GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mannokinase in Shewanella sp. ANA-3

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 7025547 Shewana3_2698 N-acetylglucosamine kinase (RefSeq)

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__ANA3:7025547
          Length = 308

 Score =  186 bits (471), Expect = 8e-52
 Identities = 108/301 (35%), Positives = 160/301 (53%), Gaps = 8/301 (2%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60
           M  G+D+GGTK E+           + RL TP  DY   + T+A  ++ A+Q  G+RGTV
Sbjct: 1   MYYGLDIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGERGTV 60

Query: 61  GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120
           G+ +PG +    G V ++N   LN +    DL+  L R V + ND  C A+SEAV G   
Sbjct: 61  GIALPGVVKA-DGTVISSNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCFALSEAVLGVGR 119

Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCY--- 177
           G   V  +I+GTG G G+  +G+ ++G N  AGE+GH  +       +  R ++P Y   
Sbjct: 120 GYSRVLGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGV----SANVACRHQLPLYVCG 175

Query: 178 CGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLA 237
           CG +GC ET++SGTG    Y+ ++G        +  +  +DP+A      Y   L   +A
Sbjct: 176 CGLEGCAETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMDILGSLMA 235

Query: 238 HVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAW 297
            +V  +DPD+IVLGGG+S V+ +   + Q  K  +F G      + A  G +SGVRGAA 
Sbjct: 236 SLVLAMDPDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSASGVRGAAL 295

Query: 298 L 298
           L
Sbjct: 296 L 296


Lambda     K      H
   0.318    0.137    0.418 

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: 330
Number of extensions: 18
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: 302
Length of database: 308
Length adjustment: 27
Effective length of query: 275
Effective length of database: 281
Effective search space:    77275
Effective search space used:    77275
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 (21.7 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