PHNO - ECOLI - GREMLIN Contacts

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PHNO - Protein PhnO

UniProt:	P16691	Sequences: MPACELRPATQYDTDAVYALICELKQAEFDHHAFRVGFNANLRDPNMRYHLALLDGEVVGMIGLHLQFHLHHVNWIGEIQELVVMPQARGLNVGSKLLAWAEEEARQAGAEMTELSTNVKRHDAHRFYLREGYEQSHFRFTKAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10724
Length:	144 (135)
Sequences:	10802 (8528)
Seq/√Len:	733.9

ECOLI - PHNO YJGM YPEA MNAT RIMI YEDL YAFP YIAC YJAB YHHY ATDA RIML YJHQ YHBS
BACSU - YHFO YHDJ YQJY YTMI RIMI PAIA YWNH YDGE YSNE YYAR YBFA YESJ YYCN YUAI SPSD YVBK YBBJ BLTD YITH YOKL YKKB YOBR YRKN YOAA YNAD YJCK YDAF YJDG
HALSA - Q9HQD2 Q9HMF0 Q9HMI8 Q9HSL3 Q9HRK6 Q9HNJ3
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
7_R	53_L	3.559	1.00
102_E	133_Y	2.999	1.00
23_E	85_M	2.982	1.00
59_V	88_A	2.455	1.00
62_I	101_A	2.435	1.00
100_W	103_E	2.347	1.00
51_L	58_V	2.286	1.00
95_S	131_E	2.138	1.00
95_S	130_R	2.097	1.00
50_H	100_W	2.090	1.00
104_E	108_A	2.066	1.00
77_G	105_A	2.028	1.00
16_A	19_A	2.005	1.00
52_A	93_V	1.932	1.00
54_L	88_A	1.814	1.00
102_E	113_T	1.799	1.00
122_H	126_R	1.793	1.00
104_E	107_Q	1.727	1.00
88_A	91_L	1.723	1.00
7_R	13_D	1.657	1.00
53_L	58_V	1.597	1.00
54_L	91_L	1.551	1.00
64_L	101_A	1.550	1.00
100_W	104_E	1.546	1.00
9_A	17_V	1.541	1.00
57_E	85_M	1.537	1.00
48_R	104_E	1.501	1.00
16_A	58_V	1.483	1.00
126_R	129_L	1.477	1.00
19_A	85_M	1.476	1.00
98_L	131_E	1.474	1.00
129_L	135_Q	1.468	1.00
125_H	129_L	1.422	1.00
57_E	87_Q	1.415	1.00
135_Q	138_F	1.397	1.00
95_S	99_A	1.394	1.00
50_H	104_E	1.391	1.00
53_L	56_G	1.388	1.00
54_L	59_V	1.366	1.00
60_G	84_V	1.352	1.00
19_A	23_E	1.345	1.00
99_A	131_E	1.336	1.00
103_E	107_Q	1.327	1.00
48_R	108_A	1.313	1.00
5_E	53_L	1.260	1.00
25_K	28_E	1.257	1.00
59_V	93_V	1.250	1.00
117_T	121_R	1.244	1.00
66_L	110_A	1.235	1.00
105_A	110_A	1.229	1.00
92_N	95_S	1.229	1.00
115_L	128_Y	1.226	1.00
102_E	106_R	1.210	1.00
66_L	108_A	1.186	1.00
11_Q	42_L	1.145	1.00
4_C	54_L	1.133	1.00
117_T	125_H	1.130	1.00
62_I	97_L	1.111	1.00
119_V	138_F	1.110	1.00
77_G	110_A	1.094	1.00
48_R	64_L	1.079	1.00
16_A	57_E	1.068	1.00
30_D	33_A	1.057	1.00
85_M	88_A	1.053	1.00
52_A	60_G	1.053	1.00
62_I	79_I	1.050	1.00
115_L	133_Y	1.046	1.00
64_L	104_E	1.040	1.00
124_A	128_Y	1.024	1.00
67_Q	78_E	1.022	1.00
9_A	51_L	1.020	1.00
96_K	99_A	1.014	1.00
79_I	98_L	1.012	1.00
76_I	112_M	1.006	1.00
122_H	125_H	0.993	1.00
125_H	135_Q	0.973	1.00
8_P	48_R	0.972	1.00
89_R	123_D	0.962	1.00
57_E	88_A	0.957	1.00
18_Y	22_C	0.952	1.00
9_A	49_Y	0.946	1.00
117_T	124_A	0.935	1.00
20_L	58_V	0.930	1.00
84_V	93_V	0.928	1.00
14_T	18_Y	0.927	1.00
35_R	39_N	0.923	1.00
39_N	42_L	0.922	1.00
105_A	113_T	0.916	1.00
94_G	127_F	0.904	1.00
34_F	37_G	0.899	1.00
76_I	114_E	0.890	1.00
23_E	86_P	0.884	1.00
15_D	19_A	0.883	1.00
54_L	57_E	0.867	1.00
39_N	43_R	0.860	1.00
37_G	41_N	0.845	1.00
99_A	102_E	0.842	1.00
98_L	133_Y	0.837	1.00
4_C	96_K	0.835	1.00
38_F	41_N	0.833	1.00
15_D	35_R	0.825	1.00
90_G	123_D	0.825	1.00
65_H	80_Q	0.821	1.00
8_P	50_H	0.816	1.00
17_V	61_M	0.811	1.00
64_L	105_A	0.809	1.00
21_I	61_M	0.802	1.00
115_L	124_A	0.800	1.00
90_G	130_R	0.799	1.00
6_L	50_H	0.796	1.00
123_D	126_R	0.795	1.00
24_L	28_E	0.790	1.00
16_A	85_M	0.787	1.00
61_M	83_V	0.779	1.00
7_R	51_L	0.778	1.00
78_E	116_S	0.775	1.00
34_F	38_F	0.775	1.00
33_A	37_G	0.770	1.00
4_C	52_A	0.767	1.00
98_L	128_Y	0.756	1.00
29_F	33_A	0.750	1.00
100_W	107_Q	0.744	1.00
6_L	96_K	0.739	1.00
11_Q	39_N	0.736	1.00
67_Q	76_I	0.732	1.00
121_R	124_A	0.730	1.00
4_C	93_V	0.717	1.00
24_L	27_A	0.715	1.00
79_I	82_L	0.708	1.00
16_A	20_L	0.707	1.00
23_E	83_V	0.707	1.00
23_E	87_Q	0.705	1.00
66_L	77_G	0.704	1.00
8_P	104_E	0.701	1.00
127_F	131_E	0.700	1.00
82_L	128_Y	0.698	1.00
96_K	100_W	0.696	1.00
78_E	114_E	0.694	1.00
102_E	131_E	0.694	1.00
103_E	106_R	0.692	1.00
98_L	127_F	0.687	1.00
37_G	40_A	0.679	1.00
13_D	53_L	0.676	1.00
20_L	24_L	0.668	1.00
66_L	75_W	0.663	1.00
49_Y	63_G	0.661	1.00
6_L	100_W	0.660	1.00
40_A	43_R	0.655	1.00
38_F	42_L	0.650	1.00
9_A	14_T	0.640	1.00
60_G	93_V	0.637	1.00
69_H	80_Q	0.633	1.00
20_L	83_V	0.630	1.00
36_V	39_N	0.626	1.00
10_T	13_D	0.617	1.00
127_F	130_R	0.616	1.00
31_H	35_R	0.614	1.00
63_G	80_Q	0.613	1.00
79_I	115_L	0.612	1.00
19_A	22_C	0.610	1.00
93_V	96_K	0.609	1.00
29_F	37_G	0.607	1.00
99_A	103_E	0.604	1.00
88_A	93_V	0.604	1.00
33_A	41_N	0.602	1.00
113_T	133_Y	0.596	1.00
71_H	74_N	0.589	1.00
48_R	66_L	0.588	1.00
24_L	83_V	0.587	1.00
78_E	81_E	0.587	1.00
36_V	40_A	0.587	1.00
90_G	94_G	0.580	1.00
112_M	136_S	0.579	1.00
34_F	41_N	0.578	1.00
46_N	75_W	0.574	1.00
129_L	134_E	0.567	1.00
16_A	51_L	0.561	1.00
52_A	97_L	0.559	1.00
60_G	97_L	0.558	1.00
9_A	13_D	0.556	1.00
122_H	129_L	0.556	1.00
52_A	59_V	0.552	1.00
22_C	31_H	0.551	1.00
22_C	26_Q	0.549	1.00
32_H	36_V	0.547	1.00
15_D	38_F	0.544	1.00
120_K	123_D	0.544	1.00
29_F	34_F	0.536	1.00
19_A	57_E	0.531	1.00
74_N	111_E	0.527	1.00
32_H	37_G	0.524	1.00
121_R	125_H	0.519	1.00
75_W	111_E	0.514	1.00
24_L	80_Q	0.513	1.00
40_A	44_D	0.513	1.00
75_W	110_A	0.513	1.00
47_M	81_E	0.511	1.00
31_H	34_F	0.509	1.00
18_Y	34_F	0.500	0.99
11_Q	14_T	0.500	0.99
84_V	97_L	0.500	0.99
21_I	81_E	0.500	0.99

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
3fynA	2	0.9375	99.9	0.289	Contact Map
2b5gA	2	0.9861	99.9	0.292	Contact Map
3t9yA	2	0.9097	99.9	0.293	Contact Map
3jvnA	2	0.7847	99.9	0.295	Contact Map
1vkcA	2	0.9722	99.9	0.299	Contact Map
1z4eA	2	0.9861	99.9	0.3	Contact Map
4yfjA	2	1	99.9	0.304	Contact Map
1s3zA	2	0.9861	99.9	0.305	Contact Map
2fe7A	3	1	99.9	0.307	Contact Map
3i9sA	4	0.9931	99.8	0.313	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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