GapMind for catabolism of small carbon sources

 

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

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate 3606718 Dshi_0149 dihydrodipicolinate synthase (RefSeq)

Query= curated2:B1W1P9
         (320 letters)



>FitnessBrowser__Dino:3606718
          Length = 291

 Score =  119 bits (299), Expect = 7e-32
 Identities = 97/283 (34%), Positives = 136/283 (48%), Gaps = 26/283 (9%)

Query: 27  DGAVDLAVFRAHVRAGIDAGAAAVFACCGTGEFHALTPEEFRLAVGAAVEESAGQVPVLA 86
           DGAVD A   A V   I  G+  +     TGE   L+ EE    V   +E +AG+VPV+A
Sbjct: 15  DGAVDFATLEALVEWQIAEGSHGLVPVGTTGESPTLSHEEHEAVVAKVIEVAAGRVPVIA 74

Query: 87  GAGYG-TALAVQYARAAEEAGADGLLAMPPYLVVADQQGLLHHYAALAAATGLETIVYQ- 144
           GAG   T  AV++ R A++AGADG L + PY     Q G++ HY ALA A  +  ++Y  
Sbjct: 75  GAGSNNTVEAVRFVRHAKDAGADGALVVTPYYNKPTQGGMIAHYTALAEAADIPIVIYNI 134

Query: 145 --RDNAVFTPETVVALARTPGVIGLKDGHGDLDLMQRIVSAVRTHRPGGDFLYFNGLPTA 202
             R     TP T+ ALA  P ++G+KD  GDL  + +   A      G +F+  +G    
Sbjct: 135 PGRSVVDMTPATMAALAALPTIVGVKDATGDLARVSQTRMAC-----GPEFIQLSGEDAT 189

Query: 203 ELTGPAYRGIGVTLYSSAVFAFAPDIALAFYRALDSGDD----ALVDGLLDHFYRPLVEL 258
            L   A+ G+G    ++ V   AP +   F  A  +GD     AL D L+       VE 
Sbjct: 190 ALGFNAHGGVGCISVTANV---APALCAQFQEATLAGDFATALALQDKLMPLHEAIFVEP 246

Query: 259 RAQGRGYAVSLVKAGVRLQGLDVGEVRTP---LTEPTAAHVKD 298
              G  YA+SL+       G    +VR P   L++ T   +KD
Sbjct: 247 GLVGAKYALSLL-------GKCSEDVRLPLLGLSDGTKVLIKD 282


Lambda     K      H
   0.322    0.138    0.405 

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: 202
Number of extensions: 15
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: 320
Length of database: 291
Length adjustment: 27
Effective length of query: 293
Effective length of database: 264
Effective search space:    77352
Effective search space used:    77352
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: 48 (23.1 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