YABB - BACSU - GREMLIN Contacts

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YABB - Uncharacterized protein YabB

UniProt:	P37543	Sequences: MVSLHDDERLDYLLAEDMKIIQSPTVFAFSLDAVLLSKFAYVPIQKGKIVDLCTGNGIVPLLLSTRSKADILGVEIQERLHDMAVRSVEYNKLDDQIQIIHDDLKNMPEKLGHNRYDVVTCNPPYFKTPKQTEQNMNEHLRIARHEIHCTLEDVISVSSKLLKQGGKAALVHRPGRLLEIFELMKAYQIEPKRVQFVYPKQGKEANTILVEGIKGGRPDLKILPPLFVYDEQNEYTKEIRTILYGDK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	247 (194)
Sequences:	7225 (5679)
Seq/√Len:	407.7

ECOLI - TRMN6 PRMC PRMB
BACSU - YABB PRMC 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
10_L	17_D	3.210	1.00
19_K	86_R	3.154	1.00
60_P	73_G	2.901	1.00
72_L	100_I	2.775	1.00
78_E	101_H	2.738	1.00
117_D	163_K	2.550	1.00
72_L	116_Y	2.413	1.00
155_I	184_M	2.369	1.00
88_V	99_I	2.337	1.00
60_P	71_I	2.315	1.00
50_V	116_Y	2.285	1.00
102_D	107_M	2.250	1.00
158_S	168_A	2.249	1.00
23_S	79_R	2.137	1.00
196_F	202_G	2.048	1.00
54_T	84_A	2.016	1.00
14_L	66_R	1.995	1.00
76_I	142_I	1.993	1.00
48_K	70_D	1.966	1.00
12_Y	17_D	1.921	1.00
63_L	120_T	1.905	1.00
16_E	65_T	1.890	1.00
81_H	99_I	1.860	1.00
19_K	90_Y	1.792	1.00
70_D	98_Q	1.750	1.00
30_S	33_A	1.745	1.00
128_T	145_H	1.742	1.00
75_E	81_H	1.721	1.00
16_E	66_R	1.714	1.00
18_M	62_L	1.701	1.00
170_L	184_M	1.694	1.00
54_T	60_P	1.693	1.00
88_V	97_I	1.684	1.00
21_I	83_M	1.680	1.00
162_L	166_G	1.658	1.00
81_H	101_H	1.627	1.00
73_G	99_I	1.627	1.00
64_S	71_I	1.577	1.00
36_L	40_A	1.567	1.00
37_S	195_Q	1.547	1.00
177_L	194_V	1.543	1.00
149_C	152_E	1.505	1.00
72_L	98_Q	1.504	1.00
61_L	93_L	1.501	1.00
155_I	183_L	1.458	1.00
12_Y	15_A	1.454	1.00
36_L	39_F	1.442	1.00
182_E	186_A	1.437	1.00
103_D	106_N	1.436	1.00
37_S	40_A	1.415	1.00
131_Q	145_H	1.399	1.00
103_D	153_D	1.391	1.00
16_E	62_L	1.372	1.00
152_E	183_L	1.360	1.00
156_S	187_Y	1.357	1.00
181_F	194_V	1.333	1.00
118_V	169_A	1.333	1.00
141_R	145_H	1.332	1.00
60_P	97_I	1.315	1.00
73_G	97_I	1.314	1.00
24_P	56_N	1.289	1.00
93_L	96_Q	1.279	1.00
105_K	161_L	1.274	1.00
64_S	96_Q	1.265	1.00
48_K	72_L	1.249	1.00
23_S	83_M	1.244	1.00
54_T	75_E	1.241	1.00
44_I	47_G	1.241	1.00
177_L	202_G	1.233	1.00
181_F	185_K	1.228	1.00
81_H	85_V	1.223	1.00
52_L	104_L	1.218	1.00
174_P	201_Q	1.214	1.00
121_C	170_L	1.214	1.00
48_K	116_Y	1.202	1.00
59_V	120_T	1.178	1.00
157_V	160_K	1.160	1.00
84_A	99_I	1.150	1.00
153_D	157_V	1.148	1.00
49_I	69_A	1.146	1.00
21_I	86_R	1.135	1.00
51_D	60_P	1.135	1.00
127_K	175_G	1.132	1.00
53_C	104_L	1.127	1.00
61_L	88_V	1.110	1.00
172_H	180_I	1.109	1.00
85_V	89_E	1.100	1.00
182_E	185_K	1.092	1.00
77_Q	80_L	1.085	1.00
37_S	41_Y	1.082	1.00
49_I	71_I	1.072	1.00
74_V	108_P	1.069	1.00
34_V	169_A	1.067	1.00
31_L	59_V	1.064	1.00
53_C	121_C	1.055	1.00
77_Q	142_I	1.050	1.00
9_R	19_K	1.050	1.00
115_R	163_K	1.046	1.00
10_L	90_Y	1.042	1.00
42_V	67_S	1.038	1.00
151_L	179_E	1.037	1.00
172_H	177_L	1.033	1.00
89_E	94_D	1.033	1.00
135_N	138_E	1.030	1.00
159_S	189_I	1.027	1.00
158_S	189_I	1.023	1.00
33_A	198_Y	1.019	1.00
38_K	169_A	1.010	1.00
48_K	114_N	1.000	1.00
18_M	61_L	0.984	1.00
178_L	182_E	0.979	1.00
162_L	168_A	0.962	1.00
151_L	183_L	0.961	1.00
14_L	62_L	0.954	1.00
61_L	91_N	0.954	1.00
39_F	67_S	0.946	1.00
38_K	42_V	0.942	1.00
104_L	153_D	0.937	1.00
41_Y	167_K	0.937	1.00
74_V	102_D	0.936	1.00
49_I	118_V	0.930	1.00
65_T	93_L	0.913	1.00
128_T	147_I	0.908	1.00
52_L	154_V	0.907	1.00
64_S	97_I	0.903	1.00
105_K	153_D	0.898	1.00
78_E	82_D	0.898	1.00
15_A	65_T	0.891	1.00
177_L	181_F	0.890	1.00
41_Y	169_A	0.883	1.00
20_I	83_M	0.878	1.00
35_L	62_L	0.870	1.00
47_G	69_A	0.869	1.00
131_Q	136_M	0.865	1.00
152_E	186_A	0.863	1.00
26_V	139_H	0.855	1.00
116_Y	119_V	0.855	1.00
86_R	90_Y	0.854	1.00
148_H	152_E	0.850	1.00
86_R	89_E	0.847	1.00
60_P	64_S	0.842	1.00
184_M	189_I	0.839	1.00
135_N	140_L	0.835	1.00
102_D	106_N	0.832	1.00
131_Q	141_R	0.830	1.00
153_D	156_S	0.828	1.00
176_R	179_E	0.824	1.00
127_K	130_K	0.824	1.00
38_K	120_T	0.820	1.00
43_P	47_G	0.818	1.00
49_I	63_L	0.818	1.00
173_R	176_R	0.817	1.00
134_Q	145_H	0.813	1.00
118_V	167_K	0.790	1.00
88_V	93_L	0.787	1.00
126_F	144_R	0.780	1.00
105_K	157_V	0.779	1.00
50_V	119_V	0.775	1.00
157_V	161_L	0.774	1.00
72_L	114_N	0.771	1.00
130_K	175_G	0.770	1.00
82_D	85_V	0.768	1.00
104_L	157_V	0.764	1.00
155_I	187_Y	0.761	1.00
152_E	187_Y	0.760	1.00
141_R	147_I	0.759	1.00
60_P	120_T	0.754	1.00
85_V	88_V	0.749	1.00
18_M	58_I	0.747	1.00
10_L	19_K	0.741	1.00
14_L	36_L	0.740	1.00
65_T	91_N	0.738	1.00
128_T	131_Q	0.736	1.00
54_T	73_G	0.729	1.00
170_L	180_I	0.728	1.00
156_S	159_S	0.726	1.00
51_D	54_T	0.726	1.00
15_A	66_R	0.721	1.00
54_T	99_I	0.717	1.00
17_D	90_Y	0.714	1.00
50_V	74_V	0.712	1.00
62_L	66_R	0.707	1.00
121_C	154_V	0.705	1.00
71_I	97_I	0.702	1.00
52_L	105_K	0.701	1.00
33_A	37_S	0.699	1.00
154_V	168_A	0.698	1.00
73_G	84_A	0.698	1.00
127_K	146_E	0.697	1.00
168_A	184_M	0.695	1.00
51_D	120_T	0.693	1.00
49_I	67_S	0.691	1.00
159_S	187_Y	0.688	1.00
46_K	70_D	0.683	1.00
183_L	187_Y	0.683	1.00
152_E	156_S	0.682	1.00
104_L	154_V	0.682	1.00
47_G	117_D	0.682	1.00
64_S	94_D	0.677	0.99
18_M	93_L	0.677	0.99
48_K	163_K	0.675	0.99
43_P	67_S	0.674	0.99
197_V	200_K	0.673	0.99
98_Q	114_N	0.672	0.99
30_S	199_P	0.665	0.99
8_E	11_D	0.663	0.99
146_E	176_R	0.663	0.99
36_L	42_V	0.663	0.99
113_H	160_K	0.662	0.99
109_E	161_L	0.662	0.99
16_E	91_N	0.662	0.99
196_F	200_K	0.660	0.99
24_P	83_M	0.659	0.99
200_K	203_K	0.655	0.99
149_C	154_V	0.652	0.99
140_L	144_R	0.648	0.99
177_L	201_Q	0.645	0.99
119_V	161_L	0.644	0.99
197_V	203_K	0.642	0.99
74_V	100_I	0.642	0.99
64_S	88_V	0.632	0.99
43_P	46_K	0.631	0.99
36_L	41_Y	0.624	0.99
119_V	162_L	0.623	0.99
20_I	24_P	0.623	0.99
185_K	190_E	0.618	0.99
179_E	182_E	0.618	0.99
126_F	173_R	0.617	0.99
109_E	113_H	0.613	0.99
100_I	114_N	0.609	0.99
41_Y	193_R	0.607	0.99
58_I	62_L	0.603	0.99
88_V	91_N	0.602	0.99
155_I	170_L	0.602	0.99
172_H	194_V	0.600	0.99
48_K	117_D	0.600	0.99
154_V	158_S	0.593	0.99
38_K	118_V	0.593	0.99
128_T	146_E	0.591	0.99
47_G	67_S	0.589	0.99
35_L	63_L	0.588	0.99
35_L	59_V	0.585	0.99
146_E	149_C	0.583	0.98
174_P	177_L	0.582	0.98
62_L	65_T	0.580	0.98
158_S	166_G	0.576	0.98
63_L	69_A	0.573	0.98
127_K	176_R	0.570	0.98
181_F	192_K	0.567	0.98
18_M	91_N	0.566	0.98
176_R	180_I	0.564	0.98
185_K	192_K	0.558	0.98
82_D	86_R	0.558	0.98
52_L	161_L	0.553	0.98
64_S	68_K	0.551	0.98
51_D	121_C	0.549	0.98
69_A	96_Q	0.549	0.98
25_T	83_M	0.544	0.98
79_R	82_D	0.544	0.98
61_L	65_T	0.544	0.98
121_C	168_A	0.539	0.98
131_Q	146_E	0.535	0.97
135_N	145_H	0.534	0.97
68_K	96_Q	0.533	0.97
79_R	139_H	0.530	0.97
106_N	109_E	0.529	0.97
105_K	119_V	0.528	0.97
50_V	161_L	0.528	0.97
83_M	87_S	0.525	0.97
146_E	150_T	0.523	0.97
134_Q	141_R	0.523	0.97
183_L	186_A	0.522	0.97
33_A	58_I	0.522	0.97
26_V	80_L	0.522	0.97
127_K	179_E	0.520	0.97
37_S	169_A	0.519	0.97
50_V	108_P	0.519	0.97
9_R	28_A	0.518	0.97
25_T	139_H	0.516	0.97
23_S	28_A	0.515	0.97
64_S	93_L	0.515	0.97
23_S	26_V	0.513	0.97
85_V	101_H	0.510	0.97
171_V	197_V	0.509	0.96
155_I	180_I	0.508	0.96
194_V	202_G	0.507	0.96
53_C	120_T	0.507	0.96
38_K	41_Y	0.503	0.96
116_Y	161_L	0.500	0.96
76_I	101_H	0.500	0.96
108_P	157_V	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
3lpmA	2	0.8988	100	0.365	Contact Map
2ozvA	2	0.7773	100	0.414	Contact Map
2b3tA	1	0.834	100	0.492	Contact Map
1nv8A	1	0.8219	100	0.511	Contact Map
3evzA	1	0.753	100	0.572	Contact Map
3c6kA	2	0.8097	99.9	0.618	Contact Map
4dzrA	2	0.6113	99.9	0.62	Contact Map
4dcmA	1	0.7126	99.9	0.629	Contact Map
3tm4A	1	0.7652	99.9	0.637	Contact Map
3v97A	1	0.7571	99.9	0.641	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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