GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
C1q - C1q domain
Pfam: PF00386 (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: CL0100
Length: 127
Sequences: 1281
Seq/Len: 10.09
HH_delta: 0.023 (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
68_N99_D0.549553.827
38_I100_T0.420952.932
43_V126_L0.342432.385
48_F90_S0.339722.366
31_A42_P0.294532.051
63_V103_V0.281551.961
51_F103_V0.261761.823
49_F124_G0.261561.822
21_F53_I0.26111.818
20_V32_Y0.253651.767
48_F125_F0.249151.735
49_F101_V0.248411.730
40_T100_T0.230751.607
44_P96_N0.225631.571
32_Y103_V0.22261.550
7_T22_D0.219141.526
66_M104_R0.2181.518
50_S90_S0.216071.505
33_N40_T0.215011.497
95_L101_V0.214161.492
21_F103_V0.210281.465
3_S25_L0.20951.459
6_L22_D0.206831.441
51_F63_V0.206581.439
3_S73_A0.205991.435
66_M102_W0.204131.422
67_K96_N0.199061.386
41_A49_F0.197641.376
4_A34_P0.197341.374
33_N100_T0.193511.348
67_K101_V0.191811.336
32_Y37_G0.189661.321
89_N121_T0.188661.314
64_E104_R0.188361.312
48_F92_V0.187661.307
21_F120_S0.186221.297
28_I94_Q0.185991.295
67_K72_V0.18581.294
2_F6_L0.184441.285
51_F89_N0.177611.237
41_A44_P0.176961.232
64_E74_S0.172561.202
51_F125_F0.167641.168
33_N36_T0.162991.135
5_S25_L0.160411.117
67_K70_N0.159711.112
50_S56_S0.159091.108
24_V34_P0.157411.096
7_T23_K0.153681.070
32_Y36_T0.153081.066
39_F49_F0.15131.054
52_T88_S0.150691.050
72_V93_L0.149431.041
38_I102_W0.148981.038
26_T92_V0.148221.032
48_F127_L0.145251.012
18_T26_T0.142850.995
39_F124_G0.142230.991
77_A87_A0.141430.985
27_N37_G0.140760.980
29_G42_P0.140490.978
24_V27_N0.137860.960
18_T102_W0.137070.955
3_S121_T0.136530.951
124_G127_L0.134530.937
36_T40_T0.133590.930
65_L91_A0.132540.923
53_I61_V0.130150.906
92_V125_F0.129790.904
52_T86_S0.128520.895
46_V94_Q0.127070.885
21_F102_W0.126890.884
33_N38_I0.126710.882
75_T108_G0.12640.880
74_S81_S0.124270.865
3_S123_S0.124050.864
13_P57_S0.123660.861
6_L32_Y0.123180.858
67_K95_L0.122920.856
19_I89_N0.120730.841
24_V91_A0.120660.840
69_G102_W0.120370.838
77_A85_D0.120210.837
62_W76_Y0.119960.835
29_G105_L0.11990.835
5_S73_A0.119580.833
82_G108_G0.119180.830
22_D35_S0.118790.827
23_K31_A0.117960.822
8_S35_S0.11790.821
24_V32_Y0.117690.820
66_M69_G0.117640.819
27_N39_F0.117560.819
16_N19_I0.117360.817
67_K93_L0.117040.815
28_I46_V0.116230.810
7_T13_P0.116180.809
58_G79_N0.11610.809
105_L108_G0.115190.802
110_G119_Y0.115080.801
38_I101_V0.115060.801
31_A41_A0.114870.800
52_T90_S0.114740.799
109_N115_G0.114420.797
5_S121_T0.114270.796
90_S113_S0.114230.796
51_F65_L0.113330.789
112_Y115_G0.11320.788
18_T104_R0.112640.785
17_Q104_R0.112240.782
101_V124_G0.112210.782
68_N72_V0.11220.781
73_A91_A0.111760.778
43_V63_V0.111760.778
86_S121_T0.111590.777
16_N71_P0.111570.777
71_P74_S0.111220.775
114_S118_P0.1110.773
50_S59_S0.110930.773
51_F126_L0.110920.773
54_M119_Y0.110660.771
74_S88_S0.11030.768
8_S17_Q0.110150.767
65_L72_V0.109940.766
33_N47_Y0.109680.764
95_L99_D0.109420.762
22_D92_V0.109330.761
61_V75_T0.109310.761
27_N30_N0.109110.760
79_N82_G0.108620.757
6_L23_K0.108490.756
30_N96_N0.108450.755
33_N42_P0.108440.755
7_T10_L0.10830.754
83_N107_S0.108130.753
123_S126_L0.107860.751
91_A106_D0.107850.751
50_S123_S0.107770.751
26_T29_G0.107690.750
17_Q35_S0.106710.743
10_L13_P0.106470.742
28_I31_A0.106370.741
92_V127_L0.105820.737
6_L20_V0.104550.728
41_A52_T0.104480.728
38_I52_T0.104230.726
35_S94_Q0.103760.723
40_T99_D0.103610.722
77_A83_N0.103560.721
27_N31_A0.102950.717
17_Q109_N0.10280.716
9_S12_P0.102560.714
60_S64_E0.102410.713
97_K100_T0.102320.713
86_S89_N0.102310.713
63_V95_L0.101740.709
65_L103_V0.10170.708
17_Q77_A0.101610.708
46_V92_V0.101530.707
48_F67_K0.101510.707
39_F47_Y0.101260.705
74_S78_S0.10090.703
107_S112_Y0.100890.703
73_A89_N0.100790.702
9_S108_G0.100680.701
18_T38_I0.100550.700
22_D113_S0.099940.696
11_S34_P0.09990.696
76_Y80_S0.099440.693
41_A47_Y0.099340.692
62_W74_S0.099260.691
31_A98_G0.098750.688
25_L88_S0.098710.687
44_P95_L0.098670.687
3_S91_A0.098580.687
67_K94_Q0.098540.686
52_T83_N0.098390.685
75_T87_A0.097730.681
27_N49_F0.097380.678
46_V54_M0.097180.677
20_V31_A0.096740.674
59_S68_N0.096620.673
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
2wnvB0.96851000.023
4douA0.96851000.023
4douA0.96851000.027
1gr3A0.96851000.033
2wnvC0.96061000.036
1o91A0.96851000.041
2wnvA0.95281000.054
2ka3A0.96061000.07
4f3jA0.98431000.073
1rj8A0.976498.90.613

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