NAM-associated - PFAM28P - GREMLIN Contacts

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NAM-associated - No apical meristem-associated C-terminal domain

PFAM:	PF14303	Sequences: KPFTLMHCWNILKDEPKWKAYLEELKKKKQKKTKNSSPSTSSSESNDSSSTGSSDNDSDEESESEESSPSKRPIGRKKAKEKRKSSYKEALDKLWAKKKELDEEKEKAKEERKKLELEKEKLELKKLKEEEKIMSMDLSSMDDEQRAYYEAKQKEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (145)
Sequences:	799 (699)
Seq/√Len:	58.1
META:	0.12

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_K	119_K	4.869	1.00
118_E	121_K	4.621	1.00
74_I	79_A	2.891	1.00
144_E	153_Q	2.735	1.00
120_E	126_K	2.667	1.00
9_W	13_K	2.610	1.00
12_L	18_W	2.567	1.00
72_R	75_G	2.536	1.00
142_D	153_Q	2.484	1.00
114_K	118_E	2.455	1.00
121_K	125_K	2.317	1.00
72_R	80_K	2.283	1.00
146_R	150_E	2.106	1.00
74_I	82_K	1.974	1.00
135_S	149_Y	1.949	1.00
89_E	93_K	1.941	1.00
149_Y	153_Q	1.940	1.00
116_E	119_K	1.829	0.99
113_K	116_E	1.748	0.99
74_I	78_K	1.726	0.99
72_R	77_K	1.720	0.99
145_Q	153_Q	1.637	0.99
109_K	112_R	1.609	0.99
93_K	99_K	1.576	0.98
125_K	128_K	1.501	0.98
81_E	84_K	1.490	0.98
30_Q	38_P	1.489	0.98
147_A	150_E	1.462	0.97
143_D	146_R	1.444	0.97
30_Q	37_S	1.428	0.97
31_K	37_S	1.424	0.97
138_L	141_M	1.408	0.97
129_E	132_K	1.399	0.97
35_N	38_P	1.372	0.96
15_E	18_W	1.327	0.96
102_D	105_K	1.307	0.95
75_G	79_A	1.264	0.94
30_Q	33_T	1.260	0.94
57_D	60_E	1.259	0.94
8_C	12_L	1.254	0.94
147_A	151_A	1.233	0.93
152_K	155_E	1.220	0.93
106_E	109_K	1.220	0.93
132_K	136_M	1.215	0.93
37_S	40_T	1.210	0.93
99_K	103_E	1.185	0.92
56_N	59_D	1.179	0.92
123_E	126_K	1.174	0.92
128_K	132_K	1.170	0.91
31_K	39_S	1.137	0.90
126_K	130_E	1.137	0.90
116_E	120_E	1.122	0.90
85_S	89_E	1.119	0.89
137_D	140_S	1.104	0.89
136_M	149_Y	1.104	0.89
77_K	80_K	1.095	0.88
101_L	104_E	1.090	0.88
93_K	107_K	1.082	0.88
102_D	106_E	1.073	0.87
98_K	105_K	1.069	0.87
95_W	98_K	1.062	0.87
91_L	94_L	1.062	0.87
127_L	130_E	1.060	0.87
32_K	35_N	1.059	0.87
36_S	39_S	1.049	0.86
153_Q	156_I	1.043	0.86
150_E	154_K	1.038	0.86
97_K	102_D	1.033	0.85
128_K	131_E	1.032	0.85
87_Y	98_K	1.023	0.85
8_C	76_R	1.020	0.85
35_N	40_T	1.014	0.84
115_L	122_L	1.013	0.84
92_D	98_K	1.009	0.84
4_T	13_K	1.006	0.84
86_S	92_D	1.004	0.84
73_P	80_K	0.994	0.83
103_E	108_A	0.991	0.83
144_E	150_E	0.986	0.83
117_L	122_L	0.984	0.82
75_G	80_K	0.982	0.82
21_Y	24_E	0.981	0.82
108_A	111_E	0.976	0.82
113_K	117_L	0.973	0.82
97_K	106_E	0.966	0.81
32_K	43_S	0.958	0.81
91_L	103_E	0.948	0.80
104_E	107_K	0.947	0.80
60_E	63_E	0.937	0.79
104_E	109_K	0.931	0.79
131_E	149_Y	0.925	0.78
130_E	133_I	0.896	0.76
95_W	99_K	0.878	0.75
100_E	103_E	0.865	0.73
88_K	97_K	0.862	0.73
95_W	105_K	0.856	0.73
107_K	111_E	0.853	0.72
62_S	65_E	0.851	0.72
92_D	96_A	0.849	0.72
38_P	43_S	0.836	0.71
34_K	42_S	0.835	0.71
35_N	42_S	0.835	0.71
86_S	91_L	0.832	0.71
31_K	43_S	0.829	0.70
77_K	140_S	0.828	0.70
37_S	42_S	0.817	0.69
35_N	43_S	0.811	0.69
30_Q	34_K	0.809	0.68
143_D	153_Q	0.803	0.68
78_K	81_E	0.801	0.68
31_K	38_P	0.791	0.67
12_L	15_E	0.790	0.67
102_D	109_K	0.780	0.66
89_E	92_D	0.777	0.65
16_P	19_K	0.774	0.65
30_Q	39_S	0.771	0.65
85_S	88_K	0.767	0.64
149_Y	152_K	0.764	0.64
29_K	39_S	0.760	0.64
140_S	153_Q	0.757	0.63
100_E	111_E	0.756	0.63
11_I	30_Q	0.756	0.63
73_P	79_A	0.748	0.62
85_S	92_D	0.745	0.62
33_T	37_S	0.744	0.62
34_K	43_S	0.744	0.62
145_Q	149_Y	0.743	0.62
126_K	129_E	0.743	0.62
93_K	97_K	0.741	0.62
89_E	94_L	0.740	0.61
85_S	99_K	0.739	0.61
93_K	100_E	0.733	0.61
119_K	123_E	0.730	0.60
97_K	104_E	0.728	0.60
39_S	42_S	0.726	0.60
92_D	104_E	0.721	0.59
66_E	71_K	0.720	0.59
114_K	121_K	0.714	0.59
73_P	77_K	0.714	0.59
39_S	43_S	0.711	0.58
144_E	154_K	0.704	0.58
107_K	110_E	0.702	0.57
57_D	61_E	0.700	0.57
95_W	102_D	0.700	0.57
31_K	34_K	0.694	0.57
138_L	146_R	0.694	0.57
87_Y	93_K	0.692	0.56
40_T	43_S	0.691	0.56
101_L	105_K	0.690	0.56
108_A	112_R	0.688	0.56
34_K	41_S	0.686	0.56
134_M	141_M	0.679	0.55
35_N	39_S	0.678	0.55
104_E	108_A	0.670	0.54
29_K	32_K	0.670	0.54
91_L	109_K	0.667	0.54
10_N	20_A	0.659	0.53
127_L	152_K	0.655	0.52
92_D	101_L	0.654	0.52
20_A	115_L	0.645	0.51
55_D	58_S	0.639	0.51
105_K	108_A	0.638	0.50
34_K	39_S	0.637	0.50
137_D	149_Y	0.637	0.50
127_L	136_M	0.633	0.50
79_A	82_K	0.633	0.50
85_S	93_K	0.633	0.50
97_K	109_K	0.627	0.49
98_K	112_R	0.624	0.49
106_E	110_E	0.620	0.48
90_A	97_K	0.620	0.48
4_T	23_E	0.619	0.48
1_K	4_T	0.618	0.48
129_E	133_I	0.616	0.48
134_M	148_Y	0.613	0.48
8_C	134_M	0.610	0.47
18_W	149_Y	0.609	0.47
101_L	110_E	0.607	0.47
8_C	11_I	0.606	0.47
87_Y	91_L	0.600	0.46
29_K	42_S	0.597	0.46
102_D	107_K	0.596	0.46
8_C	15_E	0.592	0.45
102_D	108_A	0.588	0.45
96_A	106_E	0.584	0.44
144_E	147_A	0.578	0.44
23_E	34_K	0.578	0.44
123_E	137_D	0.578	0.44
8_C	22_L	0.577	0.44
33_T	36_S	0.577	0.44
33_T	40_T	0.572	0.43
1_K	122_L	0.568	0.43
101_L	112_R	0.565	0.42
104_E	112_R	0.564	0.42
98_K	109_K	0.563	0.42
126_K	152_K	0.560	0.42
87_Y	94_L	0.558	0.42
88_K	101_L	0.553	0.41
29_K	139_S	0.552	0.41
12_L	129_E	0.548	0.41
91_L	95_W	0.530	0.39
141_M	152_K	0.526	0.38
38_P	42_S	0.526	0.38
14_D	134_M	0.524	0.38
120_E	124_L	0.522	0.38
97_K	108_A	0.521	0.38
125_K	132_K	0.521	0.38
135_S	153_Q	0.519	0.38
151_A	154_K	0.519	0.38
105_K	112_R	0.518	0.37
97_K	101_L	0.517	0.37
92_D	103_E	0.515	0.37
32_K	38_P	0.514	0.37
86_S	93_K	0.511	0.37
76_R	146_R	0.507	0.36
98_K	102_D	0.505	0.36
56_N	62_S	0.504	0.36
2_P	7_H	0.500	0.36

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4djcB	1	0.0833	3	0.936	Contact Map
4yonA	1	0.5385	2.4	0.939	Contact Map
4cr2Z	1	0.3141	1.8	0.943	Contact Map
3csuA	3	0.3333	1.4	0.946	Contact Map
4nf9C	1	0.0577	1.3	0.947	Contact Map
3ul1A	1	0.1346	1.1	0.949	Contact Map
4uvqA	2	0.3077	1.1	0.95	Contact Map
3narA	1	0.3462	1.1	0.95	Contact Map
3magA	2	0.2692	1.1	0.95	Contact Map
1juqA	3	0.2821	1	0.951	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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