GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NIR_SIR - Nitrite and sulphite reductase 4Fe-4S domain
Pfam: PF01077 (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: 157
Sequences: 3693
Seq/Len: 23.52
HH_delta: 0.199 (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
131_E139_R1.179364.171
106_P109_E0.798792.825
144_K147_E0.74822.646
29_R33_D0.645682.283
30_E107_E0.6392.260
94_R97_R0.609332.155
144_K148_E0.608672.152
94_R138_E0.57762.043
80_G104_F0.574032.030
67_I114_I0.564171.995
11_C59_C0.559571.979
82_D98_E0.554761.962
26_P30_E0.539681.908
11_C55_C0.525291.858
120_Y126_E0.524941.856
140_L144_K0.520441.840
27_L107_E0.508091.797
24_T54_G0.506061.790
8_V28_A0.499581.767
69_F114_I0.499331.766
55_C59_C0.492891.743
31_L52_I0.482971.708
58_S62_P0.475131.680
10_A28_A0.472711.672
38_R115_E0.467351.653
69_F110_V0.455481.611
48_F118_L0.438511.551
143_E146_R0.436791.545
27_L52_I0.42821.514
63_Q84_Y0.421631.491
14_S25_K0.415251.468
51_A65_N0.408151.443
84_Y98_E0.404081.429
67_I117_I0.403121.426
50_I67_I0.392471.388
83_V113_V0.389611.378
17_C55_C0.389151.376
81_F107_E0.388741.375
115_E119_E0.388211.373
105_V113_V0.383351.356
136_F140_L0.378151.337
27_L81_F0.358661.268
109_E112_E0.354321.253
69_F83_V0.354141.252
142_F146_R0.3511.241
84_Y96_G0.347571.229
117_I133_F0.345741.223
51_A60_A0.341261.207
117_I145_F0.3391.199
143_E147_E0.334771.184
53_S60_A0.334171.182
8_V31_L0.3341.181
62_P70_I0.33121.171
52_I69_F0.327031.156
72_V82_D0.322871.142
69_F81_F0.322231.140
145_F149_V0.322181.139
47_K132_R0.31041.098
100_A113_V0.304261.076
70_I84_Y0.286761.014
85_V99_L0.286381.013
11_C54_G0.28541.009
12_P15_G0.283811.004
48_F67_I0.281460.995
30_E33_D0.280680.993
22_I52_I0.276480.978
13_G17_C0.275060.973
88_G93_P0.27480.972
72_V104_F0.27450.971
28_A52_I0.273440.967
22_I107_E0.271720.961
42_P119_E0.270730.957
85_V137_I0.270560.957
26_P29_R0.268060.948
83_V105_V0.266910.944
15_G25_K0.265310.938
137_I145_F0.263250.931
100_A105_V0.262710.929
140_L145_F0.261810.926
70_I82_D0.26120.924
6_R132_R0.260190.920
6_R47_K0.25360.897
17_C54_G0.250850.887
31_L114_I0.249280.882
49_K88_G0.248430.879
68_G96_G0.247310.875
53_S58_S0.246750.873
97_R138_E0.24660.872
120_Y144_K0.24350.861
53_S62_P0.242330.857
17_C59_C0.241340.853
86_G137_I0.240960.852
81_F110_V0.239870.848
15_G23_D0.236790.837
30_E111_L0.236340.836
49_K66_D0.23410.828
137_I142_F0.233640.826
6_R66_D0.233340.825
11_C17_C0.232960.824
141_G144_K0.232920.824
120_Y149_V0.232850.823
120_Y136_F0.231610.819
88_G134_K0.231390.818
41_D115_E0.230690.816
132_R135_D0.230580.815
93_P96_G0.228970.810
133_F136_F0.227910.806
119_E125_R0.2270.803
4_T44_L0.22620.800
22_I27_L0.225560.798
44_L122_R0.225470.797
116_A120_Y0.224820.795
27_L69_F0.224780.795
88_G138_E0.224710.795
27_L110_V0.224120.793
23_D26_P0.224060.792
127_A130_K0.221020.782
133_F145_F0.220170.779
92_H135_D0.218720.773
33_D36_E0.218030.771
120_Y140_L0.215730.763
38_R41_D0.214310.758
127_A131_E0.213710.756
71_G81_F0.213140.754
14_S20_A0.212720.752
64_I89_L0.212610.752
22_I81_F0.212150.750
60_A65_N0.212050.750
98_E103_G0.207270.733
58_S63_Q0.207160.733
122_R125_R0.206920.732
16_F24_T0.206030.729
99_L113_V0.205470.727
107_E111_L0.204480.723
15_G26_P0.204280.722
119_E122_R0.204190.722
22_I71_G0.203110.718
114_I118_L0.2010.711
21_L104_F0.198460.702
120_Y148_E0.196720.696
90_G132_R0.196480.695
31_L50_I0.196180.694
97_R142_F0.196040.693
82_D104_F0.19540.691
74_K106_P0.194930.689
130_K139_R0.194390.687
38_R118_L0.193940.686
32_E40_E0.191760.678
116_A149_V0.191180.676
20_A24_T0.190270.673
33_D75_P0.190150.672
68_G87_G0.190130.672
57_N71_G0.189970.672
28_A48_F0.189320.670
49_K89_L0.189230.669
74_K104_F0.189070.669
10_A25_K0.18890.668
62_P68_G0.187620.663
42_P118_L0.185870.657
37_E43_N0.185430.656
46_R121_Y0.1850.654
74_K80_G0.184590.653
110_V114_I0.184570.653
56_P71_G0.184470.652
13_G59_C0.183090.647
54_G59_C0.181010.640
24_T52_I0.180680.639
118_L121_Y0.179240.634
144_K149_V0.177770.629
90_G93_P0.177740.629
50_I114_I0.177590.628
140_L143_E0.177550.628
64_I95_L0.177310.627
31_L111_L0.175340.620
32_E36_E0.174210.616
37_E40_E0.174170.616
92_H138_E0.173710.614
68_G90_G0.17190.608
67_I85_V0.171510.607
49_K93_P0.169920.601
84_Y95_L0.167760.593
126_E148_E0.167110.591
13_G55_C0.166130.587
140_L148_E0.166040.587
83_V114_I0.166020.587
63_Q95_L0.165470.585
126_E136_F0.165360.585
31_L110_V0.165290.585
30_E119_E0.165190.584
21_L72_V0.163760.579
53_S70_I0.163280.577
7_N46_R0.163250.577
126_E140_L0.162540.575
99_L142_F0.162160.573
5_V36_E0.161970.573
21_L71_G0.161870.572
108_E112_E0.161160.570
80_G90_G0.160730.568
47_K88_G0.159960.566
49_K132_R0.159710.565
9_T12_P0.159180.563
13_G20_A0.158770.561
44_L118_L0.158230.560
14_S23_D0.156440.553
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
2akjA0.98091000.199
3b0gA0.96821000.201
1zj8A0.96181000.204
3mm5A0.97451000.213
3or1A0.97451000.216
3or1B0.97451000.219
1aopA0.97451000.22
1zj8A0.90451000.223
4g38A0.97451000.229
1aopA0.92991000.241

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