CDC61 - HALSA - GREMLIN Contacts

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CDC61 - ORC1-type DNA replication protein 1

UniProt:	Q9HHZ9	Sequences: MITDARVLQPEFIPREVQHRDAEVNYLSSVLNPLTKGERADSALLYGPSGVGKTCIAQFLVEQLRGEVVALNYQYVNCWEDHSRFQTLYRLLDGIGKTVDIHRQSTPTDVHLNRLRTADDTSYVVILDEVDQLEDKSLLYDLYRIPHITMILIANDEEDLFASLDQRLNSRLTDCERIHFDPYHENELIPILHDRVHWGLEEDVISDSHLQLIAANAGGDARVVIGILRHSARTARETGSDQITADLIEEVTPEAKSEIKQRTVDRFTPHQELLYNIITEHGEISPQDLYDAYCTRTDDPKTKRMVRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (238)
Sequences:	9345 (4689)
Seq/√Len:	303.9

ECOLI - FTSH RARA DPO3X RUVB
BACSU - FTSH YJOB YRVN RUVB SP5K DPO3X
HALSA - CDC61 CDC69 CDC66 CDC68 CDC6A CDC65 CDC64 Q9HNS7 Q9HPV0 PAN1 CDCH PAN2 Q9HPG1 CDC62 Q9HPU1 Q9HNK6 CDC67 Q9HHW2 RFCL RFCS
SULSO - CDC61 CDC63 CDC62 Q97V06 Q97W25 Q97ZJ7 Q97ZZ9 PAN Q980U9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
189_I	211_Q	4.649	1.00
185_E	215_A	3.994	1.00
238_T	247_L	3.623	1.00
184_H	187_E	3.530	1.00
189_I	193_H	3.358	1.00
190_P	193_H	3.167	1.00
192_L	225_I	3.104	1.00
268_T	271_Q	2.710	1.00
182_P	221_A	2.685	1.00
196_V	228_L	2.649	1.00
240_S	247_L	2.612	1.00
185_E	214_A	2.582	1.00
188_L	214_A	2.559	1.00
211_Q	215_A	2.475	1.00
244_T	247_L	2.472	1.00
189_I	210_L	2.313	1.00
126_I	153_I	2.257	1.00
248_I	251_V	2.164	1.00
44_L	130_V	2.146	1.00
260_K	263_T	2.113	1.00
259_I	263_T	2.090	1.00
212_L	215_A	2.046	1.00
220_D	224_V	2.035	1.00
261_Q	265_D	2.022	1.00
263_T	266_R	2.014	1.00
196_V	210_L	1.879	1.00
94_G	98_T	1.830	1.00
116_R	119_D	1.825	1.00
79_W	138_L	1.812	1.00
90_R	93_D	1.805	1.00
193_H	207_D	1.799	1.00
130_V	152_L	1.788	1.00
268_T	272_E	1.781	1.00
246_D	250_E	1.755	1.00
221_A	224_V	1.749	1.00
209_H	212_L	1.746	1.00
228_L	248_I	1.744	1.00
23_E	181_D	1.720	1.00
269_P	272_E	1.718	1.00
45_L	180_F	1.703	1.00
222_R	225_I	1.697	1.00
141_D	145_I	1.693	1.00
192_L	213_I	1.680	1.00
21_D	187_E	1.617	1.00
220_D	223_V	1.613	1.00
192_L	210_L	1.587	1.00
20_R	23_E	1.586	1.00
29_S	237_E	1.538	1.00
34_L	37_G	1.519	1.00
220_D	225_I	1.506	1.00
185_E	189_I	1.502	1.00
250_E	253_P	1.501	1.00
266_R	270_H	1.480	1.00
14_P	62_E	1.475	1.00
246_D	249_E	1.453	1.00
56_I	180_F	1.446	1.00
212_L	245_A	1.438	1.00
267_F	274_L	1.418	1.00
240_S	244_T	1.414	1.00
252_T	255_A	1.414	1.00
205_I	208_S	1.409	1.00
197_H	201_E	1.399	1.00
206_S	209_H	1.392	1.00
216_N	249_E	1.369	1.00
267_F	271_Q	1.357	1.00
17_V	55_C	1.302	1.00
249_E	253_P	1.292	1.00
62_E	66_G	1.279	1.00
193_H	210_L	1.276	1.00
245_A	248_I	1.274	1.00
244_T	251_V	1.273	1.00
245_A	249_E	1.268	1.00
21_D	190_P	1.259	1.00
57_A	151_I	1.259	1.00
260_K	264_V	1.253	1.00
268_T	273_L	1.248	1.00
219_G	223_V	1.241	1.00
97_K	100_D	1.237	1.00
227_I	252_T	1.235	1.00
23_E	178_I	1.234	1.00
271_Q	275_Y	1.226	1.00
234_T	238_T	1.226	1.00
267_F	270_H	1.211	1.00
109_D	113_N	1.203	1.00
115_L	142_L	1.203	1.00
234_T	250_E	1.202	1.00
265_D	268_T	1.185	1.00
251_V	255_A	1.179	1.00
204_V	208_S	1.168	1.00
264_V	268_T	1.159	1.00
26_Y	29_S	1.155	1.00
26_Y	230_H	1.140	1.00
270_H	273_L	1.135	1.00
27_L	60_L	1.124	1.00
212_L	249_E	1.122	1.00
205_I	209_H	1.121	1.00
266_R	269_P	1.096	1.00
247_L	251_V	1.093	1.00
242_Q	245_A	1.087	1.00
257_S	263_T	1.084	1.00
217_A	225_I	1.077	1.00
242_Q	248_I	1.077	1.00
185_E	211_Q	1.067	1.00
202_E	228_L	1.066	1.00
272_E	275_Y	1.062	1.00
44_L	157_E	1.059	1.00
270_H	274_L	1.048	1.00
271_Q	274_L	1.046	1.00
129_E	155_N	1.038	1.00
269_P	273_L	1.033	1.00
257_S	260_K	1.018	1.00
213_I	228_L	1.018	1.00
259_I	264_V	1.015	1.00
111_H	114_R	1.005	1.00
189_I	214_A	0.990	1.00
202_E	243_I	0.990	1.00
263_T	268_T	0.989	1.00
204_V	209_H	0.986	1.00
243_I	247_L	0.976	1.00
257_S	261_Q	0.971	1.00
28_S	32_N	0.965	1.00
263_T	271_Q	0.959	1.00
235_A	238_T	0.958	1.00
205_I	232_A	0.952	1.00
73_Y	126_I	0.944	1.00
23_E	56_I	0.942	1.00
131_D	155_N	0.941	1.00
114_R	118_A	0.941	1.00
221_A	225_I	0.939	1.00
27_L	43_A	0.939	1.00
242_Q	255_A	0.934	1.00
265_D	269_P	0.932	1.00
186_N	190_P	0.932	1.00
127_L	150_M	0.926	1.00
46_Y	177_R	0.925	1.00
242_Q	252_T	0.921	1.00
220_D	227_I	0.910	1.00
234_T	237_E	0.900	1.00
270_H	275_Y	0.898	1.00
186_N	189_I	0.895	1.00
258_E	262_R	0.894	1.00
27_L	178_I	0.886	1.00
250_E	254_E	0.881	1.00
74_Q	120_D	0.873	1.00
244_T	248_I	0.869	1.00
216_N	219_G	0.869	1.00
264_V	271_Q	0.864	1.00
193_H	196_V	0.864	1.00
267_F	275_Y	0.864	1.00
264_V	270_H	0.864	1.00
256_K	259_I	0.861	1.00
266_R	271_Q	0.858	1.00
98_T	109_D	0.858	1.00
19_H	190_P	0.855	1.00
206_S	242_Q	0.845	1.00
258_E	261_Q	0.842	1.00
183_Y	191_I	0.840	1.00
210_L	213_I	0.839	1.00
245_A	252_T	0.838	1.00
207_D	211_Q	0.838	1.00
248_I	252_T	0.837	1.00
257_S	264_V	0.832	1.00
13_I	62_E	0.830	1.00
78_C	133_L	0.827	1.00
209_H	213_I	0.821	1.00
74_Q	123_Y	0.821	1.00
238_T	250_E	0.819	1.00
242_Q	251_V	0.814	1.00
72_N	122_S	0.792	1.00
248_I	255_A	0.790	1.00
113_N	116_R	0.788	1.00
46_Y	179_H	0.788	1.00
261_Q	269_P	0.787	0.99
78_C	127_L	0.787	0.99
241_D	244_T	0.784	0.99
247_L	250_E	0.783	0.99
32_N	36_K	0.783	0.99
21_D	25_N	0.780	0.99
207_D	210_L	0.779	0.99
248_I	254_E	0.779	0.99
263_T	270_H	0.775	0.99
205_I	242_Q	0.774	0.99
262_R	266_R	0.773	0.99
30_V	43_A	0.772	0.99
23_E	180_F	0.771	0.99
60_L	151_I	0.770	0.99
241_D	247_L	0.765	0.99
193_H	211_Q	0.764	0.99
268_T	275_Y	0.762	0.99
261_Q	271_Q	0.759	0.99
196_V	248_I	0.757	0.99
45_L	57_A	0.755	0.99
253_P	257_S	0.753	0.99
216_N	252_T	0.752	0.99
183_Y	188_L	0.751	0.99
266_R	272_E	0.750	0.99
143_Y	147_H	0.745	0.99
252_T	256_K	0.745	0.99
259_I	268_T	0.741	0.99
234_T	247_L	0.741	0.99
261_Q	264_V	0.739	0.99
49_S	169_N	0.736	0.99
92_L	100_D	0.736	0.99
143_Y	146_P	0.730	0.99
33_P	37_G	0.729	0.99
142_L	168_L	0.726	0.99
12_F	62_E	0.725	0.99
226_G	230_H	0.723	0.99
76_V	127_L	0.718	0.99
263_T	267_F	0.715	0.99
198_W	201_E	0.711	0.99
204_V	210_L	0.708	0.99
258_E	270_H	0.707	0.99
267_F	273_L	0.706	0.99
140_Y	167_R	0.705	0.99
262_R	265_D	0.705	0.99
35_T	40_A	0.702	0.99
78_C	90_R	0.701	0.99
212_L	216_N	0.699	0.99
15_R	34_L	0.697	0.99
64_L	73_Y	0.696	0.99
264_V	274_L	0.693	0.99
140_Y	144_R	0.687	0.99
96_G	99_V	0.687	0.99
253_P	256_K	0.685	0.99
26_Y	254_E	0.684	0.99
217_A	222_R	0.682	0.99
258_E	268_T	0.682	0.99
255_A	260_K	0.680	0.99
95_I	98_T	0.679	0.99
118_A	123_Y	0.677	0.98
17_V	24_V	0.675	0.98
48_P	156_D	0.674	0.98
28_S	63_Q	0.671	0.98
167_R	170_S	0.669	0.98
13_I	16_E	0.667	0.98
235_A	247_L	0.667	0.98
29_S	33_P	0.665	0.98
16_E	198_W	0.665	0.98
217_A	223_V	0.664	0.98
258_E	271_Q	0.662	0.98
53_K	128_D	0.661	0.98
233_R	236_R	0.658	0.98
49_S	155_N	0.655	0.98
219_G	225_I	0.653	0.98
27_L	45_L	0.651	0.98
219_G	222_R	0.648	0.98
170_S	183_Y	0.645	0.98
27_L	56_I	0.645	0.98
264_V	269_P	0.644	0.98
229_R	233_R	0.643	0.98
243_I	248_I	0.640	0.98
30_V	33_P	0.640	0.98
254_E	258_E	0.637	0.98
159_D	163_S	0.635	0.98
247_L	255_A	0.634	0.98
186_N	211_Q	0.633	0.98
266_R	273_L	0.630	0.98
118_A	125_V	0.630	0.98
256_K	264_V	0.629	0.98
61_V	73_Y	0.628	0.98
265_D	275_Y	0.626	0.97
241_D	251_V	0.626	0.97
233_R	237_E	0.625	0.97
61_V	126_I	0.625	0.97
131_D	154_A	0.624	0.97
112_L	118_A	0.622	0.97
252_T	257_S	0.619	0.97
20_R	224_V	0.619	0.97
262_R	268_T	0.618	0.97
242_Q	254_E	0.617	0.97
29_S	230_H	0.614	0.97
31_L	35_T	0.613	0.97
58_Q	75_Y	0.610	0.97
18_Q	194_D	0.609	0.97
170_S	222_R	0.607	0.97
188_L	221_A	0.605	0.97
260_K	275_Y	0.604	0.97
157_E	162_A	0.603	0.97
42_S	172_L	0.601	0.97
238_T	246_D	0.600	0.97
24_V	56_I	0.600	0.97
140_Y	143_Y	0.599	0.97
217_A	224_V	0.597	0.97
90_R	141_D	0.596	0.97
188_L	220_D	0.595	0.97
201_E	204_V	0.594	0.97
252_T	260_K	0.594	0.97
262_R	267_F	0.592	0.97
266_R	275_Y	0.592	0.97
130_V	174_D	0.591	0.96
243_I	251_V	0.591	0.96
25_N	28_S	0.590	0.96
266_R	274_L	0.590	0.96
10_P	13_I	0.590	0.96
91_L	94_G	0.587	0.96
94_G	109_D	0.583	0.96
46_Y	174_D	0.581	0.96
113_N	117_T	0.580	0.96
217_A	221_A	0.579	0.96
25_N	238_T	0.578	0.96
209_H	245_A	0.575	0.96
218_G	223_V	0.575	0.96
208_S	211_Q	0.574	0.96
47_G	52_G	0.573	0.96
156_D	162_A	0.571	0.96
30_V	37_G	0.570	0.96
77_N	144_R	0.570	0.96
112_L	115_L	0.568	0.96
261_Q	268_T	0.568	0.96
72_N	120_D	0.566	0.96
208_S	245_A	0.564	0.95
20_R	60_L	0.564	0.95
260_K	267_F	0.562	0.95
91_L	99_V	0.561	0.95
246_D	255_A	0.560	0.95
239_G	244_T	0.560	0.95
79_W	112_L	0.560	0.95
205_I	244_T	0.560	0.95
149_T	153_I	0.558	0.95
241_D	245_A	0.555	0.95
204_V	207_D	0.555	0.95
243_I	255_A	0.552	0.95
264_V	267_F	0.550	0.95
207_D	213_I	0.550	0.95
92_L	95_I	0.549	0.95
48_P	181_D	0.548	0.95
268_T	274_L	0.546	0.95
265_D	270_H	0.543	0.94
29_S	234_T	0.543	0.94
264_V	275_Y	0.542	0.94
245_A	251_V	0.541	0.94
217_A	220_D	0.539	0.94
187_E	190_P	0.537	0.94
230_H	254_E	0.537	0.94
260_K	271_Q	0.536	0.94
264_V	272_E	0.536	0.94
12_F	15_R	0.533	0.94
27_L	57_A	0.533	0.94
267_F	272_E	0.528	0.94
244_T	255_A	0.526	0.93
142_L	150_M	0.526	0.93
196_V	204_V	0.525	0.93
90_R	94_G	0.525	0.93
207_D	212_L	0.524	0.93
255_A	263_T	0.519	0.93
261_Q	267_F	0.519	0.93
36_K	40_A	0.518	0.93
192_L	214_A	0.518	0.93
193_H	197_H	0.516	0.93
165_D	170_S	0.515	0.93
24_V	59_F	0.514	0.93
29_S	233_R	0.514	0.93
91_L	100_D	0.511	0.92
251_V	254_E	0.507	0.92
231_S	251_V	0.506	0.92
256_K	260_K	0.500	0.92

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
4xgcA	1	0.8214	100	0.403	Contact Map
2v1uA	1	0.987	100	0.409	Contact Map
2qbyA	1	0.9805	100	0.41	Contact Map
2qbyB	1	0.9675	100	0.443	Contact Map
1w5sA	1	0.9838	100	0.446	Contact Map
1fnnA	1	0.9805	100	0.457	Contact Map
4ko8A	3	0.7597	100	0.48	Contact Map
4cr2L	1	0.7468	100	0.489	Contact Map
4cr2M	1	0.7695	100	0.49	Contact Map
4cr2I	1	0.7727	100	0.491	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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