GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Halomonas desiderata SP1

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_086509383.1 BZY95_RS07810 carbohydrate kinase

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



>NCBI__GCF_002151265.1:WP_086509383.1
          Length = 326

 Score =  244 bits (623), Expect = 2e-69
 Identities = 146/317 (46%), Positives = 183/317 (57%), Gaps = 2/317 (0%)

Query: 4   NILCFGEALIDFHAE--GRDAQGFPRSFIPFAGGAPANVSVAVARLGGPAAFAGMLGQDM 61
           +++ FGEAL+D  +   G  A   P++F P+AGGAPANV+VA ARLG P+ F GMLG+D 
Sbjct: 3   SVIAFGEALVDMLSSRLGDLAGDAPKTFTPYAGGAPANVAVACARLGVPSRFLGMLGEDH 62

Query: 62  FGDFLLDSLRRAGVDTAGVARTGEANTALAFVALDSHGERSFSFYRPPSADLLFRPEHFR 121
           FGDFL   L   GVDT+GV RT EA TALAFV+ D+ GER+F FYRPP+ADLL+R EH  
Sbjct: 63  FGDFLAGELAAHGVDTSGVVRTREARTALAFVSRDASGERTFDFYRPPAADLLYRLEHLP 122

Query: 122 AESFRGAAVFHVCSNSMTEPALAEATREGMRRAHTAGAWVSFDLNLRPALWPNQSASHDE 181
              F   A+ H CSNS+TEP +A+ T      A  AG  VS D NLR  LW   SA    
Sbjct: 123 PGVFAEPAIVHFCSNSLTEPEIADTTLAMADMASRAGCLVSVDANLRHNLWAGGSADITL 182

Query: 182 LWPALHLADVVKLSAEEFHWLAGDEGEEATLDRLWAGRARLLVVTDGSRTLRWFHPDASG 241
           +   +  A +VKLS +E  +L  D   EA L    A   RLLV+TDG   +R        
Sbjct: 183 VTQLIDRAGLVKLSTDELDYLRADHPAEAWLAERLAAGVRLLVITDGPGEVRAIGVGREL 242

Query: 242 EMPVYAVPTVDSTAAGDAFVGGLLHRLATVEKGADQLDHLVAELPRLHAMLRFAAACGAL 301
                 V  VD+TA GDAF+GGLL  LA              +   L   LR AA CGA 
Sbjct: 243 RHAPPRVEAVDTTAGGDAFIGGLLAELADYLGATAGDGDWHKDDDFLRRALRTAANCGAH 302

Query: 302 TVTRLGSFAAMPDEAEV 318
            VTR G++AA+P+  ++
Sbjct: 303 AVTRPGAYAALPNRGDL 319


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: 391
Number of extensions: 20
Number of successful extensions: 4
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: 326
Length adjustment: 28
Effective length of query: 298
Effective length of database: 298
Effective search space:    88804
Effective search space used:    88804
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