NTP_transf_4 - PFAM28P - GREMLIN Contacts

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NTP_transf_4 - Sugar nucleotidyl transferase

PFAM:	PF13562	Sequences: IILFDDPARENLLPLTLTRPVADLRCGILTIREKWERYLGAATVSFLTRDYLSEKFPLNVIPDDDNLLINGRVLPNEELVEAIKSLKPGEALVKGGELIAARLSEEQLEELLDDLLEDELIEYEGEVLLIEYPWDIFSLNGEAIRADFELLTKGRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (151)
Sequences:	7570 (6104)
Seq/√Len:	496.8
META:	0.937

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_D	32_R	3.332	1.00
13_L	17_L	3.301	1.00
141_G	145_R	3.069	1.00
143_A	146_A	2.915	1.00
131_E	135_D	2.485	1.00
32_R	36_E	2.413	1.00
34_K	143_A	2.341	1.00
87_K	90_E	2.241	1.00
128_L	139_L	2.215	1.00
24_L	136_I	2.173	1.00
31_I	34_K	2.066	1.00
90_E	119_E	1.996	1.00
135_D	138_S	1.977	1.00
32_R	46_F	1.931	1.00
16_T	24_L	1.916	1.00
29_L	150_L	1.915	1.00
34_K	147_D	1.886	1.00
11_N	132_Y	1.847	1.00
64_D	102_R	1.840	1.00
97_E	131_E	1.794	1.00
9_R	49_R	1.775	1.00
72_R	129_L	1.708	1.00
15_L	24_L	1.673	1.00
29_L	34_K	1.662	1.00
38_Y	77_E	1.641	1.00
128_L	142_E	1.636	1.00
72_R	97_E	1.600	1.00
128_L	143_A	1.556	1.00
139_L	142_E	1.549	1.00
37_R	150_L	1.535	1.00
22_A	71_G	1.534	1.00
12_L	21_V	1.520	1.00
73_V	129_L	1.514	1.00
29_L	37_R	1.502	1.00
73_V	99_I	1.495	1.00
82_A	123_Y	1.473	1.00
4_F	68_L	1.457	1.00
94_K	127_V	1.436	1.00
22_A	46_F	1.382	1.00
142_E	145_R	1.376	1.00
6_D	70_N	1.372	1.00
1_I	67_L	1.371	1.00
5_D	49_R	1.354	1.00
6_D	72_R	1.334	1.00
26_C	143_A	1.326	1.00
91_A	98_L	1.322	1.00
9_R	13_L	1.320	1.00
13_L	16_T	1.297	1.00
145_R	149_E	1.291	1.00
36_E	44_V	1.277	1.00
68_L	103_L	1.276	1.00
4_F	98_L	1.274	1.00
25_R	28_I	1.254	1.00
97_E	129_L	1.246	1.00
29_L	33_E	1.243	1.00
93_V	98_L	1.240	1.00
68_L	101_A	1.235	1.00
135_D	139_L	1.215	1.00
132_Y	135_D	1.210	1.00
98_L	101_A	1.207	1.00
148_F	152_T	1.180	1.00
142_E	146_A	1.158	1.00
140_N	144_I	1.152	1.00
26_C	31_I	1.142	1.00
12_L	130_I	1.121	1.00
77_E	81_E	1.119	1.00
73_V	127_V	1.083	1.00
33_E	36_E	1.075	1.00
45_S	66_N	1.060	1.00
60_V	66_N	1.050	1.00
78_E	125_G	1.045	1.00
93_V	120_L	1.040	1.00
92_L	100_A	1.039	1.00
23_D	46_F	1.034	1.00
146_A	149_E	1.022	1.00
91_A	94_K	1.015	1.00
8_A	11_N	1.014	1.00
73_V	79_L	1.004	1.00
25_R	30_T	1.001	1.00
74_L	130_I	0.993	1.00
30_T	33_E	0.988	1.00
1_I	44_V	0.987	1.00
38_Y	150_L	0.977	1.00
47_L	68_L	0.977	1.00
12_L	133_P	0.965	1.00
93_V	96_G	0.964	1.00
11_N	131_E	0.952	1.00
3_L	32_R	0.928	1.00
25_R	33_E	0.926	1.00
9_R	15_L	0.924	1.00
3_L	35_W	0.921	1.00
29_L	151_L	0.916	1.00
67_L	102_R	0.915	1.00
5_D	22_A	0.914	1.00
36_E	43_T	0.908	1.00
2_I	66_N	0.908	1.00
16_T	21_V	0.904	1.00
28_I	151_L	0.903	1.00
41_A	44_V	0.897	1.00
28_I	144_I	0.893	1.00
21_V	71_G	0.892	1.00
20_P	46_F	0.888	1.00
76_N	146_A	0.881	1.00
21_V	72_R	0.878	1.00
12_L	72_R	0.876	1.00
83_I	100_A	0.874	1.00
130_I	139_L	0.856	1.00
74_L	128_L	0.853	1.00
1_I	69_I	0.850	1.00
121_I	124_E	0.849	1.00
74_L	143_A	0.825	1.00
15_L	133_P	0.823	1.00
90_E	121_I	0.819	1.00
53_S	58_L	0.816	1.00
76_N	123_Y	0.811	1.00
58_L	61_I	0.809	1.00
2_I	68_L	0.808	1.00
26_C	136_I	0.806	1.00
112_L	115_L	0.805	1.00
26_C	74_L	0.805	1.00
94_K	126_E	0.801	1.00
94_K	97_E	0.800	1.00
86_L	92_L	0.797	1.00
47_L	50_D	0.791	1.00
26_C	130_I	0.774	1.00
103_L	107_Q	0.766	1.00
29_L	143_A	0.764	1.00
108_L	111_L	0.764	1.00
39_L	80_V	0.764	1.00
8_A	72_R	0.764	1.00
130_I	136_I	0.764	1.00
141_G	144_I	0.753	1.00
137_F	140_N	0.748	1.00
89_G	92_L	0.748	1.00
15_L	19_R	0.742	1.00
62_P	66_N	0.737	1.00
12_L	24_L	0.736	1.00
137_F	141_G	0.734	1.00
19_R	24_L	0.734	1.00
88_P	102_R	0.728	1.00
149_E	153_K	0.728	1.00
82_A	125_G	0.726	1.00
32_R	44_V	0.720	1.00
25_R	29_L	0.717	1.00
5_D	9_R	0.717	1.00
109_E	112_L	0.715	1.00
31_I	74_L	0.708	1.00
111_L	115_L	0.705	1.00
80_V	84_K	0.704	1.00
35_W	75_P	0.700	1.00
15_L	136_I	0.699	1.00
104_S	107_Q	0.696	1.00
35_W	39_L	0.689	1.00
31_I	71_G	0.684	1.00
61_I	64_D	0.682	1.00
9_R	21_V	0.660	1.00
81_E	84_K	0.659	1.00
1_I	39_L	0.654	1.00
53_S	56_F	0.653	1.00
82_A	92_L	0.651	1.00
86_L	100_A	0.650	1.00
28_I	148_F	0.648	1.00
53_S	57_P	0.646	1.00
22_A	48_T	0.643	1.00
54_E	57_P	0.643	1.00
26_C	140_N	0.642	1.00
130_I	135_D	0.641	1.00
79_L	83_I	0.639	1.00
55_K	58_L	0.638	1.00
35_W	69_I	0.637	1.00
3_L	44_V	0.635	1.00
120_L	124_E	0.631	1.00
10_E	49_R	0.627	1.00
140_N	143_A	0.625	1.00
20_P	55_K	0.625	1.00
88_P	104_S	0.625	1.00
89_G	104_S	0.624	1.00
23_D	56_F	0.624	1.00
10_E	13_L	0.620	1.00
123_Y	127_V	0.616	1.00
70_N	129_L	0.611	0.99
4_F	70_N	0.607	0.99
23_D	30_T	0.605	0.99
128_L	146_A	0.600	0.99
77_E	149_E	0.594	0.99
61_I	66_N	0.593	0.99
63_D	66_N	0.584	0.99
48_T	56_F	0.581	0.99
69_I	100_A	0.580	0.99
3_L	36_E	0.577	0.99
31_I	75_P	0.577	0.99
130_I	133_P	0.572	0.99
71_G	75_P	0.566	0.99
54_E	58_L	0.563	0.99
134_W	138_S	0.563	0.99
90_E	93_V	0.556	0.99
143_A	147_D	0.556	0.99
111_L	114_D	0.554	0.99
70_N	97_E	0.550	0.99
22_A	47_L	0.550	0.99
38_Y	80_V	0.546	0.99
21_V	24_L	0.542	0.99
34_K	74_L	0.541	0.99
48_T	52_L	0.538	0.99
94_K	129_L	0.538	0.99
26_C	139_L	0.532	0.99
39_L	84_K	0.530	0.99
2_I	45_S	0.529	0.99
78_E	82_A	0.523	0.98
27_G	144_I	0.522	0.98
91_A	101_A	0.519	0.98
16_T	19_R	0.518	0.98
3_L	22_A	0.518	0.98
18_T	51_Y	0.517	0.98
60_V	63_D	0.516	0.98
20_P	52_L	0.515	0.98
119_E	122_E	0.514	0.98
111_L	117_E	0.512	0.98
20_P	71_G	0.512	0.98
75_P	80_V	0.511	0.98
8_A	131_E	0.508	0.98
34_K	75_P	0.507	0.98
107_Q	115_L	0.506	0.98
75_P	79_L	0.504	0.98
22_A	32_R	0.504	0.98
15_L	18_T	0.500	0.98

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
1wdiA	1	0.6667	7.4	0.931	Contact Map
1vkyA	2	0.6731	6	0.934	Contact Map
3d8lA	2	0.25	4.9	0.937	Contact Map
3pqaA	4	0.4744	3.8	0.94	Contact Map
1mc3A	3	0.9295	3.8	0.94	Contact Map
4trhA	2	0.5449	3.8	0.94	Contact Map
2c42A	2	0.9872	3.6	0.941	Contact Map
1lvwA	3	0.9231	3.4	0.942	Contact Map
4ho4A	3	0.9295	3	0.943	Contact Map
1na6A	2	0.5577	2.9	0.944	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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