GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rft-1 - Rft protein
Pfam: PF04506 (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: CL0222
Length: 549
Sequences: 6090
Seq/Len: 11.09
HH_delta: 0.385 (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
328_N340_Q0.671335.010
253_R257_S0.575864.298
75_N78_Q0.573874.283
160_F163_L0.4383.269
132_E136_F0.397792.969
397_F457_S0.362982.709
67_P157_Q0.337732.520
367_S389_R0.337722.520
316_S348_L0.337142.516
42_V295_A0.328512.452
413_S416_Q0.32382.417
443_L450_L0.319272.383
366_Y369_L0.307662.296
367_S385_P0.30352.265
430_I458_L0.298092.225
328_N339_K0.297892.223
68_S321_S0.28612.135
444_G447_G0.27692.067
323_L340_Q0.268092.001
434_A451_A0.267891.999
447_G451_A0.267771.998
385_P389_R0.260871.947
320_F341_A0.259381.936
371_L384_A0.256761.916
368_P372_R0.251831.879
27_L180_F0.25111.874
7_A315_S0.24491.828
144_I213_L0.243761.819
451_A455_N0.239651.789
39_I130_Y0.238581.781
159_L322_K0.234691.751
360_V364_P0.234461.750
345_L407_F0.233181.740
386_S446_V0.229911.716
324_L341_A0.229561.713
33_S36_I0.227751.700
324_L411_V0.227751.700
66_Q258_L0.22611.687
434_A454_I0.225351.682
364_P389_R0.224881.678
264_F418_D0.224441.675
162_K166_K0.219281.636
280_L445_A0.217331.622
27_L179_T0.216821.618
104_W136_F0.213981.597
461_I465_R0.212671.587
390_A453_C0.211411.578
204_A207_A0.21041.570
280_L448_L0.21021.569
323_L328_N0.20941.563
329_S342_A0.208431.556
27_L183_V0.208271.554
72_D326_R0.207151.546
413_S466_F0.206481.541
8_S12_L0.205781.536
362_F366_Y0.205551.534
363_G370_L0.205111.531
435_S439_T0.204831.529
321_S325_S0.204511.526
438_L451_A0.204031.523
276_D294_Y0.20291.514
415_S419_R0.202471.511
390_A450_L0.201691.505
137_L209_A0.201011.500
24_L175_K0.200971.500
406_A410_S0.199511.489
387_L445_A0.19841.481
390_A446_V0.196621.467
340_Q343_N0.196571.467
322_K326_R0.195561.459
368_P385_P0.193731.446
166_K170_L0.191261.427
203_L208_F0.190911.425
129_P133_P0.188051.403
140_L143_F0.187151.397
177_I181_A0.18591.387
342_A346_S0.184081.374
130_Y133_P0.183771.371
249_Y253_R0.182771.364
366_Y370_L0.182751.364
352_Y403_I0.182191.360
320_F410_S0.180531.347
279_V436_Y0.180361.346
260_W264_F0.180111.344
83_L154_L0.179871.342
72_D325_S0.179751.341
287_T290_D0.179141.337
124_A129_P0.178631.333
438_L443_L0.178041.329
91_A147_L0.177871.327
346_S350_K0.177581.325
276_D435_S0.177161.322
178_V182_L0.176931.320
181_A186_A0.176571.318
290_D445_A0.176291.316
356_G399_A0.175061.306
323_L326_R0.174591.303
207_A211_G0.174421.302
450_L454_I0.174411.302
300_Y370_L0.173711.296
56_R146_L0.172791.290
203_L207_A0.172671.289
458_L462_Y0.172541.288
339_K343_N0.172031.284
430_I434_A0.171861.283
180_F186_A0.171671.281
279_V435_S0.17161.281
173_F177_I0.169281.263
429_A433_A0.169031.261
63_C86_S0.16871.259
369_L372_R0.16781.252
276_D452_N0.167541.250
70_S75_N0.166991.246
15_L19_L0.166921.246
174_A218_T0.164861.230
12_L165_V0.163991.224
311_P315_S0.16321.218
352_Y399_A0.162821.215
431_F452_N0.162791.215
92_V96_I0.162541.213
174_A214_A0.161691.207
159_L319_Y0.161441.205
90_Q150_P0.160781.200
343_N346_S0.160271.196
343_N347_N0.160181.195
420_Y462_Y0.159871.193
340_Q344_V0.158971.186
175_K179_T0.158191.181
11_I311_P0.158081.180
171_A215_Y0.157681.177
404_T463_S0.157351.174
427_F459_R0.157061.172
210_L214_A0.157021.172
361_A365_P0.156971.171
341_A411_V0.156961.171
70_S78_Q0.156451.168
178_V214_A0.154191.151
69_S324_L0.154081.150
181_A185_L0.152551.138
62_A258_L0.151991.134
286_L290_D0.151541.131
69_S73_K0.151191.128
27_L184_V0.150371.122
431_F435_S0.149941.119
280_L294_Y0.149941.119
156_Q161_F0.149781.118
209_A213_L0.149161.113
248_S251_F0.149131.113
69_S412_A0.148741.110
420_Y463_S0.14871.110
203_L206_L0.14851.108
71_I79_S0.148281.107
6_G9_F0.147961.104
425_V429_A0.147811.103
10_L314_E0.147381.100
350_K354_Y0.146261.092
275_G432_L0.146041.090
358_V362_F0.145761.088
364_P393_Y0.145731.088
358_V361_A0.145191.084
404_T464_L0.144751.080
136_F140_L0.144631.079
135_V139_G0.144251.077
24_L208_F0.144221.076
122_S288_F0.144191.076
16_L169_S0.144041.075
397_F460_I0.143791.073
63_C67_P0.143331.070
206_L210_L0.143281.069
25_N299_N0.142691.065
371_L385_P0.141181.054
439_T448_L0.140931.052
354_Y358_V0.140771.051
179_T183_V0.14061.049
280_L286_L0.14031.047
267_I271_L0.139911.044
213_L217_I0.139811.043
433_A437_L0.139651.042
66_Q255_L0.139431.041
368_P389_R0.13921.039
414_E418_D0.139131.038
35_E124_A0.138971.037
77_A81_N0.138451.033
434_A438_L0.137891.029
219_L223_Y0.137851.029
66_Q82_L0.13771.028
24_L179_T0.137421.026
435_S448_L0.136751.021
71_I158_M0.136431.018
296_L374_L0.136341.018
462_Y465_R0.136251.017
362_F365_P0.135621.012
161_F315_S0.13561.012
208_F212_Q0.135581.012
174_A178_V0.135481.011
213_L216_S0.135451.011
437_L440_R0.135311.010
372_R381_S0.134861.006
369_L373_L0.134541.004
256_L260_W0.133920.999
208_F211_G0.133660.998
431_F455_N0.133630.997
139_G143_F0.133550.997
345_L404_T0.133430.996
43_Q281_S0.132960.992
211_G215_Y0.13290.992
319_Y344_V0.132740.991
81_N248_S0.132670.990
339_K342_A0.132110.986
29_L296_L0.131660.983
401_N456_M0.130590.975
261_S418_D0.128920.962
65_R69_S0.12850.959
123_N129_P0.12840.958
269_K273_T0.128330.958
68_S157_Q0.128280.957
377_S380_S0.128050.956
215_Y219_L0.127520.952
297_V387_L0.127440.951
465_R468_R0.127410.951
205_I208_F0.12740.951
393_Y453_C0.127340.950
365_P369_L0.12730.950
29_L37_L0.127040.948
180_F183_V0.126540.944
178_V211_G0.126460.944
28_L204_A0.126270.942
341_A345_L0.125630.938
457_S461_I0.125250.935
80_I83_L0.125050.933
363_G367_S0.124670.930
206_L209_A0.12450.929
254_D412_A0.123860.924
443_L447_G0.123740.923
280_L291_Q0.123650.923
167_A171_A0.123360.921
6_G161_F0.123150.919
19_L172_V0.122910.917
275_G278_L0.12290.917
317_R406_A0.122150.912
147_L220_F0.121950.910
69_S72_D0.121380.906
58_A62_A0.121270.905
181_A184_V0.120610.900
317_R321_S0.120480.899
438_L447_G0.120340.898
248_S253_R0.120320.898
324_L329_S0.120260.897
295_A299_N0.120260.897
167_A219_L0.120180.897
38_G292_G0.119990.895
300_Y363_G0.119950.895
353_L357_L0.119920.895
22_F303_L0.119670.893
221_F225_W0.11880.887
227_Y230_P0.118570.885
294_Y449_I0.118550.885
91_A95_L0.118480.884
359_I366_Y0.118450.884
59_F62_A0.118270.883
28_L40_A0.118270.883
137_L140_L0.118260.883
143_F146_L0.118120.882
175_K208_F0.117970.880
30_R376_G0.117960.880
29_L374_L0.117810.879
329_S339_K0.117670.878
4_A8_S0.117550.877
401_N459_R0.11750.877
401_N405_E0.117490.877
276_D431_F0.117040.873
392_C396_P0.1170.873
78_Q81_N0.116950.873
388_L391_Y0.116910.872
313_E406_A0.116690.871
359_I362_F0.116490.869
279_V439_T0.116320.868
393_Y397_F0.116190.867
62_A72_D0.1160.866
264_F268_L0.115960.865
123_N126_V0.115940.865
404_T467_I0.115840.865
289_E379_W0.115640.863
455_N459_R0.115520.862
297_V449_I0.115470.862
22_F26_Q0.115430.861
137_L206_L0.115140.859
430_I454_I0.115050.859
73_K325_S0.115030.858
156_Q164_R0.115020.858
28_L183_V0.115020.858
217_I221_F0.114840.857
207_A212_Q0.114510.855
39_I44_L0.114440.854
409_F417_L0.114240.853
43_Q46_L0.114170.852
281_S291_Q0.114150.852
43_Q131_F0.113910.850
327_D339_K0.113850.850
270_H274_E0.113840.850
203_L216_S0.113540.847
203_L212_Q0.113330.846
323_L344_V0.113160.845
60_R152_Y0.113140.844
408_V466_F0.112640.841
169_S173_F0.112530.840
26_Q30_R0.112050.836
175_K211_G0.111160.830
26_Q374_L0.110950.828
73_K326_R0.11040.824
402_G405_E0.11020.822
182_L207_A0.110150.822
386_S389_R0.110060.821
137_L210_L0.110040.821
32_L205_I0.109420.817
13_L16_L0.109410.817
62_A66_Q0.109330.816
42_V46_L0.10890.813
78_Q251_F0.108870.812
19_L23_V0.108630.811
329_S411_V0.108440.809
210_L213_L0.108310.808
319_Y323_L0.108240.808
394_Y449_I0.108170.807
426_V429_A0.108090.807
308_L355_L0.108030.806
357_L361_A0.1080.806
431_F451_A0.107680.804
17_S21_T0.107630.803
300_Y303_L0.107450.802
24_L27_L0.106960.798
407_F467_I0.106910.798
29_L375_G0.106460.795
301_G391_Y0.106270.793
161_F165_V0.10620.793
364_P367_S0.106120.792
16_L360_V0.1060.791
408_V416_Q0.105560.788
25_N295_A0.105480.787
21_T45_E0.105240.785
26_Q29_L0.105240.785
398_L456_M0.105210.785
87_V91_A0.10520.785
183_V204_A0.105190.785
400_I460_I0.105180.785
269_K398_L0.105090.784
389_R393_Y0.105050.784
66_Q70_S0.104910.783
44_L135_V0.10490.783
69_S254_D0.104880.783
38_G42_V0.104850.782
353_L400_I0.104810.782
367_S388_L0.104570.780
65_R317_R0.104510.780
122_S125_F0.104490.780
89_L252_D0.104450.780
301_G395_I0.104250.778
290_D444_G0.104120.777
49_S302_S0.104040.776
80_I84_W0.104040.776
254_D257_S0.104020.776
28_L208_F0.103970.776
348_L403_I0.103940.776
305_A398_L0.103910.775
47_L70_S0.103650.774
34_P377_S0.103470.772
299_N374_L0.103440.772
6_G318_L0.103360.771
141_S216_S0.103330.771
151_L155_A0.103190.770
69_S325_S0.10310.769
280_L387_L0.102990.769
447_G450_L0.102940.768
126_V129_P0.102810.767
86_S255_L0.10280.767
64_L153_I0.10270.766
250_Y253_R0.102680.766
377_S381_S0.102670.766
354_Y357_L0.102620.766
62_A65_R0.102570.765
144_I148_S0.102540.765
355_L362_F0.10250.765
364_P368_P0.102470.765
35_E38_G0.10230.763
13_L168_E0.102250.763
180_F185_L0.102250.763
183_V208_F0.102140.762
464_L468_R0.102010.761
456_M459_R0.101970.761
394_Y397_F0.101890.760
304_V363_G0.101750.759
360_V396_P0.101510.758
76_W80_I0.101360.756
10_L388_L0.101050.754
81_N84_W0.100980.754
168_E172_V0.100940.753
434_A437_L0.100890.753
182_L185_L0.100840.753
87_V147_L0.100810.752
347_N350_K0.100810.752
21_T138_Y0.100530.750
291_Q295_A0.100470.750
317_R410_S0.100350.749
394_Y456_M0.100130.747
339_K346_S0.100070.747
439_T447_G0.100060.747
406_A409_F0.100040.747
316_S321_S0.099890.745
349_L400_I0.099810.745
170_L174_A0.099780.745
33_S379_W0.099740.744
258_L456_M0.099570.743
225_W229_F0.099280.741
133_P136_F0.099220.740
91_A94_N0.098930.738
235_S239_P0.098770.737
51_I55_S0.098560.736
387_L449_I0.098520.735
141_S212_Q0.09850.735
433_A439_T0.098350.734
293_V384_A0.09830.734
322_K340_Q0.098290.734
71_I322_K0.098250.733
278_L282_F0.098220.733
44_L48_Y0.098150.732
304_V391_Y0.098090.732
311_P314_E0.097930.731
62_A259_T0.097850.730
390_A449_I0.097740.729
152_Y164_R0.09770.729
435_S452_N0.097690.729
153_I157_Q0.097280.726
35_E288_F0.097230.726
16_L19_L0.097210.725
450_L453_C0.097110.725
93_V458_L0.097090.725
65_R258_L0.096890.723
170_L257_S0.096830.723
19_L22_F0.096740.722
95_L239_P0.09670.722
179_T204_A0.096510.720
43_Q291_Q0.09650.720
14_Q18_R0.096490.720
69_S321_S0.096460.720
129_P132_E0.096320.719
414_E417_L0.096110.717
249_Y252_D0.096030.717
349_L404_T0.095980.716
126_V132_E0.095870.715
92_V386_S0.095770.715
370_L374_L0.095670.714
64_L421_N0.095510.713
79_S158_M0.09540.712
292_G300_Y0.095330.711
381_S385_P0.095240.711
394_Y453_C0.095220.711
9_F162_K0.095170.710
156_Q165_V0.095030.709
137_L213_L0.094950.709
44_L138_Y0.094740.707
154_L158_M0.094530.705
419_R466_F0.094480.705
81_N251_F0.094410.705
23_V176_C0.094410.705
297_V388_L0.094350.704
67_P79_S0.094120.702
19_L173_F0.094030.702
416_Q420_Y0.093710.699
394_Y398_L0.093640.699
91_A393_Y0.093560.698
371_L381_S0.093450.697
268_L421_N0.093410.697
5_K8_S0.093090.695
10_L318_L0.093090.695
72_D75_N0.093060.695
205_I209_A0.0930.694
48_Y138_Y0.092890.693
375_G381_S0.092580.691
34_P293_V0.092570.691
352_Y356_G0.092570.691
66_Q254_D0.09250.690
324_L412_A0.092370.689
64_L156_Q0.092320.689
92_V95_L0.092250.688
262_F265_Q0.092150.688
367_S370_L0.092140.688
203_L210_L0.092070.687
329_S341_A0.091940.686
428_S431_F0.091920.686
85_L255_L0.091920.686
42_V292_G0.091830.685
134_S325_S0.091720.685
454_I457_S0.091720.685
66_Q69_S0.091680.684
274_E277_K0.091680.684
214_A378_R0.091620.684
416_Q466_F0.091560.683
314_E317_R0.091370.682
367_S371_L0.091320.682
25_N37_L0.091110.680
394_Y452_N0.091090.680
183_V211_G0.091080.680
250_Y368_P0.091010.679
204_A209_A0.091010.679
279_V282_F0.091010.679
7_A311_P0.090990.679
234_F238_L0.09080.678
34_P292_G0.090770.677
381_S465_R0.090430.675
125_F129_P0.090320.674
455_N463_S0.090240.673
376_G379_W0.090230.673
309_F313_E0.090170.673
34_P289_E0.090090.672
433_A440_R0.090040.672
89_L169_S0.089940.671
375_G378_R0.089850.671
28_L32_L0.08980.670
301_G394_Y0.08960.669
21_T172_V0.089550.668
428_S433_A0.089520.668
148_S152_Y0.089390.667
272_L456_M0.089330.667
438_L450_L0.089310.667
141_S213_L0.089210.666
163_L226_M0.089180.666
293_V297_V0.088970.664
361_A366_Y0.088940.664
420_Y466_F0.088850.663
145_E149_E0.088820.663
133_P137_L0.08870.662
204_A208_F0.088650.662
85_L252_D0.088570.661
13_L164_R0.088510.661
95_L275_G0.088410.660
78_Q82_L0.08830.659
437_L442_G0.088140.658
413_S417_L0.087850.656
92_V221_F0.087840.656
30_R34_P0.087740.655
144_I217_I0.087720.655
60_R153_I0.087630.654
35_E289_E0.087370.652
265_Q459_R0.087360.652
258_L261_S0.087360.652
93_V467_I0.087280.651
384_A387_L0.087180.651
81_N392_C0.087160.650
365_P368_P0.08710.650
297_V302_S0.08710.650
17_S20_L0.087090.650
18_R21_T0.087060.650
39_I131_F0.086990.649
91_A217_I0.086920.649
177_I180_F0.086850.648
341_A407_F0.086790.648
273_T456_M0.086770.648
316_S403_I0.086740.647
152_Y156_Q0.086730.647
225_W228_F0.086620.646
398_L409_F0.086570.646
65_R321_S0.086550.646
447_G455_N0.086490.645
152_Y161_F0.086440.645
88_P92_V0.086340.644
39_I134_S0.086320.644
239_P242_S0.086310.644
40_A205_I0.086150.643
45_E49_S0.086140.643
262_F401_N0.08610.643
268_L272_L0.086080.642
55_S60_R0.086020.642
18_R22_F0.086020.642
281_S287_T0.085980.642
342_A357_L0.085940.641
426_V433_A0.085910.641
317_R409_F0.085780.640
320_F344_V0.085710.640
305_A313_E0.08570.640
373_L408_V0.085620.639
12_L19_L0.085570.639
71_I76_W0.085260.636
432_L462_Y0.085220.636
140_L144_I0.085130.635
43_Q47_L0.085060.635
395_I398_L0.08490.634
91_A372_R0.084880.633
130_Y256_L0.084850.633
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
3w4tA0.79781000.385
3mktA0.80331000.399
4humA0.80871000.436
3w4tA0.542899.80.702
3mktA0.530199.80.709
4humA0.535599.80.716
1pw4A0.391647.40.954
3o7qA0.393411.30.966
4j05A0.404410.30.966
4apsA0.36435.30.97

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