YicC_N - PFAM28P - GREMLIN Contacts

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YicC_N - YicC-like family, N-terminal region

PFAM:	PF03755	Sequences: IKSMTGFGRAEGEDGGTITVEIRSVNHRFLDLSLRLPRELRALEPEIRELLRERLSRGKVDVSLSLERAGAAAAAVRINEELLKAYLAALRELAEELGAGPLSLSDLLRLPGVLEEEEEDDELWAALLAALEEALDALVAMREREGAALAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	151 (149)
Sequences:	37046 (26915)
Seq/√Len:	2205.0
META:	0.919

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_L	132_E	2.900	1.00
84_K	96_E	2.504	1.00
80_E	96_E	2.488	1.00
24_S	138_L	2.458	1.00
124_W	128_L	2.314	1.00
54_R	136_D	2.226	1.00
80_E	92_E	2.185	1.00
103_S	106_D	2.184	1.00
2_K	139_V	2.099	1.00
46_E	124_W	1.940	1.00
54_R	139_V	1.919	1.00
87_L	91_R	1.883	1.00
55_L	138_L	1.878	1.00
27_H	59_K	1.859	1.00
2_K	143_E	1.852	1.00
139_V	143_E	1.763	1.00
48_R	52_R	1.734	1.00
128_L	132_E	1.731	1.00
54_R	132_E	1.724	1.00
50_L	128_L	1.714	1.00
12_G	130_A	1.692	1.00
20_V	64_L	1.678	1.00
80_E	84_K	1.632	1.00
55_L	60_V	1.591	1.00
137_A	140_A	1.543	1.00
46_E	128_L	1.528	1.00
140_A	144_R	1.528	1.00
11_E	17_T	1.513	1.00
50_L	53_E	1.501	1.00
12_G	133_E	1.499	1.00
33_S	59_K	1.492	1.00
92_E	96_E	1.488	1.00
49_E	53_E	1.478	1.00
17_T	67_E	1.473	1.00
133_E	137_A	1.426	1.00
13_E	17_T	1.401	1.00
83_L	93_L	1.355	1.00
20_V	130_A	1.350	1.00
50_L	54_R	1.341	1.00
84_K	97_L	1.324	1.00
45_P	49_E	1.320	1.00
100_G	103_S	1.319	1.00
91_R	94_A	1.296	1.00
84_K	88_A	1.288	1.00
47_I	131_L	1.286	1.00
10_A	133_E	1.286	1.00
43_L	124_W	1.284	1.00
51_L	135_L	1.283	1.00
94_A	100_G	1.277	1.00
10_A	130_A	1.277	1.00
144_R	147_A	1.232	1.00
46_E	49_E	1.213	1.00
34_L	47_I	1.213	1.00
9_R	19_T	1.212	1.00
11_E	19_T	1.209	1.00
106_D	109_R	1.201	1.00
89_A	92_E	1.191	1.00
147_A	150_A	1.191	1.00
83_L	113_V	1.187	1.00
129_A	133_E	1.187	1.00
23_R	61_D	1.175	1.00
143_E	147_A	1.174	1.00
144_R	148_A	1.169	1.00
87_L	97_L	1.167	1.00
30_L	52_R	1.160	1.00
12_G	129_A	1.154	1.00
62_V	131_L	1.151	1.00
140_A	143_E	1.140	1.00
132_E	136_D	1.140	1.00
88_A	92_E	1.132	1.00
85_A	88_A	1.112	1.00
24_S	60_V	1.108	1.00
10_A	137_A	1.100	1.00
85_A	89_A	1.087	1.00
51_L	62_V	1.085	1.00
133_E	136_D	1.065	1.00
53_E	132_E	1.062	1.00
90_L	108_L	1.058	1.00
20_V	131_L	1.057	1.00
54_R	135_L	1.054	1.00
33_S	61_D	1.049	1.00
41_R	61_D	1.023	1.00
77_R	115_E	1.020	1.00
16_G	66_L	1.015	1.00
80_E	89_A	1.011	1.00
49_E	52_R	1.001	1.00
136_D	140_A	1.001	1.00
75_A	85_A	0.994	1.00
81_E	84_K	0.993	1.00
105_S	109_R	0.988	1.00
22_I	62_V	0.985	1.00
126_A	129_A	0.982	1.00
10_A	134_A	0.981	1.00
32_L	51_L	0.978	1.00
31_D	59_K	0.976	1.00
31_D	48_R	0.971	1.00
35_R	63_S	0.961	1.00
55_L	139_V	0.953	1.00
86_Y	110_L	0.949	1.00
18_I	66_L	0.943	1.00
34_L	62_V	0.940	1.00
64_L	127_L	0.938	1.00
125_A	128_L	0.937	1.00
141_M	144_R	0.934	1.00
79_N	115_E	0.934	1.00
42_A	124_W	0.923	1.00
40_L	66_L	0.919	1.00
12_G	126_A	0.914	1.00
125_A	129_A	0.909	1.00
38_R	41_R	0.898	1.00
50_L	135_L	0.896	1.00
91_R	95_E	0.894	1.00
43_L	46_E	0.889	1.00
79_N	82_L	0.884	1.00
93_L	97_L	0.878	1.00
94_A	101_P	0.870	1.00
130_A	133_E	0.857	1.00
92_E	95_E	0.857	1.00
77_R	116_E	0.856	1.00
81_E	85_A	0.844	1.00
82_L	86_Y	0.843	1.00
88_A	91_R	0.843	1.00
9_R	21_E	0.834	1.00
22_I	138_L	0.833	1.00
51_L	55_L	0.822	1.00
129_A	132_E	0.820	1.00
43_L	127_L	0.818	1.00
44_E	48_R	0.817	1.00
102_L	105_S	0.804	1.00
90_L	104_L	0.803	1.00
90_L	102_L	0.797	1.00
23_R	27_H	0.795	1.00
55_L	135_L	0.792	1.00
83_L	107_L	0.776	1.00
20_V	134_A	0.776	1.00
22_I	134_A	0.770	1.00
136_D	139_V	0.765	1.00
130_A	134_A	0.764	1.00
22_I	51_L	0.762	1.00
82_L	85_A	0.761	1.00
19_T	67_E	0.753	1.00
82_L	113_V	0.751	1.00
50_L	131_L	0.750	1.00
78_I	83_L	0.747	1.00
38_R	65_S	0.746	1.00
16_G	68_R	0.745	1.00
34_L	44_E	0.745	1.00
103_S	107_L	0.740	1.00
13_E	69_A	0.738	1.00
30_L	60_V	0.737	1.00
15_G	69_A	0.735	1.00
106_D	110_L	0.734	1.00
12_G	18_I	0.732	1.00
94_A	104_L	0.730	1.00
8_G	134_A	0.729	1.00
27_H	61_D	0.727	1.00
46_E	50_L	0.727	1.00
76_V	89_A	0.714	1.00
94_A	97_L	0.711	1.00
18_I	130_A	0.692	1.00
94_A	99_A	0.688	1.00
78_I	89_A	0.685	1.00
51_L	131_L	0.682	1.00
18_I	127_L	0.675	1.00
116_E	119_E	0.664	1.00
134_A	138_L	0.661	1.00
19_T	65_S	0.653	1.00
39_E	66_L	0.649	1.00
1_I	150_A	0.647	1.00
94_A	102_L	0.646	1.00
84_K	87_L	0.640	1.00
126_A	130_A	0.640	1.00
112_G	115_E	0.630	1.00
137_A	144_R	0.626	1.00
91_R	100_G	0.625	1.00
49_E	148_A	0.625	1.00
36_L	47_I	0.618	1.00
137_A	141_M	0.616	1.00
90_L	107_L	0.612	1.00
78_I	93_L	0.612	1.00
110_L	113_V	0.610	1.00
36_L	64_L	0.610	1.00
18_I	126_A	0.606	1.00
111_P	114_L	0.606	1.00
102_L	106_D	0.597	1.00
23_R	41_R	0.595	1.00
27_H	35_R	0.589	1.00
124_W	129_A	0.584	1.00
31_D	38_R	0.583	1.00
20_V	62_V	0.582	1.00
40_L	123_L	0.582	1.00
17_T	69_A	0.575	1.00
89_A	114_L	0.574	1.00
120_D	123_L	0.574	1.00
87_L	102_L	0.572	1.00
22_I	135_L	0.568	1.00
87_L	90_L	0.563	1.00
37_P	40_L	0.561	1.00
91_R	101_P	0.561	1.00
100_G	106_D	0.561	1.00
107_L	113_V	0.555	1.00
99_A	102_L	0.545	1.00
47_I	127_L	0.544	1.00
74_A	79_N	0.543	1.00
31_D	34_L	0.540	1.00
18_I	40_L	0.536	1.00
30_L	34_L	0.535	1.00
80_E	83_L	0.534	1.00
32_L	48_R	0.528	1.00
100_G	104_L	0.527	1.00
51_L	60_V	0.527	1.00
90_L	110_L	0.518	1.00
9_R	137_A	0.518	1.00
131_L	135_L	0.516	1.00
127_L	130_A	0.514	1.00
27_H	31_D	0.513	1.00
78_I	114_L	0.512	1.00
86_Y	90_L	0.512	1.00
95_E	98_G	0.509	1.00
123_L	127_L	0.507	1.00
36_L	44_E	0.507	1.00
51_L	54_R	0.505	1.00
87_L	107_L	0.501	1.00
10_A	20_V	0.500	1.00

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
3ghgA	2	0.6821	30.1	0.915	Contact Map
4qgkA	2	0.3642	15.4	0.925	Contact Map
4i14A	2	0.0927	13.2	0.928	Contact Map
2gqpA	1	0.5099	11.3	0.93	Contact Map
4w6yA	2	0.404	10.5	0.931	Contact Map
1rlzA	4	0.894	10.1	0.932	Contact Map
3h90A	3	0.4305	9.3	0.933	Contact Map
1deqA	1	0.8212	8.8	0.933	Contact Map
3n9uC	1	0.3444	6.3	0.937	Contact Map
2j42A	1	0	6.2	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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