GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Pseudomonas putida KT2440

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate PP_1011 PP_1011 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Putida:PP_1011
          Length = 319

 Score =  228 bits (581), Expect = 1e-64
 Identities = 131/324 (40%), Positives = 182/324 (56%), Gaps = 13/324 (4%)

Query: 3   KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVE---VKDG 59
           K+ LVGD+GGTNAR AL      ++ +   ++ +DY + E  I  YLE   +    +   
Sbjct: 2   KHLLVGDIGGTNARFALW--RDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAV 59

Query: 60  CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF 119
           C+A+A P+ GD    TN+ W  S     K L    L +INDFTA+++ +  L++    + 
Sbjct: 60  CLAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREV 119

Query: 120 GGAEPVEGKPIAVYGAGTGLGVAHLVHVDKR-WVSLPGEGGHVDFAPNSEEEAIILEILR 178
              +    +P  V G GTGLGV  L+ + ++ W +LPGEGGHVD    +  EA I + + 
Sbjct: 120 CPGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAAIHQQIH 179

Query: 179 AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSL-- 236
           ++IGHVSAE VLSG GLV LY+AI   D   P +  P  IT+ AL        RAL++  
Sbjct: 180 SQIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGE----PRALAVVE 235

Query: 237 -FCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIP 295
            FC  +GR  GN  L LG  GGV+I GG++PRF E F  SGF A+F DKG    Y   +P
Sbjct: 236 QFCRFLGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVP 295

Query: 296 VYLIVHDNPGLLGSGAHLRQTLGH 319
           V+L+  +  GL G+G  L+Q L H
Sbjct: 296 VWLVTAEFSGLEGAGVALQQALDH 319


Lambda     K      H
   0.322    0.141    0.426 

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: 333
Number of extensions: 16
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: 321
Length of database: 319
Length adjustment: 28
Effective length of query: 293
Effective length of database: 291
Effective search space:    85263
Effective search space used:    85263
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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