GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HlyD - HlyD family secretion protein
Pfam: PF00529 (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: CL0105
Length: 305
Sequences: 10138
Seq/Len: 33.24
HH_delta: 0.33 (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
14_E31_R1.460414.565
16_L31_R1.095853.425
34_P38_E1.022483.196
24_K27_Q1.012813.166
16_L28_V0.928852.903
24_K176_D0.906852.835
38_E42_A0.862642.696
111_R115_E0.856522.677
42_A45_E0.835022.610
49_Q52_Q0.803882.513
92_Q96_K0.720972.254
229_R244_E0.718912.247
164_E172_R0.702782.197
154_D157_Q0.686022.144
231_P242_H0.681552.130
81_K85_A0.656342.052
45_E157_Q0.652242.039
104_Q108_E0.650812.034
28_V164_E0.648182.026
18_K21_Q0.642072.007
83_E87_Q0.637281.992
48_L52_Q0.636581.990
41_L45_E0.629371.967
12_V30_A0.610261.907
56_K59_R0.597981.869
7_L162_Q0.592981.853
106_Q109_Q0.586051.832
147_L150_K0.584051.826
91_Q102_A0.578021.807
21_Q27_Q0.572111.788
10_G32_L0.569691.781
108_E111_R0.5681.775
109_Q113_Q0.543051.697
40_D43_Q0.537511.680
114_L118_Q0.536791.678
69_Q73_F0.521071.629
13_T31_R0.520811.628
28_V31_R0.51611.613
121_L150_K0.513941.606
92_Q111_R0.512161.601
7_L11_I0.506671.584
155_E159_Q0.502241.570
28_V172_R0.500891.566
91_Q110_A0.499771.562
157_Q161_A0.495751.550
158_R162_Q0.495011.547
52_Q150_K0.494931.547
66_E69_Q0.493321.542
272_D278_Q0.492171.538
85_A89_E0.489931.531
107_L111_R0.479231.498
196_S199_Q0.47871.496
150_K154_D0.478171.495
173_A204_V0.470761.471
95_A107_L0.470381.470
13_T33_D0.469881.469
88_R92_Q0.469711.468
13_T34_P0.467071.460
25_K176_D0.465661.456
118_Q122_K0.460141.438
80_E84_E0.458071.432
22_R179_R0.45591.425
113_Q117_Q0.45571.424
45_E49_Q0.454821.422
152_R155_E0.449311.404
41_L153_L0.448261.401
47_E50_A0.445771.393
181_I205_V0.441031.379
89_E93_A0.431621.349
47_E51_A0.430191.345
97_S101_A0.429851.344
89_E92_Q0.42651.333
229_R246_G0.426171.332
43_Q47_E0.425191.329
115_E118_Q0.420341.314
173_A176_D0.418931.309
216_L224_V0.415711.299
37_Y163_T0.412631.290
272_D276_V0.410811.284
93_A96_K0.409671.280
62_A66_E0.407511.274
90_R94_L0.405461.267
48_L146_G0.402811.259
38_E41_L0.40221.257
129_E132_Q0.401271.254
57_Q61_E0.400731.253
131_Q134_L0.39971.249
103_S106_Q0.398821.247
31_R164_E0.398391.245
248_V285_K0.397261.242
106_Q110_A0.39491.234
95_A104_Q0.39411.232
7_L36_D0.388621.215
80_E83_E0.386921.209
101_A104_Q0.380341.189
31_R34_P0.38021.188
217_K220_Q0.3781.182
224_V247_V0.376611.177
126_G129_E0.376571.177
128_L132_Q0.374371.170
86_A89_E0.36931.154
268_V282_V0.368611.152
23_V29_L0.367481.149
15_I191_V0.366651.146
214_A284_I0.364131.138
159_Q162_Q0.361961.131
192_G198_G0.360891.128
177_G204_V0.359991.125
59_R62_A0.358731.121
93_A97_S0.357161.116
41_L157_Q0.355741.112
17_V27_Q0.35541.111
191_V225_R0.353211.104
128_L148_A0.352831.103
85_A118_Q0.352781.103
132_Q136_Q0.351851.100
48_L153_L0.350671.096
40_D44_A0.348371.089
41_L107_L0.347461.086
87_Q91_Q0.344921.078
153_L157_Q0.344131.076
13_T16_L0.343711.074
65_L69_Q0.342671.071
87_Q90_R0.342661.071
212_V232_V0.342171.070
246_G287_D0.34091.066
82_A85_A0.338191.057
146_G150_K0.338081.057
156_A159_Q0.334991.047
12_V195_V0.331981.038
30_A201_L0.331481.036
113_Q116_S0.3311.035
73_F76_A0.33071.034
16_L27_Q0.329631.030
129_E133_A0.32961.030
15_I30_A0.327981.025
241_V245_G0.327931.025
84_E87_Q0.327151.023
91_Q94_L0.326371.020
195_V201_L0.325251.017
79_A82_A0.32341.011
110_A113_Q0.323231.010
231_P244_E0.321581.005
46_A49_Q0.321271.004
12_V189_V0.318870.997
22_R230_A0.318620.996
45_E153_L0.317840.993
43_Q152_R0.31180.975
83_E86_A0.308980.966
270_P280_Q0.30580.956
120_A124_A0.305440.955
85_A88_R0.303950.950
45_E48_L0.302220.945
36_D40_D0.301980.944
79_A83_E0.301420.942
30_A171_I0.300640.940
44_A48_L0.300080.938
29_L202_L0.299860.937
173_A177_G0.298590.933
70_A74_P0.298050.932
52_Q56_K0.296690.927
18_K187_R0.293450.917
44_A47_E0.293030.916
105_A109_Q0.292150.913
46_A151_A0.291960.913
102_A107_L0.289630.905
28_V227_G0.289160.904
24_K233_S0.289080.904
117_Q120_A0.288920.903
134_L138_Q0.288910.903
8_V37_Y0.287350.898
230_A245_G0.287030.897
188_S202_L0.286620.896
243_T246_G0.286330.895
82_A86_A0.284040.888
104_Q107_L0.282080.882
49_Q147_L0.281440.880
241_V246_G0.279280.873
242_H246_G0.278920.872
38_E160_L0.275980.863
256_V259_D0.27590.862
40_D159_Q0.275250.860
58_A62_A0.274950.859
134_L137_A0.274880.859
242_H245_G0.274810.859
140_A143_Q0.273190.854
246_G285_K0.272410.851
234_G237_Y0.27190.850
156_A160_L0.271250.848
116_S119_A0.271090.847
119_A122_K0.270650.846
111_R114_L0.270360.845
270_P274_G0.270130.844
143_Q146_G0.269480.842
40_D155_E0.269190.841
142_L146_G0.269090.841
67_R71_L0.267730.837
98_Q101_A0.266520.833
71_L75_A0.266020.831
88_R107_L0.265320.829
130_Q134_L0.264970.828
190_Q193_E0.262360.820
6_S201_L0.261350.817
121_L124_A0.260620.815
102_A106_Q0.260050.813
72_V76_A0.259230.810
47_E148_A0.258460.808
39_A42_A0.257530.805
12_V15_I0.256240.801
30_A131_Q0.256230.801
180_V202_L0.254650.796
206_D224_V0.254410.795
91_Q105_A0.253550.793
245_G249_S0.252370.789
127_S130_Q0.251990.788
112_A115_E0.251990.788
190_Q202_L0.251510.786
276_V279_G0.25110.785
6_S9_G0.25050.783
17_V21_Q0.248730.777
52_Q104_Q0.248440.777
212_V284_I0.247330.773
201_L229_R0.246690.771
41_L160_L0.246460.770
23_V27_Q0.245970.769
277_R280_Q0.241070.754
145_Q148_A0.240140.751
161_A172_R0.239960.750
154_D228_I0.239280.748
49_Q53_A0.238750.746
65_L68_A0.23870.746
161_A164_E0.238660.746
116_S120_A0.237550.743
11_I35_T0.237530.742
225_R228_I0.236890.740
48_L209_I0.234070.732
109_Q112_A0.233780.731
124_A127_S0.233430.730
136_Q139_L0.232750.728
4_V29_L0.231340.723
243_T247_V0.231060.722
81_K84_E0.230030.719
254_E257_P0.229650.718
187_R190_Q0.229590.718
70_A73_F0.229230.716
284_I287_D0.229040.716
143_Q147_L0.228640.715
48_L150_K0.227560.711
41_L44_A0.227270.710
37_Y41_L0.226850.709
272_D275_F0.226810.709
95_A98_Q0.225920.706
133_A137_A0.225770.706
206_D209_I0.225430.705
255_I259_D0.22530.704
172_R195_V0.225110.704
138_Q141_Q0.22490.703
270_P273_I0.224560.702
75_A80_E0.224180.701
81_K114_L0.223920.700
252_L255_I0.223420.698
11_I194_Y0.223120.697
14_E191_V0.222750.696
88_R111_R0.221690.693
200_P203_S0.221480.692
92_Q107_L0.220720.690
279_G282_V0.218960.684
37_Y40_D0.218840.684
52_Q146_G0.217840.681
20_G249_S0.2170.678
207_T210_A0.21690.678
59_R63_E0.216020.675
76_A80_E0.214730.671
160_L163_T0.214670.671
91_Q98_Q0.21440.670
264_V279_G0.214240.670
3_I203_S0.214010.669
254_E258_V0.213570.668
251_I255_I0.213040.666
11_I33_D0.2130.666
171_I174_P0.212790.665
35_T38_E0.212160.663
114_L117_Q0.211750.662
69_Q72_V0.211020.660
6_S30_A0.210990.659
121_L128_L0.210530.658
148_A152_R0.21040.658
253_M257_P0.21030.657
65_L72_V0.210.656
135_L139_L0.209330.654
48_L51_A0.20920.654
175_A204_V0.209140.654
222_R236_V0.208380.651
83_E118_Q0.207840.650
233_S242_H0.207430.648
187_R202_L0.206950.647
136_Q140_A0.206350.645
189_V193_E0.206230.645
255_I258_V0.20580.643
71_L74_P0.204960.641
6_S171_I0.204770.640
117_Q121_L0.204670.640
267_R279_G0.204640.640
17_V128_L0.204460.639
133_A136_Q0.204260.638
72_V83_E0.203810.637
35_T158_R0.203410.636
256_V260_S0.202610.633
226_P248_V0.201890.631
110_A114_L0.201740.631
73_F77_A0.201640.630
42_A46_A0.201430.630
50_A145_Q0.201370.629
131_Q135_L0.20110.629
123_S127_S0.200670.627
9_G194_Y0.200660.627
91_Q106_Q0.20040.626
65_L83_E0.200330.626
192_G195_V0.199730.624
34_P37_Y0.199680.624
122_K126_G0.19950.624
16_L19_E0.198480.620
46_A53_A0.198210.620
68_A72_V0.197810.618
108_E112_A0.197580.618
45_E111_R0.197420.617
251_I254_E0.197370.617
282_V286_L0.197120.616
70_A76_A0.197110.616
34_P163_T0.196970.616
234_G243_T0.196750.615
72_V121_L0.196550.614
235_D238_P0.196520.614
92_Q95_A0.19620.613
156_A163_T0.196020.613
39_A158_R0.195650.612
176_D208_E0.195280.610
69_Q83_E0.193880.606
44_A156_A0.193550.605
160_L164_E0.193480.605
171_I177_G0.192950.603
149_A153_L0.192920.603
114_L121_L0.192130.601
158_R161_A0.191540.599
41_L48_L0.191350.598
260_S263_P0.191150.597
48_L107_L0.190610.596
177_G180_V0.190330.595
188_S203_S0.190260.595
150_K153_L0.189830.593
130_Q133_A0.189640.593
62_A94_L0.189450.592
53_A56_K0.188880.590
241_V275_F0.188570.589
28_V118_Q0.187680.587
19_E182_Q0.18690.584
244_E287_D0.186730.584
105_A108_E0.186690.584
146_G149_A0.186660.583
124_A128_L0.186440.583
152_R156_A0.186430.583
220_Q224_V0.186410.583
102_A110_A0.186190.582
149_A152_R0.185720.581
13_T35_T0.185460.580
269_S272_D0.185320.579
252_L256_V0.18530.579
41_L156_A0.185210.579
261_L264_V0.184730.577
32_L37_Y0.184360.576
245_G248_V0.18410.575
230_A233_S0.183730.574
74_P77_A0.183520.574
16_L30_A0.182660.571
268_V280_Q0.182470.570
107_L114_L0.182460.570
127_S131_Q0.182430.570
47_E152_R0.181840.568
42_A154_D0.181520.567
22_R127_S0.181340.567
232_V286_L0.181230.566
174_P224_V0.180110.563
264_V268_V0.179940.562
256_V261_L0.179850.562
126_G130_Q0.179680.562
57_Q60_L0.178080.557
81_K98_Q0.177830.556
69_Q87_Q0.176810.553
51_A149_A0.176790.553
105_A112_A0.176480.552
138_Q142_L0.176440.551
193_E196_S0.176350.551
80_E89_E0.175440.548
22_R176_D0.175330.548
68_A74_P0.175280.548
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
3fppA0.8231000.33
4dk0A0.8231000.336
2f1mA0.780399.90.358
4l8jA0.731199.90.379
1vf7A0.734499.90.384
3lnnA0.786999.90.386
3ne5B0.698499.90.443
2k32A0.37799.50.632
1z6hA0.236198.60.759
1dczA0.229598.40.774

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