YQJY - BACSU - GREMLIN Contacts

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YQJY - Uncharacterized protein YqjY

UniProt:	P54562	Sequences: MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRLFFEHFQDTSFITSEHNSMTGFLIGFQSQSDPETAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQRGCTRVKCVTSPVNKVSIAYHTKLGFDIEKGTKTVNGISVFANYDGPGQDRVLFVKNI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	156 (128)
Sequences:	9064 (7099)
Seq/√Len:	627.5

ECOLI - RIMI YPEA PHNO YJGM MNAT YEDL YJAB YIAC YAFP YHBS
BACSU - YQJY YHFO RIMI PAIA YYAR YTMI YHDJ YWNH YSNE YUAI YESJ YBFA YVBK YYCN YDGE SPSD YBBJ BLTD YOBR
HALSA - Q9HMF0 Q9HQD2 Q9HSL3 Q9HMI8 Q9HRK6
SULSO - Y209 Q7LXZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_R	47_S	3.514	1.00
20_E	76_H	3.288	1.00
93_I	124_F	2.894	1.00
86_K	121_K	2.699	1.00
53_T	79_F	2.331	1.00
56_L	92_F	2.305	1.00
46_T	84_I	2.266	1.00
86_K	122_L	2.217	1.00
90_D	122_L	2.081	1.00
45_I	52_M	2.013	1.00
48_E	79_F	1.989	1.00
44_F	91_V	1.977	1.00
91_V	94_E	1.877	1.00
113_K	117_A	1.871	1.00
6_I	14_V	1.829	1.00
58_G	92_F	1.819	1.00
79_F	82_M	1.803	1.00
4_R	10_D	1.795	1.00
13_M	16_S	1.710	1.00
20_E	77_P	1.707	1.00
48_E	53_T	1.669	1.00
48_E	82_M	1.631	1.00
89_Y	122_L	1.630	1.00
21_W	74_G	1.593	1.00
117_A	120_T	1.574	1.00
93_I	104_V	1.549	1.00
126_I	129_G	1.543	1.00
15_T	19_N	1.542	1.00
95_T	98_Q	1.538	1.00
95_T	99_R	1.512	1.00
116_I	120_T	1.511	1.00
120_T	126_I	1.497	1.00
80_R	114_V	1.466	1.00
68_A	96_V	1.460	1.00
54_G	75_V	1.383	1.00
12_E	29_E	1.308	1.00
60_Q	101_C	1.303	1.00
106_C	119_H	1.302	1.00
44_F	95_T	1.296	1.00
43_S	57_I	1.289	1.00
16_S	20_E	1.287	1.00
86_K	90_D	1.285	1.00
51_S	78_D	1.270	1.00
6_I	45_I	1.254	1.00
47_S	50_N	1.250	1.00
91_V	95_T	1.236	1.00
51_S	76_H	1.232	1.00
115_S	119_H	1.197	1.00
96_V	104_V	1.158	1.00
17_V	21_W	1.158	1.00
47_S	52_M	1.151	1.00
13_M	52_M	1.150	1.00
20_E	78_D	1.141	1.00
27_L	31_L	1.131	1.00
10_D	47_S	1.115	1.00
42_T	99_R	1.111	1.00
42_T	95_T	1.109	1.00
76_H	79_F	1.097	1.00
6_I	43_S	1.081	1.00
110_P	129_G	1.073	1.00
108_T	115_S	1.068	1.00
30_K	34_L	1.053	1.00
116_I	126_I	1.045	1.00
3_I	44_F	1.045	1.00
21_W	80_R	1.041	1.00
48_E	51_S	1.041	1.00
56_L	70_I	1.032	1.00
56_L	88_L	1.027	1.00
16_S	76_H	1.010	1.00
17_V	52_M	0.995	1.00
75_V	84_I	0.974	1.00
83_Q	86_K	0.968	1.00
17_V	76_H	0.966	1.00
106_C	115_S	0.942	1.00
58_G	96_V	0.935	1.00
113_K	116_I	0.931	1.00
28_K	31_L	0.931	1.00
53_T	84_I	0.931	1.00
93_I	122_L	0.928	1.00
29_E	33_R	0.925	1.00
42_T	58_G	0.924	1.00
33_R	37_E	0.922	1.00
70_I	89_Y	0.922	1.00
18_L	55_F	0.911	1.00
112_N	115_S	0.906	1.00
13_M	17_V	0.902	1.00
46_T	54_G	0.901	1.00
3_I	87_Q	0.892	1.00
22_W	74_G	0.884	1.00
94_E	98_Q	0.881	1.00
13_M	51_S	0.858	1.00
26_Q	32_P	0.825	1.00
96_V	101_C	0.817	1.00
108_T	112_N	0.816	1.00
12_E	16_S	0.815	1.00
89_Y	118_Y	0.814	1.00
68_A	101_C	0.809	1.00
17_V	74_G	0.808	1.00
28_K	32_P	0.807	1.00
25_R	30_K	0.806	1.00
27_L	32_P	0.802	1.00
89_Y	119_H	0.800	1.00
13_M	76_H	0.795	1.00
87_Q	90_D	0.790	1.00
51_S	79_F	0.784	1.00
14_V	55_F	0.781	1.00
31_L	35_F	0.772	1.00
118_Y	122_L	0.771	1.00
30_K	36_F	0.761	1.00
5_T	95_T	0.758	1.00
73_S	119_H	0.756	1.00
3_I	91_V	0.755	1.00
11_Y	15_T	0.755	1.00
38_H	41_D	0.751	1.00
8_S	37_E	0.750	1.00
90_D	94_E	0.743	1.00
55_F	74_G	0.738	1.00
105_K	127_E	0.737	1.00
81_K	114_V	0.730	1.00
5_T	44_F	0.730	1.00
57_I	71_H	0.728	1.00
18_L	22_W	0.728	1.00
21_W	77_P	0.717	1.00
75_V	85_G	0.714	1.00
67_T	105_K	0.710	1.00
27_L	35_F	0.705	1.00
69_Y	105_K	0.688	1.00
32_P	35_F	0.687	1.00
69_Y	107_V	0.672	1.00
46_T	53_T	0.670	1.00
27_L	34_L	0.664	1.00
84_I	87_Q	0.659	1.00
93_I	97_K	0.658	1.00
27_L	30_K	0.652	1.00
4_R	7_T	0.650	1.00
35_F	57_I	0.648	1.00
34_L	39_F	0.645	1.00
104_V	124_F	0.640	1.00
128_K	131_K	0.629	1.00
33_R	36_F	0.626	1.00
42_T	60_Q	0.626	1.00
77_P	80_R	0.625	1.00
26_Q	34_L	0.624	1.00
18_L	72_F	0.621	1.00
67_T	103_R	0.615	1.00
29_E	32_P	0.613	1.00
106_C	124_F	0.612	1.00
61_S	64_D	0.611	1.00
59_F	71_H	0.610	1.00
81_K	117_A	0.609	1.00
13_M	45_I	0.609	1.00
64_D	67_T	0.605	1.00
16_S	51_S	0.605	1.00
111_V	116_I	0.604	1.00
54_G	88_L	0.601	1.00
26_Q	29_E	0.589	1.00
32_P	36_F	0.589	1.00
60_Q	99_R	0.584	1.00
85_G	118_Y	0.582	1.00
35_F	38_H	0.582	1.00
30_K	33_R	0.580	1.00
5_T	42_T	0.580	1.00
26_Q	30_K	0.578	1.00
31_L	34_L	0.575	1.00
25_R	35_F	0.571	1.00
16_S	19_N	0.560	1.00
108_T	116_I	0.554	1.00
73_S	89_Y	0.552	1.00
34_L	38_H	0.548	1.00
58_G	95_T	0.542	0.99
56_L	73_S	0.539	0.99
46_T	88_L	0.538	0.99
59_F	62_Q	0.537	0.99
26_Q	36_F	0.533	0.99
35_F	41_D	0.531	0.99
25_R	31_L	0.526	0.99
43_S	47_S	0.524	0.99
3_I	88_L	0.524	0.99
25_R	28_K	0.524	0.99
73_S	115_S	0.522	0.99
12_E	15_T	0.518	0.99
94_E	97_K	0.518	0.99
108_T	119_H	0.516	0.99
79_F	84_I	0.516	0.99
120_T	125_D	0.515	0.99
25_R	29_E	0.512	0.99
69_Y	72_F	0.511	0.99
114_V	117_A	0.508	0.99
64_D	105_K	0.507	0.99
22_W	72_F	0.504	0.99
54_G	84_I	0.503	0.99
112_N	119_H	0.500	0.99

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
1mk4A	2	1	99.9	0.308	Contact Map
3d3sA	2	0.9936	99.9	0.341	Contact Map
4kvxA	1	0.9295	99.9	0.347	Contact Map
3dr6A	2	0.9615	99.9	0.358	Contact Map
2reeA	1	0.9679	99.9	0.358	Contact Map
1s3zA	2	0.8782	99.9	0.364	Contact Map
2r7hA	2	0.9423	99.9	0.364	Contact Map
2j8mA	2	0.9615	99.9	0.367	Contact Map
4pv6C	3	0.9231	99.9	0.371	Contact Map
2ob0A	1	0.9423	99.9	0.377	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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