GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_NifH - 4Fe-4S iron sulfur cluster binding proteins NifHfrxC family
Pfam: PF00142 (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: CL0023
Length: 273
Sequences: 10019
Seq/Len: 36.7
HH_delta: 0.177 (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
17_A121_L1.512634.580
210_P237_E1.35764.110
82_L117_Y1.348144.082
16_T238_Y1.185043.588
27_M243_R1.183293.582
24_L119_F1.102713.338
224_T227_E1.073253.249
29_K119_F0.948392.871
26_E239_R0.921322.789
32_L117_Y0.856282.592
17_A33_Q0.808162.447
195_E199_E0.789722.391
181_I241_L0.698052.113
30_K118_D0.689912.089
214_I217_R0.686022.077
21_S33_Q0.681762.064
184_S211_R0.680872.061
16_T181_I0.676292.047
27_M239_R0.67052.030
23_A242_A0.644631.952
24_L121_L0.631721.913
21_S121_L0.60551.833
33_Q42_S0.595531.803
29_K118_D0.590711.788
243_R247_E0.581681.761
20_L245_I0.573931.738
71_E116_D0.564141.708
236_Q239_R0.554431.679
207_A241_L0.553351.675
27_M246_L0.539621.634
150_S184_S0.536821.625
144_E178_G0.536081.623
23_A226_I0.526351.594
29_K246_L0.52511.590
196_D199_E0.518881.571
207_A244_K0.518821.571
232_S235_A0.51331.554
76_E82_L0.508281.539
209_I234_Q0.499971.514
196_D200_R0.498271.509
182_C194_V0.484551.467
20_L242_A0.469411.421
54_T57_D0.468631.419
69_E72_D0.467951.417
212_S234_Q0.457561.385
21_S42_S0.457491.385
8_K11_I0.457121.384
217_R221_Y0.446971.353
195_E208_F0.444811.347
240_E243_R0.444371.345
146_Y181_I0.441491.337
25_A80_G0.432211.309
45_L154_M0.42791.295
223_K227_E0.427841.295
240_E244_K0.424851.286
212_S232_S0.420071.272
23_A239_R0.417651.264
12_G183_N0.41381.253
205_I208_F0.410181.242
229_A232_S0.408111.236
16_T148_V0.407721.234
111_G114_E0.406741.231
18_S42_S0.404061.223
215_V234_Q0.404021.223
16_T20_L0.398811.207
36_C122_Y0.395081.196
237_E240_E0.391291.185
231_D236_Q0.390961.184
125_L132_G0.390591.183
127_D132_G0.389761.180
69_E112_A0.386731.171
16_T183_N0.38541.167
241_L245_I0.383021.160
24_L31_V0.382871.159
197_F201_I0.382181.157
209_I237_E0.380951.153
191_E195_E0.379671.149
97_G100_I0.379531.149
233_E236_Q0.379351.148
44_R157_Y0.379171.148
214_I229_A0.378781.147
194_V198_A0.378151.145
18_S43_T0.377461.143
152_E155_S0.373281.130
230_P235_A0.369651.119
236_Q240_E0.368821.117
117_Y120_V0.365521.107
163_C200_R0.364831.105
223_K228_A0.364071.102
72_D75_K0.363481.100
19_N22_A0.361951.096
31_V118_D0.360851.092
32_L74_V0.360791.092
14_S42_S0.359241.088
148_V183_N0.358881.087
149_T180_I0.357451.082
8_K13_K0.355711.077
30_K116_D0.355091.075
146_Y206_I0.355081.075
119_F246_L0.354741.074
15_T215_V0.354081.072
21_S81_I0.352931.069
183_N238_Y0.35261.068
74_V82_L0.352361.067
144_E176_R0.350031.060
192_E195_E0.348461.055
105_E108_E0.34681.050
25_A81_I0.345931.047
22_A26_E0.345321.045
152_E216_Q0.344161.042
114_E143_Q0.341891.035
23_A27_M0.340921.032
239_R243_R0.340921.032
96_A99_G0.340761.032
189_D192_E0.338251.024
32_L120_V0.337341.021
19_N226_I0.33581.017
31_V119_F0.332821.008
36_C55_V0.330641.001
41_D158_A0.330341.000
179_G206_I0.329370.997
83_C88_G0.327460.991
213_E217_R0.326540.989
97_G101_I0.325990.987
78_F227_E0.325510.985
46_L81_I0.324360.982
13_K37_D0.318870.965
70_L84_V0.317990.963
161_N164_K0.316140.957
55_V58_L0.312680.947
150_S155_S0.312590.946
23_A238_Y0.312120.945
185_R208_F0.311820.944
15_T219_E0.310960.941
151_G182_C0.310760.941
144_E179_G0.309580.937
34_I120_V0.307420.931
167_K170_A0.306980.929
154_M219_E0.305240.924
192_E196_D0.302140.915
22_A226_I0.30110.912
41_D44_R0.300340.909
164_K167_K0.299090.906
18_S45_L0.297610.901
58_L73_V0.291380.882
149_T194_V0.291370.882
16_T209_I0.290410.879
126_G132_G0.289820.877
204_P244_K0.289680.877
24_L242_A0.28930.876
18_S47_L0.289290.876
9_G35_G0.28870.874
19_N238_Y0.286920.869
105_E109_E0.286880.869
99_G103_A0.28680.868
30_K117_Y0.286350.867
34_I122_Y0.286040.866
234_Q237_E0.283370.858
53_P57_D0.282790.856
186_N211_R0.282580.856
121_L245_I0.280620.850
233_E237_E0.280480.849
82_L85_E0.280090.848
221_Y228_A0.27980.847
182_C197_F0.279390.846
49_G83_C0.279110.845
195_E198_A0.279030.845
215_V219_E0.278110.842
26_E227_E0.275880.835
165_A169_F0.275110.833
212_S233_E0.274470.831
206_I244_K0.273660.829
27_M242_A0.271720.823
22_A224_T0.271690.823
20_L24_L0.27110.821
22_A227_E0.270810.820
14_S46_L0.270150.818
92_G97_G0.267650.810
32_L113_Y0.266980.808
20_L241_L0.265660.804
180_I203_T0.263410.797
26_E226_I0.263250.797
102_T105_E0.263090.797
7_G39_K0.262940.796
18_S33_Q0.26250.795
160_N164_K0.262240.794
85_E88_G0.261460.792
9_G123_D0.25920.785
125_L134_A0.25710.778
145_V166_I0.256610.777
24_L246_L0.256550.777
19_N224_T0.255220.773
213_E216_Q0.254950.772
96_A103_A0.253920.769
39_K126_G0.253440.767
173_G176_R0.252470.764
8_K123_D0.25080.759
182_C205_I0.250650.759
41_D154_M0.250460.758
104_L110_L0.250040.757
149_T162_I0.248750.753
98_R102_T0.244940.742
40_A43_T0.244920.742
28_G31_V0.244820.741
193_I196_D0.243860.738
197_F205_I0.24210.733
101_I104_L0.241830.732
86_S90_E0.241210.730
225_V235_A0.240840.729
188_D191_E0.239450.725
77_G80_G0.239410.725
226_I239_R0.23910.724
99_G102_T0.238260.721
97_G102_T0.237110.718
187_V190_E0.235080.712
230_P239_R0.235050.712
96_A102_T0.234420.710
9_G37_D0.23410.709
71_E74_V0.234090.709
13_K126_G0.23320.706
142_A176_R0.232360.703
26_E230_P0.232090.703
96_A100_I0.23140.701
38_P42_S0.231040.699
22_A81_I0.230630.698
30_K82_L0.229180.694
217_R228_A0.229040.693
9_G13_K0.227730.689
23_A26_E0.227680.689
17_A21_S0.226770.687
100_I103_A0.226650.686
23_A235_A0.224740.680
190_E194_V0.224540.680
56_L60_R0.224440.680
225_V228_A0.22440.679
10_G35_G0.224370.679
182_C185_R0.224190.679
242_A246_L0.224080.678
91_P96_A0.223390.676
16_T241_L0.22210.672
89_P92_G0.22060.668
7_G125_L0.220230.667
244_K247_E0.220180.667
188_D192_E0.219020.663
199_E202_G0.218390.661
218_A228_A0.217890.660
164_K168_N0.216970.657
113_Y116_D0.216770.656
119_F242_A0.216540.656
125_L133_F0.216140.654
152_E211_R0.21590.654
85_E89_P0.214780.650
226_I235_A0.214550.650
42_S158_A0.214290.649
13_K124_V0.213960.648
211_R216_Q0.213150.645
71_E112_A0.212360.643
179_G204_P0.212150.642
75_K85_E0.211160.639
99_G104_L0.210360.637
96_A104_L0.209850.635
88_G91_P0.208740.632
91_P99_G0.208590.632
86_S89_P0.207780.629
91_P100_I0.207740.629
97_G104_L0.206910.626
17_A42_S0.206330.625
92_G96_A0.205530.622
28_G80_G0.204910.620
31_V81_I0.204580.619
189_D193_I0.204470.619
243_R246_L0.204390.619
163_C167_K0.204050.618
126_G133_F0.203570.616
156_L220_L0.203520.616
187_V191_E0.201380.610
97_G103_A0.2010.609
36_C128_V0.199560.604
191_E198_A0.199510.604
106_L109_E0.19930.603
18_S154_M0.198560.601
58_L84_V0.197980.599
175_A179_G0.197830.599
153_F220_L0.197030.597
241_L244_K0.196410.595
33_Q121_L0.195430.592
74_V113_Y0.195140.591
33_Q81_I0.194680.589
33_Q83_C0.194220.588
155_S159_A0.194140.588
103_A107_L0.193920.587
104_L109_E0.193820.587
158_A161_N0.193740.587
34_I110_L0.193330.585
55_V84_V0.193170.585
45_L157_Y0.193030.584
127_D134_A0.192720.583
191_E194_V0.19220.582
196_D201_I0.190770.578
38_P41_D0.190670.577
39_K42_S0.190160.576
146_Y245_I0.189480.574
179_G205_I0.189430.574
18_S46_L0.189280.573
153_F157_Y0.188120.570
98_R104_L0.187930.569
8_K37_D0.187510.568
57_D62_K0.187370.567
198_A201_I0.187360.567
212_S215_V0.18690.566
225_V234_Q0.186860.566
151_G185_R0.186170.564
218_A224_T0.185890.563
215_V225_V0.185810.563
33_Q36_C0.185740.562
15_T154_M0.184630.559
6_Y158_A0.184550.559
19_N23_A0.184390.558
69_E74_V0.184260.558
7_G126_G0.184210.558
198_A204_P0.18420.558
235_A239_R0.184080.557
109_E112_A0.1840.557
78_F224_T0.183730.556
209_I241_L0.18280.553
148_V151_G0.182390.552
151_G190_E0.182220.552
216_Q220_L0.181940.551
98_R101_I0.181910.551
43_T46_L0.181850.551
114_E120_V0.181840.551
170_A176_R0.181410.549
182_C208_F0.181140.548
197_F200_R0.180910.548
198_A208_F0.180720.547
70_L113_Y0.180680.547
161_N165_A0.180660.547
18_S83_C0.179750.544
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
2afhE11000.177
1cp2A0.98171000.199
3fwyA0.95971000.232
2ynmA0.95971000.25
3endA0.95971000.263
1hyqA0.93771000.337
3ea0A0.86811000.342
3q9lA0.89381000.35
1g3qA0.84981000.357
1wcv10.88281000.361

Page generated in 0.0412 seconds.