GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Methylocystis bryophila S285

Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate WP_085771876.1 B1812_RS12430 adenosine kinase

Query= SwissProt::Q6XZ79
         (323 letters)



>NCBI__GCF_002117405.1:WP_085771876.1
          Length = 333

 Score = 61.6 bits (148), Expect = 3e-14
 Identities = 70/237 (29%), Positives = 104/237 (43%), Gaps = 12/237 (5%)

Query: 38  GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97
           GG+ AN    ++ LG    FVGK+ +DE GR  A  +R  GV         GA TA   +
Sbjct: 59  GGSAANTMAGLASLGCRVGFVGKVKEDEAGREFAHDIRKAGVAFETPFATDGAATARCLI 118

Query: 98  TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIAEPCRTAHLRAMEI 157
            +  DG+R    +    A   L   +++      A V +           + A L+A ++
Sbjct: 119 FVTPDGQRTMNTFL--GACQALGPADIDEAQAADAKVLYLEGYLWDPPAAKEAFLKAAKL 176

Query: 158 AKEAGALLSYDPNLREALWPSREEARTQILS-IWDQ-ADIVKVSEVELEFLTGIDSVEDD 215
           ++  G  ++   +L +A    R   R + L  I DQ  DIV  +E EL  L    + + D
Sbjct: 177 SRAKGRKVAL--SLSDAFCVDR--YRDEFLGLIRDQLVDIVFANESELHSL--YQTADFD 230

Query: 216 VVMKLWRPTMKLL-LVTLGDQGCKYYARDFHGAVPSFKVQQ-VDTTGAGDAFVGALL 270
             +   R    LL +VT   QG          +VP+F V++ VDTTGAGD F    L
Sbjct: 231 TALVALRAEKGLLGVVTRSAQGALVADAAGVVSVPAFAVEEIVDTTGAGDLFAAGFL 287


Lambda     K      H
   0.319    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: 224
Number of extensions: 14
Number of successful extensions: 2
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: 333
Length adjustment: 28
Effective length of query: 295
Effective length of database: 305
Effective search space:    89975
Effective search space used:    89975
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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