PAIA - BACSU - GREMLIN Contacts

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PAIA - Protease synthase and sporulation negative regulatory protein PAI 1

UniProt:	P21340	Sequences: MSVKMKKCSREDLQTLQQLSIETFNDTFKEQNSPENMKAYLESAFNTEQLEKELSNMSSQFFFIYFDHEIAGYVKVNIDDAQSEEMGAESLEIERIYIKNSFQKHGLGKHLLNKAIEIALERNKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEEQTDLIMAKTLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (145)
Sequences:	13114 (10517)
Seq/√Len:	873.4

ECOLI - YJGM MNAT RIMI YAFP YEDL YJAB YPEA PHNO YIAC ATDA YHHY RIML YJHQ RIMJ
BACSU - PAIA YUAI YTMI YWNH RIMI YHFO YQJY YSNE YDGE YBFA YYAR YYCN YHDJ YESJ BLTD YBBJ SPSD YDAF YOKL YVBK YOAA YRKN YNAD YKKB YJCK YJDG
HALSA - Q9HSL3 Q9HMF0 Q9HRK6 Q9HMI8 Q9HQD2 Q9HNJ3 Q9HRY6 Q9HMZ2
SULSO - Y209 Q7LXZ8 Q97UX1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_K	65_Y	3.280	1.00
116_I	147_F	2.950	1.00
109_K	145_M	2.907	1.00
74_V	115_A	2.816	1.00
22_E	99_K	2.767	1.00
62_F	114_K	2.370	1.00
64_I	107_L	2.316	1.00
109_K	144_K	2.239	1.00
71_A	102_F	2.190	1.00
139_I	143_K	2.145	1.00
66_F	102_F	2.124	1.00
6_K	12_D	2.078	1.00
114_K	117_E	2.027	1.00
118_I	122_R	1.979	1.00
149_Q	152_A	1.954	1.00
63_F	70_I	1.946	1.00
113_N	145_M	1.942	1.00
91_L	119_A	1.883	1.00
143_K	149_Q	1.869	1.00
8_C	16_L	1.849	1.00
72_G	98_I	1.783	1.00
112_L	145_M	1.749	1.00
116_I	127_I	1.716	1.00
76_V	115_A	1.710	1.00
66_F	105_H	1.696	1.00
66_F	71_A	1.691	1.00
103_Q	137_N	1.656	1.00
118_I	121_E	1.626	1.00
102_F	105_H	1.611	1.00
61_F	75_K	1.586	1.00
140_A	143_K	1.561	1.00
129_L	142_Y	1.559	1.00
60_Q	118_I	1.552	1.00
139_I	149_Q	1.515	1.00
15_T	18_Q	1.514	1.00
18_Q	22_E	1.394	1.00
62_F	118_I	1.366	1.00
78_I	124_K	1.337	1.00
109_K	113_N	1.336	1.00
69_E	101_S	1.336	1.00
15_T	70_I	1.334	1.00
65_Y	70_I	1.331	1.00
47_T	51_E	1.294	1.00
69_E	99_K	1.290	1.00
17_Q	21_I	1.287	1.00
77_N	94_E	1.279	1.00
119_A	127_I	1.266	1.00
114_K	118_I	1.257	1.00
14_Q	47_T	1.253	1.00
91_L	124_K	1.252	1.00
19_L	23_T	1.236	1.00
34_P	38_K	1.210	1.00
8_C	63_F	1.200	1.00
90_S	128_W	1.194	1.00
76_V	119_A	1.186	1.00
18_Q	99_K	1.185	1.00
74_V	111_L	1.174	1.00
74_V	93_I	1.160	1.00
131_V	135_N	1.149	1.00
65_Y	68_H	1.136	1.00
90_S	126_N	1.131	1.00
136_E	140_A	1.124	1.00
60_Q	122_R	1.123	1.00
5_M	62_F	1.107	1.00
7_K	118_I	1.091	1.00
133_E	152_A	1.087	1.00
138_A	142_Y	1.087	1.00
23_T	97_Y	1.081	1.00
131_V	139_I	1.078	1.00
19_L	70_I	1.075	1.00
36_N	39_A	1.072	1.00
10_R	51_E	1.063	1.00
127_I	147_F	1.058	1.00
117_E	121_E	1.054	1.00
4_K	65_Y	1.052	1.00
26_D	100_N	1.048	1.00
22_E	100_N	1.039	1.00
93_I	112_L	1.033	1.00
46_N	49_Q	1.028	1.00
136_E	139_I	1.024	1.00
89_E	125_K	1.013	1.00
66_F	69_E	0.995	1.00
20_S	73_Y	0.992	1.00
15_T	69_E	0.981	1.00
51_E	55_S	0.981	1.00
69_E	102_F	0.953	1.00
104_K	137_N	0.952	1.00
112_L	147_F	0.950	1.00
33_S	36_N	0.946	1.00
71_A	107_L	0.941	1.00
19_L	99_K	0.933	1.00
110_H	113_N	0.931	1.00
22_E	101_S	0.920	1.00
98_I	107_L	0.906	1.00
92_E	128_W	0.892	1.00
7_K	62_F	0.871	1.00
141_F	145_M	0.868	1.00
5_M	114_K	0.867	1.00
5_M	110_H	0.867	1.00
129_L	138_A	0.858	1.00
9_S	12_D	0.847	1.00
7_K	60_Q	0.847	1.00
135_N	138_A	0.834	1.00
17_Q	47_T	0.833	1.00
76_V	118_I	0.829	1.00
116_I	120_L	0.827	1.00
13_L	17_Q	0.814	1.00
113_N	117_E	0.810	1.00
20_S	50_L	0.810	1.00
119_A	124_K	0.808	1.00
112_L	142_Y	0.807	1.00
10_R	55_S	0.803	1.00
108_G	141_F	0.801	1.00
99_K	102_F	0.798	1.00
153_H	157_M	0.780	1.00
8_C	13_L	0.775	1.00
154_S	157_M	0.774	1.00
79_D	128_W	0.773	1.00
113_N	116_I	0.763	1.00
92_E	130_G	0.755	1.00
106_G	109_K	0.754	1.00
14_Q	18_Q	0.749	1.00
79_D	92_E	0.745	1.00
78_I	91_L	0.745	1.00
107_L	110_H	0.741	1.00
64_I	71_A	0.740	1.00
8_C	61_F	0.736	1.00
92_E	95_R	0.736	1.00
75_K	94_E	0.736	1.00
48_E	52_K	0.736	1.00
6_K	63_F	0.735	1.00
78_I	122_R	0.730	1.00
153_H	156_Y	0.729	1.00
64_I	111_L	0.727	1.00
52_K	56_N	0.726	1.00
20_S	24_F	0.722	1.00
21_I	25_N	0.720	1.00
64_I	110_H	0.714	1.00
16_L	73_Y	0.712	1.00
32_N	37_M	0.706	1.00
112_L	141_F	0.700	1.00
18_Q	69_E	0.690	1.00
72_G	111_L	0.688	1.00
35_E	39_A	0.685	1.00
116_I	145_M	0.684	1.00
64_I	72_G	0.684	1.00
110_H	114_K	0.684	1.00
33_S	37_M	0.681	1.00
46_N	54_L	0.681	1.00
93_I	115_A	0.669	1.00
74_V	96_I	0.662	1.00
48_E	51_E	0.655	1.00
10_R	13_L	0.655	1.00
79_D	88_A	0.652	1.00
24_F	97_Y	0.650	1.00
104_K	140_A	0.646	1.00
93_I	129_L	0.646	1.00
131_V	138_A	0.645	1.00
53_E	75_K	0.645	1.00
102_F	107_L	0.642	1.00
12_D	65_Y	0.642	1.00
15_T	19_L	0.638	1.00
126_N	150_T	0.630	1.00
96_I	142_Y	0.622	1.00
60_Q	76_V	0.619	1.00
109_K	140_A	0.618	1.00
79_D	90_S	0.612	1.00
34_P	37_M	0.611	1.00
30_E	33_S	0.606	1.00
140_A	144_K	0.595	1.00
104_K	144_K	0.594	1.00
24_F	27_T	0.594	1.00
8_C	12_D	0.593	1.00
96_I	112_L	0.589	1.00
128_W	150_T	0.587	1.00
50_L	61_F	0.583	1.00
22_E	26_D	0.581	1.00
49_Q	53_E	0.579	1.00
89_E	124_K	0.576	1.00
45_F	49_Q	0.576	1.00
13_L	51_E	0.575	1.00
112_L	116_I	0.567	1.00
46_N	50_L	0.567	1.00
14_Q	17_Q	0.566	1.00
45_F	50_L	0.563	1.00
72_G	107_L	0.562	1.00
75_K	95_R	0.560	1.00
59_S	75_K	0.559	1.00
25_N	29_K	0.556	1.00
117_E	120_L	0.550	1.00
129_L	147_F	0.549	1.00
35_E	38_K	0.547	1.00
45_F	53_E	0.547	1.00
49_Q	52_K	0.544	1.00
98_I	102_F	0.543	1.00
77_N	92_E	0.542	1.00
134_K	139_I	0.540	1.00
50_L	53_E	0.528	1.00
32_N	36_N	0.526	1.00
130_G	157_M	0.524	1.00
50_L	54_L	0.524	1.00
137_N	140_A	0.521	1.00
5_M	111_L	0.521	1.00
96_I	129_L	0.519	1.00
62_F	74_V	0.519	1.00
20_S	97_Y	0.519	1.00
24_F	28_F	0.512	1.00
22_E	25_N	0.509	1.00
26_D	103_Q	0.509	1.00
98_I	111_L	0.508	1.00
18_Q	21_I	0.507	1.00
73_Y	97_Y	0.506	1.00
64_I	98_I	0.505	1.00
20_S	95_R	0.505	1.00
76_V	91_L	0.504	1.00
60_Q	78_I	0.502	1.00
143_K	148_V	0.501	1.00
20_S	45_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
1tiqA	1	0.9942	99.9	0.25	Contact Map
3fixA	2	0.9012	99.9	0.285	Contact Map
2j8mA	2	0.9419	99.9	0.287	Contact Map
4e2aA	2	0.9826	99.9	0.3	Contact Map
3dr6A	2	0.9419	99.9	0.305	Contact Map
2cy2A	1	0.9709	99.9	0.313	Contact Map
3fncA	2	0.9302	99.9	0.319	Contact Map
4h89A	2	0.936	99.9	0.324	Contact Map
4j3gA	2	0.936	99.9	0.332	Contact Map
3kkwA	1	0.9128	99.9	0.341	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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