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:

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