GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Frischella perrara PEB0191

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_039105873.1 FPB0191_RS10250 hypothetical protein

Query= BRENDA::C4M2I2
         (294 letters)



>NCBI__GCF_000807275.1:WP_039105873.1
          Length = 294

 Score =  174 bits (440), Expect = 3e-48
 Identities = 92/291 (31%), Positives = 163/291 (56%), Gaps = 3/291 (1%)

Query: 6   IKVAGIGEVVWDCFGDVKKQGGAPCNFAMHMAQFGFESYAFIAVGNDELGKRSLEIIHSF 65
           +K+  +GE +WD   + KK GGA  NF  H    G ++    AVGND+ G+  L  ++  
Sbjct: 4   LKIIAVGEYLWDYLPNGKKIGGAAANFCYHAKSAGAQAILVSAVGNDDNGRELLNQLNIL 63

Query: 66  GV-QTIDPVVDYETSTVIITLHN-GIPSYNVKLNVAWDHLKLTDSIIEKAKE-LDAVCFG 122
           G+   +     YET  V++ L   G P+YN+   VAWD ++LT+S+ +  K+ + A+ FG
Sbjct: 64  GIPHDVQTSTHYETGKVMVELDAAGKPTYNIINPVAWDDVQLTESLQKLLKDDIVAIYFG 123

Query: 123 TIAQRSEETRKSIIQFLKLMKPNSFKVFDVNLRQHFYNDDIIQESLSLSNIVKMSDEEIQ 182
           ++ QR++   + +   +  +  N   + D+NLRQ+ Y  +I++ SL  ++I+K++DEE+ 
Sbjct: 124 SLIQRNKNNHQLLKTIVTSLPSNIKIIVDINLRQNHYTYEILRFSLEHTHILKLNDEELP 183

Query: 183 EVGKACGFQGNDLEILKQIHHQYHLKYSLLTLGEKGSYVYDGTNEIFCEPTKVNVVNTVG 242
            +      + +   +   +H  Y L+  + T G +GSY+     + +C   K+  ++TVG
Sbjct: 184 VIADLLNIKADPNVLYDYLHKNYQLELLIYTCGSEGSYLISENEQDYCPAEKITPIDTVG 243

Query: 243 AGDSFTAIFVGSILKGKSIEQAQKLASKVASYVCTQDSAMPKLTQELLSEL 293
           AGDSF A      LKG+ +++    A+ +A+YVCTQ   MP + +E++ +L
Sbjct: 244 AGDSFMATASILYLKGRKLKEINAKANHIAAYVCTQSGPMPLMPEEMVKDL 294


Lambda     K      H
   0.318    0.135    0.389 

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: 233
Number of extensions: 10
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: 294
Length of database: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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.

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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