GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HrpB_C - ATP-dependent helicase C-terminal
Pfam: PF08482 (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. )
Length: 133
Sequences: 600
Seq/Len: 4.51
HH_delta: 0.94 (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
117_R131_E0.56153.696
99_I120_M0.53143.498
29_S32_Q0.464683.059
54_I87_L0.46413.055
117_R121_R0.452172.976
67_R128_P0.433932.856
46_L66_V0.367922.422
68_L113_Y0.349372.300
71_L74_L0.343192.259
19_D22_E0.342442.254
107_S111_G0.325762.144
66_V71_L0.308172.028
121_R131_E0.29271.927
65_S90_E0.267411.760
25_R33_Q0.258881.704
44_I87_L0.253471.668
72_F128_P0.2481.632
43_H51_R0.24481.611
100_Q112_S0.243431.602
46_L52_I0.242351.595
114_P117_R0.239191.574
35_W38_R0.236551.557
46_L50_R0.234531.544
66_V70_E0.234351.543
44_I54_I0.233071.534
5_Y26_S0.231681.525
115_E118_K0.230171.515
54_I64_L0.228681.505
111_G114_P0.228241.502
42_E53_R0.227761.499
48_S70_E0.223051.468
18_L23_A0.221741.460
67_R96_G0.221731.459
63_V90_E0.22151.458
54_I62_P0.220461.451
55_D90_E0.216871.428
77_T106_A0.21081.388
76_E79_R0.208141.370
10_T14_D0.206771.361
46_L70_E0.205871.355
93_S120_M0.199371.312
1_W4_P0.197671.301
2_L6_L0.195971.290
67_R99_I0.194861.283
64_L89_L0.194851.283
21_L25_R0.194341.279
71_L89_L0.192391.266
29_S33_Q0.180281.187
107_S112_S0.174621.149
1_W93_S0.17181.131
100_Q103_Q0.170531.122
68_L72_F0.168651.110
68_L116_V0.162911.072
40_A81_A0.158541.044
25_R29_S0.158521.043
106_A110_Q0.158181.041
61_P103_Q0.157931.040
58_D61_P0.15671.031
45_T51_R0.156141.028
68_L128_P0.155791.025
127_H130_P0.15451.017
120_M125_P0.154121.014
46_L64_L0.153641.011
130_P133_P0.151670.998
90_E101_V0.150240.989
12_L17_K0.149770.986
118_K126_K0.146860.967
39_L82_G0.146380.964
62_P101_V0.145120.955
100_Q121_R0.142710.939
72_F116_V0.139960.921
112_S120_M0.139890.921
3_A58_D0.139690.919
28_L36_L0.137640.906
35_W39_L0.13720.903
38_R82_G0.136970.902
52_I64_L0.135020.889
79_R86_P0.134730.887
1_W95_A0.132640.873
39_L84_R0.131650.867
80_I103_Q0.130590.860
111_G120_M0.129850.855
39_L85_V0.129520.853
75_T110_Q0.129340.851
48_S96_G0.129320.851
50_R66_V0.129040.849
99_I112_S0.128890.848
31_E34_Q0.128040.843
50_R67_R0.127880.842
43_H53_R0.127050.836
9_V14_D0.125980.829
104_D107_S0.125970.829
15_L18_L0.12560.827
48_S88_T0.125130.824
74_L99_I0.123770.815
9_V18_L0.123670.814
14_D17_K0.12360.814
5_Y9_V0.123340.812
129_W133_P0.123070.810
31_E38_R0.122830.809
3_A7_S0.122760.808
80_I83_G0.121180.798
117_R128_P0.120010.790
96_G128_P0.119890.789
101_V107_S0.119860.789
115_E119_E0.119780.788
72_F126_K0.119510.787
29_S118_K0.119490.787
47_P74_L0.11940.786
65_S92_L0.118450.780
88_T103_Q0.11820.778
44_I77_T0.117930.776
99_I111_G0.116990.770
128_P132_D0.116990.770
40_A62_P0.115380.759
81_A85_V0.114790.756
52_I92_L0.111680.735
101_V113_Y0.110990.731
25_R37_D0.110340.726
99_I119_E0.109840.723
23_A27_L0.109310.720
34_Q118_K0.109170.719
76_E106_A0.10780.710
71_L112_S0.107180.705
40_A119_E0.104570.688
55_D59_D0.104270.686
71_L100_Q0.102810.677
51_R84_R0.102610.675
88_T119_E0.102450.674
69_Q72_F0.102110.672
48_S90_E0.10140.667
73_G78_P0.101390.667
31_E126_K0.10090.664
48_S52_I0.100880.664
30_W34_Q0.100530.662
70_E119_E0.099790.657
17_K21_L0.099660.656
127_H131_E0.099150.653
27_L35_W0.098730.650
21_L37_D0.098510.648
119_E123_R0.098070.646
127_H133_P0.097720.643
45_T87_L0.097710.643
33_Q37_D0.097330.641
45_T53_R0.096640.636
124_Y127_H0.096250.634
39_L79_R0.096240.633
29_S39_L0.096220.633
3_A6_L0.0960.632
50_R113_Y0.095860.631
95_A122_G0.095840.631
28_L35_W0.095380.628
16_K22_E0.095190.627
13_K31_E0.094790.624
88_T96_G0.094740.624
35_W55_D0.094550.622
114_P119_E0.094310.621
27_L74_L0.094280.621
28_L32_Q0.094230.620
23_A26_S0.093790.617
98_P101_V0.09320.613
34_Q38_R0.093110.613
50_R70_E0.093050.612
62_P88_T0.09260.610
20_L57_S0.092490.609
32_Q39_L0.091950.605
5_Y86_P0.091740.604
96_G122_G0.091590.603
40_A99_I0.091510.602
68_L99_I0.09120.600
9_V12_L0.090890.598
115_E123_R0.090620.596
35_W114_P0.090330.595
99_I114_P0.090150.593
120_M128_P0.090120.593
46_L90_E0.089580.590
57_S90_E0.089580.590
22_E26_S0.089480.589
14_D22_E0.089360.588
5_Y53_R0.089060.586
48_S112_S0.089010.586
2_L30_W0.088540.583
31_E39_L0.088330.581
68_L117_R0.08830.581
37_D42_E0.088240.581
21_L51_R0.088040.580
46_L92_L0.088040.580
40_A68_L0.088030.579
13_K81_A0.087910.579
2_L92_L0.087770.578
73_G130_P0.087680.577
28_L34_Q0.087410.575
74_L77_T0.086870.572
100_Q111_G0.086820.571
100_Q107_S0.086790.571
29_S38_R0.086730.571
70_E92_L0.086570.570
14_D57_S0.08630.568
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
4aefA0.466264.60.94
4bhxA0.428625.70.952
3lhrA0.428624.10.953
2jd3A0.481222.50.954
1vbwA0.496219.90.955
1mitA0.503818.20.955
2hqtA0.360916.10.956
4fddA0.443613.90.957
4aeeA0.473713.30.958
1dwmA0.511311.20.959
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