RDD - PFAM28P - GREMLIN Contacts

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RDD - RDD family

PFAM:	PF06271	Sequences: YAGFGRRLLAFLIDLLILLAVLLLLALLLGLLLAALGLGGLALAGLLALLLLLLLLLVWLLYFVLFESLRGQTPGKRLLGLRVVDDDGGPLSFGRALLRNLLRLVPFGGYLLSLLLLGLGFLWALFDPRRQRLHDLLAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (129)
Sequences:	82235 (64360)
Seq/√Len:	5666.6
META:	0.899

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_D	95_R	3.542	1.00
127_D	136_L	3.221	1.00
91_L	96_A	3.003	1.00
131_Q	136_L	2.631	1.00
63_F	67_E	2.562	1.00
68_S	93_F	2.249	1.00
61_L	66_F	2.245	1.00
65_L	69_L	2.157	1.00
2_A	81_L	2.118	1.00
72_Q	77_R	2.018	1.00
110_Y	113_S	1.969	1.00
92_S	95_R	1.965	1.00
3_G	6_R	1.957	1.00
61_L	67_E	1.884	1.00
85_D	89_G	1.848	1.00
67_E	76_K	1.831	1.00
10_A	81_L	1.739	1.00
124_A	132_R	1.738	1.00
70_R	77_R	1.700	1.00
6_R	79_L	1.680	1.00
123_W	127_D	1.623	1.00
127_D	131_Q	1.608	1.00
86_D	131_Q	1.593	1.00
9_L	79_L	1.578	1.00
11_F	63_F	1.574	1.00
13_I	79_L	1.573	1.00
71_G	82_R	1.545	1.00
123_W	133_L	1.521	1.00
120_G	132_R	1.490	1.00
68_S	96_A	1.488	1.00
122_L	126_F	1.485	1.00
62_Y	66_F	1.476	1.00
4_F	124_A	1.473	1.00
66_F	74_P	1.473	1.00
116_L	120_G	1.420	1.00
13_I	78_L	1.407	1.00
27_L	31_L	1.396	1.00
60_L	97_L	1.378	1.00
14_D	75_G	1.373	1.00
111_L	114_L	1.370	1.00
24_L	28_L	1.351	1.00
94_G	98_L	1.350	1.00
67_E	100_N	1.330	1.00
135_D	138_A	1.299	1.00
113_S	116_L	1.297	1.00
62_Y	67_E	1.254	1.00
21_V	24_L	1.254	1.00
61_L	65_L	1.253	1.00
120_G	134_H	1.215	1.00
102_L	137_L	1.200	1.00
109_G	112_L	1.156	1.00
95_R	98_L	1.151	1.00
63_F	66_F	1.150	1.00
6_R	9_L	1.145	1.00
96_A	100_N	1.144	1.00
74_P	77_R	1.141	1.00
60_L	64_V	1.123	1.00
114_L	118_G	1.117	1.00
129_R	136_L	1.117	1.00
5_G	9_L	1.112	1.00
117_L	120_G	1.086	1.00
98_L	137_L	1.078	1.00
64_V	97_L	1.058	1.00
61_L	64_V	1.041	1.00
85_D	92_S	1.025	1.00
109_G	113_S	1.020	1.00
10_A	79_L	1.016	1.00
59_W	63_F	1.002	1.00
64_V	100_N	0.997	1.00
23_L	27_L	0.992	1.00
86_D	139_G	0.985	1.00
123_W	136_L	0.981	1.00
58_V	61_L	0.965	1.00
63_F	100_N	0.953	1.00
111_L	115_L	0.951	1.00
66_F	77_R	0.943	1.00
76_K	83_V	0.939	1.00
21_V	58_V	0.923	1.00
123_W	126_F	0.907	1.00
120_G	124_A	0.905	1.00
76_K	81_L	0.900	1.00
113_S	117_L	0.896	1.00
8_L	11_F	0.883	1.00
97_L	100_N	0.879	1.00
20_A	24_L	0.871	1.00
4_F	8_L	0.866	1.00
2_A	6_R	0.864	1.00
11_F	15_L	0.854	1.00
93_F	97_L	0.852	1.00
85_D	91_L	0.852	1.00
109_G	137_L	0.849	1.00
93_F	96_A	0.838	1.00
99_R	135_D	0.829	1.00
49_L	53_L	0.827	1.00
112_L	115_L	0.825	1.00
10_A	75_G	0.822	1.00
67_E	83_V	0.821	1.00
110_Y	114_L	0.817	1.00
114_L	117_L	0.812	1.00
55_L	58_V	0.807	1.00
122_L	125_L	0.801	1.00
64_V	93_F	0.799	1.00
133_L	136_L	0.799	1.00
72_Q	76_K	0.796	1.00
71_G	90_P	0.774	1.00
111_L	116_L	0.772	1.00
74_P	78_L	0.766	1.00
83_V	99_R	0.764	1.00
17_I	74_P	0.762	1.00
24_L	27_L	0.746	1.00
5_G	8_L	0.739	1.00
18_L	22_L	0.737	1.00
95_R	138_A	0.734	1.00
133_L	137_L	0.733	1.00
48_A	52_L	0.732	1.00
64_V	68_S	0.731	1.00
16_L	20_A	0.729	1.00
98_L	138_A	0.727	1.00
64_V	67_E	0.720	1.00
92_S	96_A	0.715	1.00
21_V	25_L	0.709	1.00
58_V	62_Y	0.708	1.00
75_G	78_L	0.705	1.00
98_L	101_L	0.701	1.00
83_V	91_L	0.700	1.00
19_L	23_L	0.700	1.00
20_A	23_L	0.699	1.00
115_L	119_L	0.699	1.00
109_G	116_L	0.692	1.00
120_G	123_W	0.691	1.00
97_L	101_L	0.690	1.00
114_L	121_F	0.684	1.00
64_V	96_A	0.673	1.00
53_L	57_L	0.667	1.00
12_L	16_L	0.660	1.00
71_G	84_V	0.658	1.00
112_L	116_L	0.657	1.00
117_L	121_F	0.649	1.00
120_G	133_L	0.643	1.00
113_S	120_G	0.638	1.00
83_V	96_A	0.632	1.00
28_L	31_L	0.625	1.00
85_D	88_G	0.617	1.00
111_L	120_G	0.615	1.00
45_G	48_A	0.612	1.00
91_L	95_R	0.612	1.00
66_F	69_L	0.605	1.00
21_V	28_L	0.604	1.00
113_S	118_G	0.603	1.00
22_L	26_A	0.602	1.00
9_L	12_L	0.602	1.00
26_A	30_G	0.600	1.00
69_L	93_F	0.599	1.00
125_L	132_R	0.597	1.00
60_L	63_F	0.592	1.00
75_G	79_L	0.590	1.00
25_L	29_L	0.586	1.00
119_L	123_W	0.585	1.00
118_G	121_F	0.585	1.00
115_L	118_G	0.584	1.00
84_V	88_G	0.583	1.00
4_F	125_L	0.581	1.00
90_P	94_G	0.580	1.00
100_N	110_Y	0.576	1.00
46_L	50_L	0.571	1.00
45_G	49_L	0.571	1.00
86_D	129_R	0.567	1.00
15_L	18_L	0.566	1.00
41_L	44_A	0.564	1.00
50_L	53_L	0.563	1.00
100_N	103_R	0.562	1.00
8_L	12_L	0.559	1.00
38_L	41_L	0.558	1.00
119_L	122_L	0.557	1.00
22_L	25_L	0.556	1.00
58_V	66_F	0.554	1.00
65_L	74_P	0.549	1.00
65_L	68_S	0.548	1.00
43_L	47_L	0.540	1.00
17_I	21_V	0.538	1.00
62_Y	65_L	0.536	1.00
48_A	51_L	0.532	1.00
6_R	81_L	0.532	1.00
16_L	19_L	0.531	1.00
42_A	45_G	0.529	1.00
11_F	103_R	0.523	1.00
126_F	129_R	0.514	1.00
124_A	130_R	0.511	1.00
36_L	39_G	0.510	1.00
72_Q	82_R	0.503	1.00
62_Y	74_P	0.502	1.00
110_Y	116_L	0.502	1.00
49_L	52_L	0.501	1.00
25_L	28_L	0.500	1.00

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
3j8eG	3	0.8849	1.8	0.922	Contact Map
3ixzB	1	0.2806	1.7	0.923	Contact Map
2zxeB	1	0.295	1.6	0.925	Contact Map
4u15A	2	0.3237	1.4	0.927	Contact Map
2lx0A	1	0.0791	1.4	0.928	Contact Map
1v54I	1	0.3813	1.3	0.929	Contact Map
1ji6A	1	0.3525	1.2	0.929	Contact Map
2mofA	1	0.3022	1.1	0.931	Contact Map
2p5qA	3	0.4173	1	0.933	Contact Map
4c7rA	3	0.8273	1	0.933	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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