Q9HNM3 - HALSA - GREMLIN Contacts

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Q9HNM3 - HoxA-like transcriptional regulator

UniProt:	Q9HNM3	Sequences: MRSTEPVVLVVDDEPRVAEAFALWLEDDYEVRTATSGAAALEAADDDVSVALLDRQMPTMTGDEVLAALRERALDIRVAMVTGIDPDFDIVEMPFDEYIQKPVDGDTLHDVVARLRTLNQYDDSIDELYRVTQKLATLEAQLSERALADNDEYQRLRERKATLSEAADAALDAAGTSTDALGDEFARLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	189 (174)
Sequences:	71644 (53111)
Seq/√Len:	4026.3

ECOLI - YHJB NARP CUSR UVRY DPIA EVGA YJJQ CREB BGLJ PHOP YEDW FIMZ DCUR QSEB BASR PHOB NARL CSGD UHPA RCSA RCSB CPXR YGEK OMPR ARCA TORS BAER KDPE RSTA YPDB RSSB TORR BARA ARCB RCSC GLRR ZRAR CHEB YEHT NTRC ATOC RCSD EVGS CHEY
BACSU - YXJL DCTR MALR YFIK PHOP DEGU CITT CMPA YVFU LIAR CSSR DESR RESD YRKP GLNL YCBL YKOG YHCZ YDFI YYCF YXDJ YCLJ YVRH CHEB YVCP YBDJ YESN BCER NATR LYTT SP0A CHEV
HALSA - Q9HNM3 Q9HRE5 Q9HR09 CHEB BAT O51970 Q9HP91

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_A	33_T	3.884	1.00
18_A	35_T	3.499	1.00
22_A	33_T	3.433	1.00
11_V	40_A	2.867	1.00
41_L	68_A	2.769	1.00
38_A	59_T	2.641	1.00
32_R	48_V	2.516	1.00
60_M	68_A	2.474	1.00
37_G	60_M	2.375	1.00
36_S	59_T	2.357	1.00
45_D	72_R	2.321	1.00
24_W	105_G	2.245	1.00
7_V	32_R	2.232	1.00
34_A	43_A	2.118	1.00
22_A	26_E	2.042	1.00
56_Q	84_I	2.027	1.00
7_V	30_E	2.005	1.00
53_L	65_V	1.953	1.00
35_T	39_A	1.904	1.00
165_E	168_D	1.885	1.00
87_D	107_T	1.838	1.00
32_R	43_A	1.824	1.00
36_S	39_A	1.797	1.00
66_L	78_V	1.779	1.00
9_L	34_A	1.779	1.00
80_M	95_F	1.743	1.00
68_A	72_R	1.721	1.00
80_M	90_I	1.720	1.00
70_R	96_D	1.704	1.00
67_A	93_M	1.689	1.00
37_G	65_V	1.614	1.00
6_P	116_R	1.555	1.00
60_M	64_E	1.551	1.00
97_E	111_V	1.531	1.00
61_T	64_E	1.492	1.00
44_A	69_L	1.482	1.00
25_L	112_V	1.474	1.00
38_A	60_M	1.463	1.00
141_Q	144_E	1.447	1.00
43_A	46_D	1.443	1.00
51_A	76_I	1.430	1.00
68_A	71_E	1.412	1.00
170_A	173_A	1.394	1.00
15_P	35_T	1.393	1.00
55_R	63_D	1.374	1.00
43_A	48_V	1.312	1.00
66_L	80_M	1.295	1.00
50_V	112_V	1.264	1.00
79_A	115_L	1.263	1.00
129_Y	133_Q	1.249	1.00
63_D	90_I	1.246	1.00
41_L	65_V	1.244	1.00
64_E	67_A	1.226	1.00
89_D	93_M	1.216	1.00
29_Y	113_A	1.211	1.00
151_D	159_R	1.204	1.00
13_D	54_D	1.198	1.00
109_H	113_A	1.197	1.00
41_L	60_M	1.195	1.00
96_D	115_L	1.188	1.00
11_V	57_M	1.169	1.00
9_L	48_V	1.168	1.00
34_A	40_A	1.160	1.00
12_D	18_A	1.154	1.00
39_A	43_A	1.148	1.00
42_E	46_D	1.147	1.00
53_L	66_L	1.125	1.00
73_A	76_I	1.120	1.00
38_A	42_E	1.114	1.00
96_D	118_L	1.103	1.00
9_L	40_A	1.095	1.00
55_R	80_M	1.093	1.00
9_L	43_A	1.093	1.00
63_D	89_D	1.092	1.00
39_A	42_E	1.091	1.00
165_E	169_A	1.077	1.00
8_V	29_Y	1.075	1.00
28_D	113_A	1.068	1.00
88_F	92_E	1.044	1.00
41_L	45_D	1.031	1.00
169_A	172_D	1.030	1.00
139_E	142_L	1.014	1.00
87_D	100_Q	1.014	1.00
147_L	151_D	1.013	1.00
153_Y	156_L	1.002	1.00
110_D	114_R	0.998	1.00
131_V	134_K	0.982	1.00
50_V	116_R	0.977	1.00
34_A	39_A	0.970	1.00
7_V	49_S	0.969	1.00
22_A	31_V	0.961	1.00
40_A	65_V	0.958	1.00
130_R	133_Q	0.957	1.00
55_R	61_T	0.950	1.00
10_V	21_F	0.949	1.00
151_D	155_R	0.947	1.00
129_Y	132_T	0.947	1.00
21_F	81_V	0.933	1.00
136_A	139_E	0.933	1.00
51_A	69_L	0.931	1.00
152_E	155_R	0.927	1.00
107_T	110_D	0.924	1.00
19_E	33_T	0.923	1.00
123_D	126_D	0.922	1.00
77_R	96_D	0.917	1.00
92_E	113_A	0.913	1.00
40_A	44_A	0.910	1.00
67_A	89_D	0.901	1.00
130_R	134_K	0.898	1.00
15_P	19_E	0.895	1.00
139_E	143_S	0.890	1.00
9_L	44_A	0.889	1.00
63_D	93_M	0.884	1.00
53_L	78_V	0.882	1.00
11_V	34_A	0.880	1.00
66_L	95_F	0.874	1.00
16_R	20_A	0.870	1.00
29_Y	109_H	0.862	1.00
11_V	51_A	0.861	1.00
6_P	29_Y	0.858	1.00
42_E	45_D	0.857	1.00
168_D	171_L	0.853	1.00
171_L	175_G	0.852	1.00
6_P	120_Q	0.851	1.00
127_E	131_V	0.844	1.00
146_A	151_D	0.843	1.00
107_T	111_V	0.840	1.00
66_L	93_M	0.833	1.00
145_R	148_A	0.826	1.00
128_L	132_T	0.824	1.00
166_A	170_A	0.823	1.00
19_E	22_A	0.819	1.00
135_L	139_E	0.816	1.00
173_A	176_T	0.810	1.00
164_S	168_D	0.809	1.00
64_E	68_A	0.808	1.00
105_G	109_H	0.804	1.00
85_D	100_Q	0.789	1.00
55_R	84_I	0.787	1.00
15_P	18_A	0.778	1.00
89_D	92_E	0.775	1.00
52_L	108_L	0.773	1.00
7_V	48_V	0.771	1.00
169_A	173_A	0.771	1.00
142_L	177_S	0.763	1.00
23_L	27_D	0.762	1.00
51_A	78_V	0.759	1.00
129_Y	134_K	0.757	1.00
115_L	118_L	0.754	1.00
146_A	149_D	0.753	1.00
53_L	80_M	0.751	1.00
158_E	161_A	0.749	1.00
165_E	172_D	0.740	1.00
79_A	111_V	0.739	1.00
10_V	31_V	0.734	1.00
44_A	48_V	0.733	1.00
119_N	123_D	0.732	1.00
149_D	168_D	0.730	1.00
65_V	69_L	0.730	1.00
147_L	153_Y	0.729	1.00
52_L	81_V	0.722	1.00
122_D	127_E	0.718	1.00
114_R	117_T	0.717	1.00
114_R	119_N	0.714	1.00
44_A	73_A	0.710	1.00
17_V	103_V	0.709	1.00
57_M	65_V	0.709	1.00
140_A	144_E	0.707	1.00
60_M	65_V	0.705	1.00
149_D	159_R	0.704	1.00
163_L	166_A	0.702	1.00
148_A	151_D	0.702	1.00
56_Q	83_G	0.694	1.00
81_V	103_V	0.694	1.00
157_R	160_K	0.690	1.00
87_D	104_D	0.687	1.00
11_V	65_V	0.687	1.00
19_E	23_L	0.682	1.00
67_A	71_E	0.682	1.00
20_A	24_W	0.681	1.00
123_D	127_E	0.681	1.00
21_F	108_L	0.676	1.00
44_A	76_I	0.676	1.00
14_E	17_V	0.669	1.00
150_N	153_Y	0.665	1.00
127_E	130_R	0.665	1.00
91_V	111_V	0.660	1.00
172_D	176_T	0.654	1.00
37_G	59_T	0.650	1.00
37_G	41_L	0.645	1.00
146_A	159_R	0.644	1.00
136_A	143_S	0.642	1.00
146_A	152_E	0.640	1.00
44_A	51_A	0.637	1.00
135_L	143_S	0.637	1.00
69_L	78_V	0.634	1.00
122_D	126_D	0.633	1.00
52_L	112_V	0.632	1.00
153_Y	168_D	0.631	1.00
24_W	109_H	0.630	1.00
41_L	72_R	0.630	1.00
145_R	151_D	0.628	1.00
128_L	131_V	0.627	1.00
97_E	114_R	0.627	1.00
116_R	119_N	0.626	1.00
104_D	107_T	0.625	1.00
127_E	134_K	0.622	1.00
90_I	95_F	0.620	1.00
136_A	140_A	0.619	1.00
70_R	77_R	0.614	1.00
12_D	57_M	0.612	1.00
17_V	20_A	0.612	1.00
152_E	156_L	0.611	1.00
77_R	116_R	0.608	1.00
103_V	108_L	0.608	1.00
47_D	73_A	0.607	1.00
140_A	143_S	0.607	1.00
149_D	153_Y	0.606	1.00
146_A	150_N	0.606	1.00
128_L	133_Q	0.605	1.00
41_L	44_A	0.603	1.00
151_D	156_L	0.602	1.00
18_A	22_A	0.602	1.00
26_E	31_V	0.601	1.00
162_T	167_A	0.599	1.00
88_F	106_D	0.598	1.00
152_E	157_R	0.595	1.00
106_D	110_D	0.594	1.00
39_A	59_T	0.593	1.00
8_V	50_V	0.592	1.00
8_V	25_L	0.591	1.00
122_D	129_Y	0.579	1.00
55_R	90_I	0.579	1.00
45_D	73_A	0.578	1.00
10_V	22_A	0.577	1.00
136_A	142_L	0.576	1.00
111_V	115_L	0.573	1.00
135_L	142_L	0.571	1.00
14_E	83_G	0.571	1.00
88_F	91_V	0.570	1.00
124_S	127_E	0.569	1.00
37_G	57_M	0.568	1.00
154_Q	164_S	0.564	1.00
126_D	129_Y	0.563	1.00
45_D	68_A	0.550	1.00
155_R	159_R	0.549	1.00
79_A	97_E	0.547	1.00
92_E	110_D	0.544	1.00
10_V	33_T	0.541	1.00
153_Y	157_R	0.541	1.00
126_D	130_R	0.540	1.00
147_L	150_N	0.540	1.00
6_P	49_S	0.533	1.00
77_R	118_L	0.530	1.00
125_I	129_Y	0.521	1.00
149_D	156_L	0.518	1.00
25_L	29_Y	0.516	1.00
75_D	121_Y	0.516	1.00
66_L	70_R	0.507	1.00
69_L	74_L	0.506	1.00
20_A	23_L	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
1yioA	1	0.9841	100	0.267	Contact Map
3c3wA	2	0.9788	100	0.277	Contact Map
4gvpA	1	0.9788	100	0.281	Contact Map
3kloA	2	0.9894	100	0.295	Contact Map
4b09A	2	0.9048	100	0.297	Contact Map
1a04A	1	0.9683	100	0.298	Contact Map
4ldzA	2	0.9735	100	0.303	Contact Map
4hyeA	2	0.9735	100	0.309	Contact Map
1ys7A	2	0.9735	100	0.328	Contact Map
2gwrA	1	0.9894	100	0.332	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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