SseB - PFAM28P - GREMLIN Contacts

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SseB - SseB protein N-terminal domain

PFAM:	PF07179	Sequences: LEAALAAAAAGPDPEARPAFLRALLDARLLVPVVAEAEEEVDKGSELALVTLEGPDGRRALPVFTSEERLAAWDAGARPVPVALPGAALAALLEGAAGLVLNPGGPVGFVLPPEEVAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (114)
Sequences:	7669 (5692)
Seq/√Len:	533.1
META:	0.772

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_R	83_A	2.867	1.00
54_G	58_R	2.792	1.00
53_E	59_R	2.667	1.00
13_D	16_A	2.599	1.00
60_A	98_G	2.377	1.00
85_P	88_A	2.315	1.00
24_L	29_L	2.164	1.00
29_L	63_V	2.132	1.00
63_V	99_L	1.949	1.00
66_S	102_N	1.943	1.00
66_S	69_R	1.868	1.00
2_E	102_N	1.763	1.00
3_A	7_A	1.746	1.00
58_R	97_A	1.739	1.00
34_V	48_A	1.730	1.00
41_V	44_G	1.697	1.00
19_A	22_R	1.662	1.00
4_A	23_A	1.627	1.00
2_E	66_S	1.613	1.00
109_F	115_E	1.608	1.00
69_R	106_P	1.591	1.00
23_A	26_D	1.584	1.00
100_V	103_P	1.534	1.00
114_E	117_A	1.511	1.00
16_A	19_A	1.494	1.00
88_A	91_A	1.489	1.00
2_E	69_R	1.460	1.00
51_T	59_R	1.436	1.00
6_A	10_A	1.418	1.00
70_L	81_P	1.407	1.00
7_A	16_A	1.387	1.00
68_E	71_A	1.366	1.00
6_A	107_V	1.352	1.00
86_G	89_L	1.318	1.00
63_V	89_L	1.313	1.00
3_A	6_A	1.298	1.00
24_L	111_L	1.290	1.00
20_F	109_F	1.256	1.00
58_R	98_G	1.248	1.00
62_P	103_P	1.243	1.00
112_P	115_E	1.232	1.00
18_P	22_R	1.230	1.00
41_V	45_S	1.229	1.00
64_F	73_W	1.226	1.00
67_E	81_P	1.225	1.00
2_E	6_A	1.186	1.00
94_E	117_A	1.183	1.00
5_L	9_A	1.168	1.00
28_R	85_P	1.163	1.00
29_L	101_L	1.155	1.00
14_P	17_R	1.151	1.00
87_A	91_A	1.144	1.00
19_A	23_A	1.119	1.00
113_P	117_A	1.096	1.00
23_A	27_A	1.085	1.00
42_D	45_S	1.083	1.00
105_G	108_G	1.038	1.00
63_V	101_L	1.034	1.00
54_G	110_V	1.028	1.00
5_L	8_A	1.021	1.00
84_L	88_A	1.020	1.00
50_V	53_E	1.010	1.00
89_L	93_L	1.008	1.00
26_D	87_A	0.991	1.00
69_R	105_G	0.987	1.00
8_A	12_P	0.971	1.00
17_R	115_E	0.956	1.00
15_E	18_P	0.955	1.00
29_L	86_G	0.948	1.00
86_G	93_L	0.940	1.00
22_R	26_D	0.933	1.00
31_V	49_L	0.931	1.00
14_P	18_P	0.931	1.00
8_A	20_F	0.931	1.00
101_L	111_L	0.930	1.00
32_P	70_L	0.922	1.00
88_A	92_L	0.912	1.00
96_A	113_P	0.909	1.00
34_V	50_V	0.908	1.00
2_E	5_L	0.906	1.00
54_G	60_A	0.897	1.00
52_L	62_P	0.895	1.00
109_F	112_P	0.891	1.00
47_L	50_V	0.888	1.00
93_L	99_L	0.882	1.00
2_E	8_A	0.871	1.00
83_A	86_G	0.866	1.00
33_V	80_V	0.859	1.00
7_A	19_A	0.846	1.00
76_G	79_P	0.838	1.00
67_E	83_A	0.831	1.00
61_L	96_A	0.824	1.00
67_E	70_L	0.814	1.00
30_L	81_P	0.805	1.00
30_L	67_E	0.800	1.00
5_L	20_F	0.796	1.00
8_A	17_R	0.788	1.00
111_L	115_E	0.767	1.00
12_P	17_R	0.765	1.00
82_V	85_P	0.761	1.00
7_A	10_A	0.758	1.00
100_V	108_G	0.748	1.00
60_A	100_V	0.748	1.00
75_A	79_P	0.746	1.00
33_V	82_V	0.746	1.00
52_L	103_P	0.745	1.00
17_R	20_F	0.745	1.00
67_E	71_A	0.732	1.00
107_V	110_V	0.729	1.00
104_G	108_G	0.721	1.00
72_A	76_G	0.721	1.00
102_N	107_V	0.720	1.00
86_G	90_A	0.717	1.00
71_A	74_D	0.707	1.00
89_L	92_L	0.705	1.00
24_L	86_G	0.704	1.00
64_F	74_D	0.702	1.00
44_G	47_L	0.697	1.00
75_A	78_R	0.696	1.00
63_V	111_L	0.688	1.00
20_F	101_L	0.679	1.00
67_E	72_A	0.670	1.00
33_V	70_L	0.663	1.00
37_A	43_K	0.656	1.00
69_R	104_G	0.653	1.00
21_L	25_L	0.652	1.00
12_P	16_A	0.651	1.00
81_P	84_L	0.649	1.00
65_T	101_L	0.639	1.00
22_R	25_L	0.637	1.00
101_L	109_F	0.630	1.00
25_L	90_A	0.624	1.00
30_L	80_V	0.620	1.00
53_E	57_G	0.616	1.00
4_A	19_A	0.615	1.00
98_G	113_P	0.610	1.00
69_R	73_W	0.604	1.00
14_P	19_A	0.603	1.00
71_A	75_A	0.581	0.99
6_A	9_A	0.578	0.99
95_G	117_A	0.574	0.99
74_D	77_A	0.573	0.99
9_A	14_P	0.573	0.99
28_R	32_P	0.568	0.99
10_A	14_P	0.568	0.99
24_L	90_A	0.555	0.99
98_G	117_A	0.554	0.99
17_R	21_L	0.553	0.99
91_A	94_E	0.548	0.99
59_R	97_A	0.542	0.99
90_A	99_L	0.539	0.99
37_A	42_D	0.538	0.99
21_L	109_F	0.536	0.99
69_R	102_N	0.531	0.99
48_A	51_T	0.531	0.99
37_A	45_S	0.529	0.99
9_A	12_P	0.529	0.99
103_P	108_G	0.529	0.99
3_A	8_A	0.526	0.99
72_A	75_A	0.521	0.99
73_W	76_G	0.520	0.99
40_E	43_K	0.520	0.99
13_D	17_R	0.520	0.99
29_L	89_L	0.515	0.99
98_G	109_F	0.514	0.99
4_A	7_A	0.512	0.99
21_L	115_E	0.512	0.99
51_T	96_A	0.512	0.99
50_V	79_P	0.510	0.99
80_V	83_A	0.510	0.99
31_V	84_L	0.500	0.98

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
4ev1A	2	0.9492	24.7	0.863	Contact Map
3ihjA	2	0.9068	5.8	0.898	Contact Map
1pq4A	1	0.3475	5.6	0.898	Contact Map
4cl2A	1	0.339	5.1	0.9	Contact Map
1fg7A	2	0.8305	4.9	0.901	Contact Map
3zk9A	1	0.339	4.4	0.903	Contact Map
4mozA	5	0.8051	4.4	0.903	Contact Map
4oxrA	2	0.339	4.3	0.903	Contact Map
2jttC	1	0.2373	4	0.904	Contact Map
4lzpB	2	0.7881	3.9	0.906	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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