GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_binding_4 - Male sterility protein
Pfam: PF07993 (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: CL0063
Length: 249
Sequences: 23490
Seq/Len: 94.34
HH_delta: 0.132 (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
15_E247_R2.231323.472
4_A27_C2.148463.343
109_A113_D1.821022.833
129_R189_P1.650442.568
15_E19_Q1.550872.413
28_L67_G1.550142.412
1_L13_L1.542532.400
82_Q124_Q1.444862.248
93_H132_Y1.431492.227
12_L92_I1.323612.060
26_Y63_E1.320772.055
12_L246_A1.314362.045
26_Y65_V1.298982.021
12_L94_C1.278281.989
70_S109_A1.264781.968
2_T93_H1.242321.933
24_K63_E1.24091.931
67_G80_D1.234291.921
26_Y88_V1.224311.905
115_T175_A1.191521.854
15_E18_R1.187581.848
111_N171_S1.176851.831
179_L190_V1.176671.831
8_L198_I1.170861.822
116_R120_R1.11611.737
173_W177_R1.096671.706
4_A13_L1.091621.699
72_P120_R1.067811.662
129_R191_T1.060791.651
116_R178_L1.052091.637
219_S223_L1.051411.636
15_E246_A1.038961.617
195_P245_V1.038641.616
13_L27_C1.033071.607
131_H193_Y1.030551.604
72_P117_N1.025611.596
71_Q80_D1.025331.595
89_D128_K1.007311.567
183_A190_V0.987281.536
113_D116_R0.984481.532
240_V245_V0.982381.529
155_E158_L0.954751.486
91_I122_A0.95241.482
168_Y172_K0.94351.468
119_L182_A0.931611.450
120_R123_A0.924791.439
14_E18_R0.914531.423
242_V246_A0.907541.412
82_Q121_L0.907191.412
94_C133_I0.904691.408
15_E243_D0.902581.404
177_R180_R0.900751.402
69_L114_G0.898011.397
133_I195_P0.896241.395
31_A64_V0.891421.387
110_V114_G0.882171.373
80_D83_E0.8821.372
122_A130_F0.866641.348
118_L130_F0.864071.344
132_Y179_L0.855731.332
176_E194_R0.846651.317
27_C62_I0.841151.309
80_D84_L0.829351.290
93_H115_T0.824441.283
241_P244_Y0.822591.280
69_L95_A0.819751.276
134_S138_V0.818111.273
157_D160_P0.816511.270
132_Y175_A0.814871.268
170_Q174_V0.814731.268
108_R174_V0.810781.262
31_A34_S0.809661.260
178_L181_E0.806131.254
199_V241_P0.803271.250
180_R192_I0.800021.245
130_F179_L0.793691.235
181_E185_R0.77131.200
112_V174_V0.770571.199
82_Q125_G0.765181.191
134_S176_E0.762781.187
103_P106_E0.759051.181
123_A186_H0.758821.181
120_R124_Q0.748781.165
113_D117_N0.745211.160
132_Y192_I0.743181.156
12_L16_L0.734221.142
2_T118_L0.733841.142
11_H242_V0.733291.141
162_Q173_W0.72681.131
11_H14_E0.725331.129
7_F200_G0.724761.128
83_E86_E0.721691.123
30_R68_D0.712711.109
117_N120_R0.701271.091
181_E184_Q0.692081.077
14_E203_R0.691641.076
119_L130_F0.690981.075
11_H243_D0.688071.071
117_N121_L0.683041.063
144_G157_D0.678581.056
108_R112_V0.666351.037
2_T95_A0.665721.036
121_L125_G0.664731.034
85_A88_V0.659431.026
17_L61_R0.653311.017
5_T29_V0.653251.016
97_S110_V0.653171.016
7_F242_V0.65031.012
123_A188_L0.649251.010
198_I245_V0.647191.007
198_I240_V0.642260.999
26_Y87_E0.637770.992
10_S14_E0.634610.987
8_L245_V0.630970.982
216_L220_C0.630630.981
91_I118_L0.630150.981
17_L25_I0.629350.979
218_R222_A0.621930.968
13_L25_I0.621870.968
170_Q177_R0.617130.960
32_S66_E0.613720.955
156_D160_P0.612520.953
72_P124_Q0.609340.948
220_C225_A0.607590.945
180_R183_A0.60710.945
119_L179_L0.606490.944
180_R184_Q0.59890.932
108_R113_D0.596570.928
120_R182_A0.595990.927
121_L124_Q0.591140.920
17_L62_I0.587920.915
131_H191_T0.58610.912
156_D159_D0.583330.908
177_R181_E0.577960.899
182_A186_H0.57720.898
86_E125_G0.575140.895
38_L66_E0.575030.895
85_A91_I0.571780.890
122_A127_R0.571160.889
97_S107_L0.564390.878
90_V131_H0.563530.877
11_H246_A0.563450.877
180_R190_V0.559760.871
175_A179_L0.55820.869
215_Y218_R0.556950.867
215_Y219_S0.556020.865
24_K61_R0.55140.858
1_L16_L0.548140.853
115_T179_L0.546320.850
31_A66_E0.545850.849
136_A196_G0.545440.849
138_V176_E0.544570.847
119_L178_L0.542540.844
193_Y248_A0.541430.842
21_P90_V0.541350.842
94_C195_P0.541190.842
72_P82_Q0.539340.839
141_S165_P0.538670.838
11_H15_E0.537560.836
28_L80_D0.535010.832
195_P198_I0.533860.831
20_P25_I0.531490.827
155_E159_D0.529810.824
81_Y85_A0.528370.822
16_L20_P0.524640.816
128_K189_P0.522820.814
115_T119_L0.522020.812
105_S109_A0.516780.804
107_L171_S0.514790.801
21_P25_I0.512320.797
13_L17_L0.510590.794
81_Y121_L0.505260.786
196_G238_D0.503920.784
123_A182_A0.501470.780
82_Q86_E0.500690.779
90_V129_R0.496860.773
91_I130_F0.493020.767
220_C226_F0.491650.765
174_V177_R0.490730.764
83_E87_E0.489540.762
108_R170_Q0.484790.754
168_Y171_S0.483740.753
68_D71_Q0.483330.752
174_V178_L0.482070.750
102_A106_E0.480010.747
28_L81_Y0.477760.743
197_I237_L0.476660.742
96_A111_N0.476120.741
216_L219_S0.474710.739
170_Q181_E0.471730.734
232_D235_A0.471310.733
21_P24_K0.469330.730
29_V64_V0.468210.729
219_S222_A0.467990.728
104_Y167_G0.463980.722
70_S110_V0.463160.721
5_T30_R0.461770.719
208_N211_D0.460130.716
164_F173_W0.459860.716
13_L20_P0.455970.709
123_A187_G0.455770.709
114_G117_N0.454230.707
21_P89_D0.453730.706
213_F217_L0.4520.703
211_D215_Y0.449920.700
20_P61_R0.448160.697
213_F216_L0.446040.694
28_L84_L0.445940.694
119_L123_A0.444590.692
85_A125_G0.44230.688
178_L182_A0.438250.682
67_G71_Q0.438080.682
26_Y84_L0.435970.678
183_A189_P0.434110.675
16_L21_P0.434090.675
197_I239_L0.434040.675
14_E243_D0.432160.672
106_E109_A0.430890.670
116_R182_A0.43060.670
84_L88_V0.43020.669
65_V84_L0.430060.669
170_Q173_W0.428270.666
108_R171_S0.425680.662
144_G160_P0.425210.662
134_S192_I0.424670.661
136_A139_A0.424360.660
34_S40_R0.423930.660
158_L161_P0.423420.659
165_P184_Q0.42220.657
93_H118_L0.421720.656
112_V171_S0.420630.654
16_L92_I0.419170.652
243_D247_R0.418180.651
24_K89_D0.416780.649
7_F11_H0.416130.647
118_L122_A0.414020.644
19_Q247_R0.413720.644
214_P217_L0.413340.643
28_L65_V0.412030.641
220_C223_L0.411670.641
128_K187_G0.409590.637
240_V244_Y0.409440.637
14_E17_L0.407670.634
93_H130_F0.406010.632
229_L233_P0.40520.630
179_L192_I0.404410.629
219_S224_G0.404360.629
65_V80_D0.401990.625
27_C64_V0.400550.623
99_N102_A0.397880.619
144_G159_D0.397710.619
214_P218_R0.397460.618
59_L62_I0.396180.616
112_V116_R0.394850.614
167_G171_S0.394770.614
1_L4_A0.394590.614
135_T168_Y0.394540.614
72_P121_L0.393770.613
204_T209_S0.392930.611
5_T31_A0.392550.611
2_T28_L0.392150.610
183_A188_L0.391270.609
13_L62_I0.388330.604
166_N169_E0.386960.602
85_A122_A0.38650.601
3_G6_G0.386050.601
137_Y140_G0.383140.596
176_E192_I0.38310.596
135_T172_K0.382530.595
193_Y245_V0.380140.591
6_G10_S0.378540.589
123_A185_R0.37810.588
30_R33_S0.377290.587
214_P220_C0.376810.586
112_V175_A0.376610.586
137_Y169_E0.373540.581
81_Y84_L0.372980.580
159_D162_Q0.37090.577
182_A188_L0.366030.570
30_R70_S0.365940.569
71_Q81_Y0.364220.567
162_Q194_R0.36380.566
102_A105_S0.362560.564
162_Q177_R0.361890.563
14_E202_S0.359390.559
112_V178_L0.357660.557
218_R221_I0.356410.555
217_L220_C0.356050.554
196_G240_V0.355910.554
138_V194_R0.355350.553
158_L162_Q0.35160.547
245_V248_A0.350410.545
69_L110_V0.350270.545
220_C224_G0.348720.543
210_D215_Y0.347670.541
97_S102_A0.347580.541
164_F169_E0.346920.540
30_R34_S0.346140.539
227_P230_P0.34470.536
119_L122_A0.343680.535
90_V128_K0.34360.535
32_S39_E0.343590.535
200_G242_V0.343580.535
155_E160_P0.342960.534
115_T178_L0.342160.532
9_G13_L0.341150.531
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
4dqvA0.9881000.132
3rufA0.89161000.161
3slgA0.875599.90.18
4egbA0.871599.90.186
3m2pA0.815399.90.191
1i24A0.943899.90.194
1sb8A0.891699.90.199
4f6lB0.931799.90.201
3sxpA0.887699.90.204
4id9A0.839499.90.205

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