GREMLIN Database
ALPA - Prophage CP4-57 regulatory protein AlpA
UniProt: P33997 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12112
Length: 70 (62)
Sequences: 135 (90)
Seq/√Len: 11.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
9_I53_G3.8250.99
15_V19_T3.1080.96
28_D36_R2.8940.94
12_L19_T2.3170.83
11_R20_G1.9890.72
48_G66_R1.9810.72
18_K60_D1.8540.67
15_V59_I1.7360.61
29_W51_S1.5990.55
11_R48_G1.5740.54
47_L52_V1.5470.52
14_A17_Q1.5190.51
11_R53_G1.5110.51
11_R51_S1.4970.50
10_L55_I1.4850.49
10_L52_V1.4410.47
51_S66_R1.4370.47
55_I67_C1.4040.45
18_K56_E1.3360.42
55_I63_L1.2880.40
32_P53_G1.2580.38
30_L44_K1.2510.38
12_L16_I1.2320.37
18_K51_S1.1530.34
16_I21_M1.1220.32
33_K36_R1.1020.31
18_K48_G1.0460.29
20_G52_V1.0440.29
23_R40_T1.0350.29
34_S46_M1.0250.28
31_N45_R1.0200.28
7_V57_A1.0160.28
17_Q24_A0.9890.27
25_T35_P0.9680.26
24_A28_D0.9670.26
9_I47_L0.9390.25
50_K64_S0.9160.24
10_L14_A0.9150.24
28_D48_G0.9060.24
48_G51_S0.9030.24
17_Q37_Y0.9020.24
37_Y49_V0.8960.23
47_L66_R0.8790.23
21_M59_I0.8540.22
31_N37_Y0.8510.22
29_W48_G0.8270.21
25_T28_D0.7840.20
9_I24_A0.7550.19
28_D34_S0.7520.19
8_R56_E0.7480.19
15_V46_M0.7440.18
8_R29_W0.7380.18
10_L23_R0.7370.18
40_T43_K0.7310.18
10_L20_G0.7260.18
39_A46_M0.7240.18
44_K50_K0.7000.17
11_R66_R0.6840.17
17_Q44_K0.6800.17
40_T61_E0.6750.17
29_W36_R0.6740.17
33_K47_L0.6660.16
28_D32_P0.6590.16
7_V13_P0.6540.16
6_A13_P0.6520.16
31_N58_E0.6440.16
15_V58_E0.6350.15
50_K59_I0.6270.15
8_R63_L0.6260.15
45_R58_E0.6210.15
48_G56_E0.6190.15
39_A58_E0.6110.15
10_L60_D0.6060.15
31_N61_E0.6000.15
6_A36_R0.5960.15
58_E64_S0.5940.14
26_I30_L0.5930.14
24_A44_K0.5820.14
24_A39_A0.5800.14
9_I32_P0.5760.14
37_Y63_L0.5730.14
6_A56_E0.5730.14
22_A26_I0.5720.14
45_R50_K0.5610.14
12_L50_K0.5510.13
51_S56_E0.5420.13
39_A65_Q0.5390.13
31_N38_D0.5380.13
11_R29_W0.5300.13
14_A63_L0.5270.13
37_Y43_K0.5210.13
11_R24_A0.5200.13
20_G57_A0.5000.12
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  
1z4hA 1 0.9 98.9 0.66 Contact Map
1y6uA 1 0.7857 98.5 0.704 Contact Map
4j2nA 4 0.8 97.8 0.755 Contact Map
1j9iA 2 0.7857 97.2 0.781 Contact Map
2cobA 1 0.6857 90.2 0.849 Contact Map
1iufA 1 1 87.4 0.857 Contact Map
1ojlA 3 0.4 87.3 0.857 Contact Map
3vw4A 1 0.4571 84.3 0.863 Contact Map
2kfsA 1 0.9 84.2 0.863 Contact Map
1hlvA 1 1 82.1 0.866 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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