Q97VK8 - SULSO - GREMLIN Contacts

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Q97VK8 - Dipeptide ABC transporter ATP binding protein (DppD-3)

UniProt:	Q97VK8	Sequences: MNNMVVLQIRNLNVYYNTLISWVKVLSDVNLDVEKGEIVGVVGESGSGKSTLGHAISRILPPNARIQGDIIVDGVNLAKLKDSELQKYRGTWVFMIFQNPLNSLNPVKKVGSQLLEAVKIRYQREGKKAEEESLMRDVIEVLKDLRLPDPYSIIDRYPHQLSGGQVQRIVISMALLLKPKLLIADEPTSALDVTIQAQVVNLFKQLNKEINTSILFITHDISLAYVVSDRIVVMYAGRIMEDGKVEEVLKSPMHPYTQGLVASIPSGDKNQKLTAIPGNPPSFFALPTGCKFSNRCSKVFDICRKKEPSIIEKNGRKIRCWLYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (252)
Sequences:	66392 (39776)
Seq/√Len:	2505.7

ECOLI - OPPF OPPD FBPC PROV SAPD METN DDPD MALK DPPD CYSA POTA POTG YCJV DPPF YDCT UGPC DDPF YEHX ARAG YADG GSIA MODC MACB YHES RBSA UUP FEPC MDLA MDLB MLAF SAPF CYDC MSBA CYDD NIKE YTFR TAUB FECE LSRA FHUC HISP YOJI SSUB YECC PHNC GLNQ YPHE YHDZ PHNK LPTB XYLG GLTL ALSA LIVG ZNUC MODF ETTA SUFC LOLD PSTB LIVF ARTP FTSE MGLA BTUD YBBA THIQ FETA NIKD YEJF YDDA PHNL CCMA YNJD YBHF YBIT YHIH
BACSU - OPUCA OPUBA OPPD YVRA OPUAA APPF YKFD MSMX DPPD YURJ APPD METN TAGH YFIL YKPA YHCH OPPF YXLF YCBN YFMM YVFR YDBJ YHEH ECFA1 YHAQ RBSA YUSV SUNT YTRB YFIC YDIF YFMF FHUC BMRA YKNU YGAD YFIB YHEI YKNV YWJA YCLP BCEA CYDD YFMR YLMA TCYN SUFC YXDL YKOD YTLC ECSA CYDC YVCR ECFA2 SKFE NATA YXEO YJKB FTSE GLNQ ARTM TCYC MNTB SSUB ALBC YKNY PSTB1 YVRO YTHP PSTB2 YUFO EXPZ YCLH ZNUC YHCG YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HMX2 Q9HHQ5 Q9HNZ9 Q9HR06 Q9HMT3 Q9HMG1 Q9HMU8 Q9HRJ6 Q9HSQ7 Q9HHM2 Q9HRH8 PHNC PSTB2 Q9HMG6 Q9HNY3 Q9HRZ9 Q9HRV7 Y1631 PSTB1 Y2317 Q9HR96 Q9HHR7 Q9HT03 Q9HS04 Q9HQA8 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q97VK8 Q97YP8 Q97VF5 Q97YP7 Q97UF2 Q97YP3 Q97YY4 Q97VK9 Q97UH3 Q97UY8 Q97UJ9 Q97ZC0 Q97VF4 Q7LX64 Q97VC1 Q97VH6 Q97UD4 Q97YK2 Q97X18 Q97YQ7 Y1893 Y2030 Q97U54 Q97Z03 Q97UH4 Q980W0 Q97W42 Q7LY07 PSTB Q97V01 Q7LXM4 Q97V00 Q97VM2 Q97VY4 Q7LX80 Q97UG5 Q97Z56 Q97YP4 Q97Z96 Q97UC2 Q97ZU0 Q980K5 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
37_E	230_R	3.852	1.00
8_Q	32_D	3.126	1.00
92_W	180_K	3.119	1.00
11_N	28_D	3.036	1.00
24_K	27_S	2.932	1.00
39_V	232_V	2.930	1.00
10_R	69_D	2.897	1.00
230_R	242_D	2.695	1.00
14_V	55_A	2.632	1.00
34_E	37_E	2.569	1.00
15_Y	24_K	2.553	1.00
40_G	228_S	2.548	1.00
153_I	156_R	2.480	1.00
8_Q	71_I	2.464	1.00
244_K	247_E	2.433	1.00
69_D	76_N	2.410	1.00
73_D	180_K	2.393	1.00
13_N	67_Q	2.265	1.00
232_V	239_I	2.259	1.00
27_S	238_R	2.183	1.00
10_R	71_I	2.130	1.00
13_N	28_D	2.086	1.00
9_I	12_L	2.037	1.00
13_N	24_K	2.025	1.00
232_V	242_D	2.004	1.00
139_I	154_I	1.985	1.00
108_K	112_S	1.969	1.00
243_G	247_E	1.944	1.00
130_E	133_S	1.887	1.00
35_K	180_K	1.883	1.00
225_Y	246_E	1.822	1.00
137_D	178_K	1.782	1.00
137_D	140_E	1.780	1.00
16_Y	51_T	1.779	1.00
53_G	217_I	1.776	1.00
53_G	183_I	1.774	1.00
149_D	152_S	1.763	1.00
243_G	248_V	1.751	1.00
16_Y	25_V	1.670	1.00
14_V	60_L	1.621	1.00
156_R	160_Q	1.617	1.00
148_P	152_S	1.588	1.00
140_E	144_D	1.567	1.00
135_M	139_I	1.556	1.00
76_N	79_K	1.553	1.00
15_Y	22_W	1.552	1.00
141_V	176_L	1.537	1.00
123_Q	129_A	1.529	1.00
218_T	224_A	1.527	1.00
115_L	134_L	1.522	1.00
111_G	154_I	1.514	1.00
17_N	22_W	1.511	1.00
111_G	155_D	1.509	1.00
111_G	115_L	1.498	1.00
12_L	62_P	1.486	1.00
40_G	224_A	1.474	1.00
11_N	30_N	1.472	1.00
9_I	31_L	1.470	1.00
73_D	92_W	1.454	1.00
247_E	251_S	1.448	1.00
13_N	27_S	1.433	1.00
14_V	63_N	1.424	1.00
58_R	85_L	1.405	1.00
204_K	226_V	1.383	1.00
184_A	214_I	1.378	1.00
31_L	232_V	1.361	1.00
206_L	212_T	1.351	1.00
178_K	212_T	1.347	1.00
15_Y	63_N	1.341	1.00
37_E	229_D	1.338	1.00
33_V	39_V	1.332	1.00
109_K	112_S	1.332	1.00
153_I	161_L	1.329	1.00
115_L	138_V	1.319	1.00
119_K	134_L	1.311	1.00
9_I	56_I	1.280	1.00
31_L	52_L	1.269	1.00
85_L	89_R	1.260	1.00
114_L	142_L	1.259	1.00
255_P	258_Q	1.255	1.00
139_I	143_K	1.251	1.00
38_I	207_N	1.241	1.00
34_E	230_R	1.240	1.00
39_V	242_D	1.239	1.00
39_V	230_R	1.228	1.00
58_R	61_P	1.223	1.00
57_S	95_M	1.208	1.00
136_R	140_E	1.205	1.00
204_K	227_V	1.202	1.00
101_L	166_V	1.195	1.00
71_I	76_N	1.192	1.00
133_S	136_R	1.183	1.00
29_V	52_L	1.172	1.00
254_H	257_T	1.165	1.00
38_I	214_I	1.163	1.00
200_V	223_L	1.158	1.00
10_R	30_N	1.153	1.00
10_R	32_D	1.151	1.00
109_K	155_D	1.151	1.00
112_S	115_L	1.146	1.00
152_S	156_R	1.145	1.00
6_V	73_D	1.135	1.00
135_M	154_I	1.129	1.00
142_L	154_I	1.129	1.00
111_G	135_M	1.123	1.00
255_P	259_G	1.108	1.00
38_I	228_S	1.102	1.00
161_L	169_I	1.068	1.00
75_V	80_L	1.067	1.00
204_K	207_N	1.065	1.00
246_E	250_K	1.065	1.00
113_Q	173_M	1.050	1.00
35_K	73_D	1.049	1.00
139_I	149_D	1.048	1.00
80_L	85_L	1.047	1.00
18_T	22_W	1.045	1.00
96_I	184_A	1.039	1.00
55_A	62_P	1.035	1.00
132_E	136_R	1.027	1.00
258_Q	262_A	1.024	1.00
107_V	159_H	1.022	1.00
231_I	245_V	1.019	1.00
140_E	143_K	1.014	1.00
207_N	214_I	1.009	1.00
52_L	234_M	1.005	1.00
245_V	256_Y	1.001	1.00
143_K	148_P	0.997	1.00
257_T	261_V	0.989	1.00
149_D	154_I	0.987	1.00
41_V	215_L	0.987	1.00
111_G	138_V	0.983	1.00
115_L	119_K	0.980	1.00
203_F	214_I	0.970	1.00
131_E	135_M	0.967	1.00
41_V	52_L	0.966	1.00
60_L	63_N	0.965	1.00
56_I	215_L	0.959	1.00
148_P	153_I	0.957	1.00
247_E	250_K	0.954	1.00
110_V	161_L	0.948	1.00
182_L	214_I	0.941	1.00
54_H	59_I	0.937	1.00
114_L	176_L	0.937	1.00
182_L	212_T	0.931	1.00
11_N	67_Q	0.929	1.00
35_K	211_N	0.929	1.00
133_S	137_D	0.925	1.00
202_L	205_Q	0.925	1.00
196_Q	220_D	0.917	1.00
144_D	205_Q	0.917	1.00
146_R	205_Q	0.914	1.00
41_V	232_V	0.914	1.00
26_L	55_A	0.912	1.00
197_A	201_N	0.910	1.00
94_F	179_P	0.909	1.00
115_L	135_M	0.908	1.00
137_D	141_V	0.906	1.00
122_Y	129_A	0.906	1.00
54_H	60_L	0.903	1.00
108_K	116_E	0.900	1.00
18_T	23_V	0.900	1.00
88_Y	93_V	0.899	1.00
130_E	134_L	0.898	1.00
241_E	251_S	0.897	1.00
9_I	70_I	0.894	1.00
184_A	203_F	0.883	1.00
141_V	144_D	0.883	1.00
87_K	90_G	0.881	1.00
157_Y	160_Q	0.880	1.00
57_S	183_I	0.880	1.00
118_V	176_L	0.879	1.00
191_L	199_V	0.876	1.00
141_V	172_S	0.872	1.00
143_K	149_D	0.870	1.00
34_E	213_S	0.865	1.00
109_K	157_Y	0.865	1.00
14_V	51_T	0.861	1.00
118_V	122_Y	0.849	1.00
33_V	181_L	0.846	1.00
104_L	166_V	0.844	1.00
15_Y	27_S	0.844	1.00
266_S	269_K	0.842	1.00
201_N	226_V	0.839	1.00
129_A	134_L	0.838	1.00
196_Q	223_L	0.832	1.00
38_I	204_K	0.831	1.00
7_L	56_I	0.826	1.00
108_K	113_Q	0.825	1.00
44_E	235_Y	0.822	1.00
6_V	35_K	0.819	1.00
94_F	174_A	0.819	1.00
121_R	177_L	0.817	1.00
149_D	153_I	0.817	1.00
239_I	242_D	0.816	1.00
6_V	32_D	0.812	1.00
240_M	254_H	0.809	1.00
230_R	240_M	0.805	1.00
186_E	219_H	0.802	1.00
235_Y	240_M	0.802	1.00
38_I	216_F	0.801	1.00
207_N	229_D	0.800	1.00
110_V	169_I	0.798	1.00
96_I	171_I	0.794	1.00
38_I	227_V	0.793	1.00
47_S	234_M	0.791	1.00
145_L	172_S	0.790	1.00
25_V	51_T	0.789	1.00
134_L	138_V	0.786	1.00
6_V	34_E	0.783	1.00
12_L	55_A	0.778	1.00
158_P	169_I	0.777	1.00
123_Q	130_E	0.774	1.00
272_K	275_A	0.773	1.00
248_V	257_T	0.770	1.00
245_V	249_L	0.768	1.00
241_E	252_P	0.761	1.00
55_A	60_L	0.759	1.00
9_I	52_L	0.758	1.00
161_L	165_Q	0.758	1.00
28_D	238_R	0.753	1.00
26_L	29_V	0.748	1.00
201_N	204_K	0.748	1.00
33_V	213_S	0.748	1.00
42_V	224_A	0.742	1.00
75_V	92_W	0.742	1.00
131_E	134_L	0.740	1.00
136_R	139_I	0.734	1.00
146_R	198_Q	0.733	1.00
259_G	262_A	0.730	1.00
28_D	67_Q	0.729	1.00
93_V	181_L	0.728	1.00
14_V	26_L	0.725	1.00
181_L	213_S	0.724	1.00
216_F	227_V	0.723	1.00
259_G	263_S	0.721	1.00
183_I	215_L	0.720	1.00
118_V	121_R	0.720	1.00
216_F	228_S	0.719	1.00
55_A	70_I	0.718	1.00
235_Y	259_G	0.717	1.00
81_K	85_L	0.713	1.00
146_R	149_D	0.712	1.00
188_T	199_V	0.711	1.00
105_N	108_K	0.710	1.00
29_V	239_I	0.709	1.00
135_M	138_V	0.708	1.00
122_Y	137_D	0.708	1.00
81_K	87_K	0.702	1.00
235_Y	238_R	0.702	1.00
72_V	92_W	0.701	1.00
11_N	14_V	0.700	1.00
221_I	249_L	0.700	1.00
228_S	231_I	0.690	1.00
200_V	226_V	0.689	1.00
233_V	252_P	0.688	1.00
33_V	215_L	0.684	1.00
69_D	78_A	0.676	1.00
204_K	208_K	0.672	1.00
262_A	274_T	0.672	1.00
117_A	177_L	0.672	1.00
96_I	174_A	0.670	1.00
241_E	253_M	0.667	1.00
228_S	245_V	0.662	1.00
233_V	248_V	0.662	1.00
39_V	215_L	0.661	1.00
119_K	131_E	0.658	1.00
117_A	173_M	0.656	1.00
50_S	54_H	0.656	1.00
61_P	78_A	0.651	1.00
111_G	139_I	0.651	1.00
252_P	257_T	0.650	1.00
26_L	52_L	0.650	1.00
241_E	248_V	0.646	1.00
38_I	229_D	0.645	1.00
77_L	88_Y	0.645	1.00
80_L	88_Y	0.642	1.00
223_L	227_V	0.642	1.00
57_S	93_V	0.640	1.00
63_N	67_Q	0.638	1.00
263_S	266_S	0.637	1.00
138_V	154_I	0.634	1.00
201_N	205_Q	0.629	1.00
198_Q	201_N	0.628	1.00
72_V	88_Y	0.627	1.00
7_L	181_L	0.625	1.00
99_N	102_N	0.625	1.00
71_I	74_G	0.624	1.00
16_Y	60_L	0.624	1.00
138_V	141_V	0.620	1.00
188_T	223_L	0.619	1.00
42_V	233_V	0.617	1.00
153_I	165_Q	0.617	1.00
114_L	138_V	0.612	1.00
163_G	168_R	0.612	1.00
135_M	155_D	0.612	1.00
258_Q	261_V	0.610	1.00
123_Q	134_L	0.606	1.00
147_L	165_Q	0.604	1.00
59_I	97_F	0.603	1.00
109_K	113_Q	0.601	1.00
76_N	80_L	0.600	1.00
69_D	79_K	0.600	1.00
225_Y	249_L	0.599	1.00
72_V	181_L	0.598	1.00
138_V	142_L	0.598	1.00
247_E	253_M	0.597	1.00
180_K	212_T	0.597	1.00
251_S	254_H	0.593	1.00
129_A	133_S	0.593	1.00
218_T	223_L	0.591	1.00
7_L	72_V	0.590	1.00
6_V	72_V	0.587	1.00
102_N	166_V	0.580	1.00
113_Q	158_P	0.580	1.00
167_Q	190_A	0.580	1.00
56_I	70_I	0.580	1.00
256_Y	259_G	0.579	1.00
273_L	276_I	0.574	1.00
54_H	95_M	0.572	1.00
181_L	215_L	0.571	1.00
15_Y	67_Q	0.570	1.00
200_V	227_V	0.569	1.00
87_K	92_W	0.568	1.00
256_Y	260_L	0.565	1.00
224_A	228_S	0.564	1.00
225_Y	245_V	0.562	1.00
267_G	270_N	0.562	1.00
141_V	175_L	0.561	1.00
6_V	213_S	0.560	1.00
15_Y	25_V	0.559	1.00
118_V	129_A	0.559	1.00
117_A	120_I	0.558	1.00
133_S	142_L	0.558	1.00
260_L	264_I	0.557	1.00
98_Q	163_G	0.556	1.00
132_E	135_M	0.554	1.00
162_S	165_Q	0.553	1.00
175_L	212_T	0.551	1.00
116_E	120_I	0.551	1.00
73_D	76_N	0.551	1.00
249_L	252_P	0.550	1.00
251_S	255_P	0.548	1.00
75_V	88_Y	0.543	1.00
263_S	267_G	0.542	1.00
232_V	240_M	0.541	1.00
77_L	93_V	0.541	1.00
45_S	186_E	0.540	1.00
243_G	252_P	0.539	1.00
6_V	181_L	0.536	1.00
123_Q	133_S	0.535	1.00
62_P	78_A	0.535	1.00
104_L	113_Q	0.532	1.00
171_I	199_V	0.532	1.00
55_A	63_N	0.529	1.00
134_L	139_I	0.527	1.00
32_D	242_D	0.527	1.00
224_A	231_I	0.527	1.00
255_P	262_A	0.526	1.00
254_H	258_Q	0.526	1.00
36_G	213_S	0.524	1.00
15_Y	18_T	0.523	1.00
44_E	47_S	0.522	1.00
37_E	242_D	0.521	1.00
118_V	123_Q	0.520	1.00
111_G	114_L	0.516	1.00
104_L	169_I	0.516	1.00
58_R	78_A	0.515	1.00
70_I	78_A	0.511	1.00
224_A	245_V	0.511	1.00
11_N	68_G	0.511	1.00
241_E	257_T	0.510	1.00
24_K	28_D	0.509	1.00
8_Q	30_N	0.508	1.00
137_D	144_D	0.504	1.00
141_V	145_L	0.503	1.00
207_N	212_T	0.502	1.00
156_R	161_L	0.502	1.00
115_L	123_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
4fwiB	1	0.9383	100	0.196	Contact Map
3tuiC	2	0.9414	100	0.207	Contact Map
4ry2A	2	0.7407	100	0.216	Contact Map
4f4cA	1	0.7191	100	0.227	Contact Map
4u00A	1	0.7438	100	0.236	Contact Map
2yyzA	1	0.8981	100	0.236	Contact Map
2oljA	2	0.7469	100	0.236	Contact Map
1b0uA	2	0.7623	100	0.236	Contact Map
4mkiB	2	0.8765	100	0.237	Contact Map
4ymuJ	2	0.7407	100	0.237	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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