GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Sinorhizobium meliloti 1021

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate SM_b21217 SM_b21217 sugar kinase

Query= reanno::Dino:3609413
         (308 letters)



>FitnessBrowser__Smeli:SM_b21217
          Length = 311

 Score = 62.4 bits (150), Expect = 1e-14
 Identities = 75/243 (30%), Positives = 103/243 (42%), Gaps = 21/243 (8%)

Query: 29  GGAVFNTAVALGRLGADVGLVTGLSRDLFGEVLMTALAAADVDSDMAVLSDRPTTLAFVT 88
           GG   N A+A   LG D  +   +  D FG  L  A      +  +  +    TTL+ V 
Sbjct: 39  GGCAGNNALAWDSLGVDYVIAANVGNDQFGTWLKEAFGERSRNWPVEAVG---TTLS-VG 94

Query: 89  LTDGHAQYAFYDENTAGRMLAPADMPDPGPEV-GTLFFGGISL-----AVEPCAAAYEAL 142
           +T    +  F+   T    L     P+    + G    GG +L       +    AY+AL
Sbjct: 95  ITHPDGERTFF---TTRGHLPLFSFPEVHSMLDGNRLRGGYALLSGSFLTDALTLAYDAL 151

Query: 143 CLKAAAGRVVMLDPNIRPGFIKD--ETTFRARIDRMLAVTDIVKVSDEDLAWLMGPGDLA 200
              A A  + +    +  G+  D    T R R    L        ++ +   L G  D A
Sbjct: 152 FDWADAHEIAVA---LDTGWPLDGWTETNRLRTLGWLKRCHCALFNEVETTTLTGLSDPA 208

Query: 201 ESAAALRARGP--AVVCVTRGGAGVEAHTATGIT-HVAAEAVEVVDTVGAGDTFNAGFLA 257
           E+A +L+   P  A+V V RG  G  A    G T  V A  V+VVDT+GAGD FNAGFLA
Sbjct: 209 EAALSLKGEMPAEAIVVVKRGPHGALAIDRDGGTFSVPAPQVQVVDTIGAGDVFNAGFLA 268

Query: 258 GLA 260
            LA
Sbjct: 269 ALA 271


Lambda     K      H
   0.320    0.136    0.398 

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: 197
Number of extensions: 8
Number of successful extensions: 1
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: 308
Length of database: 311
Length adjustment: 27
Effective length of query: 281
Effective length of database: 284
Effective search space:    79804
Effective search space used:    79804
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