GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Stenotrophomonas chelatiphaga DSM 21508

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate WP_057508811.1 ABB28_RS11735 4-hydroxy-tetrahydrodipicolinate synthase

Query= curated2:A4YNH1
         (314 letters)



>NCBI__GCF_001431535.1:WP_057508811.1
          Length = 297

 Score = 99.4 bits (246), Expect = 9e-26
 Identities = 67/185 (36%), Positives = 95/185 (51%), Gaps = 5/185 (2%)

Query: 15  SGLLSFPVTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKV 74
           SGL++   TPF+AD S D   ++  +       V G+  AG TGE  +L+ AE  +++  
Sbjct: 4   SGLITALATPFRADGSLDTDGWQRLLHLQLEGGVRGVVVAGSTGEAATLSDAEYDQLLAS 63

Query: 75  AVDETKGRVPVLAGTGY-GTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAV 133
           AV+   GRVPVLAGTG  GTA   E    A  AGA   L++ P  +   Q GL AH  AV
Sbjct: 64  AVERIAGRVPVLAGTGLSGTAKTIEQTRRAAAAGATHALVVTPPYVRPTQAGLIAHYRAV 123

Query: 134 CKSVKIGVIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRL 190
                + V++YN   R    + P+T+A L    PN+VG K+ +GD   +  +    GD  
Sbjct: 124 ADHGGLPVVLYNVPGRTGCDMLPETVAELAAH-PNIVGIKEAVGDNGRVKALLALRGDDF 182

Query: 191 TYIGG 195
             + G
Sbjct: 183 AILSG 187


Lambda     K      H
   0.320    0.136    0.392 

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: 264
Number of extensions: 11
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: 314
Length of database: 297
Length adjustment: 27
Effective length of query: 287
Effective length of database: 270
Effective search space:    77490
Effective search space used:    77490
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.

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