GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Cupriavidus basilensis 4G11

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate RR42_RS06250 RR42_RS06250 dihydrodipicolinate synthase

Query= curated2:A4YNH1
         (314 letters)



>FitnessBrowser__Cup4G11:RR42_RS06250
          Length = 294

 Score =  106 bits (264), Expect = 8e-28
 Identities = 83/274 (30%), Positives = 131/274 (47%), Gaps = 15/274 (5%)

Query: 22  VTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVAVDETKG 81
           VTP + D S D    R+ +DW       G+   G TGE  ++   E  E+++VAV++   
Sbjct: 12  VTPMQEDGSLDFPALRALVDWHVAEGTDGIVIVGTTGESPTVNVDEHCELIRVAVEQADK 71

Query: 82  RVPVLAGT-GYGTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVCKSVKIG 140
           R+P++AGT G  T  A E+   A++ GAD  L + PY     QEG+  H   + ++V++ 
Sbjct: 72  RIPIIAGTGGNSTKEAIELTAFAKQVGADASLQVVPYYNKPTQEGMYRHFRTIAEAVELP 131

Query: 141 VIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRLT-YIGGL 196
           V++YN   R  A +Q DT+ RL +  P ++G K+  G+I+   ++        + Y G  
Sbjct: 132 VVLYNVPGRTVADMQHDTILRLAQ-VPGIIGVKEATGNIDRAAQLIKDAPQGFSIYSGDD 190

Query: 197 PTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIHAGLKDFILPLIAIR 256
           PTA    L    +G     S   N  P        A  K D  T     +   + L+A+ 
Sbjct: 191 PTAIALML----LGGHGNISVTANVAPRKMHELCVAALKGDAIT----ARRIHMELVALN 242

Query: 257 NRKKGYAVSI-IKAGMKVIGRDSGPVRLPLTDLT 289
                 A  I +K  ++ +GR  G +RLPLT L+
Sbjct: 243 KAMFVEANPIPVKWALQQMGRMQGGIRLPLTPLS 276


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: 201
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: 294
Length adjustment: 27
Effective length of query: 287
Effective length of database: 267
Effective search space:    76629
Effective search space used:    76629
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 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