RS12 - HALSA - GREMLIN Contacts

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RS12 - 30S ribosomal protein S12

UniProt:	P0CX00	Sequences: MTNGKYAARKLKKDRQQRRWSDSEYARRERGLGKKSDPLEGAPQGRGIVLEKVGIEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAISFIDEHDEVTIAGIGGAKGRAMGDLSGVNYKVEKVNGVSLIELVRGNAEKPVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	142 (137)
Sequences:	232 (116)
Seq/√Len:	9.9

BACSU - RS12
HALSA - RS12
SULSO - RS12

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_V	100_I	5.269	1.00
22_D	25_Y	3.604	0.97
127_V	140_P	3.307	0.96
53_V	80_T	3.153	0.94
131_E	136_N	3.073	0.93
67_C	117_V	2.675	0.87
69_R	83_C	2.375	0.80
8_A	12_K	2.310	0.78
130_I	134_R	2.298	0.77
95_H	103_I	1.804	0.58
29_E	79_V	1.797	0.58
16_Q	92_I	1.796	0.58
39_L	100_I	1.753	0.56
40_E	46_R	1.734	0.55
85_G	88_A	1.715	0.54
29_E	36_S	1.662	0.52
18_R	21_S	1.613	0.50
54_G	64_I	1.601	0.49
70_V	100_I	1.592	0.49
20_W	26_A	1.582	0.48
114_L	120_K	1.558	0.47
39_L	44_Q	1.556	0.47
55_I	135_G	1.527	0.46
50_L	134_R	1.514	0.45
63_A	131_E	1.514	0.45
42_A	79_V	1.500	0.44
82_F	86_D	1.499	0.44
111_M	114_L	1.468	0.43
59_Q	102_G	1.446	0.42
70_V	75_N	1.429	0.41
56_E	59_Q	1.395	0.40
5_K	30_R	1.393	0.40
26_A	30_R	1.388	0.39
36_S	73_I	1.346	0.38
111_M	125_N	1.342	0.37
23_S	43_P	1.299	0.36
57_A	114_L	1.294	0.35
21_S	33_G	1.291	0.35
99_T	120_K	1.288	0.35
22_D	27_R	1.279	0.35
59_Q	62_S	1.264	0.34
9_R	16_Q	1.261	0.34
78_Q	103_I	1.261	0.34
106_A	118_N	1.253	0.34
23_S	107_K	1.244	0.33
94_E	97_E	1.233	0.33
95_H	125_N	1.211	0.32
90_S	114_L	1.171	0.31
81_A	86_D	1.167	0.30
41_G	47_G	1.161	0.30
128_S	131_E	1.160	0.30
58_K	138_E	1.157	0.30
58_K	111_M	1.155	0.30
83_C	88_A	1.151	0.30
34_K	37_D	1.135	0.29
83_C	89_I	1.134	0.29
71_Q	74_K	1.133	0.29
86_D	112_G	1.131	0.29
100_I	121_V	1.126	0.29
8_A	69_R	1.125	0.29
70_V	126_G	1.122	0.29
16_Q	27_R	1.110	0.28
118_N	124_V	1.074	0.27
88_A	133_V	1.045	0.26
76_G	137_A	1.027	0.25
14_D	18_R	1.024	0.25
61_N	113_D	1.022	0.25
30_R	134_R	1.020	0.25
130_I	136_N	1.018	0.25
57_A	64_I	1.012	0.25
13_K	36_S	1.011	0.25
9_R	102_G	1.004	0.24
35_K	94_E	0.996	0.24
93_D	133_V	0.989	0.24
79_V	86_D	0.984	0.24
88_A	138_E	0.970	0.23
119_Y	130_I	0.970	0.23
23_S	110_A	0.968	0.23
71_Q	75_N	0.962	0.23
137_A	140_P	0.957	0.23
78_Q	95_H	0.950	0.23
124_V	129_L	0.946	0.23
16_Q	119_Y	0.939	0.22
119_Y	123_K	0.937	0.22
71_Q	123_K	0.929	0.22
76_G	138_E	0.923	0.22
43_P	46_R	0.921	0.22
77_K	106_A	0.916	0.22
11_L	87_G	0.910	0.21
47_G	56_E	0.906	0.21
65_R	113_D	0.902	0.21
5_K	26_A	0.890	0.21
120_K	134_R	0.886	0.21
38_P	67_C	0.880	0.21
89_I	93_D	0.872	0.20
47_G	115_S	0.872	0.20
60_P	96_D	0.867	0.20
99_T	103_I	0.854	0.20
44_Q	58_K	0.849	0.20
72_L	116_G	0.848	0.20
21_S	24_E	0.847	0.20
69_R	100_I	0.846	0.20
63_A	71_Q	0.840	0.19
87_G	90_S	0.833	0.19
10_K	91_F	0.831	0.19
62_S	102_G	0.819	0.19
4_G	8_A	0.817	0.19
46_R	78_Q	0.816	0.19
25_Y	57_A	0.809	0.19
22_D	44_Q	0.801	0.18
44_Q	123_K	0.800	0.18
7_A	28_R	0.797	0.18
72_L	75_N	0.795	0.18
25_Y	63_A	0.794	0.18
67_C	75_N	0.794	0.18
49_V	68_V	0.790	0.18
91_F	132_L	0.785	0.18
22_D	51_E	0.777	0.18
6_Y	43_P	0.776	0.18
101_A	120_K	0.775	0.18
77_K	83_C	0.770	0.17
50_L	69_R	0.770	0.17
133_V	136_N	0.767	0.17
38_P	74_K	0.764	0.17
93_D	132_L	0.764	0.17
3_N	43_P	0.760	0.17
54_G	127_V	0.756	0.17
7_A	13_K	0.755	0.17
31_G	34_K	0.739	0.17
57_A	113_D	0.731	0.16
5_K	32_L	0.730	0.16
75_N	118_N	0.730	0.16
37_D	100_I	0.728	0.16
31_G	92_I	0.725	0.16
128_S	135_G	0.722	0.16
129_L	137_A	0.717	0.16
93_D	111_M	0.716	0.16
9_R	82_F	0.711	0.16
14_D	132_L	0.703	0.16
16_Q	22_D	0.701	0.16
39_L	121_V	0.686	0.15
77_K	132_L	0.682	0.15
68_V	97_E	0.679	0.15
13_K	90_S	0.678	0.15
79_V	116_G	0.674	0.15
110_A	121_V	0.673	0.15
13_K	16_Q	0.669	0.15
120_K	124_V	0.665	0.15
18_R	134_R	0.657	0.15
89_I	92_I	0.645	0.14
40_E	91_F	0.638	0.14
53_V	91_F	0.620	0.14
38_P	47_G	0.619	0.14
7_A	53_V	0.616	0.14
60_P	84_P	0.615	0.14
73_I	127_V	0.613	0.14
41_G	117_V	0.608	0.14
27_R	78_Q	0.607	0.14
66_K	98_V	0.605	0.14
74_K	77_K	0.604	0.14
120_K	137_A	0.604	0.14
91_F	131_E	0.600	0.13
96_D	108_G	0.600	0.13
77_K	110_A	0.600	0.13
68_V	76_G	0.598	0.13
32_L	40_E	0.598	0.13
31_G	100_I	0.597	0.13
125_N	135_G	0.595	0.13
95_H	111_M	0.585	0.13
44_Q	101_A	0.584	0.13
56_E	66_K	0.584	0.13
10_K	72_L	0.581	0.13
18_R	39_L	0.578	0.13
6_Y	50_L	0.577	0.13
5_K	123_K	0.576	0.13
19_R	125_N	0.571	0.13
38_P	80_T	0.563	0.13
104_G	113_D	0.563	0.13
15_R	97_E	0.559	0.13
17_Q	37_D	0.558	0.13
123_K	127_V	0.557	0.13
107_K	128_S	0.555	0.13
86_D	140_P	0.553	0.12
63_A	116_G	0.549	0.12
10_K	20_W	0.543	0.12
32_L	95_H	0.541	0.12
128_S	137_A	0.541	0.12
88_A	95_H	0.535	0.12
14_D	26_A	0.535	0.12
7_A	139_K	0.534	0.12
45_G	136_N	0.525	0.12
12_K	61_N	0.523	0.12
107_K	110_A	0.523	0.12
17_Q	21_S	0.518	0.12
86_D	136_N	0.514	0.12
102_G	129_L	0.513	0.12
63_A	67_C	0.512	0.12
41_G	75_N	0.512	0.12
96_D	102_G	0.511	0.12
97_E	108_G	0.508	0.12
49_V	79_V	0.504	0.12
8_A	71_Q	0.503	0.12
126_G	139_K	0.503	0.12
12_K	69_R	0.502	0.11
70_V	74_K	0.502	0.11
51_E	114_L	0.500	0.11

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
3j20N	1	1	100	0.202	Contact Map
3zeyS	1	0.993	100	0.22	Contact Map
4ujpY	1	0.993	100	0.224	Contact Map
4bpeL	1	0.9648	100	0.236	Contact Map
5aj3L	1	0.7254	100	0.58	Contact Map
4ji1L	1	0.8028	100	0.587	Contact Map
4rb5L	1	0.8099	100	0.589	Contact Map
2vawA	1	0.3451	10.1	0.966	Contact Map
1ofuA	1	0.2958	8.8	0.967	Contact Map
2vxyA	2	0.2887	8.7	0.967	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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