Q9HMH5 - HALSA - GREMLIN Contacts

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Q9HMH5 - Isochorismatase

UniProt:	Q9HMH5	Sequences: MDVDPAHTAVVVVDMQNGFCHPDGSLHAPASEDALAAVTALVSRARDAGARIVYTRDVHPPGQFERTTHYDEFERWGEHVTAGSWDAQLHDKLTVAADDHVVEKHTYDAFYETELDGYLTAHGITELVFCGTLANVCVLHTAGSAGVRDYRPILAADAVGYIEASHKEYTLDHAEWLFGEVADRAAIAFA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	190 (171)
Sequences:	10025 (6963)
Seq/√Len:	532.5

ECOLI - RUTB YECD PNCA YCAC
BACSU - YWOC YAAI PNCA YDDQ YRDC
HALSA - Q9HMH5 Q9HQL7
SULSO - Q97VZ5 Q97YW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
116_D	120_T	3.275	1.00
108_D	144_S	2.796	1.00
126_E	151_R	2.785	1.00
116_D	150_Y	2.771	1.00
56_R	103_E	2.759	1.00
45_A	50_A	2.557	1.00
8_T	126_E	2.510	1.00
38_V	130_C	2.350	1.00
129_F	142_A	2.330	1.00
116_D	148_R	2.319	1.00
126_E	153_I	2.313	1.00
15_M	38_V	2.272	1.00
41_L	155_A	2.235	1.00
164_A	168_E	2.150	1.00
7_H	125_T	2.111	1.00
174_A	179_G	2.046	1.00
114_E	118_Y	2.015	1.00
18_G	86_D	2.005	1.00
9_A	124_I	1.930	1.00
139_L	143_G	1.908	1.00
37_A	158_A	1.907	1.00
17_N	85_W	1.901	1.00
44_R	48_A	1.899	1.00
37_A	40_A	1.814	1.00
145_A	152_P	1.807	1.00
109_A	141_T	1.776	1.00
102_V	118_Y	1.765	1.00
8_T	128_V	1.747	1.00
53_V	118_Y	1.686	1.00
156_A	183_D	1.666	1.00
17_N	91_D	1.662	1.00
134_A	167_K	1.646	1.00
12_V	42_V	1.639	1.00
156_A	181_V	1.636	1.00
20_C	90_H	1.584	1.00
128_V	155_A	1.563	1.00
55_T	109_A	1.548	1.00
100_H	118_Y	1.519	1.00
45_A	128_V	1.516	1.00
39_T	43_S	1.496	1.00
46_R	99_D	1.487	1.00
12_V	130_C	1.470	1.00
51_R	122_H	1.458	1.00
134_A	159_V	1.456	1.00
127_L	145_A	1.438	1.00
139_L	173_H	1.431	1.00
85_W	88_Q	1.396	1.00
161_Y	167_K	1.385	1.00
165_S	168_E	1.371	1.00
39_T	92_K	1.363	1.00
129_F	141_T	1.351	1.00
58_V	87_A	1.341	1.00
135_N	161_Y	1.334	1.00
134_A	171_L	1.331	1.00
30_A	33_D	1.296	1.00
138_V	154_L	1.291	1.00
118_Y	122_H	1.290	1.00
12_V	38_V	1.274	1.00
12_V	15_M	1.271	1.00
11_V	129_F	1.267	1.00
156_A	171_L	1.266	1.00
120_T	150_Y	1.253	1.00
36_A	92_K	1.251	1.00
168_E	172_D	1.250	1.00
37_A	157_D	1.222	1.00
82_A	103_E	1.215	1.00
34_A	38_V	1.214	1.00
154_L	159_V	1.212	1.00
139_L	170_T	1.204	1.00
117_G	121_A	1.201	1.00
56_R	89_L	1.198	1.00
10_V	45_A	1.184	1.00
144_S	148_R	1.180	1.00
43_S	47_D	1.159	1.00
13_V	137_C	1.152	1.00
58_V	103_E	1.135	1.00
128_V	153_I	1.132	1.00
41_L	158_A	1.124	1.00
56_R	101_V	1.120	1.00
17_N	88_Q	1.065	1.00
142_A	154_L	1.064	1.00
96_A	99_D	1.044	1.00
159_V	167_K	1.028	1.00
58_V	82_A	1.008	1.00
165_S	169_Y	1.007	1.00
114_E	117_G	1.003	1.00
89_L	101_V	1.003	1.00
8_T	50_A	0.991	1.00
42_V	46_R	0.986	1.00
142_A	174_A	0.979	1.00
134_A	161_Y	0.974	1.00
9_A	53_V	0.968	1.00
127_L	152_P	0.964	1.00
153_I	180_E	0.955	1.00
140_H	143_G	0.954	1.00
44_R	47_D	0.948	1.00
42_V	54_Y	0.947	1.00
60_P	82_A	0.934	1.00
167_K	171_L	0.926	1.00
171_L	181_V	0.921	1.00
34_A	160_G	0.912	1.00
40_A	44_R	0.909	1.00
153_I	182_A	0.902	1.00
163_E	166_H	0.900	1.00
118_Y	121_A	0.898	1.00
125_T	151_R	0.893	1.00
106_T	149_D	0.888	1.00
165_S	172_D	0.879	1.00
88_Q	94_T	0.878	1.00
14_D	104_K	0.874	1.00
155_A	158_A	0.872	1.00
43_S	96_A	0.868	1.00
78_E	81_T	0.858	1.00
54_Y	95_V	0.852	1.00
111_Y	148_R	0.851	1.00
54_Y	89_L	0.850	1.00
15_M	132_T	0.846	1.00
13_V	129_F	0.846	1.00
39_T	95_V	0.839	1.00
11_V	115_L	0.832	1.00
130_C	158_A	0.831	1.00
109_A	115_L	0.828	1.00
41_L	130_C	0.824	1.00
81_T	84_S	0.817	1.00
119_L	150_Y	0.815	1.00
17_N	21_H	0.813	1.00
151_R	180_E	0.812	1.00
35_L	39_T	0.808	1.00
9_A	119_L	0.802	1.00
155_A	182_A	0.801	1.00
166_H	169_Y	0.791	1.00
144_S	147_V	0.787	1.00
40_A	43_S	0.783	1.00
42_V	52_I	0.780	1.00
17_N	90_H	0.777	1.00
110_F	145_A	0.771	1.00
53_V	122_H	0.768	1.00
33_D	36_A	0.762	1.00
106_T	112_E	0.758	1.00
51_R	124_I	0.757	1.00
172_D	175_E	0.756	1.00
7_H	126_E	0.755	1.00
129_F	138_V	0.754	1.00
84_S	87_A	0.751	1.00
132_T	160_G	0.750	1.00
38_V	158_A	0.748	1.00
95_V	99_D	0.746	1.00
135_N	173_H	0.744	1.00
12_V	54_Y	0.736	1.00
36_A	39_T	0.731	1.00
36_A	40_A	0.726	1.00
170_T	174_A	0.723	1.00
72_E	75_R	0.719	1.00
62_G	65_E	0.718	1.00
54_Y	98_D	0.710	1.00
46_R	96_A	0.708	1.00
91_D	94_T	0.703	1.00
34_A	132_T	0.696	1.00
100_H	122_H	0.691	1.00
51_R	118_Y	0.690	1.00
95_V	101_V	0.686	1.00
19_F	137_C	0.685	1.00
135_N	166_H	0.682	1.00
117_G	120_T	0.680	1.00
169_Y	173_H	0.676	1.00
159_V	171_L	0.671	1.00
20_C	35_L	0.669	1.00
35_L	90_H	0.668	1.00
172_D	176_W	0.665	1.00
23_D	27_H	0.663	1.00
135_N	162_I	0.661	1.00
61_P	78_E	0.661	1.00
10_V	41_L	0.660	1.00
146_G	179_G	0.659	1.00
53_V	100_H	0.657	1.00
142_A	179_G	0.648	1.00
18_G	24_G	0.647	1.00
10_V	130_C	0.645	1.00
111_Y	147_V	0.642	1.00
129_F	152_P	0.642	1.00
133_L	136_V	0.642	1.00
39_T	94_T	0.641	1.00
152_P	155_A	0.637	1.00
7_H	123_G	0.634	1.00
29_P	32_E	0.630	1.00
166_H	172_D	0.627	1.00
54_Y	101_V	0.626	1.00
31_S	132_T	0.626	1.00
71_D	74_E	0.625	1.00
169_Y	172_D	0.622	1.00
24_G	27_H	0.622	1.00
133_L	161_Y	0.615	1.00
21_H	32_E	0.611	1.00
54_Y	99_D	0.610	1.00
136_V	162_I	0.609	1.00
60_P	63_Q	0.609	1.00
41_L	45_A	0.604	1.00
13_V	138_V	0.602	1.00
15_M	90_H	0.600	1.00
71_D	75_R	0.599	1.00
83_G	88_Q	0.599	1.00
156_A	167_K	0.595	1.00
85_W	91_D	0.591	0.99
41_L	128_V	0.591	0.99
10_V	52_I	0.589	0.99
35_L	93_L	0.588	0.99
53_V	102_V	0.588	0.99
171_L	175_E	0.584	0.99
42_V	45_A	0.583	0.99
46_R	98_D	0.581	0.99
154_L	171_L	0.580	0.99
156_A	175_E	0.580	0.99
15_M	93_L	0.579	0.99
142_A	152_P	0.575	0.99
43_S	94_T	0.574	0.99
130_C	155_A	0.574	0.99
112_E	117_G	0.573	0.99
27_H	32_E	0.571	0.99
143_G	177_L	0.565	0.99
42_V	99_D	0.559	0.99
90_H	93_L	0.559	0.99
60_P	105_H	0.556	0.99
154_L	174_A	0.555	0.99
102_V	114_E	0.554	0.99
20_C	31_S	0.553	0.99
10_V	42_V	0.553	0.99
46_R	52_I	0.541	0.99
111_Y	144_S	0.540	0.99
18_G	80_V	0.540	0.99
166_H	176_W	0.539	0.99
15_M	34_A	0.539	0.99
180_E	183_D	0.535	0.99
35_L	92_K	0.533	0.99
108_D	147_V	0.533	0.99
166_H	170_T	0.532	0.99
95_V	98_D	0.531	0.99
107_Y	141_T	0.531	0.99
56_R	88_Q	0.529	0.99
54_Y	93_L	0.528	0.99
51_R	100_H	0.525	0.99
56_R	87_A	0.523	0.99
133_L	162_I	0.519	0.99
76_W	107_Y	0.517	0.99
29_P	33_D	0.517	0.99
138_V	159_V	0.516	0.99
45_A	51_R	0.514	0.99
107_Y	146_G	0.513	0.99
146_G	177_L	0.513	0.99
128_V	157_D	0.512	0.99
107_Y	147_V	0.506	0.98
73_F	76_W	0.506	0.98
71_D	77_G	0.505	0.98
100_H	103_E	0.504	0.98
170_T	173_H	0.504	0.98
29_P	160_G	0.502	0.98
60_P	65_E	0.500	0.98

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
3irvA	2	1	100	0.139	Contact Map
3kl2A	4	1	100	0.147	Contact Map
3hb7A	3	0.9579	100	0.15	Contact Map
1nbaA	4	1	100	0.159	Contact Map
3hu5A	3	0.9684	100	0.159	Contact Map
3r2jA	2	0.9737	100	0.164	Contact Map
2fq1A	2	0.9789	100	0.164	Contact Map
4l07A	4	0.9789	100	0.181	Contact Map
2wt9A	2	0.9579	100	0.181	Contact Map
1nf9A	2	0.9632	100	0.182	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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