GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_synthase - NAD synthase
Pfam: PF02540 (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: CL0039
Length: 242
Sequences: 3528
Seq/Len: 14.58
HH_delta: 0.072 (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
170_E174_E1.027523.738
164_R170_E0.821432.988
59_E197_E0.79572.895
164_R174_E0.777192.827
19_K121_N0.736352.679
38_A125_L0.700062.547
50_V116_L0.598652.178
83_P87_A0.595392.166
33_V163_A0.588282.140
20_G122_Y0.57862.105
67_E70_E0.578372.104
103_N107_R0.571452.079
66_K76_Y0.57092.077
49_A74_I0.562332.046
48_L77_I0.549421.999
34_V151_I0.542171.972
51_I62_I0.528381.922
188_E192_G0.524261.907
161_E164_R0.508951.852
116_L120_Y0.501241.824
35_A74_I0.493941.797
62_I78_V0.492371.791
64_D171_E0.482411.755
69_A76_Y0.472361.718
20_G46_N0.471681.716
66_K70_E0.468381.704
59_E63_E0.463381.686
155_Y158_E0.456161.660
88_F104_I0.451811.644
66_K78_V0.451271.642
67_E71_K0.434291.580
22_V120_Y0.433681.578
38_A124_V0.431.564
60_E171_E0.423541.541
82_D188_E0.422241.536
13_V21_V0.415991.513
10_R14_K0.414251.507
29_I163_A0.412931.502
84_I111_T0.405341.475
21_V42_L0.404211.471
63_E67_E0.400991.459
25_L69_A0.400281.456
82_D86_D0.399551.454
16_S123_L0.393751.432
88_F103_N0.38631.405
191_L196_E0.384381.398
9_L37_L0.378091.376
19_K122_Y0.37791.375
60_E63_E0.377641.374
86_D90_K0.377211.372
7_D11_D0.366861.335
63_E78_V0.364861.327
34_V124_V0.364341.325
160_R196_E0.362911.320
51_I57_S0.362691.319
84_I88_F0.360791.313
12_Y16_S0.354571.290
24_G113_L0.35391.288
88_F111_T0.349431.271
164_R173_I0.348681.269
112_T115_A0.347921.266
107_R110_M0.344551.253
53_P78_V0.344311.253
62_I66_K0.342751.247
36_A40_K0.341531.243
11_D15_K0.335961.222
55_G82_D0.33591.222
110_M145_A0.335881.222
37_L150_P0.332851.211
87_A90_K0.332591.210
23_V124_V0.33191.207
64_D175_K0.330181.201
23_V35_A0.326071.186
57_S62_I0.325381.184
48_L75_E0.325011.182
108_I111_T0.32251.173
187_D190_E0.321671.170
36_A72_L0.316991.153
95_A129_N0.316581.152
60_E64_D0.314041.142
186_T189_D0.313141.139
84_I91_S0.312751.138
20_G48_L0.310211.129
138_F144_G0.306991.117
35_A49_A0.306261.114
36_A168_I0.306181.114
85_F108_I0.304971.110
85_F89_L0.304571.108
197_E200_A0.302991.102
88_F108_I0.302881.102
194_S197_E0.302181.099
84_I104_I0.301291.096
83_P188_E0.299511.090
12_Y15_K0.294781.072
176_P186_T0.292641.065
26_S30_D0.291461.060
192_G196_E0.290081.055
29_I173_I0.285971.040
141_Y145_A0.283321.031
55_G85_F0.282351.027
34_V38_A0.281231.023
77_I120_Y0.280651.021
192_G197_E0.274620.999
68_L172_I0.27410.997
104_I111_T0.273590.995
51_I76_Y0.273180.994
22_V50_V0.270180.983
66_K69_A0.269610.981
75_E120_Y0.269160.979
8_F11_D0.268940.978
32_A172_I0.268240.976
40_K166_L0.267950.975
92_L100_A0.265550.966
161_E165_Y0.264790.963
51_I65_A0.263140.957
104_I107_R0.259880.945
116_L119_K0.258810.942
100_A115_A0.256990.935
108_I112_T0.256160.932
179_A187_D0.255950.931
39_V72_L0.251740.916
84_I87_A0.251040.913
22_V116_L0.250330.911
83_P90_K0.250120.910
21_V38_A0.249630.908
84_I108_I0.248450.904
25_L68_L0.245660.894
129_N147_D0.245640.894
149_A152_A0.244310.889
39_V47_V0.241980.880
21_V125_L0.241380.878
11_D14_K0.240990.877
80_D83_P0.239560.872
84_I112_T0.239530.871
135_L198_L0.238240.867
50_V112_T0.238070.866
63_E66_K0.237920.866
19_K46_N0.237270.863
176_P203_R0.236140.859
9_L21_V0.235240.856
128_G146_G0.232970.848
188_E194_S0.22710.826
23_V38_A0.226950.826
20_G120_Y0.22690.825
140_K143_D0.226710.825
90_K185_Q0.225270.820
13_V42_L0.224710.818
129_N179_A0.22440.816
146_G149_A0.222180.808
159_V163_A0.221390.805
81_I108_I0.220480.802
130_K155_Y0.217550.791
55_G89_L0.216860.789
9_L150_P0.215980.786
35_A72_L0.21530.783
69_A72_L0.214860.782
107_R143_D0.214830.782
96_D119_K0.21330.776
7_D10_R0.212710.774
160_R176_P0.212060.771
36_A68_L0.211630.770
29_I159_V0.21150.769
82_D192_G0.211270.769
86_D89_L0.211070.768
154_L158_E0.210830.767
133_L138_F0.20760.755
64_D67_E0.207470.755
65_A69_A0.207120.754
140_K145_A0.207110.753
45_D75_E0.206640.752
42_L46_N0.206140.750
15_K148_I0.205010.746
115_A119_K0.204260.743
59_E200_A0.204130.743
25_L49_A0.204110.743
18_A46_N0.204040.742
163_A173_I0.203360.740
54_S85_F0.202870.738
36_A39_V0.201850.734
141_Y146_G0.201070.732
42_L47_V0.200590.730
126_G149_A0.200410.729
135_L191_L0.20020.728
54_S108_I0.199920.727
16_S148_I0.199610.726
102_G105_Q0.199520.726
59_E62_I0.198830.723
126_G145_A0.198160.721
45_D73_G0.198010.720
67_E171_E0.197670.719
179_A185_Q0.196710.716
140_K147_D0.196670.715
144_G147_D0.195750.712
128_G144_G0.195260.710
133_L149_A0.194910.709
72_L172_I0.194810.709
79_I91_S0.193920.705
177_P187_D0.19360.704
128_G138_F0.192430.700
88_F100_A0.191920.698
38_A148_I0.191460.697
29_I156_K0.191140.695
83_P91_S0.191140.695
36_A166_L0.190530.693
195_Y198_L0.190260.692
192_G195_Y0.190220.692
182_W190_E0.189850.691
129_N187_D0.189090.688
9_L125_L0.188920.687
62_I80_D0.18870.687
52_M124_V0.18850.686
103_N139_T0.188320.685
58_S180_G0.188260.685
114_Y143_D0.188170.685
8_F12_Y0.186310.678
126_G146_G0.18610.677
157_T200_A0.185920.676
111_T115_A0.185510.675
33_V37_L0.185310.674
48_L120_Y0.184610.672
110_M114_Y0.183910.669
27_G30_D0.182280.663
33_V159_V0.181720.661
200_A203_R0.18160.661
157_T203_R0.181160.659
117_A147_D0.180730.658
96_D129_N0.180490.657
68_L73_G0.180290.656
181_L195_Y0.180180.656
115_A118_N0.17990.654
32_A65_A0.179870.654
10_R41_A0.178860.651
23_V34_V0.178650.650
39_V43_G0.17850.649
48_L122_Y0.177750.647
102_G106_A0.176890.644
34_V125_L0.176150.641
176_P202_L0.175380.638
26_S31_S0.175320.638
158_E161_E0.175190.637
60_E175_K0.17450.635
58_S175_K0.173940.633
14_K46_N0.173050.630
195_Y202_L0.171440.624
114_Y140_K0.171220.623
13_V16_S0.1710.622
46_N75_E0.170920.622
110_M143_D0.170350.620
51_I78_V0.170220.619
89_L97_D0.169780.618
97_D101_R0.169460.617
160_R173_I0.16870.614
130_K153_D0.168440.613
96_D101_R0.167720.610
182_W191_L0.167120.608
61_D175_K0.166740.607
32_A71_K0.166160.605
125_L148_I0.166090.604
137_Y179_A0.165010.600
198_L202_L0.164450.598
114_Y147_D0.163980.597
104_I115_A0.163960.596
100_A119_K0.163490.595
114_Y118_N0.163120.593
57_S61_D0.162620.592
9_L148_I0.161910.589
152_A155_Y0.160430.584
39_V75_E0.160320.583
28_G31_S0.160.582
186_T190_E0.159950.582
49_A69_A0.159760.581
26_S156_K0.159540.580
105_Q180_G0.158990.578
27_G31_S0.158920.578
54_S82_D0.158430.576
21_V47_V0.158370.576
90_K93_E0.157420.573
158_E203_R0.156870.571
39_V74_I0.156710.570
106_A148_I0.156250.568
95_A128_G0.156190.568
24_G52_M0.156090.568
9_L42_L0.155980.567
53_P82_D0.155820.567
90_K188_E0.155630.566
63_E171_E0.155530.566
57_S60_E0.155460.566
49_A76_Y0.155340.565
61_D180_G0.154770.563
81_I84_I0.154390.562
84_I115_A0.154370.562
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
4f4hA0.99171000.072
3q4gA0.9381000.122
3ilvA0.99591000.147
3p52A0.97521000.147
3dpiA0.9381000.148
3n05A0.98351000.162
3fiuA0.9381000.169
1wxiA0.9381000.195
1kqpA0.9381000.206
3sdbA0.99591000.213

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