Protein Info for PP_0672 in Pseudomonas putida KT2440

Annotation: Sensory box protein

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

• TIGR00229: PAS domain S-box protein
  • amino acids 444 to 574 (131 residues), 34 bits, E=2.9e-12
  • amino acids 576 to 715 (140 residues), 39.9 bits, E=4.2e-14
  • amino acids 720 to 836 (117 residues), 60.9 bits, E=1.3e-20
• PF13426: PAS_9
  • amino acids 464 to 566 (103 residues), 21.8 bits, E=6.4e-08
  • amino acids 592 to 707 (116 residues), 23.2 bits, E=2.4e-08
  • amino acids 728 to 829 (102 residues), 58.2 bits, E=3.2e-19
• PF08447: PAS_3
  • amino acids 471 to 561 (91 residues), 37.6 bits, 7.6e-13
• PF13188: PAS_8
  • amino acids 720 to 757 (38 residues), 21.7 bits, see alignment (E = 5.4e-08)
• PF00989: PAS
  • amino acids 720 to 827 (108 residues), 39.7 bits, E=1.5e-13
• PF08448: PAS_4
  • amino acids 722 to 831 (110 residues), 32.3 bits, E=3.7e-11
• TIGR00254: diguanylate cyclase (GGDEF) domain
  • amino acids 838 to 1004 (167 residues), 135.4 bits, E=1.6e-43
• PF00990: GGDEF
  • amino acids 841 to 1002 (162 residues), 162.3 bits, E=3e-51
• PF00563: EAL
  • amino acids 1023 to 1257 (235 residues), 259.2 bits, E=1.1e-80

Best Hits

KEGG orthology group: None (inferred from 88% identity to pen:PSEEN0807)

Predicted SEED Role

"Serine hydroxymethyltransferase (EC 2.1.2.1)" in subsystem Folate Biosynthesis or Glycine Biosynthesis or Glycine and Serine Utilization or LMPTP YwlE cluster or Photorespiration (oxidative C2 cycle) or Serine-glyoxylate cycle or Serine Biosynthesis (EC 2.1.2.1)

MetaCyc Pathways

• folate transformations III (E. coli) (9/9 steps found)
• folate transformations II (plants) (10/11 steps found)
• glycine betaine degradation III (7/7 steps found)
• superpathway of L-serine and glycine biosynthesis I (4/4 steps found)
• dTMP de novo biosynthesis (mitochondrial) (3/3 steps found)
• glycine degradation (3/3 steps found)
• folate polyglutamylation (4/5 steps found)
• glycine biosynthesis I (1/1 steps found)
• glycine betaine degradation I (6/8 steps found)
• photorespiration II (7/10 steps found)
• folate transformations I (9/13 steps found)
• photorespiration I (6/9 steps found)
• photorespiration III (6/9 steps found)
• purine nucleobases degradation II (anaerobic) (16/24 steps found)
• glycine betaine degradation II (mammalian) (1/4 steps found)
• formaldehyde assimilation I (serine pathway) (7/13 steps found)

KEGG Metabolic Maps

• Cyanoamino acid metabolism
• Glycine, serine and threonine metabolism
• Methane metabolism
• One carbon pool by folate

Isozymes

Compare fitness of predicted isozymes for: 2.1.2.1

Use Curated BLAST to search for 2.1.2.1

Sequence Analysis Tools

See Q88Q26 at UniProt or InterPro

Protein Sequence (1276 amino acids)

>PP_0672 Sensory box protein (Pseudomonas putida KT2440)
MTNLTHPSSLRSAPQAPATLLRGSIKGALALLALILLGLLLWQLFAQFNHTQAELRKQSL
DASAELADHLSLNMALKAQQAVNVVQPYPDAPTPAALPSLLGTLRERLPALQSVAWLDNV
GQLRADSLAGSPDRQSLDELLVLSQGRPYFFTNSADNHLLYLLLRQDAAQGSGYWLLRLS
PDYYRELTLHLEGSGHPQWLLENSRSGEVLQRHAAADTSDEPLQSVMLAFIENSTWQLRG
LFDAKLAQQKLLPALLGKCLLVLFCALLPVLALINMRRRQRALQEDRRRYQEIFEGTGVA
LCVLDLSSLPGQLDRYHLRNRAALKHSLALDPNLRRSLLLELKITEVNQVARQLLNIDCH
EGAWQRLIDGTGDSRDSVGMQLIDALIEQRPLLELEVRLPTPQGTELHLWLMARLPLQRR
DYQAVILSISDITSRKQVELSLLERESFWSDVVRTVPDQLYVQDVPSQRMIFSNRHLGQT
LGYDRTELAQMGDRFWELLLHPEDAAHYQALRRQQRDNCHDQPLHCQLRFRHRDGSWRCY
DIREQVLTRNAEGLVTRIIGVGKDVTVQIEASQSLRDSEQRYRMLAESISDVIFSTDNQL
KLNYVSPSVQSVLGYQADWIFANGWQSIVANPAQLTGIYSLMERVSKAMGDPAQMAQLCS
QLPTQLFLFDCLRADGRKIPIELRLVLVWDDDQRFEGVLGVGRDISQQRRAEKDLRMAAT
VFEHSTSAILITDPAGYIVQANEAFSRVSGYAVSEVLDQLPGMLTVDEQQEGHLRYVVKQ
LHQRGSWEGEVWLKRRDGDHYPAWVGITAVLDDEGDLASYVCFFTDISERKASEQRIHRL
AYYDALTHLPNRTLFQDRLYNALQQAERQKAWVVLMFLDLDRFKPINDSLGHAAGDRMLK
DMALRLLACVDDDDTVARMGGDEFTLLLQPRPTREMALNRAIHVAENILGSLVRPFVLEN
REFFVTASIGIALSPQDGSELSQLMKNADTAMYHAKERGKNNFQFYQAEMNASALERLEL
ESDLRHAMEQNEFILYYQPQFSGDGKRLTGAEALLRWRHPTRGLVPPGDFIPVIEELGLV
VDVGDWVLREASRQLKAWHKAKVRVPKVSVNISARQFSDGQLGTRIANILEESGLPPACL
ELELTESILMREVNEALQILASLKNLGLSIAVDDFGTGYSSLNYLKQFPIDVLKIDRTFV
DGLPEGEQDAQIARAIIAMAHSLNLAVIAEGVETHEQLEFLREHGCDEVQGYLFGRPMPA
HQFEAQFSNETLFMFH