GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ivdG in Pseudomonas putida KT2440

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate PP_1953 PP_1953 Oxidoreductase, short chain dehydrogenase/reductase family

Query= BRENDA::Q99714
         (261 letters)



>lcl|FitnessBrowser__Putida:PP_1953 PP_1953 Oxidoreductase, short
           chain dehydrogenase/reductase family
          Length = 269

 Score =  131 bits (330), Expect = 1e-35
 Identities = 100/276 (36%), Positives = 135/276 (48%), Gaps = 31/276 (11%)

Query: 7   SVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT 66
           S +  + V+TG ASG+G ATA+ LV QGA  V +DL  S    QA     + +  P DV+
Sbjct: 2   SFQNKIVVLTGAASGIGKATAQLLVEQGAHVVAMDL-KSDLLQQAFGSEEHVLCIPTDVS 60

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYN-------------LKKGQTHTLE- 112
             + V+ A      KFGRVDV +N AGI   ++  N             +K G+  T + 
Sbjct: 61  DSEAVRAAFQAVDAKFGRVDVIINAAGINAPTREANQKMVDANVAALDAMKSGRAPTFDF 120

Query: 113 -------DFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQ 165
                  DF+RV++VNL   F  IR     M +     GG  G I+N +SVAA  G    
Sbjct: 121 LADTSDQDFRRVMEVNLFSQFYCIREGVPLMRR----AGG--GSIVNISSVAALLGVAMP 174

Query: 166 AAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPS 225
             Y ASK  ++G+T   A +LAP  IRV  IAPG   TPL+   P +V  FL S  P   
Sbjct: 175 LYYPASKAAVLGLTRAAAAELAPYNIRVNAIAPGSVDTPLMHEQPPEVVQFLVSMQPI-K 233

Query: 226 RLGDPAEYAH--LVQAIIENPFLNGEVIRLDGAIRM 259
           RL  P E A   L  A   + F+ G+ +  +G + M
Sbjct: 234 RLAQPEELAQSILFLAGEHSSFITGQTLSPNGGMHM 269


Lambda     K      H
   0.318    0.135    0.385 

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: 143
Number of extensions: 7
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: 261
Length of database: 269
Length adjustment: 25
Effective length of query: 236
Effective length of database: 244
Effective search space:    57584
Effective search space used:    57584
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 (21.7 bits)
S2: 47 (22.7 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 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