AHH - PFAM28P - GREMLIN Contacts

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AHH - A nuclease family of the HNH/ENDO VII superfamily with conserved AHH

PFAM:	PF14412	Sequences: KNLRKAAGGPRPSPGYQAHHIVPGKNKPRAPRAREILKKAGIDINDAANGVFLPRSEAPGAPGHRGPHTNAYHEAVNERLDKADKSPGGAREALLEELRKIREELRNGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (100)
Sequences:	2705 (2416)
Seq/√Len:	241.6
META:	0.787

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_A	50_G	3.835	1.00
91_R	95_L	3.424	1.00
79_R	104_E	2.765	1.00
79_R	97_E	2.660	1.00
24_G	45_N	2.555	1.00
23_P	73_H	2.532	1.00
75_A	79_R	2.055	1.00
90_A	93_A	2.032	1.00
26_N	29_R	2.000	1.00
17_Q	65_R	1.914	1.00
32_R	77_N	1.881	1.00
45_N	50_G	1.813	1.00
16_Y	52_F	1.768	1.00
97_E	100_K	1.761	1.00
26_N	73_H	1.737	1.00
18_A	52_F	1.708	1.00
99_R	102_R	1.646	1.00
53_L	64_H	1.620	1.00
31_P	35_E	1.619	1.00
48_A	95_L	1.576	1.00
102_R	106_R	1.531	1.00
33_A	37_L	1.483	1.00
24_G	44_I	1.479	1.00
87_P	90_A	1.470	1.00
43_D	46_D	1.468	1.00
12_P	16_Y	1.407	1.00
33_A	36_I	1.407	1.00
70_N	74_E	1.353	1.00
17_Q	55_R	1.336	1.00
25_K	73_H	1.330	1.00
40_A	85_K	1.310	1.00
74_E	78_E	1.277	1.00
21_I	51_V	1.266	1.00
30_A	34_R	1.263	1.00
27_K	30_A	1.244	1.00
34_R	38_K	1.242	1.00
23_P	26_N	1.235	1.00
34_R	37_L	1.206	1.00
77_N	81_D	1.193	1.00
24_G	50_G	1.121	1.00
36_I	77_N	1.106	1.00
40_A	94_L	1.105	1.00
22_V	37_L	1.102	1.00
89_G	93_A	1.102	1.00
22_V	33_A	1.095	1.00
21_I	102_R	1.055	1.00
93_A	96_E	1.053	1.00
32_R	81_D	1.053	1.00
93_A	97_E	1.050	1.00
103_E	107_N	1.041	1.00
35_E	39_K	1.040	1.00
39_K	84_D	1.038	1.00
19_H	67_P	1.037	1.00
86_S	89_G	1.010	1.00
75_A	78_E	0.996	1.00
36_I	94_L	0.947	1.00
94_L	102_R	0.941	1.00
90_A	94_L	0.932	1.00
33_A	77_N	0.929	1.00
72_Y	76_V	0.923	1.00
92_E	95_L	0.921	1.00
7_A	12_P	0.912	1.00
79_R	82_K	0.890	1.00
9_G	12_P	0.888	1.00
37_L	42_I	0.888	1.00
29_R	70_N	0.885	0.99
29_R	74_E	0.874	0.99
67_P	73_H	0.869	0.99
53_L	105_L	0.858	0.99
25_K	67_P	0.853	0.99
42_I	46_D	0.852	0.99
11_R	52_F	0.848	0.99
37_L	40_A	0.840	0.99
92_E	96_E	0.832	0.99
86_S	90_A	0.830	0.99
76_V	105_L	0.825	0.99
51_V	106_R	0.821	0.99
11_R	16_Y	0.812	0.99
103_E	106_R	0.810	0.99
48_A	91_R	0.801	0.99
48_A	99_R	0.801	0.99
19_H	51_V	0.785	0.99
19_H	72_Y	0.779	0.99
95_L	99_R	0.768	0.99
73_H	77_N	0.764	0.99
72_Y	105_L	0.758	0.98
83_A	97_E	0.753	0.98
37_L	94_L	0.750	0.98
16_Y	54_P	0.748	0.98
15_G	55_R	0.743	0.98
34_R	44_I	0.719	0.98
23_P	76_V	0.718	0.98
23_P	30_A	0.715	0.98
57_E	66_G	0.715	0.98
53_L	62_P	0.707	0.98
11_R	14_P	0.699	0.97
104_E	107_N	0.691	0.97
30_A	36_I	0.684	0.97
23_P	72_Y	0.680	0.97
55_R	60_G	0.674	0.97
28_P	31_P	0.671	0.97
98_L	102_R	0.662	0.96
30_A	73_H	0.661	0.96
47_A	50_G	0.658	0.96
17_Q	66_G	0.656	0.96
38_K	43_D	0.642	0.96
12_P	52_F	0.641	0.96
78_E	89_G	0.623	0.95
57_E	65_R	0.620	0.95
7_A	11_R	0.610	0.94
94_L	98_L	0.610	0.94
29_R	77_N	0.603	0.94
32_R	36_I	0.600	0.94
32_R	35_E	0.599	0.94
22_V	101_I	0.598	0.94
18_A	45_N	0.598	0.94
19_H	53_L	0.596	0.94
99_R	106_R	0.587	0.93
69_T	73_H	0.570	0.92
80_L	83_A	0.562	0.92
40_A	90_A	0.554	0.91
56_S	66_G	0.552	0.91
76_V	101_I	0.552	0.91
33_A	42_I	0.552	0.91
26_N	30_A	0.547	0.90
78_E	82_K	0.547	0.90
99_R	103_E	0.544	0.90
40_A	84_D	0.543	0.90
79_R	83_A	0.538	0.90
100_K	104_E	0.536	0.90
31_P	77_N	0.535	0.89
30_A	33_A	0.533	0.89
57_E	60_G	0.527	0.89
74_E	77_N	0.527	0.89
36_I	80_L	0.526	0.89
56_S	63_G	0.522	0.88
31_P	81_D	0.522	0.88
78_E	81_D	0.521	0.88
8_G	12_P	0.519	0.88
100_K	103_E	0.516	0.88
11_R	38_K	0.514	0.88
83_A	94_L	0.513	0.87
17_Q	52_F	0.513	0.87
86_S	94_L	0.512	0.87
97_E	101_I	0.509	0.87
89_G	97_E	0.508	0.87
7_A	14_P	0.506	0.87
82_K	100_K	0.503	0.86
85_K	93_A	0.503	0.86
79_R	101_I	0.500	0.86

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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
1fr2B	1	0.4404	55.2	0.841	Contact Map
3zfkA	1	0.4312	55	0.841	Contact Map
7ceiB	1	0.4404	47.8	0.847	Contact Map
4qkoB	2	0.4587	38.5	0.856	Contact Map
4uhqA	1	0.5138	32.1	0.862	Contact Map
1xreA	2	0.6514	23.6	0.87	Contact Map
3vlcE	1	0.2294	13	0.885	Contact Map
2lsoA	1	0.4128	12.6	0.886	Contact Map
3s4wB	1	0.6606	12.5	0.886	Contact Map
4ogeA	1	0.789	11.4	0.888	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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