GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HemY_N - HemY protein N-terminus
Pfam: PF07219 (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: CL0020
Length: 108
Sequences: 493
Seq/Len: 4.56
HH_delta: 0.854 (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
5_I12_I0.218382.210
3_V19_A0.210462.130
31_Y35_R0.175991.781
63_L95_N0.160181.621
31_Y34_L0.14531.471
79_E106_Q0.142581.443
79_E103_A0.141541.433
44_P63_L0.140991.427
25_L29_V0.137881.396
32_L37_L0.136451.381
66_G98_L0.13271.343
10_Y67_L0.131511.331
47_V80_K0.131241.328
7_W24_L0.129611.312
23_L32_L0.128071.296
92_P95_N0.125351.269
70_L102_A0.124461.260
4_L13_E0.124341.259
101_R105_A0.123651.252
84_K90_D0.123351.249
4_L11_R0.122971.245
25_L33_L0.122311.238
2_Y13_E0.119931.214
61_R90_D0.118891.203
55_R85_A0.117741.192
27_F31_Y0.115361.168
99_A102_A0.114191.156
42_S45_S0.114071.155
20_L40_L0.113881.153
59_A85_A0.111971.133
72_E101_R0.111891.133
5_I21_I0.111651.130
40_L61_R0.111421.128
16_L31_Y0.111071.124
59_A89_S0.110771.121
62_A85_A0.110531.119
5_I19_A0.110481.118
2_Y72_E0.110311.117
71_A107_G0.11011.114
62_A71_A0.109911.112
66_G101_R0.109351.107
57_R94_L0.109011.103
25_L28_V0.108991.103
39_R50_W0.108971.103
15_S80_K0.108421.097
66_G82_L0.107921.092
26_L84_K0.106281.076
27_F80_K0.106051.073
69_A74_D0.105961.073
20_L29_V0.105631.069
14_T18_V0.105361.066
17_W51_R0.104041.053
43_L58_K0.103821.051
77_R81_L0.103481.047
56_R65_R0.103451.047
26_L41_L0.103231.045
72_E102_A0.103151.044
37_L40_L0.1031.043
25_L102_A0.102921.042
6_S9_G0.101831.031
82_L98_L0.101831.031
28_V32_L0.100421.016
66_G78_A0.100171.014
86_A92_P0.099391.006
93_L96_Y0.099311.005
40_L76_Q0.099131.003
33_L37_L0.09911.003
20_L52_R0.098881.001
105_A108_D0.09860.998
4_L15_S0.098440.996
4_L19_A0.097210.984
25_L32_L0.096610.978
30_L33_L0.096390.976
73_G92_P0.09630.975
7_W98_L0.095820.970
68_I72_E0.095810.970
34_L41_L0.095430.966
3_V15_S0.094240.954
29_V32_L0.093880.950
28_V94_L0.092990.941
68_I107_G0.092940.941
11_R74_D0.092780.939
62_A82_L0.092380.935
35_R38_R0.092290.934
9_G31_Y0.09220.933
86_A99_A0.091790.929
27_F30_L0.091630.927
5_I29_V0.091480.926
7_W84_K0.091420.925
32_L36_L0.090980.921
28_V40_L0.090850.920
70_L97_L0.09060.917
37_L41_L0.090420.915
55_R69_A0.09010.912
23_L27_F0.089720.908
9_G14_T0.089620.907
92_P99_A0.089570.907
45_S52_R0.089570.907
72_E99_A0.089490.906
16_L97_L0.08920.903
12_I86_A0.088940.900
71_A95_N0.08890.900
36_L58_K0.088120.892
22_L30_L0.087580.886
7_W74_D0.087460.885
92_P102_A0.087080.881
49_R53_R0.086910.880
57_R84_K0.085830.869
14_T65_R0.085820.869
68_I101_R0.085240.863
13_E21_I0.084980.860
10_Y20_L0.084920.860
30_L68_I0.084910.859
46_R49_R0.084120.851
23_L37_L0.084070.851
64_S97_L0.083890.849
44_P94_L0.083860.849
18_V44_P0.083860.849
18_V22_L0.083460.845
4_L47_V0.083270.843
53_R88_L0.083210.842
32_L65_R0.082860.839
19_A31_Y0.082660.837
19_A45_S0.082660.837
27_F34_L0.082590.836
82_L96_Y0.081160.821
68_I71_A0.080810.818
66_G75_W0.080680.817
7_W105_A0.080380.814
5_I30_L0.080250.812
71_A92_P0.079420.804
79_E95_N0.079380.803
68_I85_A0.079170.801
32_L61_R0.079030.800
29_V57_R0.07890.799
83_A102_A0.078520.795
30_L108_D0.078230.792
9_G25_L0.078060.790
81_L92_P0.077880.788
40_L43_L0.077490.784
28_V31_Y0.077060.780
24_L32_L0.076510.774
4_L82_L0.076480.774
9_G27_F0.076040.770
36_L45_S0.075890.768
68_I92_P0.075810.767
69_A101_R0.075470.764
29_V56_R0.075360.763
72_E86_A0.075230.761
45_S76_Q0.075110.760
64_S101_R0.074830.757
16_L19_A0.074820.757
22_L103_A0.074390.753
29_V45_S0.074350.753
14_T43_L0.074060.750
10_Y27_F0.073980.749
55_R101_R0.073930.748
55_R102_A0.073350.742
20_L31_Y0.073240.741
38_R97_L0.073210.741
60_Q97_L0.073080.740
7_W79_E0.073010.739
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
1wao10.5093840.854
2gw1A0.580.80.858
3urzA0.490779.80.86
3upvA0.490775.30.865
2c2lA0.490773.30.867
3qkyA0.592671.20.869
2kc7A0.453770.90.87
2r5sA0.509370.30.87
3iegA0.481569.70.871
3uq3A0.490769.60.871
If you are interested in a protein containing this domain,
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