Table 2.

Nucleotide Cyclases and cNMP-Binding Proteins in Prokaryotic Species with Available Genome Sequences

Species (strain) No. ORFs 3′–5′ nucleotide cyclases[i] cNMP-binding proteins[i]
genome annotation[ii] PROBE class I[iii] PROBE class III[iv] genome annotation[v] PROBE
Archaea
 Aeropyrum pernix(K1)2694N.F.N.F.N.F.N.F.N.F.
 Archaeoglobus fulgidus(DSM4303)2407N.F.N.F.N.F.AF0971[vi] N.F.
 Methanobacterium   thermoautotrophicum(delta H)1869N.F.N.F.N.F.N.F.N.F.
 Methanococcus jannaschii   (DSM2661)1771N.F.N.F.N.F.N.F.N.F.
 Pyrococcus abyssi (GE5)1765PAB0653[vii] N.F.N.F.N.F.N.F.
PAB2098[vii]
 Pyrococcus horikoshii(OT3)1979N.F.N.F.N.F.N.F.N.F.
Eubacteria
 Aquifex aeolicus(VF5)1522N.F.N.F.N.F.N.F.aq_490 (fnr)
aq_2107
 Bacillus subtilis (168)4100N.F.N.F.N.F. P46908 (fnr) P46908 (fnr)
 Borrelia burgdorferi(B31)850N.F.N.F.N.F.N.F.N.F.
 Chlamydia pneumoniae(CWL029)1052N.F.N.F.N.F.CPn0294[viii] [ix] CPn0294[viii] [ix]
 Chlamydia trachomatis (serovar D)894CT664[x] N.F.N.F.CT235[viii] CT235[viii]
 Escherichia coli(K-12)4289 P00936 (cyaA) P00936 (cyaA)N.F. P03020 (crp) P03020 (crp)
P03019 (fnr) P03019 (fnr)
P33023 P33023
 Haemophilus influenzae RD (KW20)1707HI0604 (cyaA)HI0604 (cyaA)N.F.HI0957 (crp)HI0957 (crp)
HI1425 (fnr)HI1425 (fnr)
HI0804[viii] HI0804[viii]
 Helicobacter pylori [xi](26695)1566N.F.N.F.N.F.N.F.N.F.
  (J99)1491
 Mycobacterium tuberculosis(H37Rv)3918Rv0891cN.F.Rv0386Rv0073Rv0073
Rv1264Rv0891cRv0104Rv0104
Rv1318cRv1264Rv0998Rv0998
Rv1319cRv1318cRv2564Rv1675c
Rv1320cRv1319cRv3239cRv2434c
Rv1359Rv1320cRv3617[xii] Rv2564
Rv1625cRv1358Rv3676Rv2565
Rv2212Rv1359Rv3728Rv3239c
Rv2435cRv1625cRv3676
Rv3645Rv1647Rv3728
Rv1900c
Rv2212
Rv2435c
Rv2488c
Rv3645
 Mycoplasma genitalium(G-37)479N.F.N.F.N.F.N.F.N.F.
 Mycoplasma pneumoniae(M129)677N.F.N.F.N.F.N.F.N.F.
 Rickettsia prowazekii (Madrid E)834N.F.N.F.N.F.N.F.N.F.
 Synechocystissp. (PCC6803)3168sll0646 (cyaA)N.F.sll0646 (cyaA)sll1423sll1169
slr1991 (cyaA)sll1161slr0449sll1180
slr1991 (cyaA)slr0510sll1371
slr0593sll1423
slr0842sll1924
slr1575slr0449
slr1764[xiii] slr0510
slr0593
slr0607[viii]
slr0842
slr1529
slr1575
 Thermotoga maritima(MSB8)1846N.F.N.F.N.F.N.F.TM1171[ix]
 Treponema pallidum(Nichols)1030TP0485N.F.TP0485TP0089TP0089
TP0995TP0261
TP0262
TP0995

[i] The SWISS-PROT identifier is given for E. coli and B. subtilis proteins; other protein designations are from the respective genome projects.

[ii] SRS search (SWISS-PROT, TrEMBL, and TrEMBL_NEW) and Entrez protein query for cyclase* OR adenylate_cyc* OR adenylate_cyc*.

[iii] PROBE model for prokaryotic phosphoenolpyruvate phosphotransferase system-dependent adenylyl cyclases (see text).

[iv] PROBE model for the cyclase superfamily examined in this study (see text).

[v] SRS search (SWISS-PROT, TrEMBL, and TrEMBL_NEW) and Entrez protein query for cyclic* OR cAMP* OR cNMP*.

[vi] The gene annotation notes that AF0971 matches the Pfam cNMP-binding model; however, it does not match the PROSITE cNMP-binding patterns and is not detected by our PROBE cNMP-binding protein superfamily model. When a data set of only the archaeal proteomes was scanned with the seven cNMP-binding protein class models, the only additional protein detected was AF0971, which was detected by the class 4 (FNR/FIXK/NTCA) model.

[vii] The gene annotation for PAB0653 and PAB2098 notes homology to the cyaB cyclase (Sismeiro et al. 1998), which is not related to the class III cyclases (see Discussion).

[viii] Proteins with <30 amino acids on either side of the cNMP-binding motif.

[ix] Proteins that were not entered into the NCBI nr database at the time that the superfamily proteins were recruited, and therefore were not included in the cNMP-binding protein superfamily.

[x] The gene annotation for CT664 notes homology to nucleotide cyclases, though the region of homology is to the FHA domain of a cyanobacterial cyclase and does not extend to the cyclase domain.

[xi] Two strains of Helicobacter pylori have been sequenced: 26695 and J99. Neither encodes any cyclases or cNMP-binding proteins.

[xii] Rv3617 annotation notes a match to one of two PROSITE patterns (PS00888) for cNMP-binding (PS00888 and PS00889 together make up the PROSITE cNMP-binding pattern); Rv3617 does not match the Pfam cNMP-binding model, nor is it detected by our PROBE cNMP-binding protein superfamily model.

[xiii] slr1764 is described as a cAMP-binding protein and has some homology to D. discoideum cAMP-binding proteins (Grant and Tsang 1990) that are not related to this superfamily of cNMP-binding proteins.

[xiv] (N.F.) None found.