GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MCM_N - MCM N-terminal domain
Pfam: PF14551 (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: 121
Sequences: 1327
Seq/Len: 10.97
HH_delta: 0.143 (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
4_R44_D0.472323.190
17_K39_D0.460973.113
36_D98_N0.391462.644
6_R68_E0.371192.507
32_S95_R0.304082.053
8_F18_Y0.282521.908
53_E115_K0.269731.822
36_D97_Y0.25991.755
7_E11_E0.258411.745
66_L92_I0.250681.693
20_D24_E0.246051.662
3_R7_E0.243461.644
25_M33_L0.223171.507
10_R72_E0.222331.501
55_P114_G0.218231.474
63_E93_Q0.209191.413
18_Y39_D0.207571.402
23_R27_Q0.205721.389
40_L51_L0.202071.365
49_E53_E0.201421.360
34_Y97_Y0.198081.338
8_F12_F0.197121.331
37_L48_A0.189941.283
6_R65_A0.181681.227
17_K21_Q0.17911.209
9_L62_F0.178071.203
55_P59_L0.176871.194
67_K91_E0.17541.184
6_R10_R0.174031.175
15_E20_D0.171661.159
59_L94_V0.171431.158
35_V68_E0.170191.149
34_Y95_R0.168341.137
21_Q30_K0.167861.134
18_Y25_M0.166561.125
37_L100_P0.164021.108
12_F18_Y0.162981.101
38_D107_E0.162281.096
110_S114_G0.161851.093
94_V116_L0.161571.091
103_T112_H0.161081.088
5_F47_L0.159811.079
50_A58_Y0.159731.079
59_L69_V0.157281.062
11_E43_F0.156811.059
57_R114_G0.155251.048
12_F39_D0.154931.046
109_R112_H0.152671.031
35_V62_F0.150151.014
36_D118_S0.149981.013
4_R7_E0.149811.012
24_E30_K0.147110.993
32_S93_Q0.147050.993
55_P96_F0.146140.987
106_R113_I0.145880.985
35_V96_F0.143570.970
15_E43_F0.142040.959
93_Q119_V0.141290.954
38_D98_N0.140460.949
26_I70_V0.140190.947
71_K88_R0.140060.946
22_L25_M0.139540.942
67_K92_I0.137990.932
57_R110_S0.137270.927
57_R60_P0.137040.925
37_L99_L0.13620.920
32_S37_L0.134820.910
98_N105_I0.133760.903
54_N110_S0.133690.903
36_D64_E0.13220.893
6_R69_V0.132070.892
5_F62_F0.131950.891
7_E49_E0.131650.889
13_K16_P0.131480.888
96_F110_S0.130210.879
64_E68_E0.129920.877
16_P20_D0.129830.877
105_I109_R0.129650.876
25_M92_I0.129190.872
60_P66_L0.128920.871
99_L107_E0.12890.870
22_L104_S0.128880.870
57_R61_L0.128430.867
105_I112_H0.128320.867
63_E94_V0.128130.865
51_L61_L0.128120.865
57_R103_T0.127520.861
23_R73_L0.127450.861
45_P50_A0.127390.860
12_F116_L0.127180.859
99_L118_S0.125930.850
91_E106_R0.12560.848
104_S107_E0.125220.846
11_E42_E0.125150.845
106_R119_V0.12460.841
56_Y60_P0.124590.841
52_I100_P0.124440.840
5_F40_L0.124420.840
9_L24_E0.124260.839
16_P19_M0.124260.839
40_L97_Y0.124010.837
32_S56_Y0.122980.831
70_V92_I0.122580.828
23_R89_R0.121180.818
83_P86_L0.120520.814
56_Y95_R0.119860.809
15_E24_E0.119560.807
88_R113_I0.119060.804
30_K69_V0.118280.799
101_K107_E0.117690.795
10_R19_M0.117010.790
30_K33_L0.116720.788
95_R98_N0.116680.788
37_L83_P0.116560.787
44_D87_K0.116340.786
62_F92_I0.116020.783
58_Y61_L0.115280.779
98_N118_S0.115210.778
23_R40_L0.11510.777
35_V44_D0.114970.776
110_S120_S0.114910.776
60_P63_E0.114810.775
71_K86_L0.114760.775
36_D39_D0.11440.773
21_Q33_L0.113910.769
67_K71_K0.113150.764
19_M93_Q0.112840.762
59_L63_E0.112050.757
57_R94_V0.111950.756
16_P115_K0.111750.755
56_Y62_F0.111520.753
52_I115_K0.111420.752
6_R9_L0.110710.748
8_F43_F0.110040.743
35_V64_E0.109090.737
65_A111_S0.108760.734
16_P93_Q0.108730.734
66_L94_V0.108640.734
25_M93_Q0.107990.729
29_N62_F0.107890.729
49_E112_H0.107730.728
17_K20_D0.107490.726
45_P49_E0.107160.724
31_K65_A0.106680.720
61_L96_F0.106180.717
101_K117_V0.106170.717
9_L25_M0.106070.716
20_D23_R0.105740.714
18_Y27_Q0.105470.712
47_L51_L0.104870.708
46_D69_V0.104790.708
33_L48_A0.104550.706
9_L40_L0.104110.703
45_P113_I0.103970.702
104_S119_V0.103930.702
31_K87_K0.103890.702
83_P88_R0.103820.701
41_R72_E0.103710.700
29_N41_R0.103370.698
117_V121_G0.102930.695
47_L58_Y0.102890.695
54_N58_Y0.102750.694
19_M34_Y0.102610.693
65_A110_S0.102260.691
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
2vl6A0.933999.80.143
4fdgB0.933999.80.152
3f9vA0.933999.80.157
1ltlA0.851299.80.196
2f4mB0.504177.20.844
1pveA0.586853.30.866
1oqyA0.8678490.869
3qc5X0.471124.20.889
2lmdA0.925621.50.891
3i7fA0.553721.10.891

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