GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Dyella japonica UNC79MFTsu3.2

Align Glycolate oxidase subunit GlcE; Glycolate dehydrogenase subunit GlcE; EC 1.1.99.14 (characterized)
to candidate N515DRAFT_1999 N515DRAFT_1999 D-lactate dehydrogenase

Query= SwissProt::P52073
         (350 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1999
          Length = 456

 Score = 85.1 bits (209), Expect = 3e-21
 Identities = 72/226 (31%), Positives = 105/226 (46%), Gaps = 29/226 (12%)

Query: 22  KTPLVIQGSNSKAFLGRPVTGQTLDV---------RCHRGIVNYDPTELVITARVGTPLV 72
           + PLV +G       G   TG T+ V         R +R I+  DP   +     G    
Sbjct: 64  RVPLVARGR------GTNTTGATVPVDGGVVASFERMNR-ILRIDPDNRLAVVEPGVLNG 116

Query: 73  TIEAALESAGQMLPCEPPHYGEEATW---GGMVACGLAGPRRPWSGSVRDFVLGTRIITG 129
            ++ AL+  G   P +P      + W   GG +AC  AGPR    GS R+  LG R + G
Sbjct: 117 DLQQALKPHGFFWPPDPT----SSPWCSIGGNLACNSAGPRTVKYGSPRENTLGLRAVAG 172

Query: 130 AGKHLRFGGEVMKNVAGYDLSRLMVGSYGCLGVLTEISMKVLPRPRASLSLR---REISL 186
            G   R G    K   GYDL+RL++GS G L ++TE ++K+ P+P    +LR   R++S 
Sbjct: 173 TGVGFRCGTYTSKGSTGYDLTRLLIGSEGTLALITEATLKLTPKPSGLRTLRATYRDVS- 231

Query: 187 QEAMSEIAEWQLQPLPISGLCYFDN-ALWIRLEGGEGSVKAARELL 231
             A   +A    QP+    L + D+ AL +  + G  SV  A  +L
Sbjct: 232 -AAARAVARIMAQPVTPCALEFIDDVALKLARDHGGDSVPVAGAML 276


Lambda     K      H
   0.320    0.138    0.430 

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: 339
Number of extensions: 20
Number of successful extensions: 1
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: 350
Length of database: 456
Length adjustment: 31
Effective length of query: 319
Effective length of database: 425
Effective search space:   135575
Effective search space used:   135575
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: 50 (23.9 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