GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ivdG in Pseudomonas fluorescens FW300-N1B4

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate Pf1N1B4_730 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= uniprot:Q8EGC1
         (252 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_730
           3-oxoacyl-[acyl-carrier protein] reductase (EC
           1.1.1.100)
          Length = 252

 Score =  277 bits (709), Expect = 1e-79
 Identities = 141/253 (55%), Positives = 186/253 (73%), Gaps = 2/253 (0%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADL-GSSTEVQGYA 59
           M L DKV++ITGG  GLG +MA   A  GAKLAL+D++Q+KL+   A       E + Y 
Sbjct: 1   MQLTDKVIIITGGCQGLGRSMAEYLAGKGAKLALVDLNQEKLDATVAACKAKGVEARAYL 60

Query: 60  LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119
            ++ DEE V    A + +DFG I+ L+NNAGILRDG+L+K KDG++T +MS  Q+Q+VI+
Sbjct: 61  CNVADEEQVTHMAAQVADDFGAIHGLINNAGILRDGLLLKVKDGEMT-KMSLAQWQAVID 119

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

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

Query: 240 NGRVFEVDGGIRL 252
            GR+ E+DGG+R+
Sbjct: 240 TGRILELDGGLRI 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: 209
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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