Transglut_i_TM - PFAM28P - GREMLIN Contacts

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Transglut_i_TM - Inactive transglutaminase fused to 7 transmembrane helices

PFAM:	PF14400	Sequences: YKHLVLGFPLLPGEQREVWTVEARVEFEATGGPVKVSLALPSLQPGFTILDENFASPGYGLSIEEEDGNRRAEWSIRRASGPQTLYYRAQVYRDPSAEPPPPPPPEPEPPELEEPYATAAEALLDEARERSADPESFTRELIKRLNDPSPDQNVALLLSKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	161 (159)
Sequences:	1475 (1068)
Seq/√Len:	84.7
META:	0.765

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_L	72_A	5.224	1.00
35_K	133_D	4.828	1.00
52_E	70_R	3.570	1.00
37_S	71_R	3.488	1.00
59_Y	83_Q	3.485	1.00
2_K	8_F	3.318	1.00
127_A	141_L	2.988	1.00
75_S	136_S	2.900	1.00
77_R	131_S	2.685	1.00
29_A	34_V	2.637	1.00
24_R	84_T	2.418	1.00
114_E	118_T	2.286	1.00
124_L	137_F	2.236	1.00
60_G	77_R	2.218	1.00
76_I	79_A	2.158	1.00
35_K	75_S	2.102	1.00
29_A	79_A	2.060	1.00
138_T	142_I	2.011	1.00
2_K	6_L	1.951	1.00
112_L	120_A	1.867	1.00
25_V	38_L	1.859	1.00
27_F	59_Y	1.798	1.00
56_S	74_W	1.788	1.00
46_G	94_D	1.768	1.00
113_E	116_Y	1.741	1.00
49_I	91_V	1.667	1.00
140_E	143_K	1.659	1.00
127_A	154_V	1.651	1.00
60_G	131_S	1.642	1.00
1_Y	5_V	1.520	1.00
1_Y	6_L	1.514	1.00
26_E	84_T	1.508	0.99
133_D	136_S	1.503	0.99
25_V	36_V	1.474	0.99
123_L	154_V	1.460	0.99
27_F	83_Q	1.459	0.99
137_F	155_A	1.403	0.99
28_E	82_P	1.398	0.99
20_T	90_Q	1.309	0.99
115_P	118_T	1.304	0.99
29_A	59_Y	1.303	0.98
9_P	60_G	1.297	0.98
2_K	10_L	1.272	0.98
147_D	150_P	1.225	0.98
56_S	61_L	1.217	0.98
121_E	125_D	1.212	0.98
79_A	83_Q	1.209	0.98
10_L	92_Y	1.193	0.97
60_G	132_A	1.192	0.97
60_G	136_S	1.191	0.97
131_S	136_S	1.174	0.97
145_L	154_V	1.172	0.97
52_E	87_Y	1.170	0.97
64_E	73_E	1.165	0.97
125_D	129_E	1.153	0.97
130_R	144_R	1.139	0.96
61_L	76_I	1.116	0.96
130_R	140_E	1.095	0.96
78_R	128_R	1.095	0.96
20_T	50_L	1.057	0.95
77_R	136_S	1.053	0.95
35_K	132_A	1.048	0.94
48_T	51_D	1.035	0.94
114_E	117_A	1.026	0.94
117_A	121_E	1.017	0.93
19_W	22_E	1.000	0.93
27_F	81_G	0.989	0.92
122_A	153_N	0.985	0.92
55_A	152_Q	0.976	0.92
49_I	89_A	0.968	0.92
11_L	14_E	0.956	0.91
27_F	34_V	0.954	0.91
17_E	93_R	0.952	0.91
52_E	74_W	0.951	0.91
135_E	138_T	0.936	0.90
75_S	140_E	0.928	0.90
13_G	21_V	0.928	0.90
153_N	156_L	0.928	0.90
9_P	77_R	0.924	0.90
8_F	92_Y	0.921	0.90
33_P	157_L	0.913	0.89
22_E	27_F	0.904	0.89
140_E	156_L	0.899	0.88
134_P	138_T	0.898	0.88
9_P	85_L	0.898	0.88
145_L	150_P	0.896	0.88
25_V	71_R	0.894	0.88
66_E	69_N	0.890	0.88
62_S	75_S	0.872	0.87
29_A	81_G	0.871	0.87
39_A	71_R	0.868	0.87
131_S	137_F	0.868	0.87
72_A	86_Y	0.863	0.86
119_A	156_L	0.861	0.86
145_L	153_N	0.860	0.86
150_P	158_L	0.850	0.85
80_S	104_P	0.849	0.85
46_G	75_S	0.848	0.85
10_L	54_F	0.846	0.85
100_P	107_P	0.843	0.85
91_V	102_P	0.837	0.84
40_L	88_R	0.823	0.83
137_F	141_L	0.820	0.83
21_V	101_P	0.818	0.83
126_E	154_V	0.816	0.83
25_V	158_L	0.811	0.83
23_A	83_Q	0.811	0.83
51_D	54_F	0.808	0.82
72_A	85_L	0.806	0.82
3_H	10_L	0.805	0.82
127_A	137_F	0.804	0.82
103_P	109_P	0.796	0.81
126_E	130_R	0.794	0.81
132_A	136_S	0.791	0.81
78_R	106_E	0.786	0.81
78_R	99_P	0.785	0.80
126_E	141_L	0.779	0.80
45_P	119_A	0.776	0.80
2_K	92_Y	0.771	0.79
120_A	157_L	0.770	0.79
107_P	117_A	0.768	0.79
145_L	156_L	0.764	0.79
53_N	124_L	0.754	0.78
74_W	153_N	0.753	0.78
77_R	132_A	0.747	0.77
39_A	44_Q	0.745	0.77
54_F	110_P	0.742	0.77
21_V	91_V	0.739	0.76
9_P	131_S	0.739	0.76
47_F	93_R	0.738	0.76
54_F	61_L	0.736	0.76
105_P	134_P	0.733	0.76
56_S	60_G	0.732	0.76
43_L	101_P	0.731	0.76
59_Y	139_R	0.730	0.75
137_F	157_L	0.730	0.75
148_P	155_A	0.726	0.75
75_S	130_R	0.726	0.75
84_T	88_R	0.723	0.75
87_Y	131_S	0.721	0.75
59_Y	79_A	0.709	0.73
44_Q	90_Q	0.709	0.73
126_E	144_R	0.702	0.73
111_E	117_A	0.702	0.73
2_K	54_F	0.702	0.73
95_P	102_P	0.702	0.73
36_V	86_Y	0.696	0.72
8_F	22_E	0.695	0.72
14_E	99_P	0.692	0.72
40_L	72_A	0.686	0.71
29_A	33_P	0.685	0.71
61_L	132_A	0.684	0.71
2_K	141_L	0.684	0.71
41_P	70_R	0.682	0.70
62_S	86_Y	0.678	0.70
128_R	137_F	0.676	0.70
6_L	53_N	0.671	0.69
42_S	49_I	0.669	0.69
9_P	56_S	0.668	0.69
133_D	145_L	0.666	0.69
4_L	36_V	0.665	0.69
54_F	63_I	0.662	0.68
33_P	51_D	0.654	0.67
56_S	85_L	0.653	0.67
54_F	70_R	0.650	0.67
109_P	117_A	0.649	0.67
144_R	150_P	0.649	0.67
6_L	10_L	0.646	0.66
72_A	132_A	0.643	0.66
63_I	135_E	0.640	0.66
41_P	56_S	0.638	0.65
58_G	82_P	0.637	0.65
29_A	157_L	0.633	0.65
1_Y	123_L	0.624	0.64
142_I	146_N	0.616	0.63
37_S	73_E	0.615	0.62
11_L	58_G	0.614	0.62
62_S	73_E	0.614	0.62
116_Y	156_L	0.613	0.62
3_H	59_Y	0.612	0.62
47_F	59_Y	0.612	0.62
40_L	70_R	0.610	0.62
35_K	73_E	0.610	0.62
20_T	23_A	0.609	0.62
39_A	69_N	0.606	0.61
100_P	103_P	0.606	0.61
95_P	139_R	0.606	0.61
47_F	76_I	0.605	0.61
29_A	32_G	0.603	0.61
82_P	96_S	0.601	0.61
10_L	40_L	0.592	0.60
57_P	70_R	0.589	0.59
40_L	51_D	0.586	0.59
52_E	89_A	0.585	0.59
31_G	78_R	0.584	0.59
61_L	152_Q	0.583	0.58
113_E	156_L	0.577	0.58
18_V	46_G	0.574	0.57
63_I	72_A	0.573	0.57
55_A	74_W	0.572	0.57
78_R	108_E	0.570	0.57
52_E	105_P	0.569	0.57
74_W	146_N	0.565	0.56
113_E	118_T	0.562	0.56
38_L	59_Y	0.561	0.56
13_G	25_V	0.558	0.55
154_V	159_S	0.558	0.55
45_P	107_P	0.557	0.55
54_F	111_E	0.556	0.55
24_R	53_N	0.554	0.55
39_A	91_V	0.554	0.55
138_T	159_S	0.554	0.55
36_V	39_A	0.554	0.55
128_R	134_P	0.553	0.54
1_Y	98_E	0.547	0.54
73_E	92_Y	0.541	0.53
146_N	150_P	0.538	0.52
8_F	51_D	0.536	0.52
96_S	148_P	0.536	0.52
5_V	25_V	0.535	0.52
59_Y	98_E	0.534	0.52
12_P	87_Y	0.534	0.52
40_L	137_F	0.534	0.52
54_F	152_Q	0.533	0.52
107_P	110_P	0.531	0.52
8_F	49_I	0.530	0.51
97_A	125_D	0.526	0.51
51_D	90_Q	0.518	0.50
55_A	151_D	0.517	0.50
52_E	134_P	0.514	0.49
8_F	35_K	0.511	0.49
13_G	28_E	0.510	0.49
139_R	156_L	0.509	0.49
134_P	139_R	0.508	0.48
6_L	54_F	0.504	0.48
22_E	90_Q	0.502	0.48
139_R	157_L	0.500	0.47
6_L	93_R	0.500	0.47

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
4gmoA	1	0.3168	16.6	0.939	Contact Map
4ot9A	2	0.2671	12.9	0.942	Contact Map
2dvyA	4	0.6708	10	0.945	Contact Map
1vccA	1	0.4348	6.8	0.949	Contact Map
2wacA	1	0.441	6.7	0.949	Contact Map
4d0pA	1	0.4658	6.5	0.95	Contact Map
2zetC	1	0.3478	4.6	0.953	Contact Map
4ziqA	2	0.7764	4.2	0.954	Contact Map
2ygwA	2	0.4907	4.1	0.954	Contact Map
2vglM	1	0.4969	4	0.954	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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