c-di-GMP phosphodiesterase class II (HD-GYP) domains in various Bacteria
Acidobacteria
. Acidobacteria bacterium Ellin345 ....................... 10 hits
. Solibacter usitatus Ellin6076 .......................... 1 hit
Actinobacteria
. Acidothermus cellulolyticus 11B ........................ 1 hit
. Frankia alni ACN14a .................................... 1 hit
. Mycobacterium avium subsp. paratuberculosis str. k10 ... 1 hit
. Mycobacterium sp. KMS .................................. 1 hit
. Mycobacterium sp. MCS .................................. 1 hit
. Mycobacterium vanbaalenii PYR-1 ........................ 1 hit
. Nocardioides sp. JS614 ................................. 2 hits
. Rhodococcus sp. RHA1 ................................... 1 hit
. Rubrobacter xylanophilus DSM 9941 ...................... 3 hits
. Streptomyces avermitilis MA-4680 ....................... 1 hit*
. Streptomyces coelicolor A3(2) .......................... 1 hit
Chloroflexi
. Dehalococcoides ethenogenes 195 ........................ 3 hits
. Dehalococcoides sp. CBDB1 .............................. 3 hits
Cyanobacteria
. Anabaena variabilis ATCC 29413 ......................... 2 hits
. Gloeobacter violaceus PCC 7421 ......................... 1 hit
. Nostoc sp. PCC 7120 .................................... 2 hits
. Synechococcus elongatus PCC 6301 ....................... 2 hits
. Synechococcus sp. JA-3-3Ab ............................. 2 hits
. Synechocystis sp. PCC 6803 ............................. 2 hits
. Thermosynechococcus elongatus BP-1 ..................... 1 hit
. Trichodesmium erythraeum IMS101 ........................ 2 hits
Deinococcus-Thermus group
. Deinococcus geothermalis DSM 11300 ..................... 5 hits
. Deinococcus radiodurans R1 ............................. 4 hits
. Thermus thermophilus HB27 .............................. 5 hits
Spirochaetes
. Borrelia afzelii PKo ................................... 1 hit
. Borrelia burgdorferi B31 ............................... 1 hit
. Borrelia garinii PBi ................................... 1 hit
. Leptospira borgpetersenii serovar Hardjo-bovis L550 .... 3 hits
. Leptospira interrogans serovar Lai str. 56601 .......... 2 hits
. Treponema denticola ATCC 35405 ......................... 4 hits
. Treponema pallidum subsp. pallidum str. Nichols ........ 3 hits
Unclassified Proteobacteria
. Magnetococcus sp. MC-1 ................................. 16 hits
Other phyla
. Aquifex aeolicus VF5 ................................... 1 hit
. Pelodictyon luteolum DSM 273 ........................... 1 hit
. Rhodopirellula baltica SH 1 ............................ 6 hits
. Thermotoga maritima MSB8 ............................... 10 hits
Acidobacteria
Acidobacteria bacterium Ellin345
Acid345_0185 gi|94967216|ref|YP_589264.1| multi sensor diguanylate cycl... BLink CDD UniProt Pfam
Acid345_1178 gi|94968207|ref|YP_590255.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Acid345_2498 gi|94969525|ref|YP_591573.1| response regulator receiver m... BLink CDD UniProt Pfam
Acid345_0504 gi|94967535|ref|YP_589583.1| response regulator receiver m... BLink CDD UniProt Pfam
Acid345_3335 gi|94970362|ref|YP_592410.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Acid345_4403 gi|94971429|ref|YP_593477.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Acid345_2866 gi|94969893|ref|YP_591941.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Acid345_1904 gi|94968931|ref|YP_590979.1| response regulator receiver m... BLink CDD UniProt Pfam
Acid345_4060 gi|94971086|ref|YP_593134.1| response regulator receiver m... BLink CDD UniProt Pfam
Acid345_4432 gi|94971458|ref|YP_593506.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Solibacter usitatus Ellin6076
Acid_1223 gi|116620346|ref|YP_822502.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Actinobacteria
Acidothermus cellulolyticus 11B
Acel_0546 gi|117927754|ref|YP_872305.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Frankia alni ACN14a
FRAAL6432 gi|111225771|ref|YP_716565.1| Hypothetical protein; putati... BLink CDD UniProt Pfam
Mycobacterium avium subsp. paratuberculosis str. k10
MAP3352c gi|41409450|ref|NP_962286.1| hypothetical protein MAP3352c... BLink CDD UniProt Pfam
Mycobacterium sp. KMS
Mkms_0925 gi|119866977|ref|YP_936929.1| transcriptional regulator, L... BLink CDD UniProt Pfam
Mycobacterium sp. MCS
Mmcs_0908 gi|108797883|ref|YP_638080.1| transcriptional regulator, L... BLink CDD UniProt Pfam
Mycobacterium vanbaalenii PYR-1
Mvan_2058 gi|120403052|ref|YP_952881.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Nocardioides sp. JS614
Noca_3310 gi|119717534|ref|YP_924499.1| regulatory protein, LuxR [No... BLink CDD UniProt Pfam
Noca_4918 gi|119714219|ref|YP_919361.1| metal-dependent phosphohydro... BLink CDD UniProt Pfam
Rhodococcus sp. RHA1
RHA1_ro06927 gi|111023879|ref|YP_706851.1| hypothetical protein RHA1_ro... BLink CDD UniProt Pfam
Rubrobacter xylanophilus DSM 9941
Rxyl_1018 gi|108803859|ref|YP_643796.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Rxyl_0861 gi|108803703|ref|YP_643640.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Rxyl_1017 gi|108803858|ref|YP_643795.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Streptomyces avermitilis MA-4680
SAV3036 gi|29829578|ref|NP_824212.1| putative integral membrane pr... BLink CDD UniProt Pfam
*SAV3035 gi|29829577|ref|NP_824211.1| lipoprotein [Streptomyces ave... BLink CDD UniProt Pfam
Streptomyces coelicolor A3(2)
SCO5218 gi|21223586|ref|NP_629365.1| putative integral membrane pr... BLink CDD UniProt Pfam
Chloroflexi
Dehalococcoides ethenogenes 195
DET0624 gi|57234549|ref|YP_181366.1| response regulator [Dehalococ... BLink CDD UniProt Pfam
DET1049 gi|57234183|ref|YP_181764.1| HD domain protein [Dehalococc... BLink CDD UniProt Pfam
DET1381 gi|57233885|ref|YP_182092.1| GGDEF domain/HD domain protei... BLink CDD UniProt Pfam
Dehalococcoides sp. CBDB1
cbdbA610 gi|73748462|ref|YP_307701.1| response regulator [Dehalococ... BLink CDD UniProt Pfam
cbdbA1335 gi|73749065|ref|YP_308304.1| GGDEF domain [Dehalococcoides... BLink CDD UniProt Pfam
cbdbA1602 gi|73749301|ref|YP_308540.1| response regulator [Dehalococ... BLink CDD UniProt Pfam
Cyanobacteria
Anabaena variabilis ATCC 29413
Ava_1255 gi|75907478|ref|YP_321774.1| Predicted sensor protein [Ana... BLink CDD UniProt Pfam
Ava_1777 gi|75907998|ref|YP_322294.1| Metal dependent phosphohydrol... BLink CDD UniProt Pfam
Gloeobacter violaceus PCC 7421
gll3192 gi|37522761|ref|NP_926138.1| hypothetical protein gll3192 ... BLink CDD UniProt Pfam
Nostoc sp. PCC 7120
alr3920 gi|17231412|ref|NP_487960.1| two-component response regula... BLink CDD UniProt Pfam
all4304 gi|17231796|ref|NP_488344.1| hypothetical protein all4304 ... BLink CDD UniProt Pfam
Synechococcus elongatus PCC 6301
syc0402_c gi|56750411|ref|YP_171112.1| hypothetical protein syc0402_... BLink CDD UniProt Pfam
syc1904_d gi|56751913|ref|YP_172614.1| hypothetical protein syc1904_... BLink CDD UniProt Pfam
Synechococcus sp. JA-3-3Ab
CYA_2336 gi|86606963|ref|YP_475726.1| response regulator [Synechoco... BLink CDD UniProt Pfam
CYA_1252 gi|86605935|ref|YP_474698.1| GAF domain protein [Synechoco... BLink CDD UniProt Pfam
Synechocystis sp. PCC 6803
sll1624 gi|16330364|ref|NP_441092.1| regulatory components of sens... BLink CDD UniProt Pfam
slr2100 gi|16330586|ref|NP_441314.1| regulatory components of sens... BLink CDD UniProt Pfam
Thermosynechococcus elongatus BP-1
tlr0485 gi|22298028|ref|NP_681275.1| hypothetical protein tlr0485 ... BLink CDD UniProt Pfam
Trichodesmium erythraeum IMS101
Tery_4298 gi|113477705|ref|YP_723766.1| putative sensor protein [Tri... BLink CDD UniProt Pfam
Tery_1233 gi|113474995|ref|YP_721056.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Deinococcus-Thermus
Deinococcus geothermalis DSM 11300
Dgeo_1999 gi|94986098|ref|YP_605462.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Dgeo_0663 gi|94984770|ref|YP_604134.1| putative PAS/PAC sensor prote... BLink CDD UniProt Pfam
Dgeo_0220 gi|94984328|ref|YP_603692.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Dgeo_2833 gi|94972296|ref|YP_594336.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Dgeo_1298 gi|94985399|ref|YP_604763.1| metal dependent phosphohydrol... BLink CDD UniProt Pfam
Deinococcus radiodurans R1
DR0039 gi|15805080|ref|NP_293765.1| hypothetical protein DR0039 ... BLink CDD UniProt Pfam
DR0719 gi|15805745|ref|NP_294442.1| hypothetical protein DR0719 ... BLink CDD UniProt Pfam
DR1565 gi|15806574|ref|NP_295288.1| hypothetical protein DR1565 ... BLink CDD UniProt Pfam
DRA0342 gi|15808001|ref|NP_285665.1| GGDEF family protein [Deinoco... BLink CDD UniProt Pfam
Thermus thermophilus HB27
TTC0629 gi|46198937|ref|YP_004604.1| HD-hydrolase domain [Thermus ... BLink CDD UniProt Pfam
TTC0633 gi|46198941|ref|YP_004608.1| two-component response regula... BLink CDD UniProt Pfam
TTC1010 gi|46199312|ref|YP_004979.1| integral membrane protein/HD-... BLink CDD UniProt Pfam
TTP0079 gi|46255150|ref|YP_006062.1| hypothetical protein TTP0079 ... BLink CDD UniProt Pfam
TTP0167 gi|46255238|ref|YP_006150.1| hypothetical membrane associa... BLink CDD UniProt Pfam
Spirochaetes
Borrelia afzelii PKo
BAPKO_0383 gi|111115197|ref|YP_709815.1| hypothetical protein BAPKO_0... BLink CDD UniProt Pfam
Borrelia burgdorferi B31
BB0374 gi|15594719|ref|NP_212508.1| hypothetical protein BB0374 ... BLink CDD UniProt Pfam
Borrelia garinii PBi
BG0373 gi|51598630|ref|YP_072818.1| hypothetical protein BG0373 ... BLink CDD UniProt Pfam
Leptospira borgpetersenii serovar Hardjo-bovis L550
LBL_1652 gi|116328315|ref|YP_798035.1| Response regulator with HD-G... BLink CDD UniProt Pfam
LBL_2291 gi|116328900|ref|YP_798620.1| Response regulator with HD-G... BLink CDD UniProt Pfam
LBL_2949 gi|116329478|ref|YP_799198.1| hypothetical protein LBL_294... BLink CDD UniProt Pfam
Leptospira interrogans serovar Lai str. 56601
LA2383 gi|24215083|ref|NP_712564.1| HD-GYP domain [Leptospira int... BLink CDD UniProt Pfam
LA2847 gi|24215547|ref|NP_713028.1| cGMP-dependent 3',5'-cyclic p... BLink CDD UniProt Pfam
Treponema denticola ATCC 35405
TDE1256 gi|42526765|ref|NP_971863.1| HD domain protein [Treponema ... BLink CDD UniProt Pfam
TDE1467 gi|42526975|ref|NP_972073.1| HD domain protein [Treponema ... BLink CDD UniProt Pfam
TDE2302 gi|42527804|ref|NP_972902.1| HD domain protein [Treponema ... BLink CDD UniProt Pfam
TDE2659 gi|42528159|ref|NP_973257.1| GAF domain/HD domain protein ... BLink CDD UniProt Pfam
Treponema pallidum subsp. pallidum str. Nichols
TP0764 gi|15639751|ref|NP_219201.1| hypothetical protein TP0764 ... BLink CDD UniProt Pfam
TP0877 gi|15639862|ref|NP_219312.1| hypothetical protein TP0877 ... BLink CDD UniProt Pfam
TP0912 gi|15639897|ref|NP_219347.1| hypothetical protein TP0912 ... BLink CDD UniProt Pfam
unclassified Proteobacteria
Magnetococcus sp. MC-1
Mmc1_0199 gi|117923515|ref|YP_864132.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_0279 gi|117923595|ref|YP_864212.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_1538 gi|117924836|ref|YP_865453.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_1640 gi|117924938|ref|YP_865555.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_1813 gi|117925110|ref|YP_865727.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_1857 gi|117925154|ref|YP_865771.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_2262 gi|117925552|ref|YP_866169.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_2455 gi|117925744|ref|YP_866361.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_2526 gi|117925815|ref|YP_866432.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_2944 gi|117926224|ref|YP_866841.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_2945 gi|117926225|ref|YP_866842.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_3072 gi|117926352|ref|YP_866969.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_3124 gi|117926403|ref|YP_867020.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Mmc1_3165 gi|117926444|ref|YP_867061.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_3408 gi|117926683|ref|YP_867300.1| response regulator receiver ... BLink CDD UniProt Pfam
Mmc1_3529 gi|117926803|ref|YP_867420.1| metal dependent phosphohydro... BLink CDD UniProt Pfam
Other phyla
Aquifex aeolicus VF5
AQ_2027 gi|15607008|ref|NP_214390.1| hypothetical protein aq_2027 ... BLink CDD UniProt Pfam
Pelodictyon luteolum DSM 273
Plut_1507 gi|78187364|ref|YP_375407.1| putative PAS/PAC sensor prote... BLink CDD UniProt Pfam
Rhodopirellula baltica SH 1
RB161 gi|32470755|ref|NP_863748.1| response regulator [Rhodopire... BLink CDD UniProt Pfam
RB1009 gi|32471194|ref|NP_864187.1| response regulator [Rhodopire... BLink CDD UniProt Pfam
RB1656 gi|32471539|ref|NP_864532.1| hypothetical protein RB1656 ... BLink CDD UniProt Pfam
RB1759 gi|32471581|ref|NP_864574.1| conserved hypothetical protei... BLink CDD UniProt Pfam
RB5964 gi|32473997|ref|NP_866991.1| probable response regulatory ... BLink CDD UniProt Pfam
RB10065 gi|32476231|ref|NP_869225.1| conserved hypothetical protei... BLink CDD UniProt Pfam
Thermotoga maritima MSB8
TM0037 gi|15642812|ref|NP_227853.1| hypothetical protein TM0037 ... BLink CDD UniProt Pfam
TM0186 gi|15642960|ref|NP_228001.1| response regulator [Thermot ... BLink CDD UniProt Pfam
TM0739 gi|15643502|ref|NP_228548.1| hypothetical protein TM0739 ... BLink CDD UniProt Pfam
TM1145 gi|15643902|ref|NP_228951.1| hypothetical protein TM1145 ... BLink CDD UniProt Pfam
TM1147 gi|15643904|ref|NP_228953.1| hypothetical protein TM1147 ... BLink CDD UniProt Pfam
TM1170 gi|15643926|ref|NP_228975.1| ABC transporter, periplasmi ... BLink CDD UniProt Pfam
TM1467 gi|15644216|ref|NP_229267.1| hypothetical protein TM1467 ... BLink CDD UniProt Pfam
TM1678 gi|15644426|ref|NP_229478.1| hypothetical protein TM1678 ... BLink CDD UniProt Pfam
TM1682 gi|15644430|ref|NP_229482.1| hypothetical protein TM1682 ... BLink CDD UniProt Pfam
TM1699 gi|15644447|ref|NP_229499.1| hypothetical protein TM1699 ... BLink CDD UniProt Pfam
Please send your corrections, questions and comments to Michael Galperin