zf-LITAF-like - PFAM28P - GREMLIN Contacts

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zf-LITAF-like - LITAF-like zinc ribbon domain

PFAM:	PF10601	Sequences: DEPVQVTCPHCGQEVTTRVEYEPGTLTWLLCLLLCLFGCLPCCLIPFCIDSCKDVVHYCPNCGAVLGTYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (68)
Sequences:	2310 (1926)
Seq/√Len:	233.6
META:	0.542

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_V	60_P	3.101	1.00
19_V	55_V	2.481	1.00
10_H	64_A	2.415	1.00
17_T	57_H	2.396	1.00
28_W	47_F	2.286	1.00
21_Y	55_V	2.256	1.00
24_G	54_D	2.027	1.00
22_E	56_V	1.966	1.00
38_G	41_P	1.893	1.00
3_P	16_T	1.814	1.00
31_C	47_F	1.726	1.00
13_Q	61_N	1.717	1.00
18_R	63_G	1.660	1.00
7_T	14_E	1.611	1.00
18_R	58_Y	1.597	1.00
44_L	48_C	1.548	1.00
20_E	58_Y	1.540	1.00
41_P	44_L	1.515	1.00
5_Q	14_E	1.459	1.00
56_V	65_V	1.449	1.00
56_V	68_T	1.358	1.00
23_P	27_T	1.341	1.00
59_C	62_C	1.341	1.00
7_T	12_G	1.323	1.00
58_Y	65_V	1.304	1.00
24_G	27_T	1.256	1.00
23_P	53_K	1.246	1.00
28_W	31_C	1.181	1.00
21_Y	53_K	1.167	1.00
34_L	39_C	1.149	1.00
27_T	52_C	1.135	1.00
26_L	30_L	1.104	1.00
27_T	31_C	1.086	1.00
4_V	67_G	1.085	1.00
6_V	15_V	1.081	1.00
50_D	53_K	1.072	1.00
46_P	49_I	0.965	1.00
25_T	29_L	0.962	1.00
29_L	33_L	0.951	1.00
8_C	11_C	0.942	1.00
43_C	46_P	0.924	1.00
65_V	68_T	0.907	1.00
28_W	32_L	0.896	0.99
26_L	29_L	0.801	0.99
39_C	42_C	0.798	0.99
11_C	62_C	0.785	0.99
26_L	69_Y	0.783	0.99
19_V	57_H	0.782	0.99
42_C	45_I	0.776	0.99
40_L	44_L	0.774	0.98
9_P	12_G	0.774	0.98
15_V	57_H	0.765	0.98
6_V	66_L	0.758	0.98
31_C	35_C	0.744	0.98
27_T	53_K	0.742	0.98
57_H	67_G	0.733	0.98
4_V	7_T	0.718	0.98
17_T	66_L	0.713	0.97
21_Y	50_D	0.708	0.97
42_C	46_P	0.700	0.97
9_P	66_L	0.696	0.97
35_C	39_C	0.692	0.97
16_T	60_P	0.687	0.97
32_L	36_L	0.684	0.97
5_Q	16_T	0.676	0.96
14_E	21_Y	0.661	0.96
8_C	59_C	0.659	0.96
34_L	40_L	0.658	0.96
20_E	56_V	0.650	0.96
27_T	47_F	0.648	0.95
15_V	61_N	0.643	0.95
11_C	59_C	0.639	0.95
15_V	66_L	0.638	0.95
27_T	46_P	0.630	0.95
8_C	62_C	0.626	0.95
46_P	50_D	0.617	0.94
54_D	68_T	0.602	0.93
5_Q	12_G	0.594	0.93
58_Y	63_G	0.591	0.93
58_Y	66_L	0.590	0.93
38_G	42_C	0.588	0.93
55_V	69_Y	0.587	0.93
34_L	38_G	0.586	0.92
7_T	10_H	0.582	0.92
35_C	38_G	0.582	0.92
23_P	31_C	0.575	0.92
18_R	60_P	0.563	0.91
21_Y	56_V	0.556	0.90
13_Q	18_R	0.548	0.90
31_C	43_C	0.547	0.90
37_F	40_L	0.541	0.89
7_T	68_T	0.536	0.89
16_T	20_E	0.536	0.89
2_E	20_E	0.536	0.89
34_L	44_L	0.533	0.88
42_C	49_I	0.530	0.88
30_L	46_P	0.527	0.88
4_V	69_Y	0.524	0.88
2_E	68_T	0.524	0.88
33_L	38_G	0.521	0.87
38_G	48_C	0.509	0.86
22_E	37_F	0.500	0.85

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
4cgyA	1	0	42	0.784	Contact Map
2jrpA	1	0.8857	35.6	0.792	Contact Map
2gaiA	1	0	32.8	0.796	Contact Map
3w0fA	1	0.4571	26.5	0.806	Contact Map
1k3xA	1	0.4714	19.8	0.817	Contact Map
1k82A	1	0.4714	19.3	0.818	Contact Map
2kdxA	1	0.5	17.6	0.821	Contact Map
1gh9A	1	0.4857	16.1	0.824	Contact Map
3u6pA	1	0.4714	16	0.824	Contact Map
1twfL	1	0.4286	13.4	0.83	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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