GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_binding_6 - Ferric reductase NAD binding domain
Pfam: PF08030 (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: CL0091
Length: 156
Sequences: 1762
Seq/Len: 11.29
HH_delta: 0.306 (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
9_G144_P0.453052.883
9_G147_M0.433862.761
13_I39_L0.392692.499
11_S14_T0.345712.200
3_N36_R0.343682.187
17_L52_F0.321392.045
6_L19_I0.311731.984
36_R69_E0.308861.966
62_L65_L0.305751.946
6_L37_I0.27961.779
69_E116_Y0.277761.768
7_V151_V0.275871.756
149_D152_R0.273871.743
2_D136_R0.261251.663
16_I39_L0.259041.649
141_V151_V0.25111.598
53_S57_N0.25041.594
15_P19_I0.249571.588
7_V139_V0.248531.582
15_P18_P0.246751.570
120_D123_E0.245071.560
71_H115_H0.241881.539
2_D133_S0.234561.493
123_E126_S0.233331.485
139_V155_V0.233121.484
22_D26_R0.230261.465
41_W51_W0.223521.423
8_A16_I0.221481.410
23_L37_I0.216951.381
75_T119_P0.212861.355
48_E52_F0.207251.319
111_N115_H0.206831.316
42_V119_P0.204431.301
15_P140_F0.201311.281
20_L39_L0.200161.274
38_K71_H0.199811.272
121_L125_L0.187841.195
13_I52_F0.187431.193
9_G42_V0.187411.193
52_F56_L0.184931.177
5_V139_V0.18411.172
2_D35_R0.181651.156
41_W52_F0.179851.145
21_R25_Q0.179351.141
133_S136_R0.178741.138
57_N61_E0.178711.137
141_V148_V0.178111.134
58_E62_L0.177751.131
150_D153_N0.174521.111
122_D126_S0.169521.079
8_A56_L0.167041.063
48_E51_W0.166881.062
128_V137_V0.166031.057
50_E53_S0.16451.047
145_P148_V0.163391.040
11_S15_P0.163041.038
7_V147_M0.162591.035
13_I17_L0.162491.034
44_R76_R0.160921.024
35_R127_E0.155620.990
146_S150_D0.155590.990
13_I41_W0.155030.987
6_L140_F0.154910.986
19_I149_D0.154850.985
17_L55_E0.154840.985
20_L55_E0.152980.974
150_D154_A0.149260.950
20_L56_L0.148810.947
16_I125_L0.148670.946
3_N38_K0.1480.942
21_R62_L0.147910.941
8_A39_L0.147380.938
14_T41_W0.146470.932
45_D48_E0.144250.918
125_L128_V0.143330.912
38_K69_E0.142890.909
4_V26_R0.141290.899
43_V51_W0.139260.886
144_P147_M0.138980.884
3_N137_V0.138550.882
43_V56_L0.138020.878
49_L72_I0.137580.876
42_V147_M0.136820.871
42_V112_I0.136460.868
145_P149_D0.135980.865
2_D26_R0.135770.864
6_L16_I0.135760.864
7_V121_L0.134690.857
20_L37_I0.133860.852
139_V151_V0.132930.846
83_N86_S0.132860.846
125_L151_V0.131080.834
79_S82_S0.131040.834
56_L70_V0.130810.833
78_S82_S0.130650.831
6_L11_S0.130340.830
118_R142_C0.129840.826
3_N135_G0.12910.822
73_Y124_I0.128390.817
5_V118_R0.12790.814
42_V73_Y0.127060.809
6_L18_P0.125740.800
111_N114_V0.125570.799
125_L155_V0.125250.797
118_R139_V0.125170.797
8_A28_N0.123910.789
15_P128_V0.123630.787
47_D53_S0.123020.783
16_I55_E0.122020.777
89_S146_S0.12190.776
7_V113_S0.121750.775
40_V78_S0.121680.774
5_V40_V0.121630.774
140_F143_G0.120430.766
39_L51_W0.120420.766
35_R40_V0.120360.766
58_E63_D0.120130.765
74_V77_E0.120050.764
5_V135_G0.119620.761
53_S80_A0.119020.757
16_I19_I0.118830.756
47_D65_L0.118350.753
52_F55_E0.118320.753
117_G142_C0.118270.753
24_L34_T0.117740.749
8_A113_S0.117440.747
63_D145_P0.11650.741
14_T140_F0.116450.741
114_V118_R0.11640.741
7_V40_V0.116340.740
54_P58_E0.115750.737
123_E127_E0.115580.736
48_E148_V0.115490.735
41_W49_L0.115260.734
16_I140_F0.115210.733
122_D154_A0.114960.732
40_V73_Y0.114680.730
43_V52_F0.11450.729
58_E61_E0.114440.728
25_Q58_E0.114360.728
51_W119_P0.114170.727
133_S137_V0.113720.724
49_L74_V0.113550.723
28_N36_R0.113210.720
6_L141_V0.113070.720
2_D34_T0.112660.717
41_W70_V0.111940.712
81_P115_H0.111310.708
14_T42_V0.11120.708
4_V138_A0.110730.705
14_T52_F0.110460.703
17_L43_V0.110280.702
64_R72_I0.109420.696
3_N136_R0.109410.696
143_G147_M0.109320.696
63_D67_N0.109140.695
4_V23_L0.108920.693
8_A40_V0.108350.690
57_N139_V0.108250.689
4_V150_D0.10760.685
28_N34_T0.106350.677
76_R122_D0.105940.674
43_V49_L0.105930.674
73_Y115_H0.105530.672
80_A83_N0.105440.671
86_S89_S0.105420.671
116_Y136_R0.10530.670
75_T111_N0.104690.666
72_I121_L0.104530.665
142_C148_V0.10390.661
17_L60_L0.103650.660
11_S140_F0.103560.659
13_I19_I0.103250.657
11_S16_I0.103180.657
149_D153_N0.102920.655
121_L139_V0.102730.654
42_V75_T0.102420.652
25_Q120_D0.10240.652
83_N89_S0.102020.649
10_G15_P0.102010.649
58_E80_A0.101950.649
11_S17_L0.101520.646
10_G143_G0.101230.644
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
3a1fA0.929599.90.306
3vo2A0.788599.70.433
3jqqA0.788599.70.445
3lo8A0.775699.70.447
4g1vA0.673199.60.456
2b5oA0.788599.60.462
1gvhA0.756499.60.471
1cqxA0.7599.60.476
2r6hA0.7599.60.476
4eh1A0.692399.60.477

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