DctQ - PFAM28P - GREMLIN Contacts

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DctQ - Tripartite ATP-independent periplasmic transporters, DctQ component

PFAM:	PF04290	Sequences: MVLLVFAQVVLRYVFNSPLPWAEELARYLFVWLVFLGAAYALRRGGHIRVDLLYDRLPPRARRVLDLLGDLLFLAFCALLAWYGWFVLSLLGGGQSSPALGIPLWPVYLAIPVGFALLALQLLAELIRLLRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	132 (128)
Sequences:	87979 (57446)
Seq/√Len:	5077.5
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_F	122_L	2.537	1.00
7_A	19_L	2.497	1.00
58_P	61_A	2.479	1.00
32_W	110_A	2.467	1.00
61_A	64_V	2.194	1.00
45_G	125_E	2.173	1.00
78_A	82_W	2.121	1.00
121_Q	124_A	1.963	1.00
41_A	46_G	1.937	1.00
87_V	91_L	1.930	1.00
5_V	26_A	1.842	1.00
57_L	61_A	1.793	1.00
7_A	11_L	1.767	1.00
74_L	119_A	1.754	1.00
70_D	129_L	1.726	1.00
51_D	55_D	1.687	1.00
42_L	122_L	1.655	1.00
77_C	118_L	1.650	1.00
40_Y	44_R	1.636	1.00
43_R	121_Q	1.624	1.00
81_A	116_A	1.601	1.00
42_L	118_L	1.597	1.00
42_L	125_E	1.575	1.00
54_Y	62_R	1.565	1.00
60_R	64_V	1.553	1.00
57_L	65_L	1.550	1.00
103_P	106_P	1.485	1.00
11_L	15_F	1.476	1.00
77_C	119_A	1.459	1.00
54_Y	66_D	1.442	1.00
88_L	92_G	1.420	1.00
67_L	126_L	1.416	1.00
23_E	27_R	1.409	1.00
70_D	125_E	1.394	1.00
11_L	17_S	1.368	1.00
78_A	119_A	1.340	1.00
38_A	118_L	1.333	1.00
39_A	117_L	1.315	1.00
70_D	126_L	1.313	1.00
10_V	14_V	1.303	1.00
11_L	19_L	1.294	1.00
93_G	105_W	1.293	1.00
77_C	115_F	1.285	1.00
30_F	34_V	1.274	1.00
63_R	129_L	1.270	1.00
81_A	119_A	1.244	1.00
86_F	90_L	1.243	1.00
59_P	63_R	1.240	1.00
81_A	85_W	1.233	1.00
66_D	129_L	1.232	1.00
125_E	129_L	1.226	1.00
59_P	62_R	1.211	1.00
88_L	91_L	1.206	1.00
39_A	121_Q	1.166	1.00
8_Q	23_E	1.156	1.00
121_Q	125_E	1.153	1.00
85_W	112_P	1.151	1.00
125_E	128_R	1.135	1.00
81_A	115_F	1.134	1.00
90_L	94_G	1.128	1.00
97_S	100_L	1.117	1.00
65_L	69_G	1.115	1.00
80_L	115_F	1.093	1.00
90_L	93_G	1.088	1.00
60_R	63_R	1.087	1.00
77_C	122_L	1.069	1.00
124_A	128_R	1.059	1.00
89_S	93_G	1.057	1.00
79_L	83_Y	1.055	1.00
74_L	126_L	1.036	1.00
6_F	10_V	1.030	1.00
62_R	66_D	1.028	1.00
87_V	90_L	1.028	1.00
10_V	15_F	1.023	1.00
8_Q	22_A	1.009	1.00
28_Y	107_V	0.993	1.00
3_L	7_A	0.983	1.00
28_Y	97_S	0.972	1.00
64_V	68_L	0.966	1.00
4_L	29_L	0.950	1.00
97_S	101_G	0.949	1.00
96_S	101_G	0.945	1.00
66_D	70_D	0.922	1.00
106_P	110_A	0.918	1.00
89_S	92_G	0.910	1.00
109_L	112_P	0.907	1.00
49_R	66_D	0.905	1.00
84_G	115_F	0.899	1.00
73_F	77_C	0.891	1.00
8_Q	19_L	0.890	1.00
72_L	75_A	0.884	1.00
74_L	123_L	0.877	1.00
43_R	124_A	0.875	1.00
64_V	67_L	0.874	1.00
110_A	114_G	0.872	1.00
63_R	67_L	0.862	1.00
38_A	42_L	0.857	1.00
70_D	122_L	0.856	1.00
67_L	129_L	0.835	1.00
75_A	78_A	0.834	1.00
4_L	22_A	0.831	1.00
95_Q	104_L	0.830	1.00
104_L	108_Y	0.828	1.00
19_L	22_A	0.826	1.00
74_L	122_L	0.826	1.00
45_G	49_R	0.820	1.00
2_V	6_F	0.819	1.00
84_G	111_I	0.818	1.00
61_A	65_L	0.805	1.00
105_W	109_L	0.802	1.00
11_L	14_V	0.793	1.00
91_L	95_Q	0.789	1.00
81_A	112_P	0.788	1.00
41_A	47_H	0.786	1.00
122_L	125_E	0.781	1.00
45_G	66_D	0.774	1.00
105_W	108_Y	0.762	1.00
102_I	107_V	0.756	1.00
104_L	107_V	0.749	1.00
25_L	100_L	0.748	1.00
84_G	112_P	0.738	1.00
39_A	114_G	0.738	1.00
32_W	36_L	0.734	1.00
106_P	109_L	0.732	1.00
71_L	126_L	0.729	1.00
71_L	75_A	0.726	1.00
113_V	117_L	0.722	1.00
98_P	101_G	0.718	1.00
114_G	118_L	0.715	1.00
25_L	102_I	0.714	1.00
31_V	34_V	0.713	1.00
21_W	25_L	0.707	1.00
63_R	66_D	0.707	1.00
52_L	56_R	0.700	1.00
49_R	54_Y	0.698	1.00
35_F	111_I	0.697	1.00
62_R	65_L	0.697	1.00
82_W	85_W	0.694	1.00
74_L	78_A	0.690	1.00
109_L	113_V	0.679	1.00
123_L	127_I	0.675	1.00
8_Q	18_P	0.671	1.00
8_Q	11_L	0.668	1.00
45_G	129_L	0.666	1.00
4_L	25_L	0.665	1.00
54_Y	65_L	0.660	1.00
116_A	120_L	0.658	1.00
93_G	96_S	0.656	1.00
91_L	94_G	0.650	1.00
42_L	47_H	0.644	1.00
37_G	41_A	0.636	1.00
124_A	127_I	0.632	1.00
92_G	95_Q	0.626	1.00
53_L	56_R	0.621	1.00
86_F	89_S	0.620	1.00
120_L	124_A	0.616	1.00
89_S	105_W	0.616	1.00
96_S	100_L	0.614	1.00
68_L	72_L	0.614	1.00
86_F	93_G	0.611	1.00
10_V	13_Y	0.609	1.00
55_D	62_R	0.606	1.00
40_Y	43_R	0.603	1.00
112_P	116_A	0.600	1.00
54_Y	69_G	0.595	1.00
6_F	9_V	0.593	1.00
27_R	31_V	0.592	1.00
4_L	26_A	0.586	1.00
11_L	18_P	0.585	1.00
45_G	70_D	0.579	1.00
9_V	13_Y	0.579	1.00
30_F	33_L	0.579	1.00
59_P	64_V	0.573	1.00
119_A	122_L	0.572	1.00
25_L	29_L	0.567	1.00
66_D	69_G	0.565	1.00
69_G	73_F	0.558	1.00
38_A	47_H	0.552	1.00
82_W	87_V	0.548	1.00
67_L	71_L	0.545	1.00
46_G	49_R	0.541	1.00
42_L	70_D	0.541	1.00
87_V	94_G	0.539	1.00
5_V	8_Q	0.537	1.00
88_L	93_G	0.531	1.00
7_A	17_S	0.524	1.00
114_G	117_L	0.522	1.00
22_A	26_A	0.519	1.00
35_F	115_F	0.513	1.00
87_V	92_G	0.510	1.00
107_V	110_A	0.503	1.00
23_E	26_A	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
2wswA	3	0.6212	4.8	0.911	Contact Map
2a65A	2	0.9242	4.5	0.912	Contact Map
4humA	1	0.9773	4.1	0.914	Contact Map
2ov2I	1	0.2424	3.5	0.917	Contact Map
2odbB	1	0.2424	3.3	0.918	Contact Map
3mktA	1	0.9773	3.1	0.92	Contact Map
4xp4A	1	0.9545	2.9	0.921	Contact Map
4c7rA	3	0.9924	2.8	0.921	Contact Map
4lz6A	1	0.9848	2.8	0.922	Contact Map
2qmeI	1	0.1591	1.9	0.928	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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