GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MCM - MCM235 family
Pfam: PF00493 (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: 331
Sequences: 5985
Seq/Len: 18.08
HH_delta: 0.017 (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
311_R318_D1.298165.313
243_S246_L1.002994.105
120_A125_C0.742023.037
302_S314_V0.738423.022
305_H321_E0.700622.868
262_L299_I0.615452.519
210_E272_N0.61382.512
34_K321_E0.613482.511
200_L301_L0.604532.474
112_L152_I0.60382.471
32_I73_L0.59642.441
309_R318_D0.57262.344
263_S266_A0.5622.300
266_A319_V0.559192.289
311_R315_T0.557312.281
104_D111_V0.540332.212
144_A161_L0.539672.209
214_E268_E0.539222.207
209_D212_E0.539132.207
268_E272_N0.53262.180
290_I294_Q0.522122.137
149_T160_T0.521722.135
38_L305_H0.50472.066
273_Y323_I0.4982.038
36_I77_V0.490962.009
34_K305_H0.49012.006
130_F169_A0.484071.981
274_Y295_L0.464431.901
269_L320_E0.453571.856
72_Q76_Y0.438041.793
212_E215_R0.433851.776
148_Q164_R0.433381.774
269_L316_E0.428291.753
222_D264_E0.421821.726
199_D297_S0.415071.699
270_I299_I0.414151.695
41_F308_L0.411731.685
214_E271_I0.40461.656
34_K309_R0.40381.653
74_L168_L0.40121.642
305_H309_R0.396141.621
245_D249_K0.363091.486
270_I319_V0.363021.486
64_G69_G0.362621.484
25_S76_Y0.358281.466
210_E268_E0.356041.457
117_L150_I0.34841.426
39_Q60_I0.342251.401
37_L211_E0.34211.400
123_G164_R0.33921.388
117_L125_C0.335541.373
101_V153_A0.334631.370
36_I73_L0.334591.369
199_D301_L0.331491.357
305_H318_D0.329271.348
38_L301_L0.325931.334
153_A156_G0.3221.318
134_K137_D0.321191.315
305_H322_A0.319881.309
88_S91_G0.317391.299
210_E275_V0.314861.289
36_I60_I0.312631.280
41_F304_A0.311641.276
106_V109_E0.310771.272
38_L200_L0.308761.264
298_L323_I0.308411.262
253_Y307_K0.307711.259
38_L322_A0.307041.257
277_L290_I0.306681.255
315_T318_D0.306191.253
309_R317_E0.306041.253
31_D321_E0.300151.228
302_S319_V0.299781.227
262_L266_A0.299591.226
249_K253_Y0.297721.219
301_L322_A0.29741.217
126_C170_A0.29571.210
114_A159_T0.294761.206
213_D278_R0.293071.200
37_L41_F0.288231.180
39_Q200_L0.28821.180
263_S313_E0.284681.165
40_L81_A0.283511.160
264_E268_E0.282961.158
242_I246_L0.280891.150
264_E267_K0.278891.141
104_D107_T0.278671.141
32_I62_L0.278621.140
84_S125_C0.275551.128
41_F254_A0.274511.124
86_Y127_I0.273951.121
80_L235_I0.273491.119
64_G206_D0.272371.115
129_E172_N0.27211.114
138_R194_L0.271961.113
242_I250_Y0.271461.111
250_Y307_K0.269861.105
265_E316_E0.26971.104
267_K271_I0.269191.102
97_L117_L0.268671.100
254_A314_V0.265321.086
249_K252_A0.264571.083
38_L308_L0.263651.079
103_R108_G0.261671.071
98_T152_I0.259241.061
65_D68_T0.257811.055
112_L159_T0.257721.055
210_E214_E0.257331.053
211_E268_E0.255931.048
75_K147_Q0.253851.039
39_Q42_G0.250921.027
61_L171_A0.249881.023
37_L308_L0.247291.012
93_S96_G0.246651.010
131_D171_A0.245961.007
252_A255_R0.245621.005
29_H64_G0.245141.003
266_A269_L0.243620.997
317_E320_E0.241750.989
83_R86_Y0.241290.988
153_A158_V0.240760.985
92_S96_G0.240430.984
67_G70_K0.240250.983
228_K232_E0.238690.977
32_I205_R0.238550.976
169_A198_F0.23730.971
83_R221_L0.237190.971
151_S160_T0.236920.970
105_P108_G0.236910.970
63_V201_I0.236020.966
26_I76_Y0.235890.965
172_N197_R0.234820.961
75_K79_K0.234410.959
261_V313_E0.231030.946
254_A307_K0.23090.945
43_G163_A0.228580.936
244_E248_R0.227360.931
33_K42_G0.226640.928
68_T204_L0.226170.926
42_G304_A0.225780.924
311_R317_E0.223750.916
35_A38_L0.223680.916
269_L323_I0.223050.913
197_R293_R0.221870.908
83_R87_T0.221540.907
117_L144_A0.221350.906
222_D267_K0.220710.903
35_A322_A0.220570.903
309_R321_E0.220360.902
292_I295_L0.219710.899
39_Q44_V0.218290.893
60_I168_L0.217990.892
41_F250_Y0.217070.888
211_E215_R0.217020.888
299_I303_E0.217020.888
173_P176_G0.216960.888
296_E300_R0.216140.885
96_G99_A0.215990.884
26_I33_K0.215860.884
299_I302_S0.215450.882
103_R116_A0.21260.870
143_E147_Q0.212230.869
91_G96_G0.210630.862
265_E268_E0.209780.859
27_Y223_S0.209570.858
210_E271_I0.20910.856
86_Y97_L0.208630.854
314_V319_V0.207840.851
198_F201_I0.207810.851
255_R300_R0.207420.849
91_G94_A0.207160.848
41_F307_K0.20680.846
130_F194_L0.206610.846
246_L249_K0.206320.844
33_K41_F0.20550.841
25_S72_Q0.205410.841
220_I224_H0.2050.839
262_L270_I0.204790.838
85_V88_S0.204120.835
269_L272_N0.203060.831
94_A99_A0.202770.830
133_M139_D0.202160.827
64_G204_L0.201950.827
148_Q163_A0.201840.826
35_A200_L0.20180.826
37_L77_V0.201580.825
268_E271_I0.201440.824
82_P125_C0.200730.822
222_D226_N0.200270.820
38_L42_G0.199860.818
64_G70_K0.198990.814
87_T91_G0.198550.813
40_L77_V0.198360.812
112_L161_L0.19770.809
80_L213_D0.197430.808
113_E156_G0.196680.805
248_R296_E0.196080.803
102_S105_P0.195980.802
33_K39_Q0.195870.802
272_N275_V0.194940.798
27_Y212_E0.194810.797
39_Q168_L0.1940.794
236_K241_P0.192810.789
160_T163_A0.192670.789
266_A315_T0.192450.788
98_T114_A0.191540.784
60_I200_L0.191180.782
135_E139_D0.190810.781
248_R252_A0.189580.776
129_E197_R0.188280.771
127_I167_V0.188260.771
32_I204_L0.188140.770
30_E33_K0.18810.770
95_A99_A0.188040.770
117_L165_C0.187880.769
272_N276_E0.18780.769
254_A304_A0.185180.758
130_F190_L0.185170.758
207_K292_I0.18510.758
211_E214_E0.184970.757
271_I275_V0.184110.754
70_K197_R0.182510.747
224_H227_G0.182340.746
70_K128_D0.182180.746
95_A98_T0.182010.745
26_I69_G0.181550.743
33_K73_L0.18140.742
26_I73_L0.180960.741
222_D225_R0.180780.740
30_E212_E0.180770.740
174_K193_P0.18010.737
139_D191_P0.179410.734
267_K299_I0.179160.733
213_D295_L0.178180.729
34_K37_L0.177440.726
100_S105_P0.177280.726
226_N232_E0.176980.724
143_E151_S0.176880.724
84_S88_S0.175940.720
213_D275_V0.174330.714
32_I35_A0.173560.710
232_E235_I0.173330.709
76_Y80_L0.172880.708
224_H255_R0.170810.699
316_E320_E0.170760.699
119_L125_C0.170690.699
178_Y198_F0.170450.698
147_Q151_S0.16990.695
241_P245_D0.169340.693
131_D190_L0.169310.693
135_E138_R0.169130.692
43_G240_K0.169130.692
221_L225_R0.168840.691
233_K236_K0.168670.690
76_Y235_I0.168630.690
123_G166_S0.168170.688
91_G99_A0.168130.688
223_S227_G0.167940.687
262_L314_V0.167460.685
214_E222_D0.16740.685
150_I161_L0.166890.683
29_H32_I0.166450.681
127_I130_F0.166190.680
266_A316_E0.1660.679
104_D108_G0.165930.679
302_S305_H0.165030.675
146_E300_R0.164030.671
109_E113_E0.163660.670
232_E236_K0.1630.667
123_G162_N0.162780.666
226_N312_D0.162710.666
208_P213_D0.162470.665
263_S315_T0.16240.665
63_V171_A0.161340.660
75_K149_T0.160780.658
269_L273_Y0.160590.657
126_C168_L0.160540.657
300_R303_E0.160380.656
87_T236_K0.160360.656
250_Y254_A0.160150.655
200_L322_A0.160030.655
225_R228_K0.159920.655
162_N244_E0.15980.654
214_E267_K0.159720.654
35_A60_I0.159570.653
41_F223_S0.158880.650
83_R88_S0.157860.646
33_K37_L0.157450.644
68_T292_I0.157250.644
35_A42_G0.157120.643
128_D293_R0.157090.643
35_A202_F0.156990.643
124_I166_S0.156370.640
222_D228_K0.156230.639
35_A305_H0.155710.637
69_G197_R0.155620.637
241_P244_E0.155480.636
30_E309_R0.155450.636
269_L319_V0.155010.634
103_R111_V0.154130.631
88_S151_S0.153930.630
146_E153_A0.153830.630
67_G197_R0.153750.629
227_G234_K0.153240.627
77_V166_S0.152860.626
84_S87_T0.15280.625
42_G300_R0.152430.624
297_S301_L0.152190.623
236_K252_A0.152010.622
214_E264_E0.151930.622
66_P129_E0.151090.618
294_Q297_S0.150510.616
228_K233_K0.149840.613
98_T112_L0.14980.613
34_K41_F0.149550.612
242_I300_R0.149350.611
306_A318_D0.149260.611
261_V312_D0.149220.611
92_S100_S0.148960.610
69_G130_F0.148930.610
224_H228_K0.148510.608
41_F44_V0.147950.606
227_G232_E0.147830.605
33_K36_I0.147790.605
113_E291_T0.147620.604
93_S137_D0.147470.604
72_Q75_K0.147470.604
35_A41_F0.14730.603
99_A102_S0.14710.602
145_M198_F0.14690.601
167_V198_F0.146870.601
222_D310_L0.146460.599
215_R317_E0.146020.598
144_A162_N0.145760.597
35_A204_L0.145660.596
43_G255_R0.145640.596
253_Y312_D0.145480.595
71_S147_Q0.145260.595
98_T101_V0.144370.591
234_K246_L0.144280.591
95_A101_V0.144160.590
112_L118_V0.143840.589
61_L169_A0.143690.588
72_Q193_P0.143540.587
76_Y79_K0.14350.587
164_R241_P0.143430.587
130_F138_R0.143360.587
158_V161_L0.142790.584
270_I295_L0.142780.584
91_G95_A0.142750.584
143_E149_T0.142510.583
106_V117_L0.142170.582
92_S116_A0.141910.581
140_A194_L0.14190.581
248_R255_R0.14170.580
220_I227_G0.14170.580
114_A162_N0.141590.580
110_W140_A0.141440.579
27_Y292_I0.141340.578
144_A163_A0.14130.578
84_S120_A0.141110.578
227_G233_K0.140770.576
101_V105_P0.140750.576
223_S308_L0.140730.576
70_K293_R0.140510.575
306_A314_V0.140060.573
215_R264_E0.139660.572
59_H145_M0.139630.571
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
4fdgB0.96681000.017
3f8tA0.87921000.138
3f9vA0.96681000.179
3nbxX0.8611000.506
2r44A0.87011000.539
1g8pA0.876199.90.582
3k1jA0.827899.90.614
1um8A0.882299.80.7
1ofhA0.848999.70.716
3hwsA0.867199.70.718

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