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OPENSEQ.org

KdpA

ID: 1416984931 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 557 (557)
Sequences: 625 (378.9)
Seq/Len: 1.122
Nf(neff/√len): 16.1

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.122).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

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] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
197_N216_M3.5781.00
460_V484_L3.4761.00
78_F82_L3.4591.00
77_L132_G3.2311.00
27_L177_V3.2281.00
463_A485_L3.2271.00
276_D523_H2.9071.00
189_F255_Q2.8961.00
349_A354_F2.8651.00
70_N143_S2.7811.00
20_A268_F2.7691.00
363_M454_S2.7631.00
81_L128_S2.7531.00
219_V223_E2.7511.00
27_L269_A2.6811.00
435_A480_F2.6661.00
81_L97_L2.4700.99
31_I145_I2.4490.99
192_Q248_T2.3980.99
335_F344_C2.3680.99
335_F346_A2.3590.99
332_S349_A2.3280.99
101_L117_S2.3210.99
56_E157_R2.3130.99
227_M344_C2.2300.98
97_L128_S2.2280.98
103_L486_A2.1780.98
117_S476_A2.1480.98
119_S237_N2.1290.98
302_E323_K2.1280.98
127_F131_A2.1190.98
97_L123_T2.1150.98
30_L177_V2.1090.98
80_M127_F2.1040.98
145_I173_I2.0870.97
185_I224_A2.0660.97
227_M346_A2.0360.97
431_G484_L2.0140.97
97_L124_L2.0140.97
185_I258_A2.0010.96
31_I173_I1.9930.96
294_C365_L1.9870.96
56_E162_T1.9850.96
286_A532_I1.9570.96
495_G499_P1.9470.96
355_T358_G1.9310.95
99_W103_L1.9270.95
367_Q461_S1.9190.95
371_V535_V1.9150.95
188_F254_V1.9110.95
155_F270_F1.9080.95
477_N482_N1.8950.95
428_V465_N1.8840.94
227_M335_F1.8520.94
81_L124_L1.8300.93
78_F99_W1.7970.92
412_R416_L1.7700.92
94_L123_T1.7680.92
267_C280_G1.7570.91
82_L99_W1.7570.91
185_I254_V1.7420.91
496_V499_P1.7370.91
126_Y201_Y1.7210.90
279_Q522_T1.7150.90
366_M461_S1.6860.89
305_G355_T1.6830.89
282_M528_V1.6780.89
410_D510_K1.6480.87
15_V253_F1.6460.87
103_L483_C1.6170.86
188_F250_L1.6160.86
73_G143_S1.6140.86
156_T274_M1.5980.85
282_M286_A1.5630.83
195_L216_M1.5590.83
283_L383_M1.5270.81
358_G362_P1.5260.81
117_S459_A1.5170.81
125_S128_S1.5140.81
79_F83_G1.5130.80
446_L455_E1.5090.80
99_W483_C1.5050.80
80_M128_S1.5010.80
398_I519_T1.5000.80
390_A534_T1.4910.79
59_W502_A1.4820.79
238_A344_C1.4780.78
380_L384_M1.4730.78
260_F338_V1.4660.77
154_A508_V1.4540.77
66_I147_V1.4540.77
366_M465_N1.4470.76
276_D404_Y1.4300.75
168_V171_L1.4160.74
444_A475_S1.4110.74
286_A528_V1.4090.73
223_E335_F1.4060.73
436_M456_V1.4040.73
70_N73_G1.4000.73
276_D279_Q1.4000.73
285_W528_V1.3850.72
115_W459_A1.3820.71
343_S376_V1.3760.71
298_V337_V1.3760.71
287_M383_M1.3750.71
148_I335_F1.3750.71
206_T209_G1.3700.70
26_G30_L1.3600.70
355_T362_P1.3570.69
445_M456_V1.3530.69
101_L477_N1.3500.69
427_L464_A1.3500.69
472_A476_A1.3430.68
459_A470_A1.3380.68
57_M365_L1.3280.67
284_L288_S1.3280.67
189_F194_A1.3200.66
260_F342_A1.3160.66
453_F546_A1.3150.66
27_L31_I1.3120.66
23_L181_V1.3040.65
359_G471_F1.3020.65
73_G136_Q1.3000.65
45_V49_A1.2990.65
238_A346_A1.2940.64
383_M531_L1.2810.63
89_L127_F1.2750.62
424_T543_F1.2740.62
115_W470_A1.2720.62
474_L481_W1.2710.62
487_F491_V1.2700.62
196_Q221_S1.2670.62
219_V236_F1.2600.61
110_V136_Q1.2570.61
86_Y96_G1.2550.61
181_V185_I1.2470.60
134_T198_F1.2430.59
28_A269_A1.2420.59
341_A373_F1.2420.59
107_V490_F1.2400.59
19_L257_L1.2370.59
19_L261_L1.2360.59
94_L97_L1.2330.59
63_L501_M1.2300.58
191_Q195_L1.2280.58
403_E519_T1.2270.58
418_A428_V1.2240.58
413_E506_S1.2230.58
465_N520_L1.2160.57
92_Q201_Y1.2080.56
104_N115_W1.2070.56
17_M284_L1.2060.56
47_F171_L1.2020.56
336_A351_H1.2010.56
195_L465_N1.1990.55
148_I344_C1.1990.55
444_A478_S1.1970.55
421_I538_V1.1970.55
59_W505_G1.1950.55
336_A354_F1.1950.55
464_A488_C1.1940.55
81_L101_L1.1920.55
350_M472_A1.1850.54
145_I266_L1.1810.54
478_S482_N1.1800.54
126_Y235_F1.1790.53
439_D442_R1.1780.53
133_L137_N1.1750.53
417_T544_I1.1650.52
227_M260_F1.1640.52
470_A476_A1.1630.52
432_A457_L1.1590.52
148_I346_A1.1590.52
537_L544_I1.1570.51
85_H96_G1.1560.51
137_N222_Q1.1500.51
370_E382_G1.1410.50
31_I149_F1.1400.50
534_T537_L1.1400.50
133_L222_Q1.1400.50
10_A14_L1.1390.50
62_Y169_D1.1380.50
447_N474_L1.1350.49
23_L265_A1.1320.49
460_V481_W1.1300.49
282_M285_W1.1300.49
336_A349_A1.1260.48
337_V361_V1.1240.48
436_M445_M1.1220.48
441_G444_A1.1220.48
227_M338_V1.1190.48
126_Y197_N1.1180.48
270_F522_T1.1180.48
119_S122_T1.1140.47
267_C287_M1.1120.47
378_S381_Y1.1110.47
137_N343_S1.1060.46
101_L482_N1.1040.46
298_V333_S1.0990.46
136_Q222_Q1.0980.46
240_S255_Q1.0940.45
21_R25_S1.0930.45
153_R169_D1.0850.44
122_T419_L1.0840.44
78_F387_V1.0810.44
459_A472_A1.0780.44
432_A453_F1.0770.44
58_N61_Q1.0690.43
444_A481_W1.0680.43
78_F103_L1.0640.42
124_L128_S1.0580.42
259_I343_S1.0580.42
189_F335_F1.0580.42
483_C486_A1.0570.42
197_N201_Y1.0570.42
77_L106_A1.0560.42
55_R61_Q1.0560.42
227_M255_Q1.0540.42
117_S485_L1.0540.42
82_L387_V1.0530.41
385_L417_T1.0510.41
268_F281_R1.0480.41
264_T373_F1.0450.41
215_P325_S1.0450.41
137_N381_Y1.0410.40
305_G320_M1.0390.40
291_F338_V1.0350.40
117_S470_A1.0340.40
21_R268_F1.0340.40
202_Q216_M1.0330.40
107_V111_T1.0300.39
42_V46_L1.0260.39
333_S336_A1.0250.39
77_L81_L1.0220.39
62_Y153_R1.0210.39
260_F344_C1.0170.38
74_L418_A1.0170.38
149_F269_A1.0120.38
133_L369_G1.0100.38
12_F342_A1.0090.37
223_E344_C1.0070.37
281_R285_W1.0060.37
339_T351_H1.0050.37
155_F274_M1.0030.37
12_F338_V1.0020.37
106_A132_G1.0010.37
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Sep14)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4j7cI40.72351000.821Contact Map
3pjzA20.76399.70.933Contact Map
3qnqA40.235213.20.989Contact Map
2k1eA40.184950.991Contact Map
4krdB10.12934.70.991Contact Map
2q67A20.18314.60.991Contact Map
2l92A10.07544.20.991Contact Map
1q16C10.26214.10.992Contact Map
3sriB10.01973.70.992Contact Map
2k3cA10.05573.60.992Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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