GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagK in Dinoroseobacter shibae DFL-12

Align Glucose kinase (characterized, see rationale)
to candidate 3608251 Dshi_1655 Glucokinase (RefSeq)

Query= uniprot:Q8P6S9
         (338 letters)



>lcl|FitnessBrowser__Dino:3608251 Dshi_1655 Glucokinase (RefSeq)
          Length = 323

 Score =  131 bits (330), Expect = 2e-35
 Identities = 93/315 (29%), Positives = 148/315 (46%), Gaps = 9/315 (2%)

Query: 19  VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRG 78
           + AD+GGT+ R+ALA         +      KYR ADY  L  ++ ++  ++  A     
Sbjct: 10  LVADIGGTNTRVALA-----DGPVLRAGSVEKYRNADYSSLDSVLRSYLEKMEVAGCSGA 64

Query: 79  VIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVMQ 138
            +A AG  + +G     NL W +  + + +  G   + L+ND +A  +A  ++    +  
Sbjct: 65  CVALAG-PVRNGIGHLTNLDWRMDEDLLSEATGAPVVALLNDLQAQGFALGHLEAACLRP 123

Query: 139 -LSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVALLQEL 197
            +S P   A    L++G GTG  AA  +      +V P+EAGHA L   ++ E+ L + +
Sbjct: 124 VISRPPPAAQETRLMIGLGTGFNAASVLYTPAGRIVTPSEAGHANLPVRTEQELRLCRFV 183

Query: 198 RRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEALQTF 257
                  A E  LSG GL  +Y  L+   D P      AA   AA A ++  A +AL+ F
Sbjct: 184 ETAHGFPAVEDVLSGRGLERVYNFLSPTPDQP--QRLSAAEVMAAAAREERQALDALELF 241

Query: 258 CGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVPVR 317
            G +G+V G++ L++    GVYL GG    I  ++    FA    +KG     +   PV 
Sbjct: 242 IGLLGTVAGNLSLIHLPFGGVYLCGGVARHIGPYLGSMGFAEAFANKGRFADFMRDFPVW 301

Query: 318 IVEHGQLGVIGAASW 332
           +VE     + G AS+
Sbjct: 302 LVEDDFAALTGCASF 316


Lambda     K      H
   0.321    0.136    0.407 

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: 210
Number of extensions: 13
Number of successful extensions: 5
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: 338
Length of database: 323
Length adjustment: 28
Effective length of query: 310
Effective length of database: 295
Effective search space:    91450
Effective search space used:    91450
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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