GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IstB_IS21 - IstB-like ATP binding protein
Pfam: PF01695 (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: 178
Sequences: 3958
Seq/Len: 22.24
HH_delta: 0.265 (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
68_A113_I0.659342.959
68_A78_V0.625362.806
83_A114_L0.618492.776
32_K36_A0.5942.666
70_E73_R0.571462.565
19_L66_A0.537792.413
62_H66_A0.531382.385
64_A144_I0.514312.308
71_A111_L0.464772.086
134_I143_T0.442351.985
77_S110_D0.430871.934
64_A146_T0.415111.863
22_F63_L0.410421.842
137_R143_T0.405811.821
13_L68_A0.390751.754
76_Y110_D0.388621.744
92_Q96_D0.387941.741
79_L109_V0.381841.714
110_D141_K0.378641.699
87_L126_E0.369771.659
70_E74_K0.36751.649
114_L130_L0.357781.606
80_F146_T0.355321.595
104_K108_R0.354721.592
81_I106_L0.351961.579
64_A113_I0.351151.576
116_D146_T0.330891.485
51_I147_S0.328711.475
112_L133_I0.325411.460
150_S153_E0.317791.426
113_I146_T0.315891.418
131_F135_D0.313941.409
153_E156_E0.312781.404
89_E106_L0.304941.368
22_F62_H0.299181.343
85_D136_E0.291761.309
71_A76_Y0.290551.304
37_Q42_E0.288681.295
90_L125_W0.284521.277
93_S99_Y0.284421.276
20_E70_E0.275731.237
42_E45_E0.274531.232
117_L145_I0.272841.224
13_L65_V0.271651.219
65_V69_N0.266141.194
59_G115_D0.264831.188
67_I144_I0.262551.178
55_P58_T0.261331.173
98_S101_E0.25681.152
26_N29_G0.256111.149
31_D34_Q0.25351.138
118_G148_N0.253331.137
18_T21_N0.252461.133
83_A117_L0.250571.124
34_Q38_L0.250141.123
72_I75_G0.248311.114
56_P155_E0.246771.107
33_A37_Q0.244451.097
41_L44_I0.243931.095
92_Q100_E0.242511.088
24_F32_K0.242281.087
100_E104_K0.24211.086
90_L99_Y0.239511.075
17_A65_V0.239371.074
94_R99_Y0.238581.071
93_S96_D0.232181.042
78_V110_D0.231651.040
21_N62_H0.230411.034
45_E74_K0.228871.027
118_G147_S0.22651.016
82_T85_D0.226481.016
18_T69_N0.219840.987
62_H65_V0.219830.987
107_K133_I0.219130.983
91_K95_S0.217970.978
82_T135_D0.214120.961
90_L94_R0.213440.958
89_E102_L0.213420.958
149_L154_L0.211910.951
116_D120_E0.211010.947
86_L133_I0.210710.946
107_K136_E0.209640.941
17_A138_Y0.209090.938
49_N142_P0.208960.938
149_L153_E0.208730.937
135_D139_E0.208140.934
117_L130_L0.207590.932
117_L120_E0.204950.920
28_R33_A0.203880.915
32_K35_I0.202330.908
17_A62_H0.202130.907
72_I78_V0.202040.907
116_D148_N0.200830.901
56_P131_F0.200370.899
109_V112_L0.200170.898
43_F50_L0.200130.898
78_V113_I0.200110.898
152_S156_E0.199060.893
111_L142_P0.198880.893
33_A36_A0.198420.890
14_P61_T0.198420.890
150_S154_L0.196370.881
92_Q95_S0.195290.876
22_F148_N0.195040.875
53_Y152_S0.19370.869
118_G151_P0.192820.865
60_K115_D0.191550.860
102_L105_R0.190920.857
94_R129_L0.190420.855
29_G33_A0.189850.852
54_G131_F0.187750.843
53_Y147_S0.186420.837
41_L70_E0.186170.835
39_A50_L0.184830.829
95_S99_Y0.183130.822
88_D91_K0.182430.819
24_F36_A0.181780.816
31_D36_A0.181510.815
52_L64_A0.179620.806
25_S28_R0.17930.805
128_E132_E0.179270.805
132_E135_D0.177360.796
30_I35_I0.177360.796
84_S133_I0.177240.795
65_V80_F0.177010.794
30_I33_A0.176150.791
23_D26_N0.173370.778
24_F35_I0.172810.776
77_S109_V0.172420.774
14_P139_E0.17220.773
14_P135_D0.172110.772
106_L109_V0.171960.772
54_G58_T0.17140.769
25_S31_D0.170340.764
35_I38_L0.169350.760
51_I54_G0.168330.755
19_L39_A0.166570.748
49_N145_I0.165940.745
84_S119_Y0.165930.745
142_P154_L0.165670.743
137_R141_K0.165090.741
25_S34_Q0.164840.740
18_T66_A0.163790.735
62_H116_D0.163350.733
28_R34_Q0.162730.730
79_L105_R0.162680.730
80_F113_I0.162230.728
93_S102_L0.162140.728
88_D126_E0.162090.727
18_T73_R0.162050.727
69_N73_R0.161090.723
133_I137_R0.161040.723
31_D35_I0.160840.722
90_L102_L0.160210.719
37_Q45_E0.159930.718
48_E108_R0.159890.718
15_P21_N0.15970.717
85_D140_R0.159030.714
88_D92_Q0.15790.709
88_D129_L0.15770.708
121_P124_E0.156460.702
73_R96_D0.15610.701
108_R136_E0.155750.699
91_K94_R0.154970.695
15_P70_E0.153930.691
103_L133_I0.153210.688
38_L41_L0.153080.687
44_I71_A0.152770.686
52_L116_D0.152490.684
54_G57_G0.152480.684
118_G137_R0.151660.681
131_F134_I0.149960.673
44_I142_P0.149590.671
15_P18_T0.149440.671
61_T115_D0.148940.668
123_S126_E0.148940.668
91_K126_E0.148730.667
82_T132_E0.148180.665
138_Y145_I0.147980.664
117_L147_S0.147660.663
82_T131_F0.146920.659
101_E104_K0.14690.659
84_S88_D0.146850.659
50_L67_I0.146720.658
26_N103_L0.146630.658
134_I138_Y0.146470.657
53_Y151_P0.146380.657
119_Y149_L0.145730.654
125_W128_E0.145330.652
56_P119_Y0.145320.652
103_L128_E0.144840.650
83_A130_L0.144540.649
14_P65_V0.14440.648
103_L129_L0.143690.645
116_D131_F0.143620.645
28_R31_D0.143570.644
12_G85_D0.143420.644
62_H80_F0.143260.643
119_Y148_N0.143010.642
39_A43_F0.142950.642
90_L151_P0.141830.636
76_Y109_V0.14170.636
12_G79_L0.141450.635
21_N33_A0.141380.634
87_L123_S0.141240.634
84_S129_L0.141060.633
17_A22_F0.140840.632
127_A132_E0.140210.629
91_K123_S0.140060.629
82_T117_L0.13980.627
63_L112_L0.139540.626
20_E23_D0.139280.625
101_E105_R0.138880.623
84_S132_E0.138530.622
85_D114_L0.138470.621
19_L40_A0.137560.617
121_P127_A0.137550.617
96_D99_Y0.13690.614
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
2qgzA0.977599.90.265
2w58A0.994499.90.333
3ec2A0.938299.90.386
1l8qA0.910199.80.451
2z4sA0.949499.80.455
2kjqA0.80999.70.513
3bosA0.893399.60.524
3cmuA0.994499.50.56
3cmuA0.977599.50.563
2bjvA0.870899.50.569

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