GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SMC_hinge - SMC proteins Flexible Hinge Domain
Pfam: PF06470 (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. )
Length: 120
Sequences: 2288
Seq/Len: 19.07
HH_delta: 0.03 (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
112_D115_E0.956644.001
97_R101_E0.691872.894
13_E90_E0.674162.820
12_I100_L0.653922.735
38_E62_D0.635732.659
11_L34_V0.632942.647
46_E50_E0.622322.603
111_D115_E0.614662.571
94_E97_R0.496282.076
36_E40_T0.484472.026
83_G87_D0.458281.917
37_D40_T0.456321.909
22_V85_L0.436121.824
91_F97_R0.425341.779
84_P87_D0.423091.770
5_L36_E0.416351.741
16_P19_E0.411831.723
5_L96_Y0.403681.688
44_I58_F0.398821.668
26_L104_L0.39831.666
25_A107_V0.396031.656
88_L109_V0.388021.623
5_L95_E0.386651.617
91_F100_L0.381851.597
6_G11_L0.364141.523
110_V119_L0.353491.479
115_E118_K0.347471.453
85_L109_V0.347261.452
6_G10_D0.34381.438
4_V33_I0.340781.425
17_K111_D0.336411.407
36_E95_E0.334491.399
86_I101_E0.32581.363
43_K46_E0.319831.338
93_D96_Y0.312911.309
61_L99_A0.310451.299
85_L88_L0.301861.263
8_L103_L0.299881.254
110_V116_A0.297011.242
15_D90_E0.291631.220
7_R10_D0.291281.218
45_I58_F0.283611.186
89_I104_L0.276191.155
39_E43_K0.270591.132
47_F51_N0.269941.129
26_L103_L0.26531.110
48_L56_A0.263531.102
32_A57_T0.257661.078
29_R32_A0.257231.076
59_I64_I0.251181.051
37_D62_D0.250381.047
34_V99_A0.249081.042
42_K46_E0.24881.041
12_I26_L0.244451.022
44_I47_F0.237430.993
68_S101_E0.231720.969
35_V41_A0.231330.968
66_S98_P0.230840.966
28_G55_R0.229860.961
42_K117_R0.229790.961
86_I91_F0.227890.953
48_L53_L0.22670.948
80_G83_G0.226440.947
23_E30_L0.225980.945
86_I100_L0.221770.928
46_E114_E0.217130.908
23_E31_Q0.215180.900
3_G36_E0.215110.900
81_G110_V0.214770.898
40_T44_I0.214540.897
57_T60_P0.212180.887
26_L30_L0.210390.880
9_A30_L0.203440.851
21_A24_A0.200940.840
64_I98_P0.200540.839
85_L104_L0.198380.830
83_G88_L0.196770.823
32_A55_R0.194950.815
99_A103_L0.194320.813
38_E63_K0.192350.805
36_E62_D0.186040.778
41_A45_I0.185980.778
20_K24_A0.185490.776
5_L40_T0.1820.761
24_A31_Q0.181330.758
18_Y109_V0.179480.751
14_V19_E0.179030.749
103_L107_V0.177850.744
43_K50_E0.176910.740
96_Y99_A0.175420.734
15_D108_V0.174140.728
6_G37_D0.173790.727
48_L52_K0.173770.727
15_D18_Y0.173630.726
110_V115_E0.172630.722
14_V113_L0.172450.721
81_G115_E0.169550.709
21_A25_A0.167990.703
14_V22_V0.165390.692
81_G111_D0.164870.690
80_G115_E0.162880.681
67_R70_A0.160840.673
59_I99_A0.160390.671
39_E42_K0.159310.666
18_Y111_D0.159030.665
29_R102_F0.157250.658
54_G113_L0.156990.657
48_L54_G0.156490.655
64_I117_R0.156260.654
14_V25_A0.15580.652
9_A31_Q0.153720.643
79_P115_E0.153460.642
65_R81_G0.153390.642
17_K71_S0.153130.640
69_S72_S0.152780.639
22_V104_L0.151220.633
54_G58_F0.150440.629
65_R72_S0.150330.629
4_V39_E0.14960.626
8_L59_I0.149270.624
13_E91_F0.148370.621
96_Y100_L0.14730.616
38_E42_K0.147030.615
4_V44_I0.14680.614
98_P101_E0.146180.611
7_R23_E0.146110.611
114_E118_K0.145940.610
114_E117_R0.145330.608
78_P81_G0.144960.606
8_L29_R0.144520.604
38_E60_P0.144390.604
45_I48_L0.144240.603
7_R47_F0.144090.603
70_A79_P0.143430.600
40_T43_K0.142530.596
68_S71_S0.142360.595
28_G50_E0.141720.593
15_D19_E0.141160.590
66_S94_E0.140980.590
67_R72_S0.140890.589
60_P99_A0.140680.588
79_P118_K0.14050.588
49_K117_R0.140030.586
79_P112_D0.13960.584
109_V116_A0.139510.584
5_L68_S0.13930.583
49_K55_R0.138720.580
32_A56_A0.138270.578
68_S118_K0.137790.576
12_I96_Y0.136950.573
39_E46_E0.136650.572
42_K114_E0.135960.569
84_P108_V0.135410.566
8_L80_G0.135040.565
34_V61_L0.134280.562
39_E72_S0.134120.561
89_I100_L0.134080.561
11_L96_Y0.134020.561
16_P70_A0.133680.559
11_L91_F0.133040.556
86_I118_K0.133030.556
37_D46_E0.133010.556
19_E23_E0.132850.556
28_G42_K0.132850.556
72_S94_E0.132730.555
28_G93_D0.132680.555
35_V44_I0.132050.552
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
3l51B0.97599.80.03
3nwcA0.92599.70.077
3l51A0.97599.70.097
2wd5A0.97599.70.147
2wd5B0.9599.70.155
1gxjA0.983399.60.17
1gxlA0.983399.60.173
2zfzA0.42515.70.878
3lapA0.42515.10.88
3ibpA0.741714.20.881

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