Q9HNJ0 - HALSA - GREMLIN Contacts

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Q9HNJ0 - DNA polymerase bacteriophage-type

UniProt:	Q9HNJ0	Sequences: MDEPSQRDDTMDGAAVTACCTRCDALVESRSQVVNGDGPSDADVLFIGEAPGATEDDTGVPFVGRSGDVLDDELAAAGLAREDVRITNCVRCRPPDNRDPHSEELANCRSHLVAEVDSVDPAVIVTLGKVPSEHVLERSVAVTGEAGSVERVSLGGTTRDVVVCLHPAATLYDASQRPAFRETIEQAATMAGADGGQARLGDY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	203 (178)
Sequences:	3323 (2368)
Seq/√Len:	177.5

HALSA - Q9HNJ0 Q9HQC4
SULSO - Q97WF1 Q97VA2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_D	60_V	4.219	1.00
43_D	122_A	3.726	1.00
45_L	116_V	3.059	1.00
76_A	181_R	2.661	1.00
46_F	125_V	2.633	1.00
109_R	113_V	2.424	1.00
114_A	117_D	2.228	1.00
99_D	130_V	2.219	1.00
45_L	119_V	2.187	1.00
17_T	33_V	2.151	1.00
73_E	180_F	2.040	1.00
73_E	184_I	2.038	1.00
50_A	90_V	2.010	1.00
27_V	30_R	2.004	1.00
149_V	162_V	1.949	1.00
53_A	57_D	1.919	1.00
94_P	104_E	1.792	1.00
23_C	108_C	1.775	1.00
30_R	92_C	1.764	1.00
21_T	27_V	1.728	1.00
129_K	133_E	1.726	1.00
37_D	81_R	1.726	1.00
177_R	181_R	1.718	1.00
9_D	12_D	1.687	1.00
149_V	190_M	1.672	1.00
160_D	190_M	1.645	1.00
126_T	163_V	1.642	1.00
71_D	81_R	1.607	1.00
46_F	70_L	1.565	1.00
186_Q	189_T	1.558	1.00
20_C	23_C	1.533	1.00
14_A	18_A	1.527	1.00
126_T	161_V	1.517	1.00
24_D	103_E	1.509	1.00
17_T	35_N	1.498	1.00
125_V	187_A	1.461	1.00
151_R	160_D	1.455	1.00
153_S	158_T	1.453	1.00
162_V	187_A	1.453	1.00
10_T	40_S	1.443	1.00
169_A	173_D	1.439	1.00
146_A	183_T	1.438	1.00
44_V	187_A	1.433	1.00
99_D	129_K	1.430	1.00
151_R	158_T	1.427	1.00
120_D	159_R	1.423	1.00
92_C	108_C	1.422	1.00
20_C	108_C	1.410	1.00
45_L	87_T	1.404	1.00
13_G	118_S	1.400	1.00
85_R	115_E	1.392	1.00
54_T	57_D	1.370	1.00
24_D	28_E	1.360	1.00
141_A	144_G	1.332	1.00
124_I	159_R	1.330	1.00
99_D	133_E	1.330	1.00
20_C	92_C	1.324	1.00
76_A	177_R	1.300	1.00
74_L	84_V	1.299	1.00
143_T	165_L	1.288	1.00
91_R	115_E	1.287	1.00
173_D	176_Q	1.284	1.00
186_Q	190_M	1.271	1.00
46_F	74_L	1.266	1.00
16_V	114_A	1.238	1.00
116_V	124_I	1.225	1.00
54_T	58_T	1.211	1.00
170_T	180_F	1.193	1.00
152_V	161_V	1.189	1.00
132_S	163_V	1.182	1.00
123_V	162_V	1.164	1.00
105_L	134_H	1.157	1.00
87_T	115_E	1.154	1.00
77_A	188_A	1.153	1.00
80_A	83_D	1.120	1.00
127_L	164_C	1.119	1.00
149_V	186_Q	1.110	1.00
149_V	160_D	1.106	1.00
132_S	140_V	1.105	1.00
162_V	186_Q	1.100	1.00
126_T	132_S	1.086	1.00
165_L	179_A	1.071	1.00
73_E	181_R	1.061	1.00
31_S	57_D	1.060	1.00
126_T	135_V	1.052	1.00
50_A	94_P	1.050	1.00
44_V	191_A	1.048	1.00
12_D	15_A	1.036	1.00
34_V	61_P	1.035	0.99
125_V	164_C	1.035	0.99
178_P	182_E	1.028	0.99
72_D	177_R	1.026	0.99
52_G	55_E	1.025	0.99
140_V	145_E	1.024	0.99
125_V	184_I	1.021	0.99
89_C	134_H	1.021	0.99
44_V	125_V	1.018	0.99
162_V	190_M	1.016	0.99
98_R	104_E	1.011	0.99
55_E	63_V	1.002	0.99
46_F	127_L	0.999	0.99
123_V	190_M	0.997	0.99
123_V	187_A	0.997	0.99
15_A	19_C	0.993	0.99
22_R	110_S	0.992	0.99
58_T	63_V	0.968	0.99
102_S	106_A	0.949	0.99
77_A	184_I	0.942	0.99
136_L	161_V	0.942	0.99
23_C	92_C	0.940	0.99
18_A	33_V	0.940	0.99
182_E	185_E	0.937	0.99
15_A	18_A	0.936	0.99
169_A	176_Q	0.933	0.99
39_P	42_A	0.925	0.99
79_L	188_A	0.912	0.99
24_D	27_V	0.906	0.99
105_L	130_V	0.897	0.99
74_L	77_A	0.884	0.98
176_Q	179_A	0.879	0.98
21_T	28_E	0.878	0.98
113_V	117_D	0.876	0.98
169_A	172_Y	0.874	0.98
164_C	180_F	0.867	0.98
12_D	16_V	0.859	0.98
72_D	76_A	0.856	0.98
26_L	30_R	0.856	0.98
183_T	186_Q	0.853	0.98
54_T	65_R	0.852	0.98
47_I	126_T	0.851	0.98
47_I	135_V	0.850	0.98
109_R	134_H	0.849	0.98
47_I	112_L	0.849	0.98
48_G	62_F	0.847	0.98
14_A	35_N	0.846	0.98
87_T	112_L	0.845	0.98
114_A	118_S	0.838	0.98
45_L	124_I	0.836	0.98
69_V	177_R	0.826	0.98
36_G	85_R	0.825	0.97
138_R	145_E	0.822	0.97
73_E	77_A	0.816	0.97
10_T	118_S	0.815	0.97
53_A	93_R	0.803	0.97
132_S	145_E	0.799	0.97
123_V	160_D	0.796	0.97
178_P	181_R	0.790	0.97
11_M	15_A	0.787	0.97
63_V	88_N	0.784	0.97
44_V	79_L	0.784	0.97
68_D	71_D	0.782	0.97
24_D	101_H	0.776	0.96
142_V	163_V	0.770	0.96
94_P	97_N	0.768	0.96
46_F	84_V	0.768	0.96
106_A	137_E	0.760	0.96
116_V	135_V	0.756	0.96
116_V	159_R	0.756	0.96
130_V	133_E	0.754	0.96
27_V	33_V	0.752	0.96
32_Q	56_D	0.750	0.96
20_C	91_R	0.745	0.95
11_M	40_S	0.739	0.95
87_T	91_R	0.739	0.95
102_S	133_E	0.739	0.95
22_R	111_H	0.736	0.95
68_D	72_D	0.731	0.95
93_R	98_R	0.731	0.95
23_C	26_L	0.728	0.95
71_D	86_I	0.728	0.95
110_S	114_A	0.727	0.95
52_G	88_N	0.726	0.95
50_A	97_N	0.721	0.95
126_T	131_P	0.705	0.94
72_D	75_A	0.703	0.94
145_E	148_S	0.695	0.93
52_G	61_P	0.689	0.93
181_R	185_E	0.684	0.93
39_P	85_R	0.681	0.93
168_A	172_Y	0.680	0.93
73_E	177_R	0.676	0.92
77_A	181_R	0.671	0.92
69_V	170_T	0.671	0.92
18_A	32_Q	0.667	0.92
53_A	65_R	0.667	0.92
22_R	107_N	0.666	0.92
110_S	113_V	0.665	0.92
10_T	14_A	0.662	0.92
38_G	42_A	0.658	0.91
88_N	166_H	0.656	0.91
48_G	88_N	0.655	0.91
62_F	95_P	0.655	0.91
165_L	169_A	0.655	0.91
9_D	118_S	0.653	0.91
52_G	97_N	0.650	0.91
182_E	186_Q	0.650	0.91
48_G	166_H	0.645	0.91
13_G	17_T	0.643	0.91
11_M	14_A	0.641	0.90
14_A	40_S	0.640	0.90
124_I	135_V	0.639	0.90
165_L	176_Q	0.634	0.90
77_A	187_A	0.632	0.90
121_P	124_I	0.630	0.90
88_N	97_N	0.624	0.89
179_A	182_E	0.621	0.89
136_L	150_E	0.620	0.89
112_L	116_V	0.620	0.89
69_V	171_L	0.620	0.89
145_E	163_V	0.620	0.89
35_N	85_R	0.618	0.89
31_S	56_D	0.614	0.88
146_A	164_C	0.613	0.88
145_E	150_E	0.613	0.88
75_A	80_A	0.612	0.88
36_G	115_E	0.612	0.88
71_D	74_L	0.607	0.88
52_G	66_S	0.601	0.87
184_I	187_A	0.601	0.87
100_P	104_E	0.596	0.87
27_V	92_C	0.595	0.87
170_T	177_R	0.595	0.87
10_T	13_G	0.595	0.87
39_P	83_D	0.593	0.87
14_A	33_V	0.592	0.87
152_V	159_R	0.588	0.86
61_P	88_N	0.585	0.86
147_G	183_T	0.585	0.86
140_V	163_V	0.583	0.86
187_A	191_A	0.582	0.86
30_R	56_D	0.582	0.86
42_A	119_V	0.581	0.86
42_A	87_T	0.580	0.85
185_E	188_A	0.580	0.85
44_V	84_V	0.578	0.85
177_R	180_F	0.575	0.85
170_T	173_D	0.569	0.84
17_T	111_H	0.565	0.84
89_C	109_R	0.562	0.84
20_C	30_R	0.562	0.84
61_P	66_S	0.558	0.83
30_R	33_V	0.552	0.83
44_V	123_V	0.548	0.82
69_V	172_Y	0.545	0.82
60_V	63_V	0.543	0.82
140_V	148_S	0.541	0.81
56_D	63_V	0.540	0.81
109_R	137_E	0.538	0.81
89_C	105_L	0.529	0.80
95_P	99_D	0.529	0.80
97_N	104_E	0.526	0.79
49_E	93_R	0.526	0.79
49_E	88_N	0.524	0.79
50_A	100_P	0.522	0.79
33_V	92_C	0.522	0.79
103_E	107_N	0.521	0.79
86_I	97_N	0.519	0.79
73_E	170_T	0.509	0.77
89_C	112_L	0.508	0.77
129_K	141_A	0.507	0.77
69_V	181_R	0.506	0.77
85_R	119_V	0.506	0.77
113_V	152_V	0.504	0.77
34_V	55_E	0.504	0.77
52_G	169_A	0.503	0.76
153_S	159_R	0.501	0.76
103_E	106_A	0.500	0.76

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
1vk2A	1	0.9163	100	0.212	Contact Map
1ui0A	1	0.9113	100	0.22	Contact Map
2d3yA	1	0.9064	100	0.285	Contact Map
3ikbA	1	0.8867	100	0.31	Contact Map
1wywA	1	0.867	100	0.43	Contact Map
1oe4A	2	0.867	100	0.526	Contact Map
1mugA	1	0.7438	100	0.533	Contact Map
2c2qA	1	0.8374	99.9	0.603	Contact Map
2l3fA	1	0.7094	98.7	0.824	Contact Map
1yc5A	1	0.3842	56.5	0.938	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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