Nterm_IS4 - PFAM28P - GREMLIN Contacts

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Nterm_IS4 - Insertion element 4 transposase N-terminal

PFAM:	PF13006	Sequences: RVSLGVLTRVIPPELVDEVLAATGRAEQRRRRLPARVVVYLVLAMALFRDLSYREVLRKLVEGLRGLAGWRVPSKSAISQARQRLGAEPLRALFE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	95 (93)
Sequences:	8186 (4181)
Seq/√Len:	433.6
META:	0.954

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_R	95_E	2.872	1.00
74_S	77_A	2.669	1.00
17_D	36_R	2.629	1.00
22_A	92_A	2.518	1.00
38_V	81_A	2.429	1.00
27_E	35_A	2.200	1.00
81_A	84_R	2.184	1.00
23_T	92_A	2.099	1.00
51_L	59_K	1.990	1.00
21_A	26_A	1.983	1.00
39_V	90_L	1.960	1.00
13_P	17_D	1.915	1.00
77_A	80_Q	1.888	1.00
16_V	39_V	1.834	1.00
45_M	53_Y	1.830	1.00
35_A	85_L	1.828	1.00
76_S	80_Q	1.827	1.00
15_L	19_V	1.754	1.00
79_S	83_Q	1.710	1.00
16_V	40_Y	1.587	1.00
15_L	18_E	1.581	1.00
18_E	22_A	1.573	1.00
33_L	38_V	1.533	1.00
19_V	92_A	1.475	1.00
54_R	75_K	1.456	1.00
57_L	78_I	1.417	1.00
44_A	56_V	1.410	1.00
92_A	95_E	1.378	1.00
41_L	53_Y	1.359	1.00
75_K	79_S	1.299	1.00
6_V	9_R	1.288	1.00
13_P	36_R	1.279	1.00
86_G	89_P	1.220	1.00
51_L	55_E	1.212	1.00
20_L	26_A	1.210	1.00
55_E	58_R	1.200	1.00
74_S	80_Q	1.189	1.00
87_A	91_R	1.184	1.00
38_V	41_L	1.170	1.00
25_R	35_A	1.165	1.00
19_V	23_T	1.160	1.00
39_V	85_L	1.127	1.00
42_V	45_M	1.103	1.00
11_I	43_L	1.103	1.00
41_L	45_M	1.089	1.00
32_R	71_R	1.071	1.00
58_R	72_V	1.040	1.00
76_S	79_S	1.021	1.00
88_E	91_R	1.018	1.00
5_G	8_T	1.017	1.00
48_F	59_K	1.004	1.00
30_R	36_R	0.992	1.00
31_R	34_P	0.990	1.00
39_V	93_L	0.958	1.00
35_A	84_R	0.955	1.00
38_V	85_L	0.943	1.00
20_L	35_A	0.932	1.00
32_R	73_P	0.924	1.00
43_L	46_A	0.915	1.00
3_S	6_V	0.913	1.00
19_V	22_A	0.898	1.00
30_R	34_P	0.897	1.00
23_T	89_P	0.885	1.00
40_Y	43_L	0.876	1.00
38_V	42_V	0.866	1.00
27_E	36_R	0.830	1.00
55_E	59_K	0.813	1.00
27_E	30_R	0.808	1.00
89_P	93_L	0.800	1.00
14_E	18_E	0.793	1.00
41_L	78_I	0.790	1.00
70_W	73_P	0.771	1.00
6_V	10_V	0.761	1.00
73_P	77_A	0.754	1.00
35_A	38_V	0.753	1.00
61_V	64_L	0.753	1.00
3_S	8_T	0.752	1.00
17_D	21_A	0.741	1.00
52_S	55_E	0.731	1.00
20_L	27_E	0.729	1.00
34_P	81_A	0.722	1.00
20_L	23_T	0.712	1.00
46_A	53_Y	0.704	1.00
88_E	92_A	0.703	1.00
89_P	92_A	0.699	1.00
76_S	81_A	0.690	1.00
8_T	11_I	0.688	1.00
46_A	49_R	0.671	1.00
90_L	93_L	0.664	1.00
17_D	26_A	0.664	1.00
57_L	62_E	0.654	0.99
67_L	70_W	0.652	0.99
45_M	78_I	0.651	0.99
57_L	72_V	0.651	0.99
34_P	37_V	0.643	0.99
12_P	15_L	0.641	0.99
7_L	43_L	0.640	0.99
19_V	93_L	0.639	0.99
48_F	56_V	0.631	0.99
28_Q	35_A	0.624	0.99
39_V	43_L	0.612	0.99
63_G	66_G	0.609	0.99
73_P	78_I	0.608	0.99
31_R	77_A	0.600	0.99
55_E	75_K	0.598	0.99
5_G	47_L	0.585	0.99
15_L	93_L	0.584	0.99
44_A	47_L	0.583	0.99
52_S	56_V	0.582	0.99
80_Q	83_Q	0.582	0.99
65_R	68_A	0.582	0.99
49_R	55_E	0.580	0.99
62_E	67_L	0.576	0.99
19_V	89_P	0.574	0.99
25_R	88_E	0.574	0.99
41_L	75_K	0.562	0.98
23_T	88_E	0.561	0.98
13_P	40_Y	0.557	0.98
44_A	60_L	0.553	0.98
15_L	49_R	0.552	0.98
4_L	8_T	0.550	0.98
59_K	75_K	0.545	0.98
83_Q	92_A	0.542	0.98
45_M	56_V	0.541	0.98
28_Q	31_R	0.534	0.98
44_A	48_F	0.527	0.98
54_R	73_P	0.527	0.98
41_L	57_L	0.526	0.98
21_A	28_Q	0.525	0.98
4_L	11_I	0.524	0.98
24_G	28_Q	0.524	0.98
83_Q	87_A	0.522	0.98
33_L	78_I	0.518	0.97
37_V	57_L	0.518	0.97
67_L	72_V	0.513	0.97
50_D	53_Y	0.512	0.97
50_D	65_R	0.505	0.97
54_R	72_V	0.504	0.97
57_L	70_W	0.500	0.97
25_R	86_G	0.500	0.97

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
4d0h0	3	0.3895	4.6	0.906	Contact Map
2q1fA	1	0.4316	3.5	0.911	Contact Map
2eqaA	1	0.5684	3.4	0.912	Contact Map
1vsy5	1	0.8737	3.4	0.912	Contact Map
1pdnC	1	0.8526	3.3	0.912	Contact Map
1k78A	1	0.8842	3	0.915	Contact Map
3p8cB	1	0.2632	2.7	0.916	Contact Map
1k7jA	1	0.5789	2.5	0.918	Contact Map
1p4wA	1	0.7895	2.3	0.92	Contact Map
1yubA	1	0.5263	2.2	0.92	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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