YJCA - BACSU - GREMLIN Contacts

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YJCA - Sporulation protein YjcA

UniProt:	O31623	Sequences: MVINGLTIVLLSLAVFRLARLLVFDTIMAPLRSLFHEEKEEKDADGNIETYIVIKGTGVRAFIGELLSCYWCTGVWCAGFLILCQAVIPQAAQWLILLLAIAGLAGIIETLVSKWLQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	118 (110)
Sequences:	136 (114)
Seq/√Len:	10.8

BACSU - YJCA YNGL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_F	70_Y	4.522	1.00
18_L	99_L	4.457	1.00
84_C	92_A	3.786	0.99
34_L	67_L	3.363	0.97
63_I	103_G	2.615	0.89
43_D	47_N	2.338	0.82
21_L	27_I	1.991	0.70
33_S	95_L	1.970	0.69
29_A	44_A	1.817	0.63
34_L	94_W	1.807	0.62
10_L	96_I	1.783	0.61
87_V	112_V	1.696	0.57
20_R	38_E	1.695	0.57
59_V	63_I	1.691	0.57
20_R	65_E	1.679	0.56
30_P	34_L	1.625	0.54
38_E	51_Y	1.548	0.50
8_I	100_A	1.495	0.48
26_T	107_I	1.443	0.45
51_Y	73_T	1.436	0.45
78_A	112_V	1.415	0.44
97_L	101_I	1.414	0.44
40_E	48_I	1.383	0.42
75_V	91_A	1.369	0.42
60_R	68_S	1.343	0.41
57_T	77_C	1.339	0.40
38_E	98_L	1.333	0.40
75_V	80_F	1.324	0.40
8_I	104_L	1.282	0.38
4_N	99_L	1.279	0.38
24_F	106_G	1.272	0.37
29_A	54_I	1.270	0.37
30_P	98_L	1.261	0.37
70_Y	87_V	1.251	0.36
4_N	110_T	1.245	0.36
37_E	83_L	1.213	0.35
11_L	92_A	1.209	0.35
15_V	78_A	1.194	0.34
8_I	44_A	1.183	0.33
54_I	95_L	1.183	0.33
78_A	101_I	1.173	0.33
82_I	94_W	1.172	0.33
80_F	112_V	1.159	0.32
20_R	43_D	1.151	0.32
53_V	56_G	1.140	0.32
22_L	62_F	1.126	0.31
16_F	65_E	1.110	0.30
21_L	28_M	1.097	0.30
12_S	93_Q	1.039	0.28
38_E	50_T	1.028	0.27
26_T	30_P	1.004	0.26
36_H	82_I	0.996	0.26
12_S	105_A	0.985	0.26
99_L	102_A	0.981	0.25
36_H	68_S	0.981	0.25
28_M	67_L	0.965	0.25
55_K	70_Y	0.964	0.25
7_T	29_A	0.960	0.25
62_F	108_I	0.956	0.25
37_E	98_L	0.956	0.25
43_D	49_E	0.951	0.24
4_N	95_L	0.947	0.24
13_L	44_A	0.941	0.24
36_H	52_I	0.941	0.24
31_L	110_T	0.938	0.24
42_K	81_L	0.910	0.23
28_M	31_L	0.907	0.23
20_R	51_Y	0.902	0.23
11_L	83_L	0.896	0.23
22_L	85_Q	0.894	0.22
26_T	65_E	0.890	0.22
80_F	96_I	0.888	0.22
6_L	62_F	0.881	0.22
37_E	54_I	0.876	0.22
66_L	94_W	0.875	0.22
18_L	91_A	0.871	0.22
52_I	82_I	0.869	0.22
60_R	64_G	0.864	0.21
7_T	107_I	0.863	0.21
44_A	80_F	0.857	0.21
49_E	53_V	0.834	0.21
61_A	88_I	0.834	0.21
26_T	51_Y	0.824	0.20
20_R	40_E	0.817	0.20
16_F	64_G	0.811	0.20
75_V	99_L	0.810	0.20
62_F	110_T	0.804	0.20
16_F	68_S	0.804	0.20
5_G	103_G	0.802	0.20
96_I	99_L	0.793	0.19
23_V	46_G	0.793	0.19
24_F	109_E	0.790	0.19
79_G	98_L	0.777	0.19
12_S	84_C	0.756	0.18
79_G	99_L	0.756	0.18
42_K	70_Y	0.755	0.18
33_S	70_Y	0.750	0.18
13_L	109_E	0.748	0.18
37_E	53_V	0.748	0.18
50_T	65_E	0.736	0.18
6_L	78_A	0.736	0.18
58_G	61_A	0.729	0.17
80_F	87_V	0.728	0.17
42_K	83_L	0.726	0.17
20_R	50_T	0.723	0.17
40_E	81_L	0.722	0.17
62_F	86_A	0.721	0.17
79_G	101_I	0.718	0.17
45_D	73_T	0.702	0.17
5_G	60_R	0.702	0.17
80_F	108_I	0.702	0.17
61_A	86_A	0.695	0.17
30_P	94_W	0.686	0.16
31_L	80_F	0.682	0.16
5_G	56_G	0.680	0.16
13_L	86_A	0.676	0.16
31_L	86_A	0.676	0.16
41_E	52_I	0.675	0.16
10_L	60_R	0.667	0.16
7_T	44_A	0.652	0.15
42_K	47_N	0.651	0.15
44_A	79_G	0.643	0.15
36_H	65_E	0.641	0.15
12_S	103_G	0.641	0.15
22_L	108_I	0.640	0.15
36_H	54_I	0.632	0.15
8_I	50_T	0.627	0.15
19_A	35_F	0.626	0.15
107_I	112_V	0.620	0.15
20_R	37_E	0.618	0.15
47_N	60_R	0.616	0.15
5_G	88_I	0.615	0.15
70_Y	109_E	0.610	0.14
63_I	100_A	0.608	0.14
40_E	90_Q	0.606	0.14
84_C	93_Q	0.603	0.14
28_M	94_W	0.598	0.14
9_V	110_T	0.594	0.14
10_L	82_I	0.593	0.14
10_L	50_T	0.592	0.14
80_F	100_A	0.580	0.14
67_L	74_G	0.576	0.14
75_V	101_I	0.566	0.13
81_L	96_I	0.566	0.13
16_F	60_R	0.565	0.13
34_L	74_G	0.561	0.13
83_L	95_L	0.560	0.13
59_V	77_C	0.558	0.13
13_L	104_L	0.556	0.13
41_E	68_S	0.549	0.13
9_V	37_E	0.549	0.13
47_N	106_G	0.540	0.13
16_F	100_A	0.539	0.13
15_V	104_L	0.538	0.13
47_N	107_I	0.536	0.13
40_E	47_N	0.528	0.13
90_Q	106_G	0.525	0.13
19_A	34_L	0.524	0.12
26_T	34_L	0.516	0.12
57_T	96_I	0.511	0.12
9_V	13_L	0.506	0.12
9_V	33_S	0.506	0.12
39_K	51_Y	0.504	0.12
42_K	50_T	0.502	0.12
51_Y	62_F	0.500	0.12

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
4q9hA	1	1	10.1	0.953	Contact Map
4q4hB	1	0.9322	10	0.953	Contact Map
4hw9A	3	0.7458	7.7	0.955	Contact Map
3zdqA	2	0.9576	7.1	0.956	Contact Map
4a82A	2	0.9746	6.7	0.956	Contact Map
2mfrA	1	0.3051	5.9	0.958	Contact Map
4f4cA	1	0.9746	5.8	0.958	Contact Map
4ry2A	2	0.9661	5.7	0.958	Contact Map
4hl7A	4	0.8898	5.1	0.959	Contact Map
3wmgA	1	0.9576	5.1	0.959	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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