DUF3656 - PFAM28P - GREMLIN Contacts

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DUF3656 - Collagenase

PFAM:	PF12392	Sequences: VYRTSDPELDRALRKSLEKSPERKIPVDLEVSGRAGEPLTLTATDELEPARKRPLTEERLREQLGKLGGTPFELGELEIDLDGLFLPVSELNELRREAVEALEEARL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	107 (105)
Sequences:	12937 (10400)
Seq/√Len:	1014.9
META:	0.889

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_D	75_G	2.863	1.00
57_E	61_R	2.637	1.00
93_E	97_E	2.473	1.00
26_P	75_G	2.295	1.00
61_R	65_G	2.192	1.00
66_K	92_N	2.191	1.00
72_F	103_E	2.187	1.00
43_A	98_A	2.175	1.00
67_L	99_V	2.155	1.00
30_E	78_E	2.129	1.00
26_P	73_E	2.073	1.00
29_L	43_A	2.015	1.00
28_D	76_E	1.789	1.00
5_S	10_D	1.765	1.00
74_L	77_L	1.727	1.00
29_L	74_L	1.714	1.00
45_D	106_R	1.711	1.00
32_S	80_D	1.707	1.00
32_S	40_T	1.684	1.00
59_R	88_V	1.667	1.00
30_E	80_D	1.655	1.00
71_P	103_E	1.616	1.00
90_E	93_E	1.613	1.00
30_E	42_T	1.595	1.00
67_L	74_L	1.553	1.00
101_A	105_A	1.516	1.00
59_R	63_Q	1.511	1.00
24_K	73_E	1.463	1.00
97_E	101_A	1.453	1.00
59_R	62_E	1.395	1.00
63_Q	92_N	1.393	1.00
35_A	49_P	1.391	1.00
53_R	59_R	1.374	1.00
101_A	104_E	1.374	1.00
56_T	59_R	1.338	1.00
48_E	51_R	1.296	1.00
100_E	103_E	1.218	1.00
32_S	42_T	1.185	1.00
28_D	44_T	1.184	1.00
41_L	64_L	1.184	1.00
57_E	79_I	1.174	1.00
87_P	90_E	1.166	1.00
7_P	11_R	1.142	1.00
65_G	74_L	1.136	1.00
97_E	100_E	1.107	1.00
34_R	82_D	1.092	1.00
34_R	37_E	1.084	1.00
100_E	104_E	1.081	1.00
24_K	69_G	1.078	1.00
33_G	47_L	1.077	1.00
33_G	39_L	1.019	1.00
41_L	94_L	1.018	1.00
60_L	91_L	1.018	1.00
49_P	83_G	1.017	1.00
7_P	15_K	1.001	1.00
25_I	45_D	0.975	1.00
88_V	92_N	0.972	1.00
14_R	18_E	0.960	1.00
63_Q	66_K	0.960	1.00
58_E	62_E	0.955	1.00
39_L	47_L	0.952	1.00
60_L	79_I	0.950	1.00
3_R	6_D	0.931	1.00
52_K	55_L	0.918	1.00
15_K	18_E	0.908	1.00
47_L	84_L	0.901	1.00
29_L	41_L	0.898	1.00
12_A	16_S	0.894	1.00
63_Q	88_V	0.889	1.00
29_L	67_L	0.888	1.00
39_L	94_L	0.880	1.00
13_L	16_S	0.878	1.00
58_E	61_R	0.873	1.00
81_L	84_L	0.873	1.00
55_L	59_R	0.871	1.00
43_A	99_V	0.862	1.00
39_L	86_L	0.854	1.00
49_P	84_L	0.842	1.00
93_E	96_R	0.842	1.00
14_R	17_L	0.830	1.00
34_R	80_D	0.829	1.00
13_L	17_L	0.826	1.00
15_K	19_K	0.823	1.00
29_L	98_A	0.818	1.00
51_R	85_F	0.814	1.00
61_R	77_L	0.813	1.00
25_I	71_P	0.798	1.00
30_E	44_T	0.781	1.00
12_A	15_K	0.780	1.00
31_V	39_L	0.757	1.00
27_V	102_L	0.756	1.00
103_E	106_R	0.754	1.00
86_L	90_E	0.750	1.00
27_V	43_A	0.747	1.00
33_G	81_L	0.745	1.00
53_R	56_T	0.742	1.00
11_R	15_K	0.738	1.00
47_L	86_L	0.736	1.00
10_D	14_R	0.733	1.00
72_F	102_L	0.733	1.00
24_K	71_P	0.728	1.00
5_S	14_R	0.726	1.00
92_N	96_R	0.723	1.00
2_Y	13_L	0.720	1.00
62_E	65_G	0.707	1.00
28_D	78_E	0.704	1.00
31_V	60_L	0.679	1.00
10_D	17_L	0.663	1.00
2_Y	7_P	0.656	1.00
35_A	82_D	0.654	1.00
35_A	84_L	0.652	1.00
67_L	70_T	0.647	1.00
29_L	77_L	0.641	1.00
7_P	14_R	0.637	1.00
16_S	19_K	0.637	1.00
56_T	62_E	0.634	1.00
63_Q	91_L	0.630	1.00
60_L	81_L	0.626	1.00
59_R	85_F	0.619	1.00
70_T	99_V	0.616	1.00
90_E	97_E	0.611	1.00
98_A	102_L	0.606	1.00
72_F	99_V	0.604	1.00
46_E	75_G	0.602	1.00
9_L	12_A	0.595	1.00
50_A	54_P	0.594	1.00
64_L	91_L	0.593	1.00
43_A	102_L	0.592	1.00
98_A	101_A	0.590	1.00
27_V	67_L	0.586	1.00
85_F	88_V	0.584	1.00
32_S	37_E	0.580	1.00
25_I	106_R	0.579	1.00
30_E	40_T	0.566	1.00
7_P	13_L	0.562	1.00
37_E	40_T	0.562	1.00
27_V	72_F	0.562	1.00
65_G	77_L	0.560	1.00
2_Y	5_S	0.544	1.00
31_V	41_L	0.542	1.00
94_L	98_A	0.541	1.00
48_E	85_F	0.539	1.00
43_A	67_L	0.535	1.00
53_R	85_F	0.533	1.00
31_V	94_L	0.531	1.00
62_E	88_V	0.529	1.00
54_P	58_E	0.527	1.00
41_L	98_A	0.524	1.00
33_G	37_E	0.524	1.00
39_L	43_A	0.522	1.00
33_G	36_G	0.520	1.00
35_A	47_L	0.516	1.00
63_Q	95_R	0.516	1.00
27_V	74_L	0.515	1.00
21_P	24_K	0.512	1.00
29_L	64_L	0.508	1.00
10_D	13_L	0.504	1.00
31_V	64_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
1dc1A	2	0.7477	9.5	0.897	Contact Map
2ve7A	1	0.5981	6.2	0.905	Contact Map
1dqnA	2	0.5327	5.7	0.906	Contact Map
1szqA	2	0.9159	5.5	0.907	Contact Map
1ivzA	1	0.8598	4.6	0.911	Contact Map
3cvzA	1	0.9346	4	0.913	Contact Map
4pedA	1	0.4953	3.9	0.914	Contact Map
1m5yA	1	0.514	3.7	0.915	Contact Map
3nvtA	4	0.1495	3.6	0.915	Contact Map
1k8kE	1	0.7944	3	0.918	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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