YFIK - BACSU - GREMLIN Contacts

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YFIK - Uncharacterized transcriptional regulatory protein YfiK

UniProt:	P94439	Sequences: MIKIIITDDQDIVREGLASLLQLREELDVIATARNGQEAFEKAKELEPDIVLMDIRMPVSNGVEGTKLITSSLPSVKVLMLTTFKDSALIAEALEEGASGYLLKDMSADTIVKAVMTVHSGGMVLPPELTAQMLNEWKREKQLKGINEIEKPNELLDLTEREIEVLAELGYGLNNKEIAEKLYITEGTVKNHVSNIISKLAVRDRTQAAIYSVRYGVSVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	220 (199)
Sequences:	80167 (57690)
Seq/√Len:	4089.5

ECOLI - UVRY CUSR KDPE PHOP EVGA YEDW FIMZ CREB NARP RSTA NARL DCUR YHJB RCSB YGEK CPXR ARCA YJJQ PHOB OMPR QSEB DPIA BASR BAER RCSA UHPA BGLJ TORR CSGD YPDB BARA RSSB ARCB RCSC TORS YEHT CHEB NTRC EVGS GLRR ZRAR ATOC RCSD
BACSU - YFIK LIAR CMPA YVFU DEGU CITT YXJL YDFI YXDJ DESR MALR YVCP BCER PHOP YHCZ YKOG YCBL YYCF YVRH YCLJ RESD YRKP CSSR DCTR YESN CHEB YBDJ GLNL LYTT SP0A NATR CHEV CCDB
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
14_R	32_T	3.776	1.00
18_A	32_T	3.329	1.00
14_R	34_R	3.320	1.00
40_F	68_L	2.791	1.00
7_T	39_A	2.774	1.00
37_Q	59_V	2.583	1.00
60_S	68_L	2.302	1.00
35_N	59_V	2.302	1.00
36_G	60_S	2.230	1.00
20_L	108_A	2.114	1.00
44_K	72_S	2.104	1.00
33_A	42_K	2.041	1.00
3_K	28_D	2.037	1.00
18_A	22_Q	2.036	1.00
31_A	42_K	1.928	1.00
56_R	84_F	1.918	1.00
53_M	65_G	1.898	1.00
34_R	38_E	1.891	1.00
187_G	190_K	1.805	1.00
66_T	78_V	1.796	1.00
35_N	38_E	1.793	1.00
90_I	110_T	1.781	1.00
31_A	46_L	1.734	1.00
80_M	93_A	1.730	1.00
42_K	46_L	1.730	1.00
31_A	48_P	1.729	1.00
67_K	96_E	1.721	1.00
25_E	112_V	1.692	1.00
3_K	31_A	1.688	1.00
5_I	33_A	1.666	1.00
80_M	98_A	1.665	1.00
70_T	99_S	1.657	1.00
87_S	107_S	1.632	1.00
161_R	164_E	1.623	1.00
175_N	190_K	1.619	1.00
36_G	65_G	1.578	1.00
42_K	45_E	1.525	1.00
61_N	64_E	1.524	1.00
100_G	114_A	1.519	1.00
60_S	64_E	1.512	1.00
73_L	76_V	1.508	1.00
68_L	72_S	1.496	1.00
43_A	69_I	1.483	1.00
21_L	115_V	1.479	1.00
168_E	181_K	1.477	1.00
173_L	181_K	1.466	1.00
167_A	171_Y	1.462	1.00
192_H	195_N	1.453	1.00
84_F	89_L	1.446	1.00
68_L	71_S	1.431	1.00
51_V	76_V	1.416	1.00
174_N	177_E	1.410	1.00
11_D	34_R	1.393	1.00
66_T	80_M	1.385	1.00
37_Q	60_S	1.382	1.00
40_F	65_G	1.351	1.00
50_I	115_V	1.350	1.00
64_E	67_K	1.338	1.00
3_K	46_L	1.335	1.00
42_K	48_P	1.329	1.00
79_L	118_V	1.324	1.00
99_S	121_G	1.296	1.00
162_E	199_K	1.283	1.00
99_S	118_V	1.281	1.00
55_I	63_V	1.266	1.00
63_V	93_A	1.254	1.00
27_L	116_M	1.246	1.00
40_F	60_S	1.235	1.00
7_T	57_M	1.226	1.00
8_D	14_R	1.223	1.00
41_E	45_E	1.209	1.00
92_E	96_E	1.207	1.00
202_V	211_Y	1.201	1.00
112_V	116_M	1.172	1.00
9_D	54_D	1.171	1.00
33_A	39_A	1.171	1.00
53_M	66_T	1.170	1.00
38_E	41_E	1.160	1.00
38_E	42_K	1.150	1.00
55_I	80_M	1.136	1.00
26_E	116_M	1.136	1.00
5_I	48_P	1.127	1.00
86_D	89_L	1.118	1.00
163_I	167_A	1.118	1.00
177_E	181_K	1.116	1.00
37_Q	41_E	1.111	1.00
63_V	92_E	1.109	1.00
5_I	39_A	1.103	1.00
4_I	27_L	1.097	1.00
176_K	186_E	1.095	1.00
50_I	119_H	1.072	1.00
135_N	138_K	1.071	1.00
168_E	172_G	1.062	1.00
113_K	117_T	1.060	1.00
187_G	191_N	1.040	1.00
148_E	155_L	1.033	1.00
5_I	42_K	1.028	1.00
88_A	92_E	1.025	1.00
40_F	44_K	1.021	1.00
6_I	17_L	1.019	1.00
110_T	113_K	1.019	1.00
33_A	38_E	1.017	1.00
95_E	116_M	1.015	1.00
191_N	194_S	1.015	1.00
165_V	169_L	1.011	1.00
91_A	95_E	1.007	1.00
173_L	177_E	1.000	1.00
87_S	91_A	0.999	1.00
39_A	65_G	0.992	1.00
15_E	32_T	0.987	1.00
164_E	167_A	0.979	1.00
67_K	92_E	0.977	1.00
90_I	103_L	0.977	1.00
51_V	69_I	0.969	1.00
11_D	15_E	0.962	1.00
168_E	173_L	0.958	1.00
43_A	73_L	0.956	1.00
139_R	152_P	0.953	1.00
39_A	43_A	0.953	1.00
18_A	29_V	0.944	1.00
12_I	16_G	0.942	1.00
160_E	164_E	0.941	1.00
164_E	168_E	0.933	1.00
55_I	61_N	0.932	1.00
201_A	204_D	0.927	1.00
53_M	78_V	0.919	1.00
5_I	31_A	0.915	1.00
17_L	81_L	0.913	1.00
132_Q	135_N	0.910	1.00
41_E	44_K	0.907	1.00
66_T	98_A	0.906	1.00
7_T	33_A	0.906	1.00
63_V	96_E	0.905	1.00
188_T	192_H	0.903	1.00
66_T	96_E	0.901	1.00
87_S	90_I	0.888	1.00
52_L	111_I	0.884	1.00
150_E	155_L	0.877	1.00
51_V	78_V	0.871	1.00
7_T	51_V	0.862	1.00
15_E	18_A	0.860	1.00
64_E	68_L	0.859	1.00
27_L	112_V	0.858	1.00
5_I	43_A	0.858	1.00
11_D	14_R	0.855	1.00
55_I	89_L	0.854	1.00
79_L	114_A	0.854	1.00
53_M	80_M	0.853	1.00
161_R	183_Y	0.851	1.00
118_V	121_G	0.849	1.00
92_E	95_E	0.844	1.00
19_S	23_L	0.840	1.00
136_E	139_R	0.836	1.00
85_K	103_L	0.834	1.00
77_K	99_S	0.833	1.00
108_A	112_V	0.824	1.00
65_G	69_I	0.824	1.00
147_N	164_E	0.818	1.00
89_L	92_E	0.818	1.00
110_T	114_A	0.814	1.00
130_T	134_L	0.810	1.00
159_T	199_K	0.810	1.00
176_K	180_E	0.809	1.00
52_L	115_V	0.807	1.00
195_N	198_S	0.803	1.00
168_E	178_I	0.801	1.00
191_N	195_N	0.800	1.00
29_V	32_T	0.796	1.00
186_E	190_K	0.795	1.00
177_E	180_E	0.793	1.00
3_K	49_D	0.789	1.00
193_V	197_I	0.786	1.00
47_E	73_L	0.785	1.00
67_K	71_S	0.777	1.00
3_K	48_P	0.776	1.00
55_I	84_F	0.771	1.00
57_M	65_G	0.771	1.00
43_A	76_V	0.767	1.00
13_V	106_M	0.762	1.00
43_A	48_P	0.761	1.00
81_L	106_M	0.756	1.00
36_G	40_F	0.756	1.00
6_I	29_V	0.756	1.00
25_E	116_M	0.756	1.00
117_T	120_S	0.753	1.00
122_G	126_P	0.748	1.00
15_E	19_S	0.747	1.00
131_A	134_L	0.746	1.00
91_A	109_D	0.740	1.00
60_S	65_G	0.739	1.00
107_S	110_T	0.731	1.00
187_G	194_S	0.730	1.00
194_S	198_S	0.726	1.00
52_L	81_L	0.726	1.00
150_E	153_N	0.725	1.00
17_L	111_I	0.725	1.00
7_T	65_G	0.717	1.00
28_D	31_A	0.707	1.00
168_E	171_Y	0.707	1.00
88_A	109_D	0.693	1.00
56_R	83_T	0.692	1.00
36_G	59_V	0.691	1.00
117_T	122_G	0.687	1.00
147_N	163_I	0.686	1.00
20_L	112_V	0.685	1.00
119_H	122_G	0.682	1.00
106_M	111_I	0.680	1.00
100_G	117_T	0.673	1.00
16_G	20_L	0.673	1.00
8_D	57_M	0.668	1.00
36_G	57_M	0.667	1.00
69_I	78_V	0.665	1.00
197_I	202_V	0.664	1.00
77_K	121_G	0.664	1.00
169_L	193_V	0.662	1.00
40_F	43_A	0.662	1.00
70_T	77_K	0.659	1.00
190_K	193_V	0.656	1.00
43_A	51_V	0.653	1.00
44_K	73_L	0.653	1.00
109_D	113_K	0.653	1.00
166_L	169_L	0.653	1.00
94_L	114_A	0.653	1.00
14_R	18_A	0.651	1.00
10_Q	13_V	0.649	1.00
75_S	125_L	0.647	1.00
22_Q	29_V	0.645	1.00
6_I	18_A	0.644	1.00
175_N	186_E	0.644	1.00
69_I	74_P	0.638	1.00
114_A	118_V	0.637	1.00
44_K	68_L	0.636	1.00
93_A	98_A	0.636	1.00
95_E	113_K	0.632	1.00
52_L	79_L	0.626	1.00
180_E	183_Y	0.626	1.00
155_L	211_Y	0.624	1.00
6_I	32_T	0.623	1.00
135_N	139_R	0.621	1.00
79_L	100_G	0.617	1.00
106_M	110_T	0.614	1.00
169_L	172_G	0.610	1.00
10_Q	83_T	0.608	1.00
90_I	107_S	0.607	1.00
54_D	104_K	0.604	1.00
184_I	189_V	0.602	1.00
77_K	119_H	0.601	1.00
171_Y	181_K	0.597	1.00
4_I	50_I	0.593	1.00
82_T	90_I	0.593	1.00
63_V	89_L	0.592	1.00
4_I	21_L	0.592	1.00
21_L	27_L	0.591	1.00
131_A	135_N	0.590	1.00
151_K	201_A	0.589	1.00
66_T	70_T	0.582	1.00
77_K	125_L	0.581	1.00
75_S	124_V	0.580	1.00
87_S	109_D	0.579	1.00
55_I	93_A	0.577	1.00
161_R	192_H	0.574	1.00
166_L	170_G	0.573	1.00
175_N	179_A	0.569	1.00
151_K	154_E	0.565	1.00
151_K	203_R	0.565	1.00
38_E	59_V	0.564	1.00
53_M	69_I	0.563	1.00
113_K	116_M	0.563	1.00
172_G	181_K	0.562	1.00
158_L	162_E	0.560	1.00
114_A	117_T	0.557	1.00
82_T	104_K	0.555	1.00
9_D	82_T	0.553	1.00
88_A	91_A	0.550	1.00
116_M	120_S	0.549	1.00
13_V	16_G	0.546	1.00
162_E	165_V	0.545	1.00
40_F	72_S	0.543	1.00
35_N	57_M	0.541	1.00
185_T	188_T	0.539	1.00
23_L	26_E	0.536	1.00
167_A	170_G	0.533	1.00
69_I	76_V	0.528	1.00
70_T	76_V	0.524	1.00
22_Q	28_D	0.523	1.00
27_L	119_H	0.523	1.00
91_A	94_L	0.523	1.00
159_T	162_E	0.518	1.00
85_K	105_D	0.518	1.00
77_K	118_V	0.509	1.00
82_T	101_Y	0.507	1.00
117_T	121_G	0.505	1.00
165_V	170_G	0.505	1.00
179_A	183_Y	0.504	1.00
16_G	19_S	0.503	1.00
154_E	157_D	0.502	1.00
130_T	133_M	0.500	1.00
47_E	74_P	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
3c3wA	2	0.9591	100	0.2	Contact Map
4gvpA	1	0.9455	100	0.209	Contact Map
4ldzA	2	0.8818	100	0.225	Contact Map
1a04A	1	0.9273	100	0.23	Contact Map
1ys7A	2	0.9773	100	0.231	Contact Map
1yioA	1	0.8955	100	0.239	Contact Map
3r0jA	2	0.95	100	0.24	Contact Map
4b09A	2	0.9	100	0.249	Contact Map
1kgsA	1	0.9682	100	0.249	Contact Map
4kfcA	2	0.9682	100	0.253	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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