Supplementary table for the paper
Long-term trends in evolution of indels
in protein sequences, by Y. Wolf,
T. Madej, V. Babenko, B. Shoemaker, and A.R. Panchenko.
This table lists the protein
families from the Conserved Domain Database http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
that were used in the paper. The columns
are as follows: CDD accession, conserved domain name, number of sequences in
the CD family, number of spacers in the CD alignment, the regression
coefficient between the sum of spacer lengths (or domain size) and evolutionary
distance, and the simplified taxonomy (bacterial-specific, eukaryote-specific,
or “root”, see the paper). An asterisk
(*) next to the CDD accession indicates that the P-value for the regression
coefficient was significant (< 0.01).
Further details may be found in the paper.
|
CDD acc |
CD name |
Nseq |
Nspacer |
Regr.coef |
tax |
|
cd00001 |
PTS_IIB_man |
25 |
15 |
-0.172 |
B |
|
cd00002* |
YbaK |
61 |
12 |
4.467 |
R |
|
cd00003* |
PNPsynthase |
18 |
9 |
14.163 |
B |
|
cd00004 |
Sortase |
35 |
13 |
4.921 |
R |
|
cd00005 |
CBM9 |
19 |
10 |
-4.282 |
B |
|
cd00006 |
PTS_IIA_man |
43 |
7 |
0.088 |
B |
|
cd00007 |
35EXOc |
55 |
9 |
-2.774 |
R |
|
cd00008 |
53EXOc |
56 |
12 |
1.129 |
R |
|
cd00009* |
AAA |
350 |
6 |
-14.858 |
R |
|
cd00010* |
AAI_LTSS |
117 |
6 |
12.021 |
E |
|
cd00013 |
ADF |
51 |
11 |
-1.351 |
E |
|
cd00014 |
CH |
53 |
5 |
0.601 |
E |
|
cd00015 |
ALBUMIN |
59 |
10 |
-1.905 |
E |
|
cd00016 |
alkPPc |
29 |
15 |
-17.025 |
R |
|
cd00017* |
ANATO |
43 |
4 |
-1.49 |
E |
|
cd00018 |
AP2 |
23 |
4 |
0.467 |
E |
|
cd00019 |
AP2Ec |
40 |
16 |
3.356 |
R |
|
cd00020 |
ARM |
77 |
8 |
-0.696 |
E |
|
cd00021 |
BBOX |
55 |
4 |
-1.13 |
E |
|
cd00022 |
BIR |
64 |
5 |
0.432 |
R |
|
cd00023 |
BBI |
20 |
5 |
-0.193 |
E |
|
cd00024* |
CHROMO |
121 |
4 |
3.339 |
R |
|
cd00027 |
BRCT |
144 |
5 |
1.419 |
R |
|
cd00028 |
B_lectin |
44 |
9 |
-1.116 |
R |
|
cd00029* |
C1 |
49 |
3 |
1.731 |
E |
|
cd00031 |
CA |
168 |
19 |
2.525 |
R |
|
cd00032 |
CASc |
52 |
13 |
3.327 |
E |
|
cd00033 |
CCP |
288 |
6 |
0.732 |
R |
|
cd00034 |
ChSh |
11 |
3 |
-1.59 |
E |
|
cd00035 |
ChtBD1 |
27 |
5 |
2.176 |
E |
|
cd00036* |
ChtBD3 |
79 |
6 |
1.621 |
R |
|
cd00037* |
CLECT |
378 |
10 |
3.955 |
R |
|
cd00038 |
CAP_ED |
292 |
9 |
0.534 |
R |
|
cd00040 |
CSF2 |
14 |
2 |
1.334 |
E |
|
cd00041 |
CUB |
294 |
10 |
1.752 |
R |
|
cd00042* |
CY |
52 |
8 |
3.502 |
E |
|
cd00043* |
CYCLIN |
328 |
4 |
1.105 |
R |
|
cd00044 |
CysPc |
36 |
15 |
-2.158 |
R |
|
cd00045 |
DED |
32 |
5 |
-0.958 |
R |
|
cd00048 |
DSRM |
154 |
5 |
-0.608 |
R |
|
cd00049 |
MH1 |
19 |
10 |
-3.127 |
E |
|
cd00050 |
MH2 |
14 |
9 |
-7.693 |
E |
|
cd00051 |
EFh |
104 |
3 |
1.657 |
R |
|
cd00053* |
EGF |
862 |
6 |
1.67 |
R |
|
cd00055* |
EGF_Lam |
317 |
6 |
4.01 |
E |
|
cd00056* |
ENDO3c |
140 |
8 |
3.057 |
R |
|
cd00057 |
FA58C |
26 |
13 |
-1.802 |
R |
|
cd00058 |
FGF |
31 |
8 |
-0.573 |
R |
|
cd00059 |
FH |
48 |
4 |
1.588 |
E |
|
cd00060 |
FHA |
141 |
10 |
0.011 |
R |
|
cd00061* |
FN1 |
23 |
3 |
-1.286 |
E |
|
cd00062 |
FN2 |
25 |
2 |
0.135 |
E |
|
cd00063 |
FN3 |
741 |
12 |
0.703 |
R |
|
cd00064 |
FU |
159 |
7 |
0.279 |
E |
|
cd00065 |
FYVE |
88 |
6 |
-0.657 |
E |
|
cd00066* |
G-alpha |
63 |
24 |
45.796 |
R |
|
cd00067 |
GAL4 |
118 |
2 |
0.266 |
E |
|
cd00068 |
GGL |
27 |
3 |
-0.184 |
E |
|
cd00069* |
GHB |
32 |
7 |
-6.431 |
E |
|
cd00070* |
GLECT |
91 |
11 |
-8.836 |
R |
|
cd00072* |
GYF |
21 |
3 |
1.674 |
E |
|
cd00073* |
H15 |
70 |
4 |
3.624 |
E |
|
cd00074 |
H2A |
18 |
9 |
0.31 |
E |
|
cd00075* |
HATPase_c |
483 |
5 |
14.13 |
R |
|
cd00077* |
HDc |
247 |
6 |
3.72 |
R |
|
cd00078* |
HECTc |
48 |
26 |
19.625 |
E |
|
cd00079* |
HELICc |
130 |
11 |
5.653 |
R |
|
cd00080 |
HhH2_motif |
98 |
4 |
-0.908 |
R |
|
cd00081 |
Hint |
77 |
12 |
-58.203 |
R |
|
cd00082* |
HisKA |
574 |
1 |
-0.756 |
R |
|
cd00083 |
HLH |
145 |
1 |
-0.046 |
E |
|
cd00084 |
HMG-box |
192 |
2 |
0.444 |
R |
|
cd00085 |
HNHc |
121 |
4 |
-1.089 |
R |
|
cd00086* |
homeodomain |
317 |
2 |
1.505 |
E |
|
cd00087 |
FReD |
57 |
18 |
1.857 |
E |
|
cd00088* |
HPT |
87 |
3 |
-5.434 |
R |
|
cd00089 |
HR1 |
25 |
1 |
0.648 |
E |
|
cd00090 |
HTH_ARSR |
178 |
6 |
0.249 |
R |
|
cd00091 |
NUC |
30 |
11 |
3.021 |
R |
|
cd00092 |
HTH_CRP |
28 |
2 |
1.853 |
R |
|
cd00093 |
HTH_XRE |
557 |
4 |
0.12 |
R |
|
cd00094 |
HX |
42 |
14 |
-3.864 |
E |
|
cd00095 |
IFab |
16 |
4 |
-1.736 |
E |
|
cd00096* |
IG |
393 |
5 |
2.528 |
R |
|
cd00097 |
IG_like |
448 |
6 |
0.298 |
E |
|
cd00100 |
IL1 |
15 |
9 |
-4.634 |
E |
|
cd00101* |
IlGF |
39 |
2 |
32.103 |
E |
|
cd00102* |
IPT |
141 |
10 |
5.031 |
R |
|
cd00103 |
IRF |
26 |
6 |
-0.734 |
R |
|
cd00104* |
KAZAL |
80 |
2 |
1.642 |
E |
|
cd00105 |
KH |
262 |
4 |
1.181 |
R |
|
cd00107 |
Knot1 |
50 |
3 |
-0.075 |
E |
|
cd00108 |
KR |
38 |
5 |
0.73 |
E |
|
cd00109* |
KU |
93 |
3 |
1.021 |
E |
|
cd00111 |
Trefoil |
49 |
4 |
0.926 |
E |
|
cd00112 |
LDLa |
565 |
6 |
0.633 |
E |
|
cd00113* |
PLAT |
36 |
7 |
-12.529 |
E |
|
cd00115* |
LMWPc |
72 |
7 |
-9.984 |
R |
|
cd00116 |
LRR_RI |
16 |
22 |
2.64 |
E |
|
cd00117 |
LU |
79 |
7 |
0.878 |
R |
|
cd00118* |
LysM |
115 |
3 |
1.176 |
R |
|
cd00119* |
LYZ1 |
49 |
9 |
-7.552 |
E |
|
cd00121 |
MATH |
81 |
8 |
-1.865 |
E |
|
cd00122 |
MBD |
46 |
4 |
-0.633 |
E |
|
cd00126 |
PAH |
17 |
1 |
0.131 |
E |
|
cd00127 |
DSPc |
51 |
6 |
2.385 |
R |
|
cd00130 |
PAS |
183 |
6 |
-0.028 |
R |
|
cd00132 |
CRIB |
17 |
5 |
-0.348 |
E |
|
cd00135* |
PDGF |
18 |
5 |
3.224 |
R |
|
cd00136 |
PDZ |
67 |
7 |
1.179 |
R |
|
cd00137 |
PLCc |
14 |
14 |
31.385 |
R |
|
cd00138 |
PLDc |
59 |
13 |
2.244 |
R |
|
cd00139 |
PIPKc |
16 |
12 |
19.732 |
E |
|
cd00140 |
POL3Bc |
20 |
20 |
2.697 |
R |
|
cd00142 |
PI3Kc_family |
60 |
13 |
-0.867 |
E |
|
cd00143* |
PP2Cc |
137 |
14 |
27.131 |
R |
|
cd00144 |
PP2Ac |
19 |
15 |
8.196 |
R |
|
cd00145* |
POLBc |
73 |
18 |
12.171 |
R |
|
cd00146* |
PKD |
70 |
8 |
8.344 |
R |
|
cd00148* |
PROF |
26 |
9 |
9.329 |
E |
|
cd00152 |
PTX |
27 |
17 |
-1.404 |
E |
|
cd00153 |
RA |
65 |
4 |
-1.116 |
E |
|
cd00155 |
RasGEF |
30 |
11 |
4.764 |
E |
|
cd00156* |
REC |
307 |
10 |
1.319 |
R |
|
cd00158* |
RHOD |
311 |
8 |
5.02 |
R |
|
cd00159 |
RhoGAP |
75 |
9 |
-0.928 |
E |
|
cd00160 |
RhoGEF |
66 |
9 |
2.853 |
E |
|
cd00161 |
RICIN |
104 |
11 |
1.721 |
R |
|
cd00162 |
RING |
555 |
4 |
-0.27 |
R |
|
cd00163* |
RNAse_Pc |
37 |
6 |
10.345 |
E |
|
cd00164 |
S1 |
228 |
5 |
-1.068 |
R |
|
cd00165* |
S4 |
266 |
4 |
-6.251 |
R |
|
cd00166* |
SAM |
145 |
5 |
0.715 |
R |
|
cd00167 |
SANT |
170 |
2 |
-0.731 |
E |
|
cd00168* |
SCP |
45 |
8 |
21.363 |
E |
|
cd00169 |
Chemokine |
22 |
5 |
0.739 |
R |
|
cd00170* |
SEC14 |
109 |
8 |
-2.818 |
E |
|
cd00171* |
Sec7 |
34 |
11 |
7.27 |
R |
|
cd00172 |
SERPIN |
91 |
23 |
-1.585 |
R |
|
cd00173* |
SH2 |
197 |
6 |
1.491 |
R |
|
cd00174* |
SH3 |
276 |
3 |
2.815 |
E |
|
cd00175 |
SNc |
30 |
6 |
-1.665 |
R |
|
cd00177* |
START |
67 |
14 |
-7.096 |
R |
|
cd00178 |
STI |
51 |
13 |
-2.038 |
E |
|
cd00179* |
SynN |
69 |
4 |
3.508 |
E |
|
cd00180* |
S_TKc |
254 |
17 |
10.75 |
R |
|
cd00182 |
TBOX |
32 |
10 |
2.416 |
E |
|
cd00183 |
TFIIS_I |
29 |
3 |
-0.803 |
E |
|
cd00184* |
TNF |
33 |
10 |
-8.593 |
E |
|
cd00185* |
TNFR |
49 |
10 |
-2.495 |
R |
|
cd00186 |
TOP1Ac |
62 |
14 |
-10.716 |
R |
|
cd00187 |
TOP4c |
57 |
28 |
6.938 |
R |
|
cd00188* |
TOPRIM |
42 |
6 |
9.496 |
R |
|
cd00189* |
TPR |
137 |
5 |
1.403 |
R |
|
cd00190* |
Tryp_SPc |
177 |
21 |
9.3 |
R |
|
cd00191* |
TY |
85 |
6 |
4.723 |
E |
|
cd00194 |
UBA |
77 |
3 |
0.073 |
E |
|
cd00195 |
UBCc |
70 |
15 |
3.302 |
R |
|
cd00196 |
UBQ |
53 |
6 |
0.372 |
R |
|
cd00197 |
VHS |
20 |
6 |
1.108 |
E |
|
cd00198 |
vWFA |
165 |
14 |
1.864 |
R |
|
cd00199* |
WAP |
19 |
3 |
-6.986 |
E |
|
cd00200* |
WD40 |
90 |
34 |
10.472 |
R |
|
cd00201 |
WW |
134 |
2 |
0.035 |
R |
|
cd00202* |
ZnF_GATA |
43 |
5 |
1.961 |
E |
|
cd00203 |
ZnMc |
120 |
9 |
0.055 |
R |
|
cd00204* |
ANK |
342 |
15 |
5.105 |
R |
|
cd00207* |
fer2 |
195 |
7 |
-4.094 |
R |
|
cd00208 |
LbetaH |
181 |
11 |
0.998 |
R |
|
cd00209 |
DHFR |
127 |
13 |
-1.606 |
R |
|
cd00211 |
PTS_IIA_fru |
109 |
10 |
-0.595 |
B |
|
cd00212 |
PTS_IIB_glc |
88 |
3 |
-0.07 |
B |
|
cd00214 |
Calpain_III |
25 |
8 |
-5.404 |
E |
|
cd00215 |
PTS_IIA_lac |
27 |
1 |
0.118 |
B |
|
cd00218 |
GlcAT-I |
12 |
15 |
16.54 |
E |
|
cd00220 |
VMO-I |
11 |
11 |
0.431 |
E |
|
cd00223 |
Topo6_Spo |
25 |
16 |
-1.464 |
R |
|
cd00230 |
RPA70N |
11 |
7 |
-1.599 |
E |
|
cd00231 |
ZipA |
11 |
1 |
0.434 |
B |
|
cd00232* |
HemeO |
42 |
7 |
12.311 |
R |
|
cd00233 |
VIP2 |
13 |
12 |
14.883 |
R |
|
cd00237 |
p23 |
35 |
9 |
-0.678 |
E |
|
cd00247 |
Endostatin-like |
20 |
5 |
1.733 |
E |
|
cd00249 |
AGE |
15 |
33 |
-0.532 |
R |
|
cd00250 |
CAS_like |
20 |
18 |
-3.531 |
R |
|
cd00253 |
PL_Passenger_AT |
75 |
20 |
-0.925 |
R |
|
cd00260 |
Sialidase |
55 |
26 |
-0.812 |
R |
|
cd00264 |
BPI |
31 |
12 |
-3.234 |
E |
|
cd00269 |
DEXHc |
135 |
6 |
-24.384 |
R |
|
cd00276 |
C2_1 |
40 |
7 |
-4.972 |
E |
|
cd00279 |
YlxR |
16 |
7 |
1.187 |
B |
|
cd00284 |
Cytochrome_b _N |
11 |
9 |
-0.393 |
R |
|
cd00286* |
Tubulin/FtsZ |
33 |
23 |
23.521 |
R |
|
cd00288 |
Pyruvate_Kinase |
15 |
43 |
-0.114 |
R |
|
cd00290 |
cytochrome_b_C |
15 |
3 |
-0.326 |
R |
|
cd00292 |
EF1B |
31 |
7 |
-1.981 |
R |
|
cd00296* |
SIR2 |
121 |
13 |
10.605 |
R |
|
cd00298 |
alpha-crystallin-Hsps |
30 |
7 |
1.011 |
R |
|
cd00312 |
Esterase_lipase |
23 |
26 |
6.351 |
R |
|
cd00314* |
plant_peroxidase |
97 |
18 |
28.161 |
R |
|
cd00315 |
Cyt_C5_DNA_methylase |
36 |
19 |
1.53 |
R |
|
cd00317* |
cyclophilin |
91 |
11 |
8.866 |
R |
|
cd00318 |
Phosphoglycerate_kinase |
26 |
29 |
11.021 |
R |
|
cd00328 |
catalase |
19 |
41 |
2.73 |
R |
|
cd00333* |
MIP |
27 |
11 |
25.271 |
R |
|
cd00346 |
trp_synt_A |
24 |
18 |
-0.777 |
R |
|
cd00347* |
Flavin_utilizing_monoxygenases |
255 |
6 |
6.684 |
R |
|
cd00349 |
Ribosomal_L11 |
12 |
8 |
-0.102 |
R |
|
cd00350 |
rubredoxin_like |
72 |
3 |
1.819 |
R |
|
cd00355* |
Ribosomal_L30_L7 |
70 |
1 |
0.353 |
R |
|
cd00365* |
HMG-CoA_reductase |
30 |
21 |
-8.658 |
R |
|
cd00367 |
PTS-HPr |
16 |
5 |
1.038 |
R |
|
cd00371 |
HMA |
105 |
6 |
-0.206 |
R |
|
cd00374* |
RNase_T2 |
96 |
14 |
13.568 |
R |
|
cd00383 |
trans_reg_C |
523 |
6 |
0.275 |
R |
|
cd00385* |
Isoprenoid_Biosyn_C1 |
324 |
12 |
-8.909 |
R |
|
cd00389* |
microbial_RNases |
25 |
4 |
12.465 |
R |
|
cd00397 |
DNA_BRE_C |
25 |
13 |
10.406 |
R |
|
cd00398 |
Aldolase_II |
13 |
17 |
11.427 |
R |
|
cd00401 |
AdoHcyase |
17 |
33 |
-32.036 |
R |
|
cd00410 |
Adenylsucc_synt |
14 |
24 |
0.091 |
R |
|
cd00411* |
Asparaginase |
16 |
24 |
9.92 |
R |
|
cd00423 |
Pterin_binding |
36 |
16 |
-3.326 |
R |
|
cd00430* |
Ala_racemase |
112 |
17 |
-4.442 |
R |
|
cd00431* |
cysteine_hydrolases |
203 |
9 |
-10.094 |
R |
|
cd00433* |
Peptidase_M17 |
88 |
18 |
11.003 |
R |
|
cd00435 |
ACBP |
15 |
7 |
1.867 |
E |
|
cd00447 |
NusB_Sun |
29 |
6 |
1.736 |
R |
|
cd00449* |
PLPDE_IV |
94 |
20 |
14.19 |
R |
|
cd00457 |
PEBP_RKIP |
37 |
12 |
-1.672 |
R |
|
cd00474 |
SUI1_eIF1 |
14 |
4 |
-2.771 |
R |
|
cd00475 |
CIS_IPPS |
16 |
14 |
1.271 |
R |
|
cd00476* |
SAICAR_synt |
63 |
12 |
28.277 |
R |
|
cd00481 |
Ribosomal_L19e |
34 |
4 |
0.146 |
R |
|
cd00483 |
HPPK |
103 |
8 |
3.248 |
R |
|
cd00487* |
Pep_deformylase |
155 |
9 |
5.127 |
R |
|
cd00494 |
HMBS |
22 |
25 |
1.396 |
R |
|
cd00498 |
Hsp33 |
41 |
20 |
4.319 |
R |
|
cd00504* |
GXGXG |
72 |
8 |
-9.788 |
R |
|
cd00516* |
PRTase_typeII |
185 |
22 |
27.448 |
R |
|
cd00520 |
RRF |
24 |
5 |
0.616 |
R |
|
cd00522 |
Hemerythrin |
19 |
5 |
-6.662 |
R |
|
cd00527 |
IF6 |
18 |
8 |
-3.137 |
R |
|
cd00528 |
MoaC |
53 |
5 |
3.381 |
R |
|
cd00531* |
NTF2_like |
162 |
10 |
-2.357 |
R |
|
cd00537 |
MTHFR |
78 |
17 |
-0.878 |
R |
|
cd00545 |
MCH |
11 |
16 |
-2.328 |
R |
|
cd00550 |
ArsA_ATPase |
13 |
13 |
-8.551 |
R |
|
cd00562 |
NifX_NifB |
111 |
7 |
-0.751 |
R |
|
cd00563 |
Dtyr_deacylase |
19 |
5 |
0.712 |
R |
|
cd00567 |
ACAD |
69 |
18 |
1.174 |
R |
|
cd00571 |
UreE |
33 |
12 |
2.82 |
R |
|
cd00575 |
NOS_oxygenase |
48 |
8 |
-4.431 |
R |
|
cd00588 |
CheW_like |
52 |
10 |
-1.126 |
R |
|
cd00592* |
HTH_MERR |
233 |
6 |
-1.845 |
R |
|
cd00593* |
RIBOc |
197 |
7 |
11.75 |
R |
|
cd00594 |
KU |
24 |
20 |
12.568 |
R |
|
cd00618* |
PLA2 |
81 |
3 |
-4.713 |
E |
|
cd00625 |
ArsB_NhaD_permease |
80 |
18 |
-0.264 |
R |
|
cd00636* |
TroA-like |
367 |
8 |
6.563 |
R |
|
cd00650* |
LDH_MDH |
22 |
22 |
6.635 |
R |
|
cd00651* |
TFold |
69 |
8 |
5.227 |
R |
|
cd00657* |
Ferritin_like |
487 |
9 |
3.418 |
R |
|
cd00680* |
Ring_hydroxylating_alpha |
68 |
15 |
-8.575 |
B |
|
cd00768* |
class_II_aaRS-like_core |
17 |
15 |
-20.223 |
R |
|
cd00802 |
class_I_aaRS_core |
21 |
14 |
-5.903 |
R |
|
cd00864 |
PI3Ka |
41 |
9 |
6.719 |
R |
|
cd00900 |
PH-like |
76 |
7 |
1.226 |
R |
|
cd00945* |
Aldolase_Class_I |
117 |
14 |
7.341 |
R |
|
cd00985* |
Maf_Ham1 |
180 |
9 |
-2.672 |
R |
|
cd01037 |
Restriction_endonuclease_like |
99 |
4 |
1.127 |
R |
|
cd01066* |
APP_MetAP |
102 |
10 |
-4.272 |
R |
|
cd01292 |
metallo-dependent_hydrolases |
50 |
18 |
2.834 |
R |
|
cd01341 |
ADP_ribosyl |
17 |
8 |
5.327 |
R |
|
cd01483 |
E1_enzyme_family |
46 |
12 |
-3.014 |
R |
|
cd01948* |
EAL |
385 |
13 |
-2.529 |
B |
|
cd01949 |
GGDEF |
511 |
5 |
-1.053 |
R |
|
cd02065* |
B12-binding_like |
124 |
6 |
4.663 |
R |