GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S_locus_glycop - S-locus glycoprotein family
Pfam: PF00954 (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: 110
Sequences: 1330
Seq/Len: 12.09
HH_delta: 0.79 (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
80_C92_C0.351972.712
48_R69_W0.240271.851
52_D58_Q0.236361.821
86_C102_C0.234021.803
91_I103_L0.22631.743
4_G11_F0.222881.717
48_R60_Y0.217951.679
28_V35_Y0.217681.677
20_N23_Y0.212141.634
90_G108_P0.198751.531
30_N33_E0.196171.511
14_I17_M0.192041.479
79_Q85_F0.186121.434
82_V85_F0.178451.375
73_W104_P0.178311.374
29_S32_E0.176541.360
63_N84_G0.175941.355
28_V32_E0.175421.351
2_R5_P0.172451.329
92_C100_C0.171631.322
2_R83_Y0.168171.296
90_G103_L0.167861.293
7_N10_R0.167731.292
6_W11_F0.167041.287
88_P106_F0.165931.278
4_G8_G0.164361.266
57_L60_Y0.163571.260
102_C105_G0.162731.254
62_W67_Q0.162371.251
17_M21_S0.159331.227
17_M20_N0.158051.218
60_Y69_W0.157071.210
2_R108_P0.156911.209
63_N77_K0.156081.202
85_F107_E0.155361.197
16_E77_K0.149681.153
18_S22_L0.14941.151
58_Q89_N0.149211.150
2_R13_G0.147021.133
28_V33_E0.146191.126
79_Q99_K0.144631.114
76_P87_G0.143981.109
60_Y71_V0.14311.102
74_S85_F0.141161.087
71_V74_S0.139461.074
4_G15_P0.138361.066
58_Q71_V0.138221.065
8_G11_F0.13781.062
92_C102_C0.137131.056
76_P106_F0.135891.047
61_I84_G0.135861.047
32_E37_T0.135771.046
81_D93_N0.135021.040
63_N99_K0.134781.038
60_Y84_G0.131851.016
18_S97_S0.131671.014
93_N101_S0.131221.011
68_S85_F0.130681.007
49_L75_A0.130371.004
68_S107_E0.129180.995
67_Q84_G0.128880.993
87_G90_G0.128820.992
53_S110_N0.126980.978
57_L61_I0.12690.978
2_R6_W0.124260.957
8_G62_W0.124240.957
86_C92_C0.122960.947
57_L84_G0.12170.938
61_I73_W0.12160.937
90_G99_K0.121090.933
3_S11_F0.120630.929
42_N64_E0.120610.929
11_F16_E0.119870.923
5_P13_G0.119440.920
73_W79_Q0.118940.916
69_W76_P0.117410.905
9_Q30_N0.116860.900
54_D58_Q0.116670.899
50_V54_D0.116570.898
86_C100_C0.116350.896
16_E33_E0.11620.895
81_D109_K0.115350.889
87_G102_C0.11510.887
57_L75_A0.114860.885
57_L73_W0.114770.884
63_N79_Q0.114290.880
66_T85_F0.113710.876
13_G81_D0.111970.863
5_P8_G0.111930.862
32_E41_S0.111890.862
7_N81_D0.111630.860
84_G110_N0.111040.855
60_Y75_A0.111030.855
59_R76_P0.110850.854
51_L56_Q0.110760.853
8_G81_D0.110510.851
37_T71_V0.110310.850
38_Y73_W0.110090.848
11_F15_P0.110070.848
1_W75_A0.109690.845
55_G58_Q0.109350.842
23_Y26_S0.109070.840
25_Y30_N0.109040.840
1_W10_R0.108810.838
41_S46_L0.108550.836
53_S60_Y0.108060.832
26_S37_T0.107560.829
54_D60_Y0.107290.827
53_S89_N0.10650.820
100_C105_G0.106240.818
47_S59_R0.106030.817
81_D108_P0.106030.817
25_Y29_S0.105840.815
40_L43_S0.105740.815
13_G83_Y0.105720.814
67_Q99_K0.105670.814
67_Q85_F0.105510.813
1_W25_Y0.105510.813
47_S54_D0.105490.813
64_E67_Q0.105480.813
28_V50_V0.105450.812
49_L56_Q0.105370.812
13_G44_S0.105330.811
18_S21_S0.1050.809
69_W86_C0.104760.807
64_E99_K0.104050.802
3_S6_W0.104020.801
11_F17_M0.103990.801
38_Y76_P0.103920.801
76_P86_C0.103770.799
28_V46_L0.103760.799
6_W36_Y0.103480.797
33_E36_Y0.103320.796
63_N66_T0.10310.794
57_L93_N0.102950.793
79_Q107_E0.102850.792
23_Y57_L0.102820.792
45_V61_I0.102290.788
19_S35_Y0.101890.785
21_S24_N0.101870.785
7_N11_F0.101210.780
51_L85_F0.101020.778
46_L81_D0.100110.771
26_S32_E0.099920.770
56_Q82_V0.099720.768
2_R89_N0.09970.768
86_C105_G0.099690.768
51_L55_G0.099680.768
54_D71_V0.099580.767
65_S104_P0.099480.766
4_G42_N0.099430.766
67_Q70_S0.099030.763
6_W108_P0.098820.761
12_S19_S0.098570.759
10_R97_S0.098370.758
39_S46_L0.098120.756
52_D55_G0.097890.754
8_G44_S0.097750.753
68_S109_K0.097550.752
22_L104_P0.09740.750
42_N63_N0.097260.749
51_L71_V0.097220.749
8_G27_F0.097140.748
91_I101_S0.096540.744
51_L84_G0.096380.743
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
1dlpA0.590996.30.79
3m7hA0.895.80.8
4gc1A0.895.80.8
1b9wA0.327388.30.846
1n1iA0.381887.60.847
1ob1C0.327386.50.85
2wg3C0.927382.10.857
1haeA0.345580.90.859
3h5cB0.336479.80.861
1gl4A0.345577.60.863
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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