Q97XF9 - SULSO - GREMLIN Contacts

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Q97XF9 - dTDP-4-dehydrorhamnose reductase (RfbD-2)

UniProt:	Q97XF9	Sequences: MTDVDKCEIEKDKAYKINSQAVKHIVRAGRVVDSYVIHISTDYVFDGNKGNYKEDNIPNPINYYGLSKLLGEIFASSYDESLIIRTSGVFRNKGFPIYVYKTLKEGKTVLAFKGYYSPISARKLALAIDELLDLRKTGIIHVAGERISRYELAIKIKEKFNLPGEVKEVDEIKSWIAKRPYDSSLDISKARKLLTIDFYTLDLEGMI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	207 (191)
Sequences:	33414 (21664)
Seq/√Len:	1567.5

ECOLI - HLDD RMLB2 GALE FCL RMLB1 GM4D YEEZ RMLD YBJS YFCH
BACSU - YTCB RMLB GALE YFNG SPSK YFHF YTBQ
HALSA - Q9HSU9 Q9HSV1 Q9HPF1 Q9HRD1 Q9HSE7 Q9HS50 Q9HML4
SULSO - Q97XF9 Q7LXE6 Q7LX44 Q97VN5 Q7LXG5 Q980W1 Q97UM3 Q97XJ9 Q97XG1 Q7LXE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_I	193_L	2.855	1.00
10_E	13_K	2.753	1.00
138_G	189_K	2.559	1.00
16_K	20_Q	2.526	1.00
86_T	128_I	2.456	1.00
127_A	142_V	2.316	1.00
126_L	199_Y	2.233	1.00
191_R	197_D	2.220	1.00
84_I	131_L	2.197	1.00
108_T	167_K	2.195	1.00
110_L	167_K	2.143	1.00
39_I	128_I	2.071	1.00
188_S	192_K	2.035	1.00
150_Y	154_I	2.013	1.00
35_Y	80_E	1.970	1.00
126_L	130_E	1.883	1.00
75_A	81_S	1.855	1.00
148_S	151_E	1.854	1.00
58_P	69_L	1.837	1.00
145_E	191_R	1.818	1.00
54_E	189_K	1.784	1.00
155_K	158_E	1.766	1.00
22_V	71_G	1.746	1.00
101_K	105_E	1.725	1.00
155_K	159_K	1.705	1.00
87_S	185_L	1.675	1.00
23_K	74_F	1.655	1.00
150_Y	168_E	1.654	1.00
69_L	73_I	1.619	1.00
138_G	193_L	1.612	1.00
53_K	56_N	1.612	1.00
190_A	194_L	1.611	1.00
40_S	44_V	1.606	1.00
115_Y	146_R	1.573	1.00
143_A	185_L	1.567	1.00
129_D	133_D	1.536	1.00
20_Q	23_K	1.503	1.00
38_H	71_G	1.470	1.00
50_G	53_K	1.438	1.00
15_Y	70_L	1.437	1.00
29_G	34_S	1.436	1.00
151_E	154_I	1.422	1.00
110_L	169_V	1.417	1.00
157_K	163_P	1.416	1.00
23_K	27_R	1.403	1.00
28_A	32_V	1.402	1.00
73_I	76_S	1.390	1.00
66_L	70_L	1.369	1.00
117_S	145_E	1.365	1.00
102_T	107_K	1.360	1.00
146_R	182_D	1.346	1.00
86_T	124_L	1.337	1.00
39_I	86_T	1.332	1.00
18_N	67_S	1.324	1.00
29_G	36_V	1.318	1.00
189_K	193_L	1.306	1.00
154_I	157_K	1.301	1.00
27_R	30_R	1.294	1.00
25_I	36_V	1.290	1.00
146_R	184_S	1.290	1.00
76_S	83_I	1.287	1.00
53_K	186_D	1.281	1.00
19_S	70_L	1.281	1.00
17_I	21_A	1.263	1.00
121_A	125_A	1.258	1.00
187_I	191_R	1.257	1.00
12_D	16_K	1.254	1.00
84_I	128_I	1.238	1.00
147_I	151_E	1.236	1.00
22_V	38_H	1.233	1.00
38_H	83_I	1.231	1.00
147_I	202_D	1.229	1.00
45_F	141_H	1.228	1.00
35_Y	82_L	1.216	1.00
36_V	75_A	1.213	1.00
38_H	75_A	1.206	1.00
115_Y	182_D	1.204	1.00
90_F	120_S	1.196	1.00
95_F	99_V	1.184	1.00
143_A	187_I	1.184	1.00
52_Y	56_N	1.180	1.00
122_R	200_T	1.179	1.00
50_G	56_N	1.178	1.00
108_T	165_E	1.175	1.00
119_I	124_L	1.149	1.00
187_I	198_F	1.141	1.00
26_V	75_A	1.136	1.00
26_V	78_Y	1.130	1.00
46_D	59_N	1.119	1.00
120_S	200_T	1.112	1.00
15_Y	19_S	1.109	1.00
55_D	189_K	1.099	1.00
140_I	189_K	1.097	1.00
27_R	31_V	1.097	1.00
27_R	78_Y	1.093	1.00
76_S	81_S	1.077	1.00
115_Y	148_S	1.070	1.00
142_V	190_A	1.068	1.00
157_K	164_G	1.062	1.00
22_V	75_A	1.061	1.00
44_V	58_P	1.058	1.00
15_Y	67_S	1.055	1.00
130_E	134_L	1.049	1.00
98_Y	102_T	1.048	1.00
76_S	139_I	1.046	1.00
8_E	63_Y	1.030	1.00
26_V	36_V	1.014	1.00
188_S	191_R	1.013	1.00
66_L	73_I	1.006	1.00
127_A	190_A	0.998	1.00
85_R	139_I	0.995	1.00
89_V	124_L	0.993	1.00
28_A	31_V	0.993	1.00
66_L	77_S	0.979	1.00
131_L	194_L	0.977	1.00
126_L	200_T	0.977	1.00
20_Q	24_H	0.970	1.00
82_L	131_L	0.968	1.00
48_N	52_Y	0.964	1.00
123_K	144_G	0.963	1.00
147_I	152_L	0.961	1.00
24_H	28_A	0.956	1.00
83_I	139_I	0.955	1.00
15_Y	20_Q	0.945	1.00
40_S	72_E	0.941	1.00
76_S	79_D	0.941	1.00
155_K	202_D	0.937	1.00
96_P	152_L	0.934	1.00
30_R	78_Y	0.930	1.00
113_K	168_E	0.930	1.00
103_L	157_K	0.929	1.00
100_Y	156_I	0.923	1.00
54_E	190_A	0.923	1.00
88_G	116_Y	0.911	1.00
169_V	174_S	0.911	1.00
120_S	123_K	0.911	1.00
35_Y	135_R	0.908	1.00
72_E	85_R	0.905	1.00
51_N	182_D	0.901	1.00
130_E	194_L	0.893	1.00
98_Y	101_K	0.890	1.00
71_G	75_A	0.889	1.00
166_V	169_V	0.888	1.00
151_E	155_K	0.885	1.00
11_K	66_L	0.884	1.00
94_G	97_I	0.878	1.00
81_S	137_T	0.875	1.00
70_L	73_I	0.875	1.00
86_T	89_V	0.872	1.00
47_G	61_I	0.871	1.00
42_D	87_S	0.871	1.00
13_K	17_I	0.857	1.00
42_D	185_L	0.853	1.00
126_L	129_D	0.850	1.00
83_I	137_T	0.848	1.00
99_V	153_A	0.846	1.00
47_G	181_Y	0.841	1.00
12_D	23_K	0.834	1.00
189_K	192_K	0.828	1.00
70_L	74_F	0.821	1.00
49_K	56_N	0.819	1.00
131_L	190_A	0.818	1.00
22_V	26_V	0.811	1.00
114_G	149_R	0.811	1.00
82_L	140_I	0.806	1.00
145_E	187_I	0.805	1.00
103_L	156_I	0.798	1.00
130_E	133_D	0.792	1.00
44_V	72_E	0.788	1.00
84_I	127_A	0.783	1.00
63_Y	66_L	0.775	1.00
85_R	141_H	0.774	1.00
157_K	162_L	0.767	1.00
19_S	67_S	0.765	1.00
154_I	158_E	0.765	1.00
157_K	166_V	0.764	1.00
24_H	27_R	0.763	1.00
60_P	69_L	0.762	1.00
37_I	128_I	0.761	1.00
180_P	183_S	0.760	1.00
100_Y	104_K	0.759	1.00
106_G	162_L	0.754	1.00
191_R	198_F	0.751	1.00
58_P	139_I	0.746	1.00
136_K	193_L	0.742	1.00
14_A	67_S	0.739	1.00
9_I	176_I	0.737	1.00
100_Y	160_F	0.736	1.00
129_D	132_L	0.733	1.00
92_N	95_F	0.729	1.00
102_T	110_L	0.728	1.00
73_I	77_S	0.715	1.00
13_K	16_K	0.713	1.00
80_E	136_K	0.710	1.00
21_A	24_H	0.706	1.00
99_V	109_V	0.704	1.00
102_T	106_G	0.703	1.00
91_R	121_A	0.700	1.00
37_I	84_I	0.693	1.00
26_V	74_F	0.690	1.00
53_K	188_S	0.688	1.00
16_K	24_H	0.686	1.00
37_I	132_L	0.681	1.00
74_F	77_S	0.677	1.00
43_Y	65_G	0.674	1.00
48_N	51_N	0.670	1.00
130_E	195_T	0.662	1.00
127_A	196_I	0.661	1.00
157_K	160_F	0.660	1.00
19_S	74_F	0.656	1.00
111_A	153_A	0.652	1.00
89_V	119_I	0.652	1.00
162_L	165_E	0.647	1.00
39_I	84_I	0.639	1.00
125_A	129_D	0.637	1.00
37_I	82_L	0.634	1.00
109_V	112_F	0.632	1.00
147_I	155_K	0.631	1.00
117_S	144_G	0.628	1.00
15_Y	66_L	0.627	1.00
123_K	126_L	0.627	1.00
23_K	78_Y	0.626	1.00
153_A	157_K	0.626	1.00
29_G	32_V	0.625	1.00
102_T	105_E	0.624	1.00
11_K	63_Y	0.610	1.00
126_L	196_I	0.608	1.00
82_L	137_T	0.603	1.00
16_K	27_R	0.600	1.00
115_Y	184_S	0.599	1.00
42_D	183_S	0.598	1.00
109_V	113_K	0.592	1.00
187_I	190_A	0.589	1.00
144_G	198_F	0.584	1.00
176_I	179_R	0.584	1.00
140_I	190_A	0.582	1.00
75_A	83_I	0.582	1.00
113_K	181_Y	0.581	1.00
15_Y	23_K	0.580	1.00
87_S	143_A	0.580	1.00
22_V	25_I	0.580	1.00
93_K	97_I	0.565	1.00
122_R	126_L	0.563	1.00
118_P	149_R	0.563	1.00
84_I	142_V	0.562	1.00
94_G	98_Y	0.562	1.00
44_V	85_R	0.557	1.00
103_L	109_V	0.557	1.00
58_P	73_I	0.556	1.00
158_E	164_G	0.556	1.00
93_K	98_Y	0.554	1.00
80_E	137_T	0.553	1.00
15_Y	74_F	0.551	1.00
150_Y	166_V	0.549	1.00
187_I	196_I	0.547	1.00
19_S	23_K	0.547	1.00
26_V	29_G	0.544	1.00
101_K	107_K	0.544	1.00
152_L	202_D	0.543	1.00
95_F	149_R	0.543	1.00
25_I	29_G	0.542	1.00
48_N	56_N	0.541	1.00
116_Y	149_R	0.539	1.00
82_L	138_G	0.539	1.00
51_N	56_N	0.537	1.00
54_E	141_H	0.531	1.00
99_V	103_L	0.531	1.00
154_I	166_V	0.529	1.00
84_I	124_L	0.528	1.00
60_P	66_L	0.528	1.00
153_A	166_V	0.524	1.00
190_A	193_L	0.524	1.00
101_K	104_K	0.522	1.00
12_D	20_Q	0.519	1.00
36_V	81_S	0.517	1.00
62_N	65_G	0.516	1.00
92_N	97_I	0.515	1.00
74_F	78_Y	0.514	1.00
76_S	138_G	0.512	1.00
104_K	160_F	0.511	1.00
144_G	187_I	0.509	1.00
118_P	152_L	0.506	1.00
145_E	197_D	0.503	1.00
82_L	134_L	0.500	1.00
103_L	160_F	0.500	1.00
97_I	101_K	0.500	1.00

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
2ggsA	1	0.9952	100	0.324	Contact Map
1rkxA	3	0.9614	100	0.35	Contact Map
1i24A	4	0.9855	100	0.351	Contact Map
1n7hA	4	1	100	0.358	Contact Map
3sxpA	3	0.9662	100	0.359	Contact Map
2b69A	2	0.9807	100	0.36	Contact Map
1vl0A	3	0.9952	100	0.36	Contact Map
1sb8A	2	1	100	0.36	Contact Map
1oc2A	2	0.9807	100	0.363	Contact Map
4wkgA	5	1	100	0.365	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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