GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Synechococcus elongatus PCC 7942

Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate Synpcc7942_0116 Synpcc7942_0116 fructokinase

Query= SwissProt::Q6XZ79
         (323 letters)



>FitnessBrowser__SynE:Synpcc7942_0116
          Length = 324

 Score =  152 bits (383), Expect = 1e-41
 Identities = 106/326 (32%), Positives = 163/326 (50%), Gaps = 7/326 (2%)

Query: 1   MAAGRELVVSFGEMLIDFVPTVAGVSLAEAPAFLKAPGGAPANVAIAVSRLGGGAAFVGK 60
           M A    V+  GEML D +     +   +  ++   PGGAPANVA A+ +LG  +  +  
Sbjct: 1   MTAQAPTVICLGEMLWDCLANDRDLPAEQVQSWTPWPGGAPANVATALVKLGVQSGLITC 60

Query: 61  LGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFVTLRADGEREFMFYR----NPSAD 116
           LG D  G  L  +L+DNGV    V       T    V   A G+R+F  +     +  AD
Sbjct: 61  LGSDPEGDRLFQVLQDNGVAIAAVQRHPRLPTRQVQVLRTAQGDRQFGGFGAIACDQFAD 120

Query: 117 MLLTADELNVELIKRAAVFHYGSISLIAEPCRTAHLRAMEIAKEAGALLSYDPNLREALW 176
             L A++L     + A V   G+I L       A  +A+  A + G  +  D N R + W
Sbjct: 121 TELQAEQLPQAWFRLAKVLCLGTIPLAYPSSAIAAQQALTWANQQGMTVLLDVNWRPSFW 180

Query: 177 PSREEARTQILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQG 236
           P    A  +I +I  Q   +K++  E E+L   D+V D   ++  +P ++ +L+T GD+G
Sbjct: 181 PDPSLAPDRIRAILPQIQQLKLAREEAEWL--FDTV-DPATIQARQPQLQAVLITDGDRG 237

Query: 237 CKYYARDFHGAVPSFKVQQVDTTGAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANAC 296
           C Y+   + G  PSF V+ +DTTGAGDAFV A L +  +        +++  +I++A+A 
Sbjct: 238 CHYWVAGWQGHCPSFPVKAIDTTGAGDAFVAAWLAQNTQMDFQWTSAEQVQTAIRWASAA 297

Query: 297 GAITTTKKGAIPSLPTEAEVLQLIEK 322
           GA+TT   GAI + PT   +  L+ K
Sbjct: 298 GALTTLNPGAIAAQPTSDAIQSLLSK 323


Lambda     K      H
   0.319    0.136    0.388 

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: 262
Number of extensions: 13
Number of successful extensions: 3
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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.

Links

Downloads

Related tools

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