GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mob_synth_C - Molybdenum Cofactor Synthesis C
Pfam: PF06463 (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: 128
Sequences: 1651
Seq/Len: 12.9
HH_delta: 0.357 (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
101_L114_A0.628023.402
97_D100_P0.604063.272
85_K97_D0.566993.071
29_L63_F0.559323.030
2_D60_R0.531162.877
25_A65_S0.510162.763
107_S110_E0.493552.673
39_L53_R0.442082.395
112_K116_R0.39132.120
29_L33_E0.388682.105
122_K126_H0.388162.103
31_R34_E0.378862.052
81_T87_K0.339131.837
117_E121_R0.335311.816
32_L36_Y0.321341.741
2_D51_Y0.319361.730
30_E34_E0.305491.655
85_K95_G0.302581.639
113_E117_E0.300771.629
87_K95_G0.297461.611
51_Y60_R0.281771.526
38_L61_V0.278741.510
106_A110_E0.276371.497
30_E33_E0.26621.442
88_P96_I0.265831.440
105_G110_E0.261831.418
116_R120_A0.261811.418
39_L55_P0.253951.376
37_E55_P0.253641.374
4_R49_A0.252371.367
26_Q69_N0.246351.334
27_E31_R0.244831.326
46_N76_N0.239121.295
78_I119_I0.234091.268
113_E116_R0.228411.237
109_E113_E0.222531.205
5_F61_V0.216551.173
26_Q30_E0.214271.161
24_P27_E0.209671.136
88_P92_S0.209191.133
98_L115_I0.209111.133
22_F68_S0.204031.105
45_P48_P0.202791.098
100_P104_S0.202111.095
8_L17_W0.201761.093
119_I122_K0.199041.078
55_P58_K0.196911.067
49_A62_G0.195691.060
28_I63_F0.193421.048
23_V28_I0.192281.042
32_L35_R0.190981.034
50_R65_S0.190351.031
4_R62_G0.187251.014
27_E30_E0.187191.014
119_I124_P0.185521.005
88_P123_P0.183460.994
8_L91_F0.182240.987
48_P76_N0.181920.985
80_L98_L0.181720.984
1_I48_P0.180810.979
54_I57_G0.178410.966
95_G118_A0.177950.964
8_L67_V0.177540.962
29_L52_Y0.176380.955
5_F28_I0.17620.954
9_M62_G0.176030.954
101_L104_S0.172860.936
100_P114_A0.172380.934
10_P122_K0.172160.933
80_L103_R0.170470.923
41_S53_R0.170160.922
72_C75_C0.168070.910
67_V91_F0.167960.910
11_I14_G0.167660.908
48_P126_H0.166390.901
33_E39_L0.166190.900
17_W91_F0.164640.892
52_Y63_F0.163590.886
5_F36_Y0.162490.880
5_F64_I0.160120.867
34_E40_P0.160040.867
34_E44_R0.159330.863
40_P52_Y0.159250.863
17_W95_G0.158630.859
4_R9_M0.157720.854
11_I66_P0.157150.851
3_V61_V0.155540.843
30_E40_P0.155320.841
86_L118_A0.15330.830
110_E113_E0.15330.830
25_A63_F0.152870.828
118_A123_P0.151590.821
8_L22_F0.151250.819
10_P14_G0.151080.818
14_G81_T0.150790.817
23_V27_E0.150360.814
3_V59_G0.148980.807
75_C79_R0.148910.807
15_N19_E0.148310.803
30_E42_E0.148060.802
124_P127_H0.1480.802
88_P118_A0.147640.800
4_R64_I0.147610.800
115_I119_I0.147040.796
80_L86_L0.145260.787
26_Q109_E0.145210.787
102_L111_L0.144250.781
44_R109_E0.144170.781
38_L41_S0.14270.773
12_G47_G0.142330.771
97_D102_L0.142120.770
119_I126_H0.141920.769
65_S70_P0.141710.768
63_F69_N0.141390.766
47_G51_Y0.140260.760
115_I118_A0.140030.759
104_S107_S0.139670.757
65_S68_S0.138830.752
67_V119_I0.138360.749
99_R103_R0.137570.745
37_E56_G0.135750.735
101_L106_A0.135120.732
40_P53_R0.134470.728
27_E35_R0.133910.725
25_A28_I0.133690.724
52_Y114_A0.133370.722
71_F90_L0.133350.722
67_V126_H0.133010.720
30_E113_E0.13180.714
1_I101_L0.131630.713
110_E114_A0.130560.707
81_T95_G0.130120.705
123_P126_H0.129060.699
117_E120_A0.128590.697
66_P91_F0.12850.696
97_D101_L0.128410.696
66_P123_P0.128160.694
46_N49_A0.128130.694
13_E66_P0.127880.693
28_I42_E0.126950.688
67_V70_P0.126790.687
103_R111_L0.126730.686
52_Y58_K0.126270.684
65_S91_F0.125540.680
72_C89_C0.125270.679
16_N19_E0.125230.678
12_G91_F0.125060.677
93_N121_R0.124280.673
78_I81_T0.124160.673
35_R39_L0.124140.672
110_E117_E0.123550.669
4_R7_E0.123540.669
118_A121_R0.123530.669
72_C79_R0.123430.669
79_R90_L0.123070.667
108_D112_K0.122770.665
1_I112_K0.121680.659
8_L21_E0.121210.657
86_L95_G0.121180.656
51_Y70_P0.121150.656
31_R113_E0.121120.656
8_L32_L0.121040.656
48_P122_K0.120580.653
29_L69_N0.120380.652
33_E104_S0.120260.651
91_F95_G0.120030.650
112_K115_I0.119790.649
104_S120_A0.119670.648
34_E109_E0.119510.647
37_E119_I0.118920.644
101_L105_G0.118870.644
122_K125_R0.118510.642
114_A117_E0.118380.641
24_P70_P0.11830.641
71_F75_C0.118290.641
83_D100_P0.117930.639
96_I121_R0.117630.637
33_E55_P0.117240.635
34_E104_S0.117080.634
22_F91_F0.117050.634
75_C89_C0.1170.634
1_I15_N0.116830.633
11_I91_F0.116420.631
80_L102_L0.116140.629
69_N82_S0.115970.628
39_L42_E0.115740.627
41_S45_P0.11560.626
18_F21_E0.115430.625
11_I48_P0.115410.625
47_G62_G0.114660.621
79_R89_C0.11460.621
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
1tv8A199.90.357
2a5hA0.890691.70.888
4k36A0.929791.30.889
3l78A0.445350.40.923
4b2gA0.812537.30.928
3fz4A0.468828.60.932
4eplA0.804726.90.933
3my7A0.921925.40.934
3k9dA0.9375240.934
3gkxA0.476623.80.934

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