GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OppC_N - N-terminal TM domain of oligopeptide transport permease C
Pfam: PF12911 (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: 56
Sequences: 6513
Seq/Len: 116.3
HH_delta: 0.72 (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
47_D50_N1.473382.672
50_N53_Q1.115232.022
42_D45_Q1.101191.997
9_W13_R1.088121.973
16_K19_V1.062051.926
30_L34_F0.941541.707
48_L51_R0.938591.702
35_A38_I0.913891.657
53_Q56_S0.89031.614
34_F37_F0.87441.586
13_R19_V0.825371.497
15_N18_A0.793161.438
22_L26_L0.760421.379
23_I27_I0.750081.360
17_L21_G0.749461.359
26_L30_L0.730871.325
12_F15_N0.720291.306
35_A39_S0.712161.291
29_V33_I0.692141.255
24_I28_L0.682411.237
21_G24_I0.676721.227
12_F18_A0.636271.154
32_A35_A0.610861.108
13_R16_K0.600191.088
21_G25_L0.592671.075
12_F16_K0.559051.014
34_F38_I0.550870.999
18_A25_L0.539230.978
31_L35_A0.524870.952
16_K20_I0.512560.929
46_Q51_R0.511430.927
47_D51_R0.489180.887
20_I24_I0.484680.879
18_A22_L0.481940.874
23_I26_L0.48120.873
49_S53_Q0.480850.872
10_R13_R0.473230.858
41_Y45_Q0.45690.829
48_L52_N0.454750.825
45_Q49_S0.443630.804
44_N48_L0.435850.790
27_I31_L0.435390.790
15_N21_G0.434820.789
25_L29_V0.43190.783
11_R14_R0.428390.777
20_I23_I0.422890.767
12_F19_V0.422710.767
19_V23_I0.40790.740
49_S52_N0.394660.716
17_L20_I0.384630.697
41_Y56_S0.380370.690
28_L55_P0.365150.662
35_A40_P0.364420.661
40_P43_P0.360940.655
36_P39_S0.347360.630
41_Y46_Q0.345480.626
47_D52_N0.343680.623
10_R14_R0.339580.616
14_R18_A0.33750.612
18_A21_G0.332350.603
41_Y44_N0.33170.602
46_Q52_N0.331450.601
52_N55_P0.319650.580
9_W12_F0.314330.570
31_L38_I0.309640.561
15_N22_L0.30450.552
31_L39_S0.297910.540
24_I32_A0.285710.518
25_L32_A0.283870.515
31_L36_P0.281230.510
13_R17_L0.277580.503
12_F17_L0.274880.498
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:
PDB Cov Prob HH_delta
2kogA0.62516.40.72
3hd7B0.678610.50.741
2cvcA0.759.90.744
3hd7A0.6259.70.744
3kdpB0.96438.60.75
3s8fB0.98217.30.757
3rlfG0.89297.10.759
1z1nX0.80366.50.763
2wn4A0.80366.30.765
3vmtA0.94646.20.765
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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