GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Pseudomonas fluorescens FW300-N2C3

Align 6-phosphofructokinase (EC 2.7.1.11); 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) (characterized)
to candidate AO356_24685 AO356_24685 2-dehydro-3-deoxygluconokinase

Query= BRENDA::D4GR05
         (318 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24685
          Length = 326

 Score =  105 bits (262), Expect = 1e-27
 Identities = 89/282 (31%), Positives = 127/282 (45%), Gaps = 10/282 (3%)

Query: 4   ELVTFGETMIRLSPPEGERIETARSLEFRTAGAESNVAVAASRLGCSAAWLSKLPDSPLG 63
           ++++FGETM  L   +   + +      R AGA+SNVA+  SRLG   AWLS++    LG
Sbjct: 5   DVLSFGETMAMLVADQRGDLASVDQFHKRIAGADSNVAIGLSRLGFKVAWLSRVGADSLG 64

Query: 64  RRVTTELRTHGVE-PYVRWDDDARQGAYYIEQGRAPRPTNVIYDRADAAVTTARPDELAV 122
           R VT  L   G++  +V  D +   G  +           V Y R  +A +      +A 
Sbjct: 65  RFVTQTLENEGLDCRHVAVDPEHPTGFQFKSLTVDGSDPQVEYFRRSSAASHLSVGSIAP 124

Query: 123 DIVEDAAAFYTSGITPALSETLRETTGELLQTATEAGTTTAFDLNYRSKLW-SPSDARDA 181
            ++ DA   + +GI PALS T RE + EL+     AG + +FD N R  LW S S    A
Sbjct: 125 ALL-DARHVHATGIVPALSGTAREMSFELMSRMRAAGRSLSFDPNLRPSLWGSESTMITA 183

Query: 182 CESLFPKVDVLVAAERDIRAVLELDGDAPTLASELAGDFDFETVVVTRGEDGALARHG-- 239
              L      ++    + R +   D  A   A  L  D   E VV+  G DGA  R    
Sbjct: 184 INRLAALAHWVLPGLGEGRLLTGFDDPADIAAFYL--DQGAEIVVIKLGADGAYYRTALD 241

Query: 240 -GTVYEQPVFETDTVDAIGTGDAFVGAFLSRLIAGEPVETAL 280
            G +   PV     VD +G GD F    +S L+ G  +  A+
Sbjct: 242 QGVIPGVPV--AQVVDTVGAGDGFAVGLISALLEGRAITEAV 281


Lambda     K      H
   0.315    0.132    0.378 

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: 268
Number of extensions: 17
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: 318
Length of database: 326
Length adjustment: 28
Effective length of query: 290
Effective length of database: 298
Effective search space:    86420
Effective search space used:    86420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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