GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas fluorescens FW300-N2C3

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate AO356_24685 AO356_24685 2-dehydro-3-deoxygluconokinase

Query= SwissProt::Q0JGZ6
         (323 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24685
          Length = 326

 Score =  128 bits (321), Expect = 2e-34
 Identities = 99/318 (31%), Positives = 147/318 (46%), Gaps = 11/318 (3%)

Query: 8   VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67
           V+SFGE +   V    G  LA    F K   GA +NVAI ++RLG   A++ ++G D  G
Sbjct: 6   VLSFGETMAMLVADQRG-DLASVDQFHKRIAGADSNVAIGLSRLGFKVAWLSRVGADSLG 64

Query: 68  RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADG-EREFMFYRNPSADMLLTHAELNV 126
           R +   L + G+D   V  D    T   F +L  DG + +  ++R  SA   L+   +  
Sbjct: 65  RFVTQTLENEGLDCRHVAVDPEHPTGFQFKSLTVDGSDPQVEYFRRSSAASHLSVGSIAP 124

Query: 127 ELIKRAAVFHYGSISLIAEPCRSAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTKI 186
            L+    V   G +  ++   R      M   + AG  LS+DPNLR +LW S     T I
Sbjct: 125 ALLDARHVHATGIVPALSGTAREMSFELMSRMRAAGRSLSFDPNLRPSLWGSESTMITAI 184

Query: 187 LSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFRG 246
             +   A  V     E   LTG D   D     L +   +++++ LG  G  Y     +G
Sbjct: 185 NRLAALAHWVLPGLGEGRLLTGFDDPADIAAFYLDQGA-EIVVIKLGADGAYYRTALDQG 243

Query: 247 AVPSYKVQQ-VDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKKG 305
            +P   V Q VDT GAGD F   L+       S+L + + + EA++ AN  G+     +G
Sbjct: 244 VIPGVPVAQVVDTVGAGDGFAVGLI-------SALLEGRAITEAVQRANWIGSRAVQSRG 296

Query: 306 AIPSLPTEVEVLKLMESA 323
            +  LPT +E+L   E+A
Sbjct: 297 DMEGLPTRIELLAEFETA 314


Lambda     K      H
   0.320    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: 252
Number of extensions: 11
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: 323
Length of database: 326
Length adjustment: 28
Effective length of query: 295
Effective length of database: 298
Effective search space:    87910
Effective search space used:    87910
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