GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PseudoU_synth_2 - RNA pseudouridylate synthase
Pfam: PF00849 (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. )
Length: 164
Sequences: 9326
Seq/Len: 56.87
HH_delta: 0.097 (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
79_T147_E2.075873.766
126_R147_E1.63632.968
124_R151_I1.594222.892
81_L145_L1.405342.549
77_E149_E1.335472.423
148_C162_L1.311152.378
94_K124_R1.292022.344
60_D63_A1.236912.244
79_T149_E1.171142.124
148_C158_I1.163322.110
93_G125_Y1.154872.095
81_L147_E1.140052.068
96_N122_I1.117712.028
94_K122_I1.0951.986
69_K73_K1.065771.933
128_L147_E1.008731.830
13_V55_L0.99921.813
91_E130_S0.976981.772
97_S164_H0.948281.720
127_V144_S0.922491.673
82_A148_C0.910161.651
146_V162_L0.902731.638
122_I151_I0.892621.619
9_A52_S0.871281.580
84_V162_L0.868921.576
84_V146_V0.861751.563
47_L55_L0.852891.547
96_N120_P0.852351.546
127_V130_S0.828681.503
64_A68_S0.821781.491
124_R149_E0.813861.476
83_L145_L0.798181.448
156_H159_R0.796291.444
65_A69_K0.796071.444
4_V54_L0.793241.439
123_T148_C0.786551.427
88_P144_S0.769211.395
157_Q161_H0.760271.379
83_L143_C0.758531.376
4_V56_L0.756891.373
78_K150_L0.755571.371
23_S26_E0.743271.348
58_A64_A0.72131.308
69_K72_P0.709161.286
27_L31_S0.686331.245
99_L160_V0.682371.238
10_G49_R0.67941.232
8_P11_V0.674731.224
84_V144_S0.668171.212
42_Y64_A0.666531.209
92_E126_R0.662241.201
150_L158_I0.660071.197
95_I98_P0.655611.189
44_V67_L0.641681.164
114_P117_D0.634551.151
27_L30_L0.626171.136
62_E66_K0.625721.135
13_V43_P0.614271.114
44_V58_A0.610111.107
66_K69_K0.598131.085
3_I57_F0.598031.085
26_E30_L0.595981.081
2_L63_A0.594381.078
41_L57_F0.594281.078
26_E29_A0.586541.064
26_E31_S0.577691.048
100_G115_G0.577511.048
131_G141_A0.567661.030
27_L32_L0.567271.029
28_P31_S0.562331.020
123_T161_H0.560391.017
129_R145_L0.560321.016
23_S27_L0.554251.005
61_K65_A0.548240.994
85_E143_C0.545890.990
95_I161_H0.541750.983
82_A146_V0.535570.972
58_A63_A0.531290.964
87_G130_S0.524230.951
77_E151_I0.523830.950
101_K155_T0.523060.949
24_V28_P0.509160.924
15_P43_P0.506230.918
123_T150_L0.503050.913
25_K30_L0.499020.905
100_G117_D0.494220.897
95_I162_L0.493150.895
81_L128_L0.487110.884
50_D159_R0.483130.876
12_P49_R0.478680.868
126_R149_E0.478630.868
94_K151_I0.474510.861
35_G38_P0.472790.858
24_V27_L0.467580.848
65_A68_S0.466480.846
43_P57_F0.46240.839
90_E93_G0.461520.837
28_P33_K0.459160.833
115_G118_G0.457070.829
61_K64_A0.456440.828
13_V47_L0.45420.824
130_S144_S0.449220.815
63_A67_L0.448310.813
51_T82_A0.445770.809
125_Y162_L0.444380.806
120_P123_T0.439320.797
23_S29_A0.435860.791
150_L157_Q0.432370.784
29_A32_L0.42960.779
68_S72_P0.4280.776
3_I6_N0.42750.775
46_R153_G0.427450.775
114_P164_H0.426060.773
24_V55_L0.423030.767
119_K154_R0.423010.767
58_A67_L0.421640.765
23_S28_P0.421070.764
131_G142_G0.418760.760
114_P118_G0.41820.759
87_G142_G0.409990.744
5_V36_D0.408220.741
28_P32_L0.407410.739
12_P16_S0.406190.737
82_A162_L0.404910.735
11_V27_L0.399810.725
5_V11_V0.398610.723
95_I99_L0.398560.723
33_K36_D0.396660.720
30_L33_K0.396140.719
45_H55_L0.392810.713
2_L67_L0.39040.708
6_N52_S0.390050.708
62_E65_A0.387890.704
44_V64_A0.387750.703
29_A33_K0.379640.689
98_P161_H0.379460.688
14_H43_P0.378840.687
2_L60_D0.373060.677
48_D153_G0.372010.675
91_E127_V0.369790.671
25_K29_A0.368110.668
152_T157_Q0.36520.662
83_L131_G0.36480.662
51_T156_H0.361550.656
46_R78_K0.357740.649
84_V88_P0.351350.637
87_G141_A0.351210.637
14_H64_A0.349760.634
42_Y61_K0.347010.629
66_K75_K0.3460.628
63_A66_K0.345230.626
123_T157_Q0.344820.625
85_E142_G0.343990.624
68_S74_R0.342150.621
24_V31_S0.341650.620
12_P17_D0.340910.618
77_E124_R0.340820.618
36_D41_L0.340620.618
89_V93_G0.34040.617
87_G144_S0.340190.617
97_S161_H0.340030.617
127_V146_V0.337910.613
93_G148_C0.337020.611
48_D80_Y0.336950.611
88_P130_S0.335870.609
48_D78_K0.335440.608
95_I125_Y0.335190.608
125_Y148_C0.333760.605
34_R38_P0.333710.605
88_P146_V0.333180.604
52_S81_L0.333030.604
51_T159_R0.332930.604
130_S141_A0.331310.601
12_P18_G0.324290.588
121_A151_I0.319880.580
155_T159_R0.318730.578
160_V163_A0.317190.575
78_K151_I0.31560.572
124_R127_V0.314270.570
89_V92_E0.314080.570
5_V55_L0.311460.565
78_K153_G0.310680.564
78_K157_Q0.309460.561
89_V144_S0.308360.559
113_P118_G0.307480.558
118_G154_R0.304990.553
98_P120_P0.304630.553
23_S31_S0.304020.551
80_Y153_G0.303490.551
3_I59_K0.302450.549
48_D159_R0.301920.548
154_R161_H0.300860.546
153_G159_R0.295580.536
160_V164_H0.295360.536
153_G156_H0.291670.529
25_K28_P0.288430.523
48_D155_T0.287560.522
131_G143_C0.286540.520
14_H155_T0.285420.518
66_K74_R0.284360.516
74_R77_E0.28350.514
10_G52_S0.282950.513
43_P68_S0.282360.512
44_V56_L0.281050.510
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
1v9fA0.92071000.097
2i82A0.90241000.125
1v9kA0.91461000.127
2omlA0.89021000.182
2olwA0.89021000.196
1kskA0.804999.90.253
1vioA0.804999.90.257
2gmlA0.774499.90.267
3dh3A0.774499.90.278
2ausC0.792797.60.793

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