Cnd1_N - PFAM28P - GREMLIN Contacts

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Cnd1_N - non-SMC mitotic condensation complex subunit 1, N-term

PFAM:	PF12922	Sequences: PKLLSKLLDLLVSGLSALADALHADLESDESQDDRAAHKNALEMYAFLLQWLVSAVETKAAEKSSAAAPAARGRGKKKGKKKKKKKKDGGWDWEEQRQRALDLLCKVLQLKLSRLWGTTSERDTFISLFTRPCYLILENEQRVKNTAIRMAIFKVLCIAVKHHGHALGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (164)
Sequences:	546 (393)
Seq/√Len:	30.6
META:	0.194

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_E	122_R	3.893	1.00
134_Y	165_H	3.178	1.00
81_K	84_K	3.072	1.00
47_F	51_W	2.938	1.00
165_H	168_G	2.699	1.00
40_N	44_M	2.592	1.00
159_A	165_H	2.529	0.99
130_T	159_A	2.476	0.99
44_M	48_L	2.331	0.99
159_A	163_H	2.306	0.99
112_L	116_W	2.159	0.98
101_L	108_L	2.111	0.98
6_K	9_D	1.931	0.97
19_A	107_V	1.927	0.97
13_S	91_W	1.916	0.96
118_T	121_E	1.875	0.96
146_T	156_L	1.837	0.95
112_L	128_L	1.830	0.95
125_F	161_K	1.782	0.95
39_K	121_E	1.760	0.94
137_L	143_V	1.734	0.94
130_T	165_H	1.723	0.94
112_L	153_F	1.665	0.92
28_S	114_R	1.656	0.92
40_N	43_E	1.649	0.92
121_E	132_P	1.601	0.91
16_S	24_A	1.587	0.90
120_S	129_F	1.572	0.90
101_L	132_P	1.555	0.89
28_S	37_A	1.551	0.89
72_R	78_K	1.528	0.89
42_L	112_L	1.505	0.88
38_H	130_T	1.481	0.87
70_A	73_G	1.439	0.85
135_L	156_L	1.431	0.85
127_S	132_P	1.422	0.85
51_W	101_L	1.392	0.83
74_R	97_R	1.387	0.83
11_L	145_N	1.386	0.83
120_S	124_T	1.383	0.83
127_S	167_L	1.360	0.82
11_L	99_R	1.358	0.82
71_A	75_G	1.350	0.81
121_E	163_H	1.345	0.81
39_K	118_T	1.340	0.81
130_T	134_Y	1.332	0.81
123_D	150_M	1.324	0.80
131_R	159_A	1.321	0.80
160_V	165_H	1.315	0.80
78_K	81_K	1.269	0.77
11_L	14_G	1.263	0.77
43_E	121_E	1.259	0.77
116_W	142_R	1.257	0.76
71_A	74_R	1.257	0.76
9_D	47_F	1.253	0.76
64_S	168_G	1.252	0.76
137_L	152_I	1.233	0.75
126_I	159_A	1.220	0.74
4_L	59_K	1.210	0.74
107_V	125_F	1.208	0.74
46_A	125_F	1.202	0.73
82_K	87_K	1.199	0.73
41_A	141_Q	1.191	0.72
97_R	137_L	1.179	0.72
43_E	157_C	1.176	0.71
83_K	87_K	1.171	0.71
24_A	33_D	1.170	0.71
14_G	114_R	1.146	0.69
93_W	108_L	1.140	0.69
19_A	103_L	1.140	0.69
7_L	133_C	1.136	0.69
7_L	15_L	1.107	0.67
47_F	128_L	1.102	0.66
82_K	95_E	1.088	0.65
25_D	38_H	1.088	0.65
157_C	162_H	1.082	0.65
121_E	136_I	1.079	0.65
107_V	110_L	1.077	0.65
35_R	39_K	1.070	0.64
45_Y	144_K	1.065	0.64
150_M	154_K	1.059	0.63
23_H	116_W	1.052	0.63
132_P	148_I	1.047	0.62
27_E	32_Q	1.035	0.61
122_R	126_I	1.034	0.61
97_R	163_H	1.034	0.61
46_A	58_T	1.027	0.61
132_P	140_E	1.027	0.61
104_L	137_L	1.027	0.61
43_E	115_L	1.026	0.61
7_L	136_I	1.009	0.59
33_D	72_R	1.007	0.59
11_L	21_A	1.004	0.59
18_L	90_G	0.993	0.58
18_L	38_H	0.993	0.58
35_R	93_W	0.978	0.57
18_L	25_D	0.960	0.56
26_L	95_E	0.958	0.55
126_I	165_H	0.943	0.54
75_G	94_E	0.941	0.54
47_F	120_S	0.934	0.54
118_T	122_R	0.926	0.53
140_E	163_H	0.918	0.52
15_L	21_A	0.917	0.52
43_E	123_D	0.907	0.51
18_L	150_M	0.907	0.51
14_G	48_L	0.905	0.51
107_V	119_T	0.898	0.51
72_R	126_I	0.893	0.50
80_K	86_K	0.888	0.50
35_R	111_K	0.886	0.50
123_D	140_E	0.884	0.50
9_D	51_W	0.874	0.49
116_W	151_A	0.874	0.49
118_T	159_A	0.874	0.49
65_S	85_K	0.873	0.49
158_I	167_L	0.864	0.48
49_L	149_R	0.858	0.47
40_N	94_E	0.857	0.47
68_A	72_R	0.855	0.47
37_A	41_A	0.850	0.47
29_D	32_Q	0.844	0.46
57_E	139_N	0.839	0.46
161_K	164_G	0.832	0.45
66_A	141_Q	0.829	0.45
118_T	163_H	0.825	0.45
47_F	56_V	0.824	0.45
164_G	167_L	0.822	0.45
156_L	162_H	0.813	0.44
18_L	63_K	0.812	0.44
39_K	131_R	0.809	0.44
131_R	160_V	0.803	0.43
161_K	165_H	0.801	0.43
17_A	121_E	0.797	0.43
58_T	164_G	0.796	0.43
69_P	72_R	0.792	0.42
47_F	157_C	0.791	0.42
13_S	144_K	0.784	0.42
43_E	132_P	0.772	0.41
21_A	24_A	0.769	0.40
79_G	83_K	0.765	0.40
39_K	133_C	0.762	0.40
79_G	84_K	0.757	0.39
74_R	148_I	0.756	0.39
26_L	37_A	0.753	0.39
137_L	151_A	0.748	0.39
43_E	133_C	0.748	0.39
14_G	17_A	0.748	0.39
45_Y	56_V	0.746	0.39
79_G	82_K	0.746	0.39
52_L	116_W	0.745	0.39
74_R	81_K	0.745	0.39
61_A	139_N	0.741	0.38
42_L	87_K	0.734	0.38
103_L	114_R	0.730	0.37
159_A	164_G	0.729	0.37
59_K	137_L	0.727	0.37
39_K	164_G	0.725	0.37
112_L	119_T	0.725	0.37
136_I	152_I	0.720	0.37
7_L	52_L	0.716	0.36
160_V	166_A	0.713	0.36
43_E	46_A	0.712	0.36
22_L	148_I	0.708	0.36
27_E	158_I	0.707	0.36
149_R	159_A	0.702	0.35
105_C	139_N	0.699	0.35
26_L	34_D	0.693	0.35
15_L	45_Y	0.686	0.34
36_A	168_G	0.678	0.34
8_L	127_S	0.678	0.34
120_S	144_K	0.666	0.33
128_L	162_H	0.660	0.32
102_D	151_A	0.655	0.32
139_N	166_A	0.647	0.31
16_S	60_A	0.647	0.31
67_A	79_G	0.643	0.31
146_T	162_H	0.642	0.31
91_W	96_Q	0.642	0.31
13_S	96_Q	0.638	0.31
91_W	116_W	0.637	0.31
42_L	136_I	0.633	0.30
44_M	50_Q	0.631	0.30
94_E	97_R	0.630	0.30
28_S	95_E	0.629	0.30
11_L	17_A	0.629	0.30
58_T	152_I	0.627	0.30
98_Q	151_A	0.625	0.30
6_K	51_W	0.618	0.29
8_L	51_W	0.617	0.29
137_L	153_F	0.616	0.29
28_S	74_R	0.616	0.29
15_L	22_L	0.615	0.29
10_L	112_L	0.614	0.29
101_L	113_S	0.610	0.29
55_A	69_P	0.606	0.29
65_S	73_G	0.606	0.29
123_D	144_K	0.605	0.29
17_A	21_A	0.601	0.28
132_P	136_I	0.598	0.28
40_N	126_I	0.597	0.28
121_E	133_C	0.593	0.28
113_S	127_S	0.590	0.28
45_Y	120_S	0.587	0.27
123_D	130_T	0.586	0.27
44_M	167_L	0.580	0.27
118_T	131_R	0.578	0.27
45_Y	145_N	0.576	0.27
52_L	108_L	0.576	0.27
7_L	12_V	0.573	0.27
22_L	126_I	0.572	0.26
61_A	143_V	0.572	0.26
15_L	23_H	0.564	0.26
41_A	151_A	0.557	0.26
79_G	139_N	0.552	0.25
18_L	155_V	0.550	0.25
4_L	148_I	0.547	0.25
108_L	136_I	0.547	0.25
154_K	164_G	0.546	0.25
7_L	47_F	0.546	0.25
17_A	168_G	0.541	0.25
131_R	135_L	0.541	0.25
66_A	92_D	0.540	0.25
61_A	87_K	0.537	0.24
18_L	22_L	0.536	0.24
107_V	129_F	0.534	0.24
40_N	115_L	0.534	0.24
5_S	74_R	0.534	0.24
22_L	25_D	0.532	0.24
100_A	103_L	0.531	0.24
22_L	62_E	0.531	0.24
46_A	106_K	0.527	0.24
41_A	160_V	0.527	0.24
49_L	90_G	0.526	0.24
33_D	74_R	0.521	0.23
35_R	115_L	0.520	0.23
150_M	163_H	0.516	0.23
46_A	122_R	0.513	0.23
97_R	127_S	0.512	0.23
34_D	160_V	0.510	0.23
50_Q	131_R	0.509	0.23
8_L	29_D	0.508	0.23
119_T	149_R	0.507	0.23
21_A	26_L	0.504	0.22
125_F	138_E	0.502	0.22
19_A	71_A	0.500	0.22

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
3m62A	1	0.9053	11.7	0.935	Contact Map
3zkvA	1	0.9172	6	0.943	Contact Map
3wozA	1	0.8876	5.6	0.944	Contact Map
2gutA	1	0.3905	5.4	0.944	Contact Map
3nxbA	1	0.4497	5.3	0.945	Contact Map
2bptA	1	0.7751	4.2	0.947	Contact Map
4pjwA	1	0.8462	3.9	0.948	Contact Map
3uv5A	1	0.4852	3.9	0.948	Contact Map
1qgrA	1	0.9053	3.9	0.948	Contact Map
3ibvA	1	0.8402	3.6	0.949	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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