GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RuvA_N - RuvA N terminal domain
Pfam: PF01330 (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: CL0021
Length: 61
Sequences: 1594
Seq/Len: 26.13
HH_delta: 0.027 (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
50_L57_I1.207453.231
6_K43_E1.079552.889
52_V57_I0.885022.368
4_Y45_K0.801422.144
6_K45_K0.767652.054
17_V30_V0.762222.040
9_V44_V0.683481.829
6_K20_D0.660781.768
5_L28_V0.6591.763
16_Y27_E0.639811.712
39_P42_G0.628161.681
30_V34_T0.611271.636
4_Y10_V0.601731.610
30_V35_L0.58431.564
8_K43_E0.578841.549
16_Y29_F0.57151.529
34_T46_L0.569291.523
5_L21_V0.552981.480
3_A18_V0.548851.469
28_V48_T0.525571.406
4_Y25_G0.522541.398
18_V25_G0.514021.375
13_N16_Y0.462881.239
20_D45_K0.44011.178
28_V61_G0.435581.166
5_L19_I0.418551.120
51_I58_S0.41671.115
31_P34_T0.404661.083
30_V46_L0.399781.070
17_V46_L0.39291.051
19_I28_V0.390421.045
5_L24_V0.390171.044
51_I56_A0.386071.033
3_A27_E0.385981.033
9_V39_P0.385461.031
12_K35_L0.37340.999
32_S35_L0.367320.983
4_Y20_D0.36730.983
32_S36_S0.367170.983
10_V45_K0.35060.938
52_V56_A0.317240.849
2_I48_T0.298410.799
17_V38_L0.295120.790
5_L26_Y0.293290.785
12_K17_V0.285340.764
19_I44_V0.28280.757
10_V20_D0.280930.752
5_L48_T0.276160.739
31_P36_S0.273560.732
38_L46_L0.270980.725
7_G61_G0.270950.725
28_V46_L0.267880.717
12_K39_P0.258860.693
14_P32_S0.257260.688
51_I57_I0.256510.686
21_V24_V0.254810.682
12_K32_S0.254690.682
38_L44_V0.251540.673
19_I46_L0.24730.662
8_K45_K0.244060.653
21_V26_Y0.240120.643
13_N21_V0.23890.639
14_P30_V0.238690.639
15_D29_F0.238050.637
13_N40_E0.233520.625
15_D27_E0.23320.624
15_D32_S0.232770.623
21_V29_F0.226650.606
34_T38_L0.225950.605
3_A26_Y0.224590.601
51_I60_Y0.223320.598
12_K40_E0.22180.594
10_V18_V0.219940.589
11_E35_L0.216580.580
30_V61_G0.215850.578
8_K41_G0.214290.573
2_I5_L0.212170.568
1_M7_G0.211990.567
3_A24_V0.211940.567
24_V41_G0.205560.550
9_V19_I0.204560.547
51_I54_E0.20430.547
29_F47_Y0.204020.546
2_I7_G0.202130.541
5_L46_L0.201290.539
26_Y50_L0.198420.531
11_E47_Y0.197250.528
12_K36_S0.194890.522
9_V17_V0.19450.520
48_T57_I0.191940.514
48_T52_V0.189970.508
56_A60_Y0.183980.492
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
1cukA199.60.027
1ixrA199.60.03
2ztdA199.60.073
3b0xA0.967266.60.797
3go5A0.901665.90.798
2w9mA147.80.818
2pmuA0.54127.80.839
2hwvA0.557425.40.842
1hh2P0.967222.70.845
3r0jA0.508222.60.846

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