GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaE in Pseudomonas fluorescens FW300-N2E2

Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate Pf6N2E2_5315 Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12.17)

Query= metacyc::MONOMER-15950
         (357 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5315 Flavohemoprotein
           (Hemoglobin-like protein) (Flavohemoglobin) (Nitric
           oxide dioxygenase) (EC 1.14.12.17)
          Length = 393

 Score =  105 bits (262), Expect = 2e-27
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 17/241 (7%)

Query: 15  ETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTGVNDGELRVAIKR 74
           E+ +  S  F+ PA+         GQ++ M+  LDGEEVRR+YS+    ++G+ R+++KR
Sbjct: 166 ESSEITSFYFE-PADKGPILLAEPGQYIGMKLMLDGEEVRRNYSLSALADNGQYRISVKR 224

Query: 75  VAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAAGSGITPILSIIKTT 134
             GGR S + +     G R+++ PPSG F++    A     + ++ G GITP L++++  
Sbjct: 225 EPGGRVSNHLHHHFDVGSRIQLFPPSGDFYL---TASDKPLVLISGGVGITPTLAMLQAA 281

Query: 135 LETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSREQQDVDLYNGRIDA 194
           L+TE    V  ++  R+  +  FR+ ++DL  R+ Q    +  F    +D  L      A
Sbjct: 282 LQTE--RPVHFIHCARNGRAHAFRDWIDDLAKRHPQ----LKRFYCYDEDDGLSPA---A 332

Query: 195 DKCGQL----FSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIHFELFAAAGSA 250
           DK G L     ++W+  +    A+  GP+     V+  LKA G+  ++  +E F  A + 
Sbjct: 333 DKVGLLSQEQLAQWLPQQRDVDAYFLGPKGFMGAVKRHLKALGVPEQQSRYEFFGPAAAL 392

Query: 251 Q 251
           +
Sbjct: 393 E 393


Lambda     K      H
   0.319    0.133    0.377 

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: 252
Number of extensions: 13
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: 357
Length of database: 393
Length adjustment: 30
Effective length of query: 327
Effective length of database: 363
Effective search space:   118701
Effective search space used:   118701
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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