RBSK - ECOLI - GREMLIN Contacts

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RBSK - Ribokinase

UniProt:	P0A9J6	Sequences: MQNAGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10818
Length:	309 (278)
Sequences:	22568 (16734)
Seq/√Len:	1003.6

ECOLI - RBSK YDJH PSUK SQUV YEII YEGV PFKB K1PF KDGK FRLD INGK HLDE
BACSU - IOLC YDJE RBSK KDGK K1PF FRLD
HALSA - Q9HP13 Q9HMJ3 Q9HSM7
SULSO - KDGK Q981E2 Q97W01 Q980X6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_A	263_T	3.104	1.00
74_R	89_V	2.641	1.00
139_L	164_A	2.605	1.00
59_A	83_D	2.499	1.00
224_L	230_W	2.493	1.00
231_A	275_I	2.484	1.00
270_P	273_E	2.330	1.00
264_A	269_K	2.318	1.00
8_V	135_A	2.276	1.00
66_D	91_K	2.258	1.00
229_V	257_F	2.255	1.00
154_K	180_L	2.169	1.00
71_E	89_V	2.094	1.00
63_C	90_I	2.062	1.00
213_H	232_S	2.053	1.00
51_A	56_A	2.008	1.00
188_E	224_L	1.977	1.00
9_V	48_A	1.977	1.00
53_R	80_D	1.937	1.00
156_A	161_T	1.936	1.00
164_A	262_I	1.927	1.00
264_A	277_F	1.914	1.00
153_A	163_V	1.894	1.00
256_T	281_A	1.888	1.00
238_Q	272_P	1.865	1.00
206_A	237_G	1.833	1.00
49_V	80_D	1.823	1.00
269_K	273_E	1.805	1.00
162_I	182_D	1.795	1.00
185_T	258_N	1.794	1.00
78_A	84_I	1.792	1.00
137_A	162_I	1.791	1.00
267_E	298_R	1.790	1.00
50_A	259_G	1.754	1.00
209_A	232_S	1.732	1.00
182_D	218_R	1.702	1.00
229_V	279_H	1.684	1.00
76_Q	79_T	1.679	1.00
230_W	239_R	1.653	1.00
231_A	238_Q	1.644	1.00
63_C	124_L	1.643	1.00
75_Q	79_T	1.641	1.00
253_A	286_V	1.641	1.00
282_A	286_V	1.638	1.00
150_M	176_E	1.638	1.00
137_A	164_A	1.635	1.00
261_L	274_A	1.632	1.00
74_R	78_A	1.624	1.00
183_I	219_T	1.618	1.00
272_P	276_R	1.612	1.00
224_L	239_R	1.612	1.00
260_A	281_A	1.603	1.00
221_L	261_L	1.557	1.00
211_V	215_K	1.541	1.00
243_F	280_A	1.539	1.00
150_M	154_K	1.532	1.00
151_A	154_K	1.529	1.00
155_I	159_N	1.512	1.00
211_V	214_E	1.496	1.00
219_T	233_V	1.485	1.00
38_V	72_S	1.476	1.00
249_D	290_G	1.475	1.00
13_I	62_A	1.471	1.00
240_V	275_I	1.471	1.00
51_A	263_T	1.471	1.00
231_A	271_L	1.468	1.00
66_D	71_E	1.467	1.00
71_E	75_Q	1.453	1.00
137_A	262_I	1.450	1.00
155_I	158_Q	1.448	1.00
224_L	227_R	1.443	1.00
7_L	51_A	1.443	1.00
151_A	155_I	1.442	1.00
233_V	236_E	1.439	1.00
260_A	277_F	1.438	1.00
40_F	73_V	1.412	1.00
204_D	207_K	1.380	1.00
162_I	183_I	1.377	1.00
15_A	72_S	1.376	1.00
167_P	186_P	1.362	1.00
157_H	182_D	1.356	1.00
166_N	223_T	1.349	1.00
197_I	211_V	1.339	1.00
133_A	159_N	1.337	1.00
206_A	210_Q	1.337	1.00
45_A	77_L	1.333	1.00
66_D	89_V	1.327	1.00
181_V	184_I	1.326	1.00
157_H	180_L	1.318	1.00
243_F	276_R	1.316	1.00
245_V	287_T	1.311	1.00
240_V	279_H	1.310	1.00
210_Q	214_E	1.299	1.00
70_G	95_T	1.294	1.00
17_H	36_Y	1.273	1.00
121_S	124_L	1.266	1.00
57_N	83_D	1.263	1.00
263_T	267_E	1.259	1.00
76_Q	80_D	1.250	1.00
40_F	76_Q	1.244	1.00
74_R	87_V	1.234	1.00
162_I	218_R	1.226	1.00
229_V	275_I	1.225	1.00
219_T	261_L	1.225	1.00
219_T	265_L	1.210	1.00
261_L	265_L	1.208	1.00
224_L	228_G	1.192	1.00
260_A	278_A	1.192	1.00
122_P	151_A	1.186	1.00
210_Q	232_S	1.180	1.00
175_D	215_K	1.180	1.00
72_S	75_Q	1.173	1.00
264_A	274_A	1.172	1.00
197_I	207_K	1.171	1.00
219_T	271_L	1.169	1.00
223_T	257_F	1.161	1.00
243_F	279_H	1.158	1.00
261_L	278_A	1.157	1.00
52_G	82_I	1.157	1.00
185_T	223_T	1.156	1.00
17_H	38_V	1.156	1.00
245_V	286_V	1.145	1.00
273_E	276_R	1.142	1.00
284_I	287_T	1.141	1.00
284_I	288_R	1.141	1.00
71_E	74_R	1.140	1.00
54_S	260_A	1.133	1.00
247_A	286_V	1.126	1.00
243_F	283_A	1.116	1.00
56_A	266_L	1.105	1.00
191_A	222_I	1.104	1.00
48_A	58_I	1.098	1.00
232_S	237_G	1.097	1.00
75_Q	78_A	1.093	1.00
210_Q	237_G	1.086	1.00
183_I	261_L	1.086	1.00
154_K	158_Q	1.085	1.00
51_A	58_I	1.069	1.00
47_Q	139_L	1.069	1.00
264_A	267_E	1.068	1.00
138_L	156_A	1.054	1.00
13_I	73_V	1.054	1.00
109_V	112_I	1.053	1.00
219_T	231_A	1.042	1.00
49_V	53_R	1.040	1.00
56_A	267_E	1.039	1.00
68_S	71_E	1.038	1.00
207_K	210_Q	1.038	1.00
140_M	163_V	1.037	1.00
183_I	265_L	1.033	1.00
256_T	285_A	1.033	1.00
188_E	227_R	1.025	1.00
247_A	250_T	1.019	1.00
139_L	262_I	1.015	1.00
52_G	81_N	1.014	1.00
90_I	93_E	1.010	1.00
50_A	256_T	1.005	1.00
209_A	222_I	1.004	1.00
279_H	282_A	1.003	1.00
9_V	44_G	1.003	1.00
165_L	181_V	0.992	1.00
185_T	261_L	0.985	1.00
147_E	151_A	0.982	1.00
242_G	279_H	0.980	1.00
59_A	135_A	0.979	1.00
191_A	208_A	0.977	1.00
126_E	151_A	0.974	1.00
65_G	95_T	0.970	1.00
17_H	69_I	0.963	1.00
261_L	271_L	0.963	1.00
18_I	39_A	0.962	1.00
138_L	161_T	0.960	1.00
59_A	86_P	0.959	1.00
274_A	278_A	0.958	1.00
51_A	259_G	0.958	1.00
40_F	72_S	0.952	1.00
93_E	119_A	0.950	1.00
72_S	76_Q	0.949	1.00
64_T	70_G	0.949	1.00
139_L	258_N	0.943	1.00
276_R	280_A	0.939	1.00
13_I	45_A	0.937	1.00
120_L	125_V	0.936	1.00
54_S	281_A	0.935	1.00
64_T	74_R	0.924	1.00
67_D	95_T	0.922	1.00
74_R	84_I	0.913	1.00
19_L	99_L	0.912	1.00
140_M	153_A	0.911	1.00
130_E	133_A	0.908	1.00
263_T	298_R	0.908	1.00
52_G	57_N	0.907	1.00
13_I	60_F	0.906	1.00
109_V	113_H	0.905	1.00
59_A	131_R	0.905	1.00
135_A	161_T	0.904	1.00
263_T	277_F	0.901	1.00
8_V	61_I	0.901	1.00
17_H	97_V	0.901	1.00
247_A	287_T	0.899	1.00
236_E	272_P	0.896	1.00
64_T	87_V	0.896	1.00
195_T	208_A	0.890	1.00
166_N	185_T	0.882	1.00
188_E	192_E	0.879	1.00
84_I	87_V	0.871	1.00
154_K	176_E	0.871	1.00
269_K	277_F	0.869	1.00
33_G	111_G	0.869	1.00
227_R	239_R	0.868	1.00
207_K	211_V	0.864	1.00
209_A	220_V	0.862	1.00
179_A	216_G	0.860	1.00
64_T	89_V	0.859	1.00
10_L	138_L	0.854	1.00
111_G	114_A	0.850	1.00
187_N	190_E	0.846	1.00
228_G	242_G	0.843	1.00
248_V	289_K	0.841	1.00
240_V	276_R	0.839	1.00
265_L	274_A	0.838	1.00
45_A	292_Q	0.834	1.00
63_C	88_S	0.832	1.00
176_E	179_A	0.829	1.00
270_P	274_A	0.827	1.00
238_Q	275_I	0.826	1.00
90_I	119_A	0.823	1.00
73_V	95_T	0.817	1.00
88_S	124_L	0.815	1.00
186_P	191_A	0.814	1.00
148_S	152_A	0.812	1.00
257_F	279_H	0.811	1.00
66_D	92_G	0.805	1.00
108_N	112_I	0.803	1.00
47_Q	258_N	0.801	1.00
213_H	233_V	0.800	1.00
16_D	41_G	0.798	1.00
7_L	266_L	0.796	1.00
245_V	283_A	0.795	1.00
166_N	186_P	0.795	1.00
256_T	282_A	0.794	1.00
260_A	264_A	0.793	1.00
10_L	152_A	0.790	1.00
14_N	96_G	0.790	1.00
240_V	272_P	0.786	1.00
256_T	260_A	0.786	1.00
74_R	88_S	0.784	1.00
233_V	271_L	0.784	1.00
140_M	149_V	0.781	1.00
210_Q	213_H	0.778	1.00
132_I	135_A	0.776	1.00
137_A	266_L	0.773	1.00
178_L	181_V	0.771	1.00
124_L	127_A	0.769	1.00
120_L	124_L	0.765	1.00
48_A	60_F	0.761	1.00
38_V	69_I	0.756	1.00
52_G	58_I	0.755	1.00
206_A	239_R	0.753	1.00
171_R	175_D	0.752	1.00
164_A	185_T	0.751	1.00
112_I	115_G	0.751	1.00
280_A	284_I	0.749	1.00
246_Q	287_T	0.746	1.00
142_L	165_L	0.744	1.00
150_M	180_L	0.740	1.00
131_R	135_A	0.739	1.00
8_V	59_A	0.739	1.00
213_H	234_N	0.733	1.00
279_H	283_A	0.731	1.00
59_A	85_T	0.730	1.00
209_A	213_H	0.724	1.00
132_I	161_T	0.724	1.00
277_F	298_R	0.723	1.00
230_W	237_G	0.723	1.00
15_A	38_V	0.722	1.00
111_G	115_G	0.719	1.00
282_A	285_A	0.715	1.00
221_L	231_A	0.714	1.00
15_A	69_I	0.711	1.00
116_A	119_A	0.709	1.00
153_A	180_L	0.708	1.00
86_P	131_R	0.703	1.00
49_V	292_Q	0.700	1.00
69_I	97_V	0.697	1.00
164_A	183_I	0.695	1.00
233_V	238_Q	0.693	1.00
107_E	110_I	0.692	1.00
100_I	110_I	0.690	1.00
146_L	173_L	0.688	1.00
122_P	147_E	0.686	1.00
76_Q	292_Q	0.684	1.00
228_G	239_R	0.683	1.00
27_P	107_E	0.680	1.00
7_L	137_A	0.678	1.00
257_F	275_I	0.677	1.00
26_T	29_E	0.676	1.00
110_I	114_A	0.676	1.00
123_A	126_E	0.673	1.00
54_S	263_T	0.672	1.00
226_S	244_R	0.671	1.00
43_K	168_A	0.669	1.00
191_A	212_L	0.663	1.00
37_Q	289_K	0.660	1.00
101_F	111_G	0.658	1.00
179_A	215_K	0.657	1.00
80_D	297_W	0.656	1.00
103_N	107_E	0.656	1.00
205_A	224_L	0.656	1.00
100_I	251_I	0.654	1.00
257_F	278_A	0.654	1.00
233_V	237_G	0.653	1.00
175_D	179_A	0.651	1.00
54_S	277_F	0.649	1.00
206_A	230_W	0.648	1.00
19_L	36_Y	0.647	1.00
138_L	152_A	0.646	1.00
205_A	208_A	0.643	1.00
147_E	150_M	0.641	1.00
146_L	150_M	0.639	1.00
164_A	258_N	0.637	1.00
269_K	274_A	0.637	1.00
206_A	232_S	0.636	1.00
131_R	134_N	0.635	1.00
197_I	208_A	0.631	1.00
257_F	282_A	0.631	1.00
122_P	126_E	0.631	1.00
85_T	131_R	0.629	1.00
197_I	204_D	0.621	1.00
229_V	240_V	0.619	1.00
27_P	103_N	0.615	1.00
41_G	46_N	0.614	1.00
209_A	237_G	0.613	1.00
48_A	82_I	0.613	1.00
8_V	131_R	0.609	1.00
206_A	209_A	0.608	1.00
172_E	175_D	0.604	1.00
101_F	109_V	0.603	1.00
123_A	127_A	0.602	1.00
139_L	142_L	0.601	1.00
19_L	33_G	0.600	1.00
122_P	148_S	0.600	1.00
110_I	113_H	0.599	1.00
275_I	279_H	0.598	1.00
208_A	212_L	0.596	1.00
156_A	163_V	0.595	1.00
127_A	155_I	0.594	1.00
191_A	205_A	0.594	1.00
150_M	153_A	0.594	1.00
62_A	87_V	0.593	1.00
163_V	181_V	0.592	1.00
240_V	243_F	0.591	1.00
217_I	220_V	0.590	1.00
57_N	136_S	0.589	1.00
12_S	143_E	0.586	1.00
57_N	266_L	0.581	1.00
88_S	127_A	0.579	1.00
184_I	220_V	0.576	1.00
137_A	183_I	0.574	1.00
71_E	78_A	0.573	1.00
221_L	257_F	0.572	1.00
213_H	217_I	0.571	1.00
45_A	60_F	0.569	1.00
136_S	161_T	0.569	1.00
259_G	263_T	0.568	1.00
189_T	193_K	0.566	1.00
51_A	262_I	0.559	1.00
54_S	259_G	0.556	1.00
86_P	89_V	0.555	1.00
47_Q	262_I	0.554	1.00
152_A	156_A	0.552	1.00
265_L	268_E	0.551	1.00
216_G	220_V	0.548	1.00
98_A	112_I	0.547	1.00
273_E	277_F	0.546	1.00
185_T	221_L	0.542	1.00
67_D	70_G	0.542	1.00
96_G	117_N	0.539	1.00
122_P	125_V	0.538	1.00
137_A	265_L	0.538	1.00
251_I	291_A	0.537	1.00
52_G	80_D	0.535	1.00
127_A	130_E	0.535	1.00
40_F	292_Q	0.535	1.00
205_A	209_A	0.534	1.00
114_A	118_A	0.534	1.00
77_L	82_I	0.534	1.00
170_A	193_K	0.533	1.00
172_E	176_E	0.533	1.00
225_G	250_T	0.530	1.00
226_S	247_A	0.529	1.00
108_N	115_G	0.529	1.00
271_L	274_A	0.529	1.00
68_S	72_S	0.528	1.00
108_N	113_H	0.527	1.00
213_H	216_G	0.525	1.00
108_N	114_A	0.524	1.00
30_T	43_K	0.523	1.00
85_T	88_S	0.523	1.00
166_N	255_D	0.522	1.00
98_A	101_F	0.521	1.00
136_S	162_I	0.520	1.00
213_H	235_G	0.517	1.00
139_L	143_E	0.517	1.00
43_K	143_E	0.515	1.00
109_V	115_G	0.515	1.00
150_M	173_L	0.514	1.00
182_D	219_T	0.512	1.00
107_E	113_H	0.512	1.00
12_S	168_A	0.511	1.00
271_L	275_I	0.510	1.00
46_N	291_A	0.509	1.00
130_E	134_N	0.509	1.00
188_E	225_G	0.505	1.00
181_V	217_I	0.503	1.00
32_T	114_A	0.503	1.00
192_E	203_E	0.500	1.00

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
1rkdA	2	0.9903	100	0.155	Contact Map
2rbcA	2	0.9676	100	0.168	Contact Map
2fv7A	2	0.9806	100	0.177	Contact Map
4xdaA	2	0.9903	100	0.183	Contact Map
3ry7A	2	0.9741	100	0.183	Contact Map
1vm7A	2	0.9612	100	0.191	Contact Map
3vasA	1	0.9644	100	0.202	Contact Map
3ljsA	2	0.945	100	0.209	Contact Map
3kzhA	2	0.9871	100	0.211	Contact Map
3ikhA	2	0.9191	100	0.211	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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