GREMLIN Database
Q9HI14 - Transcription initiation factor IID
UniProt: Q9HI14 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 71 (59)
Sequences: 842 (493)
Seq/√Len: 64.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
13_F30_F3.1021.00
25_V40_G2.9541.00
20_L23_P2.6481.00
30_F38_T2.3941.00
25_V49_A2.3121.00
37_I46_A2.1221.00
13_F28_L2.0811.00
6_A16_L1.8801.00
28_L36_V1.7701.00
25_V53_I1.7090.99
20_L53_I1.6390.99
51_D55_S1.5420.99
17_V28_L1.4760.98
37_I50_V1.4240.98
27_A53_I1.4040.98
7_D20_L1.4020.98
30_F36_V1.3140.96
51_D59_D1.2670.96
13_F36_V1.1750.94
15_G30_F1.1050.91
20_L25_V1.1030.91
45_D48_H1.0970.91
7_D19_R1.0850.90
15_G28_L1.0510.89
9_D12_Q1.0210.88
35_L55_S1.0070.87
6_A18_Y1.0030.87
37_I40_G1.0020.87
12_Q16_L0.9950.86
7_D32_S0.9940.86
16_L38_T0.9690.85
41_K45_D0.9680.85
22_E48_H0.9330.82
21_D48_H0.9270.82
7_D46_A0.9260.82
44_V47_E0.9150.81
4_E11_E0.9040.80
56_R59_D0.9030.80
14_P36_V0.8980.80
42_H47_E0.8920.79
11_E15_G0.8870.79
48_H51_D0.8730.78
44_V48_H0.8640.77
42_H48_H0.8440.76
14_P18_Y0.8320.75
11_E31_G0.8120.73
18_Y56_R0.7920.71
33_G39_G0.7830.70
13_F32_S0.7760.69
43_P47_E0.7710.69
9_D18_Y0.7660.68
47_E59_D0.7640.68
26_V32_S0.7540.67
27_A35_L0.7350.65
27_A55_S0.7200.63
21_D46_A0.7150.63
46_A54_D0.7130.63
11_E24_S0.6760.59
14_P30_F0.6730.58
55_S58_E0.6640.57
7_D17_V0.6640.57
43_P46_A0.6510.56
10_P19_R0.6420.55
48_H59_D0.6360.54
22_E55_S0.6300.53
23_P45_D0.6250.53
47_E51_D0.6230.53
5_G35_L0.6210.52
36_V49_A0.6170.52
53_I60_L0.6130.51
25_V41_K0.6120.51
40_G49_A0.6020.50
48_H56_R0.6000.50
9_D27_A0.5900.49
13_F34_K0.5840.48
51_D62_L0.5720.47
13_F41_K0.5670.46
14_P28_L0.5610.45
5_G32_S0.5550.45
31_G62_L0.5510.44
15_G19_R0.5390.43
6_A12_Q0.5330.42
48_H52_T0.5290.42
30_F34_K0.5270.41
55_S60_L0.5230.41
19_R28_L0.5050.39
17_V34_K0.5010.39
10_P31_G0.5000.38
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

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  
1rm1A 1 1 99.9 0.167 Contact Map
3eikA 2 0.9859 99.9 0.168 Contact Map
4b0aA 1 0.9859 99.9 0.17 Contact Map
1ytbA 1 1 99.9 0.172 Contact Map
2z8uA 2 0.8592 99.9 0.173 Contact Map
1mp9A 2 1 99.9 0.175 Contact Map
1aisA 1 1 99.8 0.195 Contact Map
2d0bA 1 1 89.8 0.802 Contact Map
3vn5A 1 0.9155 88.3 0.808 Contact Map
4py5A 1 0.9577 83.7 0.82 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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