2. d.52.3 Prokaryotic type KH domain (KH-domain type II) Prokaryotic and eukaryotic domains share a KH-motif but have different topologies ! Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 2j02 d2j02c1 C:28-48,50-61,62-72,83-96,97-106 2j00 d2j00c1 C:28-48,50-61,62-72,83-96,97-106 1l2f d1l2fa2 A:200-213,219-228,231-240,255-266,268-274 1hh2 d1hh2p2 P:200-213,219-228,231-240,255-266,268-275 1n34 d1n34c1 C:25-52,51-61,62-71,81-96,97-104 2i2u d2i2uc1 C:24-47,50-57,61-70,82-95,96-102 2zkq d2zkqc1 C:10-30,32-43,44-54,63-79,82-91 2f4v d2f4vc1 C:25-48,50-61,62-72,81-96,97-104 1k0r d1k0ra2 A:185-198,204-213,216-225,240-251,253-260 1k0r d1k0rb2 B:185-198,204-213,216-225,240-251,253-260 1j5e d1j5ec1 C:25-48,50-61,62-72,81-96,97-106 1i94 d1i94c1 C:25-48,50-61,62-72,81-96,97-106 2atw d2atwa2 A:185-198,204-213,216-225,240-251,253-259 2atw d2atwc2 C:185-198,204-213,216-225,240-251,253-259 2hhh d2hhhc1 C:25-48,50-61,62-72,81-96,97-106 1i96 d1i96c1 C:25-48,50-61,62-72,81-96,97-106 2asb d2asba2 A:185-198,204-213,216-225,240-251,253-259 1hnz d1hnzc1 C:25-48,50-61,62-72,81-96,97-106 1hr0 d1hr0c1 C:28-48,50-61,62-72,81-96,97-106 1hnx d1hnxc1 C:25-48,50-61,62-72,81-96,97-106 1hnw d1hnwc1 C:25-48,50-61,62-72,81-96,97-106 1fjg d1fjgc1 C:25-48,50-61,62-72,81-96,97-106 2avy d2avyc1 C:24-47,50-60,61-70,80-95,96-105 2aw7 d2aw7c1 C:24-47,51-60,61-69,82-95,96-104 1n33 d1n33c1 C:25-48,50-59,64-72,81-96,99-105 1vs7 d1vs7c1 C:24-47,51-60,61-69,82-95,96-104 2qou d2qouc1 C:24-47,49-60,61-71,80-95,96-103 1vs5 d1vs5c1 C:24-47,50-60,61-70,80-95,96-105 1i95 d1i95c1 C:25-48,50-61,62-72,81-96,98-106 3df3 d3df3c1 C:24-47,52-60,61-69,80-95,96-103 2vhp d2vhpc1 C:24-47,50-60,61-70,82-95,97-104 2qbh d2qbhc1 C:24-47,49-60,61-71,80-95,96-104 2qbj d2qbjc1 C:24-47,49-60,61-71,80-95,96-104 1n36 d1n36c1 C:25-52,53-61,62-70,81-93,99-105 3df1 d3df1c1 C:24-47,49-60,61-71,80-95,96-103 1xnq d1xnqc1 C:25-48,50-61,62-72,81-96,99-106 2qb9 d2qb9c1 C:24-47,49-60,61-71,80-95,96-104 2qbb d2qbbc1 C:24-47,49-60,61-71,80-95,96-104 1wh9 d1wh9a_ A:6-21,24-34,35-44,54-69,74-82 2z4k d2z4kc1 C:24-47,49-60,61-71,80-95,96-105 2z4m d2z4mc1 C:24-47,49-60,61-71,80-95,96-105 2atw d2atwc3 C:263-273,277-286,287-295,307-318,319-326 2uxc d2uxcc1 C:25-48,50-61,62-72,81-96,99-106 2vho d2vhoc1 C:24-47,49-60,61-71,80-95,98-104 1k0r d1k0ra3 A:263-273,277-286,287-295,307-318,319-326 2qbd d2qbdc1 C:24-47,49-60,61-71,80-95,96-105 2qbf d2qbfc1 C:24-47,49-60,61-71,80-95,96-105 2qp0 d2qp0c1 C:24-47,50-60,61-70,80-95,97-105 1k0r d1k0rb3 B:263-273,277-286,287-295,307-318,319-326 2qal d2qalc1 C:24-47,49-60,61-71,80-95,96-105 2qan d2qanc1 C:24-47,49-60,61-71,80-95,96-105 2qow d2qowc1 C:24-47,50-60,61-70,80-95,98-105 2atw d2atwa3 A:263-273,277-286,287-296,307-318,319-327 1xmq d1xmqc1 C:25-48,50-61,62-72,81-96,99-106 1xmo d1xmoc1 C:25-48,50-61,62-72,81-96,99-106 1n32 d1n32c1 C:25-48,50-61,62-72,81-96,99-106 2b9o d2b9oc1 C:25-48,50-61,62-72,81-96,98-106 2b9m d2b9mc1 C:25-48,50-61,62-72,81-96,98-106 2b64 d2b64c1 C:25-48,50-61,62-72,81-96,98-106 2asb d2asba3 A:263-273,277-286,287-296,307-318,319-327 1hh2 d1hh2p3 P:278-288,292-301,302-310,322-333,334-341 1l2f d1l2fa3 A:278-288,292-301,302-310,322-333,334-341 2uuc d2uucc1 C:25-48,50-61,62-72,81-96,99-106 2uua d2uuac1 C:25-48,50-61,62-72,81-96,99-106 1xnr d1xnrc1 C:25-48,50-61,62-72,81-96,99-106 2uu9 d2uu9c1 C:25-48,50-61,62-72,79-96,99-106 2uub d2uubc1 C:25-48,50-61,62-72,81-96,99-106 2ow8 d2ow8d1 D:28-48,54-61,62-72,81-96,99-106 2e5l d2e5lc1 C:25-48,50-61,62-72,81-96,99-106 2i2p d2i2pc1 C:24-47,49-60,61-71,78-95,96-105 2qoy d2qoyc1 C:24-47,49-60,61-71,78-95,96-105 1i97 d1i97c1 C:25-48,52-61,62-71,81-96,101-106 1ega d1egab2 B:189-207,213-225,226-238,251-270,273-281 2hgi d2hgif1 F:25-48,52-59,63-71,81-95,98-106 1ega d1egaa2 A:189-207,214-225,226-238,251-270,273-282 1yl4 d1yl4f1 F:25-48,51-59,64-71,81-96,102-106 2ow8 d2ow8d1 D:28-48,50-54,62-72,81-96,99-106 2hgr d2hgrf1 F:25-48,52-59,64-71,81-95,102-106 2hgp d2hgpf1 F:25-48,52-59,64-71,81-96,102-106 1wf3 d1wf3a2 A:188-206,213-224,226-237,250-269,271-281 3. d.52.8 Fe-S cluster assembly (FSCA) domain-like similar putative active site with a conserved cysteine residue ! Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 2cu6 d2cu6a1 A:6-19,32-40,41-48,58-72,75-82 2cu6 d2cu6b1 B:6-19,32-40,41-48,58-72,75-82 1th5 d1th5a1 A:157-169,177-187,188-197,201-217,220-226 1veh d1veha_ A:12-25,34-44,45-53,58-78,81-86 1xhj d1xhja_ A:7-28,29-37,38-45,52-71,74-81 1wcj d1wcja_ A:7-19,32-40,42-49,57-73,76-83 1veh d1veha_ A:24-34,34-44,45-53,58-78,81-86 1uwd d1uwda_ A:7-19,32-40,42-49,57-73,76-81 4. d.218.1 Nucleotidyltransferase Nucleotidyltransferase core: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands: 123 1wot d1wota_ A:8-21,22-28,42-48,53-69,72-77 2o5a d2o5ab1 B:3-18,19-27,35-43,44-63,84-92 2o5a d2o5aa1 A:3-18,19-27,35-43,44-63,84-92 1ylq d1ylqa1 A:-1-13,15-21,34-41,46-62,65-72 2id1 d2id1b1 B:2-18,19-27,35-42,44-63,84-91 2id1 d2id1a1 A:2-18,19-27,35-42,44-63,84-91 1ylq d1ylqb1 B:-1-13,15-21,34-41,46-62,65-72 1no5 d1no5a_ A:10-26,28-33,46-53,58-73,77-84 1vfg d1vfga2 A:1-10,11-16,30-38,39-52,70-78 1vfg d1vfgb2 B:1-10,11-16,30-38,39-52,70-78 1xsl d1xsli3 I:388-408,410-415,427-434,443-455,486-494 1rzt d1rztm3 M:388-408,410-415,427-434,443-455,486-494 2pbe d2pbea2 A:3-19,20-27,42-50,58-66,97-107 2gws d2gwsa3 A:388-408,410-415,427-434,443-455,486-494 1rzt d1rzti3 I:388-408,410-415,427-434,443-455,486-494 1no5 d1no5b_ B:10-26,27-33,46-53,58-72,77-84 1zjm d1zjma3 A:151-171,173-178,190-197,209-222,252-260 1vj7 d1vj7b2 B:217-233,236-241,265-272,274-290,319-328 1miy d1miya2 A:2-19,21-26,41-46,48-57,75-83 1miy d1miyb2 B:2-19,21-26,41-46,48-57,75-83 2pxi d2pxia3 A:151-171,173-178,190-197,209-222,252-260 2fmq d2fmqa3 A:151-171,173-178,190-197,209-222,252-260 2iso d2isoa3 A:151-171,173-178,190-197,209-222,252-260 2isp d2ispa3 A:151-171,173-178,190-197,209-222,252-260 2nrk d2nrka1 A:9-28,30-37,50-58,66-74,95-105 2fms d2fmsa3 A:151-171,173-178,190-197,209-222,252-260 3c2l d3c2la3 A:151-171,173-178,190-197,209-222,252-260 3c2k d3c2ka3 A:151-171,173-178,190-197,209-222,252-260 2gws d2gwsi3 I:388-408,410-415,427-434,440-455,486-495 2fmp d2fmpa3 A:151-171,173-178,190-197,209-222,252-260 3c5f d3c5fb3 B:388-408,410-415,427-434,440-455,486-495 3c2m d3c2ma3 A:151-171,173-178,190-197,209-222,252-260 1zjn d1zjna3 A:151-171,172-178,190-198,209-222,252-260 1mq3 d1mq3a3 A:151-171,173-178,190-197,209-222,252-260 1miv d1miva2 A:2-19,21-26,42-46,48-57,75-83 1miv d1mivb2 B:2-19,21-26,42-46,48-57,75-83 2p66 d2p66a3 A:151-171,173-178,190-197,208-222,252-260 1xsl d1xsle3 E:388-408,410-415,427-434,442-455,486-494 1xsl d1xslm3 M:388-408,410-415,427-434,440-455,486-494 1xsl d1xsla3 A:388-408,410-415,427-434,440-455,486-494 2gws d2gwsm3 M:388-408,410-415,427-434,440-455,486-494 1rzt d1rzta3 A:388-408,410-415,427-434,440-455,486-494 8icr d8icra4 A:151-171,173-178,190-197,207-222,252-260 8icb d8icba4 A:151-171,173-178,190-197,207-222,252-260 7icf d7icfa4 A:151-171,173-178,190-197,207-222,252-260 1zqv d1zqva2 A:151-171,173-178,190-197,207-222,252-260 3c5g d3c5gb3 B:388-408,410-415,427-434,440-455,486-494 8ici d8icia4 A:151-171,173-178,190-197,207-222,252-260 1zqo d1zqoa4 A:151-171,173-178,190-197,207-222,252-260 1ueu d1ueua2 A:17-39,41-45,59-66,72-84,106-115 3c5f d3c5fa3 A:388-408,410-415,427-434,440-455,486-494 1zql d1zqla4 A:151-171,173-178,190-197,207-222,252-260 8icz d8icza4 A:151-171,173-178,190-197,207-222,252-260 1zqz d1zqza2 A:151-171,173-178,190-197,207-222,252-260 7icu d7icua4 A:151-171,173-178,190-197,207-222,252-260 1zqm d1zqma4 A:151-171,173-178,190-197,207-222,252-260 8icu d8icua4 A:151-171,173-178,190-197,207-222,252-260 1bpx d1bpxa4 A:151-171,172-178,190-198,207-222,252-260 1zqc d1zqca4 A:151-171,173-178,190-197,207-222,252-260 1miw d1miwb2 B:2-19,21-25,42-46,48-57,75-83 2gws d2gwse3 E:388-408,410-415,427-434,440-455,486-494 1rzt d1rzte3 E:388-408,410-415,427-434,440-455,486-494 1bpe d1bpea3 A:151-171,172-178,190-198,207-222,252-260 1zqk d1zqka4 A:151-171,173-178,190-197,207-222,252-260 1miw d1miwa2 A:2-19,21-25,42-46,48-57,75-83 8icv d8icva4 A:151-171,173-178,190-197,207-222,252-260 8icw d8icwa4 A:151-171,173-178,190-197,207-222,252-260 1zqn d1zqna4 A:151-171,173-178,190-197,207-222,252-260 1zqh d1zqha4 A:151-171,173-178,190-197,207-222,252-260 1zqf d1zqfa4 A:151-171,173-178,190-197,207-222,252-260 9ici d9icia4 A:151-171,173-178,190-197,207-222,252-260 8ick d8icka4 A:151-171,173-178,190-197,207-222,252-260 8icg d8icga4 A:151-171,173-178,190-197,207-222,252-260 8icx d8icxa4 A:151-171,173-178,190-197,207-222,252-260 1zqd d1zqda4 A:151-171,173-178,190-197,207-222,252-260 8icn d8icna4 A:151-171,173-178,190-197,207-222,252-260 9icu d9icua4 A:151-171,173-178,190-197,207-222,252-260 8ich d8icha4 A:151-171,173-178,190-197,207-222,252-260 8icq d8icqa4 A:151-171,173-178,190-197,207-222,252-260 1zqa d1zqaa4 A:151-171,173-178,190-197,207-222,252-260 1zqs d1zqsa4 A:151-171,173-178,190-197,207-222,252-260 9ica d9icaa4 A:151-171,173-178,190-197,207-222,252-260 1zqg d1zqga4 A:151-171,173-178,190-197,207-222,252-260 8icy d8icya4 A:151-171,172-178,190-198,207-222,252-260 1zqt d1zqta4 A:151-171,173-178,190-197,207-222,252-260 9icc d9icca4 A:151-171,173-178,190-197,207-222,252-260 1zqi d1zqia4 A:151-171,173-178,190-197,207-222,252-260 8ica d8icaa4 A:151-171,173-178,190-197,207-222,252-260 9ice d9icea4 A:151-171,173-178,190-197,207-222,252-260 9icj d9icja4 A:151-171,173-178,190-197,207-222,252-260 3c5g d3c5ga3 A:388-408,410-415,427-434,440-455,486-494 9icl d9icla4 A:151-171,173-178,190-197,207-222,252-260 8ict d8icta4 A:151-171,173-178,190-197,207-222,252-260 8icp d8icpa4 A:151-171,173-178,190-197,207-222,252-260 1zqe d1zqea4 A:151-171,173-178,190-197,207-222,252-260 8icj d8icja4 A:151-171,173-178,190-197,207-222,252-260 1zqq d1zqqa4 A:151-171,173-178,190-197,207-222,252-260 1f5a d1f5aa4 A:54-84,95-100,113-122,125-140,163-174 9icf d9icfa4 A:151-171,173-178,190-197,207-222,252-260 1q79 d1q79a2 A:54-84,95-100,113-122,125-140,163-174 9ich d9icha4 A:151-171,173-178,190-197,207-222,252-260 7ice d7icea4 A:151-171,173-178,190-197,207-222,252-260 9icn d9icna4 A:151-171,173-178,190-197,207-222,252-260 7icl d7icla4 A:151-171,173-178,190-197,207-222,252-260 9ics d9icsa4 A:151-171,173-178,190-197,207-222,252-260 9icv d9icva4 A:151-171,173-178,190-197,207-222,252-260 7icm d7icma4 A:151-171,173-178,190-197,207-222,252-260 7ict d7icta4 A:151-171,173-178,190-197,207-222,252-260 1zqp d1zqpa4 A:151-171,173-178,190-197,207-222,252-260 7icg d7icga4 A:151-171,172-178,190-198,207-222,252-260 7icv d7icva4 A:151-171,173-178,190-197,207-222,252-260 8icc d8icca4 A:151-171,173-178,190-197,207-222,252-260 9icm d9icma4 A:151-171,173-178,190-197,207-222,252-260 8icl d8icla4 A:151-171,173-178,190-197,207-222,252-260 1bpb d1bpba2 A:151-171,173-178,190-197,207-222,252-260 9icq d9icqa4 A:151-171,173-178,190-197,207-222,252-260 9ico d9icoa4 A:151-171,173-178,190-197,207-222,252-260 2bpc d2bpca2 A:151-171,173-178,190-197,207-222,252-260 7ick d7icka4 A:151-171,173-178,190-197,207-222,252-260 8icf d8icfa4 A:151-171,173-178,190-197,207-222,252-260 7ici d7icia4 A:151-171,173-178,190-197,207-222,252-260 7icq d7icqa4 A:151-171,173-178,190-197,207-222,252-260 8icm d8icma4 A:151-171,173-178,190-197,207-222,252-260 9ict d9icta4 A:151-171,173-178,190-197,207-222,252-260 1zqw d1zqwa2 A:151-171,173-178,190-197,207-222,252-260 7icn d7icna4 A:151-171,172-178,190-198,207-222,252-260 9icr d9icra4 A:151-171,173-178,190-197,207-222,252-260 1zqx d1zqxa2 A:151-171,173-178,190-197,207-222,252-260 9icy d9icya4 A:151-171,173-178,190-197,207-222,252-260 1vj7 d1vj7a2 A:210-233,236-241,267-272,274-290,319-328 7ico d7icoa4 A:151-171,172-178,190-198,207-222,252-260 9icw d9icwa4 A:151-171,173-178,190-197,207-222,252-260 2bpf d2bpfa4 A:151-171,173-178,190-197,207-222,252-260 9icg d9icga4 A:151-171,172-178,190-198,207-222,252-260 1zqj d1zqja4 A:151-171,173-178,190-197,207-222,252-260 9icb d9icba4 A:151-171,173-178,190-197,207-222,252-260 1zqu d1zqua2 A:151-171,173-178,190-197,207-222,252-260 8ico d8icoa4 A:151-171,173-178,190-197,207-222,252-260 2van d2vana2 A:151-171,173-178,190-197,207-222,252-260 1q78 d1q78a2 A:54-84,95-100,113-122,125-140,163-174 1nom d1noma2 A:151-171,173-178,190-197,207-222,252-260 9ick d9icka4 A:151-171,173-178,190-197,207-222,252-260 8ice d8icea4 A:151-171,173-178,190-197,207-222,252-260 8ics d8icsa4 A:151-171,173-178,190-197,207-222,252-260 1zqr d1zqra4 A:151-171,173-178,190-197,207-222,252-260 2q66 d2q66a2 A:41-71,82-87,100-109,112-128,150-161 1bpy d1bpya4 A:151-171,173-178,190-197,207-222,252-260 1jn3 d1jn3a2 A:151-171,173-178,190-197,207-222,252-260 1zqy d1zqya2 A:151-171,173-178,190-197,207-222,252-260 7ich d7icha4 A:151-171,173-178,190-197,207-222,252-260 2bpg d2bpgb4 B:151-171,173-178,190-197,207-222,252-260 9icx d9icxa4 A:151-171,173-178,190-197,207-222,252-260 9icp d9icpa4 A:151-171,172-178,190-198,207-222,252-260 7icp d7icpa4 A:151-171,172-178,190-198,207-222,252-260 1bpz d1bpza4 A:151-171,172-178,190-198,207-222,252-260 7ics d7icsa4 A:151-171,173-178,190-197,207-222,252-260 1rpl d1rpla2 A:151-171,173-178,190-197,207-222,252-260 1tv9 d1tv9a3 A:151-171,173-178,190-197,207-222,252-260 1zqb d1zqba4 A:151-171,173-178,190-197,207-222,252-260 2o1p d2o1pa2 A:41-71,82-87,100-109,112-128,150-161 7icj d7icja4 A:151-171,173-178,190-197,207-222,252-260 1fa0 d1fa0b4 B:41-71,82-87,100-109,112-128,150-161 7icr d7icra4 A:151-171,172-178,190-198,207-222,252-260 3c66 d3c66b2 B:41-71,82-87,100-109,112-128,150-161 1uet d1ueta2 A:17-39,41-45,59-66,71-84,106-115 2o1p d2o1pb2 B:41-71,82-87,100-109,112-128,150-161 2bpg d2bpga4 A:151-171,172-178,190-198,207-222,252-260 3c66 d3c66a2 A:41-71,82-87,100-109,112-128,150-161 2hhp d2hhpa2 A:41-71,82-87,100-109,112-128,150-161 1mq2 d1mq2a3 A:151-171,173-178,190-197,207-222,252-260 1huo d1huob4 B:151-171,173-178,190-197,207-222,252-260 1fa0 d1fa0a4 A:41-71,82-87,100-109,112-128,150-161 1huz d1huzb4 B:151-171,173-178,190-197,207-222,252-260 1tva d1tvaa3 A:151-171,173-178,190-197,207-222,252-260 2pfp d2pfpa3 A:388-408,410-415,427-434,442-455,486-494 2bcu d2bcua3 A:388-408,410-415,427-434,442-455,486-494 1xsn d1xsna3 A:388-408,410-415,427-434,442-455,486-494 1huo d1huoa4 A:151-171,173-178,190-197,207-222,252-260 2i9g d2i9ga3 A:151-171,173-178,190-197,207-222,252-260 2pfn d2pfna3 A:388-408,410-415,427-434,442-455,486-494 2bcs d2bcsa3 A:388-408,410-415,427-434,442-455,486-494 1huz d1huza4 A:151-171,173-178,190-197,207-222,252-260 2bcr d2bcra3 A:388-408,410-415,427-434,442-455,486-494 2bcv d2bcva3 A:388-408,410-415,427-434,442-455,486-494 1xsp d1xspa3 A:388-408,410-415,427-434,442-455,486-494 2pfo d2pfoa3 A:388-408,410-415,427-434,442-455,486-494 2bcq d2bcqa3 A:388-408,410-415,427-434,442-455,486-494 1bpd d1bpda3 A:151-171,173-178,190-197,207-222,252-260 1ou5 d1ou5a2 A:13-27,28-35,50-55,56-68,88-95 2pfq d2pfqa3 A:388-408,410-415,427-434,442-455,486-494 1ou5 d1ou5b2 B:13-27,28-35,50-55,56-68,88-95 1kdh d1kdha4 A:304-324,326-331,343-350,354-373,427-438 1kej d1keja4 A:304-324,326-331,343-350,354-373,427-438 1uev d1ueva2 A:17-39,41-45,59-66,70-84,106-115 1jms d1jmsa4 A:304-324,326-331,343-350,354-373,427-438 2be3 d2be3b1 B:2-34,39-47,73-80,82-96,131-144 2be3 d2be3a1 A:2-34,38-47,73-81,82-96,131-144 2b4v d2b4va2 A:53-76,78-83,97-104,110-129,264-270 2ewr d2ewra1 A:3-20,23-27,43-49,50-61,87-101 1sz1 d1sz1a2 A:18-39,41-45,59-67,71-88,106-116 1sz1 d1sz1b2 B:18-39,41-45,59-67,71-88,106-116 1px5 d1px5b2 B:24-44,52-64,71-83,93-113,140-153 1tfw d1tfwa2 A:17-39,41-45,59-66,71-87,106-115 2zha d2zhaa2 A:17-39,41-45,59-66,71-88,106-115 2dr5 d2dr5a2 A:17-39,41-45,59-67,71-87,106-116 2dr7 d2dr7a2 A:17-39,41-45,59-67,71-87,106-116 2zh6 d2zh6a2 A:17-39,41-45,59-67,71-87,106-116 2zh9 d2zh9a2 A:17-39,41-45,59-67,71-87,106-116 2zh2 d2zh2a2 A:17-39,41-45,59-66,71-87,106-116 2zh4 d2zh4a2 A:17-39,41-45,59-67,71-87,106-116 1tfy d1tfyd2 D:17-39,41-45,59-67,71-88,106-116 1tfw d1tfwc2 C:17-39,41-45,59-67,71-87,106-116 2dra d2draa2 A:17-39,41-45,59-67,71-87,106-116 2zh7 d2zh7a2 A:17-39,41-45,59-67,71-87,106-116 2zh3 d2zh3a2 A:17-39,41-45,59-67,71-87,106-116 2dr8 d2dr8a2 A:17-39,41-45,59-67,71-87,106-116 1tfy d1tfya2 A:17-39,41-45,59-67,71-87,106-116 2dvi d2dvia2 A:17-39,41-45,59-67,71-87,106-116 1r8a d1r8aa2 A:17-39,41-45,59-67,71-87,106-116 1tfy d1tfyc2 C:17-39,41-45,59-67,71-87,106-116 2zh1 d2zh1a2 A:17-39,41-45,59-67,71-87,106-116 2dr9 d2dr9a2 A:17-39,41-45,59-67,71-88,106-116 2zh8 d2zh8a2 A:17-39,41-45,59-67,71-87,106-116 2zh5 d2zh5a2 A:17-39,41-45,59-67,71-87,106-116 1tfy d1tfyb2 B:17-39,41-45,59-67,71-87,106-116 2drb d2drba2 A:17-39,41-45,59-67,71-87,106-116 2zhb d2zhba2 A:17-39,41-45,59-67,71-88,106-116 1px5 d1px5a2 A:24-44,52-63,72-83,93-112,140-153 1r8c d1r8ca2 A:17-39,41-45,59-67,71-87,106-116 1r89 d1r89a2 A:17-39,41-45,59-67,71-87,106-116 1tfw d1tfwb2 B:17-39,41-45,59-67,71-88,106-116 1r8b d1r8ba2 A:17-39,41-45,59-67,71-87,106-116 1tfw d1tfwd2 D:17-39,41-45,59-67,71-87,106-116 7. d.52.2 GMP synthetase C-terminal dimerisation domain Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 1gpm d1gpma3 A:417-439,445-453,468-478,489-505,508-514 1gpm d1gpmc3 C:417-439,445-452,469-479,489-505,509-514 1gpm d1gpmb3 B:417-439,445-453,468-479,489-505,508-514 1gpm d1gpmd3 D:417-439,445-452,469-479,489-505,509-514 8. d.333.1 UbiD C-terminal domain-like UbiD C-terminal domain-like alpha-beta(2)-alpha-beta-alpha-beta(2); 3 layers, a/b/a; mixed beta-sheet, order: 12354, strands 2,3 and 5 are parallel to each other 2idb d2idbc2 C:340-349,350-357,364-371,376-390,396-403 2idb d2idba2 A:340-349,350-357,364-371,376-390,396-403 2idb d2idbb2 B:340-349,350-356,364-371,376-390,396-403 9. d.147.1 Methenyltetrahydromethanopterin cyclohydrolase Methenyltetrahydromethanopterin cyclohydrolase consists of two alpha+beta subdomains 1qlm d1qlma_ A:3-19,24-30,32-38,45-58,163-170 1qlm d1qlma_ A:183-197,202-212,233-241,243-254,287-295 11. d.52.9 Cation efflux protein cytoplasmic domain-like Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 2qfi d2qfia1 A:211-225,229-238,240-248,257-275,280-284 2qfi d2qfib1 B:211-225,229-238,240-248,257-275,280-284 3byp d3bypb1 B:8-24,27-39,40-51,55-75,76-86 3byp d3bypa1 A:8-24,27-39,40-51,55-75,76-86 3byr d3byra1 A:8-24,27-39,40-51,55-75,76-86 13. d.307.1 Nqo5-like Nqo5-like core: alpha-beta(2)-alpha-beta(3); 2 layers, a/b; mixed beta-sheet, order 12534, strands 2 and 5 are parallel 2fug d2fuge1 E:1-15,15-20,24-29,33-43,86-94 2fug d2fugn1 N:1-15,15-20,24-29,33-43,86-95 2fug d2fug51 5:1-15,15-20,24-29,33-43,86-95 2fug d2fugw1 W:1-15,15-20,24-29,30-43,86-95 14. d.215.1 Smc hinge domain Smc hinge domain consists of 2 different alpha+beta subdomains; forms subdomain-swapped dimers 1gxj d1gxja_ A:500-510,515-519,544-549,549-564,566-574 1gxk d1gxkb_ B:500-510,515-519,544-549,549-564,565-574 1gxj d1gxjb_ B:500-510,515-519,544-549,549-564,565-574 1gxl d1gxlc_ C:500-510,515-519,544-549,549-564,565-574 1gxl d1gxla_ A:500-510,515-519,544-549,549-564,565-574 1gxl d1gxlb_ B:500-510,515-519,544-549,549-564,565-574 1gxl d1gxld_ D:500-510,515-519,544-549,549-564,565-574 1gxk d1gxkc_ C:501-510,515-519,544-549,549-564,567-574 1gxk d1gxka_ A:501-510,515-519,544-549,549-564,568-574 1gxk d1gxkd_ D:501-510,515-519,544-549,549-564,568-574 16. b.43.2 FucI/AraA C-terminal domain-like Reductase/isomerase/elongation factor common domain barrel, closed; n=6, S=10; greek-key 1fui d1fuid1 D:339-354,454-466,470-482,536-548,549-555 1fui d1fuie1 E:339-354,454-467,469-481,536-548,549-555 1fui d1fuib1 B:339-354,455-467,469-481,536-548,549-555 1fui d1fuic1 C:339-354,454-467,469-482,536-548,549-555 1fui d1fuif1 F:339-354,454-467,469-482,536-548,549-555 1fui d1fuia1 A:339-354,454-467,469-482,536-548,549-555 2ajt d2ajtb1 B:308-323,389-400,401-413,458-470,471-477 2hxg d2hxga1 A:308-323,388-400,401-413,458-470,471-477 2ajt d2ajta1 A:308-323,389-400,401-413,458-470,471-477 2ajt d2ajtc1 C:308-323,389-400,401-413,458-470,471-477 2hxg d2hxgb1 B:308-323,389-400,401-413,458-470,472-477 2hxg d2hxgc1 C:308-323,388-400,401-413,458-470,472-477 19. d.52.5 Probable GTPase Der, C-terminal domain possible distant relative of the Era C-terminal domain lacking the KH motif ! Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 1mky d1mkya3 A:361-377,382-392,395-403,408-425,431-438 20. d.130.1 S-adenosylmethionine synthetase S-adenosylmethionine synthetase duplication: consists of 3 similar intertwined domains ! structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta 1p7l d1p7ld1 D:14-35,37-47,48-58,63-76,89-94 1rg9 d1rg9d1 D:14-35,37-47,48-58,63-76,89-94 1rg9 d1rg9c1 C:14-35,37-47,48-58,63-76,89-94 1rg9 d1rg9b1 B:14-35,37-47,48-58,63-76,89-94 1p7l d1p7lc1 C:14-35,37-47,48-58,63-76,89-94 1rg9 d1rg9a1 A:14-35,37-47,48-58,63-76,89-94 1p7l d1p7lb1 B:14-35,37-47,48-58,63-76,89-94 1p7l d1p7la1 A:14-35,37-47,48-58,63-76,89-94 2p02 d2p02a1 A:51-72,74-84,85-95,100-113,126-131 1xra d1xraa1 A:14-35,37-47,48-58,63-76,89-99 1qm4 d1qm4b1 B:30-51,53-63,64-74,79-92,105-115 1mxa d1mxaa1 A:14-35,37-47,48-58,63-76,89-99 1xrc d1xrca1 A:14-35,37-47,48-58,63-76,89-99 1qm4 d1qm4a1 A:30-51,53-63,64-74,79-92,105-115 1mxb d1mxba1 A:14-35,37-47,48-58,63-76,89-99 1xrb d1xrba1 A:14-35,37-47,48-58,63-76,89-99 1mxc d1mxca1 A:14-35,37-47,48-58,63-76,89-99 1fug d1fugb1 B:14-35,37-47,48-58,63-76,89-99 1o90 d1o90a1 A:30-51,53-63,64-74,79-92,105-115 1o90 d1o90b1 B:30-51,53-63,64-74,79-92,105-115 1o92 d1o92b1 B:30-51,53-63,64-74,79-92,105-115 1o92 d1o92a1 A:30-51,53-63,64-74,79-92,105-115 1o9t d1o9ta1 A:30-51,53-63,64-74,79-92,105-115 1o9t d1o9tb1 B:30-51,53-63,64-74,79-92,105-115 1o93 d1o93a1 A:30-51,53-63,64-74,79-92,105-115 1o93 d1o93b1 B:30-51,53-63,64-74,79-92,105-115 1fug d1fuga1 A:14-35,37-47,48-58,63-76,89-98 1qm4 d1qm4b2 B:152-172,180-192,195-209,215-232,241-246 1qm4 d1qm4a2 A:152-172,180-192,195-209,215-232,241-246 1xrb d1xrba2 A:135-155,163-174,175-188,194-207,220-225 1p7l d1p7lc2 C:135-155,163-174,175-188,194-207,220-225 1xrc d1xrca2 A:135-155,163-174,175-188,194-207,220-225 1rg9 d1rg9c2 C:135-155,163-174,175-188,194-207,220-225 1mxa d1mxaa2 A:135-155,163-174,175-188,194-207,220-225 1p7l d1p7ld2 D:135-155,163-174,175-188,194-207,220-225 1rg9 d1rg9d2 D:135-155,163-174,175-188,194-207,220-225 1mxc d1mxca2 A:135-155,163-174,175-188,194-207,220-225 1p7l d1p7lb2 B:135-155,163-174,175-188,194-207,220-225 1rg9 d1rg9b2 B:135-155,163-174,175-188,194-207,220-225 1p7l d1p7la2 A:135-155,163-174,175-188,194-207,220-225 1rg9 d1rg9a2 A:135-155,163-174,175-188,194-207,220-225 1mxb d1mxba2 A:135-155,163-174,175-188,194-206,220-225 1fug d1fuga2 A:135-155,163-174,177-188,194-207,220-225 1xra d1xraa2 A:135-155,163-174,175-188,194-206,220-225 2p02 d2p02a2 A:173-193,201-214,215-230,236-254,262-267 1o93 d1o93a2 A:152-172,180-193,194-209,215-232,241-246 1o93 d1o93b2 B:152-172,180-193,194-209,215-232,241-246 1o9t d1o9ta2 A:152-172,180-193,194-209,215-232,241-246 1o9t d1o9tb2 B:152-172,180-193,194-209,215-232,241-246 1o90 d1o90a2 A:152-172,180-193,194-209,215-233,241-246 1o92 d1o92a2 A:152-172,180-193,194-209,215-233,241-246 1o90 d1o90b2 B:152-172,180-193,194-209,215-233,241-246 1o92 d1o92b2 B:152-172,180-193,194-209,215-233,241-246 1fug d1fugb2 B:135-155,163-174,178-188,194-206,220-225 23. d.52.6 BolA-like Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 1v9j d1v9ja_ A:31-44,46-53,60-68,75-88,95-103 1ny8 d1ny8a_ A:6-19,21-27,31-40,46-59,68-76 25. d.52.7 Ribosome-binding factor A, RbfA possible distant homologue of the type I KH domain lacking the KH motif ! Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 2e7g d2e7ga1 A:86-111,123-130,134-141,159-171,177-182 2r1c d2r1ca1 A:5-24,31-39,43-51,55-66,83-89 2dyj d2dyja1 A:4-24,30-39,43-52,54-66,83-90 2r1c d2r1ca1 A:5-24,31-39,43-51,65-78,83-89 2dyj d2dyjb1 B:4-24,30-39,43-52,65-78,83-90 2dyj d2dyjb1 B:4-24,30-39,43-52,54-66,83-90 1kkg d1kkga_ A:7-28,36-45,48-57,75-88,94-102 2dyj d2dyja1 A:4-24,30-39,43-52,65-78,83-90 1jos d1josa_ A:7-28,32-43,47-57,74-87,92-98 1pa4 d1pa4a_ A:7-25,33-42,45-53,55-82,87-92 1jos d1josa_ A:7-28,32-43,47-57,60-75,92-98 1kkg d1kkga_ A:7-28,36-45,48-57,61-76,94-102 2e7g d2e7ga1 A:86-111,123-130,134-141,145-160,177-182 26. d.326.1 XisI-like XisI-like alpha-beta(4)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order 1234, meander; the open side of beta-sheet provides dimerization interface 2nlv d2nlvb1 B:3-22,51-65,66-74,78-87,92-96 2nvm d2nvma1 A:2-24,65-79,80-88,91-101,106-110 2nvm d2nvmb1 B:2-24,65-79,80-88,91-101,106-110 2nwv d2nwva1 A:2-25,53-67,68-76,80-89,94-99 2nlv d2nlva1 A:0-22,51-65,66-74,78-87,92-96 27. e.69.1 Poly(A) polymerase catalytic subunit-like Central domain d2 is distantly related to the nucleotidyltransferase superfamily (scop_sf 81301) Poly(A) polymerase catalytic subunit-like 3 domains; d1: all-alpha, contains HhH motif; d2: alpha+beta of nucleotidyltransferase fold (scop_cf 81302); d3: [alpha+beta; beta(3)-alpha-beta(3)-alpha(2); 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 123654, strands 2 and 5 are antiparallel to the rest 2ga9 d2ga9d1 D:162-180,182-186,204-208,209-226,248-257 2gaf d2gafd1 D:162-180,182-186,204-208,209-226,248-257 28. d.52.10 EspE N-terminal domain-like contains extra C-terminal helix that packs against shorter N-terminal helix Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 2d27 d2d27a1 A:87-95,95-103,104-111,115-127,129-135 2d28 d2d28c1 C:87-95,95-103,104-111,115-127,129-135 2bh1 d2bh1x1 X:18-26,26-32,37-43,47-59,62-67 2bh1 d2bh1y1 Y:18-26,26-32,37-43,47-59,62-67 29. e.23.1 Acetyl-CoA synthetase-like Acetyl-CoA synthetase-like 4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta 1lci d1lcia_ A:450-462,463-474,478-488,494-506,515-519 1pg3 d1pg3b_ B:528-540,541-552,556-566,572-588,594-599 1pg4 d1pg4b_ B:528-540,541-552,556-566,572-588,594-599 1ba3 d1ba3a_ A:450-462,463-474,478-488,494-506,515-519 1pg3 d1pg3a_ A:528-540,541-552,556-566,572-588,594-599 1pg4 d1pg4a_ A:528-540,541-552,556-566,572-588,594-599 1ry2 d1ry2a_ A:587-599,603-607,618-623,640-654,660-665 1amu d1amub_ B:441-452,455-466,468-478,483-496,502-507 1amu d1amua_ A:441-453,455-466,468-478,483-495,502-507 3cw9 d3cw9a1 A:413-424,426-437,441-451,457-469,477-482 1t5h d1t5hx_ X:413-424,426-438,440-451,457-469,477-482 1md9 d1md9a_ A:441-453,454-465,469-479,484-496,504-509 1t5d d1t5dx_ X:413-424,426-438,440-451,457-469,477-482 3cw9 d3cw9b1 B:413-424,426-437,441-451,457-469,477-482 1mdb d1mdba_ A:441-453,454-465,469-479,484-496,504-509 1ult d1ulta_ A:446-458,459-470,474-484,489-501,510-514 1mdf d1mdfa_ A:441-453,454-465,469-479,484-496,504-509 1ult d1ultb_ B:446-458,462-468,476-482,489-501,509-514 31. c.109.1 PEP carboxykinase N-terminal domain PEP carboxykinase N-terminal domain contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain 2pxz d2pxzx2 X:28-38,47-51,53-58,141-153,308-312 1k3d d1k3da2 A:28-38,47-51,53-58,141-153,308-312 2py7 d2py7x2 X:28-38,47-51,53-58,141-153,308-312 2olq d2olqa2 A:28-38,47-51,53-58,141-153,308-312 2olr d2olra2 A:28-38,47-51,53-58,141-153,308-312 1oen d1oena2 A:28-38,47-51,53-58,141-153,308-312 1os1 d1os1a2 A:28-38,47-51,53-58,141-153,308-312 2pc9 d2pc9a2 A:20-32,34-38,40-45,122-134,293-297 1ii2 d1ii2a2 A:10-23,25-29,31-36,114-126,281-285 1aq2 d1aq2a2 A:28-38,47-51,53-58,141-153,308-312 1k3c d1k3ca2 A:28-38,47-51,53-58,141-153,308-312 1ayl d1ayla2 A:28-38,47-51,53-58,141-153,308-312 1xkv d1xkva2 A:20-32,34-38,40-45,122-134,293-297 1j3b d1j3bb2 B:20-32,34-38,40-45,122-134,293-297 1ii2 d1ii2b2 B:10-23,25-29,31-36,114-126,281-285 1xkv d1xkvb2 B:20-32,34-38,40-45,122-134,293-297 1j3b d1j3ba2 A:20-32,34-38,40-45,122-134,293-297 2pc9 d2pc9d2 D:20-32,34-38,40-45,122-134,293-297 2pc9 d2pc9b2 B:20-32,34-38,40-45,122-134,293-297 2pc9 d2pc9c2 C:20-32,34-38,40-45,122-134,293-297 32. d.227.1 OsmC-like OsmC-like swapped dimer of beta(3)-alpha-beta(2)-alpha(2)-beta subunits; mixed beta-sheet; order: 321[4][5][6]; buried helix 1lql d1lqli_ I:1640-1665,1667-1680,1690-1702,1719-1729,1731-1741 1lql d1lqlj_ J:1840-1865,1867-1880,1890-1902,1919-1929,1931-1941 1lql d1lqld_ D:640-665,668-680,690-701,719-729,731-741 1lql d1lqle_ E:840-865,868-880,890-901,919-929,931-941 1lql d1lqlc_ C:440-465,468-480,490-501,519-529,531-541 1lql d1lqlf_ F:1040-1065,1068-1080,1090-1101,1119-1129,1131-1141 1lql d1lqlg_ G:1240-1265,1268-1280,1290-1301,1319-1329,1331-1341 1lql d1lqla_ A:40-65,67-80,88-102,119-129,131-141 1lql d1lqlj_ J:1840-1865,1867-1880,1890-1902,1904-1919,1931-1941 1lql d1lqli_ I:1640-1665,1667-1680,1690-1702,1704-1720,1731-1741 1lql d1lqlh_ H:1440-1465,1467-1480,1488-1502,1519-1529,1531-1541 1lql d1lqlc_ C:440-465,468-480,490-501,504-519,531-541 1lql d1lqld_ D:640-665,668-680,690-701,704-719,731-741 1lql d1lqlb_ B:240-265,268-280,288-301,319-329,331-341 1ml8 d1ml8a_ A:35-60,62-76,80-94,97-114,123-134 1lql d1lqlf_ F:1040-1065,1068-1080,1090-1101,1104-1119,1131-1141 1lql d1lqle_ E:840-865,868-880,890-901,904-919,931-941 1vla d1vlab_ B:37-62,66-81,83-98,102-118,127-137 1lql d1lqlg_ G:1240-1265,1268-1280,1290-1301,1304-1319,1331-1341 1vla d1vlad_ D:37-62,66-81,83-98,102-118,127-137 1vla d1vlaa_ A:37-62,66-81,83-98,102-118,127-137 1lql d1lqla_ A:40-65,67-80,88-102,104-119,131-141 1vla d1vlac_ C:37-62,66-81,83-98,102-118,127-137 1lql d1lqlh_ H:1440-1465,1467-1480,1488-1502,1504-1519,1531-1541 1ml8 d1ml8a_ A:35-60,62-76,80-94,113-124,123-134 2pn2 d2pn2a1 A:41-66,71-82,85-97,101-115,125-132 1lql d1lqlb_ B:240-265,268-280,288-301,304-319,331-341 1usp d1uspb_ B:45-70,77-87,92-102,106-121,132-138 2d7v d2d7va1 A:64-89,91-107,109-125,131-146,154-161 1ukk d1ukka_ A:45-70,72-88,89-104,108-123,133-142 2onf d2onfb1 B:41-66,68-84,86-102,105-120,130-139 1ukk d1ukkb_ B:45-70,72-88,89-104,108-123,133-142 2d7v d2d7vb1 B:64-89,91-107,109-125,131-146,154-161 2onf d2onfa1 A:41-66,68-84,86-102,105-120,130-139 1qwi d1qwid_ D:47-72,74-90,91-106,110-125,133-143 1nye d1nyef_ F:1067-1092,1094-1110,1111-1126,1130-1145,1153-1162 1qwi d1qwic_ C:47-72,74-90,91-106,110-125,133-143 1nye d1nyea_ A:67-92,94-110,111-126,130-145,153-162 1nye d1nyed_ D:667-692,694-710,711-726,730-745,753-763 1nye d1nyeb_ B:267-292,294-310,311-326,330-345,353-362 1nye d1nyee_ E:867-892,894-910,911-926,930-945,953-963 1nye d1nyec_ C:467-492,494-510,511-526,530-545,553-563 1qwi d1qwib_ B:47-72,75-90,91-106,110-125,133-143 1qwi d1qwia_ A:47-72,75-90,91-106,110-125,133-143 1n2f d1n2fa_ A:48-73,80-92,93-105,109-124,135-142 1n2f d1n2fb_ B:48-73,80-92,93-105,109-124,135-142 1usp d1uspa_ A:45-70,77-89,90-102,106-121,133-139 33. d.52.4 YhbC-like, N-terminal domain Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta 1ib8 d1ib8a2 A:5-23,26-37,38-48,53-68,79-86