GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Laminin_G_1 - Laminin G domain
Pfam: PF00054 (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: CL0004
Length: 131
Sequences: 3104
Seq/Len: 23.69
HH_delta: 0.025 (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
56_H72_D1.229046.589
52_D56_H0.567523.042
32_E43_S0.431372.313
30_R45_R0.426972.289
3_T52_D0.399882.144
3_T51_N0.389622.089
4_S53_G0.381312.044
31_L58_V0.371771.993
33_F60_V0.368991.978
36_N40_G0.35381.897
24_L60_V0.340331.824
55_W121_R0.335821.800
26_L29_G0.331181.775
27_R32_E0.327911.758
60_V67_G0.322081.727
96_Y101_P0.321281.722
52_D72_D0.299991.608
2_R53_G0.298761.602
59_S70_S0.297021.592
24_L33_F0.295361.583
13_L22_I0.29251.568
51_N56_H0.287221.540
96_Y99_G0.28691.538
11_L22_I0.285351.530
2_R55_W0.285141.529
99_G119_C0.277871.490
33_F67_G0.27691.484
26_L50_I0.27571.478
6_P51_N0.263111.410
12_Y23_A0.260221.395
7_N27_R0.253391.358
25_E32_E0.252721.355
37_L62_R0.250931.345
68_S78_T0.247251.325
22_I33_F0.238531.279
37_L89_L0.232881.248
119_C126_N0.227651.220
66_N78_T0.225721.210
35_Y67_G0.223731.199
61_S68_S0.220181.180
54_K58_V0.219181.175
20_D90_D0.217461.166
5_E8_G0.214631.151
20_D89_L0.208651.119
32_E45_R0.207731.114
62_R65_R0.205961.104
56_H71_V0.202391.085
60_V69_L0.200491.075
75_E78_T0.200061.072
79_G86_T0.197191.057
97_V123_L0.196951.056
105_S108_R0.194061.040
116_F120_I0.193211.036
115_G119_C0.192631.033
11_L95_L0.188111.008
66_N80_E0.188091.008
7_N28_D0.187611.006
11_L24_L0.187311.004
25_E112_I0.181780.974
44_L69_L0.178340.956
34_R43_S0.176010.944
21_F41_P0.17540.940
65_R92_D0.174390.935
63_N66_N0.172740.926
5_E117_K0.171180.918
9_L12_Y0.170760.915
30_R46_S0.166540.893
6_P26_L0.165190.886
21_F34_R0.164090.880
33_F69_L0.163130.875
12_Y21_F0.161840.868
15_S91_V0.161480.866
90_D123_L0.160510.860
101_P123_L0.159890.857
36_N41_P0.159690.856
109_P112_I0.159460.855
61_S70_S0.159420.855
14_G22_I0.158710.851
35_Y62_R0.157960.847
25_E34_R0.157690.845
70_S76_V0.157040.842
81_S85_A0.155430.833
63_N79_G0.155190.832
46_S71_V0.154050.826
13_L94_P0.153550.823
2_R74_E0.153060.821
48_Q110_L0.152720.819
70_S75_E0.151670.813
106_R110_L0.151140.810
5_E57_T0.15110.810
3_T8_G0.15050.807
50_I71_V0.150440.806
25_E52_D0.149790.803
77_V82_P0.149090.799
43_S79_G0.148560.796
20_D62_R0.147690.792
110_L113_S0.14760.791
107_P110_L0.147490.791
90_D93_G0.147360.790
68_S82_P0.147080.788
82_P101_P0.147070.788
93_G100_L0.146930.788
3_T26_L0.146330.784
83_S87_Q0.146190.784
30_R49_K0.145430.780
47_P97_V0.144860.777
19_K127_G0.144280.773
61_S71_V0.143890.771
68_S75_E0.143720.770
122_N128_K0.14360.770
44_L79_G0.143560.770
12_Y15_S0.143550.770
25_E108_R0.143360.769
17_D90_D0.142210.762
27_R43_S0.141840.760
31_L127_G0.141220.757
12_Y25_E0.14010.751
13_L55_W0.13930.747
109_P115_G0.138750.744
13_L25_E0.138080.740
9_L17_D0.137680.738
12_Y115_G0.137270.736
3_T29_G0.136660.733
57_T97_V0.136530.732
42_A45_R0.136110.730
30_R50_I0.135990.729
48_Q78_T0.135980.729
44_L108_R0.13440.721
13_L91_V0.133880.718
70_S74_E0.133670.717
7_N114_P0.132390.710
8_G76_V0.131950.707
38_G89_L0.131770.706
33_F44_L0.131040.702
22_I112_I0.130870.702
21_F36_N0.130560.700
80_E86_T0.130350.699
69_L87_Q0.130140.698
42_A123_L0.129790.696
4_S28_D0.129710.695
12_Y100_L0.129570.695
29_G51_N0.129330.693
52_D119_C0.128660.690
6_P10_L0.128070.687
111_P114_P0.126670.679
106_R109_P0.126630.679
47_P74_E0.126450.678
80_E85_A0.12560.673
92_D95_L0.125490.673
36_N39_S0.125320.672
98_G118_G0.124650.668
8_G26_L0.124190.666
37_L40_G0.123480.662
6_P49_K0.123450.662
71_V126_N0.123120.660
11_L62_R0.123010.659
8_G53_G0.122570.657
93_G101_P0.122210.655
99_G124_S0.122020.654
33_F42_A0.121710.652
28_D92_D0.121540.652
29_G69_L0.120790.648
55_W71_V0.120560.646
67_G81_S0.120450.646
95_L128_K0.120240.645
81_S123_L0.119970.643
70_S119_C0.119770.642
49_K74_E0.119440.640
117_K122_N0.119240.639
79_G90_D0.119020.638
21_F62_R0.118920.638
89_L92_D0.11810.633
38_G120_I0.117960.632
29_G49_K0.117390.629
59_S73_G0.116680.626
121_R125_I0.116320.624
42_A85_A0.115930.621
13_L95_L0.115830.621
43_S85_A0.115780.621
34_R41_P0.115340.618
35_Y81_S0.115270.618
5_E10_L0.11520.618
82_P120_I0.114970.616
120_I123_L0.114760.615
82_P86_T0.114260.613
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
1dykA0.984799.90.025
2jd4A0.992499.90.025
3v64A0.992499.90.044
3pveA0.992499.90.044
1pz7A0.992499.80.047
3sh4A0.984799.80.066
1h30A0.984799.80.068
1f5fA0.992499.80.073
1d2sA0.954299.80.085
3qcwA0.984799.80.088

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