GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate Pf6N2E2_667 Dihydrolipoamide acetyltransferase component (E2) of acetoin dehydrogenase complex (EC 2.3.1.-)

Query= curated2:P19076
         (283 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_667
          Length = 370

 Score = 83.2 bits (204), Expect = 8e-21
 Identities = 77/259 (29%), Positives = 120/259 (46%), Gaps = 32/259 (12%)

Query: 29  GFPLMMIHGSGPGVTAWANWRLVMPELAKSRRVIAPDMLGFGYSERPADAQYNRDVWVDH 88
           G PL+++HG G  +    NW      LA  RRVIA D+ G G S +    + + D     
Sbjct: 132 GTPLLLVHGFGGDLN---NWLFNHEALAAGRRVIALDLPGHGESGKVLQ-RGDLDELSGV 187

Query: 89  AVGVLDALEIEQADLVGNSFGGGIALALAIRHPERVRRLVLMGSAGVSFPITEGLDAVWG 148
            + +LD L+I    LVG+S GG ++L  A   P RVR L L+GSAG+      G +    
Sbjct: 188 VLALLDHLDINAVHLVGHSMGGAVSLNTARLAPRRVRSLTLIGSAGL------GSEINGS 241

Query: 149 YNPSFAEMR-------RLLDIFAFDRNLVN----DELAELRYQASIRPGFHESFAAMFPA 197
           Y   F E         +L+ +F+ +  LVN    D++ + +    +     +  + +F  
Sbjct: 242 YLQGFVEAANRNALKPQLVQLFS-NAELVNRQMLDDMLKYKRLEGVDAALQQLSSRLFAD 300

Query: 198 PRQRWVDGLASAEAAIRALPHETLVIHGREDQIIPLQTSLTLADWIARAQLHVFGQCGHW 257
            RQ+           ++A    TLV+ G +D IIP+  S  L+     AQ+ V    GH 
Sbjct: 301 GRQQ-----TDLREVVQAGQVPTLVVWGSDDAIIPVTHSEGLS-----AQVEVLPGQGHM 350

Query: 258 TQIEHAARFASLVGDFLAE 276
            Q+E A +  SL+  F+ +
Sbjct: 351 VQMEAAEQVNSLILAFIQQ 369


Lambda     K      H
   0.323    0.137    0.424 

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: 277
Number of extensions: 18
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: 283
Length of database: 370
Length adjustment: 28
Effective length of query: 255
Effective length of database: 342
Effective search space:    87210
Effective search space used:    87210
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 (22.0 bits)
S2: 48 (23.1 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