GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Cronobacter condimenti 1330

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate WP_007680610.1 BN137_RS02010 sugar kinase

Query= SwissProt::Q0JGZ6
         (323 letters)



>NCBI__GCF_000319285.1:WP_007680610.1
          Length = 312

 Score =  113 bits (282), Expect = 7e-30
 Identities = 94/312 (30%), Positives = 133/312 (42%), Gaps = 11/312 (3%)

Query: 8   VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67
           V++ GE +  FV T  G  LA+   F K   GA  NVA  +ARLG   ++V ++G+D FG
Sbjct: 7   VITIGEAMAMFVATEPG-DLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSFG 65

Query: 68  RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADG-EREFMFYRNPSADMLLTHAELNV 126
           R + + L   G+   GV  D    T     +   DG +    ++R  SA   L+  + N 
Sbjct: 66  RFVLSQLEKEGISTRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDFNA 125

Query: 127 ELIKRAAVFHYGSISLIAEPCRSAHL-RAMEIAKEAGALLSYDPNLREALWPSREEARTK 185
            L   A   H   ++          L  A    K  G  +S+DPNLR  LW S  E   K
Sbjct: 126 PLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMVEK 185

Query: 186 ILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFR 245
           +  +   AD V     E   LTG    E      L R    +++ T  D      A   +
Sbjct: 186 LNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASGEQ 245

Query: 246 GAVPSYKVQQ-VDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKK 304
           G V + KV   VDT GAGD F   ++       S+L + K L +A    N  GA+    +
Sbjct: 246 GTVEAVKVDNVVDTVGAGDGFAVGVI-------SALLEGKTLHQAATRGNKIGALAIQVQ 298

Query: 305 GAIPSLPTEVEV 316
           G    LPT  ++
Sbjct: 299 GDSEGLPTRAQL 310


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: 221
Number of extensions: 9
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: 312
Length adjustment: 27
Effective length of query: 296
Effective length of database: 285
Effective search space:    84360
Effective search space used:    84360
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 24 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