GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Exonuc_VII_L - Exonuclease VII large subunit
Pfam: PF02601 (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: 319
Sequences: 1697
Seq/Len: 5.32
HH_delta: 0.948 (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
100_A122_I0.721944.254
68_N106_S0.661073.895
103_I123_A0.655953.865
50_S59_S0.601113.542
296_S312_D0.583733.440
34_T135_T0.577583.403
6_R104_A0.551613.250
68_N108_I0.512723.021
16_R43_E0.509053.000
111_I141_I0.497292.930
306_I317_A0.496332.925
308_I317_A0.492342.901
300_L315_I0.478452.819
1_L101_R0.476832.810
286_V308_I0.453792.674
57_A96_D0.446382.630
56_A93_A0.407532.401
310_L315_I0.389882.297
297_V312_D0.388812.291
68_N107_P0.386092.275
214_K218_K0.385942.274
31_F82_I0.382882.256
103_I110_V0.361262.129
19_V31_F0.359262.117
61_V99_V0.351852.073
18_A76_F0.35042.065
70_M75_D0.345122.034
31_F80_I0.339211.999
166_R170_K0.338431.994
100_A126_V0.338021.992
96_D99_V0.333931.968
80_I141_I0.328171.934
120_F125_F0.324021.909
64_L79_I0.323261.905
78_V141_I0.320511.889
49_A60_I0.318091.874
132_P136_A0.316091.863
286_V317_A0.315731.860
287_R309_R0.309291.823
307_E314_S0.308741.819
64_L81_I0.308061.815
67_A79_I0.30331.787
82_I113_A0.30281.784
61_V98_E0.299251.763
49_A59_S0.294921.738
18_A67_A0.279531.647
284_A308_I0.278491.641
60_I99_V0.278461.641
32_L44_I0.269951.591
117_E130_R0.268421.582
27_A118_T0.266921.573
285_I293_V0.264781.560
82_I114_I0.263931.555
294_I300_L0.263521.553
97_E101_R0.26011.533
49_A63_A0.259321.528
27_A82_I0.259321.528
271_E274_S0.258221.522
306_I319_V0.254711.501
278_I281_R0.254591.500
35_L44_I0.250211.474
92_W95_N0.249481.470
301_K304_D0.244821.443
56_A60_I0.244141.439
287_R307_E0.238051.403
50_S55_G0.23711.397
10_L129_L0.23681.395
284_A310_L0.236321.393
65_R105_A0.235391.387
39_N143_P0.23351.376
198_Q201_D0.232741.371
88_I92_W0.230391.358
47_Y67_A0.229811.354
64_L110_V0.226531.335
300_L304_D0.225551.329
18_A79_I0.224861.325
81_I123_A0.224461.323
218_K221_R0.222291.310
25_G28_I0.220591.300
104_A126_V0.21961.294
99_V102_A0.218961.290
20_I81_I0.218671.289
14_P143_P0.214941.267
37_R139_E0.214691.265
8_K107_P0.212981.255
271_E277_K0.212011.249
129_L140_L0.209811.236
274_S278_I0.208111.226
81_I112_S0.206041.214
1_L97_E0.203661.200
296_S299_Q0.201741.189
158_R162_A0.19781.166
65_R69_E0.196741.159
289_K304_D0.196661.159
33_R37_R0.195791.154
144_D147_E0.195071.149
11_P78_V0.195011.149
60_I81_I0.192771.136
55_G58_A0.192761.136
47_Y66_K0.190231.121
67_A76_F0.190171.121
61_V64_L0.189581.117
57_A98_E0.189571.117
297_V310_L0.189341.116
275_P283_Y0.188881.113
305_E316_K0.187711.106
62_S65_R0.18761.105
79_I108_I0.187511.105
300_L306_I0.186851.101
295_T299_Q0.186621.100
42_V142_V0.186381.098
122_I126_V0.184431.087
170_K173_R0.183781.083
220_Q224_N0.180821.065
60_I64_L0.178161.050
33_R132_P0.177971.049
14_P17_I0.177311.045
20_I64_L0.176671.041
206_R210_A0.175111.032
19_V44_I0.174321.027
64_L103_I0.174131.026
16_R45_I0.172021.014
18_A47_Y0.171891.013
129_L132_P0.171811.012
303_G318_E0.170681.006
17_I42_V0.170411.004
29_Q118_T0.170411.004
23_P48_P0.170061.002
39_N42_V0.169140.997
17_I78_V0.168090.990
23_P28_I0.167610.988
40_P143_P0.166290.980
61_V65_R0.164570.970
64_L99_V0.164440.969
305_E318_E0.16390.966
16_R76_F0.163190.962
171_R175_N0.163040.961
306_I315_I0.16280.959
278_I285_I0.161190.950
79_I106_S0.160080.943
20_I49_A0.15990.942
45_I76_F0.158850.936
32_L46_L0.158850.936
58_A98_E0.158350.933
57_A93_A0.157990.931
35_L142_V0.157750.930
34_T118_T0.156960.925
92_W96_D0.156620.923
205_Q209_Q0.155750.918
24_T28_I0.153980.907
145_R149_L0.153420.904
50_S58_A0.153250.903
35_L138_A0.151640.894
47_Y76_F0.151630.893
213_Q217_R0.151580.893
81_I113_A0.151480.893
271_E276_L0.151210.891
88_I118_T0.14950.881
10_L111_I0.148120.873
66_K70_M0.14810.873
275_P282_G0.147910.872
310_L313_G0.147760.871
196_Q199_R0.1470.866
39_N148_L0.14620.861
213_Q216_Q0.145920.860
64_L106_S0.145020.855
300_L310_L0.144620.852
197_Q219_R0.143630.846
131_A137_A0.143540.846
198_Q202_E0.142890.842
151_R155_L0.142390.839
65_R102_A0.142060.837
315_I319_V0.141870.836
112_S123_A0.141830.836
308_I315_I0.14130.833
216_Q220_Q0.141280.832
49_A67_A0.140730.829
34_T132_P0.140270.827
17_I35_L0.140180.826
273_L281_R0.139880.824
47_Y70_M0.139880.824
279_L282_G0.139270.821
296_S311_A0.139080.820
61_V102_A0.139070.819
10_L78_V0.139040.819
29_Q32_L0.138750.818
309_R314_S0.137970.813
26_A118_T0.136860.806
57_A61_V0.136560.805
55_G93_A0.136020.802
45_I70_M0.135570.799
64_L68_N0.134450.792
276_L309_R0.134270.791
18_A75_D0.133350.786
37_R140_L0.132810.783
28_I46_L0.132720.782
101_R105_A0.131550.775
7_K128_D0.130910.771
132_P135_T0.13090.771
55_G96_D0.130370.768
161_R165_N0.129960.766
25_G113_A0.129490.763
1_L104_A0.128630.758
61_V96_D0.128590.758
38_R139_E0.128060.755
15_K43_E0.12790.754
269_R273_L0.127730.753
118_T121_T0.12760.752
70_M108_I0.127170.749
272_A278_I0.126850.747
51_V56_A0.126770.747
171_R219_R0.126660.746
156_R160_N0.125460.739
192_K196_Q0.124650.735
287_R293_V0.123890.730
27_A31_F0.123690.729
22_S27_A0.123130.726
28_I32_L0.12280.724
286_V310_L0.121990.719
27_A113_A0.120970.713
31_F39_N0.12030.709
277_K280_K0.120070.708
292_K299_Q0.119290.703
152_L156_R0.119090.702
280_K311_A0.118810.700
25_G135_T0.118570.699
104_A135_T0.118510.698
219_R223_Q0.118270.697
39_N142_V0.118130.696
285_I309_R0.118040.696
202_E209_Q0.1180.695
51_V89_E0.11790.695
191_R195_Q0.117730.694
163_M166_R0.117560.693
279_L283_Y0.117540.693
29_Q33_R0.117440.692
274_S280_K0.117310.691
155_L158_R0.117230.691
47_Y79_I0.117020.690
37_R136_A0.116940.689
2_F7_K0.116720.688
114_I123_A0.116670.687
89_E128_D0.116360.686
71_G107_P0.116290.685
18_A45_I0.116160.684
281_R285_I0.115610.681
70_M76_F0.114910.677
67_A142_V0.114890.677
13_F42_V0.114380.674
267_E276_L0.114160.673
167_L170_K0.114160.673
118_T132_P0.114150.673
25_G39_N0.1140.672
81_I114_I0.113730.670
27_A32_L0.113570.669
34_T37_R0.113550.669
78_V108_I0.113450.669
81_I99_V0.113430.668
18_A31_F0.112750.664
278_I283_Y0.112590.663
13_F39_N0.112210.661
20_I99_V0.112090.660
49_A66_K0.1120.660
131_A140_L0.111890.659
25_G276_L0.111340.656
87_S90_D0.111020.654
63_A67_A0.110820.653
27_A76_F0.110510.651
37_R142_V0.109990.648
312_D315_I0.109920.648
269_R272_A0.109830.647
22_S136_A0.109760.647
210_A213_Q0.109650.646
20_I67_A0.109390.645
155_L159_L0.108970.642
289_K305_E0.108840.641
136_A139_E0.108640.640
26_A29_Q0.10840.639
220_Q223_Q0.108240.638
40_P144_D0.108030.637
277_K300_L0.107920.636
294_I304_D0.107840.635
5_N104_A0.107660.634
112_S130_R0.107620.634
212_Q216_Q0.107570.634
204_K208_K0.107160.631
154_E164_R0.106760.629
25_G29_Q0.106630.628
76_F79_I0.106490.627
29_Q88_I0.106110.625
106_S110_V0.105720.623
58_A268_A0.105590.622
6_R110_V0.105540.622
202_E206_R0.105410.621
48_P121_T0.10520.620
172_Q315_I0.104870.618
96_D102_A0.104660.617
33_R135_T0.104630.617
276_L280_K0.104340.615
38_R131_A0.10410.613
23_P29_Q0.104070.613
27_A67_A0.104020.613
211_I215_L0.103990.613
172_Q175_N0.103980.613
152_L155_L0.103640.611
278_I295_T0.103610.611
297_V319_V0.103590.610
71_G76_F0.103510.610
38_R137_A0.103510.610
298_K312_D0.10340.609
49_A99_V0.10340.609
25_G34_T0.103350.609
18_A81_I0.103320.609
31_F141_I0.103080.607
67_A108_I0.103040.607
150_Q153_D0.102970.607
20_I63_A0.10280.606
181_L192_K0.102740.605
128_D137_A0.10260.605
24_T33_R0.101950.601
16_R75_D0.101750.600
71_G108_I0.101560.598
120_F127_A0.101510.598
89_E95_N0.101490.598
178_A267_E0.101430.598
271_E280_K0.10120.596
165_N168_Q0.101150.596
159_L270_L0.100580.593
195_Q198_Q0.100440.592
31_F136_A0.100330.591
307_E316_K0.100320.591
135_T139_E0.100180.590
157_Q161_R0.100050.590
27_A128_D0.10.589
300_L319_V0.099950.589
20_I61_V0.099920.589
302_P305_E0.099160.584
32_L35_L0.098960.583
291_G297_V0.09890.583
192_K197_Q0.098860.583
82_I118_T0.098590.581
267_E271_E0.098590.581
168_Q172_Q0.098530.581
13_F148_L0.098510.580
161_R168_Q0.09840.580
31_F40_P0.098390.580
34_T136_A0.097920.577
150_Q154_E0.097820.576
25_G87_S0.097470.574
147_E150_Q0.097230.573
167_L307_E0.097210.573
92_W121_T0.097060.572
68_N79_I0.097020.572
2_F122_I0.096870.571
283_Y315_I0.096230.567
125_F136_A0.096220.567
159_L207_L0.096060.566
7_K89_E0.095880.565
22_S25_G0.095740.564
31_F34_T0.09570.564
51_V94_F0.095630.564
59_S63_A0.095610.563
65_R147_E0.095490.563
57_A99_V0.095320.562
214_K220_Q0.095060.560
199_R203_L0.094920.559
28_I48_P0.094780.558
297_V311_A0.094760.558
135_T182_Q0.093850.553
27_A46_L0.093850.553
29_Q120_F0.093830.553
32_L36_K0.093760.552
213_Q298_K0.093720.552
35_L135_T0.093710.552
149_L153_D0.093670.552
59_S195_Q0.093610.552
294_I306_I0.093610.552
272_A277_K0.093480.551
90_D120_F0.09340.550
23_P32_L0.093380.550
48_P139_E0.093220.549
87_S118_T0.093190.549
41_I145_R0.093150.549
135_T192_K0.093070.548
111_I142_V0.092910.547
1_L284_A0.092830.547
172_Q176_Q0.092810.547
217_R220_Q0.09270.546
21_T128_D0.092640.546
267_E270_L0.092490.545
102_A106_S0.092440.545
97_E128_D0.092260.544
88_I96_D0.092020.542
38_R143_P0.091910.542
191_R194_E0.091840.541
274_S277_K0.091690.540
80_I139_E0.091540.539
62_S222_L0.091010.536
21_T27_A0.090760.535
100_A135_T0.090550.534
200_L204_K0.090520.533
25_G48_P0.090290.532
14_P39_N0.090280.532
171_R197_Q0.089840.529
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
2csuA0.467194.50.948
3ufxB0.48991.50.953
2nu8B0.426390.10.954
2fp4B0.426383.50.959
3vivA0.664682.20.959
3r2pA0.561174.90.962
3t8bA0.705372.90.962
2xciA0.504772.90.962
3rstA0.598769.10.963
1uuyA0.448366.70.964
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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