GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pseudomonas fluorescens FW300-N1B4

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate Pf1N1B4_4506 Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)

Query= SwissProt::P0A9S1
         (382 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4506
          Length = 387

 Score =  241 bits (614), Expect = 3e-68
 Identities = 136/371 (36%), Positives = 206/371 (55%), Gaps = 4/371 (1%)

Query: 13  FGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPT 72
           FG G    + +  K  G +K L+V+D  ++  G VA V   + A G+ + +Y  V PNP 
Sbjct: 18  FGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQAQGIDFFLYSDVSPNPR 77

Query: 73  ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSV 132
           I  V  G  +++ +  D ++AIGGGSP D  K IGI+  +    ++   EG+     PS 
Sbjct: 78  IEEVMLGAELYRENHCDVIVAIGGGSPMDCGKGIGIVVAHGR--NILEFEGVDMLRMPSP 135

Query: 133 PILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAAT 192
           P++ IPTTAGT+A+V+   +I+++++R KF  V    +P V+ ID +    M P L A T
Sbjct: 136 PLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLSMDPFLSACT 195

Query: 193 GVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAG--EEMALGQYVAG 250
           G+DAL HAIE +++ G   LTD   ++A+ +I G L   +A   D    E++ LG   AG
Sbjct: 196 GIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPSDIALREKIMLGSMQAG 255

Query: 251 MGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKV 310
           + FSN  LG VH M+H LG F + PHG+ NA+L+ HV+ +N     E+++ IA   G+  
Sbjct: 256 LAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYSSAPERFKVIAETFGIDC 315

Query: 311 EGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREAT 370
            G++  +     VE + AL   +G    L   GV   DIP L+Q A+ D C   NPRE++
Sbjct: 316 RGLNHRQICGRLVEHLIALKHAIGFHETLGLHGVSTADIPFLSQHAMHDPCILTNPRESS 375

Query: 371 LEDIVELYHTA 381
             D+  +Y  A
Sbjct: 376 QRDVEVVYGEA 386


Lambda     K      H
   0.319    0.136    0.404 

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: 392
Number of extensions: 18
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: 382
Length of database: 387
Length adjustment: 30
Effective length of query: 352
Effective length of database: 357
Effective search space:   125664
Effective search space used:   125664
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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