GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas putida KT2440

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 PP_3378 PP_3378 putative 2-ketogluconokinase

Query= SwissProt::P50845
         (324 letters)



>FitnessBrowser__Putida:PP_3378
          Length = 316

 Score =  301 bits (772), Expect = 1e-86
 Identities = 161/309 (52%), Positives = 211/309 (68%), Gaps = 5/309 (1%)

Query: 4   DAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQLG 63
           D + FGE+MAMF A + G L  V  F K +AGA+SNVA GLARLGF++ W+S+VG+D LG
Sbjct: 5   DVLCFGETMAMFVAEQAGDLAGVGQFGKRIAGADSNVAIGLARLGFKVRWLSRVGDDSLG 64

Query: 64  TFILQELKKEGVDVSRVIRSQDEN-PTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121
            F+L  L+ EG+D S V    D N PTG  LK++ ++G DP V Y+R+ SAAS L+ A  
Sbjct: 65  RFVLDSLRCEGLDCSGV--EVDANYPTGFQLKARSEDGSDPAVEYFRRGSAASRLSAAMV 122

Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181
              + Q A H+H TGIP ALS   +  ++ +++ MR AG++ISFDPN+RPSLWPDQ++MV
Sbjct: 123 SPVWLQ-ARHVHATGIPLALSDSCRALSHALLDGMRAAGRSISFDPNLRPSLWPDQSSMV 181

Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241
             IN LA  ADW  PG+ EG LLTG+ TP  IA +YL +G   V IKLG  GAYF++   
Sbjct: 182 REINALAAKADWVLPGLEEGRLLTGQHTPADIAAFYLDQGVELVVIKLGDAGAYFRSAKG 241

Query: 242 EGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDGL 301
           EG +    V RVVDTVGAGD FAVGV+S +L+G    +AV RGN  G+  VQ+ GDM+GL
Sbjct: 242 EGQVAPVPVSRVVDTVGAGDAFAVGVLSALLEGRPVAEAVARGNWCGSRAVQSRGDMEGL 301

Query: 302 PTREKLASF 310
           P R +L ++
Sbjct: 302 PLRHELEAY 310


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: 318
Number of extensions: 13
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: 324
Length of database: 316
Length adjustment: 28
Effective length of query: 296
Effective length of database: 288
Effective search space:    85248
Effective search space used:    85248
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