GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Dinoroseobacter shibae DFL-12

Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate 3608243 Dshi_1647 2-dehydro-3-deoxyglucarate aldolase (RefSeq)

Query= SwissProt::Q47098
         (262 letters)



>FitnessBrowser__Dino:3608243
          Length = 260

 Score =  241 bits (614), Expect = 1e-68
 Identities = 125/255 (49%), Positives = 170/255 (66%)

Query: 2   ENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIA 61
           EN  K AL AG  QIG+WLG  +   AEL AG GFDW L+DGEH+PN+   ++ QL+A+ 
Sbjct: 5   ENQLKQALLAGDVQIGIWLGFGAPAVAELAAGCGFDWCLVDGEHSPNDPAQMIDQLRAMV 64

Query: 62  PYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSA 121
              + P+VR    +   +K+ LD+G QT++VPMV+ A +A++ VRA RYPP G+RGVG+A
Sbjct: 65  GQGAMPIVRVPVGEDWVLKRALDLGVQTIMVPMVETAAQAQQIVRAMRYPPDGVRGVGAA 124

Query: 122 LARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMG 181
           LARAS ++   +Y+  AN Q+C +VQIE+  A++ +P+I  VEGVD +FIGPADL+ADMG
Sbjct: 125 LARASGYSLDAEYVTTANAQICTIVQIESHAAVRAIPEIAAVEGVDVLFIGPADLAADMG 184

Query: 182 YAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLAR 241
           Y G    PEV A I  A+ +I  SGK PG+L  +E  A R+   GA FV VG D T LA 
Sbjct: 185 YPGRADAPEVDAVICAALGEIARSGKVPGVLAFSETDAVRFAAAGARFVGVGADVTSLAV 244

Query: 242 AAEALAARFGAQATA 256
           A   L+A   A+ ++
Sbjct: 245 ALRGLSASSRARLSS 259


Lambda     K      H
   0.317    0.133    0.387 

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: 229
Number of extensions: 9
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: 262
Length of database: 260
Length adjustment: 25
Effective length of query: 237
Effective length of database: 235
Effective search space:    55695
Effective search space used:    55695
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: 47 (22.7 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