GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1953
          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:

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