GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Cupriavidus basilensis 4G11

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate RR42_RS09470 RR42_RS09470 2-dehydro-3-deoxygluconokinase

Query= SwissProt::P50845
         (324 letters)



>FitnessBrowser__Cup4G11:RR42_RS09470
          Length = 314

 Score =  283 bits (724), Expect = 4e-81
 Identities = 152/308 (49%), Positives = 195/308 (63%), Gaps = 2/308 (0%)

Query: 3   LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62
           LD VT GE+M M  A E G L  V TF K  AGAE+NVA GL+RLG ++GW S++G+D +
Sbjct: 5   LDVVTLGEAMLMLVAGEAGPLEGVQTFHKRTAGAETNVAIGLSRLGLKVGWASRLGDDSM 64

Query: 63  GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121
             ++L E+++EGVD S+V+    E  TG   K +V +G DP V Y+R+ SAAS +     
Sbjct: 65  ARYLLGEMRREGVDCSQVVCEPGER-TGFQFKGRVDDGSDPPVEYHRRGSAASRMNPEHL 123

Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181
              + + A HLHVTG+ PAL+   +  T   +  MR AG+T+SFDPN+RP+LW     M 
Sbjct: 124 DDRWLRRARHLHVTGVFPALAEGTQAATRQAIATMRAAGRTVSFDPNLRPALWATPELMR 183

Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241
            T+N+LA   DW  PGI EG  LTG   PE IA +Y  +GA  V +KLG EGAYF     
Sbjct: 184 ETLNNLAQQCDWVLPGIEEGRFLTGHAEPERIAAFYRGRGARLVVVKLGAEGAYFDGEAG 243

Query: 242 EGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDGL 301
            G +    V+RVVDTVGAGDGFAVGVIS +L G +  DAV+RG  IGA  VQ  GD +GL
Sbjct: 244 TGHVPAFSVERVVDTVGAGDGFAVGVISALLQGRTVADAVRRGAWIGARAVQVRGDTEGL 303

Query: 302 PTREKLAS 309
           PT   LA+
Sbjct: 304 PTHALLAA 311


Lambda     K      H
   0.317    0.135    0.399 

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: 308
Number of extensions: 17
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: 324
Length of database: 314
Length adjustment: 28
Effective length of query: 296
Effective length of database: 286
Effective search space:    84656
Effective search space used:    84656
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 (21.6 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