TSCPD - PFAM28P - GREMLIN Contacts

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TSCPD - TSCPD domain

PFAM:	PF12637	Sequences: YKFKGGCGLYITVNEDEDGRPGEVFINMGKEGGCISGNLEAIARLISLALQYGVPLEEIVEKLKGIFCPSGVTFGGNKATSCPDAIARALEEHL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (91)
Sequences:	17493 (7914)
Seq/√Len:	829.7
META:	0.942

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_K	91_E	4.048	1.00
36_S	40_E	2.480	1.00
41_A	83_P	2.220	1.00
54_V	62_K	2.180	1.00
67_F	79_A	2.126	1.00
49_A	59_I	2.077	1.00
13_V	21_P	2.056	1.00
44_R	62_K	1.829	1.00
42_I	45_L	1.817	1.00
60_V	91_E	1.773	1.00
12_T	31_E	1.754	1.00
45_L	59_I	1.738	1.00
45_L	63_L	1.692	1.00
16_D	26_I	1.613	1.00
12_T	29_G	1.603	1.00
11_I	30_K	1.475	1.00
46_I	59_I	1.452	1.00
34_C	68_C	1.447	1.00
24_V	55_P	1.442	1.00
2_K	10_Y	1.429	1.00
49_A	54_V	1.390	1.00
40_E	44_R	1.370	1.00
67_F	77_N	1.365	1.00
10_Y	31_E	1.327	1.00
3_F	11_I	1.327	1.00
9_L	32_G	1.316	1.00
30_K	86_I	1.307	1.00
27_N	52_Y	1.304	1.00
54_V	58_E	1.279	1.00
26_I	43_A	1.231	1.00
44_R	66_I	1.222	1.00
60_V	90_L	1.200	1.00
5_G	8_G	1.197	1.00
48_L	62_K	1.197	1.00
58_E	62_K	1.181	1.00
3_F	6_G	1.181	1.00
72_V	78_K	1.157	1.00
55_P	58_E	1.146	1.00
45_L	49_A	1.135	1.00
48_L	58_E	1.134	1.00
65_G	84_D	1.132	1.00
64_K	88_R	1.121	1.00
60_V	87_A	1.110	1.00
73_T	76_G	1.104	1.00
64_K	87_A	1.095	1.00
84_D	88_R	1.092	1.00
34_C	82_C	1.068	1.00
66_I	83_P	1.051	1.00
9_L	31_E	1.040	1.00
7_C	82_C	1.039	1.00
16_D	22_G	1.038	1.00
35_I	38_N	1.021	1.00
10_Y	25_F	0.995	1.00
46_I	87_A	0.983	1.00
7_C	34_C	0.952	1.00
22_G	51_Q	0.947	1.00
49_A	52_Y	0.936	1.00
41_A	66_I	0.922	1.00
58_E	61_E	0.919	1.00
52_Y	55_P	0.913	1.00
42_I	46_I	0.903	1.00
16_D	20_R	0.897	1.00
73_T	78_K	0.884	1.00
56_L	60_V	0.869	1.00
68_C	82_C	0.868	1.00
38_N	42_I	0.863	1.00
26_I	52_Y	0.860	1.00
14_N	27_N	0.859	1.00
26_I	86_I	0.858	1.00
44_R	52_Y	0.846	1.00
54_V	59_I	0.840	1.00
65_G	80_T	0.839	1.00
42_I	63_L	0.838	1.00
81_S	84_D	0.834	1.00
59_I	63_L	0.810	1.00
75_G	89_A	0.804	1.00
80_T	84_D	0.804	1.00
23_E	47_S	0.795	1.00
14_N	23_E	0.792	1.00
11_I	89_A	0.791	1.00
41_A	63_L	0.788	1.00
71_G	78_K	0.788	1.00
79_A	85_A	0.785	1.00
27_N	36_S	0.782	1.00
47_S	51_Q	0.777	1.00
13_V	89_A	0.774	1.00
7_C	68_C	0.768	1.00
38_N	82_C	0.765	1.00
52_Y	58_E	0.753	1.00
3_F	9_L	0.748	1.00
38_N	83_P	0.746	1.00
27_N	40_E	0.728	1.00
59_I	87_A	0.715	1.00
60_V	64_K	0.714	1.00
67_F	83_P	0.708	1.00
15_E	21_P	0.695	1.00
73_T	77_N	0.682	1.00
46_I	63_L	0.680	1.00
63_L	87_A	0.667	1.00
2_K	9_L	0.663	1.00
88_R	92_E	0.661	1.00
7_C	28_M	0.652	1.00
40_E	66_I	0.648	1.00
24_V	46_I	0.642	1.00
56_L	90_L	0.637	1.00
29_G	32_G	0.637	1.00
74_F	78_K	0.635	1.00
15_E	56_L	0.613	1.00
19_G	24_V	0.610	1.00
79_A	88_R	0.607	1.00
23_E	55_P	0.603	1.00
23_E	51_Q	0.600	1.00
40_E	67_F	0.597	1.00
57_E	61_E	0.595	1.00
4_K	74_F	0.588	1.00
53_G	56_L	0.588	1.00
19_G	55_P	0.573	1.00
85_A	89_A	0.572	1.00
49_A	53_G	0.567	1.00
39_L	43_A	0.563	1.00
25_F	44_R	0.560	1.00
48_L	54_V	0.559	1.00
34_C	38_N	0.552	1.00
13_V	90_L	0.549	1.00
10_Y	14_N	0.548	1.00
25_F	59_I	0.546	1.00
34_C	37_G	0.541	1.00
37_G	67_F	0.540	1.00
42_I	87_A	0.540	1.00
3_F	10_Y	0.526	1.00
41_A	45_L	0.523	1.00
67_F	71_G	0.523	1.00
74_F	77_N	0.518	1.00
70_S	74_F	0.509	1.00
37_G	66_I	0.500	1.00
48_L	51_Q	0.500	1.00

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
3r07C	1	0.8511	31.2	0.873	Contact Map
2iz1A	2	0.9043	12.2	0.895	Contact Map
2zydA	2	0.9043	12.1	0.895	Contact Map
3lk4B	1	0.6489	10	0.899	Contact Map
4bbyA	2	0.8191	9.8	0.9	Contact Map
2odiA	1	0.4468	9.8	0.9	Contact Map
5by3A	1	0.9574	9.5	0.9	Contact Map
2i81A	3	0.8511	9.4	0.9	Contact Map
2p4qA	2	0.9043	9.2	0.901	Contact Map
2oa9A	1	0.4149	8	0.904	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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