GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RCC1 - Regulator of chromosome condensation (RCC1) repeat
Pfam: PF00415 (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: CL0186
Length: 51
Sequences: 5933
Seq/Len: 116.33
HH_delta: -0.008 (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
7_W27_P2.001433.580
3_R29_K1.707923.055
24_V28_T1.589972.844
38_I50_A1.354552.423
5_Y29_K1.318212.358
20_D24_V1.121262.005
10_N14_Q1.068931.912
44_G47_H0.980571.754
6_S30_V0.97631.746
6_S43_C0.959741.717
6_S49_L0.935531.673
12_Y46_D0.860791.540
6_S15_L0.839741.502
4_V38_I0.79841.428
40_Q51_L0.772731.382
43_C48_T0.752251.345
9_S14_Q0.728521.303
18_G24_V0.710811.271
9_S46_D0.681711.219
9_S12_Y0.665561.190
42_A49_L0.60241.077
14_Q48_T0.601841.076
11_D45_S0.600821.075
4_V41_V0.590751.057
4_V50_A0.581351.040
6_S48_T0.577061.032
33_L38_I0.562691.006
11_D14_Q0.553620.990
10_N15_L0.547730.980
12_Y45_S0.544370.974
27_P30_V0.535670.958
6_S18_G0.534350.956
18_G28_T0.517810.926
10_N18_G0.516670.924
19_G23_N0.462190.827
41_V50_A0.452760.810
40_Q43_C0.434240.777
18_G23_N0.420250.752
19_G22_K0.419180.750
39_V51_L0.419140.750
9_S23_N0.415110.742
31_P34_S0.393340.703
33_L50_A0.392620.702
15_L24_V0.366950.656
8_G16_G0.360780.645
18_G21_N0.357660.640
33_L36_V0.34440.616
22_K31_P0.338770.606
20_D23_N0.336850.602
31_P38_I0.330370.591
29_K34_S0.328160.587
2_G37_R0.324280.580
32_F35_G0.321930.576
32_F38_I0.310430.555
14_Q46_D0.300670.538
42_A47_H0.288910.517
29_K32_F0.287570.514
34_S39_V0.28610.512
16_G48_T0.283230.507
23_N34_S0.282080.505
32_F36_V0.28160.504
6_S16_G0.28020.501
28_T31_P0.275840.493
13_G16_G0.274240.490
10_N20_D0.27090.485
42_A51_L0.270450.484
1_D29_K0.268440.480
1_D37_R0.266280.476
16_G41_V0.26130.467
10_N19_G0.26090.467
34_S37_R0.259470.464
21_N36_V0.256140.458
25_S46_D0.253760.454
5_Y14_Q0.252780.452
11_D36_V0.251860.450
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
3kciA0.980499-0.008
4jhnA198.90.031
4jhnA0.980498.90.031
3mvdK0.980498.90.035
4l1mA0.980498.80.039
4d9sA0.980498.80.042
4d9sA0.980498.80.046
4l1mA0.980498.80.047
3kciA0.980498.80.047
3of7A198.80.047

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