GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Salinicoccus carnicancri Crm

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_017549879.1 C792_RS0112925 sugar kinase

Query= SwissProt::Q53W83
         (309 letters)



>NCBI__GCF_000330705.1:WP_017549879.1
          Length = 315

 Score =  176 bits (447), Expect = 5e-49
 Identities = 117/310 (37%), Positives = 168/310 (54%), Gaps = 11/310 (3%)

Query: 2   LEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDEL 61
           +EV+  GE +VALV +  G++R     + YV GAE+N  + L+RLG    +V  +GEDEL
Sbjct: 1   MEVIGIGESMVALVNEPKGYIRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDEL 60

Query: 62  GAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPD 121
           G ++  ++RAE VD +H       TG++ ++ LP G   V YYR+ SA S +     D D
Sbjct: 61  GELILHKVRAENVDASHVTHKDKRTGVFFKQILPDGSVDVTYYREDSAASNMDIRDIDMD 120

Query: 122 YLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLE 181
            +   + L+L+GIT +LS  A+     A+  A    V V  D N R  +WS +EAR  + 
Sbjct: 121 AIRRAKVLYLTGITLSLSSSAKEMLFEAVRIA-GDDVTVVFDPNIRLKMWSAKEARETIL 179

Query: 182 RALPGVDLLFLSEEEAELLFG--RVEEAL---RALSAPEVVLKRGAKGAWAFVDGRRVEG 236
             LP VD L    +E ++L G  R EEAL   R L   +VVLK G +GA    DG  + G
Sbjct: 180 EFLPHVDCLIAGRDEVDILMGAMRPEEALKSFRELGCSKVVLKLGKEGAVYDFDG--IGG 237

Query: 237 SA---FAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPY 293
           S       E +DPVGAGDAFAAG ++G + G   E  +  A  LG  +    GD++G P 
Sbjct: 238 SVKNPKQFEEIDPVGAGDAFAAGIISGLLNGEDPEASVEKACFLGGYITQFVGDYQGFPS 297

Query: 294 REDLEVLLKA 303
            + L   +++
Sbjct: 298 GDGLRAAMES 307


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: 250
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: 309
Length of database: 315
Length adjustment: 27
Effective length of query: 282
Effective length of database: 288
Effective search space:    81216
Effective search space used:    81216
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: 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