GREMLIN Database
PHINT_rpt - Phage-integrase repeat unit
PFAM: PF14882 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 52 (50)
Sequences: 2658 (2411)
Seq/√Len: 340.9
META: 0.882

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
5_R8_K4.3241.00
42_F46_R2.8151.00
25_K29_D2.7941.00
28_G33_T2.4041.00
46_R50_Q2.1131.00
41_T44_E2.0671.00
46_R49_A1.7041.00
15_N18_R1.6871.00
26_G29_D1.6521.00
17_D27_W1.5731.00
6_Y9_D1.5481.00
27_W31_L1.5021.00
21_K24_W1.3921.00
13_P19_V1.3511.00
28_G34_G1.3421.00
28_G36_P1.3391.00
12_L30_F1.2781.00
9_D12_L1.2521.00
40_R48_A1.2491.00
24_W27_W1.2401.00
12_L48_A1.1931.00
6_Y14_S1.1751.00
15_N19_V1.1361.00
29_D42_F1.0711.00
36_P39_Y1.0691.00
47_K51_K0.9711.00
2_Y12_L0.9381.00
39_Y48_A0.9121.00
4_K47_K0.8561.00
3_K15_N0.8391.00
22_D25_K0.8091.00
27_W30_F0.8051.00
47_K50_Q0.7961.00
42_F45_A0.7961.00
6_Y12_L0.7771.00
48_A51_K0.7671.00
37_R40_R0.7611.00
12_L39_Y0.7541.00
17_D21_K0.7210.99
2_Y5_R0.7200.99
25_K42_F0.7130.99
26_G35_R0.6930.99
8_K11_R0.6930.99
34_G47_K0.6810.99
6_Y10_P0.6710.99
15_N32_G0.6670.99
25_K28_G0.6550.99
34_G37_R0.6470.99
3_K14_S0.6430.99
21_K36_P0.6230.98
42_F48_A0.6200.98
38_K41_T0.6170.98
21_K38_K0.6050.98
14_S22_D0.6020.98
4_K36_P0.6020.98
3_K8_K0.5990.98
23_E43_E0.5930.98
12_L45_A0.5880.97
23_E42_F0.5840.97
41_T45_A0.5640.97
7_K32_G0.5560.96
33_T39_Y0.5550.96
4_K43_E0.5520.96
20_Y43_E0.5390.96
14_S34_G0.5340.96
29_D46_R0.5310.95
19_V27_W0.5210.95
7_K27_W0.5150.95
40_R43_E0.5140.95
13_P20_Y0.5120.94
42_F49_A0.5070.94
3_K17_D0.5040.94
23_E27_W0.5030.94
37_R43_E0.5030.94
24_W31_L0.5000.94
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  
1uw4B 1 0.9038 6.9 0.85 Contact Map
1yu0A 3 0.7885 5.3 0.858 Contact Map
2bpdA 2 0.6731 4.7 0.861 Contact Map
4do4A 2 0.7885 4.6 0.862 Contact Map
3wbzA 5 1 4.3 0.863 Contact Map
1gwmA 1 0.8846 4.2 0.864 Contact Map
3js8A 1 0.8269 4.2 0.864 Contact Map
1vquA 2 0.5385 4.1 0.865 Contact Map
1wcuA 1 0.8846 4 0.866 Contact Map
1dkiA 1 0.2885 3.7 0.867 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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