GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PRK - Phosphoribulokinase Uridine kinase family
Pfam: PF00485 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0023
Length: 194
Sequences: 9958
Seq/Len: 51.33
HH_delta: 0.179 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
167_R171_E0.874192.448
139_L142_E0.833692.334
156_P160_I0.803932.251
18_R21_Q0.783682.194
142_E146_Q0.756932.119
160_I164_E0.754942.114
168_P172_R0.701821.965
78_A83_G0.689381.930
20_A24_N0.6651.862
157_E161_A0.663141.857
17_K21_Q0.659211.846
4_I16_A0.658061.843
162_Q165_R0.634361.776
161_A164_E0.628361.759
3_G127_F0.627021.756
17_K20_A0.618921.733
71_L74_E0.613181.717
141_L160_I0.601931.685
136_D139_L0.578211.619
73_K77_K0.578131.619
155_S158_E0.564671.581
170_Y174_I0.558111.563
169_G172_R0.558081.563
161_A165_R0.54491.526
91_D98_D0.544731.525
143_R147_R0.537381.505
140_R143_R0.535641.500
71_L75_D0.535321.499
70_D74_E0.531821.489
75_D78_A0.529681.483
68_D71_L0.527631.477
74_E78_A0.526381.474
15_L18_R0.517451.449
93_S96_D0.511521.432
42_F75_D0.511091.431
7_P140_R0.508771.425
18_R22_I0.506191.417
159_V162_Q0.492971.380
135_A139_L0.490431.373
141_L164_E0.488161.367
162_Q166_V0.487181.364
15_L133_L0.483971.355
135_A140_R0.481721.349
158_E161_A0.480861.346
37_L42_F0.477691.338
10_S135_A0.477421.337
91_D94_T0.474471.329
91_D95_G0.471731.321
118_L130_K0.468031.311
45_D48_L0.467041.308
69_F73_K0.457511.281
93_S97_R0.452891.268
88_P91_D0.451991.266
112_V127_F0.451011.263
16_A20_A0.44651.250
4_I15_L0.442861.240
42_F45_D0.440751.234
139_L143_R0.426011.193
4_I19_L0.423451.186
6_G10_S0.421911.181
141_L145_I0.419721.175
85_I93_S0.415381.163
48_L51_R0.41471.161
140_R144_R0.414511.161
41_D45_D0.412831.156
47_H50_D0.412561.155
9_G144_R0.411391.152
40_D43_Y0.40871.144
40_D44_D0.402941.128
89_I92_F0.399511.119
102_I106_P0.396041.109
2_I129_L0.394431.104
76_L79_L0.390811.094
7_P10_S0.390251.093
87_I95_G0.389451.090
38_S41_D0.388491.088
2_I109_I0.375661.052
168_P171_E0.373611.046
78_A81_N0.371911.041
39_L43_Y0.37181.041
94_T98_D0.36971.035
15_L19_L0.369271.034
2_I131_I0.368521.032
47_H51_R0.36581.024
144_R159_V0.362611.015
46_Y49_R0.362461.015
117_A120_D0.356760.999
49_R54_R0.355130.994
86_E90_Y0.35440.992
158_E162_Q0.354130.992
10_S140_R0.352430.987
144_R147_R0.349390.978
138_D142_E0.348430.976
50_D53_G0.346720.971
44_D47_H0.345890.969
8_S144_R0.345130.966
134_D167_R0.34090.955
110_V113_E0.339720.951
171_E175_E0.338640.948
111_I114_G0.337480.945
92_F96_D0.337170.944
73_K122_E0.335440.939
41_D44_D0.334840.938
7_P163_Y0.333090.933
92_F95_G0.329420.922
8_S163_Y0.329230.922
16_A113_E0.328870.921
20_A36_I0.327920.918
95_G99_P0.327390.917
86_E89_I0.321980.902
101_I105_S0.320360.897
110_V114_G0.31850.892
119_Y130_K0.316250.886
14_T18_R0.314550.881
51_R54_R0.313970.879
67_F71_L0.310180.869
159_V163_Y0.309670.867
77_K126_L0.309450.866
137_E160_I0.306950.859
145_I159_V0.303420.850
137_E140_R0.303360.849
13_T17_K0.303220.849
37_L40_D0.302550.847
172_R175_E0.301950.845
121_E125_D0.300090.840
69_F72_L0.299560.839
143_R146_Q0.299120.838
89_I98_D0.29910.837
49_R66_A0.298710.836
121_E126_L0.29820.835
116_Y120_D0.294310.824
70_D73_K0.293280.821
65_D68_D0.292210.818
5_A120_D0.29010.812
123_L127_F0.289320.810
134_D169_G0.288660.808
153_G156_P0.288650.808
48_L52_K0.287410.805
169_G173_Y0.284620.797
102_I105_S0.284520.797
142_E145_I0.281640.789
35_I75_D0.28070.786
76_L82_G0.279550.783
113_E117_A0.278010.778
80_K83_G0.277480.777
8_S140_R0.276840.775
6_G11_G0.276340.774
50_D54_R0.276020.773
154_R159_V0.275710.772
116_Y119_Y0.275080.770
113_E116_Y0.274080.767
166_V169_G0.272670.763
84_S103_I0.272390.763
132_F167_R0.271210.759
103_I106_P0.271150.759
77_K81_N0.270790.758
54_R58_R0.269640.755
88_P92_F0.269270.754
23_L109_I0.267660.749
94_T97_R0.265260.743
89_I93_S0.262250.734
58_R61_F0.259820.728
87_I90_Y0.259780.727
96_D99_P0.258630.724
59_Y63_H0.255680.716
40_D45_D0.255660.716
39_L42_F0.253740.710
37_L41_D0.252050.706
4_I131_I0.251920.705
109_I113_E0.250170.700
72_L76_L0.248910.697
105_S108_D0.248090.695
134_D137_E0.244460.684
141_L163_Y0.243930.683
67_F72_L0.243890.683
165_R168_P0.243710.682
39_L117_A0.243710.682
154_R162_Q0.24360.682
154_R158_E0.243390.682
43_Y67_F0.24280.680
19_L23_L0.242470.679
72_L112_V0.242210.678
86_E103_I0.242210.678
68_D72_L0.239770.671
43_Y46_Y0.239230.670
115_I118_L0.238520.668
163_Y167_R0.238250.667
6_G12_K0.237150.664
137_E171_E0.237050.664
90_Y97_R0.236560.662
122_E125_D0.236360.662
16_A36_I0.2350.658
171_E174_I0.234830.658
61_F65_D0.234180.656
24_N108_D0.23390.655
37_L45_D0.231530.648
3_G92_F0.231120.647
145_I156_P0.23020.645
86_E98_D0.229490.643
141_L144_R0.228980.641
6_G23_L0.228960.641
51_R59_Y0.228030.638
107_S110_V0.226510.634
121_E173_Y0.226170.633
21_Q24_N0.225330.631
90_Y93_S0.225070.630
121_E124_R0.225050.630
112_V123_L0.223370.625
46_Y50_D0.223310.625
46_Y59_Y0.222990.624
7_P137_E0.222430.623
146_Q157_E0.222360.623
124_R127_F0.222240.622
134_D171_E0.221820.621
92_F98_D0.221570.620
73_K76_L0.218910.613
54_R59_Y0.218430.612
54_R78_A0.218130.611
77_K80_K0.217150.608
16_A41_D0.216530.606
164_E168_P0.216150.605
68_D97_R0.215970.605
49_R52_K0.215960.605
115_I119_Y0.215920.605
14_T17_K0.214830.602
86_E101_I0.213750.599
138_D143_R0.213290.597
19_L111_I0.213160.597
104_I107_S0.212720.596
16_A86_E0.212570.595
43_Y47_H0.211310.592
8_S13_T0.210510.589
48_L54_R0.210230.589
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
4gi7A0.963999.90.179
1a7jA0.979499.90.225
3tqcA0.963999.90.259
1sq5A0.963999.90.299
1uj2A199.90.306
4bfzA0.974299.80.317
1odfA0.989799.80.337
1rz3A0.896999.80.354
2ga8A0.994899.80.364
3aezA0.974299.80.371

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