Protein Info for LRK54_RS16575 in Rhodanobacter denitrificans FW104-10B01

Annotation: GGDEF domain-containing phosphodiesterase

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

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 912 transmembrane" amino acids 12 to 32 (21 residues), see Phobius details amino acids 200 to 221 (22 residues), see Phobius details TIGR00229: PAS domain S-box protein" amino acids 234 to 344 (111 residues), 53.4 bits, see alignment E=2.9e-18 amino acids 352 to 466 (115 residues), 42.5 bits, see alignment E=6.4e-15 PF00989: PAS" amino acids 236 to 295 (60 residues), 30.6 bits, see alignment 8.6e-11 amino acids 351 to 457 (107 residues), 37.5 bits, see alignment E=6.2e-13 PF13188: PAS_8" amino acids 236 to 286 (51 residues), 31.5 bits, see alignment 3.8e-11 PF13426: PAS_9" amino acids 247 to 337 (91 residues), 25.6 bits, see alignment E=3.6e-09 amino acids 358 to 459 (102 residues), 45.4 bits, see alignment E=2.6e-15 PF08448: PAS_4" amino acids 353 to 461 (109 residues), 26.4 bits, see alignment E=2.1e-09 TIGR00254: diguanylate cyclase (GGDEF) domain" amino acids 467 to 630 (164 residues), 137.5 bits, see alignment E=3.6e-44 PF00990: GGDEF" amino acids 471 to 627 (157 residues), 137.9 bits, see alignment E=8e-44 PF00563: EAL" amino acids 648 to 883 (236 residues), 241.5 bits, see alignment E=2.5e-75

Best Hits

Predicted SEED Role

"diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains) with PAS/PAC sensor(s)" in subsystem Bacterial hemoglobins

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (912 amino acids)

>LRK54_RS16575 GGDEF domain-containing phosphodiesterase (Rhodanobacter denitrificans FW104-10B01)
MLQQPLSRRMLPLAYALVVMLATILGLTWFALQTQVTLAGFLNSESVWSKAQKQAVIALD
AYAVTGSPADLAGFWQNYSVLDSDRLARDEIASGSFDQEVVDRAFVHGNVMPTAKPGMIF
VLEHFSGAPYLRDALAAWRSSDAEIAQLASIAKELEHTHAAGASSAEQAAIQRGRIHALN
DSIEPKANRFSLEIARGTTWMGHMLFIGVLSAACIAVLLWLDMARRTLVSIRGSEERYRL
LFDSAADAIVMVDEASGRILDVNRTASAWTGRSADELVGDRFVHLFTQSMAGQQTGRAAA
NVLLGAKGQTRPVETQTSLVNWGSQPVRQAIIRDISERVAMERERRIAAEALASIAEGVI
IADAGRLVISTNAAHAELTGFTSQALQGRRLDDTRRLPGGQPLPRSIWDSVAAGHNWMGE
VVSLRSDGSSYPEHLSLSTIRDADDQVVYYVAVLTDIHEAKANQHRLEQMARHDPLTGLV
NRAEFERHCAEAIAVAERERLAAVVLFIDLDAFKIVNDSYSHAIGDRLLVKVAERIRRQL
SEGDVAGRIGGDEFTVLIPRLILREDARAIVSRLLASLSEPLLVDDYEIVLSASIGVAGY
PLDGDNALALIANADAAMYAAKTEERNAFRFYTPMMHADTRRRLQLAAELRQALARNEFH
LVFQPSVELRSGRIVAVEALLRWQHPERGEVLPAEFIPVAESLGLIRRIDEWVMQTTCAQ
IQAWDLAGVPPIRVAVNISARWFGHPAFVDGVSRNLQSRRLAPGRLLLEITESAMLRLGD
DIERTMQTLHTLGIAVAIDDFGTGYSSMAYLKLPAVTCLKIDRSFVTGLPGDGNDAAITV
AMLAMAKSLGLITIAEGIETEAQHEFLLRSGCIEGQGYLYSYPLRPEEVQRLLCPSQPSV
PMRLKLVPPKRS