RHAD - ECOLI - GREMLIN Contacts

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RHAD - Rhamnulose-1-phosphate aldolase

UniProt:	P32169	Sequences: MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11866
Length:	274 (207)
Sequences:	1418 (889)
Seq/√Len:	61.8

ECOLI - RHAD FUCA SGBE ULAF ARAD YGBL
BACSU - ARAD MTNB
HALSA - Q9HQE3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_K	100_A	5.099	1.00
236_Q	240_K	4.004	1.00
181_G	204_H	3.853	1.00
253_R	257_I	3.459	1.00
146_N	240_K	3.382	1.00
83_Q	89_N	3.339	1.00
60_Q	63_P	2.972	1.00
40_A	44_P	2.720	1.00
154_L	247_M	2.699	1.00
58_L	61_P	2.655	1.00
58_L	63_P	2.613	1.00
219_P	223_E	2.487	1.00
138_V	221_L	2.379	1.00
149_A	240_K	2.179	1.00
153_V	244_M	2.176	1.00
70_F	122_F	2.140	1.00
131_A	217_S	2.088	1.00
232_E	236_Q	2.075	1.00
137_R	220_T	2.054	1.00
184_P	210_P	2.037	1.00
59_S	63_P	2.035	1.00
216_G	228_I	2.008	1.00
199_Q	202_Q	2.002	1.00
56_I	59_S	1.951	1.00
206_L	231_A	1.929	1.00
155_E	242_Y	1.926	1.00
146_N	236_Q	1.900	1.00
140_M	224_T	1.899	1.00
82_V	89_N	1.884	1.00
128_R	131_A	1.876	1.00
257_I	261_K	1.845	1.00
197_T	209_W	1.832	1.00
254_E	258_A	1.820	1.00
150_L	235_A	1.817	1.00
252_S	255_E	1.750	0.99
140_M	228_I	1.737	0.99
147_L	231_A	1.710	0.99
177_P	257_I	1.698	0.99
154_L	249_Q	1.616	0.99
147_L	214_V	1.611	0.99
73_T	125_H	1.608	0.99
71_I	92_I	1.570	0.99
43_A	47_D	1.493	0.98
239_V	244_M	1.469	0.98
206_L	216_G	1.462	0.98
71_I	90_L	1.440	0.98
41_D	222_D	1.439	0.98
241_V	248_K	1.428	0.98
144_A	147_L	1.406	0.97
66_A	69_P	1.404	0.97
153_V	239_V	1.388	0.97
41_D	44_P	1.380	0.97
154_L	210_P	1.370	0.97
47_D	53_P	1.367	0.97
69_P	92_I	1.367	0.97
124_S	201_M	1.353	0.97
170_T	176_F	1.350	0.97
77_K	89_N	1.345	0.97
96_D	126_C	1.325	0.96
127_E	198_A	1.321	0.96
171_E	174_V	1.310	0.96
146_N	232_E	1.308	0.96
143_H	212_H	1.300	0.96
152_Y	168_G	1.289	0.96
191_D	195_Q	1.287	0.96
239_V	243_S	1.278	0.95
214_V	231_A	1.272	0.95
261_K	265_V	1.263	0.95
147_L	208_L	1.252	0.95
169_S	172_C	1.236	0.94
96_D	100_A	1.231	0.94
43_A	46_H	1.228	0.94
73_T	221_L	1.182	0.93
56_I	61_P	1.180	0.93
148_I	169_S	1.171	0.93
120_A	215_F	1.153	0.92
175_V	178_D	1.137	0.92
44_P	47_D	1.132	0.91
39_D	43_A	1.120	0.91
148_I	151_T	1.117	0.91
150_L	242_Y	1.111	0.91
156_N	182_I	1.100	0.90
125_H	139_I	1.089	0.90
171_E	176_F	1.089	0.90
205_S	219_P	1.084	0.90
146_N	239_V	1.081	0.89
42_I	47_D	1.078	0.89
81_N	89_N	1.067	0.89
117_E	193_I	1.062	0.89
48_N	51_Q	1.056	0.88
93_V	122_F	1.055	0.88
253_R	256_L	1.050	0.88
220_T	223_E	1.040	0.87
196_A	199_Q	1.030	0.87
171_E	230_T	1.001	0.85
240_K	243_S	1.000	0.85
72_V	76_G	0.996	0.85
115_T	189_G	0.988	0.85
73_T	90_L	0.984	0.84
195_Q	199_Q	0.981	0.84
145_T	240_K	0.979	0.84
144_A	228_I	0.973	0.84
191_D	223_E	0.973	0.84
233_K	236_Q	0.965	0.83
142_C	228_I	0.959	0.83
43_A	87_A	0.956	0.83
61_P	64_L	0.949	0.82
144_A	232_E	0.944	0.82
58_L	79_F	0.938	0.81
257_I	260_G	0.929	0.81
210_P	249_Q	0.925	0.81
176_F	256_L	0.924	0.80
239_V	253_R	0.909	0.79
36_R	68_T	0.902	0.79
74_G	77_K	0.890	0.78
239_V	242_Y	0.887	0.78
221_L	224_T	0.870	0.76
39_D	87_A	0.869	0.76
70_F	93_V	0.865	0.76
42_I	60_Q	0.860	0.75
191_D	194_G	0.857	0.75
77_K	82_V	0.851	0.75
108_L	111_E	0.843	0.74
95_V	126_C	0.840	0.74
178_D	257_I	0.838	0.74
38_D	41_D	0.831	0.73
251_I	259_L	0.831	0.73
70_F	187_V	0.830	0.73
93_V	115_T	0.829	0.73
227_L	230_T	0.828	0.73
192_E	195_Q	0.827	0.73
108_L	139_I	0.825	0.72
169_S	173_L	0.825	0.72
45_Y	48_N	0.818	0.72
193_I	215_F	0.815	0.71
230_T	263_F	0.810	0.71
258_A	262_R	0.808	0.71
123_L	195_Q	0.806	0.71
92_I	108_L	0.801	0.70
93_V	118_L	0.798	0.70
68_T	129_I	0.796	0.70
255_E	258_A	0.790	0.69
39_D	44_P	0.788	0.69
251_I	256_L	0.787	0.69
123_L	127_E	0.786	0.69
252_S	258_A	0.781	0.68
206_L	227_L	0.780	0.68
254_E	261_K	0.779	0.68
153_V	248_K	0.774	0.68
44_P	48_N	0.774	0.68
40_A	45_Y	0.773	0.67
43_A	90_L	0.773	0.67
174_V	263_F	0.772	0.67
175_V	251_I	0.765	0.67
49_F	53_P	0.761	0.66
206_L	214_V	0.759	0.66
153_V	242_Y	0.757	0.66
205_S	217_S	0.757	0.66
127_E	202_Q	0.756	0.66
58_L	64_L	0.755	0.66
249_Q	261_K	0.753	0.65
170_T	173_L	0.748	0.65
169_S	237_V	0.747	0.65
37_L	42_I	0.745	0.65
120_A	124_S	0.745	0.65
138_V	224_T	0.744	0.64
89_N	112_A	0.740	0.64
75_S	113_V	0.739	0.64
157_D	235_A	0.739	0.64
57_P	75_S	0.738	0.64
186_M	196_A	0.730	0.63
83_Q	88_A	0.729	0.63
255_E	259_L	0.728	0.63
42_I	71_I	0.728	0.63
40_A	52_Q	0.727	0.63
242_Y	245_G	0.724	0.62
137_R	219_P	0.722	0.62
175_V	230_T	0.722	0.62
181_G	208_L	0.719	0.62
75_S	189_G	0.719	0.62
250_T	256_L	0.718	0.62
142_C	214_V	0.715	0.61
218_G	223_E	0.715	0.61
41_D	220_T	0.714	0.61
205_S	227_L	0.711	0.61
115_T	119_P	0.711	0.61
184_P	199_Q	0.708	0.61
140_M	206_L	0.705	0.60
157_D	215_F	0.702	0.60
181_G	207_V	0.698	0.59
59_S	64_L	0.695	0.59
69_P	108_L	0.693	0.59
41_D	49_F	0.691	0.59
242_Y	246_G	0.688	0.58
201_M	217_S	0.686	0.58
56_I	63_P	0.686	0.58
145_T	236_Q	0.683	0.58
77_K	112_A	0.680	0.58
45_Y	52_Q	0.680	0.58
169_S	174_V	0.679	0.57
75_S	116_S	0.678	0.57
129_I	177_P	0.676	0.57
57_P	63_P	0.675	0.57
186_M	209_W	0.673	0.57
131_A	137_R	0.672	0.57
197_T	207_V	0.671	0.56
117_E	194_G	0.663	0.56
174_V	178_D	0.663	0.56
72_V	115_T	0.662	0.55
42_I	209_W	0.658	0.55
116_S	120_A	0.658	0.55
173_L	251_I	0.655	0.55
94_K	97_S	0.655	0.55
183_L	200_E	0.651	0.54
180_V	244_M	0.648	0.54
184_P	196_A	0.646	0.54
147_L	228_I	0.646	0.54
70_F	118_L	0.644	0.53
153_V	246_G	0.643	0.53
176_F	253_R	0.640	0.53
194_G	225_F	0.640	0.53
238_L	242_Y	0.636	0.53
62_M	138_V	0.636	0.53
119_P	194_G	0.634	0.52
171_E	233_K	0.634	0.52
59_S	73_T	0.632	0.52
149_A	239_V	0.631	0.52
171_E	263_F	0.630	0.52
116_S	189_G	0.626	0.51
75_S	115_T	0.626	0.51
208_L	214_V	0.623	0.51
38_D	51_Q	0.621	0.51
178_D	264_G	0.619	0.51
129_I	137_R	0.617	0.50
44_P	51_Q	0.616	0.50
211_F	248_K	0.611	0.50
75_S	114_P	0.610	0.50
172_C	175_V	0.606	0.49
216_G	242_Y	0.605	0.49
139_I	217_S	0.603	0.49
40_A	43_A	0.602	0.49
170_T	175_V	0.602	0.49
138_V	193_I	0.600	0.48
126_C	194_G	0.598	0.48
36_R	39_D	0.598	0.48
115_T	190_T	0.597	0.48
170_T	185_W	0.595	0.48
200_E	207_V	0.593	0.48
177_P	206_L	0.591	0.47
218_G	221_L	0.591	0.47
194_G	230_T	0.589	0.47
119_P	123_L	0.582	0.46
60_Q	140_M	0.579	0.46
41_D	88_A	0.577	0.46
157_D	234_S	0.575	0.46
62_M	190_T	0.575	0.46
248_K	256_L	0.574	0.45
263_F	267_P	0.573	0.45
42_I	46_H	0.570	0.45
40_A	87_A	0.569	0.45
144_A	169_S	0.568	0.45
43_A	97_S	0.565	0.44
150_L	238_L	0.563	0.44
150_L	210_P	0.561	0.44
140_M	184_P	0.559	0.44
45_Y	49_F	0.558	0.44
211_F	249_Q	0.556	0.43
190_T	258_A	0.553	0.43
217_S	224_T	0.553	0.43
41_D	48_N	0.553	0.43
95_V	122_F	0.553	0.43
43_A	48_N	0.552	0.43
60_Q	64_L	0.551	0.43
97_S	122_F	0.547	0.42
138_V	209_W	0.546	0.42
117_E	170_T	0.543	0.42
183_L	210_P	0.541	0.42
38_D	53_P	0.541	0.42
55_Y	230_T	0.540	0.42
206_L	228_I	0.539	0.42
117_E	121_H	0.538	0.41
249_Q	252_S	0.538	0.41
141_H	212_H	0.537	0.41
73_T	117_E	0.533	0.41
120_A	191_D	0.532	0.41
177_P	254_E	0.531	0.41
223_E	259_L	0.530	0.41
153_V	241_V	0.528	0.40
117_E	189_G	0.527	0.40
74_G	89_N	0.525	0.40
119_P	191_D	0.525	0.40
171_E	188_P	0.524	0.40
120_A	193_I	0.523	0.40
51_Q	87_A	0.523	0.40
96_D	191_D	0.521	0.40
129_I	146_N	0.519	0.39
225_F	229_D	0.518	0.39
186_M	193_I	0.517	0.39
48_N	52_Q	0.513	0.39
67_N	96_D	0.511	0.39
147_L	235_A	0.511	0.39
79_F	170_T	0.511	0.39
67_N	95_V	0.510	0.38
83_Q	93_V	0.508	0.38
241_V	244_M	0.507	0.38
74_G	111_E	0.506	0.38
113_V	195_Q	0.506	0.38
152_Y	248_K	0.506	0.38
141_H	213_G	0.502	0.38
79_F	142_C	0.500	0.37

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
2v9lA	3	0.9818	100	0.263	Contact Map
4c24A	3	0.7591	100	0.375	Contact Map
1pvtA	3	0.8175	100	0.378	Contact Map
3ocrA	4	0.8212	100	0.382	Contact Map
1e4cP	3	0.7482	100	0.39	Contact Map
2opiA	3	0.7555	100	0.405	Contact Map
4xxfA	3	0.792	100	0.413	Contact Map
1k0wA	3	0.7591	100	0.416	Contact Map
2z7bA	3	0.792	100	0.422	Contact Map
4m6rA	3	0.7445	100	0.44	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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