GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Dokdonella koreensis DS-123

Align Probable 5-dehydro-4-deoxyglucarate dehydratase 2; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase 2; KDGDH 2 (uncharacterized)
to candidate WP_067648532.1 I596_RS12675 4-hydroxy-tetrahydrodipicolinate synthase

Query= curated2:Q9RDE8
         (322 letters)



>NCBI__GCF_001632775.1:WP_067648532.1
          Length = 304

 Score = 89.7 bits (221), Expect = 8e-23
 Identities = 73/244 (29%), Positives = 109/244 (44%), Gaps = 14/244 (5%)

Query: 39  EDGSF--DADGYRAYVAERLAAGPGALFPACGTGEFFSLDEDEYRQAVAIAVEETAGSVP 96
           +DG    D + +   +  ++A G  AL  A  TGE   LD+ E+   VA  VE  AG +P
Sbjct: 17  QDGELPIDFEAFGRLIDHQVAGGTRALVAAGSTGEAAMLDDAEFSALVAFTVERAAGRIP 76

Query: 97  VVAGTGY-GWAQALRFARIAEDAGADALLVMPHYLTAAPQDGLVAQMERIAAGTRLPLIA 155
           V+AGTG     + +   R A DAGA A LV+        Q+GL      +A   RLP++ 
Sbjct: 77  VLAGTGQASTRRTIEQTRRAADAGAGAALVVTPPYVRPTQEGLYRHFMDVAEHGRLPVVL 136

Query: 156 YQ---RGQVAYTAESVRRLTRVPGVIGLKDGHSDLDRLQRAVLAAPDD--FLFFNGAATA 210
           Y    R       E+V RL     ++ +K+  +D +R++R + A P    F   +G    
Sbjct: 137 YNVPGRTACDLLPETVERLAAQGNIVAIKEARADAERMERLLAARPTTRRFAILSGDDPT 196

Query: 211 EVQARAYAAVGVPAYSSAVHAFAPEIANAFLAALRGGD---TGTVDKLLRDFYVPLVELR 267
            V+A    A GV + ++ V   AP    A   A    D      +D  L+D Y  L    
Sbjct: 197 CVRAMLAGADGVISVAANV---APAALQAIAEACADADRPRAEALDAALQDLYALLAAEP 253

Query: 268 DRVP 271
           + +P
Sbjct: 254 NPIP 257


Lambda     K      H
   0.320    0.136    0.395 

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: 279
Number of extensions: 12
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: 322
Length of database: 304
Length adjustment: 27
Effective length of query: 295
Effective length of database: 277
Effective search space:    81715
Effective search space used:    81715
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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