GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Sinorhizobium meliloti 1021

Align Fructokinase-2; ZmFRK2; EC 2.7.1.4 (characterized)
to candidate SM_b21374 SM_b21374 sugar kinase

Query= SwissProt::Q6XZ78
         (335 letters)



>FitnessBrowser__Smeli:SM_b21374
          Length = 313

 Score =  130 bits (328), Expect = 3e-35
 Identities = 103/322 (31%), Positives = 148/322 (45%), Gaps = 22/322 (6%)

Query: 19  VVSFGEMLIDFVPDVAGLSLAESGGFVKA-------PGGAPANVACAIAKLGGSSAFVGK 71
           +++ GE+L++ +    G       GF KA       P GAPA       KLG   A + +
Sbjct: 4   ILTIGEILVEIIATEKG------DGFRKATPLIGPFPSGAPAIFIDQAGKLGQPCAIISR 57

Query: 72  FGDDEFGHMLVNILKQNNVNAEGCLFDKHARTALAFVTLKHDGEREFMFYRNPSADMLLT 131
            G D+FG + +  LK++ V+  G   D  A T  AFV  + DG R F+F    SA   +T
Sbjct: 58  VGGDDFGTVNLERLKRDGVDISGIEVDPLATTGSAFVRYRPDGSRAFVFNIRDSACGKIT 117

Query: 132 EAELDLGLVRRARVFHYGSISLISEPCRSAHMAAMRAAKAAGVLCSYDPNVRLPLWPSPD 191
             E    LV      H    SL +     + +AA+   KA G   S+DPN+R  +  SP 
Sbjct: 118 LDERMTRLVGECSHVHVMGSSLYAPSVVESILAAIGIVKAGGGTVSFDPNLRPEILKSP- 176

Query: 192 AAREGILSIWKEADFIKVSDDEVAFLTRGDANDEKNVLSLWFDGLKLLVVTDGDKGCRYF 251
             RE +L++  E D    S DE+ FL      + + V  L   G+K +VV  G  G  YF
Sbjct: 177 GMREALLTVLAETDLFLPSGDEL-FLFTEAKTESQAVAELLASGIKAVVVKRGAAGASYF 235

Query: 252 TKDFKGSVPGFKVDTVDTTGAGDAFVGSLLVNVAKDDSIFHNEEKLREALKFSNACGAIC 311
                 S+PGF V+ +D TGAGD F  + +       S + N    REAL+F+ A GA  
Sbjct: 236 DAGAALSLPGFPVEEIDPTGAGDCFGATFV-------SFWLNGASPREALEFAAASGARA 288

Query: 312 TTKKGAIPALPTVATAQDLIAK 333
               G +    T A  +  I++
Sbjct: 289 VMHFGPMEGASTRAELERFISE 310


Lambda     K      H
   0.320    0.136    0.403 

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: 261
Number of extensions: 13
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: 335
Length of database: 313
Length adjustment: 28
Effective length of query: 307
Effective length of database: 285
Effective search space:    87495
Effective search space used:    87495
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 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