GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Terminase_5 - Putative ATPase subunit of terminase (gpP-like)
Pfam: PF06056 (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: 58
Sequences: 20472
Seq/Len: 352.97
HH_delta: 0.117 (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
10_Y34_K2.736342.316
22_E51_A2.579882.184
17_K27_R2.471162.092
18_E22_E2.191611.855
29_T33_W2.074291.756
16_I31_Y1.934651.638
32_S37_Y1.932661.636
17_K21_E1.906241.614
14_W22_E1.90011.608
27_R31_Y1.885711.596
9_L12_Q1.836491.555
14_W18_E1.828871.548
33_W44_P1.624011.375
31_Y35_D1.587321.344
15_S18_E1.568911.328
14_W51_A1.509831.278
19_I30_V1.499851.270
28_S31_Y1.496461.267
5_Q8_S1.47231.246
25_V44_P1.410711.194
20_A30_V1.391761.178
49_E54_R1.367861.158
25_V29_T1.339871.134
44_P47_R1.335751.131
5_Q9_L1.317751.115
46_E50_E1.277741.082
29_T32_S1.242541.052
7_R11_L1.194511.011
40_D44_P1.154230.977
45_I49_E1.151320.975
39_W43_L1.13150.958
9_L54_R1.123940.951
10_Y19_I1.106420.937
42_L45_I1.105850.936
33_W40_D1.104190.935
32_S38_K1.103630.934
41_E44_P1.103080.934
12_Q53_E1.093940.926
19_I52_I1.089890.923
18_E21_E1.068590.905
20_A27_R1.063760.900
23_L51_A1.048250.887
16_I27_R1.043480.883
26_P29_T1.018690.862
25_V30_V1.001820.848
16_I34_K0.987730.836
14_W19_I0.975930.826
7_R16_I0.89660.759
12_Q52_I0.868590.735
6_A30_V0.860440.728
9_L52_I0.850130.720
48_V52_I0.843330.714
28_S32_S0.839570.711
9_L23_L0.808090.684
7_R10_Y0.77630.657
29_T38_K0.77290.654
42_L46_E0.751670.636
47_R51_A0.735360.622
19_I51_A0.731710.619
25_V47_R0.726920.615
8_S11_L0.726450.615
6_A10_Y0.726440.615
20_A23_L0.682030.577
46_E49_E0.681090.577
19_I48_V0.676280.572
33_W41_E0.673150.570
19_I23_L0.657560.557
29_T44_P0.652810.553
39_W42_L0.641990.543
25_V33_W0.616860.522
32_S36_R0.610470.517
11_L34_K0.61030.517
43_L47_R0.604330.512
49_E53_E0.599320.507
30_V34_K0.58940.499
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
4ichA197.80.117
3op9A197.70.139
3ivpA197.70.144
3mlfA197.70.145
1y9qA197.70.145
2bnmA197.70.148
2jvlA197.70.152
2kpjA197.70.158
3kz3A197.70.158
3kxaA197.60.164

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