GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GreA_GreB_N - Transcription elongation factor N-terminal
Pfam: PF03449 (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: 74
Sequences: 1548
Seq/Len: 20.92
HH_delta: -0.017 (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
12_E16_A1.335043.261
8_P12_E1.144712.796
17_E61_R1.143062.792
20_H24_V1.061162.592
22_K66_E0.98822.414
25_E54_R0.983872.403
19_E23_N0.945782.310
20_H25_E0.923662.256
26_R59_E0.815691.992
67_E71_R0.775591.894
21_L58_L0.772151.886
57_F60_A0.743841.817
11_Y15_Q0.715031.747
29_I58_L0.699321.708
64_E68_R0.699031.707
18_L62_I0.697631.704
25_E28_E0.669561.636
39_Q47_E0.666231.627
12_E15_Q0.634751.550
11_Y74_V0.627541.533
15_Q19_E0.621.514
50_A53_E0.577981.412
16_A20_H0.565181.381
35_E38_E0.537111.312
11_Y69_L0.52611.285
28_E31_E0.511891.250
33_I55_Q0.511771.250
43_S49_H0.500261.222
9_E13_K0.483811.182
31_E34_A0.453131.107
37_R42_L0.421451.029
28_E32_E0.406020.992
7_T10_G0.401610.981
35_E39_Q0.396670.969
18_L22_K0.39370.962
61_R64_E0.38880.950
31_E35_E0.383280.936
32_E35_E0.379060.926
56_A60_A0.366860.896
49_H53_E0.357990.874
32_E54_R0.355960.869
29_I55_Q0.352510.861
54_R58_L0.32860.803
54_R57_F0.319970.782
6_L69_L0.314460.768
6_L72_A0.313460.766
25_E58_L0.305340.746
9_E12_E0.305330.746
18_L66_E0.304170.743
14_L65_L0.302520.739
6_L68_R0.30160.737
30_A34_A0.299760.732
5_Y73_E0.289860.708
46_A50_A0.286190.699
14_L18_L0.284750.696
6_L11_Y0.278840.681
13_K16_A0.278460.680
63_R67_E0.277320.677
8_P11_Y0.276930.676
15_Q69_L0.274040.669
43_S47_E0.271680.664
67_E70_A0.268920.657
11_Y65_L0.268870.657
46_A49_H0.268060.655
42_L45_N0.267120.652
52_K55_Q0.267010.652
44_E51_A0.266630.651
60_A64_E0.264950.647
5_Y67_E0.257830.630
29_I54_R0.256680.627
39_Q46_A0.255250.623
36_A44_E0.253940.620
35_E47_E0.253810.620
34_A38_E0.25230.616
5_Y64_E0.24670.603
31_E39_Q0.246160.601
43_S52_K0.244090.596
21_L25_E0.241660.590
29_I32_E0.241280.589
40_G45_N0.240080.586
66_E70_A0.237620.580
36_A45_N0.236720.578
19_E22_K0.236690.578
37_R56_A0.235420.575
46_A53_E0.23390.571
69_L72_A0.230080.562
48_Y52_K0.230020.562
16_A19_E0.22970.561
37_R50_A0.229030.559
5_Y71_R0.224590.549
23_N27_P0.224360.548
39_Q49_H0.223460.546
42_L55_Q0.221010.540
45_N48_Y0.220310.538
55_Q59_E0.219990.537
16_A24_V0.218620.534
44_E48_Y0.217860.532
53_E57_F0.216920.530
36_A42_L0.216820.530
33_I37_R0.215970.528
20_H28_E0.214990.525
29_I49_H0.214420.524
62_I66_E0.212560.519
37_R53_E0.210930.515
22_K62_I0.206480.504
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
2p4vA199.8-0.017
1grjA199.80.007
2f23A0.986599.60.108
3bmbA0.554196.30.696
2pn0A0.554192.30.757
1wleA0.986562.80.822
3qneA0.918956.20.829
2dq3A0.9189520.833
2dq0A0.918951.90.833
2k48A0.9865440.84

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