NRFG - ECOLI - GREMLIN Contacts

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NRFG - Formate-dependent nitrite reductase complex subunit NrfG

UniProt:	P32712	Sequences: MKQPKIPVKMLTTLTILMVFLCVGSYLLSPKWQAVRAEYQRQRDPLHQFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRVNRTQLVESINMAKLLQRRLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11950
Length:	198 (151)
Sequences:	18384 (16396)
Seq/√Len:	1334.3

ECOLI - NRFG LPSRP HEMY NLPI YFGM BAMD YGEG YFBP YBBN YBGF PGAA YGEH BEPA CCMH BCSC CADC YJCO YPHG YBEQ
BACSU - YSOA YVCD YPIA RAPB RAPF RAPC RAPG RAPD RAPK RAPA RAPJ RAPE RAPH YRRB RAPI SUNS GLUP GUTR
HALSA - Q9HMM8
SULSO - Q97WM3 Q97ZS3 Q97V36 Q97VC4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_N	162_Q	3.018	1.00
88_D	91_N	2.880	1.00
122_S	128_Q	2.849	1.00
147_L	166_L	2.818	1.00
54_T	57_A	2.795	1.00
110_Y	132_M	2.578	1.00
46_L	62_L	2.499	1.00
76_W	95_A	2.449	1.00
80_G	96_Y	2.412	1.00
150_L	166_L	2.400	1.00
114_A	133_I	2.348	1.00
151_A	167_W	2.312	1.00
62_L	78_L	2.274	1.00
42_Q	61_A	2.182	1.00
79_L	95_A	2.176	1.00
134_D	150_L	2.053	1.00
63_Q	79_L	2.050	1.00
83_Y	91_N	1.959	1.00
154_A	166_L	1.923	1.00
97_R	113_L	1.910	1.00
117_L	132_M	1.888	1.00
154_A	162_Q	1.878	1.00
96_Y	112_A	1.868	1.00
133_I	149_L	1.867	1.00
113_L	132_M	1.833	1.00
49_F	57_A	1.781	1.00
117_L	128_Q	1.776	1.00
49_F	61_A	1.774	1.00
45_P	61_A	1.752	1.00
83_Y	95_A	1.726	1.00
93_L	97_R	1.534	1.00
130_R	134_D	1.493	1.00
121_A	126_T	1.462	1.00
164_I	168_Q	1.455	1.00
59_L	63_Q	1.418	1.00
66_I	76_W	1.412	1.00
130_R	157_Q	1.395	1.00
130_R	154_A	1.384	1.00
93_L	120_Q	1.361	1.00
49_F	54_T	1.337	1.00
83_Y	88_D	1.285	1.00
150_L	154_A	1.282	1.00
110_Y	135_K	1.270	1.00
167_W	183_L	1.261	1.00
65_K	75_Q	1.258	1.00
59_L	83_Y	1.258	1.00
93_L	113_L	1.246	1.00
100_L	110_Y	1.239	1.00
79_L	83_Y	1.238	1.00
147_L	169_K	1.229	1.00
47_H	78_L	1.226	1.00
48_Q	52_Q	1.217	1.00
113_L	117_L	1.207	1.00
137_L	147_L	1.203	1.00
66_I	75_Q	1.198	1.00
140_D	143_E	1.189	1.00
72_N	75_Q	1.188	1.00
136_A	146_A	1.169	1.00
154_A	159_N	1.162	1.00
59_L	86_Q	1.155	1.00
137_L	146_A	1.131	1.00
177_R	180_R	1.131	1.00
45_P	49_F	1.127	1.00
103_R	106_N	1.122	1.00
117_L	122_S	1.118	1.00
111_A	149_L	1.103	1.00
76_W	98_Q	1.097	1.00
99_A	109_L	1.095	1.00
100_L	109_L	1.094	1.00
174_N	177_R	1.085	1.00
39_Y	65_K	1.038	1.00
93_L	117_L	1.032	1.00
127_A	157_Q	1.029	1.00
144_I	174_N	1.028	1.00
56_E	86_Q	1.018	1.00
115_T	149_L	0.985	1.00
81_E	112_A	0.985	1.00
69_N	72_N	0.984	1.00
50_A	78_L	0.978	1.00
162_Q	165_E	0.969	1.00
130_R	150_L	0.966	1.00
57_A	60_Q	0.966	1.00
42_Q	64_D	0.964	1.00
116_V	120_Q	0.954	1.00
128_Q	131_A	0.954	1.00
59_L	82_Y	0.932	1.00
98_Q	102_L	0.928	1.00
130_R	153_D	0.926	1.00
46_L	65_K	0.921	1.00
77_A	112_A	0.920	1.00
90_S	120_Q	0.917	1.00
43_R	78_L	0.916	1.00
42_Q	65_K	0.909	1.00
73_S	99_A	0.908	1.00
50_A	62_L	0.903	1.00
43_R	47_H	0.895	1.00
144_I	170_V	0.884	1.00
64_D	68_A	0.884	1.00
59_L	79_L	0.866	1.00
169_K	173_L	0.861	1.00
135_K	139_L	0.859	1.00
148_M	152_S	0.859	1.00
107_A	136_A	0.855	1.00
152_S	155_F	0.853	1.00
153_D	157_Q	0.852	1.00
143_E	146_A	0.849	1.00
132_M	135_K	0.841	1.00
106_N	109_L	0.840	1.00
98_Q	101_Q	0.832	1.00
147_L	170_V	0.830	1.00
42_Q	68_A	0.830	1.00
77_A	81_E	0.829	1.00
47_H	51_S	0.818	1.00
73_S	103_R	0.814	1.00
111_A	115_T	0.804	1.00
89_Y	119_Y	0.802	1.00
118_Y	156_M	0.800	1.00
66_I	79_L	0.789	1.00
93_L	116_V	0.787	1.00
151_A	170_V	0.786	1.00
118_Y	149_L	0.784	1.00
155_F	167_W	0.778	1.00
80_G	99_A	0.777	1.00
166_L	169_K	0.776	1.00
169_K	172_D	0.768	1.00
81_E	85_W	0.762	1.00
76_W	102_L	0.759	1.00
149_L	152_S	0.753	1.00
130_R	159_N	0.753	1.00
126_T	153_D	0.743	1.00
95_A	98_Q	0.741	1.00
89_Y	116_V	0.729	1.00
170_V	180_R	0.722	1.00
80_G	92_S	0.720	1.00
91_N	94_L	0.715	1.00
147_L	173_L	0.712	1.00
55_P	82_Y	0.712	1.00
151_A	163_A	0.705	1.00
118_Y	126_T	0.702	1.00
61_A	64_D	0.696	1.00
107_A	140_D	0.695	1.00
126_T	156_M	0.687	1.00
100_L	113_L	0.685	1.00
118_Y	153_D	0.681	1.00
135_K	138_A	0.674	1.00
111_A	143_E	0.674	1.00
38_E	41_R	0.674	1.00
65_K	68_A	0.672	1.00
84_L	112_A	0.670	1.00
82_Y	86_Q	0.667	1.00
84_L	92_S	0.662	1.00
43_R	72_N	0.658	1.00
114_A	129_T	0.650	1.00
50_A	55_P	0.649	1.00
148_M	170_V	0.644	1.00
126_T	157_Q	0.644	1.00
50_A	85_W	0.640	1.00
134_D	154_A	0.636	1.00
171_M	180_R	0.634	1.00
152_S	183_L	0.632	1.00
155_F	160_Y	0.629	1.00
110_Y	139_L	0.629	1.00
50_A	82_Y	0.629	1.00
84_L	89_Y	0.627	1.00
49_F	52_Q	0.626	1.00
77_A	106_N	0.624	1.00
84_L	116_V	0.617	1.00
163_A	167_W	0.615	1.00
60_Q	64_D	0.614	1.00
152_S	156_M	0.607	1.00
107_A	143_E	0.606	1.00
92_S	96_Y	0.606	1.00
76_W	99_A	0.603	1.00
78_L	81_E	0.596	1.00
77_A	109_L	0.596	1.00
115_T	118_Y	0.596	1.00
136_A	139_L	0.596	1.00
148_M	183_L	0.590	1.00
128_Q	132_M	0.589	1.00
84_L	96_Y	0.588	1.00
93_L	122_S	0.587	1.00
40_Q	44_D	0.583	1.00
58_Q	62_L	0.583	1.00
129_T	153_D	0.578	1.00
148_M	177_R	0.578	1.00
64_D	67_R	0.578	1.00
110_Y	136_A	0.576	1.00
47_H	50_A	0.574	1.00
170_V	173_L	0.571	1.00
57_A	61_A	0.570	1.00
45_P	48_Q	0.569	1.00
114_A	136_A	0.569	1.00
162_Q	166_L	0.568	1.00
41_R	48_Q	0.560	1.00
154_A	157_Q	0.560	1.00
46_L	58_Q	0.560	1.00
97_R	132_M	0.550	1.00
152_S	167_W	0.550	1.00
133_I	153_D	0.550	1.00
91_N	95_A	0.549	1.00
89_Y	120_Q	0.547	1.00
84_L	119_Y	0.546	1.00
95_A	99_A	0.545	1.00
99_A	102_L	0.544	1.00
77_A	99_A	0.541	1.00
180_R	183_L	0.541	1.00
155_F	163_A	0.541	1.00
118_Y	129_T	0.536	1.00
44_D	48_Q	0.532	1.00
81_E	84_L	0.532	1.00
89_Y	93_L	0.530	1.00
168_Q	172_D	0.526	1.00
127_A	130_R	0.523	1.00
134_D	138_A	0.522	1.00
115_T	119_Y	0.517	1.00
171_M	181_T	0.517	1.00
168_Q	171_M	0.517	1.00
44_D	47_H	0.515	1.00
160_Y	164_I	0.514	1.00
131_A	135_K	0.511	1.00
166_L	170_V	0.507	1.00
83_Y	86_Q	0.504	1.00
178_V	181_T	0.504	1.00
118_Y	133_I	0.503	1.00
97_R	101_Q	0.502	1.00
43_R	75_Q	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
4gywA	2	0.8081	99.8	0.269	Contact Map
2pziA	1	0.9242	99.8	0.273	Contact Map
4l9pA	1	0.9747	99.8	0.288	Contact Map
3q7aA	1	0.9545	99.8	0.294	Contact Map
5aioA	1	0.7778	99.8	0.294	Contact Map
3dssA	1	0.9848	99.8	0.295	Contact Map
2e2eA	2	0.8081	99.8	0.304	Contact Map
2h6fA	1	0.9545	99.8	0.306	Contact Map
2vsyA	1	0.6313	99.8	0.309	Contact Map
3urzA	1	0.7828	99.8	0.31	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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