FlpD - PFAM28P - GREMLIN Contacts

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FlpD - Methyl-viologen-reducing hydrogenase, delta subunit

PFAM:	PF02662	Sequences: IVAFLCNWCSYAAADLAGTSRLQYPPNVRIIRVPCSGRVDPLFILKAFEKGADGVLVAGCHPGDCHYIEGNYRARRRVELLKKLLEELGIEPERLRLEWVSASEGEKFAEVVNEFTEKIRELG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (123)
Sequences:	17218 (8788)
Seq/√Len:	792.4
META:	0.96

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_E	92_P	3.556	1.00
96_R	118_K	3.196	1.00
5_L	30_I	2.446	1.00
93_E	118_K	2.229	1.00
46_K	50_K	2.096	1.00
27_N	116_T	2.094	1.00
82_K	92_P	2.093	1.00
98_E	111_V	2.083	1.00
62_P	75_R	2.029	1.00
54_G	119_I	1.963	1.00
106_E	110_E	1.878	1.00
25_P	113_N	1.851	1.00
46_K	49_E	1.841	1.00
10_S	58_A	1.794	1.00
107_K	111_V	1.756	1.00
33_V	39_V	1.746	1.00
3_A	28_V	1.737	1.00
56_L	98_E	1.702	1.00
110_E	114_E	1.651	1.00
114_E	118_K	1.644	1.00
78_V	95_L	1.640	1.00
48_F	95_L	1.625	1.00
54_G	115_F	1.619	1.00
116_T	120_R	1.605	1.00
75_R	79_E	1.577	1.00
2_V	52_A	1.575	1.00
36_S	57_V	1.559	1.00
62_P	99_W	1.553	1.00
36_S	59_G	1.537	1.00
7_N	32_R	1.537	1.00
75_R	99_W	1.487	1.00
69_E	73_R	1.475	1.00
104_E	107_K	1.474	1.00
56_L	112_V	1.466	1.00
59_G	99_W	1.452	1.00
58_A	98_E	1.448	1.00
62_P	72_Y	1.424	1.00
118_K	121_E	1.419	1.00
22_L	109_A	1.417	1.00
117_E	120_R	1.368	1.00
69_E	72_Y	1.365	1.00
117_E	121_E	1.349	1.00
61_H	104_E	1.318	1.00
1_I	116_T	1.290	1.00
111_V	114_E	1.289	1.00
109_A	113_N	1.288	1.00
41_P	81_L	1.235	1.00
38_R	43_F	1.223	1.00
28_V	112_V	1.213	1.00
61_H	64_D	1.210	1.00
96_R	114_E	1.201	1.00
84_L	87_E	1.201	1.00
40_D	43_F	1.168	1.00
2_V	47_A	1.166	1.00
5_L	108_F	1.141	1.00
96_R	115_F	1.131	1.00
108_F	112_V	1.125	1.00
91_E	94_R	1.114	1.00
63_G	71_N	1.108	1.00
39_V	44_I	1.101	1.00
79_E	82_K	1.100	1.00
113_N	117_E	1.091	1.00
114_E	117_E	1.088	1.00
100_V	111_V	1.050	1.00
5_L	10_S	1.046	1.00
41_P	80_L	1.025	1.00
82_K	95_L	1.024	1.00
60_C	65_C	1.020	1.00
96_R	111_V	1.019	1.00
44_I	55_V	0.998	1.00
110_E	113_N	0.987	1.00
56_L	96_R	0.984	1.00
113_N	116_T	0.979	1.00
73_R	77_R	0.958	1.00
101_S	104_E	0.956	1.00
98_E	107_K	0.942	1.00
16_L	20_S	0.939	1.00
8_W	67_Y	0.929	1.00
59_G	97_L	0.923	1.00
34_P	38_R	0.907	1.00
11_Y	15_D	0.905	1.00
105_G	109_A	0.891	1.00
74_A	97_L	0.888	1.00
45_L	81_L	0.888	1.00
5_L	58_A	0.873	1.00
83_K	86_E	0.866	1.00
84_L	88_L	0.865	1.00
3_A	56_L	0.863	1.00
58_A	100_V	0.858	1.00
35_C	65_C	0.857	1.00
18_G	24_Y	0.846	1.00
115_F	119_I	0.843	1.00
86_E	91_E	0.836	1.00
78_V	82_K	0.833	1.00
73_R	87_E	0.832	1.00
4_F	47_A	0.803	1.00
76_R	79_E	0.802	1.00
7_N	12_A	0.800	1.00
57_V	78_V	0.792	1.00
107_K	110_E	0.788	1.00
42_L	46_K	0.782	1.00
61_H	101_S	0.766	1.00
83_K	87_E	0.753	1.00
44_I	95_L	0.746	1.00
73_R	76_R	0.733	1.00
16_L	19_T	0.724	1.00
56_L	111_V	0.720	1.00
100_V	107_K	0.720	1.00
6_C	35_C	0.710	1.00
7_N	34_P	0.710	1.00
18_G	21_R	0.709	1.00
49_E	88_L	0.706	1.00
76_R	80_L	0.700	1.00
5_L	11_Y	0.694	1.00
35_C	70_G	0.693	1.00
72_Y	75_R	0.692	1.00
44_I	81_L	0.690	1.00
22_L	106_E	0.675	1.00
4_F	33_V	0.673	1.00
39_V	57_V	0.671	1.00
71_N	99_W	0.663	1.00
70_G	74_A	0.654	1.00
78_V	97_L	0.652	1.00
65_C	70_G	0.652	1.00
15_D	18_G	0.650	1.00
37_G	70_G	0.647	1.00
48_F	90_I	0.647	1.00
82_K	93_E	0.641	1.00
6_C	65_C	0.639	1.00
49_E	87_E	0.637	1.00
42_L	87_E	0.635	1.00
72_Y	76_R	0.632	1.00
14_A	30_I	0.632	1.00
106_E	109_A	0.629	1.00
58_A	108_F	0.625	1.00
90_I	94_R	0.622	1.00
4_F	31_I	0.621	1.00
44_I	47_A	0.621	1.00
11_Y	32_R	0.619	1.00
24_Y	28_V	0.619	1.00
3_A	112_V	0.612	1.00
13_A	17_A	0.608	1.00
111_V	115_F	0.606	1.00
80_L	84_L	0.604	1.00
68_I	73_R	0.604	1.00
45_L	84_L	0.603	1.00
43_F	47_A	0.601	1.00
119_I	122_L	0.593	1.00
9_C	60_C	0.592	1.00
43_F	46_K	0.592	1.00
80_L	83_K	0.591	1.00
77_R	81_L	0.588	1.00
27_N	120_R	0.584	1.00
36_S	39_V	0.584	1.00
10_S	13_A	0.582	1.00
98_E	114_E	0.571	1.00
81_L	84_L	0.567	1.00
116_T	119_I	0.561	1.00
6_C	60_C	0.551	1.00
106_E	113_N	0.542	1.00
33_V	38_R	0.540	1.00
77_R	87_E	0.539	1.00
44_I	57_V	0.538	1.00
20_S	106_E	0.536	1.00
40_D	87_E	0.535	1.00
115_F	118_K	0.530	1.00
36_S	71_N	0.526	1.00
34_P	67_Y	0.524	1.00
59_G	71_N	0.523	1.00
82_K	91_E	0.522	1.00
79_E	83_K	0.520	1.00
12_A	19_T	0.520	1.00
85_L	90_I	0.519	1.00
93_E	121_E	0.518	1.00
7_N	11_Y	0.515	1.00
4_F	39_V	0.514	1.00
47_A	55_V	0.514	1.00
45_L	88_L	0.510	1.00
41_P	45_L	0.510	1.00
23_Q	113_N	0.508	1.00
56_L	115_F	0.508	1.00
63_G	72_Y	0.507	1.00
54_G	94_R	0.501	1.00
7_N	29_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
2cndA	1	0.7073	53.5	0.878	Contact Map
4eacA	1	0.748	40.8	0.887	Contact Map
2eixA	2	0.6911	40.3	0.887	Contact Map
3w5hA	1	0.6992	39	0.888	Contact Map
2ozlB	2	0.9106	30.6	0.894	Contact Map
1gvhA	3	0.7398	29.4	0.895	Contact Map
1cqxA	2	0.748	29.2	0.895	Contact Map
4g1vA	3	0.7561	25.9	0.898	Contact Map
1tz9A	2	0.7317	25.1	0.898	Contact Map
3qe2A	1	0.9268	24.7	0.899	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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