SMTA - ECOLI - GREMLIN Contacts

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SMTA - Protein SmtA

UniProt:	P36566	Sequences: MQDRNFDDIAEKFSRNIYGTTKGQLRQAILWQDLDRVLAEMGPQKLRVLDAGGGEGQTAIKMAERGHQVILCDLSAQMIDRAKQAAEAKGVSDNMQFIHCAAQDVASHLETPVDLILFHAVLEWVADPRSVLQTLWSVLRPGGVLSLMFYNAHGLLMHNMVAGNFDYVQAGMPKKKKRTLSPDYPRDPAQVYLWLEEAGWQIMGKTGVRVFHDYLREKHQQRDCYEALLELETRYCRQEPYITLGRYIHVTARKPQSKDKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12167
Length:	261 (203)
Sequences:	11484 (8168)
Seq/√Len:	573.3

ECOLI - SMTA UBIG UBIE YJHP BIOC CMOA TAM CMOB YAFE TEHB RLMA YAFS
BACSU - YCGJ YXBB MENG YRRT YODH YBAJ YRHH YDAC YQEM YXJB
HALSA - Q9HR81 Q9HND6 Q9HMT2 Q9HR63 Q9HRX3 Q9HQ85 ARSM Q9HSK6
SULSO - Q7LXN7 Q97WT7 Q97ZU8 Q97X57 Q97WH3 Q97XD7 Q97YX4 Q97WN4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_R	68_Q	3.478	1.00
136_W	200_W	3.412	1.00
76_A	99_H	2.980	1.00
53_G	71_L	2.801	1.00
72_C	100_C	2.677	1.00
52_G	121_V	2.645	1.00
68_Q	96_Q	2.549	1.00
129_R	197_E	2.485	1.00
76_A	80_D	2.449	1.00
116_I	139_L	2.360	1.00
127_D	130_S	2.332	1.00
134_T	137_S	2.271	1.00
70_I	113_V	2.263	1.00
116_I	135_L	2.232	1.00
135_L	145_L	2.202	1.00
82_A	97_F	2.196	1.00
48_V	62_M	2.186	1.00
49_L	113_V	2.178	1.00
60_I	86_A	2.103	1.00
114_D	140_R	2.098	1.00
81_R	84_Q	2.080	1.00
139_L	145_L	2.077	1.00
129_R	133_Q	2.069	1.00
187_D	190_Q	2.035	1.00
107_S	113_V	2.030	1.00
64_E	89_K	2.014	1.00
128_P	194_W	2.007	1.00
79_I	99_H	1.938	1.00
51_A	135_L	1.928	1.00
53_G	59_A	1.924	1.00
59_A	69_V	1.921	1.00
125_V	131_V	1.836	1.00
139_L	143_G	1.822	1.00
79_I	97_F	1.820	1.00
129_R	194_W	1.783	1.00
7_D	75_S	1.765	1.00
43_P	46_L	1.728	1.00
70_I	98_I	1.715	1.00
192_Y	196_E	1.710	1.00
47_R	70_I	1.708	1.00
101_A	104_D	1.642	1.00
139_L	200_W	1.619	1.00
7_D	77_Q	1.614	1.00
134_T	138_V	1.543	1.00
110_E	137_S	1.526	1.00
59_A	71_L	1.487	1.00
47_R	113_V	1.475	1.00
74_L	101_A	1.461	1.00
80_D	83_K	1.458	1.00
130_S	133_Q	1.456	1.00
86_A	97_F	1.427	1.00
100_C	106_A	1.387	1.00
73_D	79_I	1.364	1.00
70_I	96_Q	1.350	1.00
193_L	197_E	1.341	1.00
192_Y	205_K	1.340	1.00
109_L	112_P	1.339	1.00
118_F	121_V	1.321	1.00
48_V	115_L	1.319	1.00
49_L	116_I	1.319	1.00
60_I	85_A	1.305	1.00
71_L	97_F	1.299	1.00
47_R	140_R	1.279	1.00
52_G	118_F	1.268	1.00
166_D	169_Q	1.260	1.00
84_Q	88_A	1.241	1.00
51_A	102_A	1.226	1.00
59_A	95_M	1.222	1.00
188_P	207_G	1.221	1.00
71_L	82_A	1.216	1.00
46_L	67_H	1.216	1.00
46_L	115_L	1.213	1.00
33_D	37_V	1.208	1.00
26_R	29_I	1.177	1.00
14_S	55_E	1.164	1.00
77_Q	80_D	1.156	1.00
60_I	89_K	1.149	1.00
63_A	94_N	1.143	1.00
47_R	112_P	1.139	1.00
102_A	121_V	1.130	1.00
61_K	65_R	1.122	1.00
45_K	67_H	1.118	1.00
121_V	125_V	1.117	1.00
32_Q	36_R	1.112	1.00
105_V	134_T	1.102	1.00
61_K	64_E	1.088	1.00
193_L	196_E	1.085	1.00
105_V	138_V	1.081	1.00
33_D	206_T	1.079	1.00
86_A	95_M	1.079	1.00
132_L	195_L	1.075	1.00
129_R	198_A	1.073	1.00
166_D	170_A	1.064	1.00
80_D	84_Q	1.061	1.00
75_S	78_M	1.061	1.00
98_I	107_S	1.051	1.00
83_K	87_E	1.050	1.00
116_I	138_V	1.050	1.00
72_C	98_I	1.043	1.00
23_G	26_R	1.039	1.00
133_Q	198_A	1.035	1.00
161_V	165_F	1.027	1.00
132_L	198_A	1.005	1.00
171_G	177_K	1.002	1.00
120_A	123_E	0.999	1.00
135_L	139_L	0.993	1.00
33_D	36_R	0.991	1.00
22_K	26_R	0.991	1.00
103_Q	127_D	0.986	1.00
25_L	28_A	0.977	1.00
23_G	27_Q	0.977	1.00
47_R	114_D	0.977	1.00
84_Q	87_E	0.973	1.00
131_V	135_L	0.963	1.00
53_G	82_A	0.961	1.00
62_M	117_L	0.954	1.00
79_I	83_K	0.949	1.00
122_L	125_V	0.941	1.00
35_D	65_R	0.931	1.00
58_T	119_H	0.926	1.00
49_L	138_V	0.921	1.00
60_I	64_E	0.916	1.00
53_G	73_D	0.916	1.00
56_G	97_F	0.907	1.00
179_T	182_P	0.900	1.00
85_A	88_A	0.897	1.00
20_T	27_Q	0.866	1.00
167_Y	170_A	0.864	1.00
57_Q	61_K	0.863	1.00
122_L	191_V	0.858	1.00
40_E	43_P	0.857	1.00
51_A	72_C	0.851	1.00
64_E	91_V	0.849	1.00
106_A	134_T	0.843	1.00
14_S	85_A	0.841	1.00
48_V	69_V	0.838	1.00
145_L	195_L	0.835	1.00
190_Q	193_L	0.834	1.00
161_V	164_N	0.833	1.00
22_K	25_L	0.830	1.00
45_K	66_G	0.827	1.00
171_G	174_K	0.826	1.00
46_L	144_V	0.826	1.00
167_Y	171_G	0.826	1.00
86_A	91_V	0.818	1.00
119_H	148_M	0.818	1.00
107_S	137_S	0.812	1.00
70_I	107_S	0.809	1.00
145_L	200_W	0.809	1.00
110_E	134_T	0.804	1.00
122_L	131_V	0.802	1.00
173_P	176_K	0.800	1.00
56_G	82_A	0.799	1.00
122_L	132_L	0.798	1.00
130_S	134_T	0.794	1.00
120_A	124_W	0.792	1.00
76_A	83_K	0.791	1.00
118_F	147_L	0.789	1.00
107_S	110_E	0.787	1.00
103_Q	125_V	0.780	1.00
19_G	24_Q	0.777	1.00
58_T	117_L	0.771	1.00
11_E	81_R	0.768	1.00
27_Q	31_W	0.768	1.00
176_K	179_T	0.767	1.00
37_V	206_T	0.762	1.00
7_D	76_A	0.761	1.00
21_T	25_L	0.754	1.00
123_E	149_F	0.753	1.00
6_F	124_W	0.751	1.00
50_D	71_L	0.747	1.00
51_A	116_I	0.747	1.00
136_W	198_A	0.746	1.00
19_G	23_G	0.741	1.00
102_A	131_V	0.738	1.00
55_E	85_A	0.736	1.00
133_Q	137_S	0.736	1.00
31_W	35_D	0.734	1.00
211_F	214_Y	0.732	1.00
104_D	130_S	0.728	1.00
132_L	191_V	0.727	1.00
21_T	24_Q	0.727	1.00
72_C	105_V	0.713	1.00
120_A	148_M	0.713	1.00
85_A	89_K	0.707	1.00
73_D	78_M	0.704	1.00
20_T	25_L	0.703	1.00
9_I	12_K	0.703	1.00
24_Q	28_A	0.701	1.00
162_A	165_F	0.701	1.00
118_F	125_V	0.696	1.00
194_W	198_A	0.695	1.00
105_V	113_V	0.694	1.00
25_L	29_I	0.693	1.00
48_V	117_L	0.689	1.00
132_L	147_L	0.688	1.00
79_I	82_A	0.686	1.00
77_Q	81_R	0.683	1.00
27_Q	30_L	0.680	1.00
81_R	85_A	0.676	1.00
211_F	215_L	0.674	1.00
32_Q	61_K	0.674	1.00
19_G	22_K	0.671	1.00
160_M	163_G	0.671	1.00
28_A	31_W	0.666	1.00
46_L	114_D	0.665	1.00
24_Q	27_Q	0.663	1.00
122_L	149_F	0.662	1.00
152_A	187_D	0.662	1.00
18_Y	21_T	0.658	1.00
33_D	208_V	0.656	1.00
34_L	146_S	0.649	1.00
63_A	91_V	0.647	1.00
60_I	91_V	0.646	1.00
86_A	89_K	0.644	1.00
102_A	125_V	0.643	1.00
107_S	138_V	0.642	1.00
57_Q	85_A	0.639	1.00
20_T	24_Q	0.636	1.00
133_Q	197_E	0.635	1.00
87_E	90_G	0.631	1.00
115_L	143_G	0.627	1.00
170_A	174_K	0.627	1.00
111_T	140_R	0.625	1.00
83_K	96_Q	0.625	1.00
83_K	97_F	0.623	1.00
122_L	147_L	0.622	1.00
53_G	72_C	0.616	1.00
157_M	161_V	0.616	1.00
115_L	144_V	0.609	1.00
103_Q	130_S	0.604	1.00
188_P	205_K	0.591	1.00
207_G	210_V	0.591	1.00
49_L	107_S	0.589	1.00
60_I	97_F	0.589	1.00
119_H	123_E	0.589	1.00
124_W	150_Y	0.587	1.00
22_K	27_Q	0.587	1.00
196_E	202_I	0.583	1.00
111_T	141_P	0.583	1.00
175_K	179_T	0.582	1.00
50_D	69_V	0.581	1.00
135_L	147_L	0.578	1.00
167_Y	174_K	0.578	1.00
18_Y	22_K	0.577	1.00
37_V	204_G	0.576	1.00
107_S	134_T	0.573	1.00
6_F	123_E	0.568	0.99
168_V	173_P	0.568	0.99
91_V	95_M	0.565	0.99
52_G	125_V	0.564	0.99
196_E	203_M	0.564	0.99
35_D	61_K	0.558	0.99
74_L	99_H	0.558	0.99
38_L	115_L	0.558	0.99
151_N	207_G	0.558	0.99
71_L	95_M	0.556	0.99
152_A	190_Q	0.555	0.99
55_E	78_M	0.554	0.99
195_L	200_W	0.553	0.99
104_D	134_T	0.553	0.99
112_P	137_S	0.553	0.99
189_A	193_L	0.552	0.99
36_R	65_R	0.551	0.99
86_A	90_G	0.550	0.99
175_K	178_R	0.549	0.99
59_A	97_F	0.548	0.99
62_M	115_L	0.547	0.99
195_L	198_A	0.546	0.99
26_R	30_L	0.546	0.99
113_V	138_V	0.542	0.99
158_H	162_A	0.542	0.99
48_V	66_G	0.541	0.99
39_A	43_P	0.539	0.99
158_H	161_V	0.532	0.99
8_D	11_E	0.529	0.99
123_E	150_Y	0.529	0.99
20_T	23_G	0.528	0.99
107_S	112_P	0.526	0.99
103_Q	126_A	0.524	0.99
118_F	135_L	0.523	0.99
48_V	67_H	0.522	0.99
132_L	194_W	0.522	0.99
34_L	38_L	0.521	0.99
160_M	165_F	0.520	0.99
172_M	175_K	0.517	0.99
106_A	137_S	0.516	0.99
189_A	205_K	0.515	0.99
168_V	171_G	0.514	0.99
58_T	61_K	0.514	0.99
120_A	150_Y	0.512	0.99
137_S	140_R	0.512	0.99
35_D	40_E	0.511	0.99
212_H	216_R	0.510	0.99
106_A	109_L	0.509	0.99
189_A	192_Y	0.508	0.99
190_Q	197_E	0.507	0.99
47_R	111_T	0.506	0.99
21_T	27_Q	0.504	0.99
192_Y	202_I	0.503	0.99
169_Q	173_P	0.503	0.99
5_N	9_I	0.503	0.99
50_D	124_W	0.500	0.99
110_E	138_V	0.500	0.99

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
4htfA	2	0.9617	100	0.338	Contact Map
2o57A	2	0.931	100	0.426	Contact Map
4pneA	2	0.908	100	0.427	Contact Map
4kdcA	1	0.8314	100	0.432	Contact Map
2yqzA	1	0.9425	100	0.436	Contact Map
4obxA	2	0.8084	100	0.441	Contact Map
3ccfA	1	0.8659	100	0.447	Contact Map
3busA	1	0.8582	100	0.453	Contact Map
3bkxA	2	0.9464	100	0.453	Contact Map
1vl5A	1	0.8238	100	0.454	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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