Q9HQH3 - HALSA - GREMLIN Contacts

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Q9HQH3 - Protoporphyrinogen oxidase

UniProt:	Q9HQH3	Sequences: MTDLADRRGAGADVYQPAEDTHLLATAAVGELDDPYARVLDVGTGSGYVAATVRDETGADVVGTDLNPFAVRQAADRGVPVVRGDLVAPFRDDAFDAVVFNPPYLPREDDTRDDWMDVALSGGDTGRRVIESFFDAVGRVLAPDGVVIMLVSTLTGVDEVAAYAGDRGFSAAAISEESFPFETLTVLKFRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	191 (182)
Sequences:	7210 (5251)
Seq/√Len:	389.2

ECOLI - PRMC PRMB TRMN6 RSMC
BACSU - PRMC YABB YBXB
HALSA - Q9HQH3
SULSO - Q7LXK7 Q980C4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_G	76_D	3.769	1.00
50_A	63_G	2.871	1.00
13_D	69_F	2.447	1.00
68_P	83_R	2.446	1.00
66_L	118_V	2.370	1.00
62_V	82_V	2.360	1.00
84_G	89_P	2.355	1.00
50_A	61_V	2.353	1.00
96_D	142_A	2.326	1.00
176_E	182_E	2.284	1.00
40_L	95_F	2.201	1.00
4_L	56_E	2.133	1.00
6_D	55_D	2.129	1.00
62_V	95_F	2.095	1.00
107_R	121_S	2.092	1.00
134_F	164_A	2.080	1.00
137_V	147_V	2.030	1.00
78_G	81_V	2.020	1.00
123_G	128_R	1.974	1.00
44_T	74_A	1.926	1.00
27_A	175_S	1.915	1.00
11_G	73_Q	1.890	1.00
141_L	145_G	1.814	1.00
38_R	60_D	1.803	1.00
149_M	164_A	1.797	1.00
8_R	52_T	1.729	1.00
117_D	121_S	1.717	1.00
86_L	129_V	1.653	1.00
28_A	148_I	1.649	1.00
125_T	131_E	1.647	1.00
6_D	56_E	1.634	1.00
54_R	61_V	1.616	1.00
157_V	174_I	1.613	1.00
20_D	23_L	1.605	1.00
53_V	99_V	1.600	1.00
87_V	140_V	1.579	1.00
71_V	81_V	1.564	1.00
29_V	57_T	1.563	1.00
85_D	132_S	1.552	1.00
31_E	148_I	1.544	1.00
51_A	78_G	1.510	1.00
6_D	52_T	1.510	1.00
4_L	26_T	1.482	1.00
14_V	46_S	1.471	1.00
31_E	146_V	1.455	1.00
157_V	182_E	1.418	1.00
132_S	136_A	1.411	1.00
24_L	148_I	1.384	1.00
71_V	83_R	1.375	1.00
44_T	50_A	1.363	1.00
27_A	30_G	1.347	1.00
154_L	181_F	1.333	1.00
34_D	37_A	1.323	1.00
28_A	99_V	1.297	1.00
162_A	166_D	1.291	1.00
85_D	88_A	1.278	1.00
23_L	184_L	1.276	1.00
106_P	155_T	1.275	1.00
110_D	113_D	1.233	1.00
94_A	142_A	1.213	1.00
21_T	49_V	1.201	1.00
151_V	185_T	1.201	1.00
8_R	51_A	1.197	1.00
161_A	165_G	1.192	1.00
28_A	97_A	1.192	1.00
106_P	109_D	1.187	1.00
23_L	178_S	1.186	1.00
161_A	174_I	1.181	1.00
130_I	149_M	1.175	1.00
64_T	84_G	1.172	1.00
100_F	149_M	1.171	1.00
25_A	52_T	1.168	1.00
60_D	80_P	1.167	1.00
29_V	56_E	1.159	1.00
39_V	53_V	1.154	1.00
67_N	118_V	1.153	1.00
124_D	131_E	1.152	1.00
74_A	81_V	1.149	1.00
136_A	139_R	1.147	1.00
67_N	70_A	1.145	1.00
63_G	81_V	1.142	1.00
42_V	133_F	1.140	1.00
63_G	79_V	1.129	1.00
87_V	136_A	1.124	1.00
38_R	62_V	1.112	1.00
64_T	90_F	1.108	1.00
38_R	93_D	1.105	1.00
134_F	163_Y	1.094	1.00
153_T	156_G	1.091	1.00
127_R	159_E	1.089	1.00
38_R	95_F	1.080	1.00
86_L	132_S	1.070	1.00
27_A	184_L	1.069	1.00
95_F	98_V	1.067	1.00
65_D	71_V	1.062	1.00
4_L	52_T	1.059	1.00
122_G	130_I	1.057	1.00
41_D	50_A	1.054	1.00
174_I	185_T	1.053	1.00
8_R	48_Y	1.039	1.00
62_V	80_P	1.035	1.00
39_V	61_V	1.011	1.00
49_V	99_V	1.003	1.00
50_A	54_R	1.003	1.00
135_D	167_R	0.991	1.00
10_A	73_Q	0.991	1.00
151_V	157_V	0.986	1.00
137_V	169_F	0.981	1.00
42_V	86_L	0.981	1.00
13_D	73_Q	0.969	1.00
16_Q	115_W	0.967	1.00
10_A	14_V	0.964	1.00
11_G	76_D	0.950	1.00
38_R	142_A	0.943	1.00
127_R	131_E	0.939	1.00
39_V	59_A	0.938	1.00
80_P	93_D	0.937	1.00
32_L	97_A	0.926	1.00
122_G	126_G	0.918	1.00
127_R	163_Y	0.917	1.00
175_S	184_L	0.916	1.00
122_G	129_V	0.909	1.00
5_A	55_D	0.900	1.00
157_V	161_A	0.900	1.00
44_T	65_D	0.899	1.00
109_D	155_T	0.893	1.00
151_V	160_V	0.882	1.00
100_F	133_F	0.877	1.00
50_A	79_V	0.873	1.00
174_I	182_E	0.867	1.00
52_T	56_E	0.864	1.00
41_D	44_T	0.861	1.00
98_V	140_V	0.845	1.00
130_I	160_V	0.843	1.00
44_T	63_G	0.842	1.00
27_A	31_E	0.841	1.00
135_D	163_Y	0.841	1.00
176_E	180_P	0.832	1.00
164_A	185_T	0.831	1.00
107_R	122_G	0.829	1.00
91_R	140_V	0.825	1.00
75_A	78_G	0.825	1.00
25_A	49_V	0.817	1.00
162_A	165_G	0.809	1.00
62_V	93_D	0.806	1.00
122_G	128_R	0.802	1.00
130_I	151_V	0.798	1.00
14_V	73_Q	0.797	1.00
5_A	56_E	0.790	1.00
133_F	147_V	0.777	1.00
54_R	78_G	0.774	1.00
39_V	97_A	0.772	1.00
20_D	184_L	0.771	1.00
37_A	59_A	0.769	1.00
28_A	32_L	0.765	1.00
51_A	55_D	0.762	1.00
105_L	120_L	0.761	1.00
31_E	173_A	0.758	1.00
39_V	57_T	0.750	1.00
43_G	129_V	0.748	1.00
159_E	162_A	0.744	1.00
92_D	139_R	0.741	1.00
25_A	29_V	0.735	1.00
158_D	162_A	0.735	1.00
54_R	79_V	0.734	1.00
30_G	175_S	0.733	1.00
36_Y	60_D	0.729	1.00
132_S	135_D	0.726	1.00
106_P	122_G	0.726	1.00
37_A	57_T	0.724	1.00
27_A	148_I	0.717	1.00
151_V	174_I	0.712	1.00
53_V	57_T	0.694	0.99
125_T	128_R	0.693	0.99
23_L	27_A	0.692	0.99
82_V	93_D	0.690	0.99
157_V	181_F	0.690	0.99
135_D	138_G	0.687	0.99
42_V	87_V	0.687	0.99
64_T	82_V	0.685	0.99
42_V	64_T	0.684	0.99
156_G	160_V	0.680	0.99
32_L	57_T	0.679	0.99
26_T	30_G	0.674	0.99
131_E	163_Y	0.672	0.99
34_D	58_G	0.669	0.99
134_F	149_M	0.665	0.99
102_P	160_V	0.663	0.99
97_A	148_I	0.662	0.99
69_F	72_R	0.662	0.99
61_V	79_V	0.659	0.99
37_A	96_D	0.651	0.99
5_A	8_R	0.650	0.99
11_G	69_F	0.649	0.99
71_V	75_A	0.647	0.99
134_F	167_R	0.644	0.99
20_D	179_F	0.644	0.99
107_R	123_G	0.642	0.99
52_T	55_D	0.639	0.99
161_A	172_A	0.639	0.99
128_R	131_E	0.637	0.99
68_P	72_R	0.637	0.99
43_G	86_L	0.632	0.99
129_V	132_S	0.631	0.99
19_E	22_H	0.621	0.99
159_E	163_Y	0.620	0.99
33_D	37_A	0.619	0.99
84_G	90_F	0.614	0.99
107_R	117_D	0.605	0.99
111_T	114_D	0.601	0.99
165_G	172_A	0.598	0.99
25_A	53_V	0.596	0.98
24_L	99_V	0.595	0.98
38_R	96_D	0.593	0.98
158_D	161_A	0.591	0.98
16_Q	119_A	0.591	0.98
75_A	81_V	0.587	0.98
40_L	64_T	0.585	0.98
33_D	36_Y	0.584	0.98
131_E	135_D	0.584	0.98
136_A	140_V	0.582	0.98
122_G	125_T	0.581	0.98
149_M	160_V	0.580	0.98
161_A	182_E	0.579	0.98
155_T	181_F	0.578	0.98
106_P	125_T	0.576	0.98
25_A	48_Y	0.575	0.98
138_G	167_R	0.571	0.98
67_N	71_V	0.571	0.98
44_T	81_V	0.570	0.98
160_V	163_Y	0.568	0.98
40_L	90_F	0.567	0.98
72_R	75_A	0.566	0.98
40_L	87_V	0.563	0.98
48_Y	52_T	0.561	0.98
51_A	79_V	0.561	0.98
107_R	124_D	0.560	0.98
108_E	124_D	0.559	0.98
23_L	26_T	0.553	0.98
87_V	90_F	0.553	0.98
53_V	59_A	0.552	0.98
137_V	141_L	0.550	0.97
138_G	169_F	0.548	0.97
148_I	184_L	0.547	0.97
38_R	94_A	0.547	0.97
32_L	59_A	0.543	0.97
43_G	100_F	0.542	0.97
177_E	183_T	0.542	0.97
109_D	153_T	0.541	0.97
9_G	73_Q	0.538	0.97
97_A	146_V	0.538	0.97
158_D	182_E	0.537	0.97
133_F	137_V	0.535	0.97
98_V	137_V	0.535	0.97
4_L	29_V	0.534	0.97
82_V	89_P	0.533	0.97
106_P	154_L	0.533	0.97
11_G	14_V	0.532	0.97
130_I	134_F	0.531	0.97
37_A	58_G	0.530	0.97
32_L	37_A	0.530	0.97
87_V	98_V	0.529	0.97
106_P	153_T	0.528	0.97
35_P	58_G	0.524	0.97
160_V	185_T	0.522	0.97
123_G	126_G	0.519	0.96
11_G	72_R	0.517	0.96
36_Y	58_G	0.517	0.96
13_D	116_M	0.515	0.96
105_L	112_R	0.506	0.96
106_P	121_S	0.503	0.96
86_L	90_F	0.503	0.96
28_A	31_E	0.500	0.96

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
2b3tA	1	0.9895	100	0.337	Contact Map
1nv8A	1	0.9529	100	0.348	Contact Map
4dzrA	2	0.7906	100	0.499	Contact Map
3evzA	1	0.8953	100	0.5	Contact Map
3c6kA	2	0.9215	99.9	0.581	Contact Map
3lpmA	2	0.8586	99.9	0.586	Contact Map
3tm4A	1	0.8796	99.9	0.594	Contact Map
4dcmA	1	0.8377	99.9	0.602	Contact Map
3q87B	1	0.8534	99.9	0.603	Contact Map
3dmgA	1	0.8743	99.9	0.608	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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