GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YrbL-PhoP_reg - PhoP regulatory network protein YrbL
Pfam: PF10707 (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: CL0016
Length: 199
Sequences: 8469
Seq/Len: 42.56
HH_delta: 0.161 (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
150_V164_I1.628473.913
19_Q25_N1.603243.852
19_Q98_L1.399373.363
109_T112_D1.026992.468
152_Q160_R1.004232.413
8_L16_D0.917332.204
132_R136_D0.879462.113
7_D19_Q0.860982.069
149_I161_L0.860732.068
143_D148_N0.834372.005
152_Q162_V0.821131.973
83_Y97_E0.819021.968
97_E162_V0.814031.956
126_A161_L0.770911.852
99_I162_V0.759151.824
81_R97_E0.755171.815
27_C98_L0.754321.813
126_A130_F0.74131.781
28_I95_V0.704661.693
148_N165_D0.684351.644
66_K84_G0.681971.639
67_Q171_E0.676891.626
99_I152_Q0.657511.580
26_L95_V0.641561.542
154_R160_R0.639341.536
122_E126_A0.618931.487
130_F163_L0.618041.485
123_L126_A0.614871.477
124_R128_D0.614091.476
65_Y82_F0.609661.465
109_T114_L0.601741.446
24_P83_Y0.599461.440
108_P112_D0.598931.439
131_K144_L0.590351.419
17_C27_C0.58821.413
9_I98_L0.584631.405
109_T113_Y0.577241.387
26_L29_K0.566641.362
15_R58_N0.563161.353
80_P99_I0.552621.328
144_L163_L0.539871.297
31_M58_N0.525361.262
61_E64_Y0.519011.247
130_F133_Y0.516211.240
111_E147_H0.515061.238
107_S110_L0.5061.216
75_D81_R0.495061.190
82_F85_F0.493371.186
143_D165_D0.481911.158
152_Q155_D0.476691.145
126_A129_E0.473121.137
166_G169_E0.470531.131
8_L11_Q0.468671.126
145_N148_N0.468251.125
8_L18_Y0.466251.120
76_W133_Y0.458771.102
61_E65_Y0.450731.083
125_Q129_E0.44641.073
131_K135_L0.445281.070
6_S19_Q0.442761.064
149_I163_L0.441831.062
62_L66_K0.432291.039
127_L130_F0.429291.032
108_P114_L0.42611.024
88_T91_G0.424281.019
77_S80_P0.419091.007
99_I164_I0.416231.000
133_Y137_H0.412670.992
86_V95_V0.4110.988
80_P96_V0.40840.981
6_S25_N0.406090.976
78_H160_R0.403270.969
18_Y30_V0.39830.957
139_I171_E0.397780.956
60_R64_Y0.397140.954
69_S81_R0.391840.942
33_P87_E0.386890.930
163_L166_G0.383550.922
59_R63_R0.382140.918
11_Q16_D0.379960.913
24_P81_R0.37890.910
31_M90_L0.378810.910
25_N98_L0.378530.910
83_Y86_V0.37560.903
132_R137_H0.373420.897
142_R170_K0.372720.896
62_L84_G0.372080.894
54_R60_R0.371840.893
9_I27_C0.369860.889
124_R129_E0.369730.888
139_I169_E0.368010.884
114_L120_T0.363090.872
112_D116_E0.360460.866
167_L170_K0.359430.864
151_V161_L0.354430.852
114_L118_G0.349630.840
78_H152_Q0.348890.838
76_W79_I0.346720.833
80_P97_E0.344460.828
13_G145_N0.341490.821
127_L149_I0.341150.820
9_I19_Q0.33770.811
10_A17_C0.33390.802
127_L161_L0.330250.794
126_A160_R0.327970.788
78_H97_E0.327310.786
110_L114_L0.32650.785
12_G15_R0.326480.784
66_K69_S0.325140.781
63_R66_K0.324140.779
124_R130_F0.323830.778
125_Q128_D0.322280.774
11_Q32_R0.32090.771
20_H23_D0.320050.769
128_D132_R0.318190.765
65_Y96_V0.317320.762
99_I150_V0.317170.762
14_E168_G0.312090.750
123_L128_D0.310850.747
111_E115_K0.307770.740
16_D30_V0.304910.733
123_L129_E0.302970.728
107_S111_E0.302290.726
78_H129_E0.301160.724
30_V91_G0.299710.720
80_P164_I0.299490.720
115_K118_G0.299060.719
134_L139_I0.298340.717
27_C31_M0.296690.713
113_Y117_G0.295660.710
108_P113_Y0.294830.708
51_P54_R0.294780.708
123_L161_L0.292550.703
84_G87_E0.29250.703
17_C143_D0.289750.696
108_P118_G0.289190.695
54_R57_Q0.287960.692
144_L168_G0.285460.686
64_Y139_I0.285280.685
69_S75_D0.284890.685
145_N165_D0.2820.678
114_L117_G0.281650.677
20_H24_P0.281420.676
113_Y116_E0.280260.673
110_L151_V0.280040.673
62_L82_F0.279380.671
20_H26_L0.278870.670
142_R146_P0.274750.660
64_Y169_E0.27390.658
84_G95_V0.273780.658
76_W129_E0.273080.656
26_L83_Y0.272820.656
79_I130_F0.270690.650
12_G145_N0.26950.648
82_F96_V0.269360.647
24_P97_E0.269060.647
118_G121_E0.268590.645
58_N61_E0.267440.643
111_E114_L0.264820.636
82_F94_L0.263830.634
61_E68_L0.26320.632
129_E133_Y0.259470.623
143_D167_L0.25880.622
116_E119_L0.256740.617
108_P116_E0.256560.616
60_R63_R0.255370.614
62_L94_L0.255320.614
15_R167_L0.254350.611
30_V33_P0.251470.604
141_I148_N0.251020.603
14_E167_L0.2510.603
62_L85_F0.250820.603
122_E125_Q0.250310.601
123_L127_L0.247150.594
10_A27_C0.243950.586
65_Y166_G0.243430.585
87_E90_L0.24340.585
86_V90_L0.241710.581
68_L139_I0.24130.580
134_L163_L0.241250.580
96_V164_I0.241180.580
12_G148_N0.240390.578
69_S78_H0.238810.574
16_D32_R0.235950.567
141_I144_L0.235250.565
21_P24_P0.234860.564
126_A131_K0.234820.564
135_L145_N0.234820.564
80_P162_V0.234410.563
12_G17_C0.233080.560
122_E129_E0.231510.556
117_G120_T0.231370.556
107_S112_D0.229580.552
114_L119_L0.228090.548
10_A14_E0.227980.548
10_A98_L0.227820.547
60_R170_K0.227790.547
151_V155_D0.22540.542
140_V170_K0.225320.541
78_H162_V0.225150.541
107_S114_L0.224910.540
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
4fieA0.83921000.161
4fihA0.83921000.167
4g31A0.84421000.187
4aojA0.83921000.187
3ubdA0.84921000.188
4gt4A0.844299.90.195
3omvA0.844299.90.196
3v5wA0.869399.90.197
3hyhA0.849299.90.202
4im0A0.864399.90.207

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