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OPENSEQ.org
MFD - Transcription-repair-coupling factor
UniProt: P30958 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11619
Length: 1148 (1126)
Sequences: 1492
Seq/Len: 1.33
MFD
Paralog alert: 0.01 [within 20: 0.00] - ratio of genomes with paralogs
GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
829_L 838_I 4.894 1.00
130_M 189_I 4.781 1.00
712_K 717_D 4.688 1.00
584_K 648_N 4.538 1.00
698_E 703_K 4.412 1.00
697_A 701_E 4.035 1.00
646_V 706_I 4.026 1.00
182_L 189_I 3.766 1.00
700_A 719_K 3.758 1.00
699_V 707_L 3.727 1.00
1012_L 1057_A 3.603 1.00
814_Y 886_E 3.415 1.00
650_K 722_D 3.347 1.00
616_M 645_A 3.267 1.00
654_V 669_F 3.222 1.00
693_T 697_A 3.192 1.00
169_L 184_F 3.149 1.00
726_L 742_I 3.091 1.00
681_E 695_I 3.084 1.00
856_D 861_R 3.077 1.00
689_A 693_T 3.066 1.00
694_Q 698_E 3.057 1.00
695_I 704_I 3.032 1.00
698_E 707_L 2.956 1.00
669_F 708_I 2.941 1.00
681_E 704_I 2.883 1.00
52_A 107_I 2.829 1.00
666_Y 670_R 2.791 1.00
825_A 886_E 2.715 1.00
679_R 698_E 2.682 1.00
839_A 862_F 2.558 1.00
512_T 516_D 2.543 1.00
494_A 512_T 2.53 1.00
692_Q 712_K 2.462 1.00
819_V 844_Q 2.461 1.00
612_V 626_V 2.452 1.00
642_A 727_I 2.415 1.00
43_V 282_L 2.411 0.99
613_L 644_L 2.394 0.99
45_I 113_L 2.386 0.99
234_T 319_S 2.385 0.99
131_K 208_A 2.38 0.99
802_I 812_V 2.373 0.99
826_A 866_V 2.351 0.99
802_I 833_V 2.271 0.99
698_E 701_E 2.254 0.99
877_I 880_A 2.235 0.99
491_G 511_L 2.224 0.99
570_D 574_Q 2.221 0.99
653_A 720_F 2.214 0.99
707_L 713_L 2.211 0.99
1070_A 1078_L 2.198 0.99
680_I 706_I 2.191 0.99
1029_R 1045_E 2.189 0.99
579_E 619_P 2.186 0.99
826_A 830_A 2.184 0.99
581_F 650_K 2.142 0.99
1030_I 1061_L 2.135 0.98
681_E 687_R 2.132 0.98
690_K 694_Q 2.125 0.98
146_D 162_Y 2.121 0.98
806_I 836_A 2.114 0.98
1035_T 1038_E 2.099 0.98
136_L 184_F 2.093 0.98
803_L 835_E 2.092 0.98
656_V 662_A 2.089 0.98
683_I 692_Q 2.069 0.98
1036_E 1065_R 2.046 0.98
812_V 864_V 2.044 0.98
388_S 428_G 2.039 0.98
164_T 169_L 2.013 0.98
814_Y 825_A 1.996 0.97
607_Q 611_A 1.992 0.97
815_L 871_I 1.99 0.97
839_A 853_V 1.987 0.97
696_L 718_V 1.981 0.97
698_E 704_I 1.958 0.97
646_V 678_V 1.956 0.97
131_K 134_Q 1.954 0.97
732_H 894_A 1.942 0.97
838_I 866_V 1.94 0.97
497_T 510_M 1.929 0.97
141_L 169_L 1.905 0.96
43_V 108_V 1.904 0.96
795_S 828_R 1.894 0.96
838_I 864_V 1.893 0.96
799_R 803_L 1.874 0.96
52_A 69_N 1.865 0.96
137_S 184_F 1.848 0.95
562_R 737_R 1.846 0.95
601_T 609_I 1.841 0.95
543_H 553_A 1.837 0.95
653_A 713_L 1.833 0.95
1017_I 1026_F 1.832 0.95
712_K 715_Q 1.812 0.95
1043_K 1058_R 1.801 0.94
120_H 270_P 1.793 0.94
137_S 140_A 1.786 0.94
690_K 693_T 1.785 0.94
56_H 107_I 1.777 0.94
852_R 856_D 1.771 0.94
1015_D 1056_P 1.769 0.94
816_Y 886_E 1.761 0.94
822_I 840_I 1.76 0.94
59_I 107_I 1.744 0.93
833_V 836_A 1.744 0.93
180_Y 209_I 1.737 0.93
361_L 373_A 1.731 0.93
688_S 691_E 1.729 0.93
28_A 55_L 1.721 0.93
802_I 864_V 1.718 0.92
128_L 141_L 1.697 0.92
726_L 749_V 1.692 0.92
590_Y 613_L 1.687 0.92
274_S 330_E 1.683 0.91
799_R 835_E 1.678 0.91
108_V 272_L 1.676 0.91
193_R 202_T 1.674 0.91
795_S 831_E 1.667 0.91
581_F 648_N 1.667 0.91
151_R 161_E 1.666 0.91
827_E 831_E 1.659 0.91
282_L 331_L 1.659 0.91
883_I 903_V 1.659 0.91
715_Q 978_L 1.654 0.90
180_Y 206_V 1.639 0.90
129_V 208_A 1.637 0.90
728_V 747_A 1.617 0.89
107_I 599_F 1.616 0.89
885_I 914_L 1.607 0.89
121_S 125_G 1.596 0.88
694_Q 697_A 1.585 0.88
1046_L 1061_L 1.582 0.88
561_V 970_I 1.571 0.87
642_A 669_F 1.57 0.87
323_R 326_E 1.564 0.87
581_F 616_M 1.561 0.87
601_T 606_A 1.56 0.87
567_E 570_D 1.55 0.86
31_V 283_V 1.545 0.86
407_I 424_Y 1.543 0.86
793_Y 814_Y 1.53 0.85
43_V 106_L 1.528 0.85
683_I 707_L 1.524 0.85
639_M 668_N 1.523 0.85
836_A 864_V 1.522 0.85
642_A 652_V 1.519 0.85
697_A 700_A 1.516 0.85
793_Y 886_E 1.516 0.85
957_E 962_E 1.509 0.84
567_E 744_A 1.504 0.84
841_G 853_V 1.504 0.84
1043_K 1065_R 1.495 0.83
41_P 280_T 1.494 0.83
167_A 183_D 1.493 0.83
642_A 706_I 1.492 0.83
830_A 838_I 1.487 0.83
764_N 976_M 1.485 0.83
142_R 152_H 1.483 0.83
883_I 914_L 1.479 0.82
854_M 875_I 1.47 0.82
226_L 230_Q 1.465 0.82
1026_F 1050_F 1.46 0.81
434_F 443_L 1.455 0.81
46_A 55_L 1.455 0.81
141_L 184_F 1.451 0.81
652_V 727_I 1.448 0.81
94_T 98_L 1.44 0.80
594_C 613_L 1.438 0.80
31_V 55_L 1.437 0.80
45_I 108_V 1.435 0.80
841_G 850_L 1.433 0.80
815_L 875_I 1.432 0.80
56_H 69_N 1.429 0.79
695_I 707_L 1.422 0.79
377_F 442_A 1.413 0.78
1043_K 1061_L 1.409 0.78
678_V 706_I 1.407 0.78
40_G 279_N 1.405 0.78
562_R 962_E 1.401 0.78
613_L 617_C 1.4 0.77
553_A 557_A 1.398 0.77
70_L 106_L 1.396 0.77
679_R 703_K 1.391 0.77
935_S 948_H 1.383 0.76
583_F 750_D 1.375 0.76
395_R 425_L 1.375 0.76
68_M 97_Q 1.374 0.76
1039_L 1068_Q 1.37 0.75
510_M 518_K 1.37 0.75
383_G 440_N 1.367 0.75
741_R 744_A 1.366 0.75
196_D 199_S 1.364 0.75
271_P 322_L 1.359 0.74
183_D 193_R 1.358 0.74
180_Y 194_V 1.356 0.74
138_R 169_L 1.353 0.74
816_Y 825_A 1.351 0.74
682_M 707_L 1.35 0.74
498_T 505_T 1.349 0.74
591_Q 595_D 1.348 0.74
829_L 864_V 1.346 0.73
822_I 826_A 1.346 0.73
589_Q 592_L 1.344 0.73
1005_E 1079_E 1.343 0.73
184_F 189_I 1.341 0.73
738_H 950_L 1.337 0.73
1066_L 1078_L 1.336 0.73
1073_L 1139_M 1.335 0.73
576_A 620_L 1.334 0.72
593_F 639_M 1.334 0.72
683_I 696_L 1.333 0.72
515_N 544_K 1.328 0.72
753_T 776_I 1.325 0.72
974_L 978_L 1.325 0.72
838_I 1072_K 1.321 0.71
819_V 822_I 1.317 0.71
716_S 719_K 1.317 0.71
378_L 385_V 1.31 0.71
22_L 30_L 1.31 0.71
699_V 704_I 1.305 0.70
22_L 26_A 1.303 0.70
228_R 245_Y 1.3 0.70
654_V 727_I 1.3 0.70
616_M 750_D 1.295 0.69
186_D 191_S 1.294 0.69
801_A 884_I 1.293 0.69
173_P 176_S 1.287 0.69
185_F 673_F 1.286 0.68
779_P 958_L 1.285 0.68
816_Y 821_N 1.281 0.68
247_Q 252_T 1.272 0.67
695_I 698_E 1.269 0.67
70_L 272_L 1.269 0.67
883_I 912_A 1.268 0.67
1033_A 1042_I 1.267 0.67
132_K 205_E 1.265 0.67
143_T 147_S 1.262 0.66
696_L 712_K 1.258 0.66
491_G 513_Y 1.258 0.66
662_A 766_A 1.257 0.66
680_I 708_I 1.255 0.66
490_V 543_H 1.253 0.66
609_I 612_V 1.253 0.66
135_R 186_D 1.253 0.66
583_F 616_M 1.247 0.65
669_F 706_I 1.246 0.65
590_Y 594_C 1.246 0.65
829_L 833_V 1.244 0.65
375_R 379_E 1.241 0.64
692_Q 717_D 1.241 0.64
500_E 505_T 1.238 0.64
587_R 647_D 1.238 0.64
813_Y 877_I 1.237 0.64
586_D 613_L 1.235 0.64
167_A 186_D 1.234 0.64
586_D 590_Y 1.233 0.64
578_K 748_N 1.232 0.64
611_A 626_V 1.231 0.64
69_N 107_I 1.229 0.63
43_V 280_T 1.227 0.63
812_V 1008_M 1.225 0.63
31_V 44_L 1.223 0.63
172_F 413_M 1.221 0.63
234_T 263_L 1.221 0.63
190_D 967_M 1.22 0.63
926_A 952_I 1.219 0.62
490_V 935_S 1.218 0.62
178_L 203_L 1.217 0.62
614_S 618_Q 1.216 0.62
134_Q 688_S 1.216 0.62
1026_F 1046_L 1.215 0.62
823_Q 840_I 1.212 0.62
120_H 124_H 1.211 0.62
900_R 1049_R 1.21 0.62
594_C 644_L 1.209 0.61
932_A 945_L 1.208 0.61
788_T 914_L 1.207 0.61
562_R 985_A 1.205 0.61
1013_P 1054_P 1.204 0.61
1062_D 1136_R 1.204 0.61
119_P 275_Y 1.203 0.61
1012_L 1046_L 1.202 0.61
583_F 650_K 1.201 0.61
884_I 915_L 1.2 0.61
110_V 292_A 1.2 0.61
59_I 105_V 1.2 0.61
1062_D 1065_R 1.199 0.61
916_T 922_M 1.197 0.60
950_L 955_A 1.189 0.60
726_L 746_R 1.189 0.60
572_Y 750_D 1.188 0.59
684_S 847_E 1.188 0.59
1026_F 1029_R 1.186 0.59
645_A 652_V 1.186 0.59
25_A 58_E 1.182 0.59
829_L 866_V 1.181 0.59
617_C 644_L 1.181 0.59
1043_K 1053_L 1.18 0.59
776_I 873_T 1.179 0.59
30_L 199_S 1.178 0.59
73_W 115_Q 1.174 0.58
1062_D 1129_K 1.173 0.58
293_E 324_V 1.172 0.58
838_I 845_M 1.169 0.58
825_A 828_R 1.168 0.58
227_F 264_F 1.167 0.57
78_Y 303_F 1.167 0.57
666_Y 682_M 1.162 0.57
46_A 108_V 1.161 0.57
493_Y 1029_R 1.159 0.57
794_D 1029_R 1.158 0.57
398_L 449_L 1.158 0.57
782_R 909_Q 1.156 0.56
639_M 669_F 1.153 0.56
684_S 692_Q 1.153 0.56
887_R 890_H 1.153 0.56
35_A 105_V 1.153 0.56
611_A 614_S 1.152 0.56
119_P 265_F 1.152 0.56
1133_E 1137_Q 1.152 0.56
1075_I 1078_L 1.149 0.56
608_A 626_V 1.148 0.56
714_L 738_H 1.148 0.56
887_R 917_P 1.147 0.55
42_V 281_L 1.144 0.55
1004_V 1063_I 1.143 0.55
1012_L 1030_I 1.14 0.55
793_Y 798_V 1.139 0.55
615_D 624_R 1.135 0.54
171_L 182_L 1.133 0.54
831_E 838_I 1.131 0.54
141_L 171_L 1.131 0.54
172_F 510_M 1.129 0.54
1039_L 1065_R 1.124 0.53
749_V 766_A 1.124 0.53
687_R 691_E 1.121 0.53
176_S 194_V 1.121 0.53
608_A 637_V 1.12 0.53
791_R 915_L 1.119 0.53
142_R 164_T 1.119 0.53
793_Y 828_R 1.118 0.53
1041_E 1044_V 1.112 0.52
271_P 274_S 1.109 0.52
1030_I 1068_Q 1.109 0.52
897_H 944_A 1.107 0.51
450_L 683_I 1.104 0.51
219_T 224_I 1.102 0.51
182_L 190_D 1.101 0.51
589_Q 647_D 1.101 0.51
449_L 1026_F 1.098 0.51
47_P 51_N 1.098 0.51
825_A 866_V 1.094 0.50
136_L 189_I 1.094 0.50
695_I 864_V 1.09 0.50
20_G 352_N 1.09 0.50
923_T 926_A 1.089 0.50
185_F 190_D 1.089 0.50
655_L 750_D 1.089 0.50
508_Y 916_T 1.084 0.49
1034_K 1038_E 1.082 0.49
766_A 814_Y 1.082 0.49
586_D 644_L 1.081 0.49
108_V 112_T 1.079 0.49
303_F 317_P 1.079 0.49
795_S 832_L 1.079 0.49
544_K 814_Y 1.079 0.49
506_G 524_S 1.077 0.48
583_F 644_L 1.077 0.48
616_M 644_L 1.076 0.48
897_H 934_A 1.075 0.48
1030_I 1042_I 1.075 0.48
873_T 878_P 1.075 0.48
185_F 188_E 1.075 0.48
48_D 51_N 1.075 0.48
140_A 144_Q 1.071 0.48
44_L 55_L 1.069 0.48
753_T 844_Q 1.067 0.47
1036_E 1040_E 1.067 0.47
689_A 692_Q 1.066 0.47
186_D 260_W 1.065 0.47
755_T 773_L 1.065 0.47
70_L 95_L 1.064 0.47
699_V 718_V 1.062 0.47
435_V 442_A 1.06 0.47
530_S 964_S 1.06 0.47
157_M 161_E 1.06 0.47
569_L 978_L 1.06 0.47
430_A 1012_L 1.059 0.47
131_K 206_V 1.057 0.46
1029_R 1042_I 1.057 0.46
78_Y 317_P 1.055 0.46
564_V 961_E 1.054 0.46
227_F 231_W 1.053 0.46
386_V 668_N 1.052 0.46
566_A 986_L 1.052 0.46
552_R 556_K 1.05 0.46
806_I 812_V 1.047 0.45
192_L 745_M 1.042 0.45
590_Y 644_L 1.042 0.45
1011_L 1023_R 1.041 0.45
718_V 1068_Q 1.041 0.45
184_F 649_H 1.04 0.45
1097_P 1101_I 1.039 0.45
581_F 584_K 1.037 0.44
143_T 511_L 1.037 0.44
381_F 442_A 1.036 0.44
751_I 897_H 1.035 0.44
639_M 708_I 1.033 0.44
1075_I 1139_M 1.032 0.44
219_T 226_L 1.032 0.44
799_R 860_Q 1.031 0.44
537_E 540_A 1.031 0.44
486_L 841_G 1.027 0.44
637_V 776_I 1.026 0.43
671_D 674_A 1.025 0.43
190_D 688_S 1.025 0.43
856_D 862_F 1.025 0.43
670_R 681_E 1.024 0.43
1095_V 1099_W 1.024 0.43
778_T 939_L 1.022 0.43
167_A 519_L 1.02 0.43
663_Q 667_D 1.02 0.43
562_R 961_E 1.02 0.43
696_L 812_V 1.02 0.43
183_D 517_A 1.019 0.43
141_L 182_L 1.019 0.43
704_I 722_D 1.018 0.43
683_I 718_V 1.017 0.43
138_R 142_R 1.015 0.42
826_A 840_I 1.014 0.42
560_K 764_N 1.011 0.42
325_D 329_S 1.011 0.42
178_L 194_V 1.01 0.42
581_F 750_D 1.009 0.42
619_P 978_L 1.009 0.42
394_R 397_A 1.008 0.42
77_P 83_P 1.007 0.42
681_E 707_L 1.007 0.42
68_M 94_T 1.005 0.41
185_F 616_M 1.004 0.41
667_D 767_M 1.004 0.41
606_A 610_N 1.001 0.41
199_S 571_I 1.001 0.41
683_I 869_T 1 0.41
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: 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-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
2eyqA20.99911000.369Contact Map0.675
3hjhA10.4191000.788Contact Map0.789
1gm5A10.60371000.796Contact Map0.499
2d7dA10.51051000.834Contact Map0.728
1c4oA10.52351000.838Contact Map0.722
2xgjA20.44511000.877Contact Map0.529
2fwrA40.34151000.878Contact Map0.535
2v6iA10.34761000.886Contact Map0.472
3mwyW10.48171000.887Contact Map0.344
3dmqA20.55841000.889Contact Map0.341
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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