APPF - BACSU - GREMLIN Contacts

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APPF - Oligopeptide transport ATP-binding protein AppF

UniProt:	P42065	Sequences: MTAANQETILELRDVKKYFPIRSGLFQRKVGDVKAVDGVSFSLKKGETLGIVGESGCGKSTAGRTMIRLYKPTEGQILFKGQDISNLSEEKLRKSVRKNIQMVFQDPFASLNPRKTLRSIIKEPFNTHNMYTMRERNEKVEELLARVGLHPSFAGRYPHEFSGGQRQRIGIARALTLNPELIIADEPVSALDVSIQAQVINLMEELQEEFNLTYLFISHDLSVVRHISDRVGVMYLGKMMELTGKHELYDNPLHPYTQALLSSVPVTRKRGSVKRERIVLKGELPSPANPPKGCVFHTRCPVAKPICKEQIPEFKEAAPSHFVACHLYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (265)
Sequences:	51333 (32720)
Seq/√Len:	2010.0

ECOLI - OPPF POTA FBPC SAPD PROV POTG CYSA MALK YCJV OPPD DDPF UGPC DPPF DPPD DDPD YDCT METN MODC YEHX YADG GSIA ARAG RBSA YHES MDLA MACB UUP FEPC MDLB CYDC SAPF NIKE MSBA CYDD MLAF HISP YECC TAUB YTFR YOJI FHUC FECE LSRA PHNC SSUB GLNQ PHNK LPTB YHDZ ETTA GLTL YPHE MODF SUFC ARTP XYLG LIVG ZNUC PSTB ALSA LIVF THIQ LOLD BTUD NIKD FTSE FETA MGLA YEJF YBBA YDDA CCMA PHNL YBHF YNJD YBIT YHIH
BACSU - APPF OPUCA OPUBA YKFD OPUAA YVRA MSMX YURJ OPPD APPD DPPD METN OPPF YKPA YFIL YHCH YCBN TAGH YFMM YXLF YHEH YVFR YDBJ YHAQ RBSA YFIB YDIF ECFA1 SUNT YFIC YUSV YFMF YGAD BMRA YWJA FHUC YHEI YKNV YKNU YFMR CYDD YTRB TCYN CYDC YCLP SUFC YLMA YTLC BCEA YXDL ECSA ECFA2 SKFE YVCR YKOD NATA YXEO SSUB ARTM GLNQ ALBC MNTB TCYC YJKB FTSE PSTB1 PSTB2 YVRO YTHP EXPZ YKNY YCLH YUFO YHCG ZNUC YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HHQ5 Q9HMX2 Q9HNZ9 Q9HMT3 Q9HR06 Q9HMG1 Q9HRJ6 Q9HMU8 Q9HSQ7 Q9HRH8 PSTB2 Q9HMG6 PHNC Q9HHM2 Q9HNY3 Q9HRV7 Q9HRZ9 PSTB1 Y1631 Y2317 Q9HHR7 Q9HR96 Q9HS04 Q9HT03 Q9HR21 Q9HQA8 Q9HMC1 Q9HMW1
SULSO - Q97YP7 Q97UF2 Q97UY8 Q97VF5 Q97VK8 Q97YP8 Q97UH3 Q97YY4 Q97VF4 Q97ZC0 Q97YP3 Q97UJ9 Q7LX64 Q97VC1 Q97VK9 Q97VH6 Q97UD4 Q97YK2 Q97X18 Q97YQ7 Y1893 Q97Z03 Q97U54 Y2030 Q97UH4 Q980W0 PSTB Q97W42 Q7LXM4 Q7LY07 Q97V01 Q97VM2 Q97VY4 Q97V00 Q7LX80 Q97UG5 Q97Z56 Q97YP4 Q97UC2 Q97Z96 Q980K5 Q97ZU0 Q980E6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_E	230_R	4.667	1.00
99_N	180_E	3.848	1.00
34_K	37_D	3.336	1.00
49_L	232_G	3.124	1.00
76_Q	83_D	3.038	1.00
44_K	47_E	3.000	1.00
230_R	242_L	2.926	1.00
50_G	228_S	2.842	1.00
244_G	247_E	2.829	1.00
80_K	180_E	2.806	1.00
232_G	239_M	2.618	1.00
132_T	135_E	2.612	1.00
23_S	38_G	2.603	1.00
153_F	156_R	2.600	1.00
37_D	238_K	2.368	1.00
115_K	119_S	2.318	1.00
20_P	42_S	2.278	1.00
139_K	142_E	2.160	1.00
22_R	76_Q	2.149	1.00
45_K	180_E	2.145	1.00
63_G	217_I	2.109	1.00
243_T	248_L	2.108	1.00
83_D	86_N	2.096	1.00
139_K	178_N	2.081	1.00
225_R	246_H	2.076	1.00
143_L	176_T	2.023	1.00
63_G	183_I	1.994	1.00
232_G	242_L	1.982	1.00
141_E	154_A	1.959	1.00
21_I	24_G	1.923	1.00
50_G	224_V	1.834	1.00
156_R	160_E	1.827	1.00
25_L	38_G	1.800	1.00
243_T	247_E	1.746	1.00
218_S	224_V	1.731	1.00
204_E	226_H	1.706	1.00
206_L	212_L	1.697	1.00
80_K	99_N	1.696	1.00
24_G	28_R	1.680	1.00
142_E	146_R	1.671	1.00
118_R	155_G	1.643	1.00
118_R	122_K	1.631	1.00
122_K	136_R	1.625	1.00
122_K	140_V	1.620	1.00
22_R	78_L	1.616	1.00
118_R	154_A	1.608	1.00
204_E	207_Q	1.571	1.00
41_F	62_A	1.566	1.00
116_T	119_S	1.564	1.00
41_F	232_G	1.550	1.00
126_N	136_R	1.546	1.00
247_E	251_N	1.545	1.00
48_T	207_Q	1.509	1.00
20_P	78_L	1.500	1.00
137_N	141_E	1.499	1.00
27_Q	34_K	1.469	1.00
43_L	49_L	1.468	1.00
153_F	161_F	1.443	1.00
28_R	61_T	1.438	1.00
184_A	214_Y	1.409	1.00
121_I	144_L	1.399	1.00
47_E	229_D	1.372	1.00
25_L	34_K	1.369	1.00
49_L	230_R	1.368	1.00
141_E	145_A	1.367	1.00
134_R	138_E	1.361	1.00
178_N	212_L	1.349	1.00
258_Q	262_S	1.333	1.00
48_T	228_S	1.329	1.00
25_L	74_E	1.318	1.00
26_F	65_T	1.318	1.00
67_I	102_M	1.315	1.00
114_R	159_H	1.310	1.00
137_N	154_A	1.305	1.00
23_S	26_F	1.296	1.00
39_V	62_A	1.295	1.00
68_R	71_K	1.290	1.00
144_L	154_A	1.289	1.00
78_L	83_D	1.282	1.00
200_I	223_V	1.278	1.00
108_F	166_R	1.266	1.00
116_T	155_G	1.262	1.00
207_Q	214_Y	1.260	1.00
245_K	249_Y	1.259	1.00
48_T	214_Y	1.247	1.00
103_V	184_A	1.240	1.00
119_S	122_K	1.233	1.00
82_Q	87_L	1.232	1.00
255_P	258_Q	1.215	1.00
152_S	156_R	1.212	1.00
246_H	250_D	1.208	1.00
44_K	230_R	1.206	1.00
49_L	242_L	1.205	1.00
150_H	153_F	1.199	1.00
138_E	142_E	1.195	1.00
161_F	169_I	1.191	1.00
19_F	28_R	1.188	1.00
131_Y	136_R	1.186	1.00
203_M	214_Y	1.186	1.00
132_T	136_R	1.182	1.00
65_T	72_P	1.175	1.00
23_S	28_R	1.164	1.00
142_E	145_A	1.161	1.00
120_I	173_R	1.158	1.00
45_K	80_K	1.145	1.00
191_L	199_V	1.141	1.00
62_A	234_M	1.140	1.00
19_F	24_G	1.133	1.00
101_Q	179_P	1.123	1.00
45_K	211_N	1.123	1.00
231_V	245_K	1.117	1.00
51_I	215_L	1.116	1.00
257_T	261_L	1.112	1.00
141_E	151_P	1.105	1.00
135_E	138_E	1.098	1.00
122_K	126_N	1.091	1.00
121_I	176_T	1.083	1.00
247_E	250_D	1.072	1.00
101_Q	174_A	1.065	1.00
115_K	123_E	1.065	1.00
25_L	28_R	1.062	1.00
255_P	259_A	1.061	1.00
182_I	212_L	1.057	1.00
125_F	176_T	1.055	1.00
118_R	137_N	1.047	1.00
182_I	214_Y	1.045	1.00
27_Q	73_T	1.044	1.00
133_M	136_R	1.038	1.00
145_A	151_P	1.038	1.00
136_R	140_V	1.030	1.00
65_T	70_Y	1.029	1.00
245_K	256_Y	1.015	1.00
43_L	181_L	1.006	1.00
36_V	65_T	1.005	1.00
131_Y	135_E	1.005	1.00
51_I	232_G	0.994	1.00
246_H	249_Y	0.992	1.00
96_V	100_I	0.989	1.00
207_Q	229_D	0.985	1.00
249_Y	252_P	0.981	1.00
64_R	69_L	0.976	1.00
44_K	213_T	0.973	1.00
51_I	62_A	0.973	1.00
277_R	280_L	0.969	1.00
23_S	40_S	0.963	1.00
133_M	137_N	0.960	1.00
64_R	70_Y	0.952	1.00
125_F	129_N	0.952	1.00
286_S	289_N	0.951	1.00
118_R	140_V	0.944	1.00
83_D	87_L	0.944	1.00
235_Y	240_M	0.942	1.00
57_C	234_M	0.940	1.00
284_L	287_P	0.940	1.00
66_M	215_L	0.936	1.00
115_K	120_I	0.934	1.00
196_Q	220_D	0.928	1.00
27_Q	32_D	0.926	1.00
186_E	219_H	0.925	1.00
100_I	181_L	0.924	1.00
67_I	183_I	0.922	1.00
245_K	248_L	0.922	1.00
266_V	269_K	0.921	1.00
252_P	257_T	0.914	1.00
43_L	213_T	0.910	1.00
239_M	242_L	0.904	1.00
143_L	146_R	0.904	1.00
26_F	30_V	0.903	1.00
285_P	289_N	0.902	1.00
21_I	41_F	0.896	1.00
20_P	23_S	0.895	1.00
216_F	227_I	0.893	1.00
286_S	290_P	0.889	1.00
204_E	227_I	0.889	1.00
287_P	290_P	0.886	1.00
65_T	73_T	0.884	1.00
103_V	171_I	0.884	1.00
48_T	204_E	0.883	1.00
36_V	39_V	0.882	1.00
139_K	143_L	0.878	1.00
129_N	139_K	0.878	1.00
184_A	203_M	0.874	1.00
29_K	32_D	0.874	1.00
281_K	284_L	0.871	1.00
125_F	128_H	0.864	1.00
143_L	172_A	0.861	1.00
248_L	257_T	0.850	1.00
19_F	23_S	0.849	1.00
43_L	215_L	0.846	1.00
197_A	201_N	0.840	1.00
122_K	137_N	0.837	1.00
200_I	226_H	0.836	1.00
275_R	279_V	0.833	1.00
111_L	166_R	0.830	1.00
157_Y	160_E	0.827	1.00
35_A	61_T	0.823	1.00
216_F	228_S	0.821	1.00
52_V	224_V	0.817	1.00
282_G	287_P	0.816	1.00
196_Q	223_V	0.815	1.00
202_L	205_E	0.811	1.00
112_N	115_K	0.810	1.00
262_S	278_I	0.802	1.00
65_T	77_I	0.798	1.00
28_R	35_A	0.791	1.00
146_R	205_E	0.791	1.00
148_G	205_E	0.791	1.00
117_L	169_I	0.789	1.00
147_V	172_A	0.785	1.00
23_S	30_V	0.784	1.00
183_I	215_L	0.783	1.00
259_A	263_S	0.782	1.00
88_S	95_S	0.780	1.00
128_H	177_L	0.779	1.00
116_T	157_Y	0.778	1.00
282_G	285_P	0.778	1.00
79_F	99_N	0.772	1.00
228_S	231_V	0.769	1.00
268_R	271_G	0.769	1.00
38_G	238_K	0.764	1.00
20_P	24_G	0.763	1.00
135_E	139_K	0.763	1.00
25_L	37_D	0.762	1.00
22_R	42_S	0.760	1.00
48_T	216_F	0.756	1.00
52_V	233_V	0.755	1.00
254_H	257_T	0.748	1.00
76_Q	86_N	0.748	1.00
163_G	168_R	0.748	1.00
137_N	155_G	0.746	1.00
117_L	161_F	0.741	1.00
285_P	290_P	0.741	1.00
49_L	215_L	0.740	1.00
39_V	239_M	0.737	1.00
201_N	204_E	0.732	1.00
19_F	26_F	0.732	1.00
26_F	70_Y	0.731	1.00
54_E	235_Y	0.726	1.00
48_T	227_I	0.724	1.00
82_Q	99_N	0.719	1.00
264_V	267_T	0.719	1.00
188_V	223_V	0.718	1.00
145_A	150_H	0.717	1.00
148_G	198_Q	0.717	1.00
288_A	291_P	0.714	1.00
158_P	169_I	0.711	1.00
248_L	252_P	0.710	1.00
161_F	165_Q	0.706	1.00
95_S	98_K	0.706	1.00
181_L	213_T	0.705	1.00
140_V	143_L	0.705	1.00
235_Y	238_K	0.705	1.00
223_V	227_I	0.703	1.00
89_E	95_S	0.701	1.00
283_E	287_P	0.692	1.00
141_E	149_L	0.687	1.00
95_S	99_N	0.685	1.00
22_R	40_S	0.684	1.00
24_G	72_P	0.684	1.00
259_A	262_S	0.684	1.00
98_K	129_N	0.680	1.00
121_I	140_V	0.679	1.00
116_T	120_I	0.679	1.00
241_E	251_N	0.679	1.00
233_V	252_P	0.677	1.00
120_I	158_P	0.677	1.00
124_P	177_L	0.675	1.00
140_V	154_A	0.673	1.00
103_V	174_A	0.672	1.00
276_E	280_L	0.669	1.00
124_P	173_R	0.668	1.00
277_R	281_K	0.666	1.00
64_R	102_M	0.666	1.00
126_N	133_M	0.665	1.00
67_I	100_I	0.663	1.00
124_P	127_T	0.660	1.00
287_P	291_P	0.659	1.00
276_E	279_V	0.658	1.00
240_M	254_H	0.658	1.00
21_I	66_M	0.657	1.00
69_L	104_F	0.657	1.00
90_E	95_S	0.655	1.00
132_T	141_E	0.655	1.00
233_V	248_L	0.654	1.00
143_L	175_L	0.654	1.00
285_P	291_P	0.653	1.00
76_Q	85_S	0.652	1.00
24_G	30_V	0.652	1.00
263_S	266_V	0.651	1.00
280_L	284_L	0.650	1.00
84_I	95_S	0.646	1.00
230_R	241_E	0.646	1.00
148_G	151_P	0.644	1.00
48_T	229_D	0.641	1.00
95_S	100_I	0.641	1.00
201_N	205_E	0.641	1.00
60_S	64_R	0.640	1.00
282_G	286_S	0.639	1.00
281_K	285_P	0.633	1.00
241_E	252_P	0.633	1.00
280_L	283_E	0.632	1.00
19_F	25_L	0.627	1.00
256_Y	259_A	0.627	1.00
243_T	249_Y	0.627	1.00
201_N	226_H	0.624	1.00
71_K	85_S	0.624	1.00
283_E	286_S	0.623	1.00
228_S	245_K	0.616	1.00
244_G	248_L	0.612	1.00
218_S	223_V	0.612	1.00
278_I	281_K	0.612	1.00
137_N	140_V	0.607	1.00
279_V	283_E	0.606	1.00
181_L	215_L	0.604	1.00
77_I	85_S	0.602	1.00
204_E	208_E	0.602	1.00
221_L	249_Y	0.602	1.00
36_V	62_A	0.600	1.00
111_L	120_I	0.599	1.00
286_S	291_P	0.599	1.00
134_R	137_N	0.597	1.00
285_P	288_A	0.594	1.00
79_F	181_L	0.591	1.00
28_R	31_G	0.591	1.00
34_K	38_G	0.590	1.00
136_R	141_E	0.588	1.00
26_F	61_T	0.586	1.00
224_V	228_S	0.582	1.00
79_F	84_I	0.582	1.00
66_M	77_I	0.582	1.00
198_Q	201_N	0.580	1.00
106_D	109_A	0.576	1.00
123_E	127_T	0.574	1.00
256_Y	260_L	0.573	1.00
68_R	89_E	0.571	1.00
55_S	186_E	0.571	1.00
82_Q	95_S	0.570	1.00
84_I	100_I	0.569	1.00
54_E	57_C	0.569	1.00
281_K	287_P	0.566	1.00
260_L	263_S	0.563	1.00
143_L	147_V	0.562	1.00
111_L	169_I	0.560	1.00
46_G	213_T	0.559	1.00
118_R	121_I	0.559	1.00
153_F	165_Q	0.558	1.00
26_F	73_T	0.558	1.00
274_K	277_R	0.555	1.00
23_S	74_E	0.551	1.00
78_L	81_G	0.550	1.00
284_L	289_N	0.549	1.00
38_G	74_E	0.548	1.00
175_L	212_L	0.547	1.00
283_E	288_A	0.546	1.00
264_V	268_R	0.546	1.00
121_I	135_E	0.546	1.00
55_S	195_I	0.545	1.00
284_L	290_P	0.544	1.00
149_L	153_F	0.543	1.00
42_S	242_L	0.542	1.00
270_R	274_K	0.541	1.00
45_K	213_T	0.541	1.00
149_L	165_Q	0.538	1.00
171_I	199_V	0.537	1.00
122_K	130_M	0.535	1.00
122_K	125_F	0.534	1.00
144_L	153_F	0.534	1.00
130_M	136_R	0.534	1.00
188_V	199_V	0.533	1.00
257_T	260_L	0.531	1.00
139_K	146_R	0.530	1.00
118_R	130_M	0.528	1.00
261_L	265_P	0.527	1.00
280_L	287_P	0.526	1.00
27_Q	30_V	0.526	1.00
243_T	252_P	0.525	1.00
152_S	155_G	0.524	1.00
251_N	255_P	0.523	1.00
162_S	165_Q	0.523	1.00
84_I	96_V	0.520	1.00
24_G	65_T	0.519	1.00
284_L	288_A	0.519	1.00
258_Q	261_L	0.517	1.00
110_S	170_G	0.517	1.00
275_R	278_I	0.516	1.00
19_F	70_Y	0.514	1.00
55_S	191_L	0.512	1.00
277_R	285_P	0.511	1.00
224_V	231_V	0.510	1.00
138_E	145_A	0.509	1.00
138_E	141_E	0.509	1.00
87_L	90_E	0.507	1.00
87_L	95_S	0.505	1.00
122_K	154_A	0.505	1.00
280_L	285_P	0.504	1.00
271_G	274_K	0.502	1.00
277_R	282_G	0.501	1.00
260_L	264_V	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
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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
4fwiB	1	0.9149	100	0.23	Contact Map
4ry2A	2	0.7416	100	0.242	Contact Map
4f4cA	1	0.7325	100	0.246	Contact Map
3tuiC	2	0.9362	100	0.255	Contact Map
2it1A	1	0.9149	100	0.257	Contact Map
2yyzA	1	0.9088	100	0.258	Contact Map
1oxxK	1	0.9331	100	0.258	Contact Map
1v43A	2	0.8845	100	0.26	Contact Map
3b5xA	2	0.769	100	0.261	Contact Map
4u00A	1	0.7325	100	0.261	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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