GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4405 - Domain of unknown function (DUF4405)
Pfam: PF14358 (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: CL0328
Length: 64
Sequences: 310
Seq/Len: 4.84
HH_delta: 0.663 (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
6_N63_H0.305522.405
2_R63_H0.252111.984
52_F56_I0.187731.477
20_G23_L0.182151.434
54_I58_L0.181271.427
2_R27_P0.178791.407
8_L55_L0.177671.398
15_V48_A0.177551.397
4_I21_I0.175691.383
7_L46_L0.166321.309
16_L49_G0.164731.296
6_N21_I0.163861.290
10_L62_L0.155511.224
24_S28_F0.151451.192
9_L52_F0.151281.191
61_G64_W0.148311.167
15_V19_S0.147971.165
17_A53_L0.147561.161
19_S50_Y0.147331.160
51_L61_G0.145191.143
24_S27_P0.144471.137
13_F60_L0.142971.125
8_L60_L0.142051.118
8_L17_A0.142011.118
22_L41_W0.140241.104
7_L19_S0.139881.101
3_Y51_L0.139061.094
27_P38_K0.137991.086
35_G38_K0.137231.080
20_G49_G0.136591.075
14_L57_I0.136161.072
4_I11_V0.135851.069
22_L48_A0.130721.029
18_I51_L0.126720.997
50_Y54_I0.126220.993
18_I60_L0.125380.987
17_A25_F0.125170.985
15_V54_I0.123110.969
44_I56_I0.123090.969
16_L48_A0.122510.964
12_S55_L0.11950.941
24_S63_H0.119010.937
4_I18_I0.118950.936
12_S18_I0.118050.929
11_V44_I0.116110.914
13_F49_G0.115020.905
38_K41_W0.114430.901
2_R52_F0.113340.892
10_L53_L0.112890.888
39_H58_L0.11170.879
12_S54_I0.110910.873
14_L17_A0.108730.856
43_N57_I0.107840.849
38_K42_R0.107020.842
20_G45_H0.107020.842
7_L11_V0.106490.838
42_R51_L0.106480.838
23_L46_L0.106310.837
13_F36_L0.106190.836
17_A44_I0.106110.835
9_L19_S0.106060.835
24_S29_P0.105670.832
18_I48_A0.105340.829
37_N54_I0.105170.828
34_L49_G0.104650.824
3_Y63_H0.104580.823
57_I61_G0.104140.820
6_N10_L0.104120.819
41_W53_L0.10410.819
24_S38_K0.103710.816
6_N28_F0.103680.816
26_V29_P0.102820.809
37_N43_N0.102440.806
44_I64_W0.100820.793
7_L25_F0.099880.786
5_I29_P0.099570.784
19_S44_I0.099330.782
3_Y7_L0.099160.780
17_A49_G0.098670.777
52_F60_L0.097950.771
10_L44_I0.097630.768
3_Y60_L0.09740.767
5_I62_L0.097260.765
8_L12_S0.096970.763
11_V60_L0.096740.761
40_F43_N0.096470.759
14_L34_L0.096380.759
18_I57_I0.096040.756
23_L57_I0.095970.755
19_S45_H0.09510.748
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
1kqfC0.984492.90.663
4gd3A192.70.665
1pp9C189.70.689
4h44A189.60.69
2qjyA185.10.711
3cx5C184.80.712
4gd3A0.953172.90.741
1vf5A172.10.743
2bs2C0.76566.80.849
1wrgA0.60941.90.883
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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