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_1687 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= uniprot:Q8EGC1
         (252 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1687 Dehydrogenases with
           different specificities (related to short-chain alcohol
           dehydrogenases)
          Length = 246

 Score =  108 bits (271), Expect = 8e-29
 Identities = 83/253 (32%), Positives = 127/253 (50%), Gaps = 22/253 (8%)

Query: 6   KVVVITGGAGGLGLAMAHNFAQAGAKLAL----IDVDQDKLERACADLGSSTEVQGYALD 61
           KV ++TG + G+G  +A   A  G  +A+       +  KL       G   +      D
Sbjct: 7   KVAIVTGASRGIGAVIARQLASEGFAVAINYASSATEASKLVVELRQAGH--QAIAIKAD 64

Query: 62  ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121
           + + +DV   F       GK++VLVNNAGIL+   L +  D         + F    N++
Sbjct: 65  VANADDVRRLFDETETQLGKVDVLVNNAGILKVLPLAQHSD---------ELFDQNFNIH 115

Query: 122 LTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNV-GQSNYAASKAGVAAMSVGWAKEL 180
             GTF   REAA  +   G+   I+N SS     N+ G + Y ASKA V +++  +AKE+
Sbjct: 116 ARGTFNTLREAATRLNSGGR---IINFSSSTVGMNLPGYAVYIASKAAVESLTQVFAKEM 172

Query: 181 ARYNIRSAAVAPGVIATEMTAAMK-PEALERLEKLVPVGRLGHAEEIASTVRFIIEND-- 237
              NI   AVAPG +AT++    K  E ++   K+ P+ RLG  E+IA  V F++  D  
Sbjct: 173 RGRNITVNAVAPGPVATDLFLHGKSEEQIQNFAKMPPLERLGQPEDIARVVSFLVGPDSA 232

Query: 238 YVNGRVFEVDGGI 250
           +VNG++  V+GG+
Sbjct: 233 WVNGQILRVNGGL 245


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: 166
Number of extensions: 11
Number of successful extensions: 5
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: 246
Length adjustment: 24
Effective length of query: 228
Effective length of database: 222
Effective search space:    50616
Effective search space used:    50616
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