T2SSN - PFAM28P - GREMLIN Contacts

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T2SSN - Type II secretion system (T2SS), protein N

PFAM:	PF01203	Sequences: PGVRLAGVSGTVWSGSALGLTVGGSPLGRLSWRLSPLSLLTGRLAADLELGGPGLTLPLSGRGRLGVTLRGLGGGLTLSDLRARLPAALLANPLQLGGQLRLDLDSLRLEGGGCVAADGRLEWRDAAVSRLSGLLPLGSYRLTLSGDGGALTLTLSTLGGPLQLSGTGTLSPDGRYRFDGTARARPGAPAALANLLNLLGRPDGDGRYRLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	211 (198)
Sequences:	4693 (3860)
Seq/√Len:	274.3
META:	0.851

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
123_W	126_A	5.961	1.00
78_L	81_L	3.616	1.00
83_A	102_L	3.408	1.00
34_L	46_A	2.873	1.00
114_C	146_G	2.528	1.00
9_S	16_S	2.428	1.00
82_R	103_D	2.258	1.00
153_L	168_G	2.165	1.00
105_D	118_D	2.127	1.00
125_D	128_V	2.084	1.00
203_D	207_R	2.077	1.00
5_L	17_A	2.008	1.00
157_T	185_R	2.001	1.00
104_L	107_L	1.961	1.00
194_N	197_N	1.935	1.00
140_Y	157_T	1.884	1.00
157_T	160_G	1.848	1.00
166_G	178_F	1.841	1.00
38_S	41_T	1.834	1.00
120_R	143_T	1.828	1.00
87_A	123_W	1.820	1.00
16_S	31_S	1.816	1.00
141_R	158_L	1.782	1.00
33_R	36_P	1.770	1.00
122_E	141_R	1.738	1.00
145_S	154_T	1.733	1.00
108_R	116_A	1.721	1.00
104_L	119_G	1.706	1.00
75_G	108_R	1.689	1.00
16_S	29_R	1.651	1.00
120_R	141_R	1.634	1.00
166_G	180_G	1.595	1.00
142_L	153_L	1.582	1.00
165_S	181_T	1.566	1.00
84_R	99_Q	1.558	1.00
154_T	167_T	1.555	1.00
47_D	64_R	1.542	1.00
18_L	21_T	1.534	1.00
84_R	101_R	1.526	1.00
15_G	32_W	1.498	1.00
150_A	169_T	1.489	1.00
38_S	45_A	1.466	1.00
157_T	161_P	1.463	1.00
8_V	17_A	1.453	1.00
87_A	100_L	1.446	1.00
106_S	116_A	1.443	1.00
38_S	44_L	1.442	1.00
144_L	153_L	1.437	1.00
7_G	18_L	1.435	1.00
147_D	152_T	1.433	1.00
101_R	124_R	1.411	1.00
123_W	128_V	1.403	1.00
30_L	50_L	1.397	1.00
101_R	122_E	1.392	1.00
163_Q	183_R	1.388	1.00
3_V	22_V	1.364	1.00
106_S	118_D	1.355	1.00
201_R	208_Y	1.347	1.00
155_L	164_L	1.339	1.00
31_S	49_E	1.328	1.00
79_S	106_S	1.309	1.00
50_L	61_G	1.300	1.00
142_L	155_L	1.300	1.00
124_R	139_S	1.276	1.00
171_S	177_R	1.269	1.00
171_S	175_R	1.266	1.00
20_L	26_P	1.258	1.00
13_W	46_A	1.238	1.00
35_S	45_A	1.236	1.00
17_A	32_W	1.209	1.00
38_S	43_R	1.205	1.00
17_A	20_L	1.190	1.00
119_G	125_D	1.181	1.00
14_S	33_R	1.178	1.00
70_R	73_G	1.171	1.00
141_R	156_S	1.166	1.00
35_S	47_D	1.164	1.00
163_Q	185_R	1.158	1.00
35_S	38_S	1.152	1.00
36_P	40_L	1.142	1.00
6_A	19_G	1.137	1.00
28_G	50_L	1.133	1.00
107_L	117_A	1.131	1.00
97_G	127_A	1.130	1.00
186_P	189_P	1.124	1.00
181_T	207_R	1.124	1.00
102_L	121_L	1.117	1.00
123_W	127_A	1.112	1.00
5_L	8_V	1.109	1.00
4_R	21_T	1.108	1.00
139_S	159_G	1.108	1.00
200_G	208_Y	1.106	1.00
39_L	42_G	1.099	1.00
22_V	25_S	1.094	1.00
154_T	165_S	1.084	1.00
66_G	77_T	1.076	1.00
86_P	89_L	1.072	1.00
85_L	89_L	1.070	1.00
81_L	104_L	1.069	1.00
63_G	66_G	1.067	1.00
142_L	146_G	1.066	1.00
71_G	74_G	1.062	1.00
117_A	121_L	1.062	1.00
63_G	81_L	1.059	1.00
110_E	115_V	1.058	1.00
119_G	123_W	1.055	1.00
66_G	70_R	1.053	1.00
85_L	100_L	1.041	1.00
87_A	126_A	1.040	1.00
184_A	188_A	1.038	1.00
145_S	152_T	1.034	1.00
18_L	22_V	1.017	1.00
19_G	26_P	1.015	1.00
131_L	134_L	1.013	1.00
32_W	98_G	1.005	1.00
202_P	206_G	0.997	1.00
103_D	120_R	0.996	1.00
38_S	42_G	0.992	1.00
161_P	185_R	0.981	1.00
127_A	136_P	0.976	1.00
77_T	108_R	0.968	1.00
203_D	206_G	0.964	1.00
45_A	66_G	0.960	1.00
35_S	46_A	0.950	1.00
202_P	208_Y	0.948	1.00
143_T	156_S	0.948	1.00
34_L	44_L	0.942	1.00
95_Q	130_R	0.940	1.00
140_Y	161_P	0.938	1.00
139_S	158_L	0.934	1.00
202_P	207_R	0.926	1.00
42_G	48_L	0.925	1.00
77_T	106_S	0.924	1.00
170_L	176_Y	0.921	1.00
146_G	151_L	0.920	1.00
170_L	174_G	0.918	1.00
37_L	41_T	0.917	1.00
183_R	207_R	0.914	1.00
98_G	138_G	0.914	1.00
9_S	18_L	0.902	1.00
88_A	97_G	0.891	1.00
202_P	205_D	0.883	1.00
162_L	192_L	0.879	1.00
188_A	191_A	0.875	1.00
109_L	114_C	0.873	1.00
21_T	24_G	0.871	1.00
140_Y	158_L	0.870	1.00
190_A	193_A	0.857	1.00
63_G	78_L	0.857	1.00
195_L	198_L	0.854	1.00
22_V	26_P	0.841	1.00
35_S	41_T	0.838	1.00
109_L	112_G	0.834	1.00
76_L	109_L	0.811	0.99
124_R	141_R	0.810	0.99
41_T	45_A	0.809	0.99
168_G	178_F	0.808	0.99
46_A	50_L	0.800	0.99
33_R	37_L	0.794	0.99
152_T	169_T	0.793	0.99
124_R	158_L	0.792	0.99
192_L	199_L	0.792	0.99
184_A	200_G	0.784	0.99
181_T	206_G	0.784	0.99
201_R	204_G	0.777	0.99
197_N	202_P	0.776	0.99
37_L	45_A	0.768	0.99
37_L	40_L	0.767	0.99
153_L	157_T	0.759	0.99
185_R	188_A	0.753	0.99
36_P	39_L	0.749	0.99
181_T	203_D	0.748	0.99
170_L	175_R	0.746	0.99
204_G	208_Y	0.745	0.99
78_L	101_R	0.743	0.99
42_G	45_A	0.740	0.99
10_G	15_G	0.731	0.99
203_D	208_Y	0.730	0.99
122_E	139_S	0.729	0.99
130_R	133_G	0.720	0.99
188_A	193_A	0.720	0.99
152_T	167_T	0.718	0.99
155_L	180_G	0.717	0.99
93_P	96_L	0.716	0.99
98_G	123_W	0.715	0.99
80_D	105_D	0.715	0.99
195_L	199_L	0.713	0.98
155_L	166_G	0.701	0.98
197_N	208_Y	0.698	0.98
86_P	98_G	0.690	0.98
129_S	133_G	0.688	0.98
39_L	43_R	0.686	0.98
96_L	128_V	0.686	0.98
46_A	49_E	0.685	0.98
132_S	136_P	0.684	0.98
198_L	205_D	0.682	0.98
104_L	176_Y	0.682	0.98
190_A	194_N	0.682	0.98
46_A	65_L	0.680	0.98
108_R	115_V	0.679	0.98
3_V	20_L	0.674	0.98
129_S	132_S	0.670	0.98
142_L	166_G	0.670	0.98
104_L	117_A	0.669	0.98
137_L	162_L	0.668	0.98
78_L	82_R	0.665	0.98
119_G	144_L	0.664	0.98
46_A	52_G	0.663	0.98
186_P	193_A	0.662	0.98
140_Y	160_G	0.653	0.97
194_N	201_R	0.652	0.97
29_R	51_G	0.651	0.97
182_A	208_Y	0.649	0.97
157_T	178_F	0.648	0.97
70_R	76_L	0.647	0.97
201_R	206_G	0.645	0.97
138_G	166_G	0.645	0.97
28_G	52_G	0.641	0.97
118_D	143_T	0.640	0.97
70_R	74_G	0.637	0.97
14_S	36_P	0.632	0.97
19_G	22_V	0.632	0.97
10_G	13_W	0.629	0.97
64_R	71_G	0.624	0.97
65_L	70_R	0.624	0.97
110_E	113_G	0.620	0.96
177_R	180_G	0.620	0.96
19_G	28_G	0.608	0.96
188_A	192_L	0.597	0.96
21_T	26_P	0.597	0.96
181_T	205_D	0.594	0.95
136_P	161_P	0.590	0.95
63_G	73_G	0.583	0.95
153_L	159_G	0.582	0.95
161_P	187_G	0.582	0.95
99_Q	125_D	0.582	0.95
37_L	66_G	0.579	0.95
7_G	29_R	0.579	0.95
64_R	70_R	0.579	0.95
23_G	26_P	0.578	0.95
161_P	188_A	0.577	0.95
29_R	50_L	0.576	0.95
133_G	138_G	0.574	0.94
50_L	53_P	0.568	0.94
146_G	157_T	0.564	0.94
191_A	195_L	0.564	0.94
6_A	156_S	0.563	0.94
137_L	194_N	0.563	0.94
45_A	77_T	0.561	0.94
204_G	207_R	0.559	0.94
189_P	203_D	0.557	0.94
157_T	164_L	0.557	0.94
65_L	71_G	0.556	0.93
3_V	93_P	0.555	0.93
46_A	78_L	0.551	0.93
66_G	79_S	0.548	0.93
118_D	145_S	0.548	0.93
18_L	24_G	0.547	0.93
16_S	66_G	0.545	0.93
156_S	165_S	0.545	0.93
27_L	92_N	0.541	0.93
185_R	189_P	0.540	0.92
114_C	151_L	0.539	0.92
171_S	176_Y	0.538	0.92
77_T	81_L	0.538	0.92
14_S	49_E	0.533	0.92
53_P	100_L	0.532	0.92
193_A	203_D	0.531	0.92
66_G	71_G	0.529	0.92
134_L	166_G	0.528	0.92
39_L	48_L	0.527	0.92
80_D	106_S	0.527	0.92
189_P	198_L	0.526	0.92
114_C	160_G	0.525	0.91
176_Y	180_G	0.525	0.91
136_P	139_S	0.523	0.91
162_L	195_L	0.520	0.91
78_L	107_L	0.517	0.91
99_Q	127_A	0.517	0.91
103_D	122_E	0.516	0.91
195_L	200_G	0.515	0.91
5_L	32_W	0.515	0.91
83_A	103_D	0.512	0.90
12_V	109_L	0.511	0.90
105_D	149_G	0.510	0.90
182_A	188_A	0.510	0.90
43_R	66_G	0.510	0.90
184_A	199_L	0.509	0.90
48_L	63_G	0.508	0.90
178_F	182_A	0.508	0.90
131_L	164_L	0.506	0.90
173_D	193_A	0.505	0.90
155_L	178_F	0.505	0.90
100_L	129_S	0.505	0.90
125_D	139_S	0.501	0.89
5_L	20_L	0.501	0.89
114_C	157_T	0.500	0.89

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
2xmxA	1	0.782	10.3	0.934	Contact Map
4dzgA	1	0.436	7.5	0.938	Contact Map
3butA	2	0.455	5.2	0.942	Contact Map
3szeA	1	0.91	4	0.946	Contact Map
4c1wA	1	0.3223	3.7	0.946	Contact Map
2krhA	1	0.1706	3.7	0.946	Contact Map
2jvfA	1	0.3555	3.4	0.947	Contact Map
3zf7M	1	0.4408	3.3	0.948	Contact Map
5a1uH	1	0	2.9	0.95	Contact Map
4aw7A	1	0.3223	2.7	0.95	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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