YHCV - BACSU - GREMLIN Contacts

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YHCV - CBS domain-containing protein YhcV

UniProt:	P54606	Sequences: MSSVKDTMTTQVATVSPNQTIQEAASLMKQHNVGAIPVVEQGVLKGMLTDRDIALRTTAQGRDGQTPVSEVMSTELVSGNPNMSLEDASQLMAQHQIRRLPIVDQNNLVGIVALGDLAVNQMSNESAGSALTNISHQNIH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	140 (119)
Sequences:	13341 (10247)
Seq/√Len:	939.3

ECOLI - KDSD GUTQ IMDH
BACSU - YHCV YLBB ACUB CCPN YKUL YTOI IMDH MGTE YHDT
HALSA - Q9HQD0 Q9HRK9 Q9HPF4 Q9HNT8 Q9HMW8 Q9HNB6 Q9HR38 Q9HPN8 IMDH Q9HRX1
SULSO - Q97U20 Q97U00 Q981B7 Q97VD7 Q97VN1 Q7LXY4 Q97U50 Q97V95 Q7LXN6 Q97Z58 Q97U23

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_Q	23_E	2.744	1.00
35_A	99_R	2.633	1.00
17_P	69_S	2.294	1.00
81_P	104_D	2.286	1.00
79_G	102_I	2.225	1.00
77_V	95_H	2.157	1.00
83_M	87_D	2.093	1.00
79_G	83_M	2.016	1.00
16_S	19_Q	1.979	1.00
80_N	83_M	1.927	1.00
66_T	70_E	1.878	1.00
24_A	68_V	1.777	1.00
17_P	45_K	1.770	1.00
15_V	19_Q	1.767	1.00
15_V	38_V	1.762	1.00
81_P	109_V	1.717	1.00
4_V	88_A	1.704	1.00
15_V	24_A	1.686	1.00
15_V	36_I	1.680	1.00
13_A	31_H	1.648	1.00
37_P	44_L	1.637	1.00
17_P	40_E	1.587	1.00
79_G	88_A	1.550	1.00
101_P	108_L	1.499	1.00
67_P	70_E	1.499	1.00
77_V	97_I	1.479	1.00
98_R	114_L	1.478	1.00
24_A	48_L	1.442	1.00
27_L	31_H	1.428	1.00
26_S	30_Q	1.424	1.00
91_L	95_H	1.391	1.00
88_A	100_L	1.379	1.00
40_E	43_V	1.376	1.00
48_L	53_I	1.374	1.00
80_N	105_Q	1.358	1.00
5_K	81_P	1.313	1.00
19_Q	27_L	1.307	1.00
40_E	45_K	1.303	1.00
78_S	103_V	1.298	1.00
15_V	68_V	1.291	1.00
22_Q	64_G	1.286	1.00
18_N	69_S	1.265	1.00
35_A	47_M	1.249	1.00
14_T	39_V	1.243	1.00
13_A	27_L	1.238	1.00
83_M	91_L	1.233	1.00
77_V	91_L	1.231	1.00
20_T	23_E	1.218	1.00
23_E	26_S	1.218	1.00
44_L	108_L	1.214	1.00
24_A	36_I	1.213	1.00
79_G	100_L	1.194	1.00
50_D	54_A	1.171	1.00
21_I	71_V	1.167	1.00
22_Q	26_S	1.141	1.00
104_D	107_N	1.140	1.00
38_V	72_M	1.125	1.00
66_T	71_V	1.121	1.00
5_K	82_N	1.119	1.00
48_L	71_V	1.111	1.00
47_M	101_P	1.111	1.00
84_S	87_D	1.106	1.00
90_Q	94_Q	1.105	1.00
7_T	85_L	1.077	1.00
48_L	68_V	1.075	1.00
34_G	50_D	1.049	1.00
7_T	112_V	1.033	1.00
52_D	73_S	1.029	1.00
25_A	53_I	1.023	1.00
9_T	116_D	1.021	1.00
79_G	91_L	1.010	1.00
39_V	45_K	0.989	1.00
87_D	91_L	0.972	1.00
88_A	112_V	0.972	1.00
42_G	107_N	0.970	1.00
54_A	98_R	0.961	1.00
80_N	104_D	0.958	1.00
33_V	36_I	0.956	1.00
37_P	108_L	0.951	1.00
50_D	98_R	0.947	1.00
104_D	109_V	0.933	1.00
91_L	100_L	0.922	1.00
85_L	117_L	0.917	1.00
23_E	27_L	0.913	1.00
4_V	79_G	0.907	1.00
99_R	111_I	0.907	1.00
13_A	33_V	0.903	1.00
16_S	40_E	0.901	1.00
16_S	39_V	0.897	1.00
35_A	98_R	0.895	1.00
15_V	27_L	0.891	1.00
44_L	76_L	0.880	1.00
27_L	30_Q	0.873	1.00
46_G	72_M	0.869	1.00
64_G	67_P	0.855	1.00
93_A	119_V	0.852	1.00
44_L	101_P	0.831	1.00
56_R	59_A	0.812	1.00
87_D	90_Q	0.811	1.00
8_M	102_I	0.790	1.00
27_L	36_I	0.790	1.00
22_Q	65_Q	0.789	1.00
68_V	72_M	0.789	1.00
43_V	107_N	0.782	1.00
92_M	100_L	0.776	1.00
98_R	115_G	0.772	1.00
99_R	113_A	0.752	1.00
28_M	36_I	0.745	1.00
39_V	42_G	0.739	1.00
69_S	72_M	0.729	1.00
103_V	108_L	0.724	1.00
34_G	99_R	0.722	1.00
12_V	37_P	0.711	1.00
51_R	98_R	0.709	1.00
34_G	98_R	0.708	1.00
18_N	67_P	0.708	1.00
80_N	106_N	0.708	1.00
35_A	111_I	0.707	1.00
39_V	44_L	0.705	1.00
81_P	105_Q	0.679	1.00
37_P	101_P	0.679	1.00
7_T	120_N	0.678	1.00
29_K	60_Q	0.660	1.00
24_A	28_M	0.658	1.00
115_G	119_V	0.650	1.00
33_V	37_P	0.649	1.00
49_T	52_D	0.643	1.00
47_M	99_R	0.623	1.00
4_V	112_V	0.614	1.00
50_D	99_R	0.613	1.00
76_L	101_P	0.611	1.00
43_V	106_N	0.608	1.00
8_M	109_V	0.608	1.00
58_T	61_G	0.608	1.00
13_A	36_I	0.603	1.00
53_I	57_T	0.603	1.00
9_T	12_V	0.602	1.00
14_T	42_G	0.598	1.00
37_P	45_K	0.598	1.00
45_K	72_M	0.593	1.00
34_G	51_R	0.593	1.00
34_G	114_L	0.591	1.00
47_M	73_S	0.589	1.00
83_M	88_A	0.588	1.00
21_I	57_T	0.587	1.00
25_A	50_D	0.586	1.00
86_E	90_Q	0.585	1.00
116_D	119_V	0.583	1.00
114_L	118_A	0.581	1.00
5_K	8_M	0.581	1.00
50_D	115_G	0.580	1.00
112_V	117_L	0.575	1.00
35_A	49_T	0.573	1.00
80_N	103_V	0.572	1.00
34_G	37_P	0.571	1.00
99_R	114_L	0.570	1.00
4_V	8_M	0.562	1.00
101_P	111_I	0.558	1.00
92_M	114_L	0.554	1.00
60_Q	66_T	0.550	1.00
40_E	69_S	0.550	1.00
89_S	118_A	0.547	1.00
82_N	105_Q	0.539	1.00
5_K	104_D	0.538	1.00
19_Q	36_I	0.537	1.00
34_G	52_D	0.524	1.00
57_T	61_G	0.517	1.00
118_A	122_M	0.516	1.00
61_G	64_G	0.509	1.00
57_T	62_R	0.507	1.00
47_M	76_L	0.505	1.00
74_T	77_V	0.505	1.00
120_N	123_S	0.503	1.00
51_R	56_R	0.503	1.00
115_G	118_A	0.501	1.00
4_V	7_T	0.500	1.00
25_A	48_L	0.500	1.00
56_R	62_R	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
3l2bA	2	0.8214	99.9	0.284	Contact Map
2rc3A	3	0.8786	99.8	0.295	Contact Map
4cooA	2	0.8857	99.8	0.298	Contact Map
3orgA	2	0.8214	99.8	0.305	Contact Map
3fhmA	2	0.8857	99.8	0.308	Contact Map
2o16A	2	0.9429	99.8	0.313	Contact Map
3pc3A	2	0.8929	99.8	0.318	Contact Map
1y5hA	2	0.8643	99.8	0.32	Contact Map
2ef7A	3	0.9071	99.8	0.322	Contact Map
4fryA	2	0.9357	99.8	0.322	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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