YVRH - BACSU - GREMLIN Contacts

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YVRH - Transcriptional regulatory protein YvrH

UniProt:	P94504	Sequences: MENASILIVDDEKAIVDMIKRVLEKEGYRNILDAASAEEAIPVVKANKVDLIVLDVMMGGMSGFEACTLIREYSDAPIFFLTARSSDADKLSGFAVGADDYITKPFNPLELAARIRAHLKRTYQSKETSSNQTYTYDYFTFSPQNAELIVGGEAVACSAQLLQLLQYFCEHPNVVLSKDQIYEKVWGYPSYGDNNTVMVHIRKLREKIERDPSNPEYIVTVRGLGYRFIPNPEGKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	237 (205)
Sequences:	71637 (51053)
Seq/√Len:	3565.7

ECOLI - ARCA CREB BAER YEDW RSTA KDPE OMPR PHOP CUSR TORR BASR CPXR QSEB PHOB DPIA FIMZ RCSB YGEK DCUR UVRY NARL EVGA YHJB NARP YJJQ BGLJ CHEB RCSA BARA CSGD UHPA TORS ARCB RSSB RCSC YEHT YPDB NTRC EVGS GLRR ATOC ZRAR RCSD
BACSU - YVRH YYCF YCBL YKOG CSSR YRKP RESD YXDJ PHOP YVCP YCLJ BCER CITT DEGU DCTR YBDJ YFIK YXJL MALR CMPA LIAR YDFI YHCZ YVFU DESR GLNL SP0A LYTT CHEB YESN NATR CHEV
HALSA - CHEB Q9HR09 Q9HNM3 Q9HRE5 BAT O51970 Q9HP91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_V	33_D	3.865	1.00
20_K	33_D	3.447	1.00
16_V	35_A	3.360	1.00
41_I	69_L	2.872	1.00
9_V	40_A	2.776	1.00
38_E	60_G	2.526	1.00
61_M	69_L	2.481	1.00
32_L	49_V	2.355	1.00
45_K	73_Y	2.206	1.00
37_A	61_M	2.203	1.00
26_E	112_A	2.189	1.00
32_L	43_V	2.174	1.00
36_S	60_G	2.138	1.00
34_A	43_V	2.134	1.00
32_L	47_N	2.126	1.00
20_K	24_E	2.124	1.00
22_V	108_P	2.119	1.00
5_S	32_L	2.106	1.00
57_M	84_R	1.979	1.00
5_S	29_R	1.972	1.00
43_V	47_N	1.862	1.00
67_C	78_I	1.838	1.00
36_S	39_E	1.800	1.00
167_Y	184_K	1.795	1.00
80_F	93_G	1.788	1.00
35_A	39_E	1.787	1.00
54_L	66_A	1.774	1.00
195_N	198_M	1.766	1.00
90_K	110_E	1.764	1.00
69_L	73_Y	1.720	1.00
71_R	99_D	1.699	1.00
160_Q	163_Q	1.694	1.00
176_L	184_K	1.638	1.00
68_T	96_V	1.638	1.00
7_L	34_A	1.610	1.00
166_Q	170_E	1.603	1.00
80_F	98_A	1.600	1.00
52_I	76_A	1.580	1.00
61_M	65_E	1.568	1.00
4_A	119_L	1.566	1.00
44_V	70_I	1.560	1.00
37_A	66_A	1.556	1.00
100_D	114_R	1.555	1.00
178_K	198_M	1.531	1.00
87_D	107_N	1.526	1.00
38_E	61_M	1.517	1.00
43_V	46_A	1.514	1.00
84_R	89_D	1.490	1.00
62_S	65_E	1.486	1.00
23_L	115_I	1.464	1.00
69_L	72_E	1.463	1.00
13_K	35_A	1.426	1.00
177_S	180_Q	1.400	1.00
51_L	115_I	1.377	1.00
79_F	118_H	1.354	1.00
67_C	80_F	1.334	1.00
56_V	64_F	1.329	1.00
200_H	203_K	1.322	1.00
135_T	140_T	1.320	1.00
65_E	68_T	1.318	1.00
9_V	58_M	1.300	1.00
138_Y	151_G	1.292	1.00
99_D	121_R	1.271	1.00
41_I	61_M	1.266	1.00
112_A	116_R	1.259	1.00
5_S	47_N	1.258	1.00
41_I	66_A	1.252	1.00
43_V	49_V	1.242	1.00
42_P	46_A	1.238	1.00
180_Q	184_K	1.225	1.00
64_F	93_G	1.223	1.00
28_Y	116_R	1.217	1.00
26_E	116_R	1.180	1.00
39_E	42_P	1.175	1.00
99_D	118_H	1.166	1.00
7_L	49_V	1.163	1.00
167_Y	171_H	1.163	1.00
56_V	80_F	1.160	1.00
92_S	96_V	1.149	1.00
86_S	89_D	1.147	1.00
39_E	43_V	1.141	1.00
64_F	92_S	1.140	1.00
34_A	40_A	1.137	1.00
41_I	45_K	1.136	1.00
167_Y	176_L	1.128	1.00
34_A	39_E	1.127	1.00
7_L	43_V	1.122	1.00
11_D	55_D	1.119	1.00
90_K	103_T	1.119	1.00
54_L	67_C	1.117	1.00
38_E	42_P	1.115	1.00
113_A	117_A	1.112	1.00
87_D	91_L	1.107	1.00
161_L	207_K	1.107	1.00
10_D	16_V	1.104	1.00
179_D	194_N	1.100	1.00
27_G	116_R	1.099	1.00
162_L	166_Q	1.090	1.00
199_V	202_R	1.086	1.00
29_R	32_L	1.080	1.00
6_I	28_Y	1.079	1.00
7_L	40_A	1.064	1.00
91_L	95_A	1.064	1.00
8_I	19_I	1.063	1.00
142_S	145_N	1.063	1.00
40_A	66_A	1.052	1.00
140_T	149_I	1.049	1.00
88_A	92_S	1.049	1.00
7_L	32_L	1.049	1.00
95_A	116_R	1.037	1.00
147_E	154_A	1.034	1.00
143_P	166_Q	1.032	1.00
17_D	33_D	1.020	1.00
110_E	113_A	1.006	1.00
51_L	119_L	0.997	1.00
149_I	154_A	0.994	1.00
56_V	62_S	0.992	1.00
176_L	180_Q	0.990	1.00
163_Q	166_Q	0.989	1.00
77_P	99_D	0.974	1.00
118_H	121_R	0.963	1.00
4_A	28_Y	0.953	1.00
159_A	163_Q	0.953	1.00
211_D	215_P	0.949	1.00
67_C	96_V	0.942	1.00
9_V	34_A	0.939	1.00
40_A	44_V	0.937	1.00
64_F	96_V	0.937	1.00
14_A	18_M	0.931	1.00
13_K	17_D	0.920	1.00
196_T	200_H	0.920	1.00
87_D	90_K	0.908	1.00
68_T	92_S	0.904	1.00
21_R	25_K	0.904	1.00
141_F	169_C	0.901	1.00
195_N	199_V	0.901	1.00
201_I	205_R	0.900	1.00
85_S	103_T	0.899	1.00
19_I	81_L	0.898	1.00
28_Y	112_A	0.897	1.00
52_I	70_I	0.894	1.00
5_S	50_D	0.884	1.00
141_F	162_L	0.883	1.00
42_P	45_K	0.880	1.00
7_L	44_V	0.871	1.00
211_D	214_N	0.868	1.00
194_N	198_M	0.855	1.00
65_E	69_L	0.845	1.00
117_A	122_T	0.842	1.00
17_D	20_K	0.842	1.00
4_A	123_Y	0.837	1.00
54_L	78_I	0.833	1.00
52_I	78_I	0.832	1.00
67_C	98_A	0.829	1.00
203_K	206_E	0.818	1.00
54_L	80_F	0.807	1.00
178_K	194_N	0.807	1.00
66_A	70_I	0.799	1.00
195_N	202_R	0.794	1.00
81_L	106_F	0.794	1.00
92_S	95_A	0.793	1.00
108_P	112_A	0.790	1.00
9_V	52_I	0.790	1.00
44_V	49_V	0.786	1.00
17_D	21_R	0.785	1.00
167_Y	170_E	0.784	1.00
210_R	216_E	0.784	1.00
135_T	138_Y	0.780	1.00
56_V	84_R	0.775	1.00
61_M	66_A	0.770	1.00
110_E	114_R	0.769	1.00
107_N	110_E	0.767	1.00
91_L	109_L	0.767	1.00
58_M	66_A	0.766	1.00
202_R	206_E	0.766	1.00
13_K	16_V	0.765	1.00
5_S	49_V	0.764	1.00
44_V	76_A	0.756	1.00
68_T	72_E	0.756	1.00
89_D	92_S	0.755	1.00
20_K	31_I	0.751	1.00
41_I	73_Y	0.744	1.00
53_V	111_L	0.742	1.00
117_A	120_K	0.742	1.00
146_A	163_Q	0.735	1.00
170_E	176_L	0.734	1.00
53_V	81_L	0.733	1.00
167_Y	181_I	0.730	1.00
88_A	109_L	0.729	1.00
199_V	203_K	0.729	1.00
57_M	83_A	0.723	1.00
56_V	89_D	0.723	1.00
119_L	122_T	0.721	1.00
79_F	114_R	0.721	1.00
106_F	111_L	0.715	1.00
44_V	52_I	0.705	1.00
75_D	124_Q	0.705	1.00
6_I	51_L	0.703	1.00
77_P	121_R	0.701	1.00
90_K	107_N	0.696	1.00
37_A	41_I	0.695	1.00
10_D	58_M	0.693	1.00
18_M	22_V	0.692	1.00
9_V	66_A	0.692	1.00
15_I	106_F	0.688	1.00
180_Q	183_E	0.687	1.00
160_Q	200_H	0.683	1.00
158_S	207_K	0.674	1.00
138_Y	150_V	0.672	1.00
22_V	112_A	0.671	1.00
75_D	125_S	0.670	1.00
37_A	60_G	0.667	1.00
168_F	201_I	0.663	1.00
136_Y	140_T	0.662	1.00
56_V	93_G	0.660	1.00
41_I	44_V	0.660	1.00
53_V	115_I	0.658	1.00
205_R	210_R	0.658	1.00
106_F	110_E	0.656	1.00
209_E	216_E	0.656	1.00
122_T	126_K	0.656	1.00
4_A	50_D	0.655	1.00
70_I	78_I	0.653	1.00
136_Y	139_F	0.649	1.00
113_A	116_R	0.648	1.00
179_D	183_E	0.647	1.00
95_A	113_A	0.641	1.00
67_C	71_R	0.640	1.00
146_A	162_L	0.638	1.00
170_E	184_K	0.634	1.00
16_V	20_K	0.632	1.00
114_R	118_H	0.631	1.00
109_L	113_A	0.629	1.00
37_A	58_M	0.628	1.00
19_I	111_L	0.626	1.00
71_R	77_P	0.623	1.00
87_D	109_L	0.620	1.00
100_D	117_A	0.620	1.00
12_E	83_A	0.618	1.00
23_L	28_Y	0.618	1.00
45_K	69_L	0.613	1.00
8_I	20_K	0.612	1.00
139_F	150_V	0.609	1.00
164_L	168_F	0.608	1.00
6_I	23_L	0.606	1.00
93_G	98_A	0.603	1.00
163_Q	167_Y	0.599	1.00
213_S	216_E	0.599	1.00
149_I	152_G	0.598	1.00
64_F	89_D	0.595	1.00
94_F	114_R	0.595	1.00
70_I	76_A	0.589	1.00
8_I	31_I	0.589	1.00
53_V	79_F	0.587	1.00
39_E	60_G	0.583	1.00
22_V	26_E	0.582	1.00
55_D	104_K	0.582	1.00
88_A	91_L	0.573	1.00
8_I	33_D	0.567	1.00
214_N	217_Y	0.567	1.00
150_V	153_E	0.566	1.00
71_R	76_A	0.564	1.00
77_P	119_L	0.563	1.00
215_P	218_I	0.563	1.00
21_R	24_E	0.562	1.00
210_R	219_V	0.562	1.00
150_V	209_E	0.560	1.00
198_M	201_I	0.559	1.00
134_Y	143_P	0.558	1.00
209_E	215_P	0.557	1.00
141_F	166_Q	0.556	1.00
12_E	15_I	0.552	1.00
158_S	161_L	0.547	1.00
10_D	104_K	0.542	1.00
134_Y	138_Y	0.538	1.00
121_R	125_S	0.537	1.00
216_E	220_T	0.536	1.00
44_V	73_Y	0.536	1.00
126_K	129_S	0.536	1.00
11_D	82_T	0.533	1.00
116_R	120_K	0.529	1.00
138_Y	142_S	0.529	1.00
18_M	21_R	0.529	1.00
15_I	18_M	0.525	1.00
77_P	125_S	0.525	1.00
8_I	16_V	0.525	1.00
85_S	105_P	0.524	1.00
193_D	196_T	0.522	1.00
51_L	118_H	0.522	1.00
44_V	74_S	0.520	1.00
79_F	100_D	0.520	1.00
209_E	213_S	0.519	1.00
77_P	122_T	0.517	1.00
11_D	58_M	0.515	1.00
150_V	211_D	0.514	1.00
91_L	94_F	0.513	1.00
48_K	74_S	0.513	1.00
141_F	148_L	0.512	1.00
13_K	33_D	0.512	1.00
82_T	104_K	0.511	1.00
44_V	66_A	0.509	1.00
82_T	101_Y	0.508	1.00
115_I	119_L	0.506	1.00
36_S	58_M	0.503	1.00
54_L	70_I	0.502	1.00
117_A	121_R	0.501	1.00
6_I	115_I	0.501	1.00
182_Y	191_Y	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
3r0jA	2	0.9325	100	0.182	Contact Map
2gwrA	1	0.9409	100	0.187	Contact Map
2oqrA	2	0.9536	100	0.191	Contact Map
1ys7A	2	0.9494	100	0.195	Contact Map
4b09A	2	0.9072	100	0.204	Contact Map
4kfcA	2	0.9451	100	0.212	Contact Map
1kgsA	1	0.9198	100	0.222	Contact Map
3q9sA	1	0.8861	100	0.243	Contact Map
1p2fA	1	0.9114	100	0.247	Contact Map
2hqrA	2	0.9325	100	0.249	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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