GREMLIN Database
Q9HNL2 - Transcription elongation factor Spt4
UniProt: Q9HNL2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 65 (58)
Sequences: 103 (61)
Seq/√Len: 8.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
7_A13_R2.4230.73
5_R52_M2.2660.68
15_V59_E2.1400.63
15_V23_P2.1140.62
40_I64_V2.0340.59
6_L31_T2.0300.59
61_A64_V1.9420.55
12_H52_M1.7850.49
30_L33_D1.7150.46
10_D28_N1.6760.45
7_A58_G1.5940.41
38_V48_I1.5780.41
34_W48_I1.5440.39
14_I24_Y1.5260.39
6_L50_D1.4290.35
44_D55_H1.3830.33
40_I45_T1.3700.33
37_Y58_G1.3420.32
7_A14_I1.3360.32
24_Y35_A1.3170.31
48_I53_E1.3160.31
10_D21_M1.2590.29
52_M58_G1.2050.27
6_L30_L1.2040.27
27_S38_V1.1550.25
26_S39_V1.1450.25
20_E23_P1.1430.25
42_H45_T1.0960.24
26_S51_K1.0770.23
26_S44_D1.0540.22
7_A16_E1.0430.22
33_D62_L1.0300.22
16_E59_E1.0000.21
13_R24_Y0.9790.20
20_E58_G0.9740.20
5_R51_K0.9650.20
36_G63_K0.9450.19
5_R42_H0.9320.19
32_E48_I0.9310.19
36_G62_L0.9260.19
16_E23_P0.9180.19
54_V59_E0.8910.18
40_I54_V0.8680.18
17_P41_T0.8630.17
37_Y62_L0.8630.17
28_N62_L0.8450.17
6_L23_P0.8220.16
32_E51_K0.8160.16
6_L14_I0.8090.16
32_E64_V0.7940.16
45_T54_V0.7490.15
6_L32_E0.7320.15
10_D33_D0.7310.15
47_E50_D0.7220.14
37_Y41_T0.6880.14
16_E28_N0.6860.14
14_I31_T0.6770.13
12_H41_T0.6770.13
17_P29_S0.6760.13
10_D20_E0.6740.13
17_P63_K0.6620.13
30_L64_V0.6550.13
35_A63_K0.6520.13
26_S60_F0.6450.13
12_H29_S0.6430.13
39_V56_E0.6400.13
23_P38_V0.6290.13
35_A42_H0.6170.12
5_R53_E0.6130.12
9_H24_Y0.6030.12
21_M51_K0.5900.12
29_S52_M0.5780.12
20_E54_V0.5710.12
9_H32_E0.5620.11
41_T51_K0.5550.11
7_A29_S0.5490.11
10_D39_V0.5480.11
20_E31_T0.5430.11
20_E41_T0.5420.11
29_S37_Y0.5410.11
50_D53_E0.5350.11
7_A56_E0.5340.11
30_L54_V0.5320.11
16_E60_F0.5290.11
38_V63_K0.5060.11
29_S33_D0.5010.10
50_D56_E0.5000.10
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  
3p8bA 1 0.9231 99.9 0.313 Contact Map
1ryqA 1 0.9077 99.9 0.316 Contact Map
3lpeB 1 0.8923 99.9 0.345 Contact Map
3h7hA 1 1 99.8 0.395 Contact Map
2exuA 2 0.9538 99.7 0.451 Contact Map
2ayjA 1 0.6462 87.2 0.851 Contact Map
4u3eA 2 0.8615 86.3 0.852 Contact Map
2lcqA 1 0.5538 75.3 0.869 Contact Map
1h7bA 2 0.2769 72.4 0.872 Contact Map
5aunA 1 0.6462 71.8 0.872 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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