NifQ - PFAM28P - GREMLIN Contacts

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

NifQ - NifQ

PFAM:	PF04891	Sequences: VLACILASAAAGGGALPAALGLSPAEFAALLARHFPGAALPLLLAALGAPLDAERDDEEEDLRDLLLAHRAGDSESERWLAAIIARACMGPDHLWQDLGLWSRAELSALLRRHFPALAARNTRDMKWKKFLYRQLCEREGIYLCRAPSCEVCSDYALCFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	160 (158)
Sequences:	1157 (888)
Seq/√Len:	70.7
META:	0.686

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_A	115_P	5.823	1.00
68_A	138_R	4.040	1.00
101_W	105_E	3.977	1.00
69_H	116_A	3.742	1.00
96_Q	126_K	3.305	1.00
136_C	144_C	2.759	1.00
110_L	131_L	2.625	1.00
120_R	130_F	2.530	1.00
72_G	77_E	2.455	1.00
63_R	82_A	2.342	1.00
92_D	96_Q	2.236	1.00
67_L	81_A	2.223	1.00
133_R	137_E	2.206	1.00
115_P	119_A	2.113	1.00
26_E	78_R	2.089	1.00
3_A	35_F	1.978	1.00
58_E	132_Y	1.972	1.00
60_E	64_D	1.921	1.00
146_A	150_E	1.912	1.00
8_S	12_G	1.892	1.00
69_H	120_R	1.892	1.00
8_S	13_G	1.867	1.00
23_S	26_E	1.864	1.00
67_L	70_R	1.826	1.00
120_R	134_Q	1.814	1.00
125_M	144_C	1.718	1.00
107_S	118_A	1.707	1.00
67_L	78_R	1.658	1.00
71_A	116_A	1.649	0.99
93_H	103_R	1.580	0.99
146_A	151_V	1.575	0.99
5_I	8_S	1.567	0.99
59_E	87_A	1.535	0.99
20_L	83_I	1.530	0.99
58_E	61_D	1.497	0.99
126_K	154_D	1.434	0.99
145_R	148_S	1.402	0.98
102_S	106_L	1.365	0.98
4_C	105_E	1.355	0.98
69_H	117_L	1.321	0.97
65_L	135_L	1.296	0.97
29_A	75_E	1.284	0.97
125_M	136_C	1.262	0.97
148_S	151_V	1.252	0.97
132_Y	136_C	1.248	0.96
133_R	136_C	1.229	0.96
110_L	118_A	1.210	0.96
108_A	112_R	1.209	0.96
70_R	79_W	1.202	0.96
133_R	144_C	1.156	0.95
6_L	30_L	1.156	0.95
126_K	160_G	1.153	0.94
59_E	86_R	1.148	0.94
97_D	109_L	1.141	0.94
134_Q	137_E	1.138	0.94
132_Y	144_C	1.137	0.94
123_R	150_E	1.134	0.94
71_A	77_E	1.113	0.93
80_L	84_I	1.112	0.93
110_L	122_T	1.110	0.93
134_Q	145_R	1.102	0.93
102_S	105_E	1.076	0.92
9_A	12_G	1.061	0.92
74_S	77_E	1.044	0.91
102_S	107_S	1.034	0.91
126_K	129_K	1.031	0.90
64_D	68_A	1.026	0.90
65_L	103_R	1.024	0.90
87_A	96_Q	1.000	0.89
89_M	135_L	0.994	0.89
104_A	108_A	0.989	0.88
4_C	83_I	0.987	0.88
4_C	101_W	0.978	0.88
16_L	87_A	0.977	0.88
156_A	160_G	0.973	0.88
55_R	148_S	0.966	0.87
106_L	136_C	0.963	0.87
3_A	6_L	0.962	0.87
144_C	148_S	0.960	0.87
24_P	28_A	0.959	0.87
56_D	86_R	0.947	0.86
10_A	15_A	0.946	0.86
73_D	77_E	0.937	0.86
66_L	84_I	0.924	0.85
96_Q	110_L	0.909	0.84
91_P	112_R	0.904	0.83
135_L	138_R	0.901	0.83
27_F	99_G	0.880	0.82
9_A	15_A	0.878	0.82
129_K	146_A	0.869	0.81
76_S	79_W	0.868	0.81
149_C	152_C	0.866	0.81
134_Q	159_F	0.865	0.81
84_I	110_L	0.863	0.81
92_D	97_D	0.862	0.80
106_L	144_C	0.860	0.80
142_Y	148_S	0.852	0.80
62_L	117_L	0.852	0.80
150_E	155_Y	0.844	0.79
58_E	136_C	0.842	0.79
111_R	118_A	0.842	0.79
116_A	119_A	0.835	0.78
129_K	136_C	0.832	0.78
12_G	17_P	0.831	0.78
58_E	144_C	0.825	0.77
25_A	50_P	0.825	0.77
27_F	113_H	0.818	0.77
81_A	84_I	0.804	0.76
93_H	129_K	0.804	0.76
16_L	20_L	0.800	0.75
154_D	157_L	0.799	0.75
65_L	117_L	0.798	0.75
96_Q	129_K	0.794	0.75
139_E	143_L	0.793	0.75
136_C	146_A	0.790	0.74
111_R	119_A	0.786	0.74
18_A	24_P	0.783	0.74
97_D	126_K	0.781	0.74
61_D	138_R	0.778	0.73
87_A	143_L	0.776	0.73
126_K	157_L	0.776	0.73
97_D	129_K	0.770	0.72
100_L	118_A	0.769	0.72
59_E	89_M	0.763	0.72
107_S	126_K	0.761	0.72
33_R	74_S	0.758	0.71
9_A	18_A	0.752	0.71
152_C	158_C	0.749	0.70
130_F	134_Q	0.749	0.70
104_A	124_D	0.742	0.70
110_L	115_P	0.739	0.69
72_G	131_L	0.734	0.69
58_E	135_L	0.733	0.69
3_A	7_A	0.731	0.69
34_H	79_W	0.725	0.68
143_L	146_A	0.724	0.68
90_G	97_D	0.722	0.68
49_A	53_A	0.718	0.67
62_L	131_L	0.716	0.67
3_A	36_P	0.713	0.67
47_L	52_D	0.709	0.66
151_V	156_A	0.709	0.66
25_A	29_A	0.702	0.65
4_C	12_G	0.699	0.65
64_D	69_H	0.696	0.65
5_I	80_L	0.694	0.64
132_Y	135_L	0.693	0.64
81_A	114_F	0.693	0.64
125_M	129_K	0.692	0.64
70_R	77_E	0.690	0.64
12_G	87_A	0.690	0.64
72_G	76_S	0.685	0.63
97_D	147_P	0.680	0.63
7_A	154_D	0.678	0.63
5_I	20_L	0.676	0.62
4_C	9_A	0.675	0.62
86_R	113_H	0.675	0.62
62_L	130_F	0.672	0.62
129_K	143_L	0.671	0.62
59_E	63_R	0.671	0.62
53_A	85_A	0.667	0.61
26_E	108_A	0.662	0.61
47_L	116_A	0.651	0.60
58_E	137_E	0.649	0.59
139_E	142_Y	0.649	0.59
58_E	106_L	0.646	0.59
9_A	20_L	0.641	0.58
93_H	121_N	0.639	0.58
45_A	73_D	0.638	0.58
27_F	34_H	0.638	0.58
6_L	20_L	0.632	0.57
96_Q	143_L	0.631	0.57
56_D	62_L	0.630	0.57
135_L	145_R	0.628	0.57
47_L	50_P	0.628	0.57
58_E	114_F	0.625	0.56
96_Q	157_L	0.625	0.56
61_D	137_E	0.623	0.56
35_F	107_S	0.618	0.56
125_M	133_R	0.617	0.56
14_G	17_P	0.616	0.55
86_R	133_R	0.610	0.55
34_H	76_S	0.607	0.54
146_A	153_S	0.607	0.54
98_L	146_A	0.606	0.54
84_I	123_R	0.604	0.54
7_A	35_F	0.604	0.54
144_C	147_P	0.604	0.54
106_L	132_Y	0.597	0.53
133_R	145_R	0.595	0.53
89_M	131_L	0.593	0.53
5_I	83_I	0.593	0.53
20_L	27_F	0.593	0.53
136_C	148_S	0.591	0.52
57_D	61_D	0.590	0.52
63_R	85_A	0.582	0.51
8_S	87_A	0.581	0.51
12_G	20_L	0.581	0.51
70_R	114_F	0.577	0.51
107_S	154_D	0.576	0.51
144_C	159_F	0.573	0.50
138_R	145_R	0.571	0.50
121_N	125_M	0.568	0.50
23_S	39_A	0.567	0.49
19_A	80_L	0.563	0.49
87_A	90_G	0.562	0.49
25_A	78_R	0.561	0.49
51_L	54_E	0.557	0.48
108_A	111_R	0.557	0.48
18_A	23_S	0.555	0.48
96_Q	153_S	0.552	0.48
38_A	49_A	0.549	0.47
85_A	112_R	0.546	0.47
77_E	126_K	0.543	0.47
85_A	117_L	0.543	0.47
100_L	109_L	0.542	0.46
22_L	30_L	0.542	0.46
136_C	147_P	0.539	0.46
15_A	88_C	0.536	0.46
16_L	83_I	0.535	0.46
98_L	114_F	0.534	0.45
50_P	53_A	0.531	0.45
55_R	80_L	0.530	0.45
57_D	89_M	0.530	0.45
58_E	90_G	0.526	0.44
102_S	124_D	0.525	0.44
55_R	145_R	0.525	0.44
102_S	108_A	0.524	0.44
44_L	48_G	0.523	0.44
31_L	36_P	0.523	0.44
32_A	75_E	0.520	0.44
131_L	135_L	0.516	0.43
35_F	154_D	0.515	0.43
136_C	143_L	0.514	0.43
82_A	86_R	0.507	0.42
106_L	125_M	0.507	0.42
109_L	114_F	0.500	0.41

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
3fspA	1	0.9062	71	0.929	Contact Map
1kg2A	1	0.9062	70.1	0.929	Contact Map
1ornA	1	0.9062	69.1	0.929	Contact Map
2abkA	1	0.9062	68.4	0.93	Contact Map
1keaA	2	0.9062	55	0.935	Contact Map
3n5nX	1	0.9	51.1	0.937	Contact Map
4unfA	1	0.9187	38.1	0.942	Contact Map
4uobA	1	0.9187	29.6	0.945	Contact Map
1z67A	1	0.3812	8.3	0.957	Contact Map
4fzvB	1	0.675	8.3	0.957	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 0.0066 seconds.