PqiA - PFAM28P - GREMLIN Contacts

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PqiA - Paraquat-inducible protein A

PFAM:	PF04403	Sequences: LQRTLALLLAALILYIPANLLPIMTLSLLGRSQEDTILSGVVELWESGSWPLALLVFLASIVVPLLKLLALLYLLLSLRRGRRPRGRTRLYRLVEFLGRWSMLDVFVVGILVALVKLGGLATVEPGPGLYAFAAVVVLTMLAAASFDPRLIWDRLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (153)
Sequences:	13643 (8438)
Seq/√Len:	682.2
META:	0.832

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_W	53_A	3.184	1.00
45_W	50_W	2.967	1.00
25_T	34_E	2.890	1.00
42_V	46_E	2.682	1.00
35_D	39_S	2.417	1.00
2_Q	79_R	2.408	1.00
11_A	68_L	2.311	1.00
7_L	138_L	2.212	1.00
12_L	72_L	2.156	1.00
43_E	46_E	2.134	1.00
41_V	57_F	2.121	1.00
70_A	90_L	2.103	1.00
43_E	47_S	2.082	1.00
70_A	94_V	2.038	1.00
16_I	20_L	1.896	1.00
57_F	62_V	1.855	1.00
5_L	75_L	1.817	1.00
27_S	32_S	1.816	1.00
58_L	63_V	1.771	1.00
125_P	129_L	1.758	1.00
5_L	79_R	1.704	1.00
17_P	21_L	1.676	1.00
38_L	61_I	1.675	1.00
25_T	32_S	1.652	1.00
76_L	80_R	1.634	1.00
14_L	138_L	1.625	1.00
28_L	31_R	1.616	1.00
14_L	134_A	1.589	1.00
10_A	138_L	1.584	1.00
82_R	86_G	1.570	1.00
89_R	93_L	1.536	1.00
58_L	62_V	1.532	1.00
25_T	126_G	1.490	1.00
88_T	92_R	1.465	1.00
54_L	58_L	1.458	1.00
8_L	72_L	1.431	1.00
14_L	131_A	1.428	1.00
73_Y	86_G	1.417	1.00
12_L	68_L	1.413	1.00
15_Y	135_V	1.408	1.00
128_G	131_A	1.401	1.00
4_T	75_L	1.379	1.00
8_L	68_L	1.346	1.00
3_R	145_S	1.345	1.00
23_I	128_G	1.335	1.00
67_K	98_G	1.323	1.00
8_L	12_L	1.303	1.00
105_V	129_L	1.298	1.00
15_Y	65_L	1.266	1.00
21_L	127_P	1.259	1.00
51_P	54_L	1.223	1.00
63_V	101_S	1.217	1.00
38_L	42_V	1.215	1.00
5_L	76_L	1.203	1.00
75_L	79_R	1.197	1.00
8_L	71_L	1.196	1.00
150_L	154_R	1.181	1.00
27_S	124_E	1.169	1.00
35_D	43_E	1.159	1.00
83_R	86_G	1.154	1.00
84_P	87_R	1.152	1.00
137_V	141_L	1.140	1.00
15_Y	68_L	1.126	1.00
73_Y	77_S	1.122	1.00
42_V	45_W	1.108	1.00
19_N	61_I	1.105	1.00
67_K	101_S	1.104	1.00
96_F	99_R	1.100	1.00
27_S	30_G	1.092	1.00
68_L	72_L	1.070	1.00
149_R	153_D	1.052	1.00
72_L	76_L	1.050	1.00
127_P	131_A	1.049	1.00
130_Y	134_A	1.047	1.00
44_L	56_V	1.040	1.00
76_L	79_R	1.039	1.00
17_P	131_A	1.038	1.00
73_Y	90_L	1.033	1.00
12_L	65_L	1.033	1.00
92_R	96_F	1.028	1.00
36_T	39_S	1.024	1.00
116_K	122_T	1.023	1.00
8_L	75_L	1.022	1.00
15_Y	19_N	1.012	1.00
89_R	92_R	1.010	1.00
134_A	138_L	0.998	1.00
126_G	131_A	0.996	1.00
135_V	139_T	0.992	1.00
11_A	138_L	0.991	1.00
55_L	59_A	0.989	1.00
141_L	145_S	0.987	1.00
4_T	142_A	0.987	1.00
51_P	55_L	0.976	1.00
93_L	96_F	0.968	1.00
25_T	124_E	0.964	1.00
117_L	121_A	0.948	1.00
48_G	51_P	0.936	1.00
21_L	128_G	0.935	1.00
103_L	136_V	0.933	1.00
111_L	123_V	0.931	1.00
17_P	20_L	0.927	1.00
147_D	150_L	0.921	1.00
65_L	69_L	0.915	1.00
19_N	36_T	0.913	1.00
74_L	151_I	0.912	1.00
63_V	97_L	0.901	1.00
78_L	146_F	0.894	1.00
74_L	94_V	0.892	1.00
6_A	10_A	0.891	1.00
14_L	135_V	0.890	1.00
11_A	142_A	0.885	1.00
150_L	153_D	0.882	1.00
95_E	98_G	0.882	1.00
16_I	19_N	0.877	1.00
41_V	53_A	0.873	1.00
10_A	14_L	0.870	1.00
116_K	119_G	0.865	1.00
26_L	121_A	0.862	1.00
67_K	143_A	0.853	1.00
4_T	145_S	0.845	1.00
140_M	144_A	0.842	1.00
141_L	144_A	0.835	1.00
60_S	106_F	0.830	1.00
57_F	61_I	0.821	1.00
10_A	13_I	0.806	1.00
54_L	57_F	0.795	1.00
33_Q	43_E	0.794	1.00
101_S	104_D	0.793	1.00
102_M	105_V	0.788	1.00
68_L	135_V	0.786	1.00
45_W	54_L	0.784	1.00
5_L	72_L	0.780	1.00
13_I	16_I	0.780	1.00
81_G	154_R	0.773	1.00
55_L	58_L	0.767	1.00
13_I	17_P	0.759	1.00
142_A	145_S	0.758	1.00
107_V	136_V	0.742	1.00
86_G	89_R	0.736	1.00
115_V	121_A	0.736	1.00
73_Y	82_R	0.736	1.00
4_T	8_L	0.731	1.00
28_L	121_A	0.730	1.00
8_L	142_A	0.730	1.00
109_G	113_A	0.725	1.00
67_K	94_V	0.722	1.00
2_Q	5_L	0.721	1.00
18_A	131_A	0.718	1.00
77_S	84_P	0.717	1.00
77_S	82_R	0.714	1.00
26_L	49_S	0.714	1.00
18_A	22_P	0.705	1.00
50_W	54_L	0.705	1.00
135_V	138_L	0.698	1.00
45_W	57_F	0.695	1.00
133_A	137_V	0.692	1.00
28_L	33_Q	0.691	1.00
83_R	87_R	0.689	1.00
77_S	87_R	0.679	1.00
98_G	101_S	0.673	1.00
129_L	133_A	0.672	1.00
69_L	73_Y	0.668	1.00
24_M	123_V	0.666	1.00
63_V	67_K	0.664	1.00
78_L	151_I	0.653	1.00
7_L	141_L	0.651	1.00
31_R	34_E	0.647	1.00
77_S	81_G	0.641	1.00
5_L	9_L	0.641	1.00
66_L	70_A	0.641	1.00
94_V	103_L	0.635	1.00
118_G	122_T	0.634	1.00
50_W	53_A	0.629	1.00
20_L	38_L	0.628	1.00
7_L	11_A	0.626	1.00
138_L	141_L	0.621	1.00
111_L	114_L	0.620	1.00
9_L	13_I	0.619	1.00
67_K	71_L	0.617	1.00
105_V	116_K	0.616	1.00
37_I	40_G	0.615	1.00
91_Y	94_V	0.607	1.00
72_L	75_L	0.606	1.00
82_R	87_R	0.602	1.00
82_R	85_R	0.598	1.00
67_K	132_F	0.595	1.00
73_Y	85_R	0.594	1.00
34_E	124_E	0.592	1.00
24_M	108_V	0.588	1.00
107_V	110_I	0.587	1.00
27_S	31_R	0.584	1.00
44_L	111_L	0.583	1.00
80_R	84_P	0.582	1.00
113_A	117_L	0.577	1.00
115_V	123_V	0.576	1.00
26_L	109_G	0.574	1.00
85_R	88_T	0.570	1.00
59_A	101_S	0.569	1.00
139_T	143_A	0.567	1.00
18_A	132_F	0.565	1.00
24_M	110_I	0.564	1.00
27_S	122_T	0.559	1.00
124_E	127_P	0.556	1.00
105_V	108_V	0.554	1.00
79_R	83_R	0.554	1.00
115_V	119_G	0.554	1.00
45_W	48_G	0.552	1.00
24_M	102_M	0.551	1.00
56_V	60_S	0.547	1.00
142_A	147_D	0.547	1.00
99_R	109_G	0.546	1.00
76_L	82_R	0.545	1.00
69_L	72_L	0.543	1.00
80_R	83_R	0.543	1.00
11_A	15_Y	0.538	1.00
103_L	135_V	0.535	1.00
110_I	113_A	0.534	1.00
140_M	143_A	0.528	1.00
93_L	97_L	0.524	1.00
119_G	131_A	0.522	1.00
7_L	142_A	0.519	0.99
67_K	139_T	0.519	0.99
81_G	84_P	0.518	0.99
63_V	136_V	0.516	0.99
19_N	22_P	0.509	0.99
12_L	16_I	0.506	0.99
110_I	116_K	0.506	0.99
99_R	103_L	0.503	0.99
77_S	85_R	0.502	0.99
14_L	17_P	0.500	0.99

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
2lzqA	1	0.0897	2	0.947	Contact Map
4ev6A	3	0.4103	1.7	0.949	Contact Map
2kygC	1	0.1346	1.6	0.95	Contact Map
3wu2M	2	0.2115	1.3	0.952	Contact Map
4j72A	2	0.6859	1.3	0.952	Contact Map
4xk8I	1	0.1859	1.2	0.953	Contact Map
4r0cA	3	0.3013	1.2	0.953	Contact Map
4i0uA	4	0.3974	1.1	0.955	Contact Map
2wscI	1	0.1923	1	0.956	Contact Map
2k1aA	1	0.2692	1	0.956	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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