits (316), Expect = 5e-34
 Identities = 85/258 (32%), Positives = 144/258 (55%), Gaps = 20/258 (7%)

Query: 1   MDLKDKVVVITGGAG--GLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGY 58
           M L+ KV +ITG A   G+G A A  FA+ GA + ++D+D+     A A LG      G 
Sbjct: 1   MLLQGKVAIITGAASERGIGRATAVTFARHGAHVVILDLDESAARDAAATLGEGH--LGL 58

Query: 59  ALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118
           A ++ DE  V A  A ++E +G+I++L+NNAGI +    +K  D +  D      +  V+
Sbjct: 59  AANVADEMQVKAAVAKVVERYGRIDILINNAGITQP---IKTLDIRPGD------YDKVL 109

Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAK---AGNVGQSNYAASKAGVAAMSVG 175
           +V+L GT L   +A   ++ +  +G IV +SS++     G  G  +Y+A+KAGV  +   
Sbjct: 110 DVSLRGTLLMS-QAVIPVMRTQASGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLGKA 168

Query: 176 WAKELARYNIRSAAVAPGVIATEMTAA-MKPEALERLEKLVPVGRLGHAEEIASTVRFII 234
            A+E    NIR  ++ PG+I T++T   M+ +    + + +P+GRLG A+++A+   F+ 
Sbjct: 169 MAREFGADNIRVNSITPGLIHTDITGGLMQDDRRHAIIESIPLGRLGAAQDVANAALFLA 228

Query: 235 E--NDYVNGRVFEVDGGI 250
              + Y+ G   +V+GG+
Sbjct: 229 SDLSSYLTGITLDVNGGM 246


Lambda     K      H
   0.317    0.134    0.369 

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: 134
Number of extensions: 7
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: 252
Length of database: 249
Length adjustment: 24
Effective length of query: 228
Effective length of database: 225
Effective search space:    51300
Effective search space used:    51300
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: 46 (22.3 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