1. b.57.1 Herpes virus serine proteinase, assemblin Herpes virus serine proteinase, assemblin core: barrel, closed; n=7, S=8; complex topology 1o6e d1o6eb_ B:6-15,65-75,158-167,170-187 1o6e d1o6ea_ A:6-15,65-75,158-167,170-186 1jq6 d1jq6a_ A:13-22,80-90,176-185,188-202 1fl1 d1fl1a_ A:5-14,63-73,153-161,165-180 1fl1 d1fl1b_ B:5-14,63-73,153-161,165-180 1jq7 d1jq7a_ A:1013-1021,1080-1090,1176-1185,1188-1199 2pbk d2pbkb1 B:5-14,63-73,153-161,165-180 1at3 d1at3a_ A:20-28,78-87,167-175,179-198 2pbk d2pbka1 A:5-14,63-73,153-161,165-180 1nkk d1nkkc_ C:1013-1023,1080-1090,1176-1185,1188-1202 1vzv d1vzva_ A:12-20,69-78,158-167,170-185 1nkk d1nkka_ A:13-23,80-90,176-185,188-201 1nkm d1nkmb_ B:313-323,380-390,476-485,488-500 1lay d1laya_ A:13-23,80-90,176-185,188-203 1njt d1njtb_ B:313-323,380-390,476-485,488-502 1njt d1njta_ A:13-23,80-90,176-185,188-203 1nkk d1nkkd_ D:1313-1323,1380-1390,1476-1485,1488-1500 1nkk d1nkkb_ B:313-323,380-390,476-485,488-503 1id4 d1id4a_ A:13-23,80-90,176-185,188-200 2wpo d2wpoc_ C:13-23,80-90,176-185,188-200 1wpo d1wpob_ B:13-23,80-90,176-185,188-201 1nju d1njud_ D:1313-1323,1380-1390,1476-1485,1488-1500 1nju d1njuc_ C:1013-1023,1080-1090,1176-1185,1188-1200 1ief d1iefa_ A:13-23,80-90,176-185,188-200 1ief d1iefb_ B:313-323,380-390,476-485,488-501 1ied d1iedb_ B:313-323,380-390,476-485,488-501 1ieg d1iegb_ B:313-323,380-390,476-485,488-503 1iec d1ieca_ A:13-23,80-90,176-185,188-200 1id4 d1id4b_ B:313-323,380-390,476-485,488-501 1iec d1iecb_ B:313-323,380-390,476-485,488-501 1njt d1njtd_ D:1313-1323,1380-1390,1476-1485,1488-1500 1njt d1njtc_ C:1013-1023,1080-1090,1176-1185,1188-1200 1nju d1njua_ A:13-23,80-90,176-185,188-200 1cmv d1cmva_ A:13-23,80-90,176-185,188-199 1ied d1ieda_ A:13-23,80-90,176-185,188-200 1cmv d1cmvb_ B:13-23,80-90,176-185,188-201 1wpo d1wpoa_ A:13-23,80-90,176-185,188-201 1nju d1njub_ B:313-323,380-390,476-485,488-500 1ieg d1iega_ A:13-23,80-90,176-185,188-200 2wpo d2wpob_ B:13-23,80-90,176-185,188-200 1nkm d1nkma_ A:13-23,80-90,176-185,188-200 2wpo d2wpoa_ A:13-23,80-90,176-185,188-200 2wpo d2wpod_ D:13-23,80-90,176-185,188-200 1at3 d1at3b_ B:20-30,78-87,167-175,179-198 1jq7 d1jq7b_ B:1313-1323,1380-1390,1476-1485,1488-1500 5. e.28.1 Reovirus inner layer core protein p3 Reovirus inner layer core protein p3 large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end 1uf2 d1uf2b_ B:71-80,89-98,165-174,971-980 1uf2 d1uf2a_ A:71-80,89-98,165-174,971-980 2btv d2btvb_ B:89-94,99-106,167-175,862-871 2btv d2btva_ A:89-94,100-106,167-175,862-871 9. d.157.1 Metallo-hydrolase/oxidoreductase Metallo-hydrolase/oxidoreductase duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets 1e5d d1e5da2 A:148-157,158-164,201-216,232-249 1e5d d1e5db2 B:148-157,158-164,201-216,232-249 2p97 d2p97a1 A:121-128,130-135,156-171,187-200 2bc2 d2bc2a_ A:154-160,161-168,185-201,215-227 1bc2 d1bc2b_ B:154-160,161-168,185-201,215-227 2p97 d2p97b1 B:121-128,130-135,156-171,187-200 1bc2 d1bc2a_ A:154-160,161-168,185-201,215-227 1bmc d1bmca_ A:154-160,161-168,185-201,215-227 2yz3 d2yz3a1 A:164-170,171-178,195-211,225-236 1bvt d1bvta_ A:154-160,161-168,185-201,215-227 1dxk d1dxka_ A:154-160,161-168,185-201,215-227 1mqo d1mqoa_ A:201-210,211-221,238-254,279-291 3bc2 d3bc2a_ A:154-160,161-168,185-201,215-227 2bc2 d2bc2b_ B:154-160,161-167,185-201,215-227 1vme d1vmeb2 B:153-161,162-167,205-220,235-249 1a8t d1a8ta_ A:150-156,157-164,181-197,211-230 1vme d1vmea2 A:153-161,162-167,205-220,235-249 2gkl d2gkla1 A:201-210,211-220,238-253,290-304 1x8g d1x8ga_ A:201-210,211-220,238-253,290-304 2qds d2qdsa1 A:201-210,211-220,238-253,290-304 2yz3 d2yz3b1 B:164-170,171-177,195-211,225-236 1ko3 d1ko3a_ A:201-210,211-221,238-254,279-295 1ko2 d1ko2a_ A:201-210,211-220,238-254,279-295 1kr3 d1kr3b_ B:167-173,174-181,198-214,228-247 3znb d3znba_ A:167-173,174-180,198-214,228-246 1hlk d1hlka_ A:167-173,174-181,198-214,228-247 1a7t d1a7ta_ A:150-156,157-164,181-197,211-230 1hlk d1hlkb_ B:167-173,174-181,198-214,228-247 1kr3 d1kr3a_ A:167-173,174-181,198-214,228-247 1a7t d1a7tb_ B:150-156,157-164,181-197,211-230 1ych d1ychd2 D:150-159,160-166,203-218,235-249 1ycf d1ycfb2 B:150-159,160-166,203-218,235-249 1ycg d1ycgd2 D:150-159,160-166,203-218,235-249 1ych d1ychc2 C:150-159,160-166,203-218,235-249 2znb d2znbb_ B:167-173,174-181,198-214,228-247 1ych d1ychb2 B:150-159,160-166,203-218,235-249 4znb d4znbb_ B:167-173,174-181,198-214,228-247 1ycg d1ycgb2 B:150-159,160-166,203-218,235-249 1ycg d1ycgc2 C:150-159,160-166,203-218,235-249 1ych d1ycha2 A:150-159,160-166,203-218,235-249 1ycg d1ycga2 A:150-159,160-166,203-218,235-249 1znb d1znba_ A:167-173,174-181,198-214,228-248 1ycf d1ycfd2 D:150-159,160-166,203-218,235-249 3znb d3znbb_ B:167-173,174-181,198-214,228-248 2bmi d2bmia_ A:150-156,157-164,181-197,211-231 1a8t d1a8tb_ B:150-156,157-163,181-197,211-230 2cfu d2cfua2 A:282-291,292-298,318-334,350-379 2cg2 d2cg2a2 A:282-291,292-298,318-334,350-379 2cfz d2cfza2 A:282-291,292-298,318-334,350-379 1ycf d1ycfc2 C:150-159,160-166,203-218,235-249 2doo d2dooa1 A:144-150,151-157,172-188,202-219 2doo d2doob1 B:144-150,151-157,172-188,202-219 1dd6 d1dd6a_ A:144-150,151-157,172-188,202-219 4znb d4znba_ A:167-173,174-180,198-214,228-248 1ycf d1ycfa2 A:150-159,160-166,203-218,235-249 1znb d1znbb_ B:167-173,174-181,198-214,228-248 2znb d2znba_ A:167-173,174-180,198-214,228-248 1vgn d1vgnb1 B:144-150,151-157,172-188,202-221 1x8i d1x8ia_ A:201-210,211-219,238-253,290-304 1dd6 d1dd6b_ B:144-150,151-157,172-188,202-220 1x8h d1x8ha_ A:201-210,211-219,238-253,290-304 1jje d1jjea_ A:144-150,151-157,172-188,202-222 1vgn d1vgna1 A:144-150,151-157,172-188,202-220 1jjt d1jjtb_ B:144-150,151-157,172-188,202-221 2bmi d2bmib_ B:150-156,157-164,181-197,211-232 1ddk d1ddka_ A:144-150,151-158,172-188,202-221 1jjt d1jjta_ A:144-150,151-157,172-188,202-222 1jje d1jjeb_ B:144-150,151-157,172-188,202-221 1m2x d1m2xc_ C:202-210,211-221,238-254,279-295 1m2x d1m2xa_ A:202-210,211-221,238-254,279-297 1m2x d1m2xd_ D:202-210,211-220,238-254,279-297 1m2x d1m2xb_ B:202-210,211-220,238-254,279-297 2cg3 d2cg3a2 A:284-291,292-298,318-334,350-379 1k07 d1k07b_ B:198-210,211-220,238-254,286-311 2q0i d2q0ia1 A:162-170,171-177,197-211,232-255 1l9y d1l9yb_ B:198-210,211-220,236-254,286-311 1k07 d1k07a_ A:198-210,211-220,236-254,286-311 2q0j d2q0ja1 A:162-170,171-177,197-211,232-255 1jt1 d1jt1a_ A:198-210,211-220,236-254,286-311 1l9y d1l9ya_ A:198-210,211-220,236-254,286-311 2q0j d2q0jb1 B:162-170,171-177,197-212,232-255 2gmn d2gmnb1 B:179-191,192-201,218-233,265-292 2gmn d2gmna1 A:179-191,192-201,218-233,265-292 2h6a d2h6aa1 A:198-210,211-220,239-254,295-317 2h6a d2h6ab1 B:198-210,211-220,239-254,295-317 1sml d1smla_ A:162-174,175-184,201-216,245-267 2hb9 d2hb9a1 A:198-210,211-220,239-254,295-317 2fu8 d2fu8a1 A:198-210,211-220,239-254,295-317 2fu9 d2fu9b1 B:198-210,211-220,239-254,295-317 2fu6 d2fu6a1 A:198-210,211-220,239-254,295-317 2fu9 d2fu9a1 A:198-210,211-220,239-254,295-317 2fm6 d2fm6a1 A:198-210,211-220,239-254,295-317 2aio d2aioa1 A:198-210,211-220,238-254,289-311 2qdt d2qdta1 A:162-174,175-184,201-216,245-267 2fm6 d2fm6b1 B:198-210,211-220,239-254,295-317 2fu8 d2fu8b1 B:198-210,211-220,239-254,295-317 2fu6 d2fu6b1 B:198-210,211-220,239-254,295-317 2gfk d2gfka1 A:198-210,211-220,239-254,295-317 2fu7 d2fu7b1 B:198-210,211-220,239-254,295-317 2fu7 d2fu7a1 A:198-210,211-220,239-254,295-317 2gfj d2gfja1 A:198-210,211-220,239-254,295-317 2gfk d2gfkb1 B:198-210,211-220,239-254,295-317 2gfj d2gfjb1 B:198-210,211-220,239-254,295-317 11. c.81.1 Formate dehydrogenase/DMSO reductase, domains 1-3 molybdopterine enzyme ! Formate dehydrogenase/DMSO reductase, domains 1-3 contains of two similar intertwined domains related by pseudo dyad; duplication ! core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451 1ti2 d1ti2a2 A:547-554,571-579,611-624,630-638 1vlf d1vlfu2 U:547-554,571-579,611-624,630-638 1vle d1vleu2 U:547-554,571-579,611-624,630-638 1vlf d1vlfq2 Q:547-554,571-579,611-624,630-638 1vlf d1vlfs2 S:547-554,571-579,611-624,630-638 1ti4 d1ti4c2 C:547-554,571-579,611-624,630-638 1ti2 d1ti2k2 K:547-554,571-579,611-624,630-638 1vlf d1vlfo2 O:547-554,571-579,611-624,630-638 1ti6 d1ti6c2 C:547-554,571-579,611-624,630-638 1ti6 d1ti6e2 E:547-554,571-579,611-624,630-638 1vle d1vlem2 M:547-554,571-579,611-624,630-638 1ti4 d1ti4e2 E:547-554,571-579,611-624,630-638 1vle d1vles2 S:547-554,571-579,611-624,630-638 1ti2 d1ti2c2 C:547-554,571-579,611-624,630-638 1vle d1vleo2 O:547-554,571-579,611-624,630-638 1ti2 d1ti2i2 I:547-554,571-579,611-624,630-638 1vlf d1vlfw2 W:547-554,571-579,611-624,630-638 1ti4 d1ti4k2 K:547-554,571-579,611-624,630-638 1vle d1vlew2 W:547-554,571-579,611-624,630-638 1vld d1vldq2 Q:547-554,571-579,611-624,630-638 1ti2 d1ti2g2 G:547-554,571-579,611-624,630-638 1ti6 d1ti6a2 A:547-554,571-579,611-624,630-638 1ti4 d1ti4a2 A:547-554,571-579,611-624,630-638 1vlf d1vlfm2 M:547-554,571-579,611-624,630-638 1vle d1vleq2 Q:547-554,571-579,611-624,630-638 1vld d1vldm2 M:547-554,571-579,611-624,630-638 1ti4 d1ti4g2 G:547-554,571-579,611-624,630-638 1ti6 d1ti6k2 K:547-554,571-579,611-624,630-638 1ti6 d1ti6g2 G:547-554,571-579,611-624,630-638 1ti2 d1ti2e2 E:547-554,571-579,611-624,630-638 1ti4 d1ti4i2 I:547-554,571-579,611-624,630-638 1vld d1vldo2 O:547-554,571-579,611-624,630-638 1ti6 d1ti6i2 I:547-554,571-579,611-624,630-638 1vld d1vldu2 U:547-554,571-579,611-624,630-638 1vld d1vldw2 W:547-554,571-579,611-624,630-638 1vld d1vlds2 S:546-554,571-579,611-624,630-638 1tmo d1tmoa2 A:489-496,502-510,542-563,566-574 1e60 d1e60c2 C:480-488,492-501,533-553,558-566 1e60 d1e60a2 A:480-488,492-501,533-553,558-566 1e61 d1e61a2 A:480-488,492-501,533-553,558-566 1eu1 d1eu1a2 A:480-488,492-501,533-553,558-566 4dmr d4dmra2 A:480-488,492-501,533-553,558-566 1h5n d1h5na2 A:480-488,492-501,533-553,558-566 1e18 d1e18a2 A:480-488,492-501,533-553,558-566 2dmr d2dmra2 A:480-488,492-501,533-553,558-566 1dmr d1dmra2 A:480-488,492-501,533-553,558-566 1h5n d1h5nc2 C:480-488,492-501,533-553,558-566 1dms d1dmsa2 A:480-488,492-501,533-553,558-566 1e5v d1e5vc2 C:480-488,492-501,533-553,558-566 1e5v d1e5va2 A:480-488,492-501,533-553,558-566 1e61 d1e61c2 C:480-488,492-501,533-553,558-566 3dmr d3dmra2 A:480-488,492-501,533-553,558-566 1ogy d1ogya2 A:504-512,514-522,598-612,620-628 1ogy d1ogyo2 O:504-512,514-522,598-612,620-628 1ogy d1ogyk2 K:504-512,514-522,598-612,620-628 1ogy d1ogyg2 G:504-512,514-522,598-612,620-628 1ogy d1ogye2 E:504-512,514-522,598-612,620-628 1ogy d1ogyc2 C:504-512,514-522,598-612,620-628 1ogy d1ogyi2 I:504-512,514-522,598-612,620-628 1ogy d1ogym2 M:504-512,514-522,598-612,620-628 15. a.56.1 CO dehydrogenase ISP C-domain like contains 2Fe-2S cluster ! CO dehydrogenase ISP C-domain like core: 4 helices, bundle 1rm6 d1rm6c1 C:49-54,55-60,103-119,122-134 1rm6 d1rm6f1 F:49-54,55-60,103-119,122-134 1jrp d1jrpe1 E:47-54,55-62,103-121,124-133 1jro d1jroe1 E:47-54,55-62,103-121,124-133 1jrp d1jrpc1 C:47-54,55-62,103-121,124-133 1jro d1jroc1 C:47-54,55-62,103-121,124-133 1jro d1jroa1 A:47-54,55-62,103-121,124-133 1jrp d1jrpg1 G:47-54,55-62,103-121,124-133 1jro d1jrog1 G:47-54,55-62,103-121,124-133 1jrp d1jrpa1 A:47-54,55-62,103-121,124-133 1sb3 d1sb3c1 C:49-54,55-60,101-119,122-134 1sb3 d1sb3f1 F:49-54,55-60,101-119,122-134 1fiq d1fiqa1 A:51-59,64-72,114-132,135-144 1ffv d1ffvd1 D:50-55,56-61,102-120,123-135 1t3q d1t3qd1 D:56-61,62-67,108-126,129-141 1ffu d1ffud1 D:50-55,56-61,102-120,123-135 1ffu d1ffua1 A:50-55,56-61,102-120,123-135 1t3q d1t3qa1 A:56-61,62-67,108-126,129-141 3b9j d3b9ja1 A:51-61,62-72,114-132,135-146 1v97 d1v97a1 A:51-60,63-72,114-132,135-146 1fo4 d1fo4b1 B:51-60,63-72,114-132,135-144 1v97 d1v97b1 B:51-61,62-72,114-132,135-146 1n5x d1n5xa1 A:51-61,62-72,114-132,135-147 1n5x d1n5xb1 B:51-61,62-72,114-132,135-147 1vdv d1vdvb1 B:51-61,62-72,114-132,135-144 1vdv d1vdva1 A:51-61,62-72,114-132,135-144 3b9j d3b9ji1 I:51-60,63-72,114-132,135-147 1fo4 d1fo4a1 A:51-60,63-72,114-132,135-144 1vlb d1vlba1 A:48-53,54-59,101-119,122-134 1sij d1sija1 A:48-53,54-59,101-119,122-134 1dgj d1dgja1 A:48-53,54-59,101-119,122-134 1ffv d1ffva1 A:50-55,56-61,102-114,123-135 1n62 d1n62d1 D:50-55,56-61,103-121,124-133 1n60 d1n60d1 D:50-55,56-61,103-121,124-133 1n63 d1n63d1 D:50-55,56-61,103-121,124-133 1n62 d1n62a1 A:50-55,56-61,103-121,124-133 1n60 d1n60a1 A:50-55,56-61,103-121,124-133 1n61 d1n61d1 D:50-55,56-61,103-121,124-133 1n61 d1n61a1 A:50-55,56-61,103-121,124-133 1zxi d1zxia1 A:50-55,56-61,103-121,124-133 1n63 d1n63a1 A:50-55,56-61,103-121,124-133 1zxi d1zxid1 D:50-55,56-61,103-121,124-133 1n5w d1n5wd1 D:50-55,56-61,103-121,124-133 1n5w d1n5wa1 A:50-55,56-61,103-121,124-133 16. d.192.1 YlxR-like YlxR-like alpha+beta fold; could have evolved from a glucocorticoid receptor-like zinc finger domain 1g2r d1g2ra_ A:22-30,32-37,52-63,74-95 19. e.53.1 QueA-like QueA-like 2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474) 1vky d1vkyb_ B:26-34,35-43,296-307,307-322 1vky d1vkya_ A:26-34,35-43,296-307,307-322 20. d.356.1 SP0830-like SP0830-like duplication: two beta-alpha-beta(2)-alpha-beta-alpha motifs are organized in ferredoxin-like subdomains swapped with the extra C-terminal helices 2hiy d2hiyc1 C:1-8,43-50,78-89,167-180 2hiy d2hiyb1 B:1-8,43-50,78-89,167-179 2hiy d2hiyd1 D:1-8,43-50,78-89,167-180 2hiy d2hiya1 A:1-8,43-50,78-89,167-180 22. d.58.39 Glutamyl tRNA-reductase catalytic, N-terminal domain common fold is elaborated with additional secondary structures ! Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2 1gpj d1gpja3 A:3-11,49-57,77-91,99-117 26. d.328.1 CorA soluble domain-like CorA soluble domain-like beta(2)-alpha-beta-alpha(2)-beta(4)-alpha(3); 3 layers: a/b/a; mixed beta-sheet, order 2137654; strands 3 and 7 are parallel 2bbj d2bbjd1 D:27-36,59-66,69-81,83-93 2bbj d2bbjf1 F:27-36,58-66,69-81,83-93 2hn2 d2hn2d1 D:4027-4036,4058-4066,4069-4081,4083-4093 2hn2 d2hn2e1 E:5027-5036,5058-5066,5069-5081,5083-5093 2hn2 d2hn2a1 A:1027-1036,1058-1066,1069-1081,1083-1093 2hn2 d2hn2b1 B:2027-2036,2058-2066,2069-2081,2083-2093 2hn2 d2hn2c1 C:3027-3036,3058-3066,3069-3081,3083-3093 2iub d2iubg1 G:27-36,58-66,69-81,83-93 2iub d2iube1 E:27-36,58-66,69-81,83-93 2iub d2iubc1 C:27-36,58-66,69-81,83-93 2iub d2iubf1 F:27-36,58-66,69-81,83-93 2iub d2iubd1 D:27-36,58-66,69-81,83-93 2iub d2iuba1 A:27-36,58-66,69-81,83-93 2iub d2iubj1 J:27-36,58-66,69-81,83-93 2iub d2iubi1 I:27-36,58-66,69-81,83-93 2bbj d2bbjb1 B:27-36,58-66,69-81,83-93 2iub d2iubh1 H:27-36,58-66,69-81,83-93 2iub d2iubb1 B:27-36,58-66,69-81,83-93 2bbh d2bbha1 A:27-36,59-66,69-81,83-93 2bbj d2bbja1 A:27-36,58-66,69-81,83-93 2bbj d2bbje1 E:27-36,58-66,69-81,83-93 2bbh d2bbha1 A:104-115,122-133,165-199,207-226 39. d.129.4 Cell-division protein ZipA, C-terminal domain contains a single copy of this fold ! TBP-like beta-alpha-beta(4)-alpha 1y2g d1y2ga1 A:57-65,80-89,93-113,125-142 1s1j d1s1ja_ A:54-65,80-89,93-113,125-142 1f7x d1f7xa_ A:59-64,81-88,93-113,125-144 1f7w d1f7wa_ A:59-64,81-88,93-113,125-144 1s1s d1s1sa1 A:56-64,81-88,93-113,125-144 1f47 d1f47b_ B:57-64,80-89,93-113,125-144 1s1s d1s1sb1 B:57-64,80-89,93-113,125-143 1y2f d1y2fa1 A:56-64,80-88,93-113,125-144 1y2g d1y2gb1 B:54-64,80-88,93-113,125-144 1s1j d1s1jb_ B:54-64,80-88,93-113,125-144 51. e.58.1 Viral ssDNA binding protein Viral ssDNA binding protein 2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array] 1urj d1urja_ A:18-26,154-163,163-172,233-246 1urj d1urjb_ B:18-26,154-163,163-172,233-246 61. e.71.1 AF1531-like AF1531-like 2 domains; d1: incomplete barrel similar to the OB-fold domain of ribosomal L2 protein, d2: six helices, array 2i5h d2i5ha1 A:40-49,50-59,93-112,170-186