GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Escherichia coli BW25113

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate 15892 b1774 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)

Query= SwissProt::P0DOW0
         (331 letters)



>FitnessBrowser__Keio:15892
          Length = 347

 Score =  128 bits (321), Expect = 2e-34
 Identities = 99/326 (30%), Positives = 158/326 (48%), Gaps = 21/326 (6%)

Query: 11  TMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPP------LVMGHEFSGV 64
           TM I+SA  PVP+   + ++V  VGICGS++ G+     +  PP      + +GHE +G 
Sbjct: 13  TMKIISAEIPVPKEDEVLIKVEYVGICGSDVHGFESGPFI--PPKDPNQEIGLGHECAGT 70

Query: 65  VEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGI--DFPGAYAERVL 122
           V  VG  V   K GD V   P V CG C +CL G+   C     +    ++ GA    + 
Sbjct: 71  VVAVGSRVRKFKPGDRVNIEPGVPCGHCRYCLEGKYNICPDVDFMATQPNYRGALTHYLC 130

Query: 123 VPSNQCYAVKDAID---GALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGL 179
            P +  Y + D +D   GALVEP A  + A  LA +K G   +++GAG IGLMT++    
Sbjct: 131 HPESFTYKLPDNMDTMEGALVEPAAVGMHAAMLADVKPGKKIIILGAGCIGLMTLQACKC 190

Query: 180 SGAKRIAVVDPNDERLKISQLWGATEM-----APNLGALLTDNHPQSFDCVIDAVGLSTT 234
            GA  IAVVD  ++RL +++  GAT +        +            D V +  G + T
Sbjct: 191 LGATEIAVVDVLEKRLAMAEQLGATVVINGAKEDTIARCQQFTEDMGADIVFETAGSAVT 250

Query: 235 RRDSLNALIRGGRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQK 294
            + +   ++RGG+ + +G     + ++  +I R E+ ++  F Y  + +   +  I+S +
Sbjct: 251 VKQAPYLVMRGGKIMIVGTVPGDSAINFLKINR-EVTIQTVFRYA-NRYPVTIEAISSGR 308

Query: 295 FLPVDRQWLDVRSLEEGPAAFKELVN 320
           F  V      +    +   AF+E VN
Sbjct: 309 F-DVKSMVTHIYDYRDVQQAFEESVN 333


Lambda     K      H
   0.322    0.139    0.424 

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: 305
Number of extensions: 14
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: 331
Length of database: 347
Length adjustment: 28
Effective length of query: 303
Effective length of database: 319
Effective search space:    96657
Effective search space used:    96657
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 (21.9 bits)
S2: 49 (23.5 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