OPENSEQ.org - PPDD - ECOLI GREMLIN

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PPDD - Prepilin peptidase-dependent protein D

UniProt:	P36647	Sequence MDKQRGFTLIELMVVIGIIAILSAIGIPAYQNYLRKAALTDMLQTFVPYRTAVELCALEHGGLDTCDGGSNGIPSPTTTRYVSAMSVAKGVVSLTGQESLNGLSVVMTPGWDNANGVTGWTRNCNIQSDSALQQACEDVFRFDDAN	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12107
Length:	146 (139)
Sequences:	740
Seq/Len:	5.32

PPDD
Paralog alert: 0.07 [within 20: 0.04] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
41_D	45_T	2.463	1.00
32_N	130_S	2.258	1.00
124_C	136_C	1.956	1.00
56_C	66_C	1.923	1.00
82_V	85_M	1.876	1.00
34_L	37_A	1.809	1.00
2_D	5_R	1.781	1.00
56_C	64_D	1.701	1.00
134_Q	137_E	1.631	0.99
61_G	64_D	1.618	0.99
55_L	59_E	1.597	0.99
92_V	95_T	1.514	0.99
38_A	45_T	1.487	0.99
29_A	33_Y	1.465	0.98
49_Y	73_I	1.441	0.98
40_T	44_Q	1.415	0.98
18_I	21_I	1.356	0.97
36_K	137_E	1.353	0.97
24_A	33_Y	1.35	0.97
133_Q	136_C	1.335	0.97
91_V	108_T	1.331	0.97
47_V	50_R	1.329	0.97
41_D	109_P	1.292	0.96
7_F	11_E	1.287	0.96
13_M	51_T	1.285	0.96
104_S	127_Q	1.283	0.96
8_T	12_L	1.281	0.96
126_I	132_L	1.275	0.95
46_F	94_L	1.266	0.95
69_G	73_I	1.253	0.95
41_D	46_F	1.241	0.94
20_A	29_A	1.234	0.94
29_A	32_N	1.222	0.94
39_L	42_M	1.222	0.94
16_I	23_S	1.202	0.93
6_G	11_E	1.202	0.93
38_A	100_L	1.202	0.93
45_T	94_L	1.2	0.93
12_L	29_A	1.191	0.93
41_D	94_L	1.184	0.92
53_V	90_G	1.18	0.92
35_R	38_A	1.174	0.92
31_Q	38_A	1.154	0.91
48_P	51_T	1.152	0.91
8_T	17_G	1.145	0.91
46_F	105_V	1.141	0.90
38_A	135_A	1.131	0.90
21_I	34_L	1.129	0.90
3_K	20_A	1.126	0.90
41_D	44_Q	1.125	0.90
53_V	120_W	1.121	0.89
31_Q	39_L	1.109	0.89
90_G	108_T	1.107	0.89
34_L	38_A	1.095	0.88
19_I	27_I	1.083	0.87
16_I	24_A	1.077	0.87
30_Y	33_Y	1.076	0.87
104_S	108_T	1.071	0.86
112_D	123_N	1.07	0.86
120_W	124_C	1.063	0.86
57_A	60_H	1.061	0.86
86_S	95_T	1.043	0.84
13_M	24_A	1.043	0.84
16_I	99_S	1.04	0.84
132_L	135_A	1.038	0.84
36_K	55_L	1.036	0.84
38_A	52_A	1.031	0.83
8_T	11_E	1.029	0.83
97_Q	127_Q	1.023	0.83
8_T	14_V	1.021	0.82
103_L	127_Q	1.02	0.82
24_A	29_A	1.017	0.82
9_L	12_L	1.016	0.82
56_C	60_H	1.016	0.82
5_R	128_S	1.013	0.82
42_M	94_L	1.01	0.82
38_A	48_P	1.005	0.81
44_Q	47_V	1.003	0.81
82_V	86_S	1	0.81

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
2hi2A	1	0.9041	99.9	0.392	Contact Map	0.436
3sokA	2	0.863	99.9	0.402	Contact Map	0.4
1oqwA	2	0.863	99.9	0.427	Contact Map	0.392
3jyzA	1	0.7192	99.7	0.564	Contact Map	0.398
1qveA	2	0.7534	99.7	0.578	Contact Map	0.545
1x6zA	1	0.7192	99.7	0.599	Contact Map	0.408
3sojA	2	0.6644	99.5	0.633	Contact Map	0.404
2m7gA	1	0.4178	99.5	0.641	Contact Map	0.271
3g20A	2	0.7329	98	0.791	Contact Map	0.515
2m3kA	1	0.7055	94.4	0.862	Contact Map	0.373

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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