GLNL - BACSU - GREMLIN Contacts

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GLNL - Transcriptional regulatory protein GlnL

UniProt:	P40759	Sequences: MRFFIADDDRAVRSILRQIIEDEDLGEAAGEADDGSQVEGHMLQFKQIDILLIDLLMPGRDGIETIRQIQNTYSGKIVMISQVEAKEMVGEAYSLGIEYFIHKPINRIEIVTVLQKVKERIELEHSIGAIQHSLSRLVNRTERKARPQQKSDSGLKEAGTFLLSELGMMGEGGAHDLMAVLQYLAEHEQSEPHEKQSPSLKQIFTQVAVRKLGTGASQTEVNREMKASEQRIRRAIIHSLHHFASLGTTDFSNPKFETYASKFFDFPVVSQKMKELQSKDAKPLAPARINMKKFIHVFFLEAKLLHETMKQRRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	314 (274)
Sequences:	9704 (8930)
Seq/√Len:	539.5

ECOLI - YHJB CHEB RSSB ARCA CREB YEDW QSEB UVRY BASR EVGA CUSR BAER DCUR PHOP OMPR DPIA TORR RCSC RSTA PHOB NARP BARA KDPE TORS YPDB UHPA YGEK CPXR FIMZ YJJQ NARL YEHT ARCB RCSB CSGD BGLJ
BACSU - GLNL YESN SP0A CITT YVRH CHEB YCLJ YYCF RESD MALR PHOP YFIK YRKP BCER YCBL DCTR YXDJ YXJL YVCP YVFU LYTT YDFI CMPA YKOG DEGU NATR DESR YHCZ LIAR CSSR
HALSA - CHEB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_Q	72_T	3.558	1.00
61_D	64_E	3.467	1.00
13_R	31_E	3.345	1.00
17_R	31_E	3.294	1.00
13_R	33_D	3.015	1.00
6_A	38_V	2.965	1.00
231_R	234_R	2.943	1.00
30_G	48_I	2.925	1.00
66_I	77_I	2.842	1.00
53_I	65_T	2.678	1.00
275_E	278_S	2.670	1.00
76_K	124_E	2.549	1.00
2_R	28_A	2.526	1.00
262_K	270_S	2.519	1.00
34_D	59_G	2.498	1.00
36_S	59_G	2.466	1.00
67_R	91_E	2.444	1.00
68_Q	71_N	2.393	1.00
39_E	68_Q	2.308	1.00
43_L	69_I	2.286	1.00
138_V	141_T	2.185	1.00
68_Q	72_T	2.152	1.00
99_Y	116_K	2.096	1.00
264_F	268_V	2.092	1.00
38_V	65_T	2.051	1.00
98_E	120_R	2.024	1.00
227_A	231_R	2.014	1.00
30_G	46_K	2.006	1.00
32_A	42_M	1.985	1.00
35_G	60_R	1.967	1.00
51_L	69_I	1.936	1.00
34_D	37_Q	1.910	1.00
99_Y	113_V	1.877	1.00
98_E	117_V	1.877	1.00
33_D	37_Q	1.852	1.00
66_I	79_M	1.845	1.00
121_I	125_H	1.817	1.00
4_F	32_A	1.807	1.00
43_L	48_I	1.801	1.00
76_K	120_R	1.767	1.00
43_L	73_Y	1.697	1.00
79_M	97_I	1.669	1.00
78_V	113_V	1.653	1.00
60_R	68_Q	1.636	1.00
64_E	67_R	1.623	1.00
259_Y	263_F	1.618	1.00
141_T	144_K	1.612	1.00
3_F	27_E	1.587	1.00
42_M	48_I	1.585	1.00
141_T	145_A	1.567	1.00
78_V	117_V	1.567	1.00
224_E	252_S	1.561	1.00
232_I	271_Q	1.559	1.00
55_L	79_M	1.524	1.00
79_M	92_A	1.499	1.00
239_S	243_F	1.490	1.00
131_Q	134_L	1.483	1.00
241_H	245_S	1.466	1.00
87_E	90_G	1.463	1.00
94_S	99_Y	1.457	1.00
7_D	13_R	1.431	1.00
138_V	142_E	1.421	1.00
53_I	79_M	1.415	1.00
56_L	83_V	1.409	1.00
70_Q	98_E	1.405	1.00
60_R	64_E	1.399	1.00
51_L	77_I	1.399	1.00
91_E	94_S	1.383	1.00
274_K	277_Q	1.383	1.00
127_I	131_Q	1.354	1.00
40_G	45_F	1.351	1.00
67_R	71_N	1.345	1.00
66_I	97_I	1.340	1.00
69_I	77_I	1.340	1.00
127_I	130_I	1.320	1.00
67_R	95_L	1.289	1.00
137_L	141_T	1.273	1.00
6_A	51_L	1.270	1.00
39_E	65_T	1.263	1.00
36_S	40_G	1.255	1.00
35_G	65_T	1.232	1.00
39_E	60_R	1.231	1.00
32_A	35_G	1.231	1.00
4_F	43_L	1.231	1.00
12_V	15_I	1.229	1.00
50_I	118_K	1.229	1.00
86_K	89_V	1.212	1.00
278_S	282_K	1.210	1.00
55_L	63_I	1.207	1.00
53_I	77_I	1.194	1.00
90_G	94_S	1.188	1.00
4_F	30_G	1.186	1.00
64_E	68_Q	1.184	1.00
105_I	110_I	1.182	1.00
131_Q	135_S	1.174	1.00
253_N	256_F	1.174	1.00
9_D	12_V	1.170	1.00
252_S	256_F	1.166	1.00
19_I	107_R	1.164	1.00
22_D	26_G	1.162	1.00
129_A	133_S	1.161	1.00
243_F	264_F	1.149	1.00
134_L	137_L	1.140	1.00
89_V	93_Y	1.132	1.00
138_V	144_K	1.129	1.00
113_V	117_V	1.126	1.00
247_G	260_A	1.119	1.00
51_L	65_T	1.115	1.00
32_A	38_V	1.113	1.00
56_L	82_Q	1.108	1.00
256_F	267_P	1.106	1.00
240_L	243_F	1.098	1.00
118_K	122_E	1.097	1.00
265_D	268_V	1.090	1.00
7_D	57_M	1.084	1.00
121_I	124_E	1.074	1.00
42_M	46_K	1.072	1.00
14_S	17_R	1.067	1.00
76_K	98_E	1.065	1.00
252_S	255_K	1.064	1.00
123_L	126_S	1.062	1.00
142_E	145_A	1.059	1.00
239_S	242_H	1.056	1.00
130_I	134_L	1.055	1.00
57_M	60_R	1.055	1.00
130_I	133_S	1.053	1.00
52_L	110_I	1.050	1.00
61_D	91_E	1.047	1.00
14_S	31_E	1.040	1.00
133_S	137_L	1.036	1.00
43_L	51_L	1.033	1.00
30_G	42_M	1.031	1.00
63_I	91_E	1.026	1.00
85_A	88_M	1.026	1.00
43_L	65_T	1.018	1.00
137_L	144_K	1.015	1.00
17_R	21_E	1.012	1.00
8_D	54_D	1.007	1.00
50_I	114_L	1.007	1.00
223_R	226_K	1.006	1.00
119_E	123_L	0.994	1.00
37_Q	40_G	0.994	1.00
2_R	30_G	0.992	1.00
226_K	230_Q	0.980	1.00
52_L	78_V	0.974	1.00
111_V	115_Q	0.967	1.00
126_S	129_A	0.961	1.00
134_L	138_V	0.959	1.00
12_V	82_Q	0.956	1.00
196_Q	199_S	0.954	1.00
40_G	44_Q	0.954	1.00
5_I	16_L	0.951	1.00
66_I	95_L	0.949	1.00
219_T	223_R	0.946	1.00
53_I	66_I	0.944	1.00
253_N	257_E	0.942	1.00
251_F	254_P	0.937	1.00
137_L	143_R	0.937	1.00
251_F	255_K	0.936	1.00
5_I	13_R	0.932	1.00
264_F	272_K	0.931	1.00
138_V	143_R	0.929	1.00
199_S	202_Q	0.928	1.00
139_N	143_R	0.927	1.00
115_Q	119_E	0.926	1.00
69_I	73_Y	0.923	1.00
155_L	159_G	0.923	1.00
160_T	164_S	0.917	1.00
91_E	95_L	0.910	1.00
75_G	124_E	0.906	1.00
271_Q	274_K	0.900	1.00
2_R	48_I	0.900	1.00
172_G	176_D	0.899	1.00
137_L	140_R	0.897	1.00
269_V	273_M	0.896	1.00
35_G	57_M	0.884	1.00
146_R	150_K	0.883	1.00
208_A	212_L	0.881	1.00
56_L	61_D	0.879	1.00
229_E	271_Q	0.873	1.00
266_F	269_V	0.873	1.00
23_E	26_G	0.870	1.00
54_D	103_K	0.869	1.00
156_K	160_T	0.865	1.00
234_R	237_I	0.857	1.00
63_I	92_A	0.856	1.00
89_V	109_E	0.848	1.00
176_D	180_V	0.846	1.00
271_Q	275_E	0.844	1.00
254_P	257_E	0.842	1.00
126_S	130_I	0.841	1.00
132_H	135_S	0.841	1.00
106_N	109_E	0.841	1.00
36_S	60_R	0.841	1.00
158_A	162_L	0.840	1.00
2_R	46_K	0.840	1.00
55_L	92_A	0.839	1.00
139_N	142_E	0.838	1.00
6_A	35_G	0.832	1.00
137_L	142_E	0.829	1.00
156_K	159_G	0.824	1.00
150_K	154_G	0.823	1.00
27_E	50_I	0.820	1.00
6_A	65_T	0.818	1.00
135_S	139_N	0.817	1.00
136_R	140_R	0.814	1.00
65_T	69_I	0.814	1.00
23_E	111_V	0.813	1.00
228_S	271_Q	0.812	1.00
232_I	272_K	0.812	1.00
109_E	113_V	0.811	1.00
112_T	116_K	0.807	1.00
10_R	14_S	0.806	1.00
229_E	267_P	0.804	1.00
82_Q	104_P	0.801	1.00
159_G	163_L	0.798	1.00
39_E	44_Q	0.794	1.00
159_G	162_L	0.792	1.00
55_L	88_M	0.791	1.00
167_G	171_E	0.785	1.00
137_L	145_A	0.784	1.00
128_G	131_Q	0.784	1.00
32_A	37_Q	0.781	1.00
5_I	17_R	0.776	1.00
268_V	271_Q	0.772	1.00
56_L	85_A	0.770	1.00
224_E	243_F	0.768	1.00
153_S	159_G	0.767	1.00
250_D	254_P	0.766	1.00
129_A	132_H	0.764	1.00
123_L	127_I	0.763	1.00
122_E	125_H	0.762	1.00
265_D	269_V	0.756	1.00
223_R	228_S	0.753	1.00
14_S	18_Q	0.752	1.00
151_S	155_L	0.748	1.00
4_F	38_V	0.745	1.00
219_T	222_N	0.744	1.00
234_R	242_H	0.744	1.00
225_M	260_A	0.742	1.00
119_E	122_E	0.741	1.00
109_E	112_T	0.737	1.00
207_V	211_K	0.735	1.00
75_G	128_G	0.733	1.00
90_G	93_Y	0.730	1.00
16_L	80_I	0.730	1.00
169_M	172_G	0.728	1.00
54_D	81_S	0.728	1.00
135_S	138_V	0.727	1.00
20_I	114_L	0.726	1.00
236_I	239_S	0.723	1.00
27_E	118_K	0.722	1.00
128_G	132_H	0.721	1.00
202_Q	206_Q	0.719	1.00
176_D	179_A	0.719	1.00
260_A	263_F	0.715	1.00
183_Y	187_H	0.714	1.00
150_K	153_S	0.713	1.00
49_D	121_I	0.712	1.00
270_S	274_K	0.710	1.00
140_R	143_R	0.705	1.00
268_V	272_K	0.705	1.00
125_H	128_G	0.704	1.00
105_I	109_E	0.704	1.00
140_R	144_K	0.703	1.00
4_F	42_M	0.703	1.00
83_V	88_M	0.701	1.00
153_S	156_K	0.700	1.00
116_K	120_R	0.699	1.00
184_L	187_H	0.698	1.00
255_K	258_T	0.698	1.00
174_A	178_M	0.695	1.00
124_E	128_G	0.694	1.00
138_V	145_A	0.689	1.00
10_R	13_R	0.689	1.00
223_R	227_A	0.689	1.00
4_F	48_I	0.687	1.00
264_F	269_V	0.686	1.00
84_E	89_V	0.684	1.00
60_R	65_T	0.681	1.00
132_H	136_R	0.681	1.00
66_I	70_Q	0.679	1.00
104_P	109_E	0.678	1.00
152_D	156_K	0.673	1.00
56_L	88_M	0.673	1.00
222_N	225_M	0.671	1.00
246_L	278_S	0.670	1.00
69_I	72_T	0.669	1.00
16_L	110_I	0.667	1.00
175_H	179_A	0.667	1.00
86_K	90_G	0.666	1.00
225_M	228_S	0.665	1.00
52_L	114_L	0.662	1.00
93_Y	97_I	0.659	1.00
6_A	32_A	0.658	1.00
70_Q	76_K	0.656	1.00
108_I	112_T	0.654	1.00
162_L	165_E	0.654	1.00
158_A	164_S	0.653	1.00
53_I	69_I	0.653	1.00
251_F	256_F	0.652	1.00
225_M	229_E	0.650	1.00
18_Q	22_D	0.650	1.00
275_E	279_K	0.649	1.00
155_L	158_A	0.647	1.00
53_I	57_M	0.647	1.00
80_I	83_V	0.646	1.00
107_R	111_V	0.645	1.00
124_E	127_I	0.644	1.00
98_E	116_K	0.641	1.00
8_D	81_S	0.639	1.00
161_F	165_E	0.639	1.00
233_R	275_E	0.638	1.00
195_K	199_S	0.636	1.00
80_I	105_I	0.635	1.00
157_E	161_F	0.634	1.00
8_D	57_M	0.632	1.00
139_N	145_A	0.632	1.00
246_L	249_T	0.626	1.00
6_A	57_M	0.626	1.00
6_A	53_I	0.625	1.00
157_E	162_L	0.620	1.00
79_M	98_E	0.619	1.00
251_F	257_E	0.617	1.00
176_D	181_L	0.617	1.00
134_L	144_K	0.615	1.00
153_S	157_E	0.615	1.00
135_S	141_T	0.615	1.00
20_I	111_V	0.612	1.00
263_F	266_F	0.611	1.00
221_V	225_M	0.611	1.00
70_Q	95_L	0.610	1.00
35_G	39_E	0.609	1.00
54_D	57_M	0.609	1.00
9_D	82_Q	0.608	1.00
241_H	244_A	0.606	1.00
224_E	227_A	0.603	1.00
35_G	38_V	0.602	1.00
224_E	228_S	0.601	1.00
92_A	97_I	0.599	1.00
8_D	82_Q	0.599	1.00
55_L	61_D	0.598	1.00
133_S	136_R	0.597	1.00
225_M	256_F	0.594	1.00
114_L	118_K	0.593	1.00
248_T	251_F	0.591	1.00
35_G	61_D	0.591	1.00
63_I	88_M	0.590	1.00
84_E	102_H	0.590	1.00
9_D	56_L	0.590	1.00
136_R	139_N	0.589	1.00
81_S	103_K	0.588	1.00
171_E	176_D	0.587	0.99
253_N	258_T	0.585	0.99
122_E	126_S	0.585	0.99
131_Q	141_T	0.583	0.99
92_A	100_F	0.579	0.99
113_V	116_K	0.572	0.99
79_M	95_L	0.569	0.99
90_G	109_E	0.567	0.99
79_M	89_V	0.564	0.99
167_G	170_G	0.562	0.99
69_I	74_S	0.558	0.99
170_G	174_A	0.558	0.99
204_F	236_I	0.558	0.99
27_E	114_L	0.556	0.99
55_L	66_I	0.555	0.99
116_K	119_E	0.552	0.99
250_D	253_N	0.550	0.99
161_F	164_S	0.550	0.99
27_E	115_Q	0.549	0.99
242_H	245_S	0.549	0.99
77_I	98_E	0.548	0.99
220_E	247_G	0.546	0.99
35_G	59_G	0.545	0.99
152_D	155_L	0.545	0.99
214_T	217_S	0.545	0.99
151_S	154_G	0.542	0.99
47_Q	73_Y	0.541	0.99
55_L	83_V	0.540	0.99
169_M	176_D	0.537	0.99
3_F	22_D	0.536	0.99
57_M	65_T	0.535	0.99
215_G	218_Q	0.535	0.99
80_I	89_V	0.532	0.99
3_F	52_L	0.532	0.99
170_G	173_G	0.531	0.99
111_V	114_L	0.528	0.99
134_L	141_T	0.526	0.99
233_R	237_I	0.526	0.99
115_Q	118_K	0.524	0.99
277_Q	281_A	0.523	0.99
146_R	151_S	0.522	0.99
44_Q	73_Y	0.517	0.99
34_D	57_M	0.516	0.99
221_V	260_A	0.513	0.99
76_K	117_V	0.512	0.99
54_D	82_Q	0.511	0.99
76_K	121_I	0.510	0.99
187_H	191_E	0.509	0.99
254_P	258_T	0.509	0.99
7_D	103_K	0.506	0.99
271_Q	277_Q	0.506	0.99
89_V	97_I	0.505	0.98
247_G	252_S	0.505	0.98
205_T	209_V	0.505	0.98
206_Q	233_R	0.504	0.98
5_I	52_L	0.503	0.98
146_R	152_D	0.501	0.98
151_S	156_K	0.501	0.98
84_E	87_E	0.500	0.98

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
1yioA	1	0.621	100	0.517	Contact Map
4g97A	1	0.4045	100	0.527	Contact Map
3n0rA	1	0.379	100	0.529	Contact Map
4b09A	2	0.6115	100	0.537	Contact Map
4gvpA	1	0.6369	100	0.538	Contact Map
1s8nA	1	0.5892	100	0.541	Contact Map
4ldzA	2	0.6115	99.9	0.544	Contact Map
2oqrA	2	0.6401	99.9	0.544	Contact Map
3q9sA	1	0.6115	99.9	0.546	Contact Map
3breA	4	0.9331	99.9	0.546	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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