GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SurA_N_2 - SurA N-terminal domain
Pfam: PF13623 (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: CL0262
Length: 145
Sequences: 913
Seq/Len: 6.3
HH_delta: 0.589 (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
45_N97_Q0.38793.039
98_E101_K0.343352.690
42_G86_W0.328262.572
1_L4_I0.293332.298
1_L5_R0.256952.013
132_Q137_D0.248161.944
47_E93_I0.247691.940
55_Q59_E0.239851.879
53_E93_I0.239611.877
12_I15_I0.236551.853
43_E48_K0.23521.843
18_A21_A0.232871.824
51_Y55_Q0.224751.761
83_N87_N0.221851.738
140_K143_Q0.21511.685
86_W90_V0.213571.673
54_F58_V0.210321.648
45_N94_L0.209171.639
61_A85_V0.208711.635
138_R142_K0.204441.602
139_A142_K0.204281.600
104_I137_D0.203961.598
61_A64_N0.201661.580
98_E102_L0.18671.463
132_Q140_K0.185991.457
44_V97_Q0.180651.415
12_I19_L0.179361.405
54_F85_V0.178991.402
57_R89_M0.177231.388
49_I89_M0.172081.348
24_V27_F0.171311.342
25_G28_R0.164641.290
53_E56_Q0.160991.261
19_L22_F0.156211.224
42_G49_I0.154981.214
16_G19_L0.154551.211
63_E66_K0.153941.206
50_S53_E0.153741.204
74_T77_E0.151411.186
12_I18_A0.150161.176
93_I97_Q0.14831.162
13_I16_G0.146631.149
11_L14_V0.146451.147
57_R60_Q0.144161.129
57_R92_N0.143531.124
107_S110_E0.14221.114
139_A143_Q0.141471.108
23_I28_R0.139791.095
41_V94_L0.133591.047
59_E63_E0.13341.045
58_V85_V0.132661.039
15_I19_L0.132111.035
42_G51_Y0.130171.020
2_Q6_Q0.129911.018
41_V50_S0.128841.009
40_V43_E0.128781.009
61_A88_Q0.128671.008
58_V62_T0.128221.005
83_N92_N0.128011.003
9_G16_G0.126330.990
23_I27_F0.125450.983
11_L21_A0.12490.978
21_A25_G0.123610.968
80_Q84_Q0.122640.961
98_E143_Q0.122360.959
26_D30_G0.121480.952
56_Q59_E0.121470.952
64_N68_Q0.120390.943
86_W99_F0.120280.942
101_K105_T0.119960.940
62_T66_K0.119120.933
132_Q135_Q0.118970.932
110_E113_D0.118810.931
97_Q101_K0.117870.923
43_E106_V0.117260.919
40_V48_K0.117030.917
52_Q55_Q0.116860.916
88_Q92_N0.116810.915
1_L16_G0.115990.909
8_G15_I0.115770.907
112_Q124_Q0.115490.905
69_N73_P0.115420.904
3_K6_Q0.114530.897
90_V108_D0.114350.896
114_M125_Q0.113320.888
7_R14_V0.113250.887
137_D140_K0.112550.882
17_L61_A0.112380.880
133_T139_A0.112270.880
11_L20_F0.112040.878
38_Q109_D0.111930.877
54_F86_W0.111560.874
11_L23_I0.111280.872
61_A65_Y0.110920.869
15_I18_A0.11060.866
45_N93_I0.110340.864
109_D113_D0.109970.862
26_D86_W0.109320.856
87_N91_Q0.108790.852
106_V111_L0.106990.838
81_I101_K0.106260.832
41_V54_F0.10590.830
42_G90_V0.105660.828
9_G27_F0.105430.826
19_L24_V0.104920.822
12_I21_A0.10490.822
9_G13_I0.104520.819
43_E81_I0.10440.818
115_L136_F0.1040.815
36_S91_Q0.103380.810
84_Q88_Q0.102650.804
136_F141_L0.102630.804
3_K8_G0.102280.801
76_Q80_Q0.102030.799
130_N133_T0.102020.799
87_N124_Q0.101990.799
87_N106_V0.10160.796
13_I103_G0.101280.793
87_N108_D0.101230.793
99_F130_N0.10060.788
50_S79_N0.10010.784
15_I46_G0.099970.783
10_L63_E0.099880.782
17_L99_F0.099880.782
8_G11_L0.099780.782
47_E100_E0.099610.780
114_M143_Q0.099420.779
6_Q11_L0.099280.778
85_V136_F0.098950.775
1_L11_L0.098260.770
9_G85_V0.097960.767
29_S71_R0.097890.767
75_E124_Q0.097650.765
107_S138_R0.097430.763
5_R8_G0.097350.763
36_S139_A0.096920.759
58_V82_R0.096760.758
85_V89_M0.096760.758
8_G12_I0.096610.757
36_S66_K0.096560.756
19_L25_G0.096460.756
68_Q96_E0.095940.752
64_N67_Q0.095850.751
11_L18_A0.09580.751
91_Q104_I0.09580.751
55_Q63_E0.095530.748
37_S100_E0.095440.748
47_E98_E0.095310.747
94_L136_F0.094820.743
113_D128_F0.094690.742
60_Q64_N0.094470.740
24_V28_R0.094180.738
7_R58_V0.094120.737
50_S100_E0.09410.737
41_V85_V0.093890.736
42_G54_F0.093890.736
17_L113_D0.093330.731
9_G129_F0.093180.730
114_M141_L0.092910.728
48_K52_Q0.092870.728
61_A69_N0.092820.727
115_L135_Q0.092660.726
26_D42_G0.092560.725
113_D135_Q0.092540.725
10_L76_Q0.092090.721
63_E95_L0.091770.719
24_V65_Y0.09120.714
12_I130_N0.091070.713
39_N89_M0.090850.712
84_Q137_D0.090680.710
44_V93_I0.090370.708
40_V94_L0.090190.707
52_Q102_L0.090080.706
94_L129_F0.090080.706
124_Q135_Q0.090030.705
101_K115_L0.089920.704
60_Q67_Q0.089720.703
4_I111_L0.089360.700
134_G142_K0.089290.700
60_Q97_Q0.089260.699
39_N52_Q0.089090.698
28_R112_Q0.088820.696
70_G73_P0.088820.696
25_G41_V0.08870.695
66_K71_R0.088690.695
36_S63_E0.088590.694
4_I7_R0.087660.687
90_V106_V0.087590.686
23_I26_D0.087540.686
52_Q83_N0.087530.686
68_Q142_K0.087290.684
2_Q8_G0.087140.683
47_E97_Q0.086910.681
16_G20_F0.086840.680
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
1m5yA0.675999.30.589
3nrkA0.724199.20.614
3rgcA0.544899.10.637
3rfwA0.675997.90.761
2nsaA0.841487.20.873
3i5gC0.441445.60.907
3aqpA0.827642.30.908
1t11A0.848341.40.909
3ayfA0.917234.70.913
3tz1A0.475933.30.913
If you are interested in a protein containing this domain,
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