PINR - ECOLI - GREMLIN Contacts

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PINR - Putative DNA-invertase from lambdoid prophage Rac

UniProt:	P0ADI0	Sequences: MSRIFAYCRISTLDQTTENQRREIESAGFKIKPQQIIEEHISGSAATSERPGFNRLLARLKCGDQLIVTKLDRLGCNAMDIRKTVEQLTETGIRVHCLALGGIDLTSPTGKMMMQVISAVAEFERDLLLERTHSGIVRARGAGKRFGRPPVLNEEQKQVVFERIKSGVSISAIAREFKTSRQTILRAKAKLQTPDI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13372
Length:	196 (177)
Sequences:	9691 (7193)
Seq/√Len:	540.7

ECOLI - PINR PINQ PINE YAGL YBCK
BACSU - YOKA CISA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_G	55_R	3.214	1.00
37_I	59_R	2.973	1.00
163_R	176_E	2.722	1.00
56_L	66_L	2.554	1.00
39_E	52_G	2.504	1.00
159_V	180_S	2.420	1.00
8_C	21_R	2.302	1.00
21_R	25_E	2.223	1.00
6_A	24_I	2.158	1.00
111_K	126_D	2.152	1.00
159_V	163_R	2.124	1.00
124_E	131_R	2.105	1.00
21_R	38_E	1.993	1.00
44_S	125_R	1.955	1.00
138_R	142_A	1.948	1.00
168_V	176_E	1.932	1.00
79_M	86_E	1.896	1.00
163_R	168_V	1.862	1.00
171_S	175_R	1.843	1.00
139_A	144_K	1.835	1.00
78_A	115_Q	1.799	1.00
22_R	26_S	1.789	1.00
21_R	36_I	1.748	1.00
176_E	180_S	1.732	1.00
115_Q	119_A	1.729	1.00
129_L	133_H	1.704	1.00
112_M	123_F	1.683	1.00
79_M	83_K	1.661	1.00
82_R	115_Q	1.654	1.00
81_I	118_S	1.631	1.00
88_L	93_I	1.630	1.00
122_E	126_D	1.616	1.00
168_V	172_A	1.591	1.00
164_I	173_I	1.569	1.00
87_Q	91_T	1.558	1.00
179_T	184_I	1.554	1.00
89_T	111_K	1.547	1.00
111_K	122_E	1.518	1.00
85_V	114_M	1.512	1.00
5_F	59_R	1.496	1.00
107_S	110_G	1.481	1.00
97_C	101_G	1.445	1.00
60_L	66_L	1.434	1.00
53_F	84_T	1.404	1.00
125_R	128_L	1.397	1.00
60_L	93_I	1.393	1.00
6_A	36_I	1.390	1.00
5_F	56_L	1.356	1.00
35_Q	55_R	1.355	1.00
169_S	172_A	1.346	1.00
112_M	119_A	1.338	1.00
72_D	121_A	1.323	1.00
132_T	136_I	1.318	1.00
49_E	54_N	1.317	1.00
125_R	129_L	1.299	1.00
75_G	81_I	1.296	1.00
137_V	141_G	1.281	1.00
68_V	97_C	1.277	1.00
78_A	82_R	1.255	1.00
68_V	95_V	1.240	1.00
12_T	15_Q	1.233	1.00
174_A	184_I	1.231	1.00
161_F	165_K	1.229	1.00
65_Q	96_H	1.218	1.00
25_E	36_I	1.211	1.00
159_V	176_E	1.207	1.00
163_R	173_I	1.191	1.00
138_R	141_G	1.184	1.00
171_S	181_R	1.183	1.00
78_A	118_S	1.158	1.00
160_V	173_I	1.146	1.00
162_E	166_S	1.137	1.00
22_R	138_R	1.131	1.00
35_Q	59_R	1.118	1.00
164_I	170_I	1.115	1.00
55_R	59_R	1.105	1.00
86_E	90_E	1.098	1.00
28_G	33_P	1.089	1.00
41_I	47_T	1.076	1.00
135_G	139_A	1.073	1.00
41_I	51_P	1.068	1.00
85_V	95_V	1.058	1.00
69_T	134_S	1.057	1.00
159_V	162_E	1.051	1.00
6_A	33_P	1.050	1.00
124_E	128_L	1.047	1.00
25_E	29_F	1.043	1.00
10_I	40_H	1.037	1.00
136_I	146_F	1.031	1.00
179_T	183_T	1.029	1.00
170_I	185_L	1.027	1.00
23_E	69_T	1.026	1.00
53_F	56_L	1.026	1.00
19_N	69_T	1.023	1.00
37_I	52_G	1.008	1.00
181_R	185_L	1.003	1.00
8_C	36_I	1.002	1.00
8_C	17_T	1.000	1.00
24_I	67_I	0.998	1.00
94_R	106_T	0.962	1.00
136_I	140_R	0.962	1.00
65_Q	94_R	0.958	1.00
69_T	99_A	0.945	1.00
57_L	84_T	0.944	1.00
72_D	131_R	0.941	1.00
8_C	38_E	0.941	1.00
163_R	166_S	0.931	1.00
181_R	184_I	0.929	1.00
57_L	87_Q	0.927	1.00
43_G	76_C	0.925	1.00
37_I	56_L	0.923	1.00
133_H	136_I	0.923	1.00
61_K	87_Q	0.922	1.00
112_M	120_V	0.918	1.00
71_L	121_A	0.910	1.00
179_T	182_Q	0.903	1.00
68_V	74_L	0.902	1.00
160_V	184_I	0.897	1.00
74_L	84_T	0.897	1.00
158_Q	162_E	0.893	1.00
127_L	131_R	0.893	1.00
116_V	119_A	0.888	1.00
128_L	132_T	0.886	1.00
83_K	87_Q	0.882	1.00
123_F	127_L	0.881	1.00
4_I	65_Q	0.877	1.00
8_C	24_I	0.875	1.00
140_R	146_F	0.873	1.00
153_N	156_Q	0.869	1.00
43_G	75_G	0.867	1.00
23_E	26_S	0.859	1.00
172_A	175_R	0.850	1.00
108_P	130_E	0.845	1.00
62_C	92_G	0.841	1.00
27_A	67_I	0.839	1.00
176_E	179_T	0.837	1.00
17_T	38_E	0.834	1.00
137_V	140_R	0.833	1.00
80_D	83_K	0.828	1.00
56_L	60_L	0.821	1.00
77_N	86_E	0.820	1.00
33_P	36_I	0.819	1.00
66_L	88_L	0.819	1.00
172_A	176_E	0.817	1.00
19_N	134_S	0.813	1.00
129_L	132_T	0.811	1.00
23_E	134_S	0.810	1.00
123_F	126_D	0.807	1.00
19_N	138_R	0.797	1.00
112_M	116_V	0.795	1.00
96_H	104_D	0.793	1.00
116_V	120_V	0.791	1.00
5_F	37_I	0.788	1.00
173_I	177_F	0.786	1.00
161_F	164_I	0.786	1.00
61_K	91_T	0.779	1.00
18_E	22_R	0.777	1.00
78_A	122_E	0.763	1.00
170_I	174_A	0.759	1.00
10_I	15_Q	0.756	1.00
115_Q	126_D	0.754	1.00
23_E	99_A	0.754	1.00
7_Y	39_E	0.752	1.00
26_S	29_F	0.751	1.00
130_E	134_S	0.747	1.00
27_A	98_L	0.746	1.00
19_N	23_E	0.742	1.00
44_S	47_T	0.741	1.00
22_R	25_E	0.739	1.00
113_M	117_I	0.739	1.00
27_A	96_H	0.739	1.00
4_I	28_G	0.731	1.00
55_R	58_A	0.730	1.00
127_L	130_E	0.726	1.00
19_N	70_K	0.726	1.00
56_L	59_R	0.724	1.00
25_E	33_P	0.721	1.00
182_Q	185_L	0.718	1.00
162_E	165_K	0.715	1.00
44_S	129_L	0.713	1.00
17_T	40_H	0.711	1.00
84_T	88_L	0.708	1.00
120_V	123_F	0.704	1.00
168_V	173_I	0.702	1.00
38_E	52_G	0.701	1.00
53_F	74_L	0.699	1.00
70_K	99_A	0.698	1.00
148_R	151_V	0.689	1.00
71_L	97_C	0.688	1.00
24_I	28_G	0.687	1.00
128_L	135_G	0.686	1.00
136_I	139_A	0.682	1.00
158_Q	161_F	0.681	1.00
180_S	184_I	0.677	1.00
124_E	127_L	0.674	1.00
81_I	114_M	0.673	1.00
160_V	177_F	0.672	1.00
28_G	67_I	0.672	1.00
132_T	135_G	0.669	1.00
109_T	112_M	0.667	1.00
133_H	137_V	0.662	1.00
48_S	80_D	0.658	1.00
178_K	184_I	0.657	1.00
47_T	54_N	0.654	1.00
112_M	115_Q	0.654	1.00
167_G	173_I	0.643	1.00
170_I	181_R	0.637	1.00
117_I	120_V	0.634	1.00
109_T	123_F	0.633	1.00
113_M	120_V	0.629	1.00
75_G	84_T	0.628	1.00
94_R	104_D	0.628	1.00
113_M	116_V	0.627	1.00
139_A	146_F	0.624	1.00
154_E	158_Q	0.618	1.00
170_I	184_I	0.617	1.00
87_Q	90_E	0.615	1.00
58_A	62_C	0.608	1.00
71_L	114_M	0.605	1.00
67_I	98_L	0.602	1.00
83_K	86_E	0.602	1.00
70_K	127_L	0.600	1.00
47_T	53_F	0.598	1.00
16_T	40_H	0.590	1.00
151_V	154_E	0.589	1.00
60_L	88_L	0.586	0.99
54_N	58_A	0.585	0.99
79_M	82_R	0.578	0.99
29_F	33_P	0.578	0.99
53_F	57_L	0.578	0.99
70_K	131_R	0.576	0.99
153_N	157_K	0.576	0.99
129_L	136_I	0.576	0.99
77_N	80_D	0.571	0.99
169_S	175_R	0.568	0.99
154_E	157_K	0.563	0.99
6_A	28_G	0.563	0.99
24_I	98_L	0.560	0.99
78_A	119_A	0.560	0.99
145_R	150_P	0.559	0.99
22_R	141_G	0.558	0.99
173_I	176_E	0.557	0.99
134_S	137_V	0.556	0.99
131_R	134_S	0.555	0.99
164_I	169_S	0.550	0.99
175_R	179_T	0.550	0.99
180_S	185_L	0.549	0.99
174_A	178_K	0.549	0.99
154_E	161_F	0.544	0.99
173_I	184_I	0.542	0.99
37_I	55_R	0.539	0.99
163_R	180_S	0.532	0.99
96_H	102_G	0.527	0.99
4_I	67_I	0.523	0.99
163_R	167_G	0.519	0.99
115_Q	122_E	0.519	0.99
43_G	80_D	0.515	0.99
126_D	129_L	0.513	0.99
180_S	183_T	0.511	0.99
108_P	111_K	0.510	0.99
174_A	177_F	0.510	0.99
169_S	173_I	0.507	0.99
59_R	62_C	0.506	0.99
152_L	156_Q	0.506	0.99
134_S	138_R	0.501	0.98
115_Q	118_S	0.500	0.98

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
2r0qC	3	0.9031	100	0.194	Contact Map
3uj3X	2	0.6327	100	0.196	Contact Map
1gdtA	2	0.9337	100	0.199	Contact Map
4bqqA	2	0.9286	100	0.229	Contact Map
3g13A	2	0.7449	100	0.31	Contact Map
3guvA	2	0.7041	100	0.323	Contact Map
2gm5A	4	0.6327	100	0.391	Contact Map
3lhkA	2	0.7143	100	0.435	Contact Map
3ilxA	2	0.6633	100	0.445	Contact Map
3bvpA	4	0.6378	100	0.459	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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