PilX - PFAM28P - GREMLIN Contacts

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PilX - Type IV pilus assembly protein PilX C-term

PFAM:	PF13681	Sequences: TNGLCAPAATGPPPANTAWTTVDFTDPATAVTVAYGTFTGAAFGAGAGPGVAAQPRYIIEYLGDVPDGGSAGLAGASTPRYVYRITARGFGGSPNTQVVLQSTYRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	106 (100)
Sequences:	1959 (1678)
Seq/√Len:	167.8
META:	0.866

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_T	101_Q	4.263	1.00
88_R	97_Q	3.906	1.00
60_E	84_R	3.861	1.00
36_G	39_T	3.153	1.00
48_G	51_V	3.050	1.00
93_S	96_T	2.448	1.00
33_V	37_T	2.140	1.00
82_V	105_R	2.109	1.00
53_A	94_P	2.028	1.00
61_Y	81_Y	1.959	1.00
88_R	99_V	1.909	1.00
62_L	103_T	1.720	1.00
35_Y	39_T	1.707	1.00
34_A	37_T	1.691	1.00
27_P	30_A	1.672	1.00
85_I	102_S	1.661	1.00
60_E	86_T	1.629	1.00
10_T	13_P	1.627	1.00
62_L	84_R	1.601	1.00
35_Y	38_F	1.582	1.00
58_I	86_T	1.576	1.00
33_V	38_F	1.562	1.00
24_F	28_A	1.471	1.00
53_A	90_F	1.463	1.00
91_G	96_T	1.455	1.00
7_P	12_P	1.402	1.00
33_V	36_G	1.381	1.00
84_R	101_Q	1.353	1.00
73_L	76_A	1.338	1.00
9_A	14_P	1.335	1.00
59_I	101_Q	1.302	1.00
34_A	38_F	1.299	1.00
90_F	97_Q	1.290	1.00
32_T	35_Y	1.279	1.00
32_T	37_T	1.259	1.00
82_V	103_T	1.229	1.00
98_V	101_Q	1.222	1.00
46_G	51_V	1.205	1.00
11_G	14_P	1.171	1.00
25_T	28_A	1.166	1.00
39_T	43_F	1.157	1.00
32_T	36_G	1.142	1.00
60_E	101_Q	1.091	1.00
64_D	79_P	1.083	1.00
3_G	60_E	1.055	0.99
18_A	58_I	1.050	0.99
24_F	27_P	1.025	0.99
45_A	48_G	1.015	0.99
92_G	96_T	1.012	0.99
64_D	81_Y	1.007	0.99
58_I	85_I	1.005	0.99
6_A	11_G	0.955	0.99
51_V	54_Q	0.911	0.98
22_V	25_T	0.908	0.98
10_T	14_P	0.890	0.98
52_A	55_P	0.887	0.98
38_F	41_A	0.877	0.98
43_F	54_Q	0.875	0.98
55_P	91_G	0.873	0.98
3_G	7_P	0.871	0.98
6_A	9_A	0.865	0.98
39_T	42_A	0.847	0.97
20_T	25_T	0.840	0.97
33_V	39_T	0.836	0.97
63_G	81_Y	0.830	0.97
55_P	58_I	0.825	0.97
70_S	79_P	0.817	0.97
56_R	89_G	0.816	0.97
67_D	72_G	0.816	0.97
21_T	26_D	0.811	0.97
8_A	11_G	0.806	0.97
8_A	13_P	0.804	0.97
21_T	27_P	0.794	0.96
58_I	99_V	0.788	0.96
62_L	79_P	0.776	0.96
9_A	12_P	0.762	0.95
43_F	51_V	0.759	0.95
19_W	99_V	0.757	0.95
61_Y	83_Y	0.757	0.95
74_A	78_T	0.738	0.94
99_V	103_T	0.736	0.94
58_I	101_Q	0.735	0.94
52_A	94_P	0.734	0.94
25_T	29_T	0.727	0.94
35_Y	43_F	0.726	0.94
41_A	92_G	0.725	0.94
66_P	72_G	0.714	0.93
66_P	79_P	0.710	0.93
25_T	99_V	0.696	0.93
44_G	48_G	0.691	0.92
58_I	89_G	0.676	0.91
90_F	94_P	0.675	0.91
46_G	49_P	0.665	0.91
68_G	83_Y	0.663	0.91
9_A	13_P	0.662	0.91
74_A	77_S	0.655	0.90
87_A	100_L	0.654	0.90
3_G	57_Y	0.652	0.90
8_A	14_P	0.650	0.90
7_P	10_T	0.646	0.89
56_R	91_G	0.637	0.89
52_A	90_F	0.631	0.88
78_T	87_A	0.631	0.88
18_A	26_D	0.630	0.88
68_G	80_R	0.629	0.88
41_A	50_G	0.626	0.88
7_P	11_G	0.622	0.88
5_C	61_Y	0.616	0.87
34_A	40_G	0.611	0.87
33_V	40_G	0.605	0.86
26_D	29_T	0.604	0.86
21_T	24_F	0.600	0.86
69_G	80_R	0.595	0.85
80_R	83_Y	0.593	0.85
61_Y	102_S	0.578	0.84
7_P	62_L	0.577	0.83
63_G	98_V	0.577	0.83
81_Y	104_Y	0.575	0.83
11_G	87_A	0.574	0.83
57_Y	88_R	0.574	0.83
68_G	71_A	0.569	0.83
32_T	104_Y	0.564	0.82
63_G	89_G	0.563	0.82
3_G	14_P	0.558	0.81
41_A	44_G	0.557	0.81
89_G	93_S	0.557	0.81
20_T	23_D	0.553	0.81
56_R	83_Y	0.547	0.80
45_A	51_V	0.537	0.79
94_P	97_Q	0.537	0.79
56_R	88_R	0.537	0.79
68_G	104_Y	0.534	0.79
91_G	94_P	0.533	0.78
19_W	22_V	0.532	0.78
83_Y	105_R	0.532	0.78
8_A	12_P	0.530	0.78
19_W	102_S	0.528	0.78
65_V	71_A	0.527	0.78
8_A	83_Y	0.525	0.77
43_F	46_G	0.521	0.77
88_R	98_V	0.514	0.76
64_D	93_S	0.512	0.76
22_V	104_Y	0.512	0.76
90_F	99_V	0.511	0.75
20_T	24_F	0.510	0.75
71_A	77_S	0.507	0.75
79_P	82_V	0.506	0.75
74_A	79_P	0.506	0.75
84_R	98_V	0.500	0.74
55_P	89_G	0.500	0.74

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
3s6sA	1	0.1226	3.4	0.909	Contact Map
2h57A	1	0.2358	2.2	0.917	Contact Map
2a5jA	1	0.3302	1.7	0.922	Contact Map
4lpvA	5	0.7642	1.4	0.926	Contact Map
2l53B	1	0.1698	1.4	0.927	Contact Map
3lluA	3	0.2264	1.3	0.927	Contact Map
4g97A	1	0.3585	1.3	0.927	Contact Map
4sbvA	8	0.6509	1.2	0.928	Contact Map
2h17A	1	0.2264	1.2	0.929	Contact Map
4c2lA	1	0.2358	1.2	0.929	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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