YQHL - BACSU - GREMLIN Contacts

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YQHL - Uncharacterized protein YqhL

UniProt:	P54510	Sequences: MSNMIVLIIFAAFIIYMIASYVYQQRIMKTLTEEEFRAGYRKAQLIDVREPNEFEGGHILGARNIPLSQLKQRKNEIRTDKPVYLYCQNSVRSGRAAQTLRKNGCTEIYNLKGGFKKWGGKIKAKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	126 (97)
Sequences:	7877 (5764)
Seq/√Len:	585.2

ECOLI - YIBN GLPE YGAP THTM PSPE YNJE
BACSU - YQHL YRKF YTWF YRKH
HALSA - Q9HME4 Q9HMT6 Q9HMT7 O54647 O54661 Q9HS22
SULSO - Q97VI9 Q7LX53 Q97ZB1 Q97XC6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_P	109_Y	3.015	1.00
51_P	55_E	2.956	1.00
32_T	35_E	2.422	1.00
35_E	39_G	2.366	1.00
31_L	35_E	2.285	1.00
44_Q	81_K	2.260	1.00
54_F	58_H	2.185	1.00
117_K	121_K	2.114	1.00
33_E	121_K	2.012	1.00
51_P	64_N	2.010	1.00
33_E	117_K	1.961	1.00
57_G	119_G	1.947	1.00
85_L	100_L	1.753	1.00
53_E	92_R	1.719	1.00
36_F	84_Y	1.711	1.00
73_R	76_E	1.668	1.00
82_P	107_E	1.600	1.00
39_G	42_K	1.571	1.00
78_R	81_K	1.534	1.00
36_F	111_L	1.522	1.00
113_G	117_K	1.444	1.00
86_Y	115_F	1.423	1.00
36_F	45_L	1.419	1.00
79_T	105_C	1.385	1.00
31_L	36_F	1.311	1.00
33_E	37_R	1.304	1.00
39_G	43_A	1.301	1.00
93_S	110_N	1.297	1.00
97_A	108_I	1.294	1.00
115_F	119_G	1.287	1.00
48_V	96_A	1.282	1.00
71_K	74_K	1.256	1.00
30_T	112_K	1.232	1.00
97_A	110_N	1.220	1.00
45_L	86_Y	1.220	1.00
46_I	77_I	1.218	1.00
39_G	82_P	1.206	1.00
33_E	111_L	1.194	1.00
32_T	112_K	1.151	1.00
59_I	86_Y	1.118	1.00
83_V	100_L	1.075	1.00
30_T	110_N	1.072	1.00
44_Q	63_R	1.071	1.00
87_C	93_S	1.066	1.00
50_E	53_E	1.063	1.00
71_K	99_T	1.055	1.00
31_L	109_Y	1.054	1.00
58_H	86_Y	1.047	1.00
77_I	83_V	1.041	1.00
99_T	103_N	1.034	1.00
43_A	84_Y	1.021	1.00
111_L	117_K	1.015	1.00
89_N	116_K	1.000	1.00
48_V	85_L	0.996	1.00
116_K	119_G	0.985	1.00
37_R	41_R	0.981	1.00
26_R	29_K	0.976	1.00
49_R	88_Q	0.962	1.00
72_Q	76_E	0.951	1.00
39_G	84_Y	0.948	1.00
88_Q	116_K	0.943	1.00
62_A	86_Y	0.926	1.00
101_R	106_T	0.912	1.00
116_K	120_G	0.904	1.00
31_L	84_Y	0.893	1.00
54_F	64_N	0.883	1.00
85_L	108_I	0.878	1.00
53_E	88_Q	0.877	1.00
44_Q	78_R	0.863	1.00
49_R	115_F	0.858	1.00
100_L	108_I	0.849	1.00
36_F	43_A	0.847	1.00
69_Q	73_R	0.846	1.00
70_L	74_K	0.830	1.00
59_I	62_A	0.829	1.00
111_L	118_W	0.828	1.00
111_L	114_G	0.821	1.00
60_L	118_W	0.816	1.00
94_G	110_N	0.810	1.00
34_E	38_A	0.806	1.00
87_C	90_S	0.805	1.00
57_G	115_F	0.803	1.00
101_R	108_I	0.799	1.00
97_A	101_R	0.786	1.00
88_Q	91_V	0.782	1.00
29_K	101_R	0.781	1.00
36_F	39_G	0.775	1.00
43_A	82_P	0.770	1.00
54_F	62_A	0.764	1.00
85_L	97_A	0.764	1.00
45_L	59_I	0.758	1.00
85_L	96_A	0.743	1.00
29_K	109_Y	0.742	1.00
45_L	62_A	0.736	1.00
34_E	121_K	0.735	1.00
35_E	38_A	0.733	1.00
88_Q	92_R	0.729	1.00
72_Q	75_N	0.721	1.00
37_R	40_Y	0.716	1.00
67_L	95_R	0.712	1.00
83_V	105_C	0.703	1.00
46_I	85_L	0.701	1.00
98_Q	102_K	0.699	1.00
119_G	122_I	0.683	1.00
53_E	56_G	0.682	1.00
52_N	56_G	0.682	1.00
52_N	55_E	0.677	1.00
95_R	98_Q	0.676	1.00
59_I	118_W	0.661	1.00
71_K	76_E	0.661	1.00
38_A	42_K	0.655	1.00
67_L	92_R	0.652	1.00
105_C	108_I	0.647	1.00
49_R	64_N	0.643	1.00
58_H	64_N	0.640	1.00
100_L	105_C	0.637	1.00
84_Y	111_L	0.632	1.00
36_F	40_Y	0.628	1.00
46_I	63_R	0.620	1.00
53_E	89_N	0.601	1.00
44_Q	77_I	0.593	1.00
46_I	96_A	0.586	1.00
101_R	107_E	0.560	0.99
94_G	98_Q	0.550	0.99
50_E	92_R	0.549	0.99
70_L	73_R	0.549	0.99
65_I	70_L	0.545	0.99
44_Q	83_V	0.542	0.99
70_L	75_N	0.540	0.99
78_R	82_P	0.536	0.99
49_R	89_N	0.535	0.99
29_K	97_A	0.535	0.99
37_R	121_K	0.530	0.99
104_G	107_E	0.529	0.99
50_E	66_P	0.528	0.99
89_N	92_R	0.527	0.99
50_E	68_S	0.526	0.99
45_L	84_Y	0.526	0.99
68_S	74_K	0.525	0.99
117_K	120_G	0.518	0.99
28_M	97_A	0.512	0.99
85_L	114_G	0.510	0.99
40_Y	43_A	0.504	0.99
84_Y	109_Y	0.503	0.99
33_E	40_Y	0.503	0.99
93_S	114_G	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
3fojA	1	0.7698	99.9	0.315	Contact Map
3ilmA	2	0.7619	99.9	0.317	Contact Map
3gk5A	1	0.7778	99.9	0.319	Contact Map
3d1pA	1	0.8016	99.9	0.324	Contact Map
3tp9A	2	0.9921	99.9	0.324	Contact Map
1urhA	1	0.7937	99.9	0.327	Contact Map
3iwhA	1	0.7778	99.9	0.328	Contact Map
1uarA	1	0.8254	99.9	0.329	Contact Map
1qxnA	2	0.9365	99.9	0.33	Contact Map
1yt8A	1	1	99.9	0.33	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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