GREMLIN Database
YDJA - Putative NAD(P)H nitroreductase YdjA
UniProt: P0ACY1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11134
Length: 183 (160)
Sequences: 13279 (9765)
Seq/√Len: 772.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
22_T25_Q3.5571.00
28_N125_Q3.3481.00
23_G51_E2.7701.00
47_F114_A2.5081.00
23_G27_Q2.4781.00
48_F93_V2.4771.00
29_I122_A2.3071.00
127_F162_T2.1621.00
9_N123_V2.1571.00
128_G163_P2.1541.00
25_Q125_Q2.1221.00
119_Q129_G2.1191.00
93_V152_D2.0521.00
5_E9_N1.9541.00
31_R34_M1.9251.00
47_F90_I1.8631.00
32_A121_A1.8291.00
25_Q127_F1.8211.00
59_S84_F1.7611.00
57_R145_A1.7411.00
33_G118_M1.6951.00
115_V156_G1.6851.00
19_P162_T1.6751.00
17_A164_Q1.6711.00
15_R164_Q1.6701.00
56_E84_F1.6341.00
90_I118_M1.6241.00
115_V158_L1.6041.00
95_K151_Q1.5421.00
29_I118_M1.5351.00
3_A7_L1.5011.00
109_M112_G1.4961.00
143_R154_I1.4801.00
92_V115_V1.4751.00
25_Q162_T1.4371.00
4_L28_N1.4311.00
3_A6_L1.4191.00
119_Q131_W1.4071.00
113_C116_M1.3971.00
20_A51_E1.3831.00
49_V88_L1.3791.00
93_V148_C1.3551.00
91_T157_F1.3511.00
122_A160_L1.3501.00
51_E88_L1.3211.00
119_Q158_L1.3151.00
138_E141_V1.2951.00
123_V128_G1.2881.00
25_Q28_N1.2861.00
54_G57_R1.2831.00
29_I160_L1.2771.00
127_F160_L1.2751.00
8_I35_R1.2401.00
92_V118_M1.2391.00
61_V145_A1.2391.00
141_V144_E1.2371.00
53_E56_E1.2301.00
91_T154_I1.2271.00
47_F92_V1.2211.00
46_H152_D1.2121.00
27_Q177_T1.2031.00
111_A155_V1.2021.00
174_P178_P1.1761.00
4_L8_I1.1751.00
131_W156_G1.1741.00
29_I127_F1.1531.00
89_I157_F1.1521.00
8_I31_R1.1501.00
61_V141_V1.1401.00
90_I160_L1.1191.00
4_L32_A1.1151.00
92_V111_A1.1111.00
121_A125_Q1.1051.00
56_E60_A1.1041.00
26_L88_L1.1021.00
12_S130_I1.0791.00
5_E8_I1.0621.00
32_A125_Q1.0581.00
129_G160_L1.0501.00
57_R60_A1.0481.00
21_P127_F1.0471.00
96_C153_K1.0421.00
36_A117_A1.0401.00
50_I91_T1.0331.00
30_L49_V1.0291.00
122_A129_G1.0241.00
46_H95_K1.0231.00
58_F142_V1.0171.00
27_Q31_R1.0161.00
141_V145_A1.0131.00
94_A111_A1.0111.00
106_E133_S1.0071.00
16_L159_Y1.0071.00
121_A124_A1.0031.00
116_M120_M0.9931.00
39_H106_E0.9731.00
34_M179_F0.9701.00
129_G158_L0.9611.00
92_V158_L0.9581.00
113_C131_W0.9571.00
4_L125_Q0.9571.00
94_A107_Q0.9471.00
22_T162_T0.9461.00
93_V154_I0.9411.00
24_E27_Q0.9371.00
60_A64_Q0.9331.00
49_V90_I0.9301.00
117_A120_M0.9291.00
140_P144_E0.9161.00
95_K152_D0.9071.00
3_A124_A0.9061.00
30_L33_G0.9051.00
118_M158_L0.9031.00
88_L160_L0.8971.00
48_F152_D0.8951.00
130_I159_Y0.8791.00
132_R159_Y0.8731.00
108_E155_V0.8671.00
27_Q176_P0.8591.00
97_E151_Q0.8571.00
112_G131_W0.8481.00
140_P143_R0.8481.00
4_L124_A0.8361.00
91_T146_F0.8351.00
115_V131_W0.8341.00
21_P162_T0.8221.00
143_R153_K0.8211.00
113_C117_A0.8191.00
118_M160_L0.8171.00
15_R165_L0.8161.00
109_M133_S0.8131.00
18_E85_R0.8111.00
56_E59_S0.8091.00
3_A120_M0.8081.00
38_D45_W0.8081.00
29_I125_Q0.8031.00
142_V145_A0.8021.00
20_A87_P0.7981.00
94_A155_V0.7931.00
7_L117_A0.7921.00
17_A162_T0.7921.00
81_N84_F0.7861.00
81_N85_R0.7851.00
175_D178_P0.7801.00
149_R152_D0.7711.00
19_P22_T0.7681.00
4_L121_A0.7671.00
28_N32_A0.7621.00
28_N31_R0.7621.00
104_R153_K0.7581.00
39_H133_S0.7521.00
7_L120_M0.7501.00
20_A88_L0.7481.00
21_P87_P0.7411.00
21_P24_E0.7361.00
21_P25_Q0.7311.00
139_S153_K0.7281.00
45_W111_A0.7261.00
31_R176_P0.7241.00
148_C152_D0.7211.00
139_S143_R0.7181.00
38_D43_Q0.7061.00
110_S133_S0.7011.00
26_L160_L0.6941.00
82_A85_R0.6921.00
46_H93_V0.6921.00
26_L30_L0.6881.00
108_E112_G0.6731.00
109_M113_C0.6701.00
6_L124_A0.6691.00
89_I159_Y0.6681.00
31_R35_R0.6611.00
139_S154_I0.6571.00
52_G55_R0.6461.00
57_R61_V0.6381.00
86_A89_I0.6371.00
6_L120_M0.6281.00
8_I28_N0.6281.00
30_L90_I0.6261.00
10_R37_P0.6221.00
39_H110_S0.6211.00
79_A85_R0.6201.00
15_R85_R0.6201.00
143_R148_C0.6101.00
48_F146_F0.6091.00
17_A87_P0.6061.00
79_A82_A0.5961.00
96_C151_Q0.5951.00
87_P162_T0.5931.00
120_M124_A0.5831.00
62_L83_P0.5831.00
50_I55_R0.5801.00
137_T157_F0.5801.00
116_M119_Q0.5781.00
24_E28_N0.5761.00
17_A165_L0.5751.00
3_A121_A0.5751.00
64_Q80_R0.5751.00
109_M131_W0.5691.00
26_L90_I0.5681.00
83_P159_Y0.5681.00
34_M176_P0.5641.00
143_R150_E0.5611.00
28_N121_A0.5591.00
123_V163_P0.5581.00
148_C154_I0.5571.00
165_L168_S0.5531.00
33_G47_F0.5501.00
50_I146_F0.5461.00
14_S130_I0.5411.00
16_L130_I0.5411.00
60_A63_E0.5391.00
29_I33_G0.5361.00
16_L19_P0.5361.00
63_E80_R0.5341.00
13_A128_G0.5331.00
14_S82_A0.5331.00
38_D44_P0.5331.00
45_W114_A0.5301.00
115_V119_Q0.5281.00
108_E153_K0.5281.00
33_G114_A0.5271.00
54_G145_A0.5251.00
118_M129_G0.5241.00
101_K104_R0.5241.00
58_F89_I0.5241.00
62_L157_F0.5201.00
37_P116_M0.5171.00
80_R84_F0.5141.00
13_A163_P0.5131.00
43_Q174_P0.5131.00
101_K105_W0.5111.00
163_P166_K0.5101.00
83_P89_I0.5101.00
53_E57_R0.5091.00
46_H174_P0.5061.00
13_A167_A0.5031.00
174_P179_F0.5031.00
26_L49_V0.5021.00
29_I121_A0.5001.00
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

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  
3bm1A 2 0.9727 100 0.152 Contact Map
2b67A 2 0.9071 100 0.156 Contact Map
3bemA 2 0.9071 100 0.161 Contact Map
3gagA 4 0.9016 100 0.165 Contact Map
3of4A 3 0.9071 100 0.165 Contact Map
1icrA 2 0.929 100 0.166 Contact Map
3qdlA 4 0.9071 100 0.167 Contact Map
4qlxA 2 0.9126 100 0.169 Contact Map
3ge6A 2 0.9071 100 0.17 Contact Map
1ywqA 2 0.9945 100 0.171 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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