FtsK_4TM - PFAM28P - GREMLIN Contacts

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FtsK_4TM - 4TM region of DNA translocase FtsK/SpoIIIE

PFAM:	PF13491	Sequences: SRRLREILGLLLLALALFLLLALASYSPADPSWSTAGSGDAPVHNWLGRVGAWLADLLLQLFGLAAFLLPLLLLVWGWRLLRRRPLRRLLLRLLGFLLLLLSLSALLALLFPSLGWGLPFGAGGVLGDLLAGLLASLLGFTGATLLLLALLLVGLILATGFSWLRLAERIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (163)
Sequences:	29108 (20931)
Seq/√Len:	1639.4
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_F	47_L	5.097	1.00
25_S	46_W	4.379	1.00
58_L	66_A	2.906	1.00
22_A	47_L	2.486	1.00
27_S	44_H	2.432	1.00
16_A	74_L	2.333	1.00
13_L	77_G	2.281	1.00
19_L	54_L	2.264	1.00
65_A	103_L	2.227	1.00
56_D	60_Q	2.218	1.00
19_L	58_L	2.182	1.00
14_A	149_A	2.093	1.00
108_A	131_A	2.023	1.00
128_D	132_G	1.964	1.00
16_A	73_L	1.959	1.00
16_A	70_P	1.956	1.00
16_A	77_G	1.916	1.00
24_A	67_F	1.895	1.00
105_A	147_L	1.860	1.00
138_L	146_L	1.746	1.00
9_G	77_G	1.741	1.00
78_W	82_R	1.698	1.00
156_I	163_W	1.656	1.00
109_L	131_A	1.636	1.00
21_L	47_L	1.571	1.00
32_S	56_D	1.531	1.00
49_R	53_W	1.526	1.00
34_S	56_D	1.525	1.00
59_L	67_F	1.524	1.00
155_L	159_T	1.512	1.00
23_L	67_F	1.512	1.00
129_L	133_L	1.493	1.00
141_T	144_T	1.490	1.00
26_Y	55_A	1.483	1.00
23_L	58_L	1.474	1.00
28_P	31_P	1.464	1.00
20_L	67_F	1.458	1.00
9_G	81_L	1.444	1.00
20_L	70_P	1.444	1.00
25_S	45_N	1.441	1.00
135_A	140_F	1.426	1.00
30_D	52_A	1.423	1.00
68_L	103_L	1.389	1.00
134_L	147_L	1.375	1.00
95_G	154_G	1.375	1.00
101_L	104_S	1.375	1.00
21_L	46_W	1.368	1.00
3_R	6_E	1.356	1.00
20_L	24_A	1.354	1.00
154_G	158_A	1.327	1.00
131_A	135_A	1.272	1.00
54_L	58_L	1.265	1.00
110_L	144_T	1.238	1.00
57_L	61_L	1.219	1.00
13_L	17_L	1.204	1.00
102_S	154_G	1.200	1.00
90_L	93_L	1.169	1.00
95_G	99_L	1.160	1.00
43_V	49_R	1.151	1.00
72_L	96_F	1.135	1.00
105_A	130_L	1.132	1.00
100_L	104_S	1.127	1.00
134_L	143_A	1.117	1.00
132_G	136_S	1.117	1.00
75_V	79_R	1.116	1.00
99_L	103_L	1.116	1.00
90_L	94_L	1.112	1.00
102_S	151_L	1.106	1.00
94_L	97_L	1.101	1.00
50_V	53_W	1.082	1.00
18_F	22_A	1.067	1.00
118_L	121_G	1.062	1.00
35_T	38_S	1.058	1.00
53_W	56_D	1.055	1.00
91_L	95_G	1.053	1.00
9_G	13_L	1.051	1.00
16_A	20_L	1.048	1.00
4_L	7_I	1.037	1.00
66_A	69_L	1.033	1.00
100_L	103_L	1.030	1.00
129_L	132_G	1.020	1.00
76_W	93_L	1.012	1.00
9_G	12_L	1.006	1.00
132_G	135_A	0.994	1.00
28_P	32_S	0.989	1.00
103_L	151_L	0.987	1.00
41_A	44_H	0.985	1.00
102_S	106_L	0.984	1.00
31_P	56_D	0.976	1.00
77_G	81_L	0.973	1.00
133_L	137_L	0.963	1.00
140_F	144_T	0.955	1.00
38_S	41_A	0.950	1.00
131_A	143_A	0.946	1.00
96_F	100_L	0.941	1.00
153_V	157_L	0.939	1.00
6_E	83_R	0.939	1.00
121_G	128_D	0.937	1.00
47_L	50_V	0.935	1.00
154_G	157_L	0.906	1.00
23_L	66_A	0.905	1.00
23_L	59_L	0.904	1.00
62_F	69_L	0.899	1.00
30_D	43_V	0.896	1.00
30_D	45_N	0.891	1.00
65_A	104_S	0.887	1.00
60_Q	125_V	0.876	1.00
29_A	44_H	0.876	1.00
39_G	42_P	0.874	1.00
103_L	106_L	0.861	1.00
32_S	53_W	0.856	1.00
19_L	23_L	0.856	1.00
5_R	83_R	0.855	1.00
139_G	142_G	0.850	1.00
89_L	93_L	0.830	1.00
50_V	137_L	0.829	1.00
88_R	92_R	0.828	1.00
144_T	148_L	0.827	1.00
10_L	14_A	0.824	1.00
133_L	136_S	0.823	1.00
102_S	105_A	0.822	1.00
152_L	156_I	0.822	1.00
92_R	95_G	0.822	1.00
126_L	129_L	0.819	1.00
148_L	152_L	0.819	1.00
66_A	70_P	0.817	1.00
33_W	57_L	0.813	1.00
34_S	37_G	0.803	1.00
65_A	107_L	0.803	1.00
88_R	91_L	0.792	1.00
61_L	125_V	0.788	1.00
21_L	141_T	0.786	1.00
130_L	133_L	0.781	1.00
43_V	46_W	0.779	1.00
12_L	73_L	0.773	1.00
65_A	68_L	0.767	1.00
113_S	116_W	0.766	1.00
160_G	163_W	0.766	1.00
112_P	115_G	0.766	1.00
64_L	116_W	0.764	1.00
68_L	99_L	0.764	1.00
34_S	60_Q	0.761	1.00
136_S	140_F	0.756	1.00
159_T	163_W	0.754	1.00
25_S	30_D	0.753	1.00
142_G	145_L	0.748	1.00
12_L	80_L	0.747	1.00
79_R	84_R	0.746	1.00
155_L	161_F	0.743	1.00
89_L	92_R	0.740	1.00
104_S	107_L	0.731	1.00
77_G	80_L	0.730	1.00
110_L	113_S	0.729	1.00
125_V	129_L	0.728	1.00
95_G	102_S	0.727	1.00
95_G	157_L	0.718	1.00
104_S	108_A	0.715	1.00
98_L	154_G	0.715	1.00
102_S	150_L	0.712	1.00
156_I	159_T	0.711	1.00
33_W	53_W	0.710	1.00
101_L	105_A	0.709	1.00
70_P	74_L	0.706	1.00
57_L	60_Q	0.705	1.00
73_L	76_W	0.703	1.00
49_R	136_S	0.702	1.00
64_L	107_L	0.698	1.00
7_I	153_V	0.697	1.00
8_L	12_L	0.696	1.00
92_R	96_F	0.693	1.00
13_L	16_A	0.693	1.00
92_R	99_L	0.688	1.00
48_G	51_G	0.687	1.00
50_V	138_L	0.685	1.00
45_N	52_A	0.684	1.00
117_G	120_F	0.682	1.00
12_L	77_G	0.681	1.00
33_W	56_D	0.681	1.00
149_A	153_V	0.677	1.00
37_G	41_A	0.671	1.00
95_G	98_L	0.670	1.00
45_N	51_G	0.665	1.00
5_R	80_L	0.662	1.00
53_W	57_L	0.656	1.00
80_L	83_R	0.653	1.00
36_A	39_G	0.649	1.00
94_L	98_L	0.646	1.00
14_A	18_F	0.641	1.00
95_G	100_L	0.641	1.00
50_V	54_L	0.639	1.00
96_F	99_L	0.639	1.00
98_L	102_S	0.636	1.00
162_S	165_R	0.634	1.00
62_F	100_L	0.627	1.00
9_G	16_A	0.620	1.00
29_A	32_S	0.620	1.00
87_R	92_R	0.620	1.00
135_A	143_A	0.619	1.00
8_L	11_L	0.617	1.00
107_L	123_G	0.611	1.00
99_L	154_G	0.607	1.00
97_L	101_L	0.598	1.00
144_T	147_L	0.596	1.00
43_V	52_A	0.595	1.00
3_R	9_G	0.594	1.00
161_F	165_R	0.587	1.00
93_L	97_L	0.579	1.00
31_P	55_A	0.579	1.00
134_L	138_L	0.578	1.00
79_R	83_R	0.577	1.00
105_A	108_A	0.574	1.00
102_S	108_A	0.574	1.00
151_L	155_L	0.573	1.00
27_S	30_D	0.566	1.00
135_A	139_G	0.562	1.00
8_L	80_L	0.559	1.00
70_P	73_L	0.559	1.00
126_L	130_L	0.553	1.00
150_L	154_G	0.546	1.00
37_G	40_D	0.542	1.00
147_L	151_L	0.541	1.00
111_F	114_L	0.538	1.00
91_L	94_L	0.537	1.00
145_L	148_L	0.535	1.00
4_L	8_L	0.533	1.00
158_A	161_F	0.530	1.00
108_A	123_G	0.529	1.00
19_L	70_P	0.526	1.00
143_A	147_L	0.525	1.00
68_L	71_L	0.522	1.00
94_L	99_L	0.521	1.00
156_I	161_F	0.521	1.00
32_S	60_Q	0.519	1.00
101_L	126_L	0.518	1.00
13_L	74_L	0.516	1.00
90_L	101_L	0.511	1.00
90_L	97_L	0.509	1.00
108_A	112_P	0.509	1.00
49_R	137_L	0.509	1.00
19_L	73_L	0.506	1.00
107_L	110_L	0.506	1.00
141_T	145_L	0.502	1.00
99_L	102_S	0.500	1.00
107_L	111_F	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
2q67A	3	0.4327	3.9	0.931	Contact Map
2h88D	1	0.2515	3.2	0.934	Contact Map
2k1eA	3	0.5965	2.6	0.937	Contact Map
3x29A	1	0.386	2.2	0.939	Contact Map
4p79A	1	0.4211	2	0.941	Contact Map
4xk8L	1	0.3567	1.9	0.941	Contact Map
3dinE	1	0.3801	1.9	0.942	Contact Map
3wdoA	1	0.9942	1.9	0.942	Contact Map
2acmA	1	0.1696	1.8	0.943	Contact Map
2mn6B	2	0.193	1.7	0.943	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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