GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Cronobacter condimenti 1330

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_007679976.1 BN137_RS02630 fructokinase

Query= SwissProt::P23917
         (302 letters)



>NCBI__GCF_000319285.1:WP_007679976.1
          Length = 303

 Score =  527 bits (1357), Expect = e-154
 Identities = 252/300 (84%), Positives = 275/300 (91%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60
           MRIGIDLGGTKTEVIAL D GEQ +RHR+PTPR+DY QT+ETIA LV++AE+ TG+RGTV
Sbjct: 1   MRIGIDLGGTKTEVIALSDDGEQRFRHRVPTPRNDYPQTVETIAGLVELAERETGERGTV 60

Query: 61  GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120
           G+GIPG++SPYTGVVKNANSTWLNGQ  DKDLSARL REVRLANDANC AVSEAVDGAAA
Sbjct: 61  GVGIPGTLSPYTGVVKNANSTWLNGQALDKDLSARLAREVRLANDANCFAVSEAVDGAAA 120

Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180
           GAQTVFAVIIGTGCG+G+A  GR+HIG NG AGEWGHNPLPWMD+DELRYREEVPCYCGK
Sbjct: 121 GAQTVFAVIIGTGCGSGIALGGRSHIGANGNAGEWGHNPLPWMDDDELRYREEVPCYCGK 180

Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240
           QGCIET+ISGTGFA DY RLSG  LKGSEIIRLV+E D +AELAL RYELRLAKSLAH+V
Sbjct: 181 QGCIETYISGTGFATDYHRLSGQPLKGSEIIRLVDEQDALAELALSRYELRLAKSLAHIV 240

Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLWP 300
           N+LDPDVIVLGGGMSNVDRLY+TV  L+K +VFGGECETPVRKA HGDSSGVRGAAWLWP
Sbjct: 241 NVLDPDVIVLGGGMSNVDRLYKTVPPLMKHWVFGGECETPVRKAVHGDSSGVRGAAWLWP 300


Lambda     K      H
   0.318    0.137    0.418 

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: 453
Number of extensions: 18
Number of successful extensions: 1
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: 302
Length of database: 303
Length adjustment: 27
Effective length of query: 275
Effective length of database: 276
Effective search space:    75900
Effective search space used:    75900
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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