GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucO in Escherichia coli BW25113

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate 15361 b1241 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase (NCBI)

Query= SwissProt::P0A9S1
         (382 letters)



>lcl|FitnessBrowser__Keio:15361 b1241 fused acetaldehyde-CoA
           dehydrogenase/iron-dependent alcohol
           dehydrogenase/pyruvate-formate lyase deactivase (NCBI)
          Length = 891

 Score =  206 bits (525), Expect = 2e-57
 Identities = 130/406 (32%), Positives = 222/406 (54%), Gaps = 39/406 (9%)

Query: 7   LNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDG 66
           L ++ +F RG++    DEV   G+++ALIVTD+ L   G   ++T  + AAG+   ++  
Sbjct: 456 LPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFE 515

Query: 67  VVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPE---------FAD 117
           V  +PT+++V++G  +  +   D +IA+GGGSP D  K + ++  +PE         F D
Sbjct: 516 VEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMD 575

Query: 118 VRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFID 177
           +R      P       ++A+ TT+GT +EVT   V+TD+   +K+   D    P +A +D
Sbjct: 576 IRKRIYKFPKMGVKAKMIAVTTTSGTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVD 635

Query: 178 ADMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSV-AGDK 236
           A+++  MP +L A  G+DA+THA+E Y++  A   +D   ++A++++   L  S   G K
Sbjct: 636 ANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSK 695

Query: 237 D--AGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADF 294
           +  A E +     +AG+ F+N  LG+ H MAH LG+ ++ PHG+ANA+L+ +V+RYNA+ 
Sbjct: 696 NPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNAND 755

Query: 295 TGEK---------------YRDIARVMGVKVEGMSLEEARNAAVEAVFA----LNRDVGI 335
              K               Y +IA  +G+   G    +   A +E + A    L  ++GI
Sbjct: 756 NPTKQTAFSQYDRPQARRRYAEIADHLGLSAPG----DRTAAKIEKLLAWLETLKAELGI 811

Query: 336 PPHLRDVGVRKED----IPALAQAALDDVCTGGNPREATLEDIVEL 377
           P  +R+ GV++ D    +  L++ A DD CTG NPR   + ++ ++
Sbjct: 812 PKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQI 857


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: 813
Number of extensions: 35
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: 382
Length of database: 891
Length adjustment: 36
Effective length of query: 346
Effective length of database: 855
Effective search space:   295830
Effective search space used:   295830
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: 53 (25.0 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 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