GREMLIN Database
Phage_pRha - Phage regulatory protein Rha (Phage_pRha)
PFAM: PF09669 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 88 (87)
Sequences: 8422 (6654)
Seq/√Len: 713.4
META: 0.765

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
58_D84_N2.8261.00
82_A85_E2.6341.00
35_L38_E2.6221.00
46_Q50_Y2.5471.00
57_K87_E2.3001.00
22_R51_P2.2591.00
44_D50_Y2.2451.00
16_N19_R2.1621.00
62_L73_A2.1061.00
58_D81_D1.9671.00
2_T52_C1.8601.00
13_R16_N1.7711.00
62_L77_A1.6831.00
16_N38_E1.6541.00
4_R52_C1.6531.00
5_E9_L1.6131.00
56_T59_G1.5381.00
41_T49_K1.5221.00
16_N35_L1.4621.00
74_E78_A1.3871.00
43_K49_K1.3841.00
14_H18_L1.3831.00
15_K19_R1.3061.00
61_T75_F1.2761.00
20_D67_F1.2521.00
19_R38_E1.2221.00
15_K39_E1.2041.00
3_S21_I1.2021.00
45_S50_Y1.1711.00
27_D73_A1.1471.00
66_G76_K1.1471.00
61_T84_N1.1401.00
28_L31_F1.1361.00
44_D48_R1.1361.00
5_E8_E1.1281.00
18_L22_R1.1111.00
57_K84_N1.1011.00
2_T5_E1.0941.00
3_S14_H1.0731.00
11_G71_K1.0721.00
1_T5_E1.0561.00
39_E42_Y1.0451.00
57_K61_T1.0401.00
2_T54_L1.0331.00
18_L51_P1.0241.00
31_F34_L1.0191.00
12_K20_D1.0001.00
29_E32_G0.9911.00
43_K46_Q0.9781.00
40_S46_Q0.9721.00
40_S44_D0.9241.00
43_K47_G0.9171.00
27_D70_K0.9121.00
44_D47_G0.9051.00
82_A87_E0.8941.00
24_L63_L0.8931.00
16_N20_D0.8931.00
62_L65_M0.8891.00
60_F64_A0.8781.00
61_T79_Y0.8721.00
40_S52_C0.8721.00
77_A81_D0.8571.00
42_Y52_C0.8551.00
81_D85_E0.8551.00
45_S48_R0.8541.00
9_L75_F0.8541.00
42_Y50_Y0.8531.00
24_L73_A0.8381.00
25_I29_E0.8341.00
6_I55_L0.8301.00
65_M79_Y0.8281.00
20_D23_N0.8201.00
78_A82_A0.7791.00
23_N27_D0.7791.00
65_M76_K0.7731.00
41_T46_Q0.7711.00
13_R19_R0.7671.00
4_R8_E0.7671.00
28_L32_G0.7571.00
46_Q49_K0.7511.00
40_S48_R0.7491.00
71_K74_E0.7431.00
22_R25_I0.7411.00
65_M73_A0.7391.00
9_L78_A0.7301.00
59_G62_L0.7281.00
42_Y45_S0.7221.00
82_A86_M0.7131.00
78_A81_D0.7061.00
80_I84_N0.7041.00
40_S50_Y0.7021.00
55_L59_G0.6971.00
42_Y46_Q0.6871.00
60_F83_F0.6851.00
39_E44_D0.6831.00
21_I53_Y0.6701.00
64_A75_F0.6651.00
1_T9_L0.6601.00
40_S54_L0.6581.00
42_Y47_G0.6531.00
15_K18_L0.6491.00
61_T80_I0.6401.00
58_D61_T0.6391.00
39_E51_P0.6381.00
30_E77_A0.6361.00
41_T48_R0.6241.00
18_L53_Y0.6101.00
55_L63_L0.6031.00
68_T74_E0.5951.00
58_D62_L0.5941.00
41_T44_D0.5821.00
59_G77_A0.5811.00
65_M75_F0.5801.00
47_G50_Y0.5801.00
19_R23_N0.5741.00
25_I28_L0.5661.00
27_D74_E0.5571.00
15_K35_L0.5551.00
68_T75_F0.5551.00
17_V67_F0.5511.00
27_D77_A0.5311.00
58_D77_A0.5301.00
70_K74_E0.5241.00
58_D80_I0.5161.00
75_F82_A0.5080.99
36_N39_E0.5060.99
12_K16_N0.5060.99
73_A77_A0.5040.99
43_K48_R0.5030.99
40_S49_K0.5000.99
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

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  
1xmkA 1 0.6023 55.2 0.814 Contact Map
2p4wA 2 0.9205 50.4 0.819 Contact Map
1l8qA 1 0.5455 49.8 0.82 Contact Map
1hsjA 2 0.75 49.1 0.821 Contact Map
2qwwA 2 0.9091 48.6 0.821 Contact Map
3l4gA 2 0.8636 47.9 0.822 Contact Map
2z4sA 1 0 47.2 0.823 Contact Map
2frhA 2 0.8295 47 0.823 Contact Map
3pvvA 1 0.5455 44.7 0.825 Contact Map
2fxaA 4 0.875 43.9 0.826 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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