SUCD - ECOLI - GREMLIN Contacts

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SUCD - Succinyl-CoA ligase [ADP-forming] subunit alpha

UniProt:	P0AGE9	Sequences: MSILIDKNTKVICQGFTGSQGTFHSEQAIAYGTKMVGGVTPGKGGTTHLGLPVFNTVREAVAATGATASVIYVPAPFCKDSILEAIDAGIKLIITITEGIPTLDMLTVKVKLDEAGVRMIGPNCPGVITPGECKIGIQPGHIHKPGKVGIVSRSGTLTYEAVKQTTDYGFGQSTCVGIGGDPIPGSNFIDILEMFEKDPQTEAIVMIGEIGGSAEEEAAAYIKEHVTKPVVGYIAGVTAPKGKRMGHAGAIIAGGKGTADEKFAALEAAGVKTVRSLADIGEALKTVLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10982
Length:	289 (273)
Sequences:	4788 (2811)
Seq/√Len:	170.1

ECOLI - SUCD PKA FDRA YAHF
BACSU - SUCD
HALSA - Q9HPP0
SULSO - Q97XD9 Q97VX2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_K	202_E	5.161	1.00
56_T	59_E	3.387	1.00
255_G	273_T	3.202	1.00
55_N	59_E	3.102	1.00
118_R	185_G	2.916	1.00
63_A	66_A	2.905	1.00
86_I	115_A	2.780	1.00
83_L	111_K	2.671	1.00
263_F	273_T	2.608	1.00
58_R	84_E	2.491	1.00
93_I	117_V	2.435	1.00
60_A	66_A	2.429	1.00
149_G	173_S	2.428	1.00
47_T	50_G	2.340	1.00
262_K	266_L	2.317	1.00
266_L	271_V	2.316	1.00
83_L	107_T	2.311	1.00
173_S	201_T	2.281	1.00
82_I	93_I	2.272	1.00
101_P	105_M	2.263	1.00
274_V	283_A	2.222	1.00
73_V	81_S	2.171	1.00
58_R	87_D	2.115	1.00
232_G	266_L	2.086	1.00
186_S	191_I	2.032	1.00
69_S	85_A	1.950	1.00
158_T	175_C	1.949	1.00
79_K	107_T	1.946	1.00
85_A	90_I	1.907	1.00
73_V	77_F	1.906	1.00
38_G	62_A	1.899	1.00
204_I	226_V	1.892	1.00
19_S	22_T	1.891	1.00
198_D	201_T	1.879	1.00
176_V	191_I	1.815	1.00
80_D	84_E	1.799	1.00
149_G	201_T	1.769	1.00
95_T	108_V	1.765	1.00
196_E	227_T	1.764	1.00
163_K	167_D	1.752	1.00
112_L	119_M	1.748	1.00
83_L	87_D	1.736	1.00
106_L	110_V	1.734	1.00
205_V	280_I	1.725	1.00
86_I	117_V	1.696	1.00
221_Y	271_V	1.694	1.00
42_G	60_A	1.687	1.00
232_G	271_V	1.683	1.00
148_V	203_A	1.677	1.00
205_V	284_L	1.629	1.00
83_L	114_E	1.611	1.00
203_A	284_L	1.606	1.00
14_Q	69_S	1.594	1.00
206_M	232_G	1.558	1.00
168_Y	285_K	1.551	1.00
192_L	204_I	1.523	1.00
129_T	132_E	1.517	1.00
63_A	88_A	1.515	1.00
220_A	224_E	1.515	1.00
57_V	85_A	1.506	1.00
86_I	111_K	1.502	1.00
103_L	107_T	1.484	1.00
204_I	224_E	1.482	1.00
71_I	81_S	1.469	1.00
78_C	100_I	1.453	1.00
69_S	90_I	1.433	1.00
110_V	114_E	1.427	1.00
67_T	91_K	1.418	1.00
221_Y	230_V	1.394	1.00
124_C	177_G	1.383	1.00
146_G	171_G	1.376	1.00
7_K	132_E	1.373	1.00
148_V	284_L	1.359	1.00
149_G	195_F	1.358	1.00
40_T	54_F	1.353	1.00
26_E	30_A	1.342	1.00
78_C	95_T	1.332	1.00
41_P	51_L	1.304	1.00
237_V	275_R	1.294	1.00
11_V	134_K	1.289	1.00
16_F	25_S	1.288	1.00
188_F	208_G	1.285	1.00
80_D	83_L	1.283	1.00
82_I	111_K	1.282	1.00
95_T	119_M	1.278	1.00
12_I	37_G	1.271	1.00
150_I	172_Q	1.257	1.00
25_S	49_L	1.257	1.00
265_A	269_A	1.256	1.00
13_C	35_M	1.249	1.00
109_K	113_D	1.245	1.00
196_E	224_E	1.238	1.00
48_H	53_V	1.235	1.00
151_V	191_I	1.228	1.00
120_I	127_V	1.228	1.00
213_S	217_E	1.223	1.00
213_S	216_E	1.212	1.00
120_I	191_I	1.208	1.00
231_V	274_V	1.206	1.00
118_R	186_S	1.195	1.00
44_G	55_N	1.195	1.00
54_F	61_V	1.191	1.00
264_A	268_A	1.184	1.00
68_A	135_I	1.180	1.00
13_C	28_A	1.178	1.00
103_L	106_L	1.174	1.00
57_V	88_A	1.165	1.00
27_Q	96_I	1.158	1.00
46_T	55_N	1.155	1.00
196_E	226_V	1.154	1.00
16_F	48_H	1.149	1.00
29_I	32_G	1.146	1.00
210_I	250_A	1.132	1.00
174_T	195_F	1.118	1.00
109_K	182_P	1.102	1.00
176_V	195_F	1.095	1.00
46_T	53_V	1.092	1.00
56_T	84_E	1.091	1.00
193_E	223_K	1.089	1.00
109_K	112_L	1.088	1.00
60_A	63_A	1.086	1.00
22_T	25_S	1.084	1.00
157_L	277_L	1.081	1.00
111_K	115_A	1.079	1.00
174_T	201_T	1.075	1.00
193_E	197_K	1.071	1.00
28_A	51_L	1.063	1.00
25_S	29_I	1.046	0.99
82_I	108_V	1.044	0.99
75_A	97_T	1.039	0.99
129_T	174_T	1.022	0.99
189_I	220_A	1.019	0.99
275_R	279_D	1.019	0.99
218_A	265_A	1.012	0.99
255_G	263_F	1.006	0.99
29_I	49_L	1.004	0.99
272_K	283_A	1.003	0.99
94_I	127_V	1.001	0.99
181_D	212_G	0.998	0.99
196_E	223_K	0.997	0.99
193_E	216_E	0.989	0.99
145_P	200_Q	0.983	0.99
263_F	267_E	0.982	0.99
14_Q	57_V	0.972	0.99
107_T	110_V	0.969	0.99
82_I	117_V	0.969	0.99
61_V	66_A	0.962	0.99
276_S	279_D	0.961	0.99
18_G	47_T	0.958	0.99
217_E	221_Y	0.957	0.99
81_S	84_E	0.948	0.99
209_E	247_H	0.945	0.99
42_G	55_N	0.944	0.99
74_P	77_F	0.943	0.99
79_K	108_V	0.942	0.99
27_Q	30_A	0.942	0.99
110_V	113_D	0.940	0.99
10_K	38_G	0.940	0.99
18_G	49_L	0.940	0.99
105_M	180_G	0.937	0.99
68_A	94_I	0.934	0.99
211_G	262_K	0.932	0.99
12_I	66_A	0.927	0.99
40_T	62_A	0.923	0.99
151_V	178_I	0.916	0.99
11_V	33_T	0.912	0.98
83_L	115_A	0.903	0.98
151_V	195_F	0.900	0.98
230_V	271_V	0.898	0.98
130_P	173_S	0.897	0.98
181_D	188_F	0.893	0.98
99_G	102_T	0.893	0.98
197_K	223_K	0.892	0.98
162_V	175_C	0.892	0.98
40_T	60_A	0.891	0.98
61_V	88_A	0.886	0.98
208_G	232_G	0.885	0.98
172_Q	175_C	0.882	0.98
104_D	108_V	0.882	0.98
134_K	137_I	0.873	0.98
16_F	22_T	0.870	0.98
31_Y	39_V	0.867	0.98
152_S	158_T	0.866	0.98
267_E	275_R	0.860	0.98
92_L	118_R	0.860	0.98
131_G	200_Q	0.859	0.98
71_I	78_C	0.852	0.98
60_A	88_A	0.851	0.98
192_L	196_E	0.849	0.98
86_I	108_V	0.847	0.98
125_P	159_Y	0.844	0.98
41_P	54_F	0.842	0.97
40_T	44_G	0.842	0.97
133_C	137_I	0.841	0.97
7_K	131_G	0.840	0.97
131_G	145_P	0.838	0.97
231_V	283_A	0.833	0.97
22_T	48_H	0.830	0.97
14_Q	81_S	0.825	0.97
28_A	41_P	0.822	0.97
95_T	112_L	0.821	0.97
165_T	172_Q	0.821	0.97
89_G	115_A	0.819	0.97
37_G	51_L	0.818	0.97
150_I	165_T	0.817	0.97
205_V	231_V	0.811	0.97
47_T	51_L	0.810	0.97
5_I	92_L	0.805	0.97
125_P	156_T	0.802	0.97
151_V	206_M	0.799	0.97
92_L	120_I	0.798	0.97
187_N	190_D	0.797	0.96
190_D	216_E	0.796	0.96
77_F	81_S	0.796	0.96
23_F	138_Q	0.791	0.96
83_L	86_I	0.789	0.96
93_I	112_L	0.787	0.96
19_S	25_S	0.784	0.96
68_A	92_L	0.783	0.96
149_G	174_T	0.782	0.96
79_K	86_I	0.778	0.96
112_L	116_G	0.777	0.96
86_I	93_I	0.775	0.96
79_K	104_D	0.775	0.96
244_R	248_A	0.775	0.96
68_A	136_G	0.775	0.96
87_D	115_A	0.771	0.96
237_V	263_F	0.771	0.96
192_L	206_M	0.771	0.96
222_I	271_V	0.769	0.96
10_K	67_T	0.763	0.96
28_A	70_V	0.761	0.95
6_D	132_E	0.761	0.95
12_I	41_P	0.759	0.95
6_D	176_V	0.759	0.95
120_I	186_S	0.758	0.95
62_A	88_A	0.753	0.95
155_G	249_G	0.750	0.95
246_G	250_A	0.750	0.95
58_R	88_A	0.749	0.95
279_D	282_E	0.743	0.95
143_H	162_V	0.742	0.95
84_E	87_D	0.742	0.95
144_K	166_T	0.737	0.95
164_Q	281_G	0.737	0.95
186_S	194_M	0.731	0.94
98_E	248_A	0.730	0.94
11_V	31_Y	0.728	0.94
188_F	206_M	0.725	0.94
100_I	180_G	0.724	0.94
203_A	231_V	0.722	0.94
174_T	194_M	0.719	0.94
14_Q	85_A	0.713	0.94
264_A	267_E	0.712	0.94
107_T	111_K	0.712	0.94
79_K	83_L	0.712	0.94
66_A	90_I	0.710	0.93
196_E	220_A	0.707	0.93
27_Q	70_V	0.702	0.93
41_P	53_V	0.701	0.93
247_H	250_A	0.700	0.93
123_N	180_G	0.699	0.93
39_V	51_L	0.699	0.93
72_Y	96_I	0.699	0.93
18_G	48_H	0.699	0.93
11_V	35_M	0.699	0.93
41_P	52_P	0.699	0.93
192_L	220_A	0.697	0.93
247_H	251_I	0.689	0.92
135_I	138_Q	0.689	0.92
193_E	220_A	0.688	0.92
165_T	281_G	0.684	0.92
79_K	111_K	0.680	0.92
47_T	52_P	0.679	0.92
89_G	117_V	0.678	0.92
219_A	222_I	0.677	0.92
86_I	112_L	0.676	0.92
244_R	250_A	0.673	0.92
86_I	114_E	0.672	0.91
168_Y	282_E	0.669	0.91
98_E	156_T	0.669	0.91
86_I	89_G	0.668	0.91
105_M	182_P	0.665	0.91
62_A	66_A	0.665	0.91
244_R	247_H	0.661	0.91
191_I	195_F	0.658	0.91
189_I	216_E	0.658	0.91
16_F	51_L	0.658	0.91
150_I	162_V	0.655	0.90
35_M	38_G	0.655	0.90
75_A	100_I	0.654	0.90
261_E	265_A	0.652	0.90
246_G	251_I	0.651	0.90
274_V	280_I	0.650	0.90
152_S	207_I	0.645	0.90
100_I	104_D	0.644	0.90
102_T	180_G	0.641	0.89
256_K	261_E	0.640	0.89
13_C	25_S	0.638	0.89
234_I	273_T	0.635	0.89
40_T	55_N	0.630	0.89
9_T	68_A	0.627	0.88
97_T	124_C	0.627	0.88
13_C	41_P	0.626	0.88
16_F	24_H	0.625	0.88
112_L	115_A	0.624	0.88
75_A	99_G	0.623	0.88
155_G	209_E	0.620	0.88
57_V	69_S	0.616	0.87
253_A	256_K	0.614	0.87
46_T	52_P	0.612	0.87
58_R	62_A	0.611	0.87
108_V	112_L	0.609	0.87
241_K	244_R	0.609	0.87
16_F	41_P	0.608	0.87
40_T	61_V	0.606	0.87
114_E	117_V	0.605	0.87
211_G	217_E	0.605	0.87
178_I	181_D	0.605	0.87
75_A	79_K	0.600	0.86
102_T	105_M	0.599	0.86
118_R	194_M	0.598	0.86
11_V	67_T	0.597	0.86
28_A	39_V	0.596	0.86
134_K	138_Q	0.595	0.86
123_N	247_H	0.595	0.86
74_P	155_G	0.594	0.86
28_A	35_M	0.594	0.86
48_H	51_L	0.593	0.85
105_M	109_K	0.592	0.85
121_G	179_G	0.591	0.85
133_C	136_G	0.591	0.85
196_E	225_H	0.587	0.85
91_K	117_V	0.586	0.85
193_E	196_E	0.584	0.85
136_G	139_P	0.583	0.84
221_Y	226_V	0.580	0.84
89_G	116_G	0.577	0.84
77_F	80_D	0.576	0.84
215_E	219_A	0.574	0.84
84_E	88_A	0.574	0.84
187_N	213_S	0.573	0.83
223_K	226_V	0.571	0.83
178_I	191_I	0.567	0.83
124_C	152_S	0.567	0.83
69_S	93_I	0.567	0.83
29_I	51_L	0.567	0.83
111_K	114_E	0.563	0.82
263_F	275_R	0.561	0.82
195_F	204_I	0.558	0.82
100_I	105_M	0.558	0.82
150_I	161_A	0.557	0.82
262_K	273_T	0.554	0.81
13_C	31_Y	0.553	0.81
166_T	172_Q	0.551	0.81
40_T	66_A	0.551	0.81
66_A	89_G	0.551	0.81
5_I	133_C	0.549	0.81
223_K	268_A	0.547	0.81
127_V	134_K	0.546	0.80
173_S	228_K	0.544	0.80
193_E	226_V	0.544	0.80
220_A	268_A	0.543	0.80
239_A	242_G	0.542	0.80
206_M	230_V	0.541	0.80
210_I	249_G	0.541	0.80
133_C	138_Q	0.539	0.80
17_T	24_H	0.539	0.80
44_G	59_E	0.537	0.79
220_A	223_K	0.536	0.79
210_I	253_A	0.536	0.79
82_I	112_L	0.535	0.79
7_K	129_T	0.533	0.79
7_K	194_M	0.532	0.79
23_F	72_Y	0.532	0.79
207_I	235_A	0.531	0.79
149_G	229_P	0.531	0.79
113_D	185_G	0.528	0.78
12_I	42_G	0.528	0.78
10_K	40_T	0.527	0.78
16_F	49_L	0.525	0.78
5_I	127_V	0.524	0.78
178_I	188_F	0.524	0.78
101_P	249_G	0.520	0.77
196_E	221_Y	0.520	0.77
218_A	222_I	0.519	0.77
128_I	137_I	0.519	0.77
195_F	201_T	0.519	0.77
130_P	149_G	0.519	0.77
165_T	284_L	0.519	0.77
82_I	119_M	0.517	0.77
155_G	247_H	0.516	0.77
132_E	145_P	0.516	0.77
158_T	177_G	0.516	0.77
12_I	69_S	0.516	0.77
76_P	104_D	0.515	0.77
252_I	256_K	0.515	0.77
244_R	252_I	0.514	0.76
78_C	97_T	0.514	0.76
91_K	118_R	0.510	0.76
113_D	116_G	0.509	0.76
6_D	174_T	0.508	0.76
187_N	216_E	0.508	0.76
21_G	26_E	0.505	0.75
135_I	139_P	0.503	0.75
38_G	52_P	0.502	0.75
90_I	117_V	0.502	0.75
130_P	174_T	0.501	0.75
74_P	97_T	0.501	0.75
246_G	249_G	0.500	0.74

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
2csuA	2	0.91	100	0.199	Contact Map
3pffA	2	0.9204	100	0.22	Contact Map
3mwdB	1	0.9308	100	0.264	Contact Map
2fp4A	1	0.9862	100	0.318	Contact Map
2yv1A	1	0.9031	100	0.335	Contact Map
2nu8A	1	0.9792	100	0.335	Contact Map
1oi7A	1	0.917	100	0.346	Contact Map
2yv2A	1	0.9135	100	0.361	Contact Map
3dmyA	2	0.7232	100	0.374	Contact Map
3ff4A	1	0.4152	99.9	0.716	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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