DUF1738 - PFAM28P - GREMLIN Contacts

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DUF1738 - Domain of unknown function (DUF1738)

PFAM:	PF08401	Sequences: DVYQEVTDRIIAALEAGVAPWRKPWSAAGGLGLPRNAVTGKPYRGINVLLLWAAAMERGYSSPRWLTFKQAQELGGQVRKGEKGTPVVFWKRLEKEEEDDDGGEPVDDEEGGEEEERKRIPFLRYYTVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (120)
Sequences:	11229 (7752)
Seq/√Len:	707.7
META:	0.907

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_G	127_T	5.145	1.00
66_L	71_A	4.475	1.00
4_Q	8_D	3.123	1.00
68_F	72_Q	2.895	1.00
68_F	77_Q	2.449	1.00
23_K	27_A	2.258	1.00
37_A	66_L	2.121	1.00
92_R	121_P	2.096	1.00
65_W	85_T	2.051	1.00
12_A	16_A	1.992	1.00
34_P	48_V	1.991	1.00
79_R	82_E	1.971	1.00
54_A	85_T	1.867	1.00
54_A	58_R	1.854	1.00
69_K	72_Q	1.853	1.00
13_A	16_A	1.851	1.00
35_R	64_R	1.732	1.00
71_A	76_G	1.704	1.00
72_Q	77_Q	1.622	1.00
48_V	52_W	1.617	1.00
8_D	12_A	1.576	1.00
86_P	127_T	1.541	1.00
93_L	120_I	1.537	1.00
2_V	5_E	1.530	1.00
86_P	125_Y	1.529	1.00
41_K	44_R	1.493	1.00
55_A	65_W	1.490	1.00
38_V	73_E	1.457	1.00
69_K	73_E	1.429	1.00
71_A	78_V	1.422	1.00
36_N	41_K	1.372	1.00
38_V	74_L	1.356	1.00
5_E	9_R	1.349	1.00
9_R	57_E	1.333	1.00
91_K	122_F	1.312	1.00
37_A	41_K	1.288	1.00
66_L	70_Q	1.246	1.00
14_L	19_A	1.234	1.00
12_A	15_E	1.228	1.00
17_G	20_P	1.222	1.00
36_N	39_T	1.221	1.00
95_K	120_I	1.210	1.00
93_L	122_F	1.207	1.00
78_V	82_E	1.196	1.00
94_E	118_K	1.195	1.00
35_R	40_G	1.190	1.00
37_A	64_R	1.183	1.00
9_R	54_A	1.179	1.00
90_W	121_P	1.168	1.00
9_R	13_A	1.168	1.00
97_E	100_D	1.163	1.00
54_A	65_W	1.141	1.00
19_A	22_R	1.135	1.00
46_I	50_L	1.131	1.00
87_V	128_V	1.111	1.00
46_I	88_V	1.083	1.00
5_E	8_D	1.081	1.00
3_Y	88_V	1.081	1.00
9_R	12_A	1.055	1.00
33_L	48_V	1.040	1.00
99_D	102_G	1.026	1.00
94_E	116_E	1.021	1.00
5_E	86_P	1.015	1.00
60_Y	65_W	1.006	1.00
35_R	42_P	0.990	1.00
68_F	78_V	0.974	1.00
87_V	126_Y	0.973	1.00
70_Q	73_E	0.965	1.00
5_E	125_Y	0.963	1.00
11_I	15_E	0.942	1.00
33_L	52_W	0.926	1.00
12_A	57_E	0.913	1.00
13_A	53_A	0.912	1.00
92_R	118_K	0.908	1.00
34_P	65_W	0.907	1.00
104_E	112_G	0.870	1.00
118_K	121_P	0.849	1.00
88_V	123_L	0.847	1.00
60_Y	82_E	0.845	1.00
35_R	63_P	0.828	1.00
34_P	52_W	0.827	1.00
33_L	42_P	0.825	1.00
23_K	26_S	0.814	1.00
2_V	88_V	0.808	1.00
82_E	85_T	0.808	1.00
95_K	117_R	0.800	1.00
13_A	20_P	0.799	1.00
68_F	84_G	0.799	1.00
66_L	76_G	0.796	1.00
95_K	98_E	0.785	1.00
50_L	54_A	0.775	1.00
50_L	86_P	0.773	1.00
99_D	103_G	0.769	1.00
13_A	18_V	0.765	1.00
34_P	51_L	0.760	1.00
36_N	70_Q	0.760	1.00
49_L	52_W	0.756	1.00
3_Y	7_T	0.753	1.00
97_E	117_R	0.749	1.00
89_F	122_F	0.747	1.00
39_T	70_Q	0.745	1.00
6_V	50_L	0.736	1.00
96_E	116_E	0.734	1.00
38_V	66_L	0.732	1.00
7_T	10_I	0.729	1.00
68_F	80_K	0.726	1.00
92_R	95_K	0.725	1.00
36_N	66_L	0.718	1.00
7_T	11_I	0.713	1.00
35_R	41_K	0.711	1.00
40_G	64_R	0.703	1.00
10_I	14_L	0.695	1.00
68_F	129_F	0.691	1.00
95_K	99_D	0.691	1.00
89_F	92_R	0.688	1.00
37_A	71_A	0.685	1.00
14_L	23_K	0.684	1.00
90_W	123_L	0.677	1.00
67_T	126_Y	0.673	1.00
21_W	24_P	0.663	1.00
84_G	129_F	0.658	1.00
99_D	115_E	0.655	1.00
50_L	85_T	0.652	1.00
113_E	116_E	0.651	1.00
54_A	60_Y	0.649	1.00
37_A	74_L	0.644	1.00
98_E	102_G	0.641	1.00
112_G	115_E	0.636	1.00
96_E	99_D	0.633	1.00
96_E	114_E	0.629	1.00
60_Y	85_T	0.625	1.00
102_G	112_G	0.615	1.00
4_Q	7_T	0.612	1.00
81_G	129_F	0.611	1.00
53_A	56_M	0.605	1.00
44_R	90_W	0.604	1.00
14_L	17_G	0.603	1.00
78_V	129_F	0.598	1.00
112_G	116_E	0.589	1.00
115_E	118_K	0.585	1.00
9_R	85_T	0.584	1.00
95_K	100_D	0.580	1.00
68_F	81_G	0.577	1.00
100_D	104_E	0.568	1.00
20_P	71_A	0.568	1.00
13_A	19_A	0.566	1.00
78_V	81_G	0.565	1.00
10_I	13_A	0.560	1.00
96_E	100_D	0.560	1.00
92_R	122_F	0.560	1.00
50_L	53_A	0.558	1.00
91_K	124_R	0.554	1.00
98_E	101_D	0.552	1.00
58_R	82_E	0.551	1.00
35_R	38_V	0.550	1.00
28_A	32_G	0.550	1.00
3_Y	6_V	0.544	1.00
70_Q	74_L	0.542	1.00
114_E	117_R	0.539	1.00
89_F	126_Y	0.537	1.00
2_V	125_Y	0.537	1.00
66_L	74_L	0.536	1.00
27_A	31_L	0.534	1.00
14_L	18_V	0.528	1.00
32_G	63_P	0.525	1.00
101_D	113_E	0.523	1.00
67_T	90_W	0.520	1.00
53_A	57_E	0.519	1.00
80_K	129_F	0.516	1.00
36_N	45_G	0.515	1.00
97_E	101_D	0.514	1.00
13_A	22_R	0.513	1.00
29_G	32_G	0.511	0.99
51_L	87_V	0.509	0.99
103_G	112_G	0.508	0.99
99_D	112_G	0.505	0.99
68_F	71_A	0.504	0.99
80_K	83_K	0.503	0.99
55_A	58_R	0.500	0.99
122_F	126_Y	0.500	0.99

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
5aj3G	1	0.3333	6.6	0.923	Contact Map
1lvmA	2	0.3411	4.6	0.929	Contact Map
4hw4A	2	0.3023	2.8	0.936	Contact Map
3p0jA	1	0.3256	2.6	0.937	Contact Map
3l32A	2	0.3023	2.6	0.937	Contact Map
3sp7A	1	0.2791	2.6	0.937	Contact Map
3hm6X	1	0.2868	2	0.941	Contact Map
4k5aA	1	0.2946	1.9	0.942	Contact Map
4kiyG	1	0.2946	1.8	0.942	Contact Map
3hgtA	2	0.3023	1.8	0.942	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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