GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Marinobacter algicola DG893

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_007152220.1 MDG893_RS02890 carbohydrate kinase

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



>NCBI__GCF_000170835.1:WP_007152220.1
          Length = 328

 Score =  270 bits (689), Expect = 5e-77
 Identities = 147/320 (45%), Positives = 197/320 (61%), Gaps = 6/320 (1%)

Query: 5   ILCFGEALIDFHA------EGRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLG 58
           ++ FGEAL+D  +      +  ++      F  F GGAPANV+ A+ +LGG + FAG +G
Sbjct: 4   VISFGEALVDMLSSRVSEDQSENSDSVNERFTKFPGGAPANVAAAIGKLGGDSYFAGKVG 63

Query: 59  QDMFGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPE 118
            DMFGDFL+ SL    V T  + +T EA TALAFV+LD  GERSF FYR PSADL+F P 
Sbjct: 64  ADMFGDFLVKSLESMHVRTDYLLQTSEAKTALAFVSLDKTGERSFEFYRGPSADLIFAPH 123

Query: 119 HFRAESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSAS 178
            F+ E F    +FH CSN++TEP + EAT+ G+ +A +AG  VSFD+NLR  LWP  +  
Sbjct: 124 EFQPEWFDDQGIFHFCSNTLTEPGILEATQAGLEKARSAGWLVSFDMNLRNNLWPKGTDP 183

Query: 179 HDELWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFHPD 238
              +W  +  AD+VKLSAEE  +L   + E   L ++    A L++VTDG + LR+  P 
Sbjct: 184 FAPVWACVEQADLVKLSAEELAFLCRHQNETEVLKQILNAGASLVLVTDGEKPLRYLTPS 243

Query: 239 ASGEMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVAELPRLHAMLRFAAAC 298
             G +    V  VDSTAAGDAFVGGLL+RL+ +   A  L  L  +  +L  ML FA+AC
Sbjct: 244 HYGSIEPRNVQMVDSTAAGDAFVGGLLYRLSDLNITAASLKALGEDPEQLEDMLTFASAC 303

Query: 299 GALTVTRLGSFAAMPDEAEV 318
           GA  VT  G+F ++P   +V
Sbjct: 304 GAHAVTHPGAFTSLPGLQDV 323


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: 328
Number of extensions: 12
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: 326
Length of database: 328
Length adjustment: 28
Effective length of query: 298
Effective length of database: 300
Effective search space:    89400
Effective search space used:    89400
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: 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