GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pseudomonas fluorescens FW300-N2C3

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate AO356_28020 AO356_28020 alcohol dehydrogenase

Query= SwissProt::P0A9S1
         (382 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28020
          Length = 392

 Score =  253 bits (646), Expect = 6e-72
 Identities = 141/380 (37%), Positives = 212/380 (55%), Gaps = 4/380 (1%)

Query: 4   RMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAI 63
           R  ++    FG G    + +  K  G +K LIVTD  ++  G VA V   + A G+ + I
Sbjct: 14  RKFVSPEIMFGAGCRHNVGNYAKTFGARKVLIVTDPGVIAAGWVADVEASLQAQGIDYCI 73

Query: 64  YDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEG 123
           Y  V PNP +  V  G  +++ +  D ++A+GGGSP D  K IGI+  +     +   EG
Sbjct: 74  YSAVSPNPRVEEVMLGADLYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGR--SILEFEG 131

Query: 124 LSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDG 183
           +   N PS P++ IPTTAGT+A+V+   +I+++++R KF  V    +P V+ ID +    
Sbjct: 132 VDTLNVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLS 191

Query: 184 MPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAG--EE 241
           M P L A TG+DAL HAIE +++ G   LTD   ++A+ +I G L   +A   D    E+
Sbjct: 192 MDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPADIALREK 251

Query: 242 MALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRD 301
           + LG   AG+ FSN  LG VH M+H LG F + PHG+ NA+L+ HV+ +N +   E+++ 
Sbjct: 252 IMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKV 311

Query: 302 IARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVC 361
           IA  +G+   G++  E R   VE + AL   +G    L   GV   DIP L+Q A+ D C
Sbjct: 312 IAETLGIDCRGLNHREIRTRLVEHLIALKHTIGFHETLGLHGVSTSDIPFLSQHAMHDPC 371

Query: 362 TGGNPREATLEDIVELYHTA 381
              NPRE++  D+  +Y  A
Sbjct: 372 ILTNPRESSQRDVEVVYGEA 391


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: 427
Number of extensions: 26
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: 392
Length adjustment: 30
Effective length of query: 352
Effective length of database: 362
Effective search space:   127424
Effective search space used:   127424
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.

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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