SpoIIM - PFAM28P - GREMLIN Contacts

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SpoIIM - Stage II sporulation protein M

PFAM:	PF01944	Sequences: SFLLFLLGALIGALLAAENFTENIEGVYSSGSAAAMFLFIFTNNIRVAFLAFALGITLFGIGTLFLLFYNGLMLGAVAGLFAQAGLGLLFLLFILPHGILELPAIFIAGAAGLRLGWALRSRREALREAGRDALKLLLGVVPLLVVAALIEGFVTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (148)
Sequences:	19736 (14198)
Seq/√Len:	1167.1
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_R	50_L	3.480	1.00
48_A	108_A	3.294	1.00
48_A	144_L	3.036	1.00
120_R	128_E	2.843	1.00
58_L	62_G	2.754	1.00
41_F	145_V	2.722	1.00
41_F	148_A	2.593	1.00
121_S	124_E	2.592	1.00
18_E	25_E	2.540	1.00
104_A	143_L	2.313	1.00
37_F	152_G	2.242	1.00
67_L	109_G	2.145	1.00
100_L	143_L	1.944	1.00
123_R	127_R	1.911	1.00
82_A	91_L	1.902	1.00
42_T	46_R	1.892	1.00
52_F	133_A	1.890	1.00
96_P	150_I	1.860	1.00
82_A	87_G	1.824	1.00
78_A	90_F	1.763	1.00
100_L	103_P	1.701	1.00
131_R	135_K	1.671	1.00
8_G	12_G	1.628	1.00
129_A	132_D	1.611	1.00
100_L	104_A	1.567	1.00
124_E	127_R	1.558	1.00
124_E	128_E	1.509	1.00
90_F	94_I	1.502	1.00
65_F	69_Y	1.484	1.00
80_L	84_A	1.467	1.00
99_I	103_P	1.419	1.00
37_F	149_L	1.417	1.00
51_A	66_L	1.410	1.00
149_L	153_F	1.409	1.00
54_L	62_G	1.405	1.00
32_S	35_A	1.390	1.00
70_N	73_M	1.378	1.00
9_A	13_A	1.360	1.00
130_G	133_A	1.340	1.00
64_L	113_L	1.334	1.00
95_L	99_I	1.327	1.00
79_G	83_Q	1.326	1.00
87_G	91_L	1.321	1.00
104_A	144_L	1.319	1.00
78_A	91_L	1.318	1.00
127_R	131_R	1.316	1.00
93_F	155_T	1.285	1.00
132_D	135_K	1.282	1.00
36_M	40_I	1.282	1.00
118_A	129_A	1.274	1.00
38_L	42_T	1.263	1.00
102_L	106_F	1.249	1.00
97_H	101_E	1.233	1.00
40_I	152_G	1.227	1.00
114_R	117_W	1.218	1.00
145_V	149_L	1.199	1.00
100_L	146_V	1.189	1.00
13_A	17_A	1.177	1.00
37_F	153_F	1.177	1.00
108_A	140_V	1.171	1.00
50_L	66_L	1.158	1.00
133_A	136_L	1.158	1.00
74_L	94_I	1.136	1.00
59_F	62_G	1.122	1.00
128_E	132_D	1.103	1.00
92_L	96_P	1.102	1.00
105_I	144_L	1.102	1.00
114_R	129_A	1.100	1.00
125_A	128_E	1.089	1.00
95_L	102_L	1.083	1.00
86_L	89_L	1.055	1.00
26_G	29_S	1.031	1.00
48_A	105_I	1.030	1.00
79_G	82_A	1.026	1.00
6_L	9_A	1.024	1.00
136_L	139_G	1.021	1.00
88_L	92_L	1.017	1.00
129_A	133_A	1.010	1.00
37_F	41_F	0.992	1.00
114_R	118_A	0.989	1.00
8_G	16_A	0.982	1.00
44_N	101_E	0.971	1.00
89_L	93_F	0.957	1.00
4_L	8_G	0.955	1.00
60_G	117_W	0.949	1.00
60_G	63_T	0.947	1.00
39_F	42_T	0.940	1.00
150_I	154_V	0.927	1.00
12_G	16_A	0.923	1.00
8_G	68_F	0.914	1.00
103_P	106_F	0.901	1.00
111_A	136_L	0.899	1.00
45_I	141_V	0.894	1.00
114_R	132_D	0.889	1.00
4_L	64_L	0.882	1.00
13_A	79_G	0.878	1.00
41_F	45_I	0.876	1.00
100_L	150_I	0.868	1.00
28_Y	31_G	0.865	1.00
47_V	66_L	0.860	1.00
5_F	8_G	0.845	1.00
59_F	119_L	0.843	1.00
3_L	7_L	0.835	1.00
8_G	14_L	0.828	1.00
132_D	136_L	0.822	1.00
50_L	54_L	0.816	1.00
111_A	140_V	0.813	1.00
51_A	109_G	0.810	1.00
11_I	14_L	0.808	1.00
28_Y	33_A	0.805	1.00
96_P	100_L	0.802	1.00
13_A	16_A	0.800	1.00
135_K	142_P	0.799	1.00
120_R	125_A	0.793	1.00
120_R	123_R	0.792	1.00
34_A	38_L	0.790	1.00
110_A	114_R	0.787	1.00
58_L	116_G	0.786	1.00
137_L	140_V	0.784	1.00
28_Y	32_S	0.783	1.00
40_I	43_N	0.781	1.00
78_A	82_A	0.766	1.00
134_L	142_P	0.764	1.00
51_A	67_L	0.763	1.00
77_V	90_F	0.761	1.00
5_F	12_G	0.761	1.00
11_I	68_F	0.761	1.00
91_L	95_L	0.761	1.00
27_V	30_S	0.753	1.00
10_L	14_L	0.751	1.00
133_A	137_L	0.751	1.00
134_L	138_L	0.746	1.00
123_R	126_L	0.746	1.00
122_R	125_A	0.746	1.00
140_V	144_L	0.741	1.00
43_N	70_N	0.735	1.00
62_G	65_F	0.733	1.00
78_A	94_I	0.733	1.00
68_F	72_L	0.729	1.00
74_L	102_L	0.727	1.00
2_F	6_L	0.721	1.00
89_L	92_L	0.719	1.00
6_L	10_L	0.717	1.00
36_M	39_F	0.709	1.00
122_R	126_L	0.708	1.00
49_F	137_L	0.708	1.00
100_L	147_A	0.707	1.00
7_L	14_L	0.706	1.00
101_E	144_L	0.694	1.00
104_A	147_A	0.693	1.00
98_G	101_E	0.692	1.00
131_R	134_L	0.678	1.00
31_G	35_A	0.671	1.00
29_S	33_A	0.667	1.00
71_G	75_G	0.664	1.00
80_L	83_Q	0.651	1.00
77_V	81_F	0.651	1.00
125_A	129_A	0.647	1.00
35_A	38_L	0.646	1.00
36_M	152_G	0.644	1.00
29_S	32_S	0.634	1.00
8_G	15_L	0.631	1.00
130_G	134_L	0.630	1.00
96_P	99_I	0.630	1.00
51_A	63_T	0.628	1.00
2_F	106_F	0.627	1.00
127_R	130_G	0.626	1.00
81_F	84_A	0.625	1.00
135_K	139_G	0.624	1.00
7_L	11_I	0.620	1.00
138_L	142_P	0.617	1.00
85_G	89_L	0.617	1.00
26_G	30_S	0.613	1.00
120_R	124_E	0.610	1.00
73_M	77_V	0.609	1.00
2_F	5_F	0.604	1.00
91_L	96_P	0.600	1.00
69_Y	72_L	0.596	1.00
43_N	46_R	0.592	1.00
11_I	15_L	0.590	1.00
103_P	107_I	0.589	1.00
117_W	129_A	0.589	1.00
5_F	106_F	0.589	1.00
7_L	10_L	0.589	1.00
30_S	33_A	0.585	1.00
70_N	74_L	0.582	1.00
9_A	12_G	0.582	1.00
69_Y	73_M	0.581	1.00
54_L	63_T	0.578	1.00
6_L	14_L	0.577	1.00
40_I	101_E	0.573	1.00
98_G	102_L	0.572	1.00
49_F	141_V	0.571	1.00
118_A	125_A	0.565	1.00
136_L	142_P	0.565	1.00
12_G	15_L	0.565	1.00
52_F	111_A	0.564	1.00
148_A	152_G	0.561	1.00
66_L	70_N	0.559	1.00
70_N	98_G	0.555	1.00
51_A	105_I	0.549	1.00
126_L	129_A	0.548	1.00
90_F	93_F	0.547	1.00
136_L	140_V	0.547	1.00
64_L	68_F	0.539	1.00
43_N	47_V	0.536	1.00
11_I	16_A	0.535	1.00
42_T	45_I	0.534	1.00
55_G	63_T	0.526	1.00
74_L	98_G	0.522	1.00
121_S	125_A	0.521	1.00
60_G	116_G	0.514	1.00
78_A	83_Q	0.511	1.00
92_L	95_L	0.509	1.00
48_A	51_A	0.509	1.00
33_A	37_F	0.507	1.00
35_A	39_F	0.506	1.00
66_L	69_Y	0.504	1.00
121_S	127_R	0.501	1.00
143_L	147_A	0.501	1.00
113_L	116_G	0.501	1.00
48_A	140_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
1scfA	4	0	4.7	0.914	Contact Map
4httA	1	0.7115	1.8	0.931	Contact Map
4ogqF	1	0.1346	0.9	0.943	Contact Map
4b4aA	1	0.7115	0.9	0.943	Contact Map
3rkoL	1	0.8333	0.9	0.943	Contact Map
2kv5A	1	0.2115	0.8	0.945	Contact Map
4lz6A	1	0.75	0.8	0.946	Contact Map
2onkC	2	0.7115	0.7	0.946	Contact Map
4p6vD	1	0.6603	0.7	0.947	Contact Map
1pfiA	7	0.2885	0.6	0.948	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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