PilW - PFAM28P - GREMLIN Contacts

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PilW - Type IV Pilus-assembly protein W

PFAM:	PF16074	Sequences: IYYVANDSDGGIPTLYRKELDASGGGGAGTAQPLVEGVEDLQVLYGVDTDGDGVVDRYVTADAVTAAAAADWARVVAVRVALLARSTEPDPGYTDTKTYTLGGATVTPANDDRYRRRVFTTTVALRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (120)
Sequences:	10988 (9149)
Seq/√Len:	835.2
META:	0.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_V	84_A	3.824	1.00
85_R	114_Y	3.051	1.00
39_E	116_R	3.049	1.00
46_G	77_A	2.453	1.00
14_T	33_P	2.396	1.00
44_L	79_R	2.389	1.00
5_A	16_Y	2.360	1.00
39_E	85_R	2.150	1.00
37_G	87_T	2.136	1.00
7_D	10_G	2.027	1.00
18_K	31_A	2.008	1.00
16_Y	33_P	1.933	1.00
48_D	56_D	1.907	1.00
81_A	118_V	1.901	1.00
55_V	76_V	1.855	1.00
52_D	56_D	1.778	1.00
47_V	59_V	1.753	1.00
80_V	123_V	1.750	1.00
81_A	101_L	1.667	1.00
81_A	102_G	1.610	1.00
44_L	81_A	1.607	1.00
41_L	82_L	1.599	1.00
16_Y	31_A	1.595	1.00
60_T	63_A	1.564	1.00
17_R	32_Q	1.562	1.00
43_V	80_V	1.557	1.00
81_A	120_T	1.547	1.00
58_Y	77_A	1.499	1.00
72_W	75_V	1.496	1.00
84_A	119_F	1.488	1.00
90_D	93_Y	1.406	1.00
2_Y	17_R	1.404	1.00
45_Y	61_A	1.392	1.00
89_P	113_R	1.376	1.00
90_D	115_R	1.328	1.00
106_V	109_A	1.324	1.00
99_Y	102_G	1.322	1.00
83_L	118_V	1.321	1.00
43_V	78_V	1.299	1.00
48_D	52_D	1.291	1.00
46_G	58_Y	1.271	1.00
13_P	85_R	1.270	1.00
12_I	37_G	1.258	1.00
7_D	33_P	1.246	1.00
3_Y	31_A	1.245	1.00
59_V	63_A	1.238	1.00
77_A	122_T	1.207	1.00
44_L	60_T	1.202	1.00
19_E	32_Q	1.185	1.00
107_T	110_N	1.181	1.00
100_T	103_G	1.181	1.00
71_D	74_R	1.159	1.00
100_T	105_T	1.148	1.00
20_L	24_G	1.124	1.00
24_G	27_G	1.115	1.00
65_T	69_A	1.111	1.00
79_R	122_T	1.104	1.00
101_L	104_A	1.101	1.00
47_V	74_R	1.066	1.00
95_D	99_Y	1.044	1.00
66_A	69_A	1.020	1.00
89_P	93_Y	1.020	1.00
7_D	16_Y	1.016	1.00
6_N	9_D	0.998	1.00
6_N	10_G	0.988	1.00
3_Y	18_K	0.986	1.00
50_D	56_D	0.982	1.00
18_K	29_G	0.951	1.00
63_A	66_A	0.946	1.00
5_A	31_A	0.922	1.00
64_V	70_A	0.918	1.00
108_P	111_D	0.906	1.00
45_Y	75_V	0.901	1.00
40_D	106_V	0.900	1.00
107_T	111_D	0.888	1.00
45_Y	78_V	0.855	1.00
92_G	113_R	0.852	1.00
17_R	20_L	0.842	1.00
9_D	12_I	0.842	1.00
47_V	57_R	0.837	1.00
59_V	71_D	0.836	1.00
36_E	87_T	0.832	1.00
83_L	101_L	0.826	1.00
78_V	81_A	0.825	1.00
101_L	118_V	0.823	1.00
48_D	76_V	0.822	1.00
89_P	114_Y	0.821	1.00
79_R	120_T	0.815	1.00
44_L	103_G	0.814	1.00
48_D	53_G	0.806	1.00
47_V	75_V	0.802	1.00
98_T	101_L	0.800	1.00
98_T	105_T	0.795	1.00
7_D	12_I	0.788	1.00
14_T	36_E	0.783	1.00
42_Q	81_A	0.777	1.00
62_D	65_T	0.773	1.00
49_T	57_R	0.770	1.00
64_V	67_A	0.767	1.00
46_G	55_V	0.767	1.00
24_G	28_A	0.765	1.00
99_Y	103_G	0.754	1.00
89_P	92_G	0.750	1.00
27_G	31_A	0.743	1.00
100_T	104_A	0.733	1.00
4_V	41_L	0.732	1.00
80_V	121_T	0.727	1.00
103_G	106_V	0.722	1.00
96_T	99_Y	0.717	1.00
62_D	66_A	0.712	1.00
40_D	101_L	0.712	1.00
58_Y	79_R	0.704	1.00
44_L	102_G	0.701	1.00
120_T	124_A	0.697	1.00
93_Y	97_K	0.695	1.00
3_Y	16_Y	0.695	1.00
94_T	113_R	0.685	1.00
55_V	77_A	0.679	1.00
12_I	36_E	0.679	1.00
102_G	106_V	0.674	1.00
9_D	36_E	0.667	1.00
13_P	17_R	0.664	1.00
41_L	80_V	0.662	1.00
12_I	114_Y	0.661	1.00
100_T	106_V	0.659	1.00
51_G	74_R	0.654	1.00
33_P	36_E	0.654	1.00
20_L	25_G	0.644	1.00
58_Y	61_A	0.643	1.00
7_D	14_T	0.643	1.00
49_T	56_D	0.631	1.00
53_G	56_D	0.620	1.00
18_K	30_T	0.613	1.00
12_I	85_R	0.612	1.00
83_L	99_Y	0.611	1.00
40_D	83_L	0.611	1.00
63_A	67_A	0.609	1.00
61_A	65_T	0.607	1.00
39_E	83_L	0.605	1.00
48_D	55_V	0.602	1.00
95_D	98_T	0.602	1.00
117_R	124_A	0.600	1.00
14_T	17_R	0.600	1.00
102_G	105_T	0.597	1.00
5_A	10_G	0.596	1.00
59_V	62_D	0.595	1.00
20_L	29_G	0.595	1.00
64_V	69_A	0.594	1.00
86_S	115_R	0.583	1.00
94_T	98_T	0.583	1.00
97_K	101_L	0.582	1.00
47_V	70_A	0.576	1.00
57_R	71_D	0.569	1.00
61_A	64_V	0.569	1.00
98_T	102_G	0.568	1.00
62_D	67_A	0.565	1.00
91_P	94_T	0.563	1.00
78_V	125_L	0.561	1.00
43_V	116_R	0.555	1.00
106_V	110_N	0.549	1.00
47_V	71_D	0.546	1.00
46_G	79_R	0.546	1.00
28_A	31_A	0.542	1.00
35_V	38_V	0.536	1.00
6_N	12_I	0.533	1.00
39_E	43_V	0.532	1.00
52_D	55_V	0.525	1.00
49_T	52_D	0.525	1.00
115_R	118_V	0.523	1.00
79_R	117_R	0.518	1.00
82_L	119_F	0.517	1.00
93_Y	96_T	0.514	1.00
65_T	70_A	0.512	1.00
57_R	61_A	0.510	1.00
59_V	64_V	0.510	1.00
42_Q	103_G	0.509	1.00
85_R	116_R	0.504	1.00
24_G	29_G	0.503	1.00
65_T	71_D	0.502	1.00
90_D	113_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
2retB	2	0.6457	63.3	0.846	Contact Map
3ci0J	1	0.6299	49.9	0.858	Contact Map
3njeA	1	0.7323	30.4	0.874	Contact Map
4ov8A	1	0.9291	7.1	0.906	Contact Map
4kyzA	1	0.6299	2.7	0.923	Contact Map
3weuA	4	0.0709	2.1	0.928	Contact Map
4tx1A	5	0.252	2	0.929	Contact Map
4jutA	4	0.5197	1.9	0.929	Contact Map
4phqA	1	0.3386	1.1	0.939	Contact Map
3w3sA	2	0.6299	1	0.94	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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