PRP38 - PFAM28P - GREMLIN Contacts

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PRP38 - PRP38 family

PFAM:	PF03371	Sequences: KSIHGTNPQFLIEKILRERIYDSPYWKEQCFGLTAYETLVDKAVEHLKYIGGWTYGGNRKPSPFLCLLLKLLQLQPEKEIVLEYLKNEDFKYLRALGAFYLRLTGPPVDVYKWLEPLLNDYRKLRRRNRDGEFDPKGFELTTMDEFVDDLLTKERVCDTILPRLPKRIVLEELD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	174 (163)
Sequences:	683 (454)
Seq/√Len:	35.6
META:	0.329

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_L	97_G	5.427	1.00
95_A	124_L	4.827	1.00
107_P	165_P	4.391	1.00
95_A	143_M	4.035	1.00
68_L	99_F	3.744	1.00
142_T	145_E	2.995	1.00
101_L	105_G	2.945	1.00
14_K	18_E	2.751	1.00
40_V	84_Y	2.740	1.00
101_L	110_V	2.490	1.00
95_A	146_F	2.399	1.00
149_D	153_K	2.386	1.00
124_L	143_M	2.375	1.00
44_V	93_L	2.309	0.99
82_L	113_W	2.293	0.99
16_L	65_L	2.236	0.99
97_G	101_L	2.167	0.99
43_A	47_L	2.127	0.99
98_A	117_L	2.039	0.99
29_Q	42_K	1.888	0.98
98_A	114_L	1.852	0.97
64_F	96_L	1.768	0.96
19_R	63_P	1.755	0.96
37_E	83_E	1.751	0.96
114_L	147_V	1.746	0.96
68_L	96_L	1.730	0.96
113_W	119_N	1.549	0.93
50_I	95_A	1.527	0.92
124_L	146_F	1.522	0.92
98_A	147_V	1.511	0.92
44_V	89_D	1.487	0.91
33_L	39_L	1.442	0.90
128_N	139_E	1.441	0.89
167_R	170_L	1.432	0.89
9_Q	21_Y	1.411	0.88
31_F	70_K	1.396	0.88
34_T	37_E	1.364	0.87
43_A	96_L	1.352	0.86
71_L	81_V	1.344	0.86
5_G	8_P	1.330	0.85
20_I	69_L	1.316	0.85
130_D	137_G	1.307	0.84
83_E	86_K	1.305	0.84
56_G	59_R	1.302	0.84
99_F	103_L	1.279	0.83
126_R	129_R	1.259	0.82
150_L	161_L	1.244	0.81
17_R	64_F	1.218	0.80
71_L	84_Y	1.217	0.80
6_T	10_F	1.208	0.79
85_L	101_L	1.207	0.79
85_L	105_G	1.206	0.79
94_R	120_D	1.196	0.78
87_N	93_L	1.186	0.78
25_Y	42_K	1.176	0.77
64_F	148_D	1.175	0.77
87_N	97_G	1.157	0.76
50_I	140_L	1.156	0.76
126_R	149_D	1.123	0.74
71_L	74_L	1.123	0.74
106_P	165_P	1.119	0.74
84_Y	93_L	1.109	0.73
22_D	155_R	1.080	0.71
57_G	60_K	1.079	0.71
155_R	160_I	1.068	0.70
141_T	149_D	1.033	0.67
97_G	105_G	0.991	0.64
82_L	86_K	0.960	0.62
39_L	71_L	0.958	0.62
82_L	101_L	0.956	0.61
30_C	33_L	0.951	0.61
42_K	172_E	0.943	0.60
89_D	97_G	0.942	0.60
40_V	93_L	0.939	0.60
140_L	145_E	0.939	0.60
3_I	104_T	0.930	0.59
6_T	9_Q	0.927	0.59
65_L	80_I	0.926	0.59
55_Y	146_F	0.924	0.59
54_T	59_R	0.922	0.59
117_L	143_M	0.911	0.58
90_F	93_L	0.897	0.56
16_L	164_L	0.895	0.56
68_L	163_R	0.890	0.56
110_V	165_P	0.887	0.56
21_Y	69_L	0.884	0.55
115_E	118_L	0.881	0.55
74_L	137_G	0.879	0.55
89_D	93_L	0.879	0.55
6_T	11_L	0.870	0.54
109_D	152_T	0.865	0.54
19_R	22_D	0.855	0.53
166_K	170_L	0.852	0.53
107_P	169_V	0.850	0.52
7_N	10_F	0.850	0.52
91_K	122_R	0.846	0.52
125_R	128_N	0.845	0.52
76_P	84_Y	0.830	0.51
55_Y	127_R	0.823	0.50
78_K	82_L	0.817	0.50
42_K	45_E	0.816	0.49
13_E	160_I	0.814	0.49
108_V	168_I	0.814	0.49
33_L	42_K	0.814	0.49
77_E	80_I	0.809	0.49
20_I	79_E	0.808	0.49
13_E	155_R	0.807	0.49
15_I	158_D	0.805	0.49
51_G	62_S	0.805	0.49
32_G	70_K	0.802	0.48
58_N	149_D	0.800	0.48
26_W	73_Q	0.798	0.48
150_L	157_C	0.796	0.48
54_T	58_N	0.795	0.48
31_F	37_E	0.795	0.48
164_L	167_R	0.794	0.48
111_Y	167_R	0.793	0.47
146_F	157_C	0.792	0.47
93_L	97_G	0.784	0.47
13_E	157_C	0.780	0.46
25_Y	67_L	0.771	0.46
68_L	126_R	0.769	0.45
100_Y	109_D	0.768	0.45
160_I	163_R	0.768	0.45
35_A	70_K	0.766	0.45
27_K	31_F	0.760	0.45
10_F	24_P	0.758	0.44
3_I	143_M	0.755	0.44
55_Y	60_K	0.754	0.44
126_R	156_V	0.754	0.44
71_L	93_L	0.753	0.44
150_L	156_V	0.752	0.44
2_S	68_L	0.752	0.44
146_F	156_V	0.751	0.44
23_S	95_A	0.734	0.42
20_I	103_L	0.734	0.42
64_F	67_L	0.734	0.42
48_K	159_T	0.733	0.42
23_S	66_C	0.733	0.42
92_Y	117_L	0.727	0.42
94_R	97_G	0.725	0.42
16_L	54_T	0.724	0.42
150_L	160_I	0.720	0.41
26_W	43_A	0.715	0.41
30_C	114_L	0.711	0.40
143_M	146_F	0.708	0.40
41_D	44_V	0.700	0.40
30_C	67_L	0.699	0.39
123_K	142_T	0.695	0.39
16_L	99_F	0.695	0.39
124_L	127_R	0.694	0.39
41_D	90_F	0.687	0.39
107_P	130_D	0.685	0.38
124_L	130_D	0.683	0.38
155_R	161_L	0.679	0.38
17_R	21_Y	0.679	0.38
39_L	129_R	0.678	0.38
90_F	111_Y	0.675	0.38
25_Y	33_L	0.674	0.37
50_I	64_F	0.669	0.37
127_R	130_D	0.666	0.37
39_L	43_A	0.664	0.37
163_R	172_E	0.655	0.36
47_L	51_G	0.650	0.36
8_P	171_E	0.650	0.36
86_K	113_W	0.647	0.35
165_P	169_V	0.643	0.35
91_K	144_D	0.641	0.35
91_K	140_L	0.634	0.34
26_W	69_L	0.630	0.34
68_L	159_T	0.629	0.34
109_D	113_W	0.627	0.34
44_V	90_F	0.623	0.33
99_F	159_T	0.622	0.33
33_L	70_K	0.621	0.33
96_L	109_D	0.620	0.33
26_W	34_T	0.620	0.33
99_F	146_F	0.620	0.33
23_S	172_E	0.616	0.33
34_T	139_E	0.615	0.33
35_A	41_D	0.614	0.33
34_T	70_K	0.614	0.33
12_I	18_E	0.614	0.33
18_E	22_D	0.613	0.33
12_I	16_L	0.611	0.32
48_K	109_D	0.608	0.32
20_I	48_K	0.606	0.32
63_P	129_R	0.600	0.32
39_L	70_K	0.595	0.31
40_V	44_V	0.595	0.31
98_A	150_L	0.592	0.31
123_K	144_D	0.592	0.31
149_D	152_T	0.592	0.31
15_I	57_G	0.591	0.31
130_D	138_F	0.591	0.31
104_T	112_K	0.590	0.31
81_V	101_L	0.590	0.31
114_L	151_L	0.589	0.31
19_R	59_R	0.589	0.31
101_L	113_W	0.588	0.31
13_E	49_Y	0.584	0.30
24_P	163_R	0.584	0.30
98_A	115_E	0.580	0.30
26_W	76_P	0.580	0.30
57_G	118_L	0.579	0.30
43_A	93_L	0.576	0.30
98_A	157_C	0.574	0.30
49_Y	81_V	0.574	0.30
65_L	103_L	0.571	0.30
17_R	92_Y	0.569	0.29
91_K	123_K	0.563	0.29
47_L	67_L	0.563	0.29
62_S	65_L	0.562	0.29
106_P	129_R	0.552	0.28
94_R	165_P	0.552	0.28
54_T	57_G	0.551	0.28
43_A	50_I	0.548	0.28
47_L	96_L	0.544	0.28
12_I	24_P	0.543	0.28
118_L	151_L	0.542	0.27
165_P	168_I	0.538	0.27
20_I	143_M	0.535	0.27
169_V	172_E	0.535	0.27
39_L	68_L	0.532	0.27
30_C	66_C	0.531	0.27
7_N	27_K	0.527	0.26
10_F	13_E	0.525	0.26
12_I	49_Y	0.524	0.26
41_D	93_L	0.524	0.26
31_F	84_Y	0.524	0.26
40_V	140_L	0.523	0.26
85_L	104_T	0.521	0.26
5_G	67_L	0.520	0.26
10_F	106_P	0.518	0.26
40_V	48_K	0.518	0.26
81_V	84_Y	0.516	0.26
22_D	27_K	0.516	0.26
77_E	88_E	0.516	0.26
12_I	165_P	0.515	0.26
35_A	39_L	0.513	0.26
13_E	137_G	0.503	0.25
30_C	84_Y	0.501	0.25
37_E	79_E	0.500	0.25
42_K	97_G	0.500	0.25

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
4l8tA	1	0.908	27	0.946	Contact Map
3gmiA	1	0.4885	15.6	0.951	Contact Map
3l9tA	1	0.9195	8.9	0.956	Contact Map
4lx2A	1	0.908	8.6	0.956	Contact Map
4lc2A	1	0.2471	7.3	0.958	Contact Map
4x8qA	1	0.8621	5.2	0.961	Contact Map
3d19A	5	0.908	4	0.963	Contact Map
2khzA	2	0.3391	3.8	0.963	Contact Map
3ee4A	2	0.4655	3.3	0.964	Contact Map
3j8bL	1	0	3.1	0.965	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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