GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MCP_N - Vibrio chemotaxis protein N terminus
Pfam: PF05581 (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: 103
Sequences: 3084
Seq/Len: 29.94
HH_delta: 0.53 (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
24_L28_S0.790823.633
54_Q58_N0.441632.029
30_V34_I0.401061.843
82_Q86_E0.390491.794
20_S24_L0.390191.793
46_V50_A0.384191.765
60_K94_F0.383451.762
31_R35_R0.381291.752
56_W60_K0.355721.634
25_Q29_T0.346091.590
77_D80_Y0.340011.562
28_S32_N0.339841.561
19_V22_L0.332671.528
44_E48_G0.319231.467
26_Q30_V0.313211.439
34_I37_Q0.3091.420
41_S44_E0.306291.407
42_V46_V0.29441.353
36_S40_S0.292161.342
61_K65_Q0.291881.341
80_Y83_S0.289561.330
7_I11_S0.286241.315
95_L98_G0.28241.297
36_S39_E0.280371.288
37_Q41_S0.279591.285
63_L91_K0.276991.273
63_L88_P0.27671.271
12_S18_T0.275681.267
35_R38_V0.26941.238
19_V23_S0.261831.203
89_K97_V0.257481.183
71_I74_D0.257251.182
43_N47_D0.257071.181
48_G52_T0.255381.173
24_L32_N0.2541.167
86_E90_L0.245261.127
79_D83_S0.243081.117
58_N62_S0.242911.116
30_V33_E0.241621.110
27_Y31_R0.240061.103
55_S58_N0.239061.098
35_R39_E0.238871.097
67_T88_P0.238121.094
33_E36_S0.237471.091
67_T84_V0.235171.080
49_V56_W0.232741.069
60_K63_L0.231531.064
85_L97_V0.229511.054
94_F97_V0.22871.051
60_K64_A0.224221.030
86_E89_K0.224011.029
62_S65_Q0.222661.023
14_L18_T0.22061.014
11_S15_L0.220251.012
50_A54_Q0.217861.001
79_D82_Q0.20990.964
94_F98_G0.208620.958
50_A53_I0.207740.954
38_V60_K0.205780.945
19_V26_Q0.205140.943
67_T97_V0.202850.932
3_F6_K0.202470.930
15_L18_T0.201120.924
83_S86_E0.200420.921
38_V46_V0.200250.920
22_L64_A0.197140.906
4_S8_V0.196490.903
29_T32_N0.194640.894
44_E47_D0.194550.894
61_K94_F0.193560.889
11_S18_T0.191420.879
28_S31_R0.190940.877
12_S16_L0.190790.877
23_S27_Y0.188850.868
56_W59_G0.188710.867
5_H9_L0.187870.863
42_V50_A0.187840.863
65_Q69_Q0.186640.858
5_H12_S0.186260.856
5_H8_V0.18540.852
51_N55_S0.184250.847
96_L100_G0.184040.846
27_Y30_V0.183820.845
64_A100_G0.183470.843
42_V45_I0.180940.831
68_T71_I0.180890.831
18_T21_L0.180330.829
53_I57_L0.179790.826
34_I38_V0.179370.824
91_K94_F0.179180.823
12_S15_L0.178960.822
96_L99_L0.178830.822
65_Q68_T0.178440.820
23_S42_V0.176680.812
26_Q31_R0.175680.807
62_S93_S0.175620.807
25_Q28_S0.174290.801
12_S95_L0.174210.800
62_S69_Q0.173150.796
39_E43_N0.172910.794
47_D72_E0.172750.794
66_S70_T0.172250.791
76_S79_D0.172160.791
59_G62_S0.172120.791
66_S91_K0.1720.790
33_E37_Q0.170810.785
90_L93_S0.169870.780
24_L27_Y0.169530.779
8_V13_L0.168680.775
81_V99_L0.167820.771
3_F26_Q0.167750.771
68_T73_L0.167520.770
38_V41_S0.166620.766
63_L92_S0.16450.756
42_V49_V0.164120.754
45_I49_V0.1640.753
88_P91_K0.162790.748
78_P101_Y0.162070.745
87_Q90_L0.16160.742
64_A68_T0.16150.742
49_V52_T0.161460.742
36_S79_D0.161290.741
53_I56_W0.160080.735
78_P82_Q0.15920.731
58_N80_Y0.15880.730
12_S27_Y0.158080.726
9_L13_L0.157250.722
48_G67_T0.157050.722
25_Q73_L0.156970.721
8_V19_V0.156770.720
81_V96_L0.156670.720
95_L99_L0.156290.718
41_S45_I0.156120.717
22_L26_Q0.154970.712
58_N61_K0.154690.711
46_V88_P0.153840.707
69_Q87_Q0.15340.705
37_Q44_E0.153020.703
89_K96_L0.152830.702
43_N90_L0.152740.702
59_G69_Q0.152290.700
84_V87_Q0.151310.695
8_V12_S0.150420.691
60_K96_L0.150330.691
48_G51_N0.150060.689
16_L19_V0.149810.688
83_S87_Q0.149050.685
81_V94_F0.14890.684
58_N90_L0.148720.683
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
4dahA0.747696.40.53
3licA0.728296.10.545
3lifA0.757396.10.547
3libA0.757395.90.553
3li9A0.76795.80.556
3c8cA0.679695.40.571
3e4oA0.980694.80.588
3by9A0.708793.40.613
3lidA0.776788.60.657
2kseA183.30.68
If you are interested in a protein containing this domain,
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