GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas fluorescens FW300-N1B4

Align fructokinase; EC 2.7.1.4 (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)

Query= CharProtDB::CH_006622
         (307 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765
          Length = 339

 Score =  114 bits (286), Expect = 2e-30
 Identities = 95/315 (30%), Positives = 148/315 (46%), Gaps = 29/315 (9%)

Query: 9   GDAVVDLLPESEGRLLQCP------GGAPANVAVGVARLGGNSGFIGAVGGDPFGRYMRH 62
           G+ +   + E  G L           GA +NVA+G++RLG N  ++  VG D  GR++  
Sbjct: 10  GETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGADSLGRFVID 69

Query: 63  TLQQEQVDVSHMYLDDQHRTSTVVVD-LDDQGERTFTFMVRPSADLFL-VEEDLPQFAAG 120
           TL+++ +D SH+ +D  H T   +    DD  +    +  R SA   L V+   PQ    
Sbjct: 70  TLEKQGLDCSHVDIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQSIAPQLLEA 129

Query: 121 QWLHVCSI--ALSAEPSRSTTFAAMESIRSAGGRVSFDPNIRPDLWQDQALLLACLDRAL 178
           + LH   I  ALSA  +R  +F  M  +R+AG  VSFDPN+RP LW  +  ++  ++R  
Sbjct: 130 RHLHATGIPPALSA-AAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQMIREINRLA 188

Query: 179 HMANVVKLSEEELVFISSSNDLAYGIASVTERYQPELLLVTRGKAGVLAAFQQKFTHFNA 238
            +A+ V     E   ++   D A  IA+       E + +  G AG         TH + 
Sbjct: 189 ALAHWVLPGLSEGRLLTGFEDPA-DIAAFYLDQGAEAVAIKLGPAGAYYR-----THLDE 242

Query: 239 RPVAS------VDTTGAGDAFVAGLLASLAANGMPTDMTALEPTLTLAQTCGALATTAKG 292
             VA       VDT GAGD F  GL+++L  N       ++   +  A   G+ A  ++G
Sbjct: 243 GFVAGVPVETVVDTVGAGDGFAVGLISALLEN------HSVAQAVQRANWIGSRAVQSRG 296

Query: 293 AMTALPYQRDLNRQF 307
            M  LP + ++  +F
Sbjct: 297 DMEGLPTRLEMFAEF 311


Lambda     K      H
   0.320    0.133    0.392 

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: 235
Number of extensions: 12
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: 307
Length of database: 339
Length adjustment: 28
Effective length of query: 279
Effective length of database: 311
Effective search space:    86769
Effective search space used:    86769
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