ImpA_N - PFAM28P - GREMLIN Contacts

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ImpA_N - ImpA, N-terminal, type VI secretion system

PFAM:	PF06812	Sequences: LAPISGDNPCGEDLRYDPEFDALEEARRKDDEDQFREAKEPDWREVIELALELLATRSKDLRVAAWLTEALLRLEGFAGLADGLALLRGLLERFWDTLHPQLDDDDLEARANALAWLND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (118)
Sequences:	9768 (7160)
Seq/√Len:	659.1
META:	0.829

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_G	93_R	2.544	1.00
10_C	97_T	2.473	1.00
47_I	51_L	2.430	1.00
47_I	74_L	2.319	1.00
52_E	56_T	2.289	1.00
47_I	71_L	2.267	1.00
25_E	28_R	2.156	1.00
88_R	92_E	2.099	1.00
47_I	70_A	2.096	1.00
68_T	83_G	2.082	1.00
19_E	57_R	2.035	1.00
42_D	45_E	1.998	1.00
64_A	90_L	1.997	1.00
50_A	67_L	1.862	1.00
45_E	49_L	1.836	1.00
8_N	12_E	1.805	1.00
53_L	63_V	1.790	1.00
47_I	75_E	1.725	1.00
50_A	63_V	1.723	1.00
64_A	87_L	1.655	1.00
61_L	98_L	1.644	1.00
14_L	58_S	1.641	1.00
19_E	22_A	1.637	1.00
19_E	53_L	1.611	1.00
17_D	57_R	1.568	1.00
22_A	49_L	1.507	1.00
67_L	71_L	1.483	1.00
71_L	83_G	1.477	1.00
85_A	89_G	1.456	1.00
59_K	94_F	1.441	1.00
22_A	45_E	1.433	1.00
54_L	58_S	1.432	1.00
19_E	52_E	1.425	1.00
44_R	74_L	1.386	1.00
102_L	107_L	1.373	1.00
45_E	48_E	1.371	1.00
12_E	57_R	1.332	1.00
104_D	107_L	1.330	1.00
26_A	45_E	1.304	1.00
33_D	36_R	1.302	1.00
27_R	66_W	1.297	1.00
43_W	70_A	1.284	1.00
71_L	75_E	1.281	1.00
75_E	82_D	1.250	1.00
97_T	101_Q	1.238	1.00
49_L	52_E	1.237	1.00
51_L	67_L	1.237	1.00
79_G	83_G	1.235	1.00
21_D	24_E	1.221	1.00
10_C	94_F	1.211	1.00
51_L	55_A	1.208	1.00
21_D	25_E	1.166	1.00
26_A	29_K	1.121	1.00
53_L	58_S	1.120	1.00
12_E	99_H	1.120	1.00
65_A	87_L	1.115	1.00
13_D	101_Q	1.110	1.00
62_R	113_A	1.103	1.00
15_R	62_R	1.095	1.00
8_N	101_Q	1.058	1.00
24_E	28_R	1.031	1.00
32_E	35_F	1.027	1.00
68_T	87_L	1.026	1.00
72_L	80_L	1.009	1.00
68_T	117_L	1.009	1.00
81_A	85_A	1.009	1.00
5_S	8_N	1.004	1.00
23_L	63_V	1.004	1.00
104_D	108_E	1.001	1.00
90_L	98_L	0.994	1.00
26_A	49_L	0.985	1.00
95_W	110_R	0.979	1.00
22_A	25_E	0.973	1.00
46_V	50_A	0.958	1.00
23_L	50_A	0.955	1.00
71_L	82_D	0.950	1.00
111_A	115_A	0.949	1.00
3_P	6_G	0.946	1.00
30_D	39_K	0.941	1.00
64_A	86_L	0.939	1.00
27_R	69_E	0.934	1.00
46_V	70_A	0.930	1.00
109_A	113_A	0.892	1.00
9_P	97_T	0.889	1.00
12_E	17_D	0.889	1.00
64_A	83_G	0.885	1.00
16_Y	21_D	0.881	1.00
94_F	97_T	0.875	1.00
4_I	8_N	0.862	1.00
71_L	74_L	0.856	1.00
89_G	92_E	0.845	1.00
80_L	84_L	0.828	1.00
52_E	57_R	0.822	1.00
29_K	40_E	0.816	1.00
20_F	62_R	0.814	1.00
28_R	31_D	0.802	1.00
82_D	85_A	0.798	1.00
69_E	73_R	0.781	1.00
24_E	62_R	0.756	1.00
24_E	66_W	0.747	1.00
32_E	38_A	0.746	1.00
4_I	59_K	0.744	1.00
19_E	49_L	0.742	1.00
78_A	81_A	0.739	1.00
54_L	90_L	0.730	1.00
91_L	114_L	0.727	1.00
18_P	22_A	0.723	1.00
91_L	98_L	0.718	1.00
5_S	12_E	0.709	1.00
54_L	59_K	0.708	1.00
112_N	115_A	0.688	1.00
44_R	48_E	0.686	1.00
48_E	52_E	0.683	1.00
14_L	63_V	0.678	1.00
85_A	88_R	0.675	1.00
65_A	113_A	0.666	1.00
86_L	90_L	0.665	1.00
30_D	38_A	0.663	1.00
30_D	41_P	0.661	1.00
87_L	117_L	0.659	1.00
71_L	79_G	0.655	1.00
20_F	24_E	0.652	1.00
40_E	73_R	0.646	1.00
59_K	90_L	0.644	1.00
86_L	89_G	0.641	1.00
29_K	41_P	0.636	1.00
18_P	21_D	0.633	1.00
52_E	55_A	0.631	1.00
23_L	66_W	0.629	1.00
2_A	93_R	0.619	1.00
75_E	79_G	0.616	1.00
27_R	46_V	0.612	1.00
106_D	109_A	0.607	1.00
47_I	50_A	0.605	1.00
14_L	53_L	0.605	1.00
8_N	99_H	0.605	1.00
91_L	95_W	0.604	1.00
105_D	108_E	0.596	1.00
54_L	64_A	0.594	1.00
14_L	17_D	0.591	1.00
58_S	63_V	0.584	1.00
47_I	67_L	0.581	1.00
50_A	54_L	0.581	1.00
10_C	98_L	0.581	1.00
58_S	99_H	0.579	1.00
67_L	86_L	0.569	1.00
36_R	39_K	0.568	1.00
13_D	62_R	0.566	1.00
103_D	107_L	0.559	1.00
76_G	79_G	0.559	1.00
81_A	84_L	0.558	1.00
75_E	78_A	0.552	1.00
20_F	63_V	0.552	1.00
43_W	47_I	0.546	1.00
64_A	68_T	0.542	1.00
81_A	88_R	0.542	1.00
1_L	89_G	0.541	1.00
13_D	16_Y	0.539	1.00
43_W	69_E	0.539	1.00
26_A	46_V	0.538	1.00
79_G	82_D	0.535	1.00
3_P	93_R	0.532	1.00
15_R	109_A	0.528	0.99
78_A	82_D	0.526	0.99
113_A	118_N	0.524	0.99
77_F	84_L	0.520	0.99
65_A	117_L	0.519	0.99
30_D	36_R	0.516	0.99
113_A	116_W	0.516	0.99
111_A	118_N	0.514	0.99
80_L	83_G	0.508	0.99
38_A	41_P	0.508	0.99
87_L	114_L	0.504	0.99
39_K	42_D	0.503	0.99
46_V	53_L	0.501	0.99
4_I	9_P	0.501	0.99
101_Q	110_R	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
1mhqA	1	0.7731	34.5	0.887	Contact Map
1juqA	3	0.8487	25.1	0.895	Contact Map
3g2sA	1	0.8319	21.2	0.898	Contact Map
3zyqA	1	0.7731	20.5	0.899	Contact Map
1elkA	1	0.8739	17.7	0.902	Contact Map
4fgvA	1	0.6891	15.6	0.904	Contact Map
3ldzA	1	0.8235	12.5	0.908	Contact Map
1x5bA	1	0.9076	11.9	0.909	Contact Map
1dvpA	2	0.8235	11.8	0.91	Contact Map
2kmfA	1	0.8655	6.9	0.918	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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