GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Kinesin - Kinesin motor domain
Pfam: PF00225 (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: 335
Sequences: 3835
Seq/Len: 11.45
HH_delta: -0.041 (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
59_Y110_D0.81614.163
70_V215_V0.682693.482
310_V325_T0.576462.940
91_T309_I0.561382.863
233_R298_D0.541722.763
133_L171_L0.534122.724
310_V329_A0.519752.651
132_Y189_G0.513472.619
49_F61_E0.492312.511
271_N289_D0.491762.508
92_M236_F0.480092.449
101_P109_R0.479232.444
155_L168_I0.479212.444
178_S181_E0.462732.360
56_E60_E0.455392.323
199_K249_G0.442582.257
257_K260_S0.438552.237
66_L76_A0.433962.213
49_F58_V0.43152.201
60_E64_S0.418212.133
108_L182_A0.413662.110
129_S173_E0.407162.077
130_V211_F0.405232.067
55_Q106_R0.40032.042
69_S305_K0.399052.035
253_G256_L0.397322.027
68_D114_Q0.395462.017
86_S311_C0.387821.978
133_L168_I0.386481.971
115_I128_V0.386471.971
132_Y209_A0.38351.956
158_R169_K0.381221.944
268_A271_N0.377781.927
79_F308_L0.366871.871
47_R61_E0.363421.854
212_T235_T0.354281.807
53_A57_D0.348571.778
64_S110_D0.347291.771
43_F323_L0.344381.757
248_S253_G0.343061.750
127_S175_E0.342911.749
301_G306_T0.341161.740
256_L260_S0.329641.681
294_R297_K0.328641.676
261_N264_K0.31981.631
245_L259_S0.319621.630
330_S334_E0.313031.597
54_T57_D0.312721.595
291_K294_R0.310261.583
177_K181_E0.308551.574
287_Y301_G0.301361.537
267_S271_N0.29821.521
125_E218_K0.295931.509
129_S216_E0.294181.501
166_V294_R0.294031.500
176_V182_A0.292331.491
131_S171_L0.289621.477
95_S101_P0.286491.461
248_S259_S0.284221.450
275_A286_P0.284051.449
114_Q118_R0.280581.431
245_L256_L0.279111.424
133_L295_L0.278581.421
107_A236_F0.274471.400
308_L332_A0.266791.361
173_E214_H0.266471.359
168_I171_L0.265871.356
328_F335_I0.263041.342
116_E119_K0.262281.338
174_V188_K0.261031.331
50_D53_A0.259071.321
196_A255_R0.257721.315
245_L260_S0.256151.307
201_N204_S0.255511.303
90_Y100_E0.254021.296
139_K154_P0.253621.294
115_I126_F0.253241.292
198_T201_N0.251881.285
108_L213_I0.246911.259
114_Q117_E0.246131.255
68_D72_D0.245881.254
198_T204_S0.245421.252
63_V103_L0.242881.239
82_G87_G0.241821.233
56_E106_R0.241051.230
200_M247_K0.240291.226
250_A253_G0.240021.224
70_V234_L0.239081.219
137_N261_N0.238471.216
140_V157_I0.238211.215
201_N206_R0.236461.206
188_K192_N0.236221.205
46_D333_R0.235831.203
260_S264_K0.234961.198
129_S175_E0.234171.194
68_D110_D0.23411.194
95_S100_E0.232311.185
77_T299_S0.229031.168
313_S318_D0.22791.162
127_S216_E0.227051.158
247_K318_D0.227021.158
186_L211_F0.226741.157
63_V78_I0.225431.150
303_N306_T0.224731.146
288_R293_T0.223531.140
258_E262_I0.22291.137
198_T205_S0.221721.131
308_L328_F0.219241.118
134_E141_Y0.218661.115
55_Q58_V0.218461.114
129_S214_H0.217661.110
71_L114_Q0.217321.108
132_Y190_Q0.216831.106
159_E166_V0.216371.104
87_G91_T0.215521.099
323_L327_R0.215521.099
112_F176_V0.215131.097
144_L189_G0.214321.093
271_N275_A0.214281.093
104_I211_F0.213331.088
214_H231_H0.212811.085
113_S117_E0.211821.080
201_N205_S0.211541.079
302_G306_T0.208861.065
132_Y211_F0.20841.063
109_R179_A0.207761.060
233_R299_S0.204271.042
245_L250_A0.203371.037
75_N232_S0.202041.031
156_K169_K0.200611.023
198_T206_R0.199751.019
41_K327_R0.199141.016
188_K191_K0.197171.006
110_D113_S0.197141.006
184_Q188_K0.197011.005
82_G88_K0.196141.000
322_T326_L0.195330.996
70_V232_S0.195010.995
69_S76_A0.194290.991
250_A259_S0.193870.989
67_V107_A0.192010.979
181_E184_Q0.191330.976
250_A256_L0.190990.974
112_F128_V0.190210.970
34_S37_S0.189510.967
71_L111_L0.188940.964
125_E220_R0.187720.957
179_A183_L0.186140.949
93_F190_Q0.185940.948
199_K202_A0.185140.944
110_D114_Q0.183610.937
254_Q257_K0.182410.930
138_E290_S0.181340.925
285_V288_R0.181090.924
53_A58_V0.181030.923
79_F235_T0.18050.921
212_T233_R0.180420.920
93_F186_L0.180350.920
315_S318_D0.179690.917
66_L307_I0.178860.912
130_V176_V0.178460.910
272_V287_Y0.178090.908
259_S267_S0.177630.906
247_K317_E0.177040.903
41_K323_L0.176910.902
107_A234_L0.176640.901
77_T294_R0.17630.899
320_E328_F0.176220.899
292_L296_L0.176190.899
170_G173_E0.176060.898
69_S72_D0.175920.897
130_V182_A0.175450.895
94_G102_G0.175390.895
308_L329_A0.175160.893
57_D61_E0.174990.893
81_Y84_T0.174520.890
310_V328_F0.174040.888
199_K203_R0.173810.887
239_L243_E0.173690.886
63_V67_V0.173140.883
126_F217_Q0.172920.882
190_Q209_A0.172810.881
43_F46_D0.172180.878
273_I328_F0.172180.878
43_F327_R0.171620.875
216_E231_H0.170930.872
268_A289_D0.170930.872
104_I132_Y0.170180.868
258_E263_N0.169960.867
312_V322_T0.169770.866
140_V155_L0.168880.861
219_D222_P0.168650.860
184_Q187_K0.167980.857
307_I311_C0.167680.855
32_V36_N0.167640.855
247_K259_S0.167360.854
193_R209_A0.167030.852
332_A335_I0.16610.847
63_V107_A0.166070.847
238_D241_G0.165640.845
108_L179_A0.165620.845
260_S265_S0.165040.842
174_V185_L0.164780.840
174_V181_E0.164610.840
279_G283_S0.16440.839
258_E266_L0.164110.837
88_K91_T0.16410.837
217_Q230_K0.164090.837
270_G274_R0.163950.836
287_Y293_T0.163670.835
255_R258_E0.163530.834
235_T299_S0.163370.833
278_Q282_Q0.163070.832
155_L169_K0.163040.832
31_S34_S0.162720.830
219_D230_K0.16270.830
271_N274_R0.162040.827
84_T89_T0.161880.826
262_I266_L0.161840.825
63_V307_I0.161740.825
67_V110_D0.16170.825
180_E184_Q0.161360.823
72_D118_R0.161250.822
84_T87_G0.161160.822
243_E266_L0.160870.821
107_A110_D0.160680.820
103_L309_I0.160650.819
90_Y95_S0.160410.818
84_T88_K0.160050.816
112_F182_A0.159850.815
201_N208_H0.158590.809
185_L188_K0.157920.805
189_G209_A0.157750.805
64_S68_D0.157430.803
84_T241_G0.156540.798
166_V297_K0.156530.798
248_S256_L0.155510.793
128_V213_I0.155150.791
267_S324_S0.154960.790
290_S293_T0.154680.789
240_A243_E0.154610.789
31_S36_N0.153990.785
57_D60_E0.153790.784
256_L259_S0.153680.784
73_G82_G0.153330.782
247_K260_S0.153120.781
55_Q105_P0.152690.779
124_Y217_Q0.150910.770
271_N331_R0.150840.769
83_Q200_M0.150180.766
298_D301_G0.149310.762
159_E297_K0.148420.757
70_V76_A0.148260.756
308_L319_Y0.148250.756
272_V276_L0.148150.756
84_T243_E0.14760.753
128_V176_V0.147570.753
141_Y194_R0.147420.752
93_F209_A0.14690.749
77_T83_Q0.146730.748
205_S208_H0.14660.748
238_D242_S0.146250.746
107_A111_L0.145910.744
279_G282_Q0.145770.744
204_S207_S0.14430.736
76_A234_L0.143960.734
98_P101_P0.143390.731
244_R308_L0.143360.731
140_V168_I0.142790.728
134_E194_R0.142180.725
242_S262_I0.141780.723
244_R253_G0.141680.723
216_E229_V0.141560.722
102_G106_R0.141390.721
102_G105_P0.141310.721
240_A262_I0.1410.719
327_R330_S0.140880.719
157_I291_K0.13960.712
208_H240_A0.139520.712
92_M104_I0.13950.712
118_R126_F0.139140.710
214_H233_R0.13910.709
233_R310_V0.13870.707
112_F115_I0.138630.707
313_S322_T0.138530.707
81_Y88_K0.138520.707
265_S269_L0.138520.707
62_V307_I0.138250.705
267_S328_F0.138060.704
128_V215_V0.137320.700
237_V240_A0.137110.699
290_S296_L0.136930.698
71_L215_V0.136880.698
67_V234_L0.136840.698
87_G94_G0.136530.696
293_T296_L0.136330.695
74_Y301_G0.135680.692
260_S267_S0.135680.692
67_V111_L0.135590.692
63_V76_A0.135560.691
258_E265_S0.135550.691
76_A307_I0.135390.691
204_S241_G0.135260.690
62_V65_P0.135210.690
45_F48_V0.135070.689
311_C325_T0.13470.687
201_N262_I0.134580.686
200_M248_S0.134530.686
272_V286_P0.134350.685
44_R333_R0.134110.684
103_L107_A0.133990.683
284_H288_R0.133810.683
31_S35_N0.13340.680
130_V185_L0.133140.679
146_P188_K0.132790.677
198_T258_E0.132740.677
85_G88_K0.132460.676
193_R206_R0.132380.675
86_S89_T0.131820.672
204_S208_H0.131740.672
249_G253_G0.131670.672
263_N288_R0.131510.671
325_T328_F0.131260.670
160_D167_Y0.131180.669
84_T200_M0.130870.668
248_S255_R0.130790.667
208_H265_S0.130740.667
250_A255_R0.13070.667
145_S172_T0.130640.666
204_S262_I0.130580.666
193_R198_T0.130530.666
35_N38_Q0.130470.665
141_Y202_A0.130090.664
215_V232_S0.130040.663
276_L302_G0.129890.663
206_R238_D0.129720.662
180_E183_L0.129640.661
84_T242_S0.129410.660
201_N207_S0.129260.659
66_L78_I0.129230.659
44_R254_Q0.129030.658
276_L287_Y0.128930.658
157_I166_V0.128420.655
274_R331_R0.128190.654
193_R204_S0.127830.652
204_S238_D0.127830.652
131_S173_E0.127530.650
138_E142_D0.127470.650
87_G90_Y0.127430.650
118_R121_K0.127410.650
113_S116_E0.127380.650
218_K224_D0.127050.648
206_R262_I0.126740.646
311_C332_A0.126550.645
124_Y219_D0.126450.645
241_G262_I0.126190.644
95_S98_P0.126080.643
126_F215_V0.125740.641
31_S37_S0.12560.641
218_K229_V0.125550.640
324_S333_R0.125440.640
159_E167_Y0.125430.640
159_E294_R0.125290.639
152_R155_L0.125280.639
206_R241_G0.124640.636
130_V213_I0.124290.634
83_Q88_K0.12420.633
94_G265_S0.124180.633
36_N39_K0.124130.633
98_P109_R0.123990.632
82_G86_S0.123730.631
82_G85_G0.123670.631
75_N303_N0.123550.630
80_A83_Q0.122320.624
262_I265_S0.122180.623
201_N240_A0.121680.621
325_T331_R0.121590.620
250_A267_S0.121330.619
67_V70_V0.121280.619
197_S202_A0.121150.618
157_I168_I0.120870.617
272_V275_A0.120830.616
201_N243_E0.120720.616
47_R53_A0.120630.615
265_S311_C0.120470.614
272_V297_K0.120440.614
119_K125_E0.120340.614
34_S38_Q0.120310.614
103_L110_D0.120180.613
243_E258_E0.119960.612
155_L158_R0.119780.611
244_R256_L0.119740.611
109_R125_E0.119660.610
55_Q94_G0.119270.608
213_I334_E0.119250.608
155_L171_L0.119070.607
83_Q237_V0.118920.607
59_Y107_A0.118870.606
145_S153_K0.118830.606
275_A310_V0.118830.606
288_R296_L0.118450.604
188_K195_T0.118420.604
198_T208_H0.118320.604
237_V242_S0.118050.602
319_Y323_L0.118040.602
238_D243_E0.117760.601
136_Y262_I0.117720.600
264_K267_S0.117620.600
108_L192_N0.11750.599
187_K190_Q0.117150.598
32_V37_S0.116870.596
308_L333_R0.116740.595
301_G304_S0.116680.595
66_L134_E0.116580.595
266_L269_L0.116560.595
243_E263_N0.116510.594
256_L264_K0.116360.594
297_K317_E0.116360.594
273_I331_R0.11610.592
201_N241_G0.115960.591
49_F55_Q0.11580.591
198_T241_G0.115780.591
40_E157_I0.115520.589
60_E65_P0.115420.589
66_L72_D0.115420.589
55_Q59_Y0.115120.587
70_V128_V0.114870.586
274_R278_Q0.11480.586
76_A305_K0.114630.585
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
2zfiA0.9731100-0.041
3lreA0.9642100-0.035
2owmA0.9821100-0.035
2vvgA0.9552100-0.033
3bfnA0.9522100-0.031
1gojA0.9433100-0.031
3b6uA0.9672100-0.031
1bg2A0.9284100-0.028
2y65A0.9403100-0.028
1t5cA0.9463100-0.026

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