Computational Molecular Biology, 2018, Vol.8, No.1, 1-13
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Table 3 Protein family distributions in the proteins encoded by all genes and by genes with pre-mRNA alternative splicing (AS genes)
in cotton
PFam ID Total
AS
% Pfam
Pfam description
pfam00078 3419
470
13.7 RVT_1
Reverse transcriptase
pfam00069 1538
590
38.4 Pkinase
Protein kinase domain
pfam07727 1201
142
11.8 RVT_2
Reverse transcriptase
pfam08284 1191
43
3.6
RVP_2
Retroviral aspartyl protease
pfam03732 1049
220
21.0 Retrotrans_gag
Retrotransposon gag protein
pfam07714 1014
326
32.1 Pkinase_Tyr
Protein tyrosine kinase
pfam13041 667
191
28.6 PPR_2
PPR repeat family
pfam00067 655
108
16.5 p450
Cytochrome P450
pfam00931 531
108
20.3 NB-ARC
NB-ARC domain
pfam13639 520
174
33.5 zf-RING_2
Ring finger domain
pfam14223 485
42
8.7
UBN2
gag-polypeptide of LTR copia-type
pfam13456 445
62
13.9 RVT_3
Reverse transcriptase-like
pfam00249 428
127
29.7 Myb_DNA-binding Myb-like DNA-binding domain
pfam00076 410
233
56.8 RRM_1
RNA recognition motif
pfam13976 398
13
3.3
gag_pre-integrs
GAG-pre-integrase domain
pfam00847 354
40
11.3 AP2
AP2 domain
pfam12776 292
143
49.0 Myb_DNA-bind_3 Myb/SANT-like DNA-binding domain
pfam13359 254
33
13.0 DDE_Tnp_4
DDE superfamily endonuclease
pfam03171 251
70
27.9 2OG-FeII_Oxy
2OG-Fe (II) oxygenase superfamily
pfam00201 240
27
11.3 UDPGT
UDP-glucoronosyl and UDP-glucosyl transferase
pfam00481 226
108
47.8 PP2C
Protein phosphatase 2C
pfam02365 221
86
38.9 NAM
No apical meristem (NAM) protein
pfam00071 216
75
34.7 Ras
Ras family
pfam03106 200
74
37.0 WRKY
WRKY DNA-binding domain
pfam00010 193
77
39.9 HLH
Helix-loop-helix DNA-binding domain
pfam10536 190
17
8.9
PMD
Plant mobile domain
pfam00153 187
66
35.3 Mito_carr
Mitochondrial carrier protein
pfam13966 186
52
28.0 zf-RVT
zinc-binding in reverse transcriptase
pfam13499 186
48
25.8 EF-hand_7
EF-hand domain pair
pfam02519 185
24
13.0 Auxin_inducible
Auxin responsive protein
pfam00141 178
47
26.4 peroxidase
Peroxidase
pfam12796 175
54
30.9 Ank_2
Ankyrin repeats (3 copies)
pfam14432 175
32
18.3 DYW_deaminase
DYW family of nucleic acid deaminases
pfam00106 171
49
28.7 adh_short
short chain dehydrogenase
pfam00004 168
56
33.3 AAA
ATPase family associated with various cellular
pfam00083 164
66
40.2 Sugar_tr
Sugar (and other) transporter
pfam02458 162
15
9.3
Transferase
Transferase family
pfam00665 160
25
15.6 rve
Integrase core domain
pfam00225 159
75
47.2 Kinesin
Kinesin motor domain
pfam03004 158
80
50.6 Transposase_24
Plant transposase (Ptta/En/Spm family)
pfam14244 155
72
46.5 UBN2_3
gag-polypeptide of LTR copia-type
pfam01095 155
20
12.9 Pectinesterase
Pectinesterase
pfam00657 150
30
20.0 Lipase_GDSL
GDSL-like Lipase/Acylhydrolase
