RecT - PFAM28P - GREMLIN Contacts

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RecT - RecT family

PFAM:	PF03837	Sequences: ERFIRSALTAIKRNPKLAKCTPESLLLALLQAAQLGLDPFKGQAYLVPYNKKGGGEAQFQIGYKGLIKLARRSGQYKGINAEVVYEGDEFEYDLGTEEPEHEHKPFDEGDRGKIIGAYAVVKLKDGGEPFVEVMSKEEIEKHRKKSSKANSGPWKTDPDEMAKKTAIRRALRKAFPLSLEGAYTADEMEQADEEKDVTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	199 (186)
Sequences:	11077 (9270)
Seq/√Len:	679.7
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_Y	62_G	3.728	1.00
43_Q	68_K	3.179	1.00
119_A	170_A	3.129	1.00
136_K	140_E	2.914	1.00
158_P	162_A	2.842	1.00
46_L	57_A	2.765	1.00
49_Y	60_Q	2.726	1.00
44_A	59_F	2.653	1.00
68_K	72_R	2.409	1.00
122_K	128_E	2.364	1.00
77_K	124_K	2.343	1.00
16_K	19_K	2.334	1.00
86_E	113_K	2.215	1.00
116_G	133_V	2.190	1.00
77_K	127_G	1.918	1.00
140_E	158_P	1.879	1.00
152_G	156_T	1.869	1.00
139_I	162_A	1.869	1.00
66_L	168_R	1.862	1.00
67_I	167_I	1.857	1.00
82_E	94_L	1.854	1.00
7_A	29_L	1.831	1.00
134_M	166_A	1.824	1.00
50_N	53_G	1.788	1.00
145_K	157_D	1.761	1.00
80_N	120_V	1.735	1.00
132_E	169_R	1.720	1.00
135_S	138_E	1.707	1.00
77_K	122_K	1.687	1.00
28_A	46_L	1.651	1.00
157_D	160_E	1.608	1.00
136_K	162_A	1.590	1.00
117_A	162_A	1.569	1.00
85_Y	114_I	1.563	1.00
49_Y	58_Q	1.557	1.00
152_G	155_K	1.555	1.00
61_I	66_L	1.523	1.00
142_H	169_R	1.513	1.00
21_T	24_S	1.493	1.00
147_S	150_N	1.487	1.00
81_A	163_K	1.473	1.00
75_Q	124_K	1.468	1.00
70_A	171_L	1.456	1.00
117_A	166_A	1.426	1.00
117_A	139_I	1.421	1.00
12_K	22_P	1.413	1.00
160_E	169_R	1.410	1.00
160_E	163_K	1.407	1.00
99_P	103_H	1.405	1.00
134_M	138_E	1.402	1.00
121_V	170_A	1.399	1.00
121_V	175_F	1.394	1.00
32_A	44_A	1.393	1.00
83_V	114_I	1.387	1.00
87_G	112_G	1.358	1.00
47_V	60_Q	1.335	1.00
136_K	158_P	1.331	1.00
153_P	161_M	1.327	1.00
97_E	101_H	1.321	1.00
83_V	163_K	1.321	1.00
32_A	39_P	1.313	1.00
19_K	55_G	1.300	1.00
114_I	162_A	1.278	1.00
138_E	159_D	1.271	1.00
63_Y	67_I	1.244	1.00
76_Y	79_I	1.233	1.00
37_L	65_G	1.224	1.00
42_G	64_K	1.217	1.00
38_D	41_K	1.193	1.00
16_K	55_G	1.192	1.00
48_P	55_G	1.182	1.00
109_G	112_G	1.178	1.00
140_E	143_R	1.165	1.00
51_K	54_G	1.158	1.00
91_E	102_E	1.148	1.00
83_V	117_A	1.147	1.00
146_S	149_A	1.141	1.00
20_C	57_A	1.108	1.00
99_P	102_E	1.094	1.00
134_M	169_R	1.087	1.00
153_P	157_D	1.081	1.00
77_K	125_D	1.057	1.00
32_A	59_F	1.056	1.00
83_V	159_D	1.052	1.00
114_I	117_A	1.050	1.00
64_K	177_L	1.048	1.00
91_E	100_E	1.045	1.00
5_R	9_T	1.045	1.00
101_H	105_P	1.039	1.00
140_E	150_N	1.022	1.00
25_L	57_A	1.021	1.00
100_E	103_H	1.004	1.00
92_Y	133_V	1.004	1.00
10_A	13_R	0.998	1.00
50_N	54_G	0.995	1.00
153_P	156_T	0.982	1.00
140_E	144_K	0.981	1.00
122_K	127_G	0.969	1.00
28_A	57_A	0.963	1.00
16_K	48_P	0.959	1.00
42_G	62_G	0.958	1.00
148_K	151_S	0.957	1.00
37_L	61_I	0.955	1.00
97_E	100_E	0.954	1.00
97_E	103_H	0.949	1.00
38_D	43_Q	0.947	1.00
91_E	104_K	0.946	1.00
21_T	56_E	0.941	1.00
71_R	75_Q	0.941	1.00
35_L	59_F	0.935	1.00
101_H	104_K	0.934	1.00
9_T	13_R	0.931	1.00
34_Q	38_D	0.929	1.00
82_E	118_Y	0.928	1.00
31_Q	34_Q	0.918	1.00
114_I	158_P	0.912	1.00
35_L	61_I	0.908	1.00
111_R	137_E	0.892	1.00
141_K	157_D	0.892	1.00
24_S	57_A	0.891	1.00
171_L	175_F	0.877	1.00
123_L	129_P	0.875	1.00
20_C	46_L	0.874	1.00
76_Y	175_F	0.873	1.00
96_T	99_P	0.866	1.00
30_L	33_A	0.863	1.00
134_M	139_I	0.863	1.00
117_A	159_D	0.862	1.00
75_Q	125_D	0.854	1.00
99_P	104_K	0.854	1.00
90_F	133_V	0.849	1.00
167_I	174_A	0.848	1.00
98_E	103_H	0.842	1.00
181_G	185_A	0.837	1.00
183_Y	188_M	0.836	1.00
67_I	174_A	0.836	1.00
114_I	159_D	0.825	1.00
93_D	102_E	0.820	1.00
75_Q	123_L	0.819	1.00
89_E	102_E	0.812	1.00
78_G	122_K	0.811	1.00
96_T	102_E	0.796	1.00
48_P	57_A	0.796	1.00
3_F	33_A	0.795	1.00
26_L	30_L	0.791	1.00
67_I	79_I	0.791	1.00
126_G	129_P	0.788	1.00
168_R	172_R	0.787	1.00
77_K	126_G	0.783	1.00
126_G	130_F	0.777	1.00
151_S	155_K	0.777	1.00
138_E	141_K	0.774	1.00
24_S	48_P	0.772	1.00
10_A	40_F	0.770	1.00
123_L	126_G	0.769	1.00
15_P	18_A	0.769	1.00
23_E	27_L	0.768	1.00
149_A	155_K	0.768	1.00
132_E	163_K	0.757	1.00
163_K	173_K	0.756	1.00
80_N	129_P	0.756	1.00
15_P	19_K	0.754	1.00
85_Y	113_K	0.751	1.00
167_I	173_K	0.750	1.00
102_E	105_P	0.741	1.00
114_I	136_K	0.740	1.00
72_R	178_S	0.740	1.00
84_V	116_G	0.736	1.00
70_A	76_Y	0.729	1.00
31_Q	59_F	0.729	1.00
87_G	111_R	0.728	1.00
81_A	167_I	0.722	1.00
66_L	171_L	0.722	1.00
68_K	178_S	0.721	1.00
138_E	169_R	0.716	1.00
120_V	128_E	0.712	1.00
50_N	55_G	0.712	1.00
90_F	95_G	0.711	1.00
98_E	102_E	0.708	1.00
145_K	156_T	0.708	1.00
8_L	12_K	0.704	1.00
100_E	104_K	0.701	1.00
143_R	158_P	0.699	1.00
82_E	163_K	0.698	1.00
24_S	28_A	0.693	1.00
144_K	149_A	0.693	1.00
11_I	18_A	0.693	1.00
132_E	166_A	0.693	1.00
184_T	187_E	0.692	1.00
113_K	136_K	0.692	1.00
71_R	76_Y	0.689	1.00
80_N	122_K	0.687	1.00
160_E	173_K	0.686	1.00
83_V	118_Y	0.684	1.00
109_G	137_E	0.683	1.00
150_N	155_K	0.681	1.00
149_A	152_G	0.678	1.00
137_E	140_E	0.677	1.00
73_S	76_Y	0.677	1.00
86_E	115_I	0.676	1.00
70_A	175_F	0.666	1.00
13_R	23_E	0.666	1.00
31_Q	35_L	0.660	1.00
129_P	170_A	0.654	1.00
124_K	127_G	0.653	1.00
63_Y	167_I	0.653	1.00
146_S	150_N	0.651	1.00
134_M	165_T	0.650	1.00
98_E	101_H	0.648	1.00
117_A	158_P	0.644	1.00
67_I	71_R	0.640	1.00
146_S	157_D	0.637	1.00
87_G	110_D	0.636	1.00
65_G	69_L	0.633	1.00
23_E	26_L	0.627	1.00
181_G	184_T	0.626	1.00
98_E	104_K	0.617	1.00
135_S	159_D	0.613	1.00
89_E	104_K	0.612	1.00
145_K	148_K	0.612	1.00
84_V	90_F	0.612	1.00
129_P	174_A	0.612	1.00
97_E	102_E	0.611	1.00
14_N	41_K	0.606	1.00
182_A	185_A	0.606	1.00
119_A	166_A	0.601	1.00
143_R	150_N	0.600	1.00
6_S	38_D	0.598	1.00
61_I	69_L	0.591	1.00
123_L	127_G	0.591	1.00
4_I	7_A	0.590	1.00
93_D	100_E	0.588	1.00
49_Y	147_S	0.582	1.00
110_D	137_E	0.580	1.00
28_A	32_A	0.577	1.00
51_K	55_G	0.575	1.00
80_N	128_E	0.573	1.00
85_Y	111_R	0.572	1.00
170_A	175_F	0.572	1.00
139_I	143_R	0.572	1.00
9_T	12_K	0.570	1.00
144_K	150_N	0.565	1.00
35_L	182_A	0.561	1.00
21_T	54_G	0.559	1.00
69_L	72_R	0.557	1.00
163_K	167_I	0.555	1.00
27_L	31_Q	0.553	1.00
47_V	58_Q	0.549	1.00
52_K	56_E	0.547	1.00
171_L	177_L	0.546	1.00
31_Q	40_F	0.545	1.00
143_R	155_K	0.544	1.00
133_V	138_E	0.539	1.00
96_T	103_H	0.537	1.00
77_K	128_E	0.536	1.00
43_Q	62_G	0.536	1.00
144_K	151_S	0.535	1.00
78_G	129_P	0.531	1.00
163_K	169_R	0.527	1.00
35_L	69_L	0.527	1.00
184_T	188_M	0.526	1.00
88_D	94_L	0.524	1.00
86_E	112_G	0.521	0.99
116_G	119_A	0.521	0.99
85_Y	88_D	0.520	0.99
132_E	170_A	0.519	0.99
79_I	167_I	0.518	0.99
134_M	142_H	0.518	0.99
104_K	107_D	0.515	0.99
146_S	151_S	0.514	0.99
116_G	135_S	0.513	0.99
103_H	106_F	0.512	0.99
52_K	55_G	0.510	0.99
76_Y	121_V	0.509	0.99
100_E	105_P	0.508	0.99
22_P	26_L	0.505	0.99
20_C	25_L	0.503	0.99
141_K	145_K	0.501	0.99
17_L	25_L	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
2dmpA	1	0.3618	14.1	0.93	Contact Map
2d5vA	1	0.2714	13	0.931	Contact Map
4ndlB	1	0.2261	8.5	0.937	Contact Map
3a03A	1	0.2663	8.2	0.937	Contact Map
3rkqA	1	0.2613	7.1	0.939	Contact Map
3d1nI	2	0.2714	6.9	0.939	Contact Map
3a02A	1	0.2563	6.7	0.94	Contact Map
4uzzB	1	0.3065	6.6	0.94	Contact Map
3l1pA	2	0.2714	6.5	0.94	Contact Map
2e19A	1	0.2864	6.4	0.94	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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