GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Sinorhizobium meliloti 1021

Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate SMc01103 SMc01103 ribokinase

Query= SwissProt::D4GYE6
         (305 letters)



>FitnessBrowser__Smeli:SMc01103
          Length = 299

 Score = 68.6 bits (166), Expect = 2e-16
 Identities = 71/245 (28%), Positives = 101/245 (41%), Gaps = 8/245 (3%)

Query: 36  AGGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRLDADGIASDFV-TVDADTRLNTT 93
           AGGKG N A  A    A V  +G +G   F +     L   G   D   TV   T     
Sbjct: 35  AGGKGANQALAARRAGASVRMAGAVGSDAFAEGALALLKEAGTDLDLTKTVGEPTGTAHI 94

Query: 94  VLAADGEYKLNH-NGPQIRAADVDELVETAQANEPDTLLVGGSLPPGM---SLSDVDRLA 149
           ++  DGE  +        R +  D     AQ +  DTL++   +P      +LS+  R  
Sbjct: 95  IVGGDGENVIVVVASANARVSGDDAANVVAQMSAGDTLMLQLEIPSASVEKALSEAKRRG 154

Query: 150 RAGDWKIAVDMGGEYLAELDADYYVCKPNRSELAAATGRTVETEADAVEAAEELHARGFE 209
                 IA            AD  +      EL A  G+     A+  EA   LHA   +
Sbjct: 155 IRSIINIAPLTPDAARLGRMADIVIANETEFELLA--GKAGIAGAEREEAMNGLHAETRQ 212

Query: 210 YVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFLAAREHGLSDADALRMG 269
            V+ +LGA+G + + + E+  A  L +E VDTVGAGD       A  + GL+ ++ALR  
Sbjct: 213 TVIVTLGAEGVVAIHEGELHRAKGLTIEPVDTVGAGDTFCGYLAAGLDAGLAFSEALRRA 272

Query: 270 VLTAS 274
            +  S
Sbjct: 273 AIAGS 277


Lambda     K      H
   0.315    0.133    0.375 

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: 224
Number of extensions: 11
Number of successful extensions: 2
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: 305
Length of database: 299
Length adjustment: 27
Effective length of query: 278
Effective length of database: 272
Effective search space:    75616
Effective search space used:    75616
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