Download Distribution of Class III nucleotide cyclases in bacteria and

Supplementary information for Shenoy AR & Visweswariah SS, FEBS Lett. 2004;561:11-21
Sandhya’s Group
Distribution of Class III nucleotide cyclases in bacteria and
archaebacteria
A total of 193 cyclases were identified in bacteria and archaebacteria using PSI-BLAST and HMM methods
(Class III nucleotide cyclases in bacteria and archaebacteria: lineage specific expansion of adenylyl cyclases
and a dearth of guanylyl cyclases. FEBS Lett. 2004;561:11-21.) and these have been listed here. In the table
below, cyclases (gene identifiers enlisted) identified in the study were classified as described in the section
on Analysis Procedures.
To search for cyclases of a particular type/domain composition/with a particular no. of transmembrane
helices/from a particular genome etc. use the Search cyclases link on the side bar. The row totals indicate
the number of genes present in each genome. Three cyclases marked by * (one each in B. japonicum, C.
crescentus and L. interrogans) have two cyclase domains and therefore the cyclase domain tally in these
organisms is one more than the total number of cyclase genes identified. The numbers in the last row
therefore add up to 195 cyclase domains that are present in a total of 193 gene products. One gene product is
a characterized guanylyl cyclase and is not listed (see below).
α
and
β
represent cyclases present on the pSymA and pSymB mega-plasmids of S. meliloti respectively.
$
The cyclases found in this organism are present on a catabolic plasmid.
^
Only one cyclase in Synechocystis is known to be a guanylyl cyclase (gi|16329561) and is not listed in the
above table. The total number of cyclases in this genome is therefore three.
AC, adenylyl cyclase; AmbiCyc, ambiguous cyclase; C1, cyclase domain with C1-like functional residues; C2,
cyclase domain with C2-like functional residues; Cyclike, cyclase domain lacking both C1-like and C2-like
residues.
Kindgom
Bacteria
Clade
αproteobacteria
Organism
Agrobacterium tumefaciens
Agrobacterium tumefaciens str.
C58 (U. Washington)
AC
AmbiCyc
15888487
15889837
15890956
17935056
17936455
17937709
1
C1
C2
Cyclike
Total
3
3
Supplementary information for Shenoy AR & Visweswariah SS, FEBS Lett. 2004;561:11-21
Kindgom
Clade
Organism
AC
AmbiCyc
C1
C2
Cyclike
Total
Bradyrhizobium japonicum
27375667
27375681
27376781
27377349
27377375
27377399
27377449
27377743
27377954
27377964
27377975
27379375
27379880
27380157
27380758
27381069
27381163
27381857
27382097
27382367
27382735
27382775
27382827
27382848
27382902
27383034
27375470
27375549
27380748
27381818
27376782*
27377378
27380154
27382988
27383122
27376782*
27382802
27382803
37
16126936
16125664
16126933*
16126933*
13471136
13472842
13473854
13470781
13474495
15965819
16263440α
15965803
15965848
16262695α
16264509β
Caulobacter crescentus CB15
Mesorhizobium loti
Sinorhizobium meliloti
βproteobacteria
γproteobacteria
Nitrosomonas europaea ATCC
19718
Coxiella burnetii RSA 493
Pseudomonas aeruginosa PA01
Shewanella oneidensis MR-1
Xanthomonas axonopodis pv.
citri str. 306
13471135
13472826
13472848
13472852
13472853
13473448
13475404
15964012
15964224
15964342
15964943
15965714
15965754
15966204
15966522
15966612
15966747
16262751α
16262756α
16263020α
16263053α
16263314α
16263319α
16263728α
16263995β
16264038β
16264092β
16264266β
16265162β
16265216β
30248121
30249799
30249278
13472512
13
16264413β
31
3
29654377
1
1
1
21241033
1
15598413
24372907
2
16264510β
3
Supplementary information for Shenoy AR & Visweswariah SS, FEBS Lett. 2004;561:11-21
Kindgom
Clade
Organism
AC
AmbiCyc
Xanthomonas campestris pv.
campestris str. ATCC 33913
Arthrobacter nicotinovorans
$
Corynebacterium efficiens YS314
Corynebacterium glutamicum
ATCC 13032
Mycobacterium bovis subsp.
bovis AF2122/97
Mycobacterium leprae
Actinobacteria
Mycobacterium tuberculosis
CDC1551
Mycobacterium tuberculosis
H37Rv
Streptomyces avermitilis MA4680
Streptomyces coelicolor A3(2)
Nostoc sp. PCC 7120
Cyanobacteria
Synechocystis sp. PCC 6803⊥
Thermosynechococcus elongatus
BP-1
Spirochaetes
Others
25169176
25169179
Leptospira interrogans serovar
lai str. 56601
Treponema pallidum
Fusobacterium nucleatum
subsp. nucleatum ATCC 25586
C1
C2
Cyclike
Total
21229718
1
25169178
3
25026866
1
19551561
1
31792456
31792513
31792514
31792515
31792811
31792834
31793391
31794815
15827006
15827733
15828261
15840710
15840770
15840771
15840772
15840773
15841080
15841103
15841703
15843257
15608404
15608458
15608459
15608460
15608763
15608785
15609349
15610781
31791563
31792079
31792314
31793093
31793667
31792554
31792555
31793615
16
15827939
4
15839770
15840309
15840558
15841371
15842015
15840814
15840815
15841955
17
15607527
15608031
15608260
15609037
15609625
15608498
15608499
15609572
16
29829871
1
21223302
17228157
17228238
17228613
17229396
17229758
17232455
16330472
1
22299953
24212988
24213265
24213693
24213770
24213884
24214119
24215236
24215344
24215534
24215667
24215740
24215933
24215985
24216542
24217155
24217179
15639476
6
16330418
22299823
2
24216707*
24216707*
24212727
18
1
19704882
3
3⊥
1
Supplementary information for Shenoy AR & Visweswariah SS, FEBS Lett. 2004;561:11-21
Kindgom
Archae
Clade
Organism
Euryarchaeota
Chlorobium tepidum TLS
Methanosarcina acetivorans str.
C2A
Methanopyrus kandleri
Methanothermobacter
thermautotrophicus
Grand Total
AC
AmbiCyc
C1
C2
Cyclike
Total
21673885
1
20090420
1
20093547
123
Sandhya’s Group
4
21
29
1
4
15678208
1
18
193