GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Neptunomonas antarctica S3-22

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_054342057.1 Nant_RS12790 carbohydrate kinase

Query= reanno::Dyella79:N515DRAFT_1919
         (326 letters)



>NCBI__GCF_001305295.1:WP_054342057.1
          Length = 330

 Score =  264 bits (674), Expect = 3e-75
 Identities = 142/323 (43%), Positives = 199/323 (61%), Gaps = 7/323 (2%)

Query: 3   RNILCFGEALIDFHAE------GRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGM 56
           + ++ FGEAL+D  +       G+       SF  F GGAPANV+ AV +LGG + F G 
Sbjct: 2   QKVISFGEALVDMLSSKVSKPAGKTEAASHESFTKFPGGAPANVAAAVGKLGGNSVFVGQ 61

Query: 57  LGQDMFGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFR 116
           +G DMFGDF+  SL  AGVDT  + ++ E  TALAFV+LD HGERSF FYR  SADLLF 
Sbjct: 62  VGADMFGDFMKASLEDAGVDTRYLLQSDEGKTALAFVSLDDHGERSFEFYRNASADLLFS 121

Query: 117 PEHFRAESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQS 176
            + F+   F G  +FH CSN++TEPA+  AT  G+ +A +AG  +SFD+NLR  LWP  +
Sbjct: 122 ADDFQESCFEGGGLFHFCSNTLTEPAIRAATLAGIDKAKSAGCIISFDVNLRLNLWPEGA 181

Query: 177 ASHDELWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFH 236
              + +W  L  AD+VKL  EE +++   + +   ++RL +    L++VTDG + LR+  
Sbjct: 182 DPFEFIWACLERADIVKLCVEELNFICRGQVQAQVIERLLSLGIALVLVTDGGKPLRYHT 241

Query: 237 PDASGEMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVA-ELPRLHAMLRFA 295
            + +G +   +V  VDSTAAGDAF+GGLL+ LA     A  L   VA E   L + L FA
Sbjct: 242 QERTGTIQPPSVAMVDSTAAGDAFIGGLLYALAEQNISAPLLSDFVAIESALLKSALTFA 301

Query: 296 AACGALTVTRLGSFAAMPDEAEV 318
           +ACGA  V   G+F+++P + ++
Sbjct: 302 SACGAYAVAHQGAFSSLPGKEDL 324


Lambda     K      H
   0.322    0.135    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: 319
Number of extensions: 9
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: 326
Length of database: 330
Length adjustment: 28
Effective length of query: 298
Effective length of database: 302
Effective search space:    89996
Effective search space used:    89996
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 (22.0 bits)
S2: 49 (23.5 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