GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TniB - Bacterial TniB protein
Pfam: PF05621 (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: CL0023
Length: 302
Sequences: 4474
Seq/Len: 14.81
HH_delta: 0.518 (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
278_T281_I0.516063.135
34_D83_R0.458192.784
245_R249_E0.41542.524
219_F240_S0.386732.349
140_L149_L0.377682.295
239_A242_E0.3732.266
55_Y266_A0.35442.153
215_L248_H0.342412.080
274_E281_I0.335812.040
175_L178_E0.313441.904
190_E193_R0.313121.902
35_R83_R0.31111.890
226_F259_S0.310951.889
157_L168_F0.309421.880
150_I186_V0.297811.809
174_F177_N0.297171.805
99_V149_L0.295351.794
78_I150_I0.294861.791
277_I282_L0.287661.748
242_E279_R0.286491.741
203_S256_G0.285121.732
223_L238_L0.278261.691
153_E204_R0.277361.685
125_R135_Q0.26671.620
142_R174_F0.258421.570
237_N262_L0.257231.563
220_R223_L0.250611.523
280_E283_D0.247471.503
240_S244_A0.244451.485
239_A276_R0.243061.477
233_R236_S0.239681.456
265_A269_A0.237261.441
129_R132_K0.236981.440
154_F185_G0.235611.431
99_V144_L0.235191.429
257_E260_R0.234541.425
265_A281_I0.232271.411
279_R283_D0.231521.407
66_I81_F0.230211.399
182_P186_V0.229581.395
241_P279_R0.228111.386
245_R279_R0.223081.355
78_I186_V0.221331.345
141_L179_L0.221021.343
230_L259_S0.21671.317
98_V150_I0.216541.316
276_R280_E0.216011.312
66_I210_L0.215821.311
38_G42_A0.21431.302
174_F178_E0.213731.298
173_K176_G0.211781.287
67_V209_E0.211641.286
239_A278_T0.211261.283
181_I185_G0.204161.240
98_V102_Q0.203761.238
77_I210_L0.201851.226
223_L258_L0.198581.206
103_M151_I0.197951.203
241_P244_A0.197831.202
238_L242_E0.197021.197
125_R128_D0.195461.187
60_R229_A0.195061.185
88_Q145_G0.194331.181
226_F229_A0.193691.177
39_Y42_A0.193521.176
272_S281_I0.192851.172
185_G188_T0.191761.165
253_G257_E0.191651.164
71_N256_G0.191481.163
246_R249_E0.191341.162
49_L81_F0.190561.158
126_P132_K0.188721.147
224_A228_R0.186431.133
124_Y128_D0.186311.132
140_L143_R0.185991.130
49_L77_I0.184711.122
71_N203_S0.184571.121
186_V190_E0.184571.121
177_N194_A0.18381.117
183_I186_V0.180361.096
268_A271_R0.180211.095
148_M184_V0.180021.094
110_R163_R0.178711.086
59_H62_P0.178521.085
53_L59_H0.178291.083
182_P190_E0.178081.082
265_A282_L0.177771.080
241_P245_R0.177541.079
247_I250_R0.177031.076
175_L194_A0.175671.067
154_F157_L0.174871.062
226_F255_I0.174611.061
237_N261_L0.174381.059
74_K152_D0.174371.059
202_A207_P0.172491.048
107_P110_R0.171931.045
101_V149_L0.171631.043
227_E234_K0.171631.043
140_L173_K0.171491.042
276_R279_R0.171291.041
49_L53_L0.17041.035
191_A194_A0.16911.027
67_V192_Y0.16881.026
279_R282_L0.168221.022
182_P185_G0.167921.020
247_I251_S0.167621.018
186_V189_R0.166731.013
67_V207_P0.166041.009
273_G280_E0.165331.004
47_D50_E0.164551.000
80_R83_R0.164330.998
146_V175_L0.163460.993
182_P188_T0.163330.992
153_E156_N0.162950.990
173_K177_N0.162480.987
243_L247_I0.162210.985
235_P276_R0.162060.985
101_V140_L0.161520.981
225_S230_L0.160620.976
75_T152_D0.15990.971
204_R256_G0.159730.970
251_S261_L0.159710.970
189_R194_A0.159680.970
155_H188_T0.158880.965
227_E237_N0.158350.962
224_A240_S0.158270.962
181_I188_T0.156860.953
227_E230_L0.156440.950
108_D111_R0.15570.946
242_E282_L0.155650.946
275_E280_E0.155620.945
240_S276_R0.155310.944
274_E278_T0.154080.936
163_R166_R0.153690.934
179_L188_T0.153460.932
219_F248_H0.153160.930
251_S254_L0.152350.926
244_A248_H0.152020.924
50_E54_E0.151980.923
181_I190_E0.151450.920
243_L249_E0.150840.916
75_T170_N0.150670.915
187_G191_A0.15010.912
69_D214_E0.148880.904
72_N76_M0.148810.904
238_L265_A0.14880.904
249_E279_R0.148620.903
68_G71_N0.148340.901
70_S155_H0.148290.901
247_I254_L0.148190.900
188_T193_R0.148190.900
63_N185_G0.148140.900
226_F258_L0.147490.896
141_L149_L0.146950.893
146_V173_K0.14690.892
268_A272_S0.14680.892
66_I78_I0.145990.887
269_A281_I0.145870.886
181_I189_R0.145860.886
65_L154_F0.145860.886
216_D220_R0.145830.886
179_L186_V0.145240.882
63_N205_F0.145160.882
253_G256_G0.144920.880
181_I186_V0.144760.879
155_H189_R0.144740.879
239_A243_L0.144480.878
146_V177_N0.144460.878
79_E100_Y0.144150.876
124_Y129_R0.144130.876
232_L235_P0.144030.875
34_D279_R0.143560.872
55_Y236_S0.142880.868
242_E245_R0.142870.868
106_E157_L0.142830.868
223_L243_L0.142440.865
188_T200_Q0.142220.864
216_D277_I0.1420.863
184_V199_P0.141870.862
50_E84_L0.141580.860
227_E232_L0.141530.860
244_A262_L0.141510.860
239_A280_E0.141030.857
245_R248_H0.140790.855
169_L173_K0.140720.855
273_G276_R0.14010.851
41_R142_R0.139350.847
75_T100_Y0.138750.843
146_V174_F0.138720.843
241_P280_E0.138370.841
107_P178_E0.137820.837
222_L225_S0.137650.836
59_H259_S0.137530.836
268_A273_G0.137270.834
249_E252_E0.136840.831
179_L193_R0.136060.827
54_E270_I0.136040.826
45_A50_E0.135580.824
266_A270_I0.135240.822
126_P131_A0.135010.820
156_N170_N0.134730.819
47_D267_I0.134030.814
35_R38_G0.133690.812
235_P278_T0.13360.812
274_E277_I0.133420.811
105_P108_D0.132330.804
220_R224_A0.13230.804
200_Q205_F0.132260.804
192_Y207_P0.131860.801
221_R225_S0.131350.798
222_L226_F0.131220.797
223_L244_A0.131210.797
261_L277_I0.130980.796
141_L171_A0.130960.796
100_Y149_L0.130930.795
131_A134_E0.130880.795
138_L142_R0.130660.794
53_L56_P0.130630.794
273_G278_T0.130030.790
100_Y205_F0.130010.790
275_E281_I0.130.790
70_S204_R0.129770.788
155_H200_Q0.129670.788
203_S254_L0.129520.787
127_R153_E0.129480.787
242_E246_R0.129380.786
185_G205_F0.129290.785
154_F169_L0.129230.785
256_G260_R0.128970.784
179_L184_V0.128950.783
85_H148_M0.128720.782
174_F194_A0.128680.782
179_L182_P0.128580.781
245_R283_D0.128290.779
184_V238_L0.128030.778
68_G74_K0.127670.776
35_R39_Y0.127560.775
79_E98_V0.127180.773
138_L143_R0.127050.772
237_N265_A0.127010.772
153_E256_G0.126970.771
104_P166_R0.126880.771
52_L64_L0.126580.769
138_L179_L0.126410.768
45_A48_R0.125980.765
235_P280_E0.12570.764
177_N275_E0.125530.763
79_E187_G0.125260.761
242_E251_S0.125240.761
246_R261_L0.125220.761
179_L185_G0.125220.761
36_W39_Y0.124930.759
126_P133_L0.12480.758
215_L249_E0.124590.757
243_L250_R0.124320.755
223_L279_R0.1240.753
157_L165_Q0.123260.749
251_S258_L0.123110.748
149_L267_I0.123020.747
46_L77_I0.122950.747
106_E112_F0.122740.746
48_R51_E0.122730.746
99_V140_L0.12260.745
271_R280_E0.122340.743
130_V133_L0.122150.742
239_A244_A0.122030.741
87_P180_Q0.121850.740
236_S269_A0.121830.740
276_R283_D0.121680.739
225_S255_I0.121650.739
149_L235_P0.12110.736
77_I139_R0.12090.735
113_Y164_K0.120830.734
144_L149_L0.120470.732
218_E258_L0.120250.731
188_T203_S0.120250.731
153_E188_T0.119960.729
63_N141_L0.119940.729
245_R250_R0.119440.726
108_D112_F0.119140.724
59_H136_Q0.118970.723
165_Q168_F0.118940.723
63_N154_F0.118930.723
176_G194_A0.118880.722
189_R192_Y0.118860.722
228_R232_L0.118860.722
146_V275_E0.118690.721
268_A274_E0.118580.720
82_R156_N0.118350.719
157_L166_R0.118120.718
219_F222_L0.118110.718
143_R275_E0.118050.717
78_I153_E0.118040.717
72_N153_E0.118020.717
182_P189_R0.117730.715
244_A249_E0.117250.712
243_L279_R0.117150.712
146_V176_G0.117090.711
66_I221_R0.1170.711
64_L81_F0.116520.708
105_P109_E0.116460.708
257_E261_L0.116140.706
81_F85_H0.116030.705
69_D212_R0.115620.702
205_F210_L0.115440.701
254_L258_L0.115270.700
271_R276_R0.115020.699
51_E217_E0.114720.697
98_V147_R0.11470.697
107_P174_F0.114530.696
238_L282_L0.114310.694
210_L213_W0.114170.694
210_L267_I0.114060.693
106_E110_R0.113580.690
227_E274_E0.113510.690
229_A259_S0.113430.689
36_W80_R0.11330.688
241_P276_R0.113240.688
139_R211_P0.113130.687
72_N210_L0.112950.686
183_I193_R0.112890.686
75_T153_E0.112880.686
139_R142_R0.112720.685
99_V106_E0.11260.684
146_V180_Q0.112240.682
237_N276_R0.11180.679
239_A249_E0.111780.679
218_E221_R0.111410.677
227_E262_L0.111370.677
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
2v1uA0.917299.90.518
1fnnA0.877599.90.531
2qbyA0.907399.90.534
3te6A0.887499.90.535
2qbyB0.900799.90.549
1w5sA0.937199.90.554
3pvsA0.837799.90.558
3uk6A0.920599.90.559
4b4tI0.870999.90.57
4b4tM0.867599.90.579
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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