PINQ - ECOLI - GREMLIN Contacts

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PINQ - Putative DNA-invertase from lambdoid prophage Qin

UniProt:	P77170	Sequences: MSQIFAYCRISTLDQTTENQRREIESAGFKIKPQQIIEEHISGSAATSERPGFNRLLARLKCGDQLIVTKLDRLGCNAMDIRKTVEQLTETGIRVHCLALGGIDLTSPTGKMMMQVISAVAEFERDLLLERTHSGIVRARGAGKRFGRPPVLNEEQKQAVFERIKSGVSISAIAREFKTSRQTILRAKAKLQTPDI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13824
Length:	196 (179)
Sequences:	9801 (7382)
Seq/√Len:	551.7

ECOLI - PINQ PINR 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	3.201	1.00
37_I	59_R	3.080	1.00
159_A	180_S	2.801	1.00
163_R	176_E	2.725	1.00
39_E	52_G	2.609	1.00
56_L	66_L	2.595	1.00
8_C	21_R	2.343	1.00
124_E	131_R	2.304	1.00
21_R	25_E	2.289	1.00
111_K	126_D	2.182	1.00
6_A	24_I	2.166	1.00
159_A	163_R	2.128	1.00
176_E	180_S	2.022	1.00
21_R	38_E	1.991	1.00
44_S	125_R	1.979	1.00
138_R	142_A	1.901	1.00
168_V	176_E	1.876	1.00
163_R	168_V	1.875	1.00
171_S	175_R	1.864	1.00
22_R	26_S	1.846	1.00
78_A	115_Q	1.831	1.00
139_A	144_K	1.824	1.00
79_M	86_E	1.813	1.00
112_M	123_F	1.780	1.00
115_Q	119_A	1.731	1.00
21_R	36_I	1.724	1.00
81_I	118_S	1.653	1.00
88_L	93_I	1.648	1.00
122_E	126_D	1.645	1.00
129_L	133_H	1.626	1.00
82_R	115_Q	1.605	1.00
79_M	83_K	1.602	1.00
111_K	122_E	1.576	1.00
164_I	173_I	1.565	1.00
89_T	111_K	1.553	1.00
168_V	172_A	1.509	1.00
87_Q	91_T	1.496	1.00
5_F	59_R	1.481	1.00
125_R	128_L	1.470	1.00
97_C	101_G	1.469	1.00
112_M	119_A	1.454	1.00
60_L	66_L	1.445	1.00
53_F	84_T	1.432	1.00
85_V	114_M	1.429	1.00
5_F	56_L	1.420	1.00
35_Q	55_R	1.408	1.00
107_S	110_G	1.407	1.00
6_A	36_I	1.406	1.00
60_L	93_I	1.395	1.00
132_T	136_I	1.378	1.00
72_D	121_A	1.366	1.00
184_I	187_A	1.338	1.00
12_T	15_Q	1.317	1.00
49_E	54_N	1.305	1.00
125_R	129_L	1.300	1.00
75_G	81_I	1.296	1.00
162_E	166_S	1.282	1.00
169_S	172_A	1.276	1.00
68_V	95_V	1.275	1.00
68_V	97_C	1.268	1.00
137_V	141_G	1.268	1.00
28_G	33_P	1.245	1.00
163_R	173_I	1.244	1.00
25_E	36_I	1.242	1.00
78_A	82_R	1.234	1.00
138_R	141_G	1.222	1.00
160_V	173_I	1.172	1.00
157_K	161_F	1.166	1.00
55_R	59_R	1.151	1.00
78_A	118_S	1.140	1.00
86_E	90_E	1.139	1.00
65_Q	96_H	1.139	1.00
151_V	154_E	1.119	1.00
19_N	69_T	1.117	1.00
22_R	138_R	1.101	1.00
124_E	128_L	1.097	1.00
171_S	181_R	1.092	1.00
41_I	51_P	1.092	1.00
69_T	134_S	1.085	1.00
159_A	176_E	1.085	1.00
6_A	33_P	1.083	1.00
135_G	139_A	1.080	1.00
35_Q	59_R	1.073	1.00
53_F	56_L	1.067	1.00
161_F	165_K	1.055	1.00
41_I	47_T	1.048	1.00
159_A	162_E	1.041	1.00
8_C	36_I	1.037	1.00
85_V	95_V	1.033	1.00
8_C	17_T	1.023	1.00
176_E	179_T	1.023	1.00
136_I	146_F	1.019	1.00
72_D	131_R	1.001	1.00
25_E	29_F	0.994	1.00
174_A	184_I	0.982	1.00
37_I	52_G	0.982	1.00
164_I	170_I	0.974	1.00
65_Q	94_R	0.972	1.00
37_I	56_L	0.963	1.00
23_E	69_T	0.950	1.00
71_L	121_A	0.944	1.00
57_L	84_T	0.942	1.00
136_I	140_R	0.935	1.00
69_T	99_A	0.920	1.00
24_I	67_I	0.916	1.00
112_M	120_V	0.915	1.00
156_Q	159_A	0.912	1.00
133_H	136_I	0.911	1.00
5_F	37_I	0.910	1.00
127_L	131_R	0.909	1.00
10_I	15_Q	0.902	1.00
74_L	84_T	0.900	1.00
61_K	87_Q	0.896	1.00
8_C	38_E	0.891	1.00
94_R	106_T	0.890	1.00
172_A	175_R	0.885	1.00
116_V	119_A	0.884	1.00
170_I	185_L	0.878	1.00
8_C	24_I	0.877	1.00
140_R	146_F	0.873	1.00
68_V	74_L	0.869	1.00
43_G	76_C	0.869	1.00
108_P	130_E	0.868	1.00
152_L	155_E	0.867	1.00
83_K	87_Q	0.855	1.00
57_L	87_Q	0.855	1.00
43_G	75_G	0.854	1.00
128_L	132_T	0.851	1.00
19_N	134_S	0.851	1.00
123_F	126_D	0.851	1.00
174_A	178_K	0.846	1.00
163_R	166_S	0.844	1.00
157_K	160_V	0.844	1.00
33_P	36_I	0.843	1.00
56_L	60_L	0.842	1.00
62_C	92_G	0.839	1.00
66_L	88_L	0.839	1.00
27_A	67_I	0.830	1.00
123_F	127_L	0.825	1.00
137_V	140_R	0.825	1.00
80_D	83_K	0.825	1.00
158_Q	162_E	0.821	1.00
129_L	132_T	0.817	1.00
179_T	184_I	0.813	1.00
181_R	185_L	0.812	1.00
23_E	26_S	0.808	1.00
4_I	65_Q	0.805	1.00
153_N	156_Q	0.800	1.00
157_K	187_A	0.791	1.00
38_E	52_G	0.790	1.00
17_T	38_E	0.787	1.00
18_E	22_R	0.784	1.00
27_A	98_L	0.783	1.00
172_A	176_E	0.781	1.00
19_N	70_K	0.778	1.00
173_I	177_F	0.776	1.00
115_Q	126_D	0.775	1.00
23_E	134_S	0.770	1.00
44_S	129_L	0.768	1.00
10_I	40_H	0.756	1.00
26_S	29_F	0.754	1.00
61_K	91_T	0.753	1.00
112_M	116_V	0.752	1.00
27_A	96_H	0.748	1.00
116_V	120_V	0.744	1.00
127_L	130_E	0.744	1.00
55_R	58_A	0.744	1.00
163_R	180_S	0.743	1.00
4_I	28_G	0.742	1.00
7_Y	39_E	0.742	1.00
19_N	138_R	0.736	1.00
130_E	134_S	0.735	1.00
56_L	59_R	0.733	1.00
77_N	86_E	0.732	1.00
162_E	165_K	0.729	1.00
124_E	127_L	0.728	1.00
44_S	47_T	0.721	1.00
17_T	40_H	0.715	1.00
120_V	123_F	0.714	1.00
78_A	122_E	0.713	1.00
113_M	116_V	0.709	1.00
96_H	104_D	0.700	1.00
113_M	117_I	0.700	1.00
160_V	184_I	0.698	1.00
19_N	23_E	0.697	1.00
23_E	99_A	0.695	1.00
156_Q	160_V	0.695	1.00
71_L	97_C	0.692	1.00
152_L	156_Q	0.692	1.00
28_G	67_I	0.689	1.00
60_L	88_L	0.684	1.00
53_F	74_L	0.684	1.00
109_T	112_M	0.682	1.00
22_R	25_E	0.681	1.00
84_T	88_L	0.678	1.00
170_I	174_A	0.677	1.00
128_L	135_G	0.674	1.00
156_Q	182_Q	0.672	1.00
25_E	33_P	0.671	1.00
156_Q	177_F	0.671	1.00
182_Q	185_L	0.667	1.00
158_Q	161_F	0.665	1.00
133_H	137_V	0.665	1.00
24_I	28_G	0.662	1.00
70_K	131_R	0.660	1.00
160_V	177_F	0.659	1.00
70_K	99_A	0.651	1.00
161_F	164_I	0.645	1.00
47_T	54_N	0.641	1.00
136_I	139_A	0.641	1.00
170_I	184_I	0.638	1.00
160_V	187_A	0.632	1.00
168_V	173_I	0.622	1.00
179_T	183_T	0.620	1.00
179_T	187_A	0.618	1.00
113_M	120_V	0.617	1.00
132_T	135_G	0.616	1.00
170_I	181_R	0.614	1.00
71_L	114_M	0.613	1.00
77_N	80_D	0.610	1.00
112_M	115_Q	0.606	1.00
54_N	58_A	0.605	1.00
48_S	80_D	0.601	1.00
16_T	40_H	0.594	1.00
117_I	120_V	0.594	1.00
87_Q	90_E	0.592	1.00
139_A	146_F	0.590	1.00
169_S	175_R	0.590	1.00
94_R	104_D	0.590	1.00
81_I	114_M	0.589	1.00
131_R	134_S	0.588	1.00
174_A	177_F	0.586	1.00
167_G	173_I	0.584	1.00
154_E	158_Q	0.583	1.00
145_R	150_P	0.582	1.00
129_L	136_I	0.579	0.99
182_Q	186_R	0.579	0.99
58_A	62_C	0.578	0.99
67_I	98_L	0.569	0.99
75_G	84_T	0.568	0.99
175_R	179_T	0.567	0.99
47_T	53_F	0.563	0.99
79_M	82_R	0.562	0.99
22_R	141_G	0.560	0.99
53_F	57_L	0.559	0.99
145_R	148_R	0.556	0.99
164_I	169_S	0.556	0.99
70_K	127_L	0.556	0.99
181_R	184_I	0.553	0.99
78_A	119_A	0.553	0.99
28_G	34_Q	0.547	0.99
109_T	123_F	0.543	0.99
48_S	75_G	0.543	0.99
104_D	107_S	0.541	0.99
83_K	86_E	0.540	0.99
24_I	98_L	0.534	0.99
151_V	155_E	0.532	0.99
108_P	123_F	0.529	0.99
134_S	137_V	0.527	0.99
43_G	80_D	0.523	0.99
173_I	176_E	0.521	0.99
178_K	184_I	0.514	0.99
13_L	40_H	0.510	0.99
115_Q	122_E	0.509	0.99
53_F	80_D	0.508	0.99
183_T	187_A	0.508	0.99
75_G	118_S	0.502	0.99
96_H	102_G	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
3uj3X	2	0.6327	100	0.199	Contact Map
4bqqA	2	0.9337	100	0.201	Contact Map
1gdtA	2	0.9337	100	0.203	Contact Map
2r0qC	3	0.9031	100	0.213	Contact Map
3g13A	2	0.7449	100	0.295	Contact Map
3guvA	2	0.7041	100	0.315	Contact Map
2gm5A	4	0.6327	100	0.377	Contact Map
3lhkA	2	0.7143	100	0.412	Contact Map
3ilxA	2	0.6633	100	0.428	Contact Map
3bvpA	4	0.6378	100	0.442	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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