DUF2956 - PFAM28P - GREMLIN Contacts

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DUF2956 - Protein of unknown function (DUF2956)

PFAM:	PF11169	Sequences: SPETQDEAMKIAKATQKPGQTKEQTKLIAQGIQKGIAQYKKQQKAKARELDKKRKKAQKAKQQQQSQEEDEEEVEEKIVYRQHWLPWLLLVLSWLGFAAYLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (99)
Sequences:	665 (510)
Seq/√Len:	51.3
META:	0.68

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_Q	37_A	5.032	1.00
93_S	97_F	4.670	1.00
50_L	54_R	2.808	1.00
50_L	53_K	2.551	1.00
47_A	50_L	2.532	1.00
54_R	58_Q	2.465	1.00
38_Q	42_Q	2.390	1.00
78_I	81_R	2.171	1.00
13_K	16_Q	1.977	1.00
45_A	49_E	1.775	0.99
95_L	101_L	1.772	0.99
88_L	91_V	1.628	0.98
54_R	57_A	1.597	0.98
90_L	94_W	1.570	0.98
38_Q	56_K	1.533	0.97
65_Q	70_D	1.516	0.97
38_Q	45_A	1.507	0.97
37_A	53_K	1.483	0.97
3_E	57_A	1.479	0.97
43_Q	47_A	1.473	0.96
36_I	40_K	1.459	0.96
36_I	39_Y	1.458	0.96
50_L	57_A	1.417	0.96
14_A	44_K	1.397	0.95
30_Q	43_Q	1.365	0.95
37_A	50_L	1.342	0.94
98_A	101_L	1.331	0.94
9_M	15_T	1.313	0.93
2_P	5_Q	1.301	0.93
17_K	30_Q	1.277	0.92
53_K	57_A	1.276	0.92
12_A	25_T	1.259	0.92
24_Q	27_L	1.253	0.92
63_Q	72_E	1.194	0.90
3_E	44_K	1.184	0.89
43_Q	50_L	1.178	0.89
1_S	4_T	1.166	0.88
78_I	83_H	1.151	0.88
11_I	14_A	1.148	0.88
15_T	41_K	1.146	0.87
65_Q	68_E	1.143	0.87
62_Q	76_E	1.128	0.87
79_V	83_H	1.112	0.86
27_L	36_I	1.104	0.85
61_K	66_S	1.096	0.85
51_D	54_R	1.096	0.85
68_E	72_E	1.053	0.83
42_Q	55_K	1.012	0.80
7_E	56_K	1.009	0.80
5_Q	42_Q	1.009	0.80
49_E	53_K	0.998	0.79
21_T	24_Q	0.990	0.79
19_G	45_A	0.983	0.78
78_I	82_Q	0.961	0.76
89_L	94_W	0.957	0.76
3_E	46_K	0.953	0.76
84_W	88_L	0.951	0.76
45_A	99_A	0.928	0.74
51_D	97_F	0.918	0.73
19_G	99_A	0.911	0.72
47_A	56_K	0.911	0.72
11_I	38_Q	0.902	0.72
79_V	82_Q	0.885	0.70
33_Q	50_L	0.856	0.68
3_E	45_A	0.848	0.67
26_K	41_K	0.847	0.67
14_A	39_Y	0.846	0.67
52_K	55_K	0.845	0.67
68_E	73_E	0.801	0.63
4_T	44_K	0.800	0.62
90_L	93_S	0.800	0.62
13_K	19_G	0.789	0.61
84_W	97_F	0.780	0.60
66_S	74_V	0.778	0.60
67_Q	74_V	0.769	0.59
83_H	88_L	0.769	0.59
3_E	38_Q	0.758	0.58
15_T	34_K	0.758	0.58
33_Q	56_K	0.757	0.58
62_Q	92_L	0.753	0.58
25_T	31_G	0.749	0.57
66_S	69_E	0.741	0.57
5_Q	50_L	0.738	0.56
67_Q	88_L	0.735	0.56
64_Q	75_E	0.731	0.56
83_H	86_P	0.726	0.55
80_Y	83_H	0.720	0.54
66_S	75_E	0.711	0.53
77_K	83_H	0.707	0.53
64_Q	72_E	0.705	0.53
44_K	51_D	0.703	0.53
69_E	74_V	0.698	0.52
10_K	101_L	0.694	0.52
65_Q	72_E	0.690	0.51
42_Q	58_Q	0.690	0.51
26_K	71_E	0.689	0.51
16_Q	23_E	0.688	0.51
8_A	12_A	0.686	0.51
73_E	76_E	0.682	0.50
14_A	43_Q	0.666	0.49
96_G	100_Y	0.659	0.48
6_D	14_A	0.652	0.47
21_T	85_L	0.651	0.47
7_E	45_A	0.651	0.47
58_Q	96_G	0.649	0.47
2_P	49_E	0.648	0.47
23_E	28_I	0.647	0.47
37_A	55_K	0.642	0.46
68_E	71_E	0.640	0.46
22_K	36_I	0.639	0.46
94_W	97_F	0.638	0.46
6_D	78_I	0.638	0.46
37_A	52_K	0.637	0.46
13_K	95_L	0.628	0.45
66_S	101_L	0.624	0.44
63_Q	69_E	0.608	0.43
6_D	63_Q	0.604	0.42
17_K	53_K	0.597	0.42
68_E	78_I	0.589	0.41
17_K	41_K	0.588	0.41
17_K	55_K	0.587	0.41
27_L	40_K	0.585	0.41
2_P	38_Q	0.584	0.40
13_K	23_E	0.578	0.40
91_V	95_L	0.572	0.39
26_K	56_K	0.570	0.39
89_L	93_S	0.560	0.38
10_K	57_A	0.559	0.38
31_G	46_K	0.558	0.38
33_Q	58_Q	0.558	0.38
41_K	93_S	0.555	0.38
66_S	70_D	0.553	0.37
96_G	99_A	0.541	0.36
43_Q	101_L	0.540	0.36
97_F	101_L	0.535	0.36
67_Q	99_A	0.533	0.35
68_E	88_L	0.533	0.35
71_E	82_Q	0.528	0.35
15_T	37_A	0.523	0.34
14_A	52_K	0.519	0.34
4_T	38_Q	0.515	0.34
64_Q	67_Q	0.515	0.34
66_S	78_I	0.506	0.33
27_L	39_Y	0.504	0.33
37_A	44_K	0.503	0.33
9_M	18_P	0.503	0.33
72_E	75_E	0.501	0.32
5_Q	40_K	0.500	0.32

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
4zw9A	1	0.2549	20.1	0.931	Contact Map
4j05A	3	0.1765	12.7	0.937	Contact Map
1pw4A	1	0.3824	10.4	0.939	Contact Map
4l6vi	1	0.2647	10.3	0.939	Contact Map
1jb0I	1	0.2647	8.9	0.941	Contact Map
4twkA	2	0.2843	7.2	0.943	Contact Map
2wscI	1	0.2059	6.8	0.944	Contact Map
2onkC	2	0.2059	6.3	0.945	Contact Map
4binA	1	0.402	6.3	0.945	Contact Map
3wu2L	1	0.3333	6	0.945	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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