GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Pseudomonas putida KT2440

Align Glucose kinase (characterized, see rationale)
to candidate PP_1011 PP_1011 glucokinase

Query= uniprot:Q8P6S9
         (338 letters)



>FitnessBrowser__Putida:PP_1011
          Length = 319

 Score =  141 bits (356), Expect = 2e-38
 Identities = 105/317 (33%), Positives = 153/317 (48%), Gaps = 18/317 (5%)

Query: 19  VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRG 78
           +  D+GGT+ R AL  ++        + +   +   DY    + + A+   L    + RG
Sbjct: 5   LVGDIGGTNARFALWRDNQ-------LHEVNVFATVDYTNPEQAIEAY---LESQGIARG 54

Query: 79  VIASAGYALE---DGRVIT-ANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGN 134
            +A+   A+    DG      N  W L+     + L ++ L L+NDF A+A     +   
Sbjct: 55  GLAAVCLAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREG 114

Query: 135 QVMQLSGPAQGAPG-PALVLGPGTGLGAALWIPNGGNS-VVLPTEAGHAALAAASDLEVA 192
           +  ++  P Q  P  PALV+GPGTGLG    +  G      LP E GH  L   +  E A
Sbjct: 115 EFREVC-PGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAA 173

Query: 193 LLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHE 252
           + Q++     HV+ E  LSG GL+ LY A+  L      H TPA +T AAL G+   A  
Sbjct: 174 IHQQIHSQIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGEP-RALA 232

Query: 253 ALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALE 312
            ++ FC F+G V G+ +L  G R GVY+ GG +P+ A+   RS FAA   DKG +     
Sbjct: 233 VVEQFCRFLGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFT 292

Query: 313 QVPVRIVEHGQLGVIGA 329
            VPV +V     G+ GA
Sbjct: 293 GVPVWLVTAEFSGLEGA 309


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: 225
Number of extensions: 9
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: 319
Length adjustment: 28
Effective length of query: 310
Effective length of database: 291
Effective search space:    90210
Effective search space used:    90210
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