GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_int_SAM_5 - Phage integrase SAM-like domain
Pfam: PF13102 (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: CL0469
Length: 138
Sequences: 1405
Seq/Len: 10.18
HH_delta: 0.733 (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
115_F132_D0.495853.325
88_D109_L0.495653.324
111_H133_F0.400112.683
51_L54_A0.341292.289
88_D113_K0.340022.280
92_E95_K0.298172.000
112_L129_F0.298141.999
88_D92_E0.295531.982
108_T133_F0.29061.949
133_F137_L0.283121.899
87_F108_T0.277311.860
128_K132_D0.269461.807
44_K47_N0.268141.798
84_L113_K0.264581.774
116_C129_F0.262361.759
101_T105_Y0.260071.744
47_N51_L0.253681.701
35_P38_D0.237541.593
95_K106_K0.231391.552
111_H136_Y0.230911.549
84_L109_L0.229431.539
91_I102_A0.227761.527
83_F122_F0.221711.487
83_F120_I0.219131.470
95_K102_A0.215631.446
20_T23_G0.214471.438
84_L116_C0.209521.405
131_E134_E0.2091.402
112_L116_C0.205941.381
134_E138_R0.204291.370
17_L30_L0.203571.365
8_L13_A0.201011.348
40_D43_K0.20031.343
125_I129_F0.198651.332
13_A36_P0.197521.325
32_L53_K0.196691.319
109_L113_K0.192391.290
127_Y131_E0.190091.275
11_G14_P0.187961.260
26_K69_K0.186561.251
100_G104_N0.185191.242
87_F109_L0.184781.239
15_I34_V0.184161.235
111_H114_R0.183331.229
12_K33_Y0.182921.227
64_E71_G0.17831.196
81_I89_E0.176491.184
114_R136_Y0.172831.159
15_I32_L0.169871.139
122_F125_I0.167911.126
56_A60_K0.16731.122
16_Y29_S0.165861.112
82_D85_D0.165651.111
107_S111_H0.164691.104
48_R51_L0.164421.103
62_I65_L0.161921.086
101_T104_N0.160991.080
53_K57_I0.160121.074
22_N124_D0.154981.039
86_Y122_F0.153751.031
17_L27_Y0.153491.029
111_H137_L0.151021.013
15_I30_L0.148280.994
104_N108_T0.145960.979
83_F87_F0.14530.974
119_K132_D0.14390.965
98_G102_A0.143570.963
106_K110_N0.142780.958
94_L97_K0.141480.949
87_F91_I0.141470.949
89_E126_D0.141360.948
115_F136_Y0.141330.948
90_Y93_E0.141250.947
63_L67_N0.139060.933
52_N59_A0.138170.927
14_P39_W0.136840.918
26_K130_I0.134130.899
112_L115_F0.133950.898
51_L61_R0.133710.897
97_K138_R0.133340.894
120_I129_F0.13240.888
114_R127_Y0.131280.880
10_N33_Y0.130390.874
110_N113_K0.130280.874
46_Q61_R0.12970.870
61_R64_E0.129230.867
7_K13_A0.128840.864
14_P18_R0.128480.862
63_L66_Q0.126360.847
56_A96_K0.125430.841
48_R55_E0.125420.841
45_E48_R0.125380.841
83_F86_Y0.12490.838
8_L12_K0.124620.836
86_Y100_G0.12410.832
86_Y89_E0.123970.831
60_K63_L0.123820.830
113_K117_K0.123560.829
68_K72_F0.123070.825
121_P124_D0.12290.824
103_R107_S0.122150.819
28_I61_R0.122020.818
16_Y27_Y0.122010.818
102_A106_K0.121610.816
40_D123_D0.121470.815
20_T25_R0.120610.809
97_K104_N0.120560.808
45_E49_E0.120330.807
52_N56_A0.120060.805
50_I53_K0.119820.804
81_I85_D0.119710.803
54_A61_R0.119540.802
110_N114_R0.117950.791
86_Y110_N0.117790.790
89_E99_K0.117680.789
98_G101_T0.116440.781
30_L54_A0.116430.781
60_K64_E0.116040.778
49_E52_N0.115750.776
62_I66_Q0.115690.776
47_N54_A0.115360.774
94_L98_G0.115360.774
82_D121_P0.115080.772
28_I58_R0.115020.771
96_K118_K0.113780.763
82_D86_Y0.113520.761
94_L99_K0.112850.757
18_R39_W0.112840.757
38_D44_K0.111890.750
15_I29_S0.111170.746
19_I28_I0.110920.744
16_Y30_L0.11090.744
122_F129_F0.110050.738
51_L65_L0.109410.734
75_K78_K0.109230.733
61_R65_L0.108890.730
9_K106_K0.108840.730
18_R27_Y0.107730.722
90_Y104_N0.107660.722
47_N61_R0.107550.721
35_P43_K0.107390.720
100_G103_R0.107150.719
91_I106_K0.107110.718
20_T129_F0.106480.714
40_D134_E0.106220.712
54_A57_I0.106020.711
64_E67_N0.105920.710
86_Y93_E0.105780.709
17_L28_I0.105490.707
49_E58_R0.105350.706
69_K73_K0.105340.706
68_K71_G0.105040.704
45_E106_K0.104920.704
38_D45_E0.104860.703
114_R118_K0.104030.698
12_K35_P0.103930.697
79_S128_K0.103730.696
38_D47_N0.103560.694
103_R110_N0.103510.694
97_K124_D0.10340.693
27_Y98_G0.102920.690
49_E54_A0.102670.689
84_L120_I0.102310.686
115_F129_F0.102120.685
89_E131_E0.101960.684
55_E62_I0.101940.684
9_K13_A0.101670.682
34_V57_I0.101670.682
113_K116_C0.101550.681
8_L33_Y0.101120.678
14_P34_V0.1010.677
104_N107_S0.100990.677
7_K99_K0.100490.674
50_I62_I0.100330.673
84_L110_N0.100320.673
61_R98_G0.100180.672
130_I134_E0.099680.668
32_L36_P0.099580.668
33_Y122_F0.099510.667
34_V41_K0.099360.666
60_K72_F0.099330.666
48_R116_C0.09890.663
51_L55_E0.09880.663
8_L11_G0.098130.658
44_K48_R0.09810.658
78_K126_D0.097850.656
36_P41_K0.097770.656
21_H126_D0.09770.655
58_R61_R0.097640.655
36_P52_N0.097460.654
40_D45_E0.097450.654
92_E106_K0.097440.653
106_K132_D0.097410.653
115_F133_F0.097140.651
44_K65_L0.097110.651
100_G127_Y0.097050.651
47_N57_I0.096840.649
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
2keyA0.463897.40.733
3lysA0.4493970.753
1z19A0.41396.50.768
1z1bA0.840696.50.769
1xo0A0.427596.30.775
2oxoA0.41396.30.775
2kd1A0.449396.10.779
2kiwA0.398696.10.78
2kkpA0.4565960.783
2khqA0.420395.90.785
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0307 seconds.