Alignments for a candidate for dgoD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Escherichia coli BW25113

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Keio:14407
          Length = 655

 Score =  186 bits (471), Expect = 3e-51
 Identities = 175/552 (31%), Positives = 264/552 (47%), Gaps = 72/552 (13%)

Query: 42  DGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEA---GGFPLEVPVFSASENTFRPT- 97
           DGRP+    +T        GH  E+  +++A   E    GG P    V    +   + T 
Sbjct: 77  DGRPIALGYHT--------GHW-EIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTH 127

Query: 98  ----AMMYRNLAALAVEEAIRGQPMDGCVLLVG-CDKTTPSLLMG-AASCDLPSIVVTGG 151
               ++ YRN AA+     IR  P    V+ V  CDK  P+ ++  AA  DLP+I+V GG
Sbjct: 128 GMFDSLPYRNDAAIVFRRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGG 187

Query: 152 PMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRS-SGTCNTMGTASTMA 210
             L     GE  G    +          E++  E  E       S  G C  +GTA T  
Sbjct: 188 ATLPPTV-GEDAGK---VQTIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQ 243

Query: 211 SMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTN 270
            +AEALG+AL  +A  P   +    +A+ + R + ++    +   +I++ +A ENA+  +
Sbjct: 244 VVAEALGLALPHSALAPSGQAVWLEIARQSARAVSELDSRGITTRDILSDKAIENAMVIH 303

Query: 271 AAIGGSTNAVIHLLAIAGRVGIDL-SLDDWDRCGRDVPTIVNLMPSGK--YLMEEFFYAG 327
           AA GGSTN ++H+ AIA   G  +  ++ W R  R VP +V+++P+G   +     F AG
Sbjct: 304 AAFGGSTNLLLHIPAIAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAG 363

Query: 328 GLPVVLKRLGEAGLLHKDALTVSGETVWDEV------------------KDVVNWNEDVI 369
           G+P V+  L + GLLH DA+TV+G+TV + +                  +D V   +DVI
Sbjct: 364 GVPEVMLHLRDLGLLHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVE-PDDVI 422

Query: 370 LPAEKA----LTSSGGIVVLRGNLAPKGAVLKPSAASPHLL------VHKGRAVVFEDID 419
           LP EKA    LTS+  +    GN+AP+G+V+K +A  P ++       H GR  VF  + 
Sbjct: 423 LPPEKAKAKGLTST--VCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVF--VS 478

Query: 420 DYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARM 479
           + +A       +I +  IMV+   GP G  GM E   +    K +  G   +  I+DAR 
Sbjct: 479 EAQAIKAIKREEIVQGDIMVVIGGGPSG-TGMEETYQLTSALKHISWG-KTVSLITDARF 536

Query: 480 SGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRL----------HLDISDEELA 529
           SG + G    H SPEA  GGP+  +++ D+IE+ V    L             ++ EE A
Sbjct: 537 SGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAVDRLTLTGSVNFIGTADNPLTPEEGA 596

Query: 530 RRLAEWQPNHDL 541
           R LA  Q + DL
Sbjct: 597 RELARRQTHPDL 608


Lambda     K      H
   0.318    0.135    0.408 

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: 1028
Number of extensions: 66
Number of successful extensions: 6
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: 579
Length of database: 655
Length adjustment: 37
Effective length of query: 542
Effective length of database: 618
Effective search space:   334956
Effective search space used:   334956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources