YCIB - BACSU - GREMLIN Contacts

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YCIB - Putative L,D-transpeptidase YciB

UniProt:	C0SP99	Sequences: MKLSLFIIAVLMPVILLSACSDHAEEHASINTKKTVENITDVRKTAKTSIDWTKPSGGEYPDIKQKHVWIDVNVKEQKAYIKEGSNTIYTMMISSGLDQTKDDATPKGTFYVEPERGEWFFSEGYQEGAEYWVSWKNHGEFLFHSVPMTKDQKVIKTEAEKLGTKASHGCIRLTIPDAKWVYENIPEHTKVVIS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	194 (167)
Sequences:	236 (203)
Seq/√Len:	15.7

BACSU - YCIB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_E	138_H	4.016	1.00
158_E	172_R	3.240	0.99
131_Y	178_A	3.116	0.99
130_E	154_V	3.057	0.98
133_V	181_V	3.029	0.98
69_W	192_V	2.988	0.98
77_Q	95_S	2.953	0.98
70_I	81_I	2.867	0.98
149_T	153_K	2.788	0.97
158_E	161_K	2.782	0.97
167_S	170_C	2.762	0.97
109_T	190_K	2.608	0.96
179_K	183_E	2.577	0.95
71_D	82_K	2.555	0.95
79_A	93_I	2.343	0.92
144_H	170_C	2.329	0.92
144_H	167_S	2.300	0.91
91_M	173_L	2.145	0.88
69_W	190_K	2.125	0.88
119_W	148_M	2.121	0.88
81_I	185_I	2.084	0.87
134_S	138_H	1.991	0.84
142_L	168_H	1.860	0.80
68_V	189_T	1.673	0.72
134_S	140_E	1.667	0.71
119_W	130_E	1.657	0.71
23_H	26_E	1.645	0.70
120_F	168_H	1.643	0.70
185_I	189_T	1.631	0.70
82_K	87_T	1.593	0.68
133_V	182_Y	1.588	0.68
81_I	181_V	1.572	0.67
70_I	181_V	1.550	0.66
161_K	166_A	1.498	0.63
74_V	107_K	1.492	0.62
113_E	134_S	1.478	0.62
142_L	170_C	1.473	0.61
115_E	134_S	1.453	0.60
166_A	172_R	1.416	0.58
135_W	141_F	1.408	0.58
142_L	167_S	1.402	0.58
22_D	29_S	1.381	0.56
117_G	132_W	1.341	0.54
117_G	120_F	1.321	0.53
37_E	126_Q	1.315	0.53
68_V	185_I	1.311	0.52
79_A	143_F	1.279	0.51
80_Y	90_T	1.264	0.50
145_S	185_I	1.260	0.49
115_E	139_G	1.234	0.48
23_H	28_A	1.232	0.48
113_E	138_H	1.210	0.47
129_A	147_P	1.208	0.46
27_H	31_N	1.182	0.45
73_N	183_E	1.178	0.45
158_E	166_A	1.167	0.44
122_S	125_Y	1.158	0.44
61_P	89_Y	1.151	0.43
68_V	181_V	1.115	0.41
109_T	192_V	1.104	0.41
112_V	185_I	1.103	0.41
23_H	30_I	1.103	0.41
120_F	142_L	1.099	0.40
24_A	30_I	1.086	0.40
144_H	168_H	1.079	0.39
128_G	132_W	1.066	0.39
119_W	154_V	1.058	0.38
51_D	54_K	1.055	0.38
45_T	71_D	1.053	0.38
148_M	154_V	1.047	0.37
69_W	109_T	1.039	0.37
50_I	174_T	1.025	0.36
96_G	172_R	1.018	0.36
110_F	135_W	1.017	0.36
32_T	35_T	1.001	0.35
120_F	128_G	0.990	0.34
31_N	34_K	0.988	0.34
154_V	188_H	0.987	0.34
94_S	147_P	0.980	0.34
63_I	185_I	0.979	0.34
128_G	147_P	0.971	0.33
25_E	32_T	0.966	0.33
125_Y	161_K	0.945	0.32
70_I	175_I	0.924	0.31
52_W	89_Y	0.923	0.31
106_P	129_A	0.912	0.31
106_P	147_P	0.903	0.30
122_S	168_H	0.882	0.29
95_S	112_V	0.880	0.29
25_E	35_T	0.879	0.29
73_N	135_W	0.873	0.29
94_S	166_A	0.873	0.29
62_D	193_I	0.872	0.29
79_A	173_L	0.872	0.29
94_S	191_V	0.863	0.28
55_P	58_G	0.860	0.28
134_S	159_A	0.853	0.28
31_N	35_T	0.848	0.28
147_P	191_V	0.845	0.27
44_K	55_P	0.845	0.27
24_A	32_T	0.840	0.27
78_K	92_M	0.838	0.27
95_S	168_H	0.833	0.27
56_S	89_Y	0.831	0.27
68_V	82_K	0.828	0.27
67_H	84_G	0.827	0.27
105_T	143_F	0.824	0.26
58_G	97_L	0.823	0.26
22_D	26_E	0.819	0.26
61_P	91_M	0.818	0.26
47_K	121_F	0.815	0.26
28_A	39_I	0.811	0.26
27_H	30_I	0.803	0.26
29_S	38_N	0.800	0.25
55_P	92_M	0.798	0.25
147_P	180_W	0.797	0.25
52_W	55_P	0.789	0.25
37_E	40_T	0.786	0.25
57_G	141_F	0.786	0.25
24_A	31_N	0.786	0.25
140_E	177_D	0.786	0.25
65_Q	175_I	0.785	0.25
57_G	92_M	0.783	0.25
46_A	49_S	0.783	0.25
81_I	136_K	0.781	0.25
96_G	105_T	0.772	0.24
136_K	140_E	0.763	0.24
117_G	134_S	0.763	0.24
36_V	41_D	0.758	0.24
106_P	128_G	0.756	0.24
127_E	168_H	0.756	0.24
121_F	128_G	0.756	0.24
97_L	181_V	0.752	0.23
90_T	177_D	0.751	0.23
180_W	191_V	0.750	0.23
105_T	172_R	0.749	0.23
105_T	167_S	0.747	0.23
112_V	191_V	0.746	0.23
132_W	147_P	0.744	0.23
169_G	191_V	0.742	0.23
26_E	34_K	0.738	0.23
91_M	146_V	0.737	0.23
63_I	88_I	0.735	0.23
25_E	28_A	0.734	0.23
63_I	68_V	0.733	0.23
136_K	139_G	0.732	0.23
132_W	185_I	0.731	0.22
98_D	103_D	0.730	0.22
97_L	166_A	0.728	0.22
52_W	56_S	0.723	0.22
28_A	33_K	0.720	0.22
60_Y	134_S	0.718	0.22
66_K	88_I	0.717	0.22
146_V	166_A	0.716	0.22
181_V	189_T	0.713	0.22
122_S	154_V	0.713	0.22
28_A	35_T	0.712	0.22
26_E	33_K	0.706	0.22
88_I	113_E	0.705	0.21
77_Q	98_D	0.705	0.21
143_F	173_L	0.699	0.21
95_S	182_Y	0.698	0.21
24_A	39_I	0.698	0.21
27_H	33_K	0.696	0.21
50_I	54_K	0.695	0.21
131_Y	182_Y	0.690	0.21
33_K	44_K	0.683	0.21
48_T	70_I	0.682	0.21
115_E	140_E	0.680	0.21
77_Q	155_I	0.679	0.20
98_D	104_A	0.679	0.20
24_A	35_T	0.679	0.20
122_S	140_E	0.676	0.20
22_D	27_H	0.673	0.20
79_A	146_V	0.671	0.20
105_T	170_C	0.671	0.20
117_G	128_G	0.669	0.20
78_K	89_Y	0.666	0.20
33_K	39_I	0.662	0.20
116_R	132_W	0.662	0.20
31_N	107_K	0.654	0.20
29_S	33_K	0.654	0.20
63_I	186_P	0.653	0.20
55_P	60_Y	0.647	0.19
28_A	36_V	0.647	0.19
153_K	181_V	0.646	0.19
106_P	180_W	0.640	0.19
122_S	127_E	0.639	0.19
26_E	36_V	0.636	0.19
130_E	141_F	0.633	0.19
28_A	31_N	0.630	0.19
62_D	84_G	0.628	0.19
32_T	40_T	0.628	0.19
79_A	171_I	0.625	0.19
23_H	36_V	0.620	0.18
146_V	158_E	0.617	0.18
130_E	148_M	0.616	0.18
154_V	175_I	0.613	0.18
36_V	151_D	0.607	0.18
105_T	169_G	0.603	0.18
51_D	55_P	0.599	0.18
28_A	38_N	0.595	0.18
135_W	191_V	0.595	0.18
61_P	177_D	0.592	0.17
61_P	159_A	0.591	0.17
22_D	39_I	0.587	0.17
34_K	39_I	0.587	0.17
122_S	142_L	0.586	0.17
89_Y	177_D	0.586	0.17
25_E	37_E	0.583	0.17
33_K	38_N	0.582	0.17
44_K	49_S	0.582	0.17
125_Y	148_M	0.580	0.17
52_W	61_P	0.576	0.17
83_E	193_I	0.575	0.17
42_V	193_I	0.571	0.17
23_H	29_S	0.566	0.17
84_G	132_W	0.565	0.17
80_Y	89_Y	0.564	0.17
79_A	91_M	0.561	0.16
81_I	126_Q	0.559	0.16
24_A	28_A	0.556	0.16
25_E	30_I	0.554	0.16
96_G	170_C	0.554	0.16
22_D	32_T	0.551	0.16
53_T	175_I	0.551	0.16
77_Q	132_W	0.546	0.16
52_W	78_K	0.546	0.16
33_K	37_E	0.545	0.16
121_F	178_A	0.540	0.16
56_S	90_T	0.528	0.15
167_S	182_Y	0.528	0.15
76_E	151_D	0.525	0.15
122_S	128_G	0.520	0.15
47_K	58_G	0.519	0.15
149_T	193_I	0.518	0.15
98_D	184_N	0.517	0.15
65_Q	121_F	0.516	0.15
125_Y	155_I	0.515	0.15
25_E	34_K	0.513	0.15
93_I	173_L	0.512	0.15
148_M	158_E	0.511	0.15
73_N	76_E	0.511	0.15
23_H	35_T	0.506	0.15
33_K	110_F	0.506	0.15
94_S	106_P	0.505	0.15
128_G	155_I	0.505	0.15
50_I	53_T	0.502	0.15
56_S	80_Y	0.500	0.15
96_G	167_S	0.500	0.15

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
4xxtA	1	0.8557	100	0.597	Contact Map
5bmqA	3	0.8969	99.9	0.648	Contact Map
4k73A	1	0.9278	99.9	0.651	Contact Map
4qtfA	2	0.9227	99.9	0.655	Contact Map
3vypA	1	0.9227	99.9	0.655	Contact Map
4jmnA	1	0.9227	99.9	0.659	Contact Map
4xvoA	1	0.8196	99.9	0.661	Contact Map
1zatA	1	0.8711	99.9	0.665	Contact Map
4a1kA	2	0.8299	99.9	0.678	Contact Map
4lpqA	1	0.8969	99.9	0.678	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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