GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pseudomonas fluorescens FW300-N2E2

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate Pf6N2E2_5603 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5603
          Length = 252

 Score =  277 bits (709), Expect = 1e-79
 Identities = 141/253 (55%), Positives = 188/253 (74%), Gaps = 2/253 (0%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSS-TEVQGYA 59
           M L DKV++ITGG  GLG +MA   A  GAKLAL+D++Q+KL++A A   +   E + Y 
Sbjct: 1   MQLTDKVIIITGGCQGLGRSMAEYLAGKGAKLALVDLNQEKLDQAVAACAAKGVEARAYL 60

Query: 60  LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119
            ++ +EE V    A + EDFG I+ L+NNAGILRDG+L+K KDG++T +MS  Q+Q+VI+
Sbjct: 61  CNVANEEQVSDMVARVAEDFGAIHGLINNAGILRDGLLLKVKDGEMT-KMSLAQWQAVID 119

Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKE 179
           VNLTG FLC RE AA M+E   +G I+NISS+++AGNVGQ+NY+A+KAGVAA +V WAKE
Sbjct: 120 VNLTGVFLCTREVAAKMVELKNSGAIINISSISRAGNVGQTNYSAAKAGVAAATVTWAKE 179

Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIENDYV 239
           LARY IR A +APG I TEMT  MKPEALE++   +P+ R+G  EEIA +  +I ENDY 
Sbjct: 180 LARYGIRVAGIAPGFIETEMTLGMKPEALEKMTSGIPLKRMGKPEEIAHSAAYIFENDYY 239

Query: 240 NGRVFEVDGGIRL 252
            GR+ E+DGG+R+
Sbjct: 240 TGRILEMDGGLRI 252


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: 217
Number of extensions: 5
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: 252
Length of database: 252
Length adjustment: 24
Effective length of query: 228
Effective length of database: 228
Effective search space:    51984
Effective search space used:    51984
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