Helicase_C_3 - PFAM28P - GREMLIN Contacts

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Helicase_C_3 - Helicase conserved C-terminal domain

PFAM:	PF13625	Sequences: LIVQSDLTILLEVDHPLAPEARDALARFAELESSPEHAHTYRLTPLSLWRALAAGLTAEEILAFLERYSRYPVPQNVLYLIRDWARRYGRLRLGRGAGLLLRSDDPALLAELLADKKLAPLLLRRLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (121)
Sequences:	10009 (6199)
Seq/√Len:	563.6
META:	0.856

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_E	78_L	3.230	1.00
32_E	42_R	3.122	1.00
78_L	82_R	2.888	1.00
62_L	82_R	2.848	1.00
62_L	78_L	2.705	1.00
94_G	102_R	2.678	1.00
103_S	109_L	2.674	1.00
30_E	44_T	2.413	1.00
27_R	56_L	2.369	1.00
24_A	64_F	2.234	1.00
75_Q	79_Y	2.137	1.00
9_I	43_L	2.076	1.00
57_T	60_E	2.049	1.00
61_I	85_A	1.988	1.00
63_A	67_R	1.957	1.00
58_A	85_A	1.901	1.00
94_G	100_L	1.819	1.00
56_L	60_E	1.770	1.00
30_E	50_R	1.745	1.00
59_E	82_R	1.676	1.00
7_L	80_L	1.591	1.00
80_L	84_W	1.572	1.00
64_F	68_Y	1.529	1.00
110_A	114_A	1.472	1.00
24_A	27_R	1.457	1.00
21_A	68_Y	1.452	1.00
33_S	40_T	1.448	1.00
111_E	115_D	1.446	1.00
90_R	104_D	1.412	1.00
49_W	53_A	1.375	1.00
28_F	61_I	1.353	1.00
11_L	17_L	1.340	1.00
58_A	81_I	1.332	1.00
24_A	56_L	1.303	1.00
110_A	113_L	1.303	1.00
3_V	9_I	1.301	1.00
106_P	110_A	1.296	1.00
62_L	81_I	1.289	1.00
44_T	47_S	1.286	1.00
52_L	85_A	1.278	1.00
48_L	84_W	1.253	1.00
48_L	61_I	1.223	1.00
79_Y	83_D	1.212	1.00
79_Y	82_R	1.202	1.00
62_L	66_E	1.191	1.00
43_L	77_V	1.184	1.00
63_A	66_E	1.176	1.00
113_L	122_L	1.172	1.00
75_Q	78_L	1.158	1.00
60_E	63_A	1.135	1.00
52_L	88_Y	1.120	1.00
26_A	31_L	1.109	1.00
59_E	63_A	1.090	1.00
103_S	112_L	1.081	1.00
76_N	80_L	1.061	1.00
17_L	20_E	1.047	1.00
48_L	85_A	1.033	1.00
92_R	102_R	1.020	1.00
17_L	67_R	1.014	1.00
31_L	39_H	1.000	1.00
21_A	64_F	0.998	1.00
53_A	88_Y	0.992	1.00
51_A	56_L	0.983	1.00
4_Q	10_L	0.977	1.00
7_L	77_V	0.972	1.00
56_L	61_I	0.970	1.00
7_L	76_N	0.966	1.00
47_S	51_A	0.956	1.00
29_A	41_Y	0.950	1.00
91_L	112_L	0.934	1.00
27_R	64_F	0.933	1.00
69_S	73_V	0.933	1.00
1_L	68_Y	0.929	1.00
48_L	52_L	0.928	1.00
26_A	41_Y	0.911	1.00
80_L	83_D	0.893	1.00
24_A	67_R	0.884	1.00
113_L	119_A	0.882	1.00
17_L	68_Y	0.877	1.00
28_F	51_A	0.876	1.00
118_L	123_L	0.867	1.00
27_R	54_A	0.867	1.00
103_S	108_L	0.859	1.00
43_L	65_L	0.858	1.00
24_A	68_Y	0.835	1.00
91_L	103_S	0.828	1.00
30_E	42_R	0.826	1.00
34_S	39_H	0.820	1.00
73_V	78_L	0.817	1.00
83_D	86_R	0.814	1.00
87_R	111_E	0.814	1.00
12_E	70_R	0.809	1.00
45_P	84_W	0.793	1.00
92_R	104_D	0.788	1.00
56_L	64_F	0.782	1.00
51_A	61_I	0.781	1.00
108_L	111_E	0.780	1.00
28_F	43_L	0.775	1.00
105_D	108_L	0.775	1.00
107_A	111_E	0.771	1.00
10_L	40_T	0.767	1.00
10_L	38_A	0.766	1.00
4_Q	8_T	0.764	1.00
112_L	115_D	0.758	1.00
93_L	101_L	0.749	1.00
8_T	32_E	0.745	1.00
22_R	26_A	0.740	1.00
45_P	87_R	0.739	1.00
18_A	21_A	0.732	1.00
58_A	62_L	0.732	1.00
98_G	102_R	0.725	1.00
76_N	79_Y	0.722	1.00
9_I	25_L	0.722	1.00
30_E	46_L	0.721	1.00
6_D	42_R	0.711	1.00
7_L	84_W	0.706	1.00
59_E	62_L	0.697	1.00
107_A	110_A	0.690	1.00
87_R	90_R	0.678	1.00
111_E	114_A	0.676	1.00
49_W	88_Y	0.674	1.00
22_R	39_H	0.674	1.00
1_L	64_F	0.671	1.00
12_E	89_G	0.667	1.00
118_L	122_L	0.665	1.00
109_L	113_L	0.665	1.00
5_S	76_N	0.650	1.00
12_E	38_A	0.649	1.00
8_T	42_R	0.648	1.00
66_E	72_P	0.647	1.00
90_R	105_D	0.646	1.00
115_D	119_A	0.640	1.00
77_V	80_L	0.637	1.00
3_V	73_V	0.635	1.00
24_A	28_F	0.627	1.00
82_R	86_R	0.626	1.00
25_L	64_F	0.618	1.00
62_L	73_V	0.613	1.00
3_V	69_S	0.610	1.00
9_I	21_A	0.604	1.00
13_V	36_E	0.602	1.00
72_P	78_L	0.601	1.00
28_F	56_L	0.599	1.00
31_L	34_S	0.591	1.00
8_T	40_T	0.586	1.00
52_L	58_A	0.582	1.00
58_A	82_R	0.581	1.00
49_W	52_L	0.577	1.00
19_P	23_D	0.575	1.00
81_I	85_A	0.574	0.99
18_A	23_D	0.573	0.99
115_D	118_L	0.572	0.99
30_E	47_S	0.568	0.99
90_R	108_L	0.565	0.99
1_L	9_I	0.565	0.99
46_L	50_R	0.565	0.99
11_L	22_R	0.564	0.99
28_F	64_F	0.564	0.99
32_E	40_T	0.559	0.99
72_P	75_Q	0.557	0.99
64_F	67_R	0.556	0.99
86_R	104_D	0.554	0.99
117_K	120_P	0.552	0.99
28_F	65_L	0.547	0.99
71_Y	74_P	0.539	0.99
61_I	64_F	0.537	0.99
112_L	118_L	0.530	0.99
57_T	61_I	0.530	0.99
75_Q	80_L	0.524	0.99
88_Y	91_L	0.522	0.99
20_E	24_A	0.515	0.99
50_R	54_A	0.515	0.99
13_V	17_L	0.513	0.99
105_D	109_L	0.512	0.99
13_V	37_H	0.507	0.99
24_A	61_I	0.505	0.99
116_K	119_A	0.504	0.99
107_A	114_A	0.504	0.99
66_E	73_V	0.503	0.99
85_A	88_Y	0.503	0.99
76_N	84_W	0.500	0.99
74_P	77_V	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
3domA	1	0.4252	32.9	0.883	Contact Map
2nn6H	1	0.6614	21.3	0.893	Contact Map
3dgpA	1	0.2913	18.4	0.896	Contact Map
3psfA	1	0.8425	16.3	0.898	Contact Map
3psiA	1	0.748	16.2	0.898	Contact Map
3a1yG	1	0.7165	15.1	0.9	Contact Map
4dn7A	2	0.6457	13.6	0.902	Contact Map
3dgpB	1	0.2677	13.6	0.902	Contact Map
4ifdH	1	0.6457	11.4	0.905	Contact Map
3vfdA	1	0.6772	8.1	0.911	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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