PSCyt3 - PFAM28P - GREMLIN Contacts

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PSCyt3 - Protein of unknown function (DUF1588)

PFAM:	PF07627	Sequences: RGGLLTQGSVLTVTSYPTRTSPVLRGKWVLENLLGTPPPPPPPNVPALPPDAAGALTLRERLEQHRANPACASCHARMDPLGFALENFDAIGRWRTTD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (97)
Sequences:	45340 (21385)
Seq/√Len:	2171.3
META:	0.988

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_N	94_W	4.318	1.00
89_D	93_R	2.780	1.00
30_L	36_T	2.590	1.00
27_K	31_E	2.397	1.00
16_Y	24_L	2.361	1.00
2_G	7_Q	2.251	1.00
27_K	78_M	2.047	1.00
72_A	76_A	1.984	1.00
60_E	63_E	1.972	1.00
64_Q	67_A	1.951	1.00
70_A	73_S	1.823	1.00
81_L	84_A	1.747	1.00
87_N	96_T	1.729	1.00
56_L	64_Q	1.675	1.00
31_E	37_P	1.655	1.00
2_G	6_T	1.650	1.00
21_S	24_L	1.616	1.00
57_T	60_E	1.592	1.00
63_E	66_R	1.581	1.00
64_Q	68_N	1.540	1.00
20_T	86_E	1.491	1.00
10_V	28_W	1.478	1.00
63_E	67_A	1.414	1.00
69_P	72_A	1.356	1.00
10_V	14_T	1.339	1.00
49_P	52_A	1.307	1.00
30_L	81_L	1.305	1.00
56_L	60_E	1.293	1.00
16_Y	19_R	1.290	1.00
52_A	55_A	1.267	1.00
65_H	79_D	1.263	1.00
22_P	58_L	1.238	1.00
58_L	62_L	1.234	1.00
30_L	38_P	1.214	1.00
29_V	81_L	1.213	1.00
66_R	79_D	1.202	1.00
59_R	63_E	1.201	1.00
86_E	95_R	1.192	1.00
16_Y	21_S	1.192	1.00
42_P	45_V	1.179	1.00
78_M	81_L	1.172	1.00
25_R	85_L	1.091	1.00
51_D	54_G	1.083	1.00
36_T	77_R	1.071	1.00
59_R	83_F	1.070	1.00
22_P	83_F	1.063	1.00
28_W	32_N	1.044	1.00
77_R	80_P	1.043	1.00
51_D	55_A	1.042	1.00
20_T	58_L	1.034	1.00
58_L	61_R	1.026	1.00
23_V	62_L	1.007	1.00
23_V	79_D	0.984	1.00
66_R	76_A	0.983	1.00
30_L	77_R	0.981	1.00
73_S	76_A	0.971	1.00
35_G	77_R	0.949	1.00
4_L	10_V	0.939	1.00
31_E	38_P	0.936	1.00
53_A	56_L	0.928	1.00
7_Q	10_V	0.916	1.00
62_L	66_R	0.913	1.00
4_L	7_Q	0.913	1.00
46_P	49_P	0.897	1.00
28_W	33_L	0.896	1.00
89_D	95_R	0.886	1.00
67_A	72_A	0.874	1.00
38_P	41_P	0.865	1.00
26_G	82_G	0.862	1.00
71_C	74_C	0.854	1.00
22_P	62_L	0.851	1.00
49_P	54_G	0.817	1.00
11_L	14_T	0.810	1.00
26_G	78_M	0.804	1.00
8_G	12_T	0.802	1.00
47_A	50_P	0.796	1.00
88_F	94_W	0.794	1.00
29_V	33_L	0.794	1.00
5_L	33_L	0.793	1.00
19_R	58_L	0.791	1.00
19_R	61_R	0.789	1.00
27_K	38_P	0.789	1.00
79_D	83_F	0.784	1.00
62_L	83_F	0.780	1.00
52_A	56_L	0.774	1.00
62_L	65_H	0.774	1.00
24_L	27_K	0.758	1.00
66_R	72_A	0.751	1.00
49_P	53_A	0.748	1.00
44_N	70_A	0.741	1.00
90_A	93_R	0.736	1.00
68_N	72_A	0.728	1.00
71_C	75_H	0.728	1.00
12_T	15_S	0.723	1.00
38_P	78_M	0.720	1.00
67_A	70_A	0.710	1.00
37_P	40_P	0.710	1.00
61_R	65_H	0.709	1.00
40_P	43_P	0.708	1.00
84_A	87_N	0.687	1.00
50_P	53_A	0.684	1.00
7_Q	12_T	0.663	1.00
27_K	32_N	0.656	1.00
13_V	32_N	0.649	1.00
48_L	52_A	0.647	1.00
3_G	75_H	0.643	1.00
93_R	97_T	0.642	1.00
50_P	54_G	0.638	1.00
23_V	78_M	0.636	1.00
63_E	83_F	0.634	1.00
49_P	64_Q	0.630	1.00
23_V	27_K	0.628	1.00
6_T	88_F	0.626	1.00
14_T	28_W	0.620	1.00
66_R	83_F	0.615	1.00
50_P	55_A	0.607	1.00
6_T	11_L	0.604	1.00
11_L	88_F	0.602	1.00
14_T	24_L	0.599	1.00
30_L	34_L	0.598	1.00
15_S	20_T	0.596	1.00
41_P	45_V	0.589	1.00
77_R	81_L	0.583	1.00
50_P	61_R	0.583	1.00
73_S	77_R	0.582	1.00
3_G	74_C	0.577	1.00
2_G	8_G	0.574	1.00
5_L	29_V	0.571	1.00
12_T	91_I	0.569	1.00
65_H	68_N	0.567	1.00
47_A	52_A	0.566	1.00
7_Q	17_P	0.565	1.00
56_L	61_R	0.555	1.00
20_T	95_R	0.553	1.00
29_V	32_N	0.548	1.00
10_V	13_V	0.542	1.00
13_V	17_P	0.535	1.00
39_P	45_V	0.529	1.00
51_D	64_Q	0.524	1.00
11_L	15_S	0.514	1.00
27_K	40_P	0.513	1.00
69_P	76_A	0.512	1.00
39_P	42_P	0.512	1.00
60_E	64_Q	0.503	1.00
24_L	31_E	0.502	1.00
38_P	77_R	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
3m97X	1	0.5918	27.9	0.891	Contact Map
4wqdA	1	0.6224	22.2	0.896	Contact Map
2zxyA	2	0.3878	20.7	0.898	Contact Map
3u99A	1	0.3878	19.8	0.899	Contact Map
4xxlA	1	0.4286	19.8	0.899	Contact Map
1iqcA	2	0.6327	18.8	0.9	Contact Map
3cp5A	1	0.5714	17.5	0.901	Contact Map
1cchA	1	0.3776	16	0.903	Contact Map
3mk7B	1	0.8061	15.1	0.904	Contact Map
1i8oA	2	0.3776	12.9	0.907	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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