GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sigma70_r4 - Sigma-70 region 4
Pfam: PF04545 (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: CL0123
Length: 50
Sequences: 52994
Seq/Len: 1059.88
HH_delta: -0.084 (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
35_S38_R3.254952.027
21_L29_R3.046481.897
23_L38_R2.935451.828
8_R40_I2.907481.810
15_L29_R2.730551.700
24_E34_R2.7191.693
23_L41_L2.59781.617
34_R38_R2.553921.590
21_L25_E2.468441.537
6_P9_E2.38931.488
15_L21_L2.364361.472
22_T25_E2.244861.398
9_E40_I2.145621.336
16_R41_L2.128141.325
16_R26_I2.067221.287
39_R43_R1.977521.231
35_S39_R1.909421.189
36_T40_I1.852811.154
27_A37_V1.751971.091
35_S42_K1.747881.088
36_T39_R1.643561.023
32_I40_I1.635091.018
9_E43_R1.622811.010
23_L34_R1.596510.994
24_E28_E1.596260.994
32_I37_V1.585690.987
39_R42_K1.562880.973
17_Y45_L1.561670.972
8_R11_E1.546050.963
41_L45_L1.51310.942
33_S36_T1.482440.923
12_V44_A1.447480.901
11_E15_L1.423070.886
10_R14_R1.390070.866
23_L37_V1.386680.863
27_A34_R1.384940.862
42_K46_K1.366960.851
8_R32_I1.343350.836
13_I17_Y1.329020.828
32_I36_T1.324390.825
38_R42_K1.309720.815
7_P11_E1.245950.776
16_R44_A1.236110.770
12_V40_I1.233640.768
25_E29_R1.138920.709
16_R23_L1.126090.701
11_E30_L1.094150.681
24_E38_R1.083060.674
26_I37_V1.072720.668
9_E44_A1.063290.662
28_E31_G1.040190.648
25_E28_E0.995580.620
5_L9_E0.991960.618
40_I43_R0.951560.592
5_L44_A0.950320.592
15_L19_E0.94120.586
15_L30_L0.919150.572
9_E12_V0.913420.569
15_L26_I0.893370.556
11_E14_R0.888430.553
43_R46_K0.884070.550
12_V30_L0.859520.535
6_P40_I0.814340.507
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
3vfzA197.8-0.084
4kn7X197.8-0.078
3vdoA197.8-0.077
2q1zA197.8-0.072
1or7A197.8-0.07
3iydF197.8-0.07
2lfwA197.8-0.067
1rp3A197.8-0.067
1l0oC0.9897.8-0.067
3hugA197.8-0.064

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