GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Dyella japonica UNC79MFTsu3.2

Align Glucose kinase (characterized, see rationale)
to candidate N515DRAFT_2652 N515DRAFT_2652 glucokinase

Query= uniprot:Q8P6S9
         (338 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2652
          Length = 355

 Score =  263 bits (672), Expect = 5e-75
 Identities = 154/320 (48%), Positives = 194/320 (60%), Gaps = 10/320 (3%)

Query: 18  FVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRR 77
           F+AAD+GGTH RL L      P     VL YR +RCAD+P L +I+  F AEL   P R 
Sbjct: 33  FLAADIGGTHARLGLVAAQ--PEGAPRVLAYRSFRCADHPHLDDIVRMFCAELDARP-RE 89

Query: 78  GVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVM 137
            V+ASAGY L  G V+  NL W L P  +  +L ++ +  +NDFEA+A+A  Y+  +  +
Sbjct: 90  LVLASAGY-LHAGVVVNRNLAWPLVPATLAHELRLERVRFLNDFEALAHAIAYVDEHSSV 148

Query: 138 QLS---GPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVALL 194
            L     P  G  GP  V+GPGTGLGAA+W P G    V+ TEAG   LAA   LE  +L
Sbjct: 149 SLKTAFAPDAGK-GPIAVIGPGTGLGAAVWFP-GEPPRVIATEAGQIQLAARGGLEREVL 206

Query: 195 QELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEAL 254
             +  +  H   E  LSGPGL  LY AL  + D     A PA V AAA AGD+V A+EA+
Sbjct: 207 DRIAPSDCHTPYEAVLSGPGLHRLYAALCAVYDRYPSCAEPADVVAAAEAGDEV-AYEAV 265

Query: 255 QTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQV 314
           Q F G+MGS  GD+ +LYG   GVYLAGGFL +I D +       R LDKG +RP L +V
Sbjct: 266 QMFGGWMGSFAGDLAMLYGATGGVYLAGGFLSRIVDLLRCGPLVERFLDKGVMRPFLHKV 325

Query: 315 PVRIVEHGQLGVIGAASWFL 334
           P+R+V+HGQLGV+GAASW L
Sbjct: 326 PIRVVDHGQLGVVGAASWHL 345


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: 284
Number of extensions: 13
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: 338
Length of database: 355
Length adjustment: 29
Effective length of query: 309
Effective length of database: 326
Effective search space:   100734
Effective search space used:   100734
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 (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