GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucO in Pseudomonas fluorescens FW300-N2E3

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate AO353_22415 AO353_22415 alcohol dehydrogenase

Query= SwissProt::P0A9S1
         (382 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_22415 AO353_22415 alcohol
           dehydrogenase
          Length = 387

 Score =  243 bits (621), Expect = 5e-69
 Identities = 135/371 (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  FGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQALGIDYCLYSAVSPNPR 77

Query: 73  ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSV 132
           +  V  G  +++ +  D ++A+GGGSP D  K IGI+  +     +   EG+     PS 
Sbjct: 78  VEEVMLGAEIYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGR--SILEFEGVDMIRVPSP 135

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

Query: 193 GVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAG--EEMALGQYVAG 250
           G+DAL HAIE +++ G   LTD   ++A+ +I G L   +A   D    E++ LG   AG
Sbjct: 196 GIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPTDIALREKIMLGSMQAG 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+DD C   NPRE++
Sbjct: 316 RGLNHRQICGRLVEHLIALKHAIGFHETLGLHGVGTSDIPFLSQHAMDDPCILTNPRESS 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: 406
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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