GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Escherichia coli BW25113

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate 15892 b1774 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Keio:15892
          Length = 347

 Score =  258 bits (659), Expect = 2e-73
 Identities = 144/350 (41%), Positives = 201/350 (57%), Gaps = 24/350 (6%)

Query: 12  AVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI---- 67
           A++     +KI +  +P    DEVLIKV  VGICGSD+H + +G         PFI    
Sbjct: 6   AILQVPGTMKIISAEIPVPKEDEVLIKVEYVGICGSDVHGFESG---------PFIPPKD 56

Query: 68  ------LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLA 121
                 LGHECAG + AVGS V +FK GDRV +EPGV CG C  C EG+YN+CPDV F+A
Sbjct: 57  PNQEIGLGHECAGTVVAVGSRVRKFKPGDRVNIEPGVPCGHCRYCLEGKYNICPDVDFMA 116

Query: 122 TPP-VDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMG 180
           T P   GA   Y+   + F + +PD++   E AL+EP +VG+HAA    ++PG  I I+G
Sbjct: 117 TQPNYRGALTHYLCHPESFTYKLPDNMDTMEGALVEPAAVGMHAAMLADVKPGKKIIILG 176

Query: 181 MGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDR 240
            G +GLM + A K  GA  I V D+   RL  A+++GAT +IN  ++D +   +  T D 
Sbjct: 177 AGCIGLMTLQACKCLGATEIAVVDVLEKRLAMAEQLGATVVINGAKEDTIARCQQFTEDM 236

Query: 241 GVDVAWETAGNPAALQSALASVRRGGKLAIVG-LPSQNEIPLNVPFIADNEIDIYGIFRY 299
           G D+ +ETAG+   ++ A   V RGGK+ IVG +P  + I        + E+ I  +FRY
Sbjct: 237 GADIVFETAGSAVTVKQAPYLVMRGGKIMIVGTVPGDSAINF---LKINREVTIQTVFRY 293

Query: 300 ANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVMV 349
           AN YP  IE ++SG  D K +VT  Y     Q A E ++  K + +K ++
Sbjct: 294 ANRYPVTIEAISSGRFDVKSMVTHIYDYRDVQQAFEESVNNKRDIIKGVI 343


Lambda     K      H
   0.320    0.137    0.401 

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: 333
Number of extensions: 16
Number of successful extensions: 4
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: 353
Length of database: 347
Length adjustment: 29
Effective length of query: 324
Effective length of database: 318
Effective search space:   103032
Effective search space used:   103032
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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