Q9HS34 - HALSA - GREMLIN Contacts

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Q9HS34 - DNA-directed RNA polymerase subunit

UniProt:	Q9HS34	Sequences: MEFCDDCGSMMKADDELWVCSSCGHKQPKDPSASFVVTEGQEETEVVDVSDAQDRGLPTTSVVCPDCDNDEAHWYMQQIRSADESETRFFICTECEHRWREDDN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	104 (100)
Sequences:	518 (384)
Seq/√Len:	38.4

HALSA - Q9HS34 Q9HP96
SULSO - Q980K2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_N	93_T	5.534	1.00
59_T	71_E	3.759	1.00
91_I	98_R	3.297	1.00
76_M	88_R	3.142	1.00
17_L	26_K	2.897	1.00
2_E	27_Q	2.787	1.00
52_A	55_R	2.432	1.00
76_M	86_E	2.366	1.00
66_D	97_H	2.227	0.99
91_I	96_E	2.132	0.99
63_V	70_D	1.857	0.98
75_Y	98_R	1.800	0.97
95_C	99_W	1.664	0.96
57_L	91_I	1.653	0.96
92_C	95_C	1.646	0.96
14_D	17_L	1.624	0.95
80_R	83_D	1.623	0.95
73_H	93_T	1.621	0.95
50_S	53_Q	1.590	0.95
61_S	71_E	1.587	0.95
85_S	90_F	1.587	0.95
4_C	7_C	1.579	0.94
5_D	25_H	1.487	0.92
75_Y	91_I	1.468	0.92
12_K	21_S	1.460	0.92
39_E	42_E	1.448	0.91
54_D	57_L	1.436	0.91
79_I	85_S	1.416	0.90
40_G	43_E	1.405	0.90
92_C	99_W	1.404	0.90
9_S	22_S	1.307	0.87
43_E	47_V	1.296	0.86
61_S	70_D	1.290	0.86
60_T	74_W	1.276	0.85
69_N	72_A	1.231	0.83
3_F	7_C	1.229	0.83
88_R	101_E	1.162	0.79
79_I	87_T	1.098	0.75
9_S	24_G	1.096	0.75
32_S	36_V	1.078	0.74
65_P	80_R	1.077	0.74
46_V	49_V	1.067	0.73
70_D	94_E	1.038	0.71
9_S	12_K	1.025	0.70
6_D	94_E	1.023	0.70
46_V	50_S	0.966	0.65
81_S	86_E	0.964	0.65
61_S	68_D	0.958	0.65
62_V	65_P	0.953	0.64
54_D	58_P	0.949	0.64
57_L	74_W	0.921	0.62
68_D	94_E	0.911	0.61
43_E	51_D	0.909	0.61
41_Q	49_V	0.883	0.58
39_E	45_E	0.882	0.58
39_E	46_V	0.867	0.57
50_S	54_D	0.850	0.55
34_S	37_V	0.843	0.55
20_C	23_C	0.830	0.54
77_Q	87_T	0.820	0.53
13_A	16_E	0.816	0.52
72_A	90_F	0.808	0.52
56_G	91_I	0.807	0.52
45_E	49_V	0.802	0.51
69_N	94_E	0.798	0.51
13_A	27_Q	0.797	0.51
49_V	54_D	0.796	0.51
6_D	68_D	0.788	0.50
41_Q	48_D	0.774	0.49
94_E	98_R	0.774	0.49
34_S	55_R	0.771	0.48
34_S	38_T	0.759	0.47
79_I	100_R	0.757	0.47
87_T	98_R	0.753	0.47
80_R	101_E	0.753	0.47
86_E	101_E	0.744	0.46
16_E	33_A	0.741	0.46
77_Q	86_E	0.739	0.45
6_D	11_M	0.733	0.45
26_K	68_D	0.728	0.44
49_V	56_G	0.728	0.44
43_E	46_V	0.722	0.44
26_K	33_A	0.718	0.44
74_W	86_E	0.714	0.43
47_V	54_D	0.711	0.43
41_Q	46_V	0.711	0.43
38_T	41_Q	0.708	0.43
40_G	46_V	0.698	0.42
32_S	38_T	0.698	0.42
63_V	68_D	0.697	0.42
22_S	75_Y	0.691	0.41
71_E	98_R	0.683	0.41
76_M	80_R	0.681	0.40
96_E	100_R	0.681	0.40
25_H	28_P	0.678	0.40
57_L	73_H	0.677	0.40
24_G	27_Q	0.671	0.39
51_D	55_R	0.660	0.39
92_C	100_R	0.649	0.38
6_D	10_M	0.641	0.37
49_V	55_R	0.639	0.37
62_V	101_E	0.638	0.37
73_H	80_R	0.633	0.36
24_G	86_E	0.633	0.36
11_M	88_R	0.625	0.36
18_W	32_S	0.622	0.35
61_S	79_I	0.621	0.35
21_S	97_H	0.619	0.35
75_Y	79_I	0.613	0.35
47_V	50_S	0.610	0.34
38_T	94_E	0.608	0.34
6_D	15_D	0.601	0.34
45_E	51_D	0.600	0.34
62_V	79_I	0.593	0.33
36_V	70_D	0.591	0.33
35_F	52_A	0.586	0.32
21_S	29_K	0.584	0.32
57_L	60_T	0.582	0.32
4_C	67_C	0.572	0.31
57_L	77_Q	0.565	0.31
60_T	73_H	0.564	0.31
3_F	23_C	0.563	0.31
14_D	19_V	0.559	0.30
68_D	98_R	0.555	0.30
45_E	71_E	0.553	0.30
7_C	11_M	0.551	0.30
39_E	79_I	0.551	0.30
22_S	98_R	0.549	0.30
38_T	61_S	0.548	0.30
58_P	77_Q	0.546	0.29
53_Q	73_H	0.546	0.29
23_C	28_P	0.537	0.29
48_D	53_Q	0.536	0.29
72_A	76_M	0.530	0.28
37_V	40_G	0.527	0.28
60_T	93_T	0.525	0.28
82_A	101_E	0.523	0.28
19_V	35_F	0.520	0.27
12_K	62_V	0.516	0.27
36_V	90_F	0.516	0.27
23_C	84_E	0.514	0.27
52_A	61_S	0.512	0.27
37_V	44_T	0.508	0.27
79_I	86_E	0.507	0.27
85_S	101_E	0.506	0.26
36_V	42_E	0.506	0.26
59_T	74_W	0.506	0.26
14_D	94_E	0.502	0.26
3_F	69_N	0.501	0.26
48_D	68_D	0.500	0.26

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
4c2mI	1	0.9808	100	0.279	Contact Map
3h0gI	1	0.9808	100	0.282	Contact Map
1twfI	1	1	100	0.289	Contact Map
3qt1I	1	0.375	100	0.294	Contact Map
1qypA	1	0.5481	99.8	0.562	Contact Map
4cgyA	1	0	99.8	0.563	Contact Map
1tfiA	1	0.4808	99.7	0.588	Contact Map
1pqvS	1	0.9615	99.7	0.594	Contact Map
3po3S	1	0.9712	99.7	0.613	Contact Map
2k4xA	1	0.3462	97.4	0.827	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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