CbiZ - PFAM28P - GREMLIN Contacts

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CbiZ - Adenosylcobinamide amidohydrolase

PFAM:	PF01955	Sequences: RFPEPLRVLSSAVLGGGLREARAVLNHQVPEGYDRDDPEAYLAELAAELGLPPGDTVGLLTAADMENAAVATESFGDLTVTAVVTAGVESNAVRAGDDPGAPPRPGTINIIVLVNAPLTDAALVNAVITATEAKTAALQDLGVRSRYSGGATGTGTDAVVVAAPPRGPPPLTYAGPHTKLGELIGRAVREAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	192 (187)
Sequences:	3867 (2736)
Seq/√Len:	200.1
META:	0.787

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_A	184_I	4.055	1.00
108_I	138_L	3.588	1.00
84_V	191_A	3.401	1.00
9_L	124_V	2.838	1.00
7_R	120_D	2.749	1.00
112_V	184_I	2.709	1.00
73_E	190_E	2.502	1.00
140_D	189_R	2.483	1.00
84_V	110_I	2.384	1.00
91_N	155_G	2.347	1.00
123_L	163_A	2.308	1.00
68_A	83_V	2.296	1.00
82_A	112_V	2.280	1.00
73_E	186_R	2.271	1.00
70_V	81_T	2.183	1.00
28_Q	63_A	2.059	1.00
24_V	111_I	2.047	1.00
112_V	130_A	2.029	1.00
9_L	18_L	2.014	1.00
155_G	177_H	2.012	1.00
72_T	81_T	1.994	1.00
124_V	127_V	1.943	1.00
22_R	55_D	1.936	1.00
135_T	139_Q	1.929	1.00
130_A	159_V	1.912	1.00
82_A	187_A	1.892	1.00
41_Y	45_L	1.812	1.00
21_A	57_V	1.738	1.00
74_S	79_T	1.734	1.00
27_H	45_L	1.727	1.00
59_L	160_V	1.717	1.00
71_A	190_E	1.674	1.00
65_M	68_A	1.638	1.00
117_P	164_P	1.575	1.00
128_I	131_T	1.570	1.00
7_R	20_E	1.565	1.00
33_Y	41_Y	1.532	1.00
28_Q	65_M	1.522	1.00
127_V	159_V	1.516	1.00
42_L	58_G	1.483	1.00
74_S	77_D	1.457	1.00
97_D	145_S	1.453	1.00
93_V	176_P	1.451	1.00
8_V	21_A	1.439	1.00
11_S	124_V	1.414	1.00
126_A	161_V	1.404	1.00
136_A	152_T	1.401	1.00
24_V	162_A	1.386	1.00
25_L	58_G	1.386	1.00
116_A	171_L	1.377	1.00
131_T	159_V	1.372	1.00
59_L	158_A	1.366	1.00
127_V	131_T	1.359	1.00
18_L	120_D	1.358	1.00
131_T	135_T	1.350	1.00
38_P	42_L	1.308	1.00
126_A	174_A	1.244	1.00
70_V	83_V	1.240	1.00
45_L	49_L	1.238	1.00
110_I	192_V	1.233	1.00
133_A	137_A	1.223	1.00
129_T	176_P	1.212	1.00
95_A	129_T	1.203	1.00
93_V	155_G	1.200	1.00
180_L	183_L	1.198	1.00
18_L	123_L	1.191	1.00
97_D	148_S	1.190	1.00
39_E	172_T	1.180	1.00
4_E	166_R	1.178	1.00
145_S	148_S	1.171	1.00
51_L	56_T	1.170	1.00
179_K	183_L	1.164	1.00
123_L	161_V	1.161	1.00
114_V	180_L	1.157	1.00
40_A	43_A	1.149	1.00
92_A	151_A	1.134	1.00
182_E	186_R	1.130	1.00
94_R	139_Q	1.124	1.00
57_V	160_V	1.112	1.00
45_L	48_E	1.101	1.00
8_V	162_A	1.099	1.00
6_L	113_L	1.098	1.00
78_L	183_L	1.087	1.00
59_L	111_I	1.080	1.00
15_G	19_R	1.071	1.00
72_T	79_T	1.067	1.00
95_A	185_G	1.059	1.00
132_E	176_P	1.052	1.00
133_A	188_V	1.045	1.00
44_E	48_E	1.029	1.00
14_L	42_L	1.028	1.00
42_L	46_A	1.018	1.00
136_A	189_R	1.017	1.00
130_A	188_V	1.004	1.00
64_D	67_N	0.995	1.00
38_P	41_Y	0.990	1.00
37_D	40_A	0.984	1.00
5_P	22_R	0.984	1.00
119_T	122_A	0.979	1.00
92_A	143_V	0.978	1.00
118_L	122_A	0.971	0.99
94_R	150_G	0.968	0.99
137_A	189_R	0.963	0.99
88_V	92_A	0.953	0.99
6_L	164_P	0.953	0.99
136_A	140_D	0.952	0.99
125_N	129_T	0.951	0.99
26_N	59_L	0.950	0.99
94_R	140_D	0.946	0.99
23_A	55_D	0.943	0.99
40_A	44_E	0.942	0.99
8_V	57_V	0.941	0.99
175_G	178_T	0.931	0.99
143_V	151_A	0.927	0.99
116_A	164_P	0.921	0.99
174_A	184_I	0.920	0.99
24_V	160_V	0.919	0.99
29_V	60_L	0.919	0.99
127_V	130_A	0.918	0.99
31_E	62_A	0.908	0.99
183_L	187_A	0.905	0.99
43_A	47_A	0.901	0.99
7_R	18_L	0.899	0.99
88_V	138_L	0.893	0.99
171_L	180_L	0.891	0.99
46_A	56_T	0.883	0.99
20_E	165_P	0.880	0.99
7_R	117_P	0.874	0.99
6_L	162_A	0.871	0.99
138_L	143_V	0.869	0.99
8_V	24_V	0.861	0.99
92_A	154_T	0.860	0.99
125_N	128_I	0.857	0.99
38_P	46_A	0.855	0.99
135_T	152_T	0.836	0.98
93_V	147_Y	0.829	0.98
38_P	60_L	0.811	0.98
5_P	20_E	0.809	0.98
107_T	156_T	0.808	0.98
42_L	60_L	0.805	0.98
179_K	182_E	0.803	0.98
137_A	141_L	0.799	0.98
80_V	183_L	0.797	0.98
62_A	107_T	0.792	0.98
41_Y	46_A	0.785	0.98
26_N	111_I	0.782	0.98
28_Q	31_E	0.781	0.98
10_S	57_V	0.776	0.98
95_A	135_T	0.770	0.97
186_R	190_E	0.769	0.97
98_D	102_P	0.765	0.97
117_P	169_P	0.762	0.97
110_I	130_A	0.756	0.97
136_A	139_Q	0.755	0.97
175_G	181_G	0.751	0.97
79_T	115_N	0.749	0.97
118_L	174_A	0.747	0.97
132_E	153_G	0.739	0.97
12_A	57_V	0.736	0.97
30_P	33_Y	0.735	0.97
130_A	184_I	0.730	0.96
25_L	46_A	0.729	0.96
82_A	188_V	0.729	0.96
23_A	51_L	0.728	0.96
53_P	56_T	0.727	0.96
73_E	187_A	0.727	0.96
98_D	101_A	0.727	0.96
185_G	189_R	0.727	0.96
130_A	161_V	0.723	0.96
80_V	114_V	0.715	0.96
85_T	107_T	0.712	0.96
39_E	43_A	0.712	0.96
94_R	189_R	0.712	0.96
29_V	33_Y	0.710	0.96
111_I	162_A	0.709	0.96
12_A	16_G	0.701	0.95
88_V	143_V	0.695	0.95
44_E	47_A	0.691	0.95
80_V	180_L	0.678	0.95
155_G	176_P	0.677	0.95
84_V	192_V	0.674	0.94
75_F	179_K	0.673	0.94
137_A	192_V	0.673	0.94
85_T	109_N	0.672	0.94
60_L	158_A	0.671	0.94
26_N	156_T	0.667	0.94
11_S	158_A	0.664	0.94
76_G	179_K	0.657	0.94
9_L	127_V	0.656	0.94
13_V	158_A	0.656	0.94
78_L	116_A	0.655	0.94
100_G	105_P	0.653	0.93
81_T	113_L	0.652	0.93
118_L	180_L	0.647	0.93
69_A	83_V	0.646	0.93
99_P	103_P	0.641	0.93
90_S	146_R	0.639	0.93
29_V	158_A	0.637	0.93
100_G	103_P	0.637	0.93
134_K	158_A	0.633	0.92
97_D	147_Y	0.632	0.92
125_N	174_A	0.632	0.92
114_V	184_I	0.629	0.92
11_S	128_I	0.628	0.92
119_T	172_T	0.627	0.92
98_D	104_R	0.624	0.92
8_V	160_V	0.623	0.92
31_E	34_D	0.622	0.92
69_A	190_E	0.619	0.92
38_P	173_Y	0.615	0.91
95_A	176_P	0.614	0.91
114_V	118_L	0.614	0.91
115_N	164_P	0.609	0.91
113_L	162_A	0.607	0.91
109_N	156_T	0.605	0.91
73_E	183_L	0.605	0.91
94_R	136_A	0.603	0.90
46_A	49_L	0.598	0.90
120_D	123_L	0.598	0.90
147_Y	150_G	0.597	0.90
132_E	152_T	0.595	0.90
12_A	59_L	0.595	0.90
11_S	127_V	0.591	0.90
166_R	169_P	0.583	0.89
91_N	156_T	0.580	0.89
177_H	182_E	0.578	0.88
110_I	188_V	0.578	0.88
114_V	164_P	0.577	0.88
46_A	58_G	0.577	0.88
27_H	60_L	0.576	0.88
47_A	117_P	0.575	0.88
114_V	174_A	0.573	0.88
42_L	45_L	0.572	0.88
117_P	163_A	0.570	0.88
63_A	69_A	0.568	0.88
75_F	78_L	0.565	0.87
33_Y	38_P	0.565	0.87
42_L	48_E	0.565	0.87
128_I	156_T	0.565	0.87
118_L	126_A	0.561	0.87
101_A	105_P	0.561	0.87
31_E	35_R	0.561	0.87
25_L	56_T	0.559	0.87
82_A	110_I	0.559	0.87
173_Y	178_T	0.559	0.87
80_V	187_A	0.556	0.87
40_A	50_G	0.554	0.86
96_G	152_T	0.552	0.86
113_L	121_A	0.550	0.86
125_N	177_H	0.546	0.86
145_S	151_A	0.546	0.86
143_V	154_T	0.546	0.86
117_P	166_R	0.545	0.85
174_A	178_T	0.544	0.85
43_A	53_P	0.543	0.85
29_V	173_Y	0.540	0.85
73_E	80_V	0.539	0.85
63_A	68_A	0.538	0.85
92_A	155_G	0.537	0.85
158_A	173_Y	0.535	0.84
27_H	41_Y	0.529	0.84
72_T	100_G	0.529	0.84
26_N	65_M	0.526	0.83
35_R	41_Y	0.525	0.83
153_G	157_D	0.525	0.83
43_A	54_G	0.525	0.83
33_Y	62_A	0.523	0.83
13_V	39_E	0.520	0.83
47_A	53_P	0.516	0.82
41_Y	44_E	0.514	0.82
79_T	114_V	0.513	0.82
101_A	104_R	0.512	0.82
14_L	43_A	0.511	0.82
30_P	62_A	0.511	0.82
83_V	111_I	0.507	0.81
24_V	57_V	0.506	0.81
93_V	156_T	0.504	0.81
36_D	47_A	0.504	0.81
92_A	96_G	0.503	0.81
88_V	154_T	0.500	0.80

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
2eo2A	1	0.3698	19.4	0.945	Contact Map
3frrA	1	0.3177	9	0.953	Contact Map
2lekA	1	0.3646	6.1	0.956	Contact Map
4r84A	1	0.3177	5.7	0.957	Contact Map
1f0zA	1	0.3281	5.5	0.957	Contact Map
4ffjA	2	0.3594	5.3	0.958	Contact Map
2cu3A	2	0.3177	5.1	0.958	Contact Map
2k5pA	1	0.375	3.5	0.961	Contact Map
4wlrB	1	0.25	3.2	0.962	Contact Map
3mioA	2	0.349	3.1	0.962	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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