SWRB - BACSU - GREMLIN Contacts

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SWRB - Swarming motility protein SwrB

UniProt:	P40405	Sequences: MSTLLWLLSFMLHGVLLYAVIILYTRLAAVKETEKQQKQILEETENTLAAFLLELKEENEKLIENKASSASQSDEESQKSGLQTSETYQERDPVQEAENLPEHIEGLITEVDRREELVNSEVQSFEDQVIELYEQGYSASQIAQKMKSGKTEIELFLKFRSKGVKDS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	167 (155)
Sequences:	120 (113)
Seq/√Len:	9.1

BACSU - SWRB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_S	13_H	4.926	1.00
52_L	151_T	4.172	0.99
45_E	57_E	3.148	0.93
62_L	133_Y	2.746	0.86
44_T	48_L	2.585	0.83
125_F	153_I	2.434	0.78
51_F	158_K	2.208	0.71
58_E	150_K	2.093	0.67
18_Y	22_I	2.016	0.64
6_W	9_S	2.006	0.63
13_H	31_K	1.964	0.61
13_H	28_A	1.959	0.61
44_T	51_F	1.955	0.61
13_H	48_L	1.934	0.60
34_E	151_T	1.868	0.57
16_L	20_V	1.849	0.57
53_L	63_I	1.826	0.56
13_H	27_L	1.825	0.56
3_T	7_L	1.784	0.54
20_V	144_Q	1.784	0.54
37_Q	153_I	1.779	0.54
5_L	29_A	1.760	0.53
1_M	20_V	1.729	0.51
5_L	9_S	1.684	0.49
41_L	44_T	1.671	0.49
43_E	57_E	1.621	0.47
26_R	74_D	1.621	0.47
43_E	139_A	1.614	0.46
27_L	31_K	1.603	0.46
140_S	150_K	1.539	0.43
19_A	144_Q	1.470	0.40
129_V	156_F	1.453	0.40
22_I	25_T	1.424	0.38
148_S	153_I	1.415	0.38
61_K	65_N	1.407	0.38
7_L	21_I	1.403	0.37
24_Y	156_F	1.402	0.37
148_S	151_T	1.400	0.37
8_L	51_F	1.381	0.37
64_E	68_S	1.375	0.36
25_T	151_T	1.367	0.36
56_K	159_F	1.353	0.35
17_L	53_L	1.341	0.35
47_T	140_S	1.297	0.33
20_V	23_L	1.295	0.33
45_E	159_F	1.292	0.33
132_L	142_I	1.286	0.33
52_L	55_L	1.269	0.32
74_D	135_Q	1.264	0.32
12_L	20_V	1.245	0.31
10_F	147_K	1.244	0.31
67_A	70_A	1.242	0.31
37_Q	44_T	1.230	0.31
21_I	24_Y	1.209	0.30
37_Q	160_R	1.203	0.30
28_A	65_N	1.199	0.30
44_T	49_A	1.184	0.29
12_L	39_Q	1.173	0.29
41_L	48_L	1.173	0.29
13_H	26_R	1.169	0.28
86_E	138_S	1.168	0.28
51_F	54_E	1.154	0.28
62_L	156_F	1.141	0.27
8_L	39_Q	1.118	0.27
16_L	144_Q	1.112	0.26
110_E	116_E	1.104	0.26
49_A	52_L	1.099	0.26
148_S	156_F	1.089	0.26
107_L	110_E	1.086	0.26
53_L	147_K	1.086	0.26
125_F	128_Q	1.079	0.25
84_T	156_F	1.073	0.25
29_A	44_T	1.072	0.25
64_E	86_E	1.034	0.24
28_A	61_K	1.020	0.23
41_L	62_L	1.016	0.23
12_L	50_A	1.016	0.23
1_M	150_K	1.012	0.23
10_F	44_T	1.006	0.23
60_E	63_I	1.006	0.23
13_H	132_L	1.004	0.23
16_L	141_Q	0.994	0.23
15_V	86_E	0.972	0.22
140_S	161_S	0.971	0.22
2_S	134_E	0.965	0.22
7_L	14_G	0.960	0.22
18_Y	55_L	0.959	0.22
33_T	74_D	0.958	0.22
7_L	50_A	0.948	0.21
18_Y	21_I	0.939	0.21
46_N	56_K	0.937	0.21
135_Q	153_I	0.932	0.21
17_L	159_F	0.925	0.21
4_L	133_Y	0.918	0.20
5_L	54_E	0.915	0.20
63_I	83_Q	0.907	0.20
6_W	147_K	0.897	0.20
2_S	88_Y	0.883	0.19
10_F	139_A	0.882	0.19
70_A	122_V	0.882	0.19
22_I	60_E	0.881	0.19
72_Q	81_G	0.880	0.19
145_K	156_F	0.878	0.19
151_T	158_K	0.877	0.19
12_L	160_R	0.867	0.19
9_S	130_I	0.865	0.19
36_Q	45_E	0.858	0.19
136_G	152_E	0.852	0.19
143_A	152_E	0.852	0.19
136_G	143_A	0.852	0.19
143_A	149_G	0.852	0.19
149_G	152_E	0.852	0.19
136_G	149_G	0.852	0.19
44_T	144_Q	0.847	0.18
105_E	109_T	0.834	0.18
44_T	161_S	0.833	0.18
90_E	153_I	0.832	0.18
154_E	158_K	0.825	0.18
9_S	124_S	0.824	0.18
17_L	113_R	0.823	0.18
52_L	58_E	0.813	0.18
84_T	88_Y	0.804	0.17
34_E	37_Q	0.800	0.17
29_A	157_L	0.800	0.17
75_E	145_K	0.794	0.17
112_D	127_D	0.787	0.17
53_L	132_L	0.783	0.17
34_E	49_A	0.782	0.17
138_S	141_Q	0.777	0.17
142_I	157_L	0.776	0.17
14_G	45_E	0.775	0.17
13_H	16_L	0.771	0.17
137_Y	145_K	0.769	0.17
82_L	94_V	0.768	0.16
25_T	135_Q	0.767	0.16
40_I	61_K	0.765	0.16
25_T	34_E	0.753	0.16
79_K	128_Q	0.745	0.16
150_K	154_E	0.743	0.16
14_G	148_S	0.741	0.16
10_F	17_L	0.739	0.16
45_E	60_E	0.737	0.16
127_D	153_I	0.734	0.16
50_A	129_V	0.730	0.16
85_S	140_S	0.725	0.15
19_A	55_L	0.718	0.15
59_N	146_M	0.718	0.15
78_Q	132_L	0.715	0.15
41_L	51_F	0.715	0.15
7_L	51_F	0.714	0.15
11_M	123_Q	0.711	0.15
79_K	94_V	0.704	0.15
25_T	72_Q	0.704	0.15
155_L	159_F	0.703	0.15
52_L	144_Q	0.703	0.15
66_K	76_E	0.702	0.15
55_L	63_I	0.700	0.15
66_K	113_R	0.699	0.15
68_S	117_L	0.698	0.15
103_H	107_L	0.696	0.15
78_Q	157_L	0.695	0.15
4_L	123_Q	0.691	0.15
54_E	62_L	0.690	0.15
61_K	66_K	0.675	0.14
13_H	124_S	0.670	0.14
7_L	81_G	0.670	0.14
80_S	85_S	0.667	0.14
13_H	41_L	0.660	0.14
32_E	56_K	0.660	0.14
75_E	133_Y	0.659	0.14
42_E	46_N	0.655	0.14
4_L	148_S	0.645	0.14
142_I	155_L	0.645	0.14
27_L	57_E	0.643	0.14
66_K	148_S	0.643	0.14
10_F	135_Q	0.642	0.14
34_E	52_L	0.640	0.14
23_L	60_E	0.638	0.14
79_K	138_S	0.634	0.14
19_A	129_V	0.627	0.13
55_L	137_Y	0.621	0.13
144_Q	161_S	0.614	0.13
46_N	54_E	0.610	0.13
25_T	148_S	0.610	0.13
29_A	37_Q	0.610	0.13
21_I	60_E	0.607	0.13
66_K	135_Q	0.599	0.13
55_L	70_A	0.598	0.13
4_L	19_A	0.596	0.13
46_N	126_E	0.595	0.13
10_F	144_Q	0.591	0.13
4_L	26_R	0.590	0.13
21_I	68_S	0.578	0.12
79_K	83_Q	0.574	0.12
48_L	54_E	0.574	0.12
56_K	155_L	0.574	0.12
47_T	134_E	0.572	0.12
107_L	118_V	0.571	0.12
15_V	67_A	0.568	0.12
119_N	133_Y	0.568	0.12
56_K	157_L	0.567	0.12
49_A	151_T	0.565	0.12
38_K	51_F	0.563	0.12
59_N	143_A	0.558	0.12
59_N	152_E	0.558	0.12
59_N	149_G	0.558	0.12
59_N	136_G	0.558	0.12
45_E	62_L	0.557	0.12
62_L	69_S	0.557	0.12
48_L	62_L	0.549	0.12
71_S	161_S	0.548	0.12
66_K	70_A	0.545	0.12
132_L	157_L	0.544	0.12
13_H	45_E	0.543	0.12
78_Q	91_R	0.538	0.12
103_H	139_A	0.535	0.12
45_E	49_A	0.535	0.12
13_H	133_Y	0.534	0.12
1_M	4_L	0.532	0.12
62_L	148_S	0.530	0.12
7_L	16_L	0.527	0.11
48_L	52_L	0.522	0.11
1_M	151_T	0.522	0.11
118_V	138_S	0.520	0.11
21_I	55_L	0.514	0.11
15_V	127_D	0.514	0.11
4_L	13_H	0.509	0.11
138_S	144_Q	0.506	0.11
68_S	80_S	0.504	0.11
42_E	47_T	0.503	0.11
104_I	110_E	0.502	0.11
60_E	123_Q	0.500	0.11

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
1tc3C	1	0.3054	68.4	0.922	Contact Map
2rnjA	1	0.3054	64.1	0.924	Contact Map
1je8A	2	0.3114	60.8	0.926	Contact Map
1jkoC	1	0.2754	56.4	0.928	Contact Map
2jpcA	1	0.2635	54.7	0.929	Contact Map
2x48A	1	0.3174	52.7	0.929	Contact Map
3iuoA	4	0.2994	52.5	0.929	Contact Map
3ulqB	1	0.2814	51.4	0.93	Contact Map
3c57A	2	0.2754	49.8	0.931	Contact Map
2m8eA	1	0.3293	43.6	0.933	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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