GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PSCyt1 - Planctomycete cytochrome C
Pfam: PF07635 (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: CL0318
Length: 59
Sequences: 833
Seq/Len: 14.12
HH_delta: 0.711 (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
36_D39_E0.960694.864
41_L44_Q0.529432.680
41_L45_R0.402812.039
19_R23_L0.385541.952
18_S21_S0.384411.946
48_S54_R0.355551.800
43_W47_T0.353721.791
6_G10_Q0.34291.736
45_R48_S0.304531.542
22_L32_I0.286431.450
25_G29_G0.281431.425
2_F17_D0.277681.406
13_G27_D0.245491.243
27_D30_P0.241511.223
48_S51_D0.240271.216
48_S53_G0.240071.215
37_P43_W0.23821.206
3_S9_K0.234791.189
25_G31_A0.223081.129
26_G29_G0.22211.124
11_K58_K0.216981.099
6_G17_D0.216361.095
3_S45_R0.213461.081
6_G9_K0.212541.076
36_D40_S0.205961.043
33_V39_E0.205331.040
2_F6_G0.199871.012
49_Q53_G0.198671.006
28_S31_A0.194440.984
2_F10_Q0.191250.968
16_L22_L0.191130.968
37_P40_S0.19020.963
7_P15_R0.190090.962
2_F19_R0.188170.953
7_P10_Q0.18730.948
12_G15_R0.18010.912
18_S22_L0.178560.904
32_I35_G0.176570.894
3_S48_S0.176320.893
16_L45_R0.17450.883
27_D52_D0.170110.861
50_D53_G0.168580.853
30_P33_V0.166790.844
11_K24_K0.164980.835
23_L32_I0.163530.828
7_P21_S0.15770.798
7_P22_L0.154820.784
23_L26_G0.149550.757
8_D21_S0.148780.753
14_L45_R0.147410.746
15_R23_L0.146050.739
30_P57_P0.14530.736
11_K17_D0.145060.734
16_L51_D0.143560.727
8_D32_I0.141250.715
15_R18_S0.141190.715
16_L42_L0.1410.714
47_T50_D0.139810.708
14_L29_G0.139590.707
20_E24_K0.139430.706
49_Q52_D0.139180.705
2_F8_D0.138170.700
12_G28_S0.138070.699
6_G31_A0.13690.693
12_G58_K0.136470.691
29_G42_L0.135320.685
31_A41_L0.133750.677
14_L42_L0.133230.675
2_F16_L0.133230.675
50_D54_R0.133010.673
19_R34_P0.132650.672
22_L41_L0.131550.666
24_K28_S0.131320.665
18_S23_L0.130720.662
14_L40_S0.130530.661
10_Q30_P0.129630.656
35_G40_S0.128820.652
40_S52_D0.128730.652
3_S43_W0.126870.642
13_G45_R0.126770.642
2_F32_I0.126210.639
25_G30_P0.126030.638
27_D48_S0.126010.638
14_L21_S0.125430.635
2_F18_S0.12490.632
17_D21_S0.123930.627
1_C4_C0.12360.626
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
1qksA0.745892.60.711
1nirA0.745892.10.715
2d0sA0.813690.30.727
1a56A0.830588.80.735
2exvA0.847587.80.739
1ls9A0.796687.70.74
1cyiA0.796687.40.742
1c6rA0.796686.70.744
3dmiA0.864485.90.746
1yiqA0.779785.80.747
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0492 seconds.