GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MreD - rod shape-determining protein MreD
Pfam: PF04093 (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: CL0315
Length: 160
Sequences: 1125
Seq/Len: 7.03
HH_delta: 0.753 (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
57_G83_G0.294532.964
17_A20_L0.237732.393
49_G87_G0.211972.133
53_G83_G0.204922.062
37_L60_I0.189191.904
45_A83_G0.188691.899
35_D79_Y0.174581.757
83_G87_G0.17381.749
58_F76_A0.171191.723
53_G57_G0.170371.715
38_L82_I0.167781.689
35_D110_L0.166151.672
49_G53_G0.162761.638
131_L137_P0.148911.499
101_P105_V0.147491.484
57_G87_G0.145351.463
53_G87_G0.144161.451
47_Y158_R0.143831.448
41_L83_G0.142361.433
78_A109_F0.13821.391
14_F60_I0.137831.387
35_D38_L0.13651.374
37_L85_L0.132061.329
113_V146_A0.129161.300
93_F139_L0.128651.295
14_F17_A0.127641.285
64_Q79_Y0.126841.277
110_L147_I0.121791.226
45_A86_V0.121111.219
77_L90_R0.121071.219
56_L59_I0.119711.205
43_F47_Y0.118851.196
45_A87_G0.118731.195
77_L81_L0.117821.186
75_Y79_Y0.117171.179
17_A40_V0.11591.166
36_L67_Y0.115841.166
139_L145_I0.1151.157
42_V86_V0.114871.156
17_A21_Q0.11481.155
39_L46_L0.114541.153
35_D68_Y0.113811.145
49_G83_G0.113721.145
59_I124_I0.112421.131
63_L92_R0.112051.128
38_L67_Y0.111641.124
62_L111_L0.111541.123
54_L83_G0.110451.112
65_D73_G0.109991.107
105_V109_F0.10891.096
139_L147_I0.108691.094
119_L129_S0.107411.081
62_L72_L0.105311.060
14_F20_L0.105221.059
115_L119_L0.105191.059
15_L21_Q0.10311.038
36_L152_P0.103071.037
54_L57_G0.102351.030
70_G124_I0.102331.030
47_Y60_I0.101721.024
127_L134_R0.101431.021
49_G93_F0.100891.015
34_P69_G0.099581.002
36_L104_L0.099361.000
27_F63_L0.099260.999
15_L146_A0.098550.992
61_G65_D0.098010.986
38_L145_I0.097940.986
75_Y78_A0.097020.976
30_F145_I0.09630.969
49_G151_P0.096050.967
16_I106_F0.095580.962
85_L89_L0.095320.959
54_L87_G0.095310.959
39_L42_V0.095240.959
64_Q102_V0.094660.953
75_Y142_N0.094530.951
125_L131_L0.094410.950
20_L24_P0.094190.948
18_L37_L0.09410.947
19_L30_F0.093880.945
128_L149_L0.093830.944
73_G77_L0.093250.939
58_F80_V0.093240.938
111_L156_L0.093170.938
50_N84_Y0.093020.936
21_Q79_Y0.092950.936
53_G62_L0.092590.932
134_R156_L0.092360.930
59_I82_I0.09220.928
24_P105_V0.091660.923
28_P141_L0.091650.922
14_F19_L0.091380.920
117_Y153_V0.091230.918
86_V93_F0.091190.918
79_Y82_I0.091140.917
59_I83_G0.090970.916
65_D76_A0.090860.914
50_N158_R0.090820.914
47_Y154_F0.090230.908
54_L155_K0.089820.904
110_L130_F0.089690.903
45_A60_I0.089240.898
59_I148_I0.089140.897
41_L57_G0.089070.896
64_Q75_Y0.089040.896
147_I156_L0.088240.888
81_L125_L0.088170.887
118_F136_L0.087950.885
77_L148_I0.087640.882
16_I58_F0.087520.881
108_L116_I0.087330.879
46_L93_F0.087210.878
39_L85_L0.087170.877
72_L77_L0.087150.877
139_L146_A0.086890.875
129_S133_F0.086850.874
88_K102_V0.086840.874
130_F138_T0.086430.870
72_L150_Y0.086160.867
33_V81_L0.086120.867
23_L125_L0.086080.866
31_G140_L0.085670.862
50_N120_F0.085650.862
39_L65_D0.085610.862
121_G149_L0.085520.861
38_L79_Y0.084690.852
33_V79_Y0.084390.849
53_G74_I0.084330.849
18_L76_A0.084290.848
66_I72_L0.084240.848
58_F62_L0.083810.844
74_I77_L0.083420.840
84_Y114_F0.083330.839
20_L36_L0.083290.838
43_F58_F0.083270.838
33_V70_G0.083180.837
19_L38_L0.083170.837
91_K124_I0.082750.833
32_I152_P0.082650.832
24_P34_P0.082540.831
64_Q149_L0.08240.829
76_A121_G0.082170.827
66_I88_K0.081730.823
34_P109_F0.08170.822
78_A139_L0.081650.822
139_L157_L0.081580.821
35_D82_I0.081460.820
42_V72_L0.081350.819
21_Q35_D0.080950.815
59_I74_I0.080880.814
79_Y137_P0.080870.814
127_L133_F0.080760.813
115_L143_A0.080760.813
75_Y101_P0.080720.812
67_Y117_Y0.080670.812
32_I141_L0.080660.812
100_L105_V0.080260.808
70_G116_I0.080210.807
101_P104_L0.080160.807
127_L137_P0.080160.807
57_G80_V0.080130.806
19_L127_L0.080.805
40_V45_A0.079850.804
41_L79_Y0.079710.802
34_P53_G0.079650.802
103_W121_G0.079590.801
88_K145_I0.079590.801
47_Y90_R0.079540.801
55_W59_I0.079440.800
70_G75_Y0.079330.798
71_P85_L0.079070.796
23_L27_F0.079050.796
40_V111_L0.078790.793
15_L112_L0.078730.792
68_Y130_F0.078550.791
112_L115_L0.078520.790
17_A24_P0.078510.790
55_W95_K0.077950.785
110_L114_F0.077880.784
71_P82_I0.077570.781
28_P32_I0.07750.780
59_I132_I0.077370.779
53_G91_K0.077260.778
36_L71_P0.077220.777
14_F122_L0.077010.775
67_Y75_Y0.076940.774
130_F139_L0.07680.773
131_L140_L0.076480.770
111_L140_L0.076260.768
69_G150_Y0.076040.765
100_L127_L0.076030.765
60_I63_L0.075940.764
58_F155_K0.075760.762
63_L122_L0.075660.761
54_L123_T0.075610.761
68_Y71_P0.075560.760
15_L69_G0.075340.758
152_P156_L0.07530.758
101_P150_Y0.075250.757
41_L60_I0.075180.757
86_V100_L0.074820.753
91_K94_F0.074530.750
119_L123_T0.074510.750
42_V106_F0.074440.749
36_L145_I0.074330.748
16_I157_L0.07430.748
124_I155_K0.074070.745
45_A156_L0.074020.745
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
4hzuS0.981297.10.753
3p5nA196.40.777
3rlbA0.9812960.786
4huqS0.968890.70.83
2ksfA0.587548.90.881
4dveA0.987517.80.904
4dx5A0.92550.924
3dh4A0.85622.80.932
3w9iA0.91872.60.933
3ne5A0.9252.30.935
If you are interested in a protein containing this domain,
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