GREMLIN Database
SBCD - Nuclease SbcCD subunit D
UniProt: P23479 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 391 (356)
Sequences: 3909 (3060)
Seq/√Len: 162.2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
44_V179_A5.0851.00
38_E268_Q4.3651.00
253_S269_E3.7411.00
34_I254_V3.7041.00
4_L40_I3.4771.00
40_I256_I3.4161.00
38_E270_V3.2051.00
31_L240_P3.1211.00
251_A271_L3.1111.00
3_I42_A3.0471.00
256_I270_V2.9471.00
35_V43_I2.9331.00
2_R258_D2.8711.00
79_V127_V2.7361.00
33_T37_D2.7321.00
358_K375_V2.6311.00
34_I270_V2.5451.00
352_S355_D2.5181.00
6_T45_M2.5011.00
34_I38_E2.4591.00
235_R255_T2.4301.00
7_A237_S2.4041.00
258_D268_Q2.4041.00
46_A179_A2.3871.00
255_T267_W2.3741.00
29_D69_A2.3311.00
38_E256_I2.2971.00
126_A174_A2.2771.00
6_T9_W2.2401.00
3_I257_V2.2241.00
63_F67_L2.2001.00
120_S123_E2.0581.00
187_G221_L1.9961.00
5_H217_A1.9781.00
42_A79_V1.9621.00
28_L66_S1.9561.00
44_V127_V1.9211.00
280_K305_D1.9161.00
286_G289_E1.8951.00
36_K73_R1.8881.00
77_P104_H1.8571.00
42_A127_V1.8531.00
30_E273_S1.8401.00
178_A213_A1.8231.00
258_D266_T1.8141.00
25_A62_L1.8001.00
226_T232_T1.7701.00
362_E368_A1.7601.00
259_A265_A1.7591.00
254_V272_L1.7231.00
117_E126_A1.7131.00
33_T69_A1.7101.00
245_F305_D1.6991.00
35_V70_L1.6961.00
6_T31_L1.6861.00
376_K380_E1.6711.00
255_T269_E1.6651.00
282_K307_E1.6621.00
23_E303_W1.6491.00
20_R23_E1.6381.00
27_V240_P1.6381.00
31_L254_V1.6371.00
35_V76_R1.6251.00
224_P255_T1.6201.00
178_A216_V1.6121.00
119_P124_L1.6041.00
216_V234_A1.6041.00
5_H215_Y1.5981.00
125_L177_I1.5871.00
49_A80_V1.5721.00
257_V267_W1.5641.00
124_L174_A1.5591.00
35_V40_I1.5561.00
27_V31_L1.5531.00
127_V177_I1.5381.00
4_L256_I1.5361.00
126_A176_K1.5321.00
11_L63_F1.5201.00
375_V379_L1.5161.00
79_V129_A1.5061.00
4_L254_V1.4991.00
23_E276_K1.4881.00
22_S26_D1.4851.00
36_K69_A1.4841.00
224_P253_S1.4821.00
9_W45_M1.4811.00
4_L34_I1.4781.00
7_A46_A1.4701.00
160_R164_E1.4451.00
29_D33_T1.4371.00
293_W296_E1.4121.00
242_A277_P1.4091.00
29_D66_S1.4001.00
15_L20_R1.3981.00
1_M258_D1.3881.00
128_G213_A1.3791.00
235_R267_W1.3771.00
248_A280_K1.3661.00
163_F166_M1.3651.00
80_V105_L1.3651.00
367_G370_P1.3651.00
27_V272_L1.3641.00
106_I129_A1.3601.00
213_A216_V1.3501.00
354_E379_L1.3381.00
81_I179_A1.3261.00
13_K243_Y1.3221.00
67_L78_I1.3221.00
4_L35_V1.3211.00
224_P269_E1.3211.00
2_R38_E1.3071.00
62_L66_S1.2961.00
171_R174_A1.2941.00
282_K309_R1.2941.00
280_K307_E1.2941.00
355_D358_K1.2711.00
320_H323_R1.2681.00
45_M78_I1.2661.00
279_V302_A1.2641.00
239_S243_Y1.2631.00
25_A29_D1.2391.00
229_R233_L1.2291.00
56_P59_A1.2261.00
30_E33_T1.2201.00
127_V179_A1.2081.00
161_Q164_E1.2001.00
288_S292_S1.1941.00
128_G176_K1.1841.00
323_R327_P1.1831.00
158_K162_A1.1771.00
48_D85_H1.1751.00
32_N66_S1.1721.00
317_E320_H1.1641.00
63_F80_V1.1591.00
24_Q243_Y1.1561.00
49_A63_F1.1541.00
13_K51_D1.1501.00
161_Q165_H1.1441.00
44_V257_V1.1421.00
257_V265_A1.1201.00
175_V259_A1.1131.00
260_K264_E1.1111.00
162_A165_H1.1101.00
25_A65_E1.1081.00
51_D243_Y1.0981.00
26_D29_D1.0981.00
30_E272_L1.0961.00
125_L175_V1.0931.00
377_L381_L1.0921.00
319_I323_R1.0830.99
94_A98_T1.0830.99
33_T36_K1.0720.99
27_V241_L1.0690.99
3_I44_V1.0660.99
307_E335_V1.0650.99
351_V359_K1.0620.99
291_Y294_L1.0610.99
36_K72_D1.0550.99
292_S295_D1.0550.99
129_A179_A1.0530.99
370_P373_E1.0520.99
34_I37_D1.0490.99
118_V123_E1.0480.99
378_F382_A1.0470.99
115_H126_A1.0420.99
256_I268_Q1.0390.99
9_W49_A1.0380.99
42_A177_I1.0370.99
44_V217_A1.0310.99
120_S175_V1.0280.99
292_S296_E1.0270.99
205_A208_S1.0240.99
73_R76_R1.0210.99
5_H218_L1.0190.99
347_E350_H1.0170.99
44_V177_I1.0130.99
245_F278_L1.0120.99
224_P235_R1.0080.99
305_D331_H1.0060.99
85_H222_H1.0000.99
32_N70_L0.9990.99
177_I259_A0.9980.99
117_E124_L0.9970.99
185_A203_T0.9940.99
184_V227_I0.9900.99
48_D84_N0.9870.99
357_F378_F0.9830.99
48_D222_H0.9780.99
376_K379_L0.9730.99
36_K76_R0.9690.99
204_V208_S0.9660.99
359_K362_E0.9660.99
287_L291_Y0.9580.99
289_E293_W0.9530.99
307_E333_R0.9520.99
323_R326_H0.9490.99
43_I78_I0.9490.99
181_H220_H0.9380.99
82_A107_G0.9250.98
239_S252_K0.9250.98
318_E321_R0.9240.98
322_L325_A0.9230.98
82_A131_A0.9190.98
190_T193_E0.9190.98
354_E357_F0.9150.98
64_Y96_P0.9150.98
121_A124_L0.9020.98
176_K214_A0.8990.98
166_M169_R0.8980.98
23_E241_L0.8970.98
94_A97_L0.8970.98
215_Y235_R0.8910.98
66_S69_A0.8900.98
359_K363_K0.8890.98
12_G59_A0.8850.98
226_T235_R0.8830.98
369_V373_E0.8830.98
335_V339_Q0.8810.98
288_S291_Y0.8730.98
26_D275_G0.8710.98
282_K335_V0.8680.98
70_L78_I0.8650.98
56_P60_E0.8640.97
354_E358_K0.8570.97
158_K161_Q0.8570.97
325_A328_G0.8520.97
9_W28_L0.8510.97
159_I162_A0.8510.97
50_F63_F0.8470.97
159_I163_F0.8450.97
371_D375_V0.8430.97
10_H222_H0.8410.97
6_T240_P0.8390.97
360_F364_Q0.8390.97
254_V270_V0.8380.97
358_K362_E0.8340.97
37_D270_V0.8330.97
332_I337_E0.8320.97
22_S25_A0.8320.97
12_G55_P0.8300.97
20_R241_L0.8270.97
223_R250_Y0.8260.97
21_L58_L0.8170.96
5_H237_S0.8170.96
368_A371_D0.8110.96
131_A236_Y0.8110.96
9_W240_P0.8070.96
180_S218_L0.8070.96
347_E351_V0.8060.96
118_V121_A0.8060.96
3_I259_A0.8030.96
84_N222_H0.8030.96
277_P302_A0.7980.96
330_I334_P0.7970.96
324_K327_P0.7970.96
69_A73_R0.7940.96
42_A257_V0.7900.96
165_H169_R0.7880.96
46_A81_I0.7880.96
21_L62_L0.7870.96
123_E175_V0.7850.96
85_H181_H0.7850.96
217_A235_R0.7840.96
57_A60_E0.7840.96
10_H48_D0.7810.95
130_L180_S0.7790.95
24_Q241_L0.7790.95
71_S103_I0.7770.95
329_F332_I0.7740.95
20_R24_Q0.7730.95
319_I329_F0.7720.95
289_E292_S0.7710.95
177_I257_V0.7710.95
158_K163_F0.7700.95
80_V103_I0.7700.95
171_R176_K0.7690.95
353_I357_F0.7670.95
46_A67_L0.7670.95
43_I73_R0.7660.95
40_I43_I0.7650.95
28_L32_N0.7650.95
343_R346_I0.7640.95
42_A125_L0.7610.95
31_L35_V0.7610.95
261_P264_E0.7500.94
291_Y325_A0.7490.94
299_D302_A0.7490.94
46_A237_S0.7480.94
134_S137_R0.7470.94
218_L236_Y0.7460.94
175_V214_A0.7460.94
24_Q50_F0.7450.94
159_I166_M0.7410.94
120_S124_L0.7400.94
42_A77_P0.7370.94
71_S102_G0.7350.94
31_L40_I0.7350.94
6_T43_I0.7350.94
206_A234_A0.7320.94
61_Q99_H0.7320.94
2_R256_I0.7310.94
15_L245_F0.7310.94
43_I76_R0.7300.94
31_L43_I0.7280.93
115_H121_A0.7270.93
225_Q229_R0.7270.93
181_H222_H0.7230.93
51_D252_K0.7220.93
286_G291_Y0.7200.93
367_G371_D0.7200.93
115_H119_P0.7180.93
115_H118_V0.7180.93
264_E267_W0.7130.93
158_K165_H0.7130.93
25_A69_A0.7120.93
119_P123_E0.7080.92
346_I376_K0.7070.92
61_Q65_E0.7050.92
372_E376_K0.7010.92
10_H220_H0.7000.92
242_A252_K0.6990.92
34_I256_I0.6960.92
162_A170_F0.6960.92
23_E26_D0.6960.92
113_P118_V0.6960.92
170_F176_K0.6960.92
229_R232_T0.6930.92
371_D376_K0.6910.92
215_Y257_V0.6860.91
281_W306_L0.6820.91
68_S72_D0.6780.91
11_L56_P0.6770.91
32_N36_K0.6760.91
114_I118_V0.6750.91
176_K182_I0.6750.91
92_S107_G0.6730.90
351_V354_E0.6720.90
239_S244_S0.6700.90
290_V294_L0.6690.90
350_H353_I0.6690.90
111_T114_I0.6670.90
366_G369_V0.6670.90
32_N69_A0.6670.90
8_D12_G0.6660.90
331_H334_P0.6650.90
233_L265_A0.6650.90
42_A118_V0.6650.90
344_E348_V0.6640.90
85_H220_H0.6630.90
373_E376_K0.6630.90
119_P122_G0.6620.90
260_K263_E0.6610.90
21_L24_Q0.6610.90
367_G373_E0.6610.90
69_A72_D0.6610.90
84_N132_Y0.6590.90
185_A205_A0.6590.90
50_F94_A0.6580.89
29_D62_L0.6560.89
226_T267_W0.6520.89
226_T229_R0.6500.89
333_R337_E0.6490.89
253_S272_L0.6490.89
63_F105_L0.6490.89
59_A131_A0.6460.89
13_K239_S0.6450.89
112_E115_H0.6440.88
228_K232_T0.6430.88
353_I382_A0.6410.88
240_P272_L0.6400.88
26_D274_S0.6380.88
18_R330_I0.6360.88
329_F334_P0.6350.88
321_R324_K0.6340.88
20_R239_S0.6340.88
344_E347_E0.6330.88
55_P88_P0.6330.88
320_H326_H0.6330.88
84_N181_H0.6310.87
4_L31_L0.6310.87
352_S357_F0.6300.87
228_K233_L0.6290.87
131_A180_S0.6290.87
335_V338_E0.6270.87
43_I70_L0.6260.87
334_P337_E0.6240.87
126_A171_R0.6230.87
87_N183_Y0.6210.87
241_L275_G0.6200.87
82_A105_L0.6190.86
162_A166_M0.6180.86
333_R340_N0.6180.86
297_G300_Q0.6160.86
305_D333_R0.6150.86
183_Y198_V0.6140.86
343_R359_K0.6130.86
322_L328_G0.6130.86
6_T254_V0.6110.86
51_D55_P0.6100.86
158_K166_M0.6080.85
7_A200_G0.6080.85
279_V283_A0.6080.85
23_E239_S0.6070.85
329_F335_V0.6050.85
107_G110_T0.6050.85
50_F60_E0.6040.85
132_Y183_Y0.6040.85
290_V306_L0.6020.85
32_N35_V0.5990.85
63_F93_A0.5990.85
27_V30_E0.5980.85
232_T235_R0.5960.84
352_S358_K0.5960.84
87_N135_E0.5950.84
41_D77_P0.5950.84
10_H85_H0.5940.84
317_E321_R0.5940.84
15_L88_P0.5920.84
41_D119_P0.5920.84
321_R328_G0.5920.84
36_K40_I0.5880.84
166_M170_F0.5850.83
70_L76_R0.5850.83
2_R39_Q0.5840.83
82_A88_P0.5830.83
11_L28_L0.5830.83
32_N73_R0.5820.83
45_M49_A0.5800.83
43_I66_S0.5790.83
188_N207_E0.5790.83
21_L59_A0.5790.83
318_E323_R0.5760.82
14_T51_D0.5760.82
3_I125_L0.5750.82
319_I322_L0.5750.82
9_W66_S0.5750.82
13_K20_R0.5740.82
12_G243_Y0.5740.82
78_I93_A0.5720.82
367_G379_L0.5700.82
55_P87_N0.5690.82
356_R360_F0.5690.82
217_A237_S0.5680.81
3_I177_I0.5670.81
329_F336_F0.5670.81
353_I364_Q0.5660.81
288_S295_D0.5650.81
104_H107_G0.5650.81
41_D258_D0.5650.81
4_L43_I0.5650.81
172_T212_D0.5640.81
331_H335_V0.5620.81
378_F381_L0.5620.81
330_I333_R0.5610.81
337_E340_N0.5610.81
21_L25_A0.5600.81
318_E327_P0.5600.81
24_Q252_K0.5590.80
355_D359_K0.5580.80
62_L237_S0.5560.80
184_V209_L0.5550.80
359_K376_K0.5550.80
268_Q271_L0.5540.80
51_D91_L0.5540.80
7_A217_A0.5540.80
198_V203_T0.5540.80
295_D298_R0.5530.80
161_Q324_K0.5530.80
240_P254_V0.5530.80
291_Y295_D0.5500.79
318_E326_H0.5490.79
12_G56_P0.5490.79
194_R221_L0.5490.79
227_I255_T0.5490.79
209_L234_A0.5450.79
48_D181_H0.5440.79
175_V261_P0.5400.78
98_T101_N0.5400.78
375_V378_F0.5390.78
99_H114_I0.5380.78
225_Q228_K0.5380.78
329_F338_E0.5350.77
87_N131_A0.5340.77
124_L175_V0.5330.77
24_Q239_S0.5330.77
369_V381_L0.5310.77
299_D304_I0.5310.77
128_G178_A0.5310.77
87_N91_L0.5300.77
243_Y252_K0.5290.77
287_L315_S0.5280.77
9_W31_L0.5270.76
55_P63_F0.5270.76
243_Y360_F0.5260.76
35_V77_P0.5260.76
112_E116_I0.5250.76
66_S70_L0.5240.76
286_G309_R0.5240.76
235_R269_E0.5220.76
105_L109_P0.5200.75
319_I325_A0.5190.75
132_Y221_L0.5180.75
144_D161_Q0.5180.75
115_H129_A0.5180.75
26_D30_E0.5180.75
132_Y247_E0.5170.75
42_A123_E0.5170.75
31_L66_S0.5170.75
337_E341_K0.5170.75
361_Y365_T0.5160.75
242_A274_S0.5160.75
251_A269_E0.5150.75
125_L259_A0.5140.75
373_E377_L0.5130.74
201_A204_V0.5110.74
255_T258_D0.5110.74
84_N220_H0.5100.74
361_Y366_G0.5070.74
351_V355_D0.5070.74
322_L329_F0.5060.73
99_H102_G0.5060.73
182_I245_F0.5050.73
335_V341_K0.5050.73
206_A227_I0.5040.73
122_G175_V0.5030.73
79_V106_I0.5030.73
227_I306_L0.5030.73
8_D222_H0.5020.73
177_I265_A0.5020.73
20_R55_P0.5010.73
228_K320_H0.5010.73
54_N64_Y0.5010.73
377_L380_E0.5000.73
342_D346_I0.5000.73
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
4ltyC 1 0.8312 100 0.363 Contact Map
3thoB 2 0.8951 100 0.378 Contact Map
4nzvA 1 0.7877 100 0.443 Contact Map
1ii7A 2 0.7673 100 0.446 Contact Map
3av0A 1 0.867 100 0.462 Contact Map
4ykeA 2 0.7826 100 0.477 Contact Map
4fbwA 2 0.7903 100 0.492 Contact Map
3t1iA 2 0.8414 100 0.496 Contact Map
4fbkA 2 0.8031 100 0.5 Contact Map
3d03A 5 0.6598 99.9 0.716 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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