GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Caulobacter crescentus NA1000

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 CCNA_01356 CCNA_01356 5-dehydro-2-deoxygluconokinase IolC

Query= SwissProt::Q53W83
         (309 letters)



>FitnessBrowser__Caulo:CCNA_01356
          Length = 642

 Score =  113 bits (283), Expect = 1e-29
 Identities = 96/326 (29%), Positives = 137/326 (42%), Gaps = 27/326 (8%)

Query: 2   LEVVTAGEPLVALVPQEPG-HLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDE 60
           L+++  G   V L  Q+ G  L        Y+GG+  N A   ARLG+K G + RVG D 
Sbjct: 8   LDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLLTRVGADH 67

Query: 61  LGAMVEERLRAEGVDLTHFRRAPG-FTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFD 119
           +G  + E+L  EGVD+      P   T L +          + +YR+  A  AL P   D
Sbjct: 68  MGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMALEPSDVD 127

Query: 120 PDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLW-------- 171
             +      + ++G T    P     SL A    K  G RV+ D++YR  LW        
Sbjct: 128 EAWFAQAGAVLING-THLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGLTGKDAG 186

Query: 172 -----SPEEARGFLERALPGVDLLFLSEEEAELLFGRVE-----EALRALSAPEVVLKRG 221
                  ++    L+  +   DL+  +EEE  +L G  +      A+R  S   +V KRG
Sbjct: 187 ENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDALLVCKRG 246

Query: 222 AKGAWAFVDG------RRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLAN 275
            +G  AF           V    F VE  + +GAGDAF AG+L G +    VE      N
Sbjct: 247 PEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVETCCEWGN 306

Query: 276 LLGASVAASRGDHEGAPYREDLEVLL 301
             GA V +  G     P   +L+  L
Sbjct: 307 ACGAIVVSRHGCTPAMPTWIELQAFL 332


Lambda     K      H
   0.320    0.139    0.407 

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: 449
Number of extensions: 22
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: 309
Length of database: 642
Length adjustment: 32
Effective length of query: 277
Effective length of database: 610
Effective search space:   168970
Effective search space used:   168970
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: 51 (24.3 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