GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DEAD - DEADDEAH box helicase
Pfam: PF00270 (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: 169
Sequences: 44885
Seq/Len: 265.59
HH_delta: 0.035 (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
35_A47_V1.995213.149
32_I64_L1.831612.891
61_F65_R1.660762.621
31_Y158_L1.641642.591
21_A25_S1.566272.472
11_I156_I1.548122.443
5_Q9_E1.390882.195
128_A157_L1.344052.121
74_R97_D1.288812.034
46_R121_S1.233591.947
37_N41_E1.22861.939
61_F77_L1.183621.868
31_Y124_V1.129591.783
29_L63_R1.124081.774
23_T160_A1.074671.696
76_V96_A1.069731.688
51_V60_Q1.066311.683
137_R141_K1.047361.653
10_A17_V1.033231.631
47_V122_L1.009151.593
63_R66_K0.995151.571
12_I37_N0.985371.555
101_T106_L0.976621.541
48_L120_L0.974241.538
19_I158_L0.950521.500
56_L59_Q0.936041.477
7_A30_A0.929931.468
11_I34_P0.912891.441
36_L40_Q0.894871.412
21_A30_A0.886631.399
38_R122_L0.872551.377
83_S87_D0.838711.324
63_R67_F0.832261.314
61_F75_V0.82691.305
51_V57_A0.81251.282
11_I17_V0.80981.278
9_E13_S0.802171.266
122_L156_I0.800731.264
123_I155_I0.798941.261
138_A141_K0.795311.255
6_E10_A0.790991.248
49_I60_Q0.789861.247
8_I12_I0.783431.236
138_A142_S0.778491.229
139_M142_S0.773851.221
46_R97_D0.772851.220
28_T60_Q0.767721.212
60_Q63_R0.764271.206
38_R42_G0.758371.197
137_R140_L0.757841.196
84_I89_R0.756281.194
30_A34_P0.755751.193
85_S90_E0.75071.185
7_A19_I0.745111.176
58_E62_E0.7231.141
76_V91_V0.721791.139
37_N40_Q0.720881.138
24_G27_K0.715711.130
142_S145_R0.715471.129
87_D91_V0.714621.128
96_A99_L0.707681.117
62_E66_K0.701741.108
108_D112_N0.70131.107
48_L123_I0.699591.104
141_K145_R0.698941.103
20_S162_L0.698871.103
107_L111_S0.688551.087
17_V156_I0.687111.084
6_E9_E0.683361.079
9_E12_I0.683021.078
88_Q91_V0.676411.068
48_L55_A0.670521.058
142_S146_R0.66881.056
64_L75_V0.662481.046
10_A13_S0.654361.033
33_L36_L0.653721.032
107_L142_S0.644951.018
88_Q92_L0.640771.011
137_R142_S0.638981.008
146_R149_R0.625010.986
64_L98_I0.623340.984
104_E107_L0.619960.978
38_R121_S0.618730.977
8_I33_L0.615180.971
159_S162_L0.6140.969
62_E65_R0.608940.961
105_Q108_D0.604420.954
50_I106_L0.601880.950
64_L100_V0.59120.933
75_V78_L0.589930.931
130_H133_D0.58520.924
8_I34_P0.582840.920
33_L37_N0.579710.915
61_F100_V0.579030.914
43_K121_S0.572830.904
59_Q63_R0.570020.900
31_Y60_Q0.567560.896
39_L47_V0.564280.891
22_P25_S0.558790.882
36_L39_L0.55680.879
139_M144_L0.555690.877
7_A10_A0.55320.873
51_V100_V0.550650.869
107_L139_M0.548120.865
31_Y49_I0.542160.856
32_I63_R0.539610.852
50_I101_T0.539290.851
85_S89_R0.536770.847
29_L67_F0.535040.844
34_P122_L0.533410.842
49_I52_P0.531920.840
12_I15_K0.53010.837
123_I153_I0.529840.836
7_A11_I0.525510.829
80_G83_S0.522540.825
74_R77_L0.521260.823
101_T105_Q0.520510.822
58_E61_F0.519760.820
18_L162_L0.519170.819
57_A77_L0.516830.816
108_D111_S0.513860.811
89_R92_L0.511170.807
87_D90_E0.509010.803
76_V79_H0.50780.801
31_Y34_P0.507380.801
58_E77_L0.505440.798
98_I102_T0.50440.796
46_R119_R0.504330.796
53_T104_E0.501280.791
75_V79_H0.499840.789
105_Q109_L0.499690.789
140_L143_I0.498350.787
23_T56_L0.497720.786
8_I30_A0.497190.785
89_R93_S0.496220.783
84_I87_D0.494470.780
109_L112_N0.493670.779
99_L120_L0.492610.777
139_M143_I0.491630.776
80_G84_I0.487220.769
122_L154_Q0.486110.767
59_Q62_E0.484220.764
57_A100_V0.483580.763
34_P37_N0.482440.761
4_Q7_A0.477060.753
81_G84_I0.476260.752
123_I144_L0.47540.750
105_Q111_S0.475360.750
111_S142_S0.475130.750
148_K155_I0.472480.746
144_L148_K0.471720.745
39_L97_D0.471430.744
75_V80_G0.467340.738
84_I88_Q0.467240.737
144_L147_L0.466040.736
35_A124_V0.465080.734
60_Q100_V0.464650.733
77_L82_Q0.463110.731
79_H83_S0.462160.729
85_S88_Q0.460860.727
137_R144_L0.459810.726
107_L110_I0.459260.725
29_L33_L0.459230.725
103_P125_I0.458190.723
36_L68_F0.458070.723
55_A59_Q0.457820.723
127_E161_T0.456690.721
38_R154_Q0.456430.720
34_P38_R0.454630.718
52_P56_L0.45270.714
116_N119_R0.451730.713
82_Q85_S0.449950.710
129_H132_S0.44990.710
77_L81_G0.447920.707
96_A106_L0.44690.705
35_A39_L0.446170.704
15_K154_Q0.443130.699
140_L144_L0.442240.698
136_F140_L0.442140.698
79_H82_Q0.439540.694
129_H159_S0.438890.693
47_V98_I0.431830.682
82_Q91_V0.430630.680
141_K144_L0.427360.674
14_G154_Q0.422850.667
154_Q157_L0.422150.666
127_E160_A0.421310.665
124_V158_L0.419150.662
19_I156_I0.417860.659
16_N157_L0.417460.659
87_D92_L0.417190.658
117_I120_L0.416340.657
18_L128_A0.415510.656
38_R41_E0.414140.654
93_S96_A0.41090.649
145_R148_K0.410320.648
49_I100_V0.41020.647
66_K69_S0.408670.645
140_L146_R0.407940.644
82_Q88_Q0.406960.642
54_R57_A0.404270.638
102_T106_L0.403890.637
19_I30_A0.403310.637
35_A122_L0.40160.634
124_V156_I0.401170.633
16_N154_Q0.400610.632
21_A27_K0.399490.631
39_L42_G0.396940.626
23_T28_T0.396540.626
47_V124_V0.396470.626
143_I146_R0.394960.623
23_T129_H0.394740.623
77_L84_I0.391240.617
24_G161_T0.391190.617
82_Q87_D0.390830.617
95_Q98_I0.390580.616
69_S120_L0.389620.615
65_R69_S0.388350.613
56_L127_E0.387480.612
73_V97_D0.387390.611
141_K146_R0.385130.608
32_I67_F0.384710.607
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
2db3A0.994199.90.035
3ly5A0.982299.90.055
3fe2A0.982299.90.056
1wrbA0.994199.90.062
3l9oA0.905399.90.063
3borA0.988299.90.066
3eiqA0.988299.90.069
3sqwA199.90.073
3iuyA0.976399.90.076
2i4iA0.994199.90.076

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