SEED Subsystem: Proline, 4-hydroxyproline uptake and utilization in Pseudomonas putida KT2440

Experiments:

Role Gene Name P. putida Missley MOI 0.1  
1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22) PP_1257 -0.1
4-hydroxyproline epimerase (EC 5.1.1.8) PP_1258 +0.2
Aldehyde dehydrogenase (EC 1.2.1.3) in 4-hydroxyproline catabolic gene cluster No genes
Amino acid permease in 4-hydroxyproline catabolic gene cluster No genes
D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster PP_1255 -0.9
D-amino-acid oxidase (EC 1.4.3.3) No genes
D-proline reductase, 23 kDa subunit (EC 1.21.4.1) No genes
D-proline reductase, 26 kDa subunit (EC 1.21.4.1) No genes
D-proline reductase, 45 kDa subunit (EC 1.21.4.1) No genes
Delta 1-pyrroline-5-carboxylate dehydrogenase domain protein No genes
Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) PP_4947 +0.0
Dipeptidyl peptidase IV in 4-hydroxyproline catabolic gene cluster No genes
Hypothetical, similar to sarcosine oxidase alpha subunit, 2Fe-2S domain No genes
Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) PP_1256 +0.2
  PP_2585 +0.5
  PP_3602 -0.1
L-Proline/Glycine betaine transporter ProP PP_0702 -0.2
  PP_2392 -0.8
  PP_2411 -0.6
  PP_2553 -0.5
  PP_2914 -0.1
  PP_3203 -0.2
  PP_3566 +0.2
  PP_3666 -0.1
  PP_4206 -0.4
  PP_4433 +0.7
  PP_4461 +0.9
  PP_5330 -0.2
Microbial collagenase, secreted (EC 3.4.24.3) No genes
Not a Proline racemase, nor 4-hydroxyproline epimerase [missing catalytic residues] No genes
Predicted 4-hydroxyproline dipeptidase No genes
Predicted regulator PutR for proline utilization, GntR family PP_0163 +1.2
  PP_3649 -0.1
ProQ: influences osmotic activation of compatible solute ProP No genes
Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) PP_4947 +0.0
Proline iminopeptidase (EC 3.4.11.5) PP_5028 +1.4
Proline racemase (EC 5.1.1.4) No genes
Proline-specific permease proY No genes
Proline/sodium symporter PutP (TC 2.A.21.2.1) No genes
PutR, transcriptional activator of PutA and PutP No genes
Putative beta-galactosidase in 4-hydroxyproline catabolic gene cluster No genes
Putative oxidoreductase in 4-hydroxyproline catabolic gene cluster No genes
Similar to eukaryotic Peptidyl prolyl 4-hydroxylase, alpha subunit (EC 1.14.11.2) No genes
Transcriptional repressor of PutA and PutP PP_4947 +0.0
Ureidoglycolate/malate/sulfolactate dehydrogenase family (EC 1.1.1.-) No genes
putPA fragment of control region No genes

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