GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Chryseobacterium viscerum 687B-08

Align Fructokinase; EC 2.7.1.4 (uncharacterized)
to candidate WP_103231942.1 C1634_RS03565 ROK family protein

Query= curated2:P43468
         (288 letters)



>NCBI__GCF_002899945.2:WP_103231942.1
          Length = 322

 Score = 62.4 bits (150), Expect = 1e-14
 Identities = 73/297 (24%), Positives = 118/297 (39%), Gaps = 50/297 (16%)

Query: 6   IEAGGTKFVCATGAENGQVSDRISIPTTTPVETMTAVDD-YFTTHPV-DAIGIGS-FGPI 62
           ++ GGT          G+V D+ ++ T    +    +D  Y +  P+ +  G  + F  I
Sbjct: 14  VDIGGTNTKFGIVNHRGEVLDKGNLRTDAYDKVEDFIDALYESVRPMMEKYGTEAHFDGI 73

Query: 63  GVNPHDPKY--GYITTTPKPGW-GDFDFLGHLKSQFNIPLYWTTDVNEAAYGESMIGIAK 119
           GV   +  Y  G I   P   W G   F   + ++FN+P   T D N AA GE + G A+
Sbjct: 74  GVGAPNANYYKGTIELAPNLPWKGVIPFAELMTAKFNLPCTVTNDANAAALGEMLFGAAR 133

Query: 120 DVPNSIYMTIGTGVGAGVISQNHIFNGRT--HTELGHMRLNRLPGDDFKSNCPYHDICLE 177
            + + I +T+GTGVG+G+I+   +  G      ELGH  +   PG   K      +  LE
Sbjct: 134 GMKDFIMITLGTGVGSGIIANGSLIYGHDGFAGELGHTIVK--PGGR-KHWSTGSEGSLE 190

Query: 178 GLAAGPAVGKRTGKAGKDIP----------------------VDDPVWPIITDY----IA 211
             A+   +     K   + P                       +DP+   +  Y    + 
Sbjct: 191 AYASATGITITAKKMRAEFPESMLNQYPEDEINSKTVYECAMKEDPIAIEVFRYTGQKLG 250

Query: 212 QACVNLTVAFAPDKIILNGGVMN-------------QRQLFPMIREKFAAYLNGYEE 255
           +A  N  +  +P  I+L GGV+              +R L P+ R K     +  +E
Sbjct: 251 EAIANFVMFSSPQAILLFGGVIKAGDFILKPAKLHMERNLLPIFRNKVQLVFSELDE 307


Lambda     K      H
   0.319    0.140    0.434 

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: 243
Number of extensions: 14
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: 288
Length of database: 322
Length adjustment: 27
Effective length of query: 261
Effective length of database: 295
Effective search space:    76995
Effective search space used:    76995
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 (21.7 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