GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Burkholderia phytofirmans PsJN

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 BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase

Query= SwissProt::P50845
         (324 letters)



>FitnessBrowser__BFirm:BPHYT_RS11300
          Length = 327

 Score =  333 bits (854), Expect = 3e-96
 Identities = 168/313 (53%), Positives = 219/313 (69%), Gaps = 2/313 (0%)

Query: 3   LDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQL 62
           LD +T+GE+MAMF A E G L  V  F+K +AGA+ NVA GL+RLGF++GWMS+VGND  
Sbjct: 8   LDVITYGEAMAMFVAAETGPLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSF 67

Query: 63  GTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAEY 121
           G ++   L KEG+D    + + +  PTG  LKSK  +G DP + Y+RK SAAS L+ A+Y
Sbjct: 68  GQYVRDTLTKEGIDQG-CVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHLSLADY 126

Query: 122 PRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATMV 181
             DY   A HLH+TG+ PA+SA  ++  +H+  +MR AGKTISFDPN+RP+LWP +A MV
Sbjct: 127 AADYVLQARHLHLTGVAPAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPSRAAMV 186

Query: 182 HTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGTS 241
             +N LA LADW  PGI EGE+LTG   P+ IA +YL++GA  V IKLG +GAYF+T   
Sbjct: 187 EGLNALAALADWVLPGIGEGEILTGYTQPDDIAKFYLEQGARGVIIKLGAQGAYFRTADD 246

Query: 242 EGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDGL 301
              + G  V +VVDTVGAGDGFAVGV+S +L+G S   AV RGN IGAL +Q  GD +GL
Sbjct: 247 AAMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALAIQVIGDSEGL 306

Query: 302 PTREKLASFLSAQ 314
           P+R +L +  +AQ
Sbjct: 307 PSRAELDALEAAQ 319


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: 340
Number of extensions: 7
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: 327
Length adjustment: 28
Effective length of query: 296
Effective length of database: 299
Effective search space:    88504
Effective search space used:    88504
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