GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Dechlorosoma suillum PS

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate Dsui_0578 Dsui_0578 homocitrate synthase NifV

Query= BRENDA::P9WMK5
         (346 letters)



>FitnessBrowser__PS:Dsui_0578
          Length = 384

 Score = 74.3 bits (181), Expect = 5e-18
 Identities = 87/289 (30%), Positives = 125/289 (43%), Gaps = 48/289 (16%)

Query: 4   MWDVRITDTSLRDGSHHKRHQFTKDEVGAIVAALDAAGVPVIEVTHGDGLGGSSFNYGFS 63
           M  + I DT+LRDG       FT  E  AI  AL AAGVP +EV    G+          
Sbjct: 1   MTTITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEV----GIPAMG------ 50

Query: 64  KTPEQELIKLAAATAKEARIAFLMLPGVGTKDDIKEARDNGGSICRIATHCTEADV---- 119
              EQE+I+  A     +R   LM+ G     D++  R     I  ++   ++  +    
Sbjct: 51  -EQEQEVIRAIAGLGLSSR---LMVWGRMCAADLEVTRRCNAHIVNLSIPVSDQQIRHKL 106

Query: 120 ---------SIQHF-GLARELGLETV--------GFLMMAHTIAPEKLAAQARIMADAGC 161
                    SI+ F   AR  GLE            L   H +     AAQA     AG 
Sbjct: 107 NKDHRWVLDSIRRFVPEARAAGLEVCVGGEDSSRADLDFLHRVME---AAQA-----AGA 158

Query: 162 QCVYVVDSAGALVLDGVADRVSALVAELGEDAQVGFHGHENLGLGVANSVAAVRAGAKQI 221
           +     D+ G L       R++AL A    D ++  H H++LGL  AN++AAV AGA  I
Sbjct: 159 RRFRFADTLGVLDPFITHQRIAALRAR--SDLEIEIHAHDDLGLATANTLAAVTAGATHI 216

Query: 222 DGSCRRFGAGAGNAPV-EALIGVFDKIGVKTGIDFFDIADAAEDVVRPA 269
           + +    G  AGNAP+ E++I +     + +G+D   +  A  D+V  A
Sbjct: 217 NTTVNGLGERAGNAPLEESVIALRHLYDIDSGVDPLQL-PAISDLVAKA 264


Lambda     K      H
   0.320    0.136    0.393 

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: 335
Number of extensions: 27
Number of successful extensions: 2
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: 346
Length of database: 384
Length adjustment: 29
Effective length of query: 317
Effective length of database: 355
Effective search space:   112535
Effective search space used:   112535
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.

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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