OPENSEQ.org - YDCZ - ECOLI GREMLIN

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YDCZ - Inner membrane protein YdcZ

UniProt:	P76111	Sequence MNQSLTLAFLIAAGIGLVVQNTLMVRITQTSSTILIAMLLNSLVGIVLFVSILWFKQGMAGFGELVSSVRWWTLIPGLLGSFFVFASISGYQNVGAATTIAVLVASQLIGGLMLDIFRSHGVPLRALFGPICGAILLVVGAWLVARRSF	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13769
Length:	149 (144)
Sequences:	836
Seq/Len:	5.81

YDCZ
Paralog alert: 0.38 [within 20: 0.26] - 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
39_L	46_I	2.129	1.00
112_L	134_A	2.031	1.00
38_M	81_S	1.945	1.00
20_Q	41_N	1.833	1.00
25_V	88_I	1.827	1.00
135_I	139_V	1.819	1.00
26_R	29_Q	1.796	1.00
75_I	78_L	1.765	1.00
81_S	84_V	1.631	1.00
38_M	42_S	1.614	0.99
136_L	143_L	1.601	0.99
85_F	89_S	1.591	0.99
17_L	107_Q	1.562	0.99
131_I	135_I	1.559	0.99
52_I	56_K	1.468	0.99
87_S	99_T	1.45	0.99
27_I	76_P	1.438	0.98
109_I	112_L	1.354	0.98
87_S	103_L	1.348	0.97
51_S	55_F	1.339	0.97
113_M	134_A	1.314	0.97
100_I	104_V	1.313	0.97
31_S	40_L	1.311	0.97
10_L	90_G	1.305	0.97
91_Y	94_V	1.305	0.97
102_V	113_M	1.296	0.97
133_G	140_G	1.294	0.96
28_T	71_W	1.293	0.96
100_I	140_G	1.285	0.96
127_L	135_I	1.271	0.96
83_F	103_L	1.266	0.96
38_M	41_N	1.26	0.96
41_N	80_G	1.258	0.96
42_S	45_G	1.238	0.95
114_L	119_S	1.227	0.95
92_Q	106_S	1.226	0.95
116_I	130_P	1.209	0.94
105_A	138_V	1.209	0.94
136_L	139_V	1.192	0.94
97_A	104_V	1.188	0.94
130_P	134_A	1.186	0.94
47_V	56_K	1.175	0.93
13_A	86_A	1.165	0.93
39_L	43_L	1.162	0.93
18_V	22_T	1.157	0.92
68_S	73_T	1.135	0.91
28_T	31_S	1.131	0.91
21_N	91_Y	1.106	0.90
18_V	91_Y	1.105	0.90
124_L	131_I	1.09	0.89
132_C	138_V	1.084	0.89
132_C	136_L	1.083	0.89
8_A	49_F	1.08	0.88
128_F	135_I	1.078	0.88
17_L	46_I	1.075	0.88
20_Q	24_M	1.072	0.88
32_S	36_I	1.071	0.88
17_L	83_F	1.066	0.88
68_S	71_W	1.057	0.87
41_N	49_F	1.049	0.86
8_A	12_A	1.037	0.86
61_G	64_E	1.035	0.85
47_V	51_S	1.031	0.85
35_L	89_S	1.028	0.85
130_P	141_A	1.028	0.85
23_L	42_S	1.027	0.85
16_G	79_L	1.025	0.85
70_R	73_T	1.023	0.85
21_N	83_F	1.021	0.84
18_V	76_P	1.02	0.84
22_T	122_V	1.016	0.84
127_L	130_P	1.013	0.84
38_M	85_F	1.007	0.83
21_N	42_S	1.005	0.83
128_F	131_I	1	0.83

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
2i68A	2	0.7047	90.5	0.857	Contact Map	0.009
3b5dA	2	0.7047	82.5	0.874	Contact Map	0.089
3kcuA	5	0.906	4.3	0.94	Contact Map	0.248
3wdoA	1	0.6376	4.3	0.94	Contact Map	0.228
3zbiC	14	0.255	3.4	0.943	Contact Map	0
3klyA	5	0.9396	3.1	0.944	Contact Map	0.278
3tdsE	5	0.8926	2.6	0.946	Contact Map	0.223
1u7gA	1	0.8523	2.6	0.946	Contact Map	0.27
4ldsA	2	0.6174	2.5	0.947	Contact Map	0.329
4apsA	2	0.5772	2	0.949	Contact Map	0.183

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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