GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Cronobacter condimenti 1330

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 WP_007680610.1 BN137_RS02010 sugar kinase

Query= SwissProt::P50845
         (324 letters)



>NCBI__GCF_000319285.1:WP_007680610.1
          Length = 312

 Score =  314 bits (805), Expect = 2e-90
 Identities = 162/307 (52%), Positives = 207/307 (67%), Gaps = 3/307 (0%)

Query: 3   LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62
           LD +T GE+MAMF A E G L +V  F K +AGAE NVA GLARLG  + W+S+VGND  
Sbjct: 5   LDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSF 64

Query: 63  GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121
           G F+L +L+KEG+  +R +   D  PTG  LKSKV +G DP V Y+RK SAAS L+  ++
Sbjct: 65  GRFVLSQLEKEGIS-TRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDF 123

Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181
               F  A HLH++G+  ALS    +   H    M+  GKTISFDPN+RP LW  +A MV
Sbjct: 124 NAPLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMV 183

Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241
             +N LA LADW  PG+ EG +LTG++ PEGIAD+YL +G   V IK G +GA+++T + 
Sbjct: 184 EKLNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASG 243

Query: 242 E-GFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300
           E G +E  +VD VVDTVGAGDGFAVGVIS +L+G +   A  RGN IGAL +Q  GD +G
Sbjct: 244 EQGTVEAVKVDNVVDTVGAGDGFAVGVISALLEGKTLHQAATRGNKIGALAIQVQGDSEG 303

Query: 301 LPTREKL 307
           LPTR +L
Sbjct: 304 LPTRAQL 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: 338
Number of extensions: 14
Number of successful extensions: 4
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: 312
Length adjustment: 27
Effective length of query: 297
Effective length of database: 285
Effective search space:    84645
Effective search space used:    84645
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 24 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