Pfam Information-PF04055.9

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IDENTIFICATION: Radical_SAM
DEFINITION: Radical SAM superfamily
COMMENT:

Pfam Reference(s)

MEDLINE AUTHOR TITLE PUBLICATION COMMENT
11222759 Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE; Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 2001;29:1097-1106.

Family Structure

0....|....10...|....20...|....30...|....40...|....50...|....60...|....70...|....80...|....90...|....100..|....110..|....120..|....130..|....140..|....150..|....160..|....170..|....180..|....190..|....200..|....210..|....220..|....230..|....240..|....250..|....260..|....270..|....280..|....290..|....300..|....310..|....320..|....330..|....340..|....350..|....360..|....370..|....380..|....390..|....400..|....410..|....420..|....430..|....440..|....450..|....460..|....470..|....480..|....490..|....500..|....510..|....520..|....530..|....540..|....550..|....560..|....570..|....
STRUCTURE EECCCCCSCC...........CTTCCCTCCCCT.............................................................................................CCCCCCHHHCCCHHHHHHHHHHHT.CCCT...CC.EEEEE.....................CSCGGGS......................................................CCHHHHHHHHCCCCHS......................................................CEECCCEEEEEECSTTCC...............-.-.-................---CHHHHHHHHCT....................CCEEEEECCCCCHH........................................HHHHHHT...CCCCH...........HHHHHHHHHHHHTT..........................CCS..................C..-.EEEEEECCTTCC.H....HHHHHHHHHH
ACCESSIBILITY 0100121122...........142222465327.............................................................................................747215642312251034005207.4222...02.20100.....................1100021......................................................6431211223343830......................................................513653210000001406...............-.-.-................---46204303822....................03300000101436........................................1016203...26152...........53014003204724..........................051..................0..-.010001013622.2....7103600630
CONSENSUS h.hstsCshp...........CpaCthst.....................................................................................................ttttt.hshcplhpthpph..hp.t...hp.tlhhs.....................uupshhh......................................................hshhthhhthttt.............................................................thplplposshhh........................................tchhctltchs....................hstlslslpshspp.........................................hhphht...pttsh...........pphhcslcthppts..........................ht........................stshhhshssps.p....pphtphhchh

Co-evolving pairs with Z>=4 and Sequence Distance > 10

MUTATION COUNT COL 1 H1 COL 2 H2 H12 MI SEQUENCE DISTANCE AVG DISTANCE STDEV AVG RANDOM DISTANCE STDEV
561 188 3.371 412 3.383 6.189 0.565 63 8.4 0.2 24.6 10.7
1102 8 4.046 189 3.179 6.663 0.562 50 6.2 0.5 27.1 10
946 8 3.951 414 3.054 6.493 0.512 114 8.3 1.6 29.8 7.1
942 8 3.957 412 2.948 6.414 0.491 112 7.6 3.6 29.1 7.7
675 189 3.474 414 3.047 6.032 0.488 64 10.7 1.5 26.2 9.9
574 188 3.285 414 3.21 6.008 0.487 65 11.3 2 26 8.3
886 25 3.975 412 3.091 6.586 0.481 105 12 0.4 28.8 6.4
658 189 3.515 412 3.309 6.345 0.479 62 7.6 0.9 23.8 10.7
698 26 3.995 412 2.96 6.481 0.473 104 12.8 2.6 28.7 7.7
965 2 3.735 412 3.075 6.34 0.47 118 14 0.2 31 7.8
1369 2 3.807 193 3.988 7.329 0.467 60 4.4 2.8 25.2 9.3
846 330 3.839 412 3.095 6.47 0.463 30 4.3 0.7 22.3 7.6
774 26 4.013 188 2.951 6.503 0.461 42 9.1 4.1 24 10.4
942 1 3.887 412 3.061 6.489 0.459 119 13.8 0.9 29.8 8.3
693 190 3.497 412 3.452 6.492 0.457 61 8.7 0.4 23.7 8.6
1026 5 3.794 188 2.681 6.021 0.454 52 3.5 0.5 26.1 10.5
866 188 2.808 410 4.097 6.453 0.453 61 9.2 0.6 25.2 11
903 26 3.948 190 3.285 6.78 0.453 44 13.5 3.5 24.2 10.8
884 188 3.254 330 3.909 6.713 0.451 33 6.7 0 21 8.2
887 26 3.986 410 4.058 7.596 0.449 102 16.1 4.6 29.3 8.5
914 3 3.75 188 2.906 6.208 0.448 54 3.4 0.1 25.1 9.8

Z>=4 average 3D distance: 9.1 stdev: 3.7

Co-evolving pairs with Z=3 and Sequence Distance > 10

MUTATION COUNT COL 1 H1 COL 2 H2 H12 MI SEQUENCE DISTANCE AVG DISTANCE STDEV AVG RANDOM DISTANCE STDEV
1067 25 3.975 410 4.021 7.55 0.446 103 14.7 0.1 28.8 7.5
1075 1 3.918 26 3.962 7.435 0.445 15 14 2.2 21.1 7.3
1009 3 3.672 189 3.242 6.473 0.442 55 3.4 0.1 26.4 10.6
1108 1 3.862 410 3.957 7.378 0.441 117 12.8 0.8 29.8 8
1183 188 2.358 560 3.806 5.727 0.437 112 21.3 2 30 6.9
936 189 3.147 410 4.075 6.785 0.437 60 7.8 0.7 24.4 10.2
812 3 3.74 414 3.093 6.397 0.436 119 15.8 2.2 29 9.4
1088 2 3.703 26 3.983 7.25 0.436 14 13.8 6.8 20 7.4
1287 189 2.874 560 3.747 6.187 0.433 111 21.2 2.2 30.1 7.2
1221 1 3.915 25 3.975 7.462 0.428 14 10.8 3.5 20.9 7.2
1112 8 4.028 190 2.985 6.584 0.428 51 10 1 24.5 9.5
866 26 3.962 189 3.19 6.727 0.424 43 10.8 2.7 25.9 10.6
976 329 3.212 412 3.143 5.931 0.424 31 3.1 0.2 21.8 8.4
919 3 3.728 187 2.868 6.175 0.422 53 3.2 0 23.9 10.2
1003 3 3.565 26 3.984 7.128 0.421 13 11.9 3.2 19.1 6.2
1033 26 3.923 330 3.578 7.08 0.421 74 11.8 0.9 27.2 10.4
1255 189 2.918 554 3.852 6.351 0.42 105 11.7 1.3 29.8 8.4
1265 3 3.499 193 4.054 7.137 0.416 59 4.3 0.3 25.4 9.7
1251 8 3.998 331 3.357 6.94 0.415 83 7.2 2 29.4 10.8
1025 193 4.138 412 3.143 6.871 0.411 58 14.9 0.5 24.8 10.8
1152 3 3.673 330 3.606 6.868 0.41 87 9.9 0.2 29.8 10.1
844 330 3.817 414 2.938 6.345 0.41 32 7.7 0.6 21.2 9.9
1040 191 3.742 414 3.001 6.334 0.409 62 13.9 1.9 24.3 10.9
1445 8 3.789 554 3.781 7.161 0.409 154 12.1 1.4 32.4 8.6
926 328 3.945 412 3.135 6.672 0.409 32 4.9 1.2 23.1 9.1
1040 3 3.581 410 4.038 7.211 0.408 115 13 0.9 29.5 7.3
1061 4 4.059 188 2.681 6.332 0.407 53 4 0.4 25.7 10.8
559 187 3.218 414 3.313 6.125 0.406 66 12.7 2.2 24.6 10.4
708 190 3.463 414 3.109 6.166 0.406 63 13 1.7 25.3 10.7
927 5 3.942 412 3.025 6.561 0.406 115 12.3 0 30.4 9.7
1007 25 3.96 189 3.306 6.86 0.405 44 7.7 3 22.6 10.7
1165 8 3.817 410 3.984 7.397 0.404 110 12.1 2.5 29.2 7.8
580 187 3.115 412 3.384 6.095 0.403 64 10 0.6 24.9 10.4
891 25 3.993 414 3.025 6.615 0.402 107 9.7 0.4 30 7
1256 1 3.928 328 3.844 7.37 0.402 87 8.3 0.9 27.6 10.2
830 3 3.746 412 3.199 6.544 0.401 117 13.1 0.2 30.8 8.2
1039 1 3.952 188 2.71 6.26 0.401 56 5.9 2.2 27.3 10.7
960 25 3.972 188 3.003 6.574 0.401 43 5.7 2 20.8 8.9
1533 8 3.824 332 4.024 7.448 0.401 84 4.2 0.1 29.1 8.6
1070 5 3.846 26 3.984 7.429 0.4 11 10.6 1.1 16.7 5.4
552 23 2.604 414 3.335 5.539 0.399 109 4.3 2.2 29.5 7.1
1129 5 3.739 190 2.992 6.331 0.399 54 5.4 0.4 24.9 10.9
862 331 3.562 412 3.19 6.353 0.399 29 4.7 1.3 22.6 7.4
1097 5 3.751 189 3.159 6.511 0.399 53 3 0 27.1 11.3
1077 330 3.591 410 4.043 7.236 0.398 28 5.5 0.1 21.9 7.5
1159 3 3.628 25 4.038 7.268 0.397 12 8.4 2.9 17.9 5.8
1274 332 4.01 412 2.968 6.581 0.396 28 7.2 0.3 21.2 7.4
1161 26 3.968 193 4.048 7.621 0.396 47 17.3 1.9 24.1 8.9
1214 189 3.05 552 3.679 6.335 0.395 103 12.5 0.4 29.3 10.4
962 190 3.171 410 4.058 6.836 0.394 59 7.5 0.1 26.1 11
1255 2 3.737 25 4.026 7.369 0.393 13 10 1.3 19.7 6.2
1089 414 3.025 556 3.718 6.35 0.393 43 3.6 0.5 21.2 10.2
1020 412 2.987 555 3.929 6.523 0.392 44 4.3 1.7 22.2 9.8
1379 8 3.948 193 4.029 7.585 0.392 54 11.6 0.1 25.8 8.9
927 4 4.124 414 3.145 6.877 0.392 118 15.3 1.8 30.6 7.7
1055 4 4.071 187 2.772 6.452 0.392 52 5.2 0.3 24.9 9.3
1203 7 3.697 410 3.923 7.229 0.391 111 12.2 0.8 30.1 7
1129 26 3.976 163 3.949 7.534 0.391 37 17.3 5.6 22.9 10.1
1146 2 3.715 410 4.057 7.382 0.391 116 12.8 0.3 28.5 8.1
1371 8 3.957 191 3.595 7.162 0.39 52 10.1 0.4 24 10.7
862 331 3.52 414 2.909 6.04 0.389 31 9 1.7 22 9
1049 191 3.76 412 3.187 6.559 0.388 60 9.4 0.8 25.5 13.1
931 189 3.443 330 3.884 6.94 0.388 32 3 0.5 22 9.8
1365 4 3.976 193 3.991 7.58 0.387 58 7.3 0.1 25.4 10.2
1282 25 3.956 406 3.832 7.401 0.386 99 20.1 1 27.7 9.2
1216 3 3.598 406 3.873 7.085 0.386 111 12.4 3.3 30.5 8
909 5 3.979 414 2.924 6.517 0.386 117 14.2 1.6 28.6 8.2
1209 8 4.011 330 3.595 7.221 0.386 82 4.2 1.7 27.5 9.6
1086 328 3.917 410 4.069 7.601 0.384 30 3.3 0.1 21.6 8.6
1304 190 2.672 560 3.695 5.983 0.384 110 23.7 1.3 30.9 8.6
1056 25 3.983 190 3.313 6.912 0.384 45 10.5 2.3 22.5 9.8
1031 193 4.133 414 2.903 6.654 0.382 60 18.7 2 23.8 9.8
1231 26 3.988 560 3.763 7.371 0.38 153 16 1.2 31.6 9.4
1057 2 3.731 188 2.843 6.194 0.38 55 5.7 1 23.4 9.8
1017 3 3.668 190 3.175 6.464 0.379 56 4.2 0.3 28.1 11
891 188 3.295 331 3.707 6.624 0.379 34 9.3 0.4 23.2 10.2
972 7 3.903 412 3.177 6.702 0.378 113 10.3 1.4 29.7 7.1

Z=3 average 3D distance: 10.1 stdev: 4.9

Download

Click to download File Size
MI: mi_pdb_PF04055.9_full_pfam.xml.gz 785 KB
Pfam: pdb_PF04055.9_full_pfam.xml.gz 448 KB

X3D PDB Models

The following X3D models currently only work with BS Contact for Windows. X3D is a new ISO standard and so not all VRML viewers have full support for the newer X3D features. Please see X3DPDB for additional information.

Click to download File Size
PDB: mi_pdb_PF04055.9_full_pfam_1tv8_B.x3dz 110 KB
PDB: mi_pdb_PF04055.9_full_pfam_1tv8_A.x3dz 111 KB
PDB: mi_pdb_PF04055.9_full_pfam_1olt_A.x3dz 143 KB


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