GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NTP_transferase - Nucleotidyl transferase
Pfam: PF00483 (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: CL0110
Length: 248
Sequences: 13728
Seq/Len: 55.35
HH_delta: 0.142 (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
30_K39_E1.679913.752
48_E74_K1.325932.961
152_E161_R1.231962.751
154_D158_R1.183482.643
35_D39_E1.105742.469
84_L88_G1.092652.440
152_E160_I1.030812.302
59_E63_E1.030332.301
48_E76_E1.028622.297
189_F214_Q0.9862.202
2_A46_I0.932272.082
35_D64_H0.929272.075
32_P35_D0.922952.061
209_P213_E0.907812.027
124_E128_E0.907052.026
41_L109_L0.850211.899
91_L94_L0.848411.895
158_R217_K0.844741.887
60_Q63_E0.832081.858
78_I92_Q0.82741.848
131_A219_Y0.823441.839
2_A41_L0.806031.800
210_K214_Q0.802651.793
189_F210_K0.784361.752
58_E62_E0.783951.751
141_P173_N0.781621.746
122_M181_I0.77741.736
154_D160_I0.760721.699
126_H136_T0.759861.697
121_D124_E0.759761.697
120_Q124_E0.757881.693
210_K213_E0.739051.651
185_E216_K0.738571.649
58_E79_V0.736811.646
161_R209_P0.734971.641
238_Y242_N0.728591.627
118_D121_D0.724241.617
20_I60_Q0.703421.571
14_R18_D0.701631.567
158_R219_Y0.699961.563
3_V93_A0.694431.551
125_F129_S0.692441.546
125_F221_F0.68711.535
139_V222_I0.681991.523
141_P222_I0.676921.512
139_V220_A0.675181.508
184_P188_D0.670391.497
62_E79_V0.667161.490
25_L238_Y0.664341.484
206_D209_P0.661041.476
144_D147_R0.645991.443
159_V220_A0.634111.416
185_E189_F0.633191.414
30_K36_Y0.620871.387
163_V170_N0.618041.380
174_L222_I0.616511.377
24_L60_Q0.610491.363
76_E96_F0.606061.354
232_I241_A0.603331.347
239_L242_N0.595141.329
20_I26_P0.591731.322
36_Y40_N0.590671.319
21_P60_Q0.588681.315
33_L232_I0.581841.299
151_V159_V0.581691.299
129_S219_Y0.578971.293
13_L25_L0.569761.272
32_P64_H0.56361.259
26_P242_N0.563031.257
26_P32_P0.561691.254
32_P36_Y0.561531.254
121_D125_F0.559641.250
34_I61_I0.558811.248
189_F207_A0.558591.248
88_G92_Q0.556831.244
239_L243_M0.556441.243
57_K60_Q0.555251.240
54_N58_E0.554481.238
235_P239_L0.552051.233
62_E66_G0.549921.228
139_V173_N0.545111.217
106_F184_P0.544851.217
185_E188_D0.53851.203
236_E240_E0.536451.198
90_L108_V0.536021.197
153_V174_L0.533721.192
40_N43_N0.53311.191
186_I216_K0.526821.177
54_N62_E0.524931.172
94_L188_D0.5241.170
107_L181_I0.523121.168
12_R22_K0.517311.155
125_F128_E0.513951.148
149_G164_E0.51141.142
59_E62_E0.50961.138
8_G21_P0.509181.137
53_V58_E0.506681.132
124_E127_R0.500451.118
126_H181_I0.500221.117
109_L119_L0.49891.114
118_D228_Y0.496441.109
30_K35_D0.492931.101
153_V220_A0.492321.100
101_D184_P0.490821.096
126_H183_K0.490251.095
110_N178_G0.4871.088
45_G120_Q0.484191.081
35_D68_G0.478811.069
44_A120_Q0.47841.068
107_L123_L0.477551.067
39_E43_N0.475731.062
24_L64_H0.475231.061
80_Q83_P0.47361.058
234_T237_D0.469811.049
66_G77_Y0.468681.047
228_Y244_D0.468141.045
152_E172_S0.467771.045
10_G22_K0.467091.043
34_I65_L0.459531.026
110_N113_I0.45481.016
130_N183_K0.447480.999
230_I240_E0.445230.994
134_T183_K0.445020.994
98_E188_D0.444360.992
98_E184_P0.4420.987
135_V182_F0.440820.984
39_E42_A0.439020.980
36_Y245_L0.43790.978
26_P29_G0.435480.973
167_D170_N0.435350.972
29_G36_Y0.433880.969
38_L42_A0.4310.963
63_E66_G0.427180.954
88_G91_L0.425110.949
28_G242_N0.424710.949
86_T110_N0.423890.947
237_D240_E0.42350.946
146_S167_D0.422170.943
38_L65_L0.419610.937
139_V151_V0.417530.932
205_T209_P0.417050.931
28_G245_L0.411770.920
139_V174_L0.40830.912
94_L187_F0.407770.911
42_A74_K0.405940.907
185_E214_Q0.403460.901
54_N77_Y0.401640.897
176_N180_Y0.400110.894
230_I244_D0.399640.893
125_F220_A0.396270.885
4_I111_G0.39430.881
152_E163_V0.393940.880
13_L235_P0.392930.878
51_V93_A0.391910.875
230_I241_A0.390630.872
240_E243_M0.390470.872
162_I176_N0.390330.872
157_G222_I0.387830.866
108_V182_F0.387050.864
125_F219_Y0.386720.864
62_E77_Y0.386590.863
33_L37_V0.385560.861
3_V106_F0.384720.859
150_V175_I0.382950.855
6_A34_I0.379630.848
158_R218_V0.377780.844
182_F208_I0.377120.842
7_G23_P0.376070.840
240_E244_D0.375980.840
142_V173_N0.375820.839
97_I106_F0.375040.838
54_N79_V0.374640.837
121_D221_F0.374570.837
63_E67_S0.373410.834
91_L95_D0.372130.831
38_L75_I0.370990.829
206_D210_K0.37060.828
152_E170_N0.37020.827
101_D183_K0.367980.822
58_E61_I0.36450.814
40_N44_A0.361340.807
126_H221_F0.360960.806
7_G53_V0.360360.805
6_A51_V0.354590.792
160_I163_V0.354370.791
123_L127_R0.352610.787
211_L216_K0.35170.785
28_G36_Y0.351170.784
4_I37_V0.351120.784
25_L235_P0.350740.783
85_G88_G0.350440.783
207_A210_K0.349950.782
46_I123_L0.346720.774
35_D38_L0.346660.774
211_L215_G0.341930.764
64_H67_S0.341450.763
186_I211_L0.341440.763
122_M136_T0.340860.761
129_S218_V0.339990.759
208_I218_V0.338840.757
147_R237_D0.338460.756
91_L202_D0.336440.751
3_V51_V0.335780.750
99_E184_P0.332440.742
101_D185_E0.332220.742
43_N120_Q0.332030.742
23_P61_I0.330920.739
122_M138_L0.330020.737
123_L181_I0.329930.737
78_I96_F0.329570.736
19_T60_Q0.328360.733
9_K83_P0.325950.728
168_N172_S0.324810.725
189_F216_K0.324490.725
96_F99_E0.32390.723
6_A52_V0.323410.722
81_P92_Q0.32330.722
2_A109_L0.322510.720
27_I238_Y0.322410.720
219_Y222_I0.322280.720
27_I242_N0.317160.708
233_G237_D0.316590.707
97_I187_F0.315870.705
46_I107_L0.315830.705
115_F241_A0.315780.705
199_R203_F0.315560.705
5_L110_N0.315330.704
201_E204_L0.315040.704
159_V218_V0.313840.701
68_G77_Y0.313190.699
142_V145_P0.313130.699
25_L242_N0.312620.698
54_N57_K0.311550.696
47_K74_K0.31150.696
22_K112_D0.311350.695
137_L151_V0.310740.694
50_I96_F0.309880.692
24_L61_I0.304820.681
80_Q88_G0.303880.679
121_D224_E0.301740.674
78_I93_A0.30080.672
151_V162_I0.299120.668
204_L209_P0.298480.667
27_I245_L0.298080.666
37_V109_L0.296750.663
135_V139_V0.292730.654
80_Q89_A0.292550.653
2_A107_L0.292220.653
59_E79_V0.292040.652
196_E199_R0.291980.652
35_D65_L0.291440.651
38_L50_I0.289610.647
155_E160_I0.289190.646
80_Q84_L0.288610.645
165_K233_G0.288250.644
146_S165_K0.286860.641
76_E79_V0.286590.640
26_P238_Y0.286550.640
2_A44_A0.28620.639
36_Y39_E0.285110.637
81_P84_L0.284590.636
154_D157_G0.283650.633
90_L93_A0.279790.625
5_L108_V0.278060.621
236_E239_L0.275240.615
24_L32_P0.274320.613
172_S176_N0.273730.611
134_T216_K0.273620.611
131_A216_K0.271850.607
224_E228_Y0.271520.606
8_G12_R0.269650.602
159_V162_I0.268860.600
93_A96_F0.268460.600
100_E184_P0.267360.597
157_G160_I0.267340.597
27_I241_A0.266870.596
140_V175_I0.265660.593
5_L86_T0.265650.593
7_G52_V0.26560.593
5_L90_L0.265410.593
147_R165_K0.26510.592
146_S168_N0.265040.592
125_F131_A0.264040.590
21_P57_K0.263210.588
186_I189_F0.262620.587
127_R130_N0.262570.586
9_K14_R0.262420.586
12_R165_K0.261610.584
84_L202_D0.261070.583
3_V53_V0.260620.582
125_F134_T0.260270.581
65_L75_I0.259980.581
52_V93_A0.259340.579
118_D223_F0.259290.579
142_V146_S0.259140.579
3_V90_L0.258730.578
231_D237_D0.258460.577
126_H130_N0.256750.573
177_T223_F0.256650.573
60_Q64_H0.255970.572
222_I225_G0.255870.571
7_G83_P0.255290.570
53_V57_K0.254080.567
50_I78_I0.253980.567
134_T217_K0.253410.566
232_I238_Y0.252970.565
145_P150_V0.252910.565
116_D228_Y0.251710.562
131_A218_V0.251550.562
122_M221_F0.251370.561
144_D165_K0.250890.560
82_E88_G0.250870.560
118_D122_M0.250850.560
153_V157_G0.250720.560
145_P168_N0.249210.557
56_Y60_Q0.249120.556
83_P88_G0.24830.555
110_N180_Y0.247920.554
42_A47_K0.247380.552
7_G10_G0.247370.552
137_L220_A0.247180.552
117_D120_Q0.247170.552
114_I241_A0.246840.551
183_K186_I0.246430.550
80_Q85_G0.244510.546
163_V166_P0.244130.545
33_L114_I0.242610.542
8_G22_K0.241250.539
5_L89_A0.240690.538
32_P68_G0.239990.536
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
3jukA0.95161000.142
4ecmA0.94761000.162
1mc3A0.95561000.192
1fxoA0.95561000.194
1lvwA0.95561000.197
2pa4A0.96371000.201
2ux8A0.95161000.202
2e3dA0.94351000.204
3pnnA0.93551000.207
3brkX0.96371000.213

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