GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NfeD - NfeD-like C-terminal partner-binding
Pfam: PF01957 (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: CL0252
Length: 144
Sequences: 1810
Seq/Len: 12.57
HH_delta: 0.523 (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
107_V116_A0.755033.927
129_R141_E0.729623.795
126_D142_P0.612813.187
93_E127_R0.540162.810
92_K110_D0.530592.760
123_P126_D0.479982.497
106_R113_R0.465382.421
94_G128_V0.456942.377
93_E129_R0.449542.338
6_G26_G0.419292.181
96_V122_I0.385372.004
10_L26_G0.378111.967
12_A22_L0.374651.949
6_G10_L0.36991.924
117_R139_I0.360021.873
109_V130_V0.35571.850
94_G130_V0.345681.798
28_A32_A0.336391.750
132_G139_I0.335481.745
3_L33_G0.331661.725
56_F60_A0.331131.722
94_G109_V0.322621.678
131_V141_E0.32261.678
25_G28_A0.314591.636
118_S122_I0.295691.538
95_T125_G0.288611.501
117_R134_E0.282461.469
17_P23_G0.278481.448
95_T127_R0.272991.420
5_L9_L0.272351.417
134_E139_I0.271671.413
2_W29_A0.264951.378
96_V128_V0.26461.376
16_I22_L0.261681.361
104_S115_R0.25581.330
89_L109_V0.253931.321
114_W138_L0.252411.313
6_G33_G0.251831.310
107_V138_L0.24721.286
105_G140_V0.243911.269
94_G116_A0.240371.250
106_R115_R0.238081.238
129_R143_V0.233751.216
35_L40_P0.232631.210
93_E143_V0.232021.207
24_W28_A0.22671.179
52_Q56_F0.221441.152
122_I140_V0.21971.143
50_T54_V0.218691.137
6_G30_F0.216691.127
119_E141_E0.214771.117
31_I59_S0.212711.106
96_V116_A0.211991.103
13_E23_G0.209581.090
2_W52_Q0.205551.069
119_E131_V0.204361.063
122_I126_D0.201251.047
32_A35_L0.195371.016
96_V124_K0.194381.011
17_P21_F0.193941.009
98_E123_P0.191310.995
3_L30_F0.190280.990
59_S63_L0.189850.987
90_I132_G0.188530.981
69_P73_K0.185620.965
2_W56_F0.185290.964
9_L13_E0.184670.961
18_G21_F0.183350.954
128_V140_V0.181050.942
98_E101_L0.180680.940
100_P103_G0.180490.939
95_T108_K0.179310.933
96_V125_G0.179270.932
120_D141_E0.17910.932
33_G37_L0.175330.912
96_V126_D0.175210.911
96_V99_I0.175190.911
105_G116_A0.175150.911
82_S85_G0.174180.906
13_E18_G0.172140.895
60_A63_L0.171980.895
108_K113_R0.170840.889
117_R137_T0.170820.888
122_I128_V0.169930.884
104_S117_R0.169280.880
8_V12_A0.169150.880
127_R143_V0.169110.880
7_L27_I0.167350.870
63_L68_F0.166280.865
105_G128_V0.166140.864
68_F72_K0.165350.860
94_G105_G0.164520.856
6_G9_L0.164330.855
25_G29_A0.163920.853
2_W36_G0.163840.852
108_K111_G0.161410.840
133_V138_L0.15710.817
99_I103_G0.154680.805
78_K141_E0.153170.797
120_D142_P0.151910.790
55_F59_S0.149760.779
96_V105_G0.149220.776
24_W67_R0.14840.772
119_E139_I0.147730.768
26_G30_F0.146730.763
72_K76_K0.146640.763
87_D90_I0.144910.754
13_E19_F0.144770.753
54_V58_V0.143770.748
60_A64_A0.142320.740
10_L23_G0.1420.739
100_P118_S0.141410.736
56_F68_F0.141220.735
28_A59_S0.140860.733
19_F23_G0.139860.727
21_F64_A0.138660.721
94_G140_V0.138230.719
89_L92_K0.137970.718
96_V107_V0.137230.714
89_L110_D0.137090.713
99_I116_A0.135220.703
7_L11_I0.134540.700
2_W23_G0.133990.697
35_L38_F0.133870.696
11_I64_A0.133680.695
13_E17_P0.132010.687
53_I124_K0.131320.683
99_I105_G0.130940.681
72_K75_L0.130180.677
115_R137_T0.130.676
131_V143_V0.129960.676
108_K124_K0.129060.671
102_N115_R0.128930.671
8_V11_I0.128140.666
100_P123_P0.128080.666
98_E124_K0.126360.657
85_G136_N0.126340.657
75_L84_T0.124960.650
86_E132_G0.124730.649
68_F136_N0.124450.647
101_L104_S0.124360.647
116_A122_I0.124210.646
58_V127_R0.1240.645
9_L29_A0.123730.644
26_G33_G0.123720.644
60_A125_G0.123620.643
67_R72_K0.123110.640
86_E133_V0.122920.639
64_A68_F0.122850.639
65_F73_K0.122760.639
1_I5_L0.121790.633
6_G17_P0.121470.632
49_W53_I0.121210.630
80_N83_S0.120220.625
5_L66_L0.119810.623
2_W28_A0.119690.623
130_V138_L0.119670.622
65_F68_F0.119590.622
94_G106_R0.119560.622
92_K120_D0.119460.621
101_L122_I0.119270.620
118_S140_V0.11790.613
3_L10_L0.117470.611
15_F49_W0.116470.606
59_S62_L0.11570.602
89_L94_G0.115620.601
9_L30_F0.115450.600
123_P143_V0.115420.600
91_G133_V0.11540.600
40_P58_V0.11520.599
25_G38_F0.115080.599
102_N109_V0.114610.596
109_V116_A0.113930.593
5_L29_A0.11330.589
111_G114_W0.113280.589
65_F79_R0.1130.588
64_A137_T0.112860.587
98_E103_G0.112720.586
39_F55_F0.112640.586
10_L29_A0.112370.584
63_L75_L0.112350.584
51_L71_R0.11230.584
34_L114_W0.112290.584
65_F72_K0.111810.582
57_I88_D0.111710.581
24_W29_A0.111370.579
104_S118_S0.111270.579
84_T121_E0.111140.578
18_G24_W0.110950.577
22_L56_F0.109910.572
19_F27_I0.109870.571
29_A56_F0.109680.570
27_I71_R0.109670.570
50_T53_I0.109480.569
57_I119_E0.109480.569
24_W32_A0.109410.569
76_K79_R0.108630.565
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
3cp0A0.548699.30.523
2exdA0.486199.20.546
2k5hA0.659799.20.554
2k14A0.520899.10.582
3giaA0.631942.40.894
1iz6A0.3819290.903
2w1tA0.3472290.903
2l66A0.326425.40.906
3mhxA0.395824.90.906
3ougA0.437519.70.91
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