GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3656 - Collagenase
Pfam: PF12392 (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: 122
Sequences: 609
Seq/Len: 4.99
HH_delta: 0.91 (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
83_F115_E0.476533.710
77_K104_N0.403993.146
42_L110_A0.370122.882
27_D86_E0.341862.662
78_L111_V0.334622.606
28_L42_L0.27462.138
78_L85_L0.263452.051
41_T51_E0.242211.886
68_E72_R0.234421.825
74_Q104_N0.231161.800
3_R97_F0.229481.787
3_R6_D0.224811.750
72_R76_S0.218411.701
7_K11_K0.214771.672
58_P96_L0.213891.665
29_K89_E0.213711.664
28_L110_A0.209131.628
74_Q103_L0.206671.609
74_Q77_K0.200421.561
33_K93_D0.194531.515
39_K53_T0.191991.495
28_L85_L0.18851.468
104_N108_R0.182381.420
27_D87_N0.178961.393
6_D118_R0.173351.350
85_L88_I0.168311.311
23_K84_E0.164141.278
29_K91_D0.16361.274
112_E115_E0.162491.265
2_Y9_L0.16181.260
30_L38_L0.16081.252
105_E109_E0.158071.231
33_K36_E0.155721.213
64_R70_R0.151841.182
98_L102_E0.15151.180
116_E120_A0.148511.156
109_E112_E0.148151.154
39_K51_E0.146971.144
77_K97_F0.146161.138
29_K41_T0.144651.126
42_L111_V0.144361.124
43_S49_S0.141781.104
102_E105_E0.140671.095
28_L40_L0.138641.080
28_L75_L0.135671.056
4_T9_L0.135661.056
38_L54_S0.135611.056
30_L75_L0.13491.050
23_K80_N0.132731.033
75_L110_A0.132521.032
6_D9_L0.132441.031
60_P95_G0.130091.013
48_N118_R0.129211.006
26_V110_A0.128521.001
31_S91_D0.128310.999
26_V114_L0.127940.996
59_E62_K0.126880.988
3_R16_S0.123750.964
110_A118_R0.123260.960
54_S106_L0.123250.960
112_E116_E0.123170.959
69_E72_R0.123160.959
63_K104_N0.122950.957
13_L16_S0.122910.957
2_Y58_P0.122370.953
2_Y7_K0.121790.948
113_K117_K0.12130.944
78_L81_T0.120850.941
40_L106_L0.119270.929
70_R103_L0.119240.928
8_K105_E0.11670.909
34_K94_E0.116470.907
30_L71_I0.116180.905
30_L40_L0.116150.904
34_K96_L0.115510.899
65_P95_G0.114470.891
26_V72_R0.114040.888
79_G101_S0.113870.887
7_K58_P0.113270.882
6_D13_L0.113170.881
90_I93_D0.112040.872
12_E94_E0.111720.870
31_S39_K0.111280.866
42_L89_E0.110080.857
50_V106_L0.108760.847
77_K85_L0.108660.846
40_L75_L0.108150.842
100_I104_N0.107380.836
25_P84_E0.106190.827
10_E13_L0.106020.826
16_S21_E0.105140.819
114_L118_R0.104090.810
28_L88_I0.10340.805
77_K107_R0.103110.803
34_K60_P0.103080.803
36_E53_T0.102860.801
81_T111_V0.102170.796
52_V106_L0.102080.795
115_E119_L0.10190.793
60_P86_E0.101740.792
1_V13_L0.101530.791
11_K15_K0.101450.790
36_E113_K0.101330.789
1_V93_D0.101230.788
70_R98_L0.099360.774
24_I118_R0.097410.758
73_K106_L0.097290.758
97_F101_S0.097180.757
33_K37_P0.096870.754
78_L102_E0.096270.750
72_R106_L0.095920.747
67_D115_E0.095780.746
41_T49_S0.095510.744
30_L37_P0.095410.743
40_L50_V0.094520.736
15_K19_S0.094460.736
58_P93_D0.094430.735
31_S41_T0.094410.735
31_S116_E0.094090.733
67_D70_R0.093840.731
50_V113_K0.093530.728
5_S10_E0.09350.728
29_K51_E0.093190.726
24_I110_A0.092560.721
3_R45_E0.092520.720
74_Q100_I0.092150.718
69_E109_E0.092050.717
6_D23_K0.091630.713
104_N107_R0.09140.712
99_P108_R0.091330.711
9_L54_S0.091210.710
24_I88_I0.091150.710
25_P68_E0.090650.706
66_L98_L0.090240.703
25_P86_E0.089970.701
88_I100_I0.089860.700
70_R101_S0.089730.699
55_E99_P0.08920.695
11_K48_N0.08870.691
50_V114_L0.088680.691
85_L90_I0.088650.690
35_G89_E0.088150.686
1_V4_T0.08810.686
38_L104_N0.087870.684
2_Y119_L0.087650.682
60_P94_E0.087640.682
66_L88_I0.087250.679
55_E109_E0.087210.679
4_T7_K0.086820.676
5_S80_N0.086760.676
67_D73_K0.086750.675
60_P69_E0.086730.675
8_K12_E0.086670.675
1_V120_A0.08640.673
66_L104_N0.086350.672
13_L82_P0.086160.671
52_V110_A0.08580.668
65_P68_E0.085790.668
38_L78_L0.085740.668
13_L64_R0.085130.663
26_V87_N0.085090.663
26_V89_E0.084750.660
53_T116_E0.084030.654
37_P66_L0.083930.654
100_I107_R0.083750.652
7_K71_I0.083330.649
47_G50_V0.083130.647
73_K105_E0.0830.646
26_V56_I0.082910.646
66_L70_R0.08290.645
9_L37_P0.082790.645
63_K77_K0.082770.644
3_R13_L0.082760.644
83_F118_R0.08260.643
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
1914A0.696729.70.91
2bkfA0.5984150.921
1f1eA0.836114.70.921
2ct9A0.53289.80.927
1qwrA0.97547.80.93
4gxwA0.90167.10.931
2ewdA0.64756.70.932
3zey40.72136.70.932
3lgdA0.88526.40.932
2xzm30.66396.40.932
If you are interested in a protein containing this domain,
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