CopD - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

CopD - Copper resistance protein D

PFAM:	PF05425	Sequences: AAALRRFSRLALVAVAVLVATGLVNAWLLLGLSALWGTPYGRLLLAKLALVAVLLALAAVNRFRLVPRLARARPAAGAALRRRLRRLVAVELALGLAVLALAAVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (100)
Sequences:	35268 (25242)
Seq/√Len:	2524.2
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_L	95_G	2.675	1.00
23_L	48_L	2.443	1.00
42_R	46_A	2.371	1.00
59_A	63_F	2.299	1.00
45_L	49_A	2.193	1.00
39_P	42_R	2.176	1.00
62_R	66_V	2.018	1.00
31_G	34_A	1.912	1.00
19_V	55_L	1.855	1.00
24_V	28_L	1.811	1.00
21_T	25_N	1.796	1.00
50_L	98_V	1.786	1.00
60_V	64_R	1.747	1.00
9_R	13_V	1.691	1.00
15_V	55_L	1.683	1.00
64_R	68_R	1.673	1.00
33_S	37_G	1.646	1.00
32_L	35_L	1.640	1.00
46_A	101_L	1.600	1.00
98_V	102_A	1.585	1.00
50_L	94_L	1.585	1.00
25_N	29_L	1.567	1.00
26_A	30_L	1.530	1.00
26_A	44_L	1.465	1.00
35_L	41_G	1.458	1.00
60_V	65_L	1.456	1.00
5_R	9_R	1.405	1.00
38_T	41_G	1.368	1.00
32_L	36_W	1.355	1.00
50_L	101_L	1.353	1.00
23_L	27_W	1.344	1.00
42_R	45_L	1.310	1.00
15_V	18_L	1.274	1.00
61_N	87_L	1.262	1.00
57_L	87_L	1.248	1.00
16_A	20_A	1.206	1.00
47_K	51_V	1.203	1.00
77_G	81_R	1.192	1.00
12_L	62_R	1.187	1.00
25_N	28_L	1.184	1.00
19_V	51_V	1.171	1.00
56_A	60_V	1.140	1.00
12_L	15_V	1.140	1.00
10_L	14_A	1.131	1.00
82_R	86_R	1.120	1.00
76_A	79_A	1.108	1.00
45_L	48_L	1.108	1.00
33_S	36_W	1.094	1.00
11_A	58_A	1.063	1.00
10_L	13_V	1.051	1.00
13_V	17_V	1.049	1.00
39_P	43_L	1.031	1.00
43_L	101_L	1.027	1.00
9_R	12_L	1.020	1.00
6_R	10_L	1.015	1.00
76_A	80_L	1.013	1.00
13_V	16_A	1.006	1.00
8_S	62_R	0.994	1.00
44_L	48_L	0.982	1.00
85_R	89_A	0.976	1.00
88_V	91_E	0.963	1.00
60_V	87_L	0.958	1.00
46_A	50_L	0.953	1.00
49_A	53_V	0.950	1.00
57_L	90_V	0.950	1.00
93_A	97_A	0.940	1.00
79_A	82_R	0.930	1.00
81_R	86_R	0.909	1.00
91_E	95_G	0.903	1.00
63_F	67_P	0.892	1.00
78_A	82_R	0.885	1.00
46_A	49_A	0.874	1.00
34_A	37_G	0.865	1.00
78_A	81_R	0.859	1.00
12_L	63_F	0.845	1.00
83_R	86_R	0.845	1.00
92_L	96_L	0.841	1.00
66_V	69_L	0.830	1.00
75_A	80_L	0.822	1.00
89_A	92_L	0.822	1.00
73_R	76_A	0.814	1.00
77_G	80_L	0.813	1.00
36_W	45_L	0.813	1.00
75_A	79_A	0.810	1.00
48_L	52_A	0.809	1.00
54_L	94_L	0.807	1.00
85_R	88_V	0.797	1.00
65_L	87_L	0.787	1.00
8_S	12_L	0.769	1.00
88_V	92_L	0.763	1.00
89_A	93_A	0.762	1.00
102_A	105_L	0.756	1.00
58_A	62_R	0.750	1.00
30_L	40_Y	0.746	1.00
57_L	61_N	0.735	1.00
20_A	24_V	0.732	1.00
83_R	87_L	0.730	1.00
12_L	16_A	0.729	1.00
80_L	83_R	0.729	1.00
18_L	21_T	0.725	1.00
35_L	45_L	0.714	1.00
16_A	19_V	0.713	1.00
17_V	21_T	0.710	1.00
52_A	56_A	0.697	1.00
43_L	104_V	0.680	1.00
51_V	55_L	0.674	1.00
86_R	90_V	0.673	1.00
26_A	48_L	0.664	1.00
76_A	81_R	0.659	1.00
24_V	27_W	0.655	1.00
58_A	61_N	0.647	1.00
74_P	78_A	0.647	1.00
4_L	84_L	0.640	1.00
79_A	83_R	0.638	1.00
60_V	83_R	0.638	1.00
74_P	79_A	0.637	1.00
65_L	68_R	0.635	1.00
92_L	95_G	0.630	1.00
7_F	61_N	0.625	1.00
73_R	77_G	0.621	1.00
96_L	100_A	0.619	1.00
100_A	104_V	0.615	1.00
14_A	18_L	0.615	1.00
57_L	94_L	0.613	1.00
4_L	66_V	0.605	1.00
55_L	59_A	0.602	1.00
86_R	89_A	0.600	1.00
80_L	85_R	0.598	1.00
95_G	99_L	0.592	1.00
99_L	102_A	0.583	1.00
27_W	31_G	0.573	1.00
6_R	9_R	0.569	1.00
74_P	77_G	0.555	1.00
53_V	94_L	0.554	1.00
97_A	101_L	0.554	1.00
47_K	58_A	0.550	1.00
61_N	65_L	0.547	1.00
4_L	88_V	0.546	1.00
65_L	83_R	0.544	1.00
37_G	42_R	0.541	1.00
21_T	24_V	0.539	1.00
50_L	97_A	0.537	1.00
56_A	59_A	0.532	1.00
98_V	101_L	0.529	1.00
35_L	38_T	0.528	1.00
20_A	23_L	0.521	1.00
30_L	35_L	0.520	1.00
43_L	105_L	0.511	1.00
58_A	91_E	0.508	1.00
78_A	83_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
4i0uA	4	0.5905	64.8	0.787	Contact Map
4ev6A	3	0.6095	62.1	0.791	Contact Map
2qjyA	2	0.9143	16	0.849	Contact Map
1kqfC	3	1	14.7	0.851	Contact Map
1kf6C	1	0.9714	12.8	0.855	Contact Map
3cx5C	2	0.9143	12.4	0.856	Contact Map
4ogqA	2	0.9143	7.4	0.869	Contact Map
4humA	1	0.981	5.9	0.876	Contact Map
4gd3A	2	0.9143	5.9	0.876	Contact Map
1pp9C	2	0.8952	5.2	0.878	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.

Page generated in 0.0054 seconds.