RskA - PFAM28P - GREMLIN Contacts

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RskA - Anti-sigma-K factor rskA

PFAM:	PF10099	Sequences: PPPALRARILAAIAAEPAAAPAAAAAAARPPRARRRRRRRRWAAAAAAAVLALALGQLAALQAALAALRAAAAAAAAVVAVLAAPAAAGASATVVWSPSGGRAVLVASGLPPLPAGKVYQLWLIPGGGAPVSAGVFDADGSGTVTLPLPPDLAGAAALAVTLEPAGGSQPTPTGPVVLSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	180 (177)
Sequences:	25990 (22024)
Seq/√Len:	1655.4
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_R	10_L	3.412	1.00
117_K	162_L	3.197	1.00
120_Q	132_S	3.143	1.00
124_I	159_A	2.991	1.00
123_L	133_A	2.726	1.00
124_I	157_A	2.427	1.00
124_I	130_P	2.358	1.00
118_V	166_G	2.356	1.00
4_A	8_R	2.264	1.00
118_V	135_V	2.201	1.00
114_P	117_K	2.054	1.00
58_L	61_L	1.955	1.00
123_L	155_A	1.928	1.00
118_V	165_A	1.919	1.00
116_G	165_A	1.913	1.00
64_A	69_R	1.750	1.00
92_A	96_W	1.749	1.00
10_L	13_I	1.692	1.00
66_A	69_R	1.672	1.00
164_P	168_S	1.656	1.00
97_S	100_G	1.636	1.00
120_Q	135_V	1.612	1.00
60_A	64_A	1.607	1.00
57_Q	62_Q	1.600	1.00
117_K	164_P	1.539	1.00
46_A	49_A	1.523	1.00
81_V	85_P	1.507	1.00
130_P	159_A	1.506	1.00
61_L	65_L	1.489	1.00
57_Q	60_A	1.488	1.00
7_A	11_A	1.476	1.00
113_L	162_L	1.461	1.00
61_L	64_A	1.458	1.00
31_P	35_R	1.433	1.00
58_L	62_Q	1.429	1.00
64_A	67_A	1.425	1.00
102_R	105_L	1.414	1.00
164_P	173_T	1.412	1.00
72_A	75_A	1.399	1.00
65_L	68_L	1.383	1.00
8_R	12_A	1.381	1.00
172_P	176_V	1.369	1.00
75_A	78_V	1.355	1.00
62_Q	66_A	1.335	1.00
65_L	69_R	1.334	1.00
52_A	56_G	1.330	1.00
103_A	107_A	1.322	1.00
7_A	10_L	1.278	1.00
60_A	63_A	1.276	1.00
25_A	28_A	1.276	1.00
161_T	176_V	1.276	1.00
121_L	158_L	1.272	1.00
68_L	72_A	1.269	1.00
125_P	129_A	1.260	1.00
81_V	84_A	1.253	1.00
113_L	116_G	1.253	1.00
168_S	171_T	1.244	1.00
78_V	82_L	1.230	1.00
78_V	83_A	1.227	1.00
103_A	106_V	1.221	1.00
120_Q	167_G	1.220	1.00
62_Q	65_L	1.219	1.00
63_A	66_A	1.206	1.00
32_R	35_R	1.196	1.00
44_A	50_V	1.192	1.00
113_L	119_Y	1.184	1.00
76_A	80_A	1.172	1.00
45_A	56_G	1.170	1.00
47_A	50_V	1.160	1.00
29_R	33_A	1.159	1.00
137_D	141_S	1.155	1.00
12_A	15_A	1.154	1.00
162_L	177_V	1.149	1.00
71_A	75_A	1.148	1.00
35_R	39_R	1.143	1.00
4_A	7_A	1.123	1.00
33_A	37_R	1.116	1.00
72_A	76_A	1.111	1.00
5_L	9_I	1.110	1.00
35_R	38_R	1.106	1.00
75_A	79_V	1.105	1.00
69_R	72_A	1.103	1.00
92_A	95_V	1.100	1.00
59_A	62_Q	1.083	1.00
102_R	106_V	1.080	1.00
159_A	176_V	1.078	1.00
32_R	36_R	1.078	1.00
113_L	117_K	1.068	1.00
92_A	105_L	1.067	1.00
77_A	80_A	1.063	1.00
57_Q	61_L	1.051	1.00
123_L	158_L	1.051	1.00
71_A	74_A	1.043	1.00
125_P	128_G	1.036	1.00
126_G	129_A	1.019	1.00
168_S	173_T	1.017	1.00
63_A	67_A	1.012	1.00
28_A	32_R	1.009	1.00
137_D	140_G	1.005	1.00
146_L	149_P	1.005	1.00
10_L	14_A	1.003	1.00
33_A	36_R	0.999	1.00
93_T	96_W	0.995	1.00
77_A	81_V	0.989	1.00
162_L	175_P	0.973	1.00
142_G	146_L	0.970	1.00
34_R	37_R	0.962	1.00
90_A	94_V	0.962	1.00
70_A	73_A	0.957	1.00
79_V	82_L	0.953	1.00
24_A	28_A	0.951	1.00
36_R	39_R	0.950	1.00
37_R	41_R	0.947	1.00
6_R	9_I	0.943	1.00
39_R	42_W	0.935	1.00
133_A	136_F	0.933	1.00
94_V	97_S	0.925	1.00
93_T	97_S	0.925	1.00
68_L	71_A	0.923	1.00
48_A	52_A	0.922	1.00
37_R	40_R	0.919	1.00
24_A	27_A	0.915	1.00
76_A	79_V	0.911	1.00
80_A	83_A	0.907	1.00
96_W	99_S	0.903	1.00
132_S	135_V	0.894	1.00
29_R	32_R	0.893	1.00
107_A	110_L	0.891	1.00
45_A	48_A	0.890	1.00
30_P	34_R	0.889	1.00
144_V	147_P	0.885	1.00
80_A	84_A	0.873	1.00
173_T	176_V	0.870	1.00
26_A	30_P	0.860	1.00
67_A	70_A	0.856	1.00
52_A	55_L	0.852	1.00
44_A	51_L	0.851	1.00
163_E	166_G	0.848	1.00
45_A	50_V	0.843	1.00
59_A	63_A	0.843	1.00
23_A	26_A	0.832	1.00
135_V	167_G	0.830	1.00
71_A	76_A	0.829	1.00
91_S	96_W	0.827	1.00
91_S	94_V	0.827	1.00
142_G	145_T	0.821	1.00
45_A	52_A	0.818	1.00
2_P	8_R	0.816	1.00
43_A	47_A	0.815	1.00
18_A	21_P	0.810	1.00
20_A	23_A	0.806	1.00
27_A	30_P	0.805	1.00
66_A	70_A	0.803	1.00
27_A	31_P	0.803	1.00
138_A	142_G	0.799	1.00
73_A	76_A	0.798	1.00
121_L	133_A	0.797	1.00
70_A	74_A	0.792	1.00
25_A	29_R	0.789	1.00
36_R	40_R	0.785	1.00
9_I	12_A	0.778	1.00
96_W	103_A	0.776	1.00
67_A	71_A	0.771	1.00
38_R	42_W	0.770	1.00
45_A	49_A	0.767	1.00
34_R	39_R	0.766	1.00
10_L	15_A	0.765	1.00
30_P	33_A	0.755	1.00
44_A	56_G	0.752	1.00
46_A	50_V	0.751	1.00
106_V	109_G	0.750	1.00
6_R	13_I	0.749	1.00
94_V	103_A	0.749	1.00
31_P	34_R	0.747	1.00
50_V	53_L	0.743	1.00
23_A	28_A	0.738	1.00
21_P	24_A	0.737	1.00
126_G	156_A	0.736	1.00
53_L	56_G	0.733	1.00
143_T	146_L	0.728	1.00
50_V	54_A	0.726	1.00
38_R	41_R	0.725	1.00
37_R	42_W	0.717	1.00
44_A	48_A	0.710	1.00
43_A	46_A	0.710	1.00
44_A	47_A	0.710	1.00
114_P	162_L	0.706	1.00
16_E	19_A	0.704	1.00
79_V	83_A	0.703	1.00
36_R	41_R	0.699	1.00
138_A	144_V	0.696	1.00
110_L	178_L	0.692	1.00
119_Y	160_V	0.691	1.00
121_L	136_F	0.689	1.00
137_D	142_G	0.688	1.00
78_V	85_P	0.687	1.00
11_A	15_A	0.687	1.00
74_A	78_V	0.681	1.00
17_P	20_A	0.680	1.00
138_A	141_S	0.672	1.00
12_A	16_E	0.671	1.00
19_A	22_A	0.670	1.00
87_A	90_A	0.666	1.00
174_G	178_L	0.665	1.00
103_A	123_L	0.661	1.00
49_A	52_A	0.660	1.00
5_L	8_R	0.658	1.00
20_A	24_A	0.658	1.00
28_A	31_P	0.657	1.00
26_A	29_R	0.650	1.00
78_V	81_V	0.650	1.00
64_A	68_L	0.649	1.00
22_A	25_A	0.647	1.00
57_Q	65_L	0.641	1.00
44_A	54_A	0.639	1.00
92_A	107_A	0.635	1.00
94_V	98_P	0.635	1.00
91_S	95_V	0.631	1.00
60_A	65_L	0.631	1.00
34_R	38_R	0.630	1.00
136_F	160_V	0.629	1.00
144_V	148_L	0.628	1.00
82_L	85_P	0.619	1.00
74_A	77_A	0.615	1.00
2_P	5_L	0.614	1.00
110_L	119_Y	0.611	1.00
147_P	150_P	0.610	1.00
170_P	174_G	0.606	1.00
94_V	158_L	0.606	1.00
3_P	7_A	0.597	1.00
30_P	35_R	0.594	1.00
67_A	72_A	0.593	1.00
22_A	26_A	0.591	1.00
76_A	82_L	0.588	1.00
96_W	100_G	0.588	1.00
90_A	93_T	0.582	1.00
79_V	84_A	0.578	1.00
143_T	147_P	0.578	1.00
125_P	130_P	0.577	1.00
90_A	96_W	0.576	1.00
123_L	156_A	0.574	1.00
43_A	48_A	0.570	1.00
6_R	12_A	0.562	1.00
35_R	40_R	0.557	1.00
89_G	94_V	0.557	1.00
30_P	36_R	0.552	1.00
65_L	71_A	0.547	1.00
145_T	149_P	0.544	1.00
18_A	22_A	0.542	1.00
9_I	13_I	0.539	1.00
135_V	166_G	0.539	1.00
25_A	30_P	0.536	1.00
49_A	56_G	0.532	1.00
159_A	162_L	0.530	1.00
120_Q	133_A	0.530	1.00
32_R	37_R	0.530	1.00
95_V	106_V	0.529	1.00
31_P	36_R	0.528	1.00
11_A	14_A	0.522	1.00
127_G	156_A	0.515	1.00
125_P	156_A	0.514	1.00
35_R	42_W	0.511	1.00
44_A	49_A	0.509	1.00
29_R	34_R	0.509	1.00
75_A	80_A	0.502	1.00
29_R	35_R	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
4aqzA	1	0.7278	4.1	0.931	Contact Map
4v3iA	2	0.1222	4.1	0.931	Contact Map
1or7C	1	0.0889	3.3	0.934	Contact Map
2pftA	1	0.3278	3.2	0.934	Contact Map
4v33A	1	0.5	2.8	0.937	Contact Map
3q48A	1	0.4778	2.4	0.938	Contact Map
2w0cP	4	0.1278	2.4	0.938	Contact Map
2kt5B	1	0.2167	1.6	0.944	Contact Map
1rq6A	1	0.1167	1.4	0.946	Contact Map
1s4zC	1	0.0611	1.3	0.947	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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