Query gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62] Match_columns 354 No_of_seqs 197 out of 4149 Neff 8.4 Searched_HMMs 33803 Date Wed Jun 1 12:51:31 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780406.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >1v9f_A Ribosomal large subuni 100.0 7.8E-41 2.8E-45 276.6 -2.6 244 1-244 4-278 (325) 2 >2gml_A Ribosomal large subuni 100.0 5.9E-33 1.7E-37 227.0 11.2 181 60-246 1-181 (237) 3 >1ksk_A Ribosomal small subuni 100.0 2.1E-32 6.3E-37 223.5 12.4 174 70-245 2-176 (176) 4 >3dh3_A Ribosomal large subuni 100.0 1.4E-31 4.1E-36 218.3 12.9 170 71-246 2-171 (227) 5 >2oml_A Ribosomal large subuni 100.0 5E-31 1.5E-35 214.8 12.6 168 69-238 7-189 (189) 6 >1vio_A Ribosomal small subuni 100.0 1.3E-30 3.9E-35 212.2 13.6 178 69-248 1-179 (186) 7 >1v9k_A Ribosomal large subuni 99.9 8.4E-27 2.5E-31 188.2 -2.3 172 69-240 5-195 (228) 8 >2i82_A Ribosomal large subuni 99.9 6.8E-25 2E-29 176.2 -1.3 169 57-225 2-186 (217) 9 >2olw_A Ribosomal large subuni 99.8 1.2E-20 3.6E-25 149.4 1.8 102 28-139 2-103 (119) 10 >1dm9_A Hypothetical 15.5 KD p 99.8 1.5E-19 4.4E-24 142.6 4.3 122 6-129 1-132 (133) 11 >2olw_A Ribosomal large subuni 99.5 6E-14 1.8E-18 107.3 10.0 83 139-221 1-98 (98) 12 >1vio_A Ribosomal small subuni 99.5 2.7E-14 8.1E-19 109.4 6.2 56 13-68 2-57 (57) 13 >1ksk_A Ribosomal small subuni 99.5 4.5E-14 1.3E-18 108.1 6.3 57 12-68 2-58 (58) 14 >3dh3_A Ribosomal large subuni 99.4 3.8E-13 1.1E-17 102.2 7.3 61 10-71 3-63 (63) 15 >1p9k_A ORF, hypothetical prot 99.2 1.5E-12 4.4E-17 98.5 0.3 65 5-69 12-77 (79) 16 >3hp7_A Hemolysin, putative; s 99.2 1.3E-11 3.8E-16 92.6 3.3 62 8-69 1-65 (65) 17 >2k6p_A Uncharacterized protei 99.1 1.1E-11 3.1E-16 93.1 -1.3 76 14-90 1-91 (92) 18 >2vqe_D 30S ribosomal protein 98.8 7.8E-09 2.3E-13 75.0 6.5 53 15-67 1-54 (94) 19 >2cqj_A BRMS2, U3 small nucleo 98.5 7E-08 2.1E-12 69.1 3.5 56 11-66 5-63 (71) 20 >1h3f_A Tyrosyl-tRNA synthetas 98.5 3.9E-07 1.1E-11 64.4 6.3 52 12-63 18-70 (83) 21 >3i1m_D 30S ribosomal protein 98.4 1.8E-07 5.4E-12 66.4 3.2 51 15-65 1-52 (94) 22 >2jan_A Tyrosyl-tRNA synthetas 98.3 2E-07 5.8E-12 66.2 2.6 70 9-78 7-77 (88) 23 >3bbn_D Ribosomal protein S4; 98.3 3E-07 9E-12 65.0 2.6 53 14-66 8-61 (120) 24 >2aus_C Pseudouridine synthase 98.2 9.8E-06 2.9E-10 55.5 9.2 157 73-246 16-195 (215) 25 >1s1h_D 40S ribosomal protein 98.1 2.2E-06 6.6E-11 59.6 3.4 54 13-66 8-62 (99) 26 >2apo_A Probable tRNA pseudour 97.9 0.00011 3.3E-09 48.9 9.7 156 73-245 16-193 (216) 27 >1jil_A Tyrrs, tyrosyl-tRNA sy 97.4 2.9E-05 8.7E-10 52.5 0.0 69 9-77 102-171 (174) 28 >2ts1_A Tyrosyl-tRNA synthetas 97.0 0.00013 4E-09 48.4 0.0 64 10-73 103-167 (174) 29 >3kbg_A 30S ribosomal protein 96.0 0.012 3.6E-07 36.0 4.9 42 26-67 22-63 (81) 30 >1c05_A Ribosomal protein S4 d 91.5 0.16 4.7E-06 29.0 3.1 26 40-65 2-27 (83) 31 >1k8w_A TRNA pseudouridine syn 90.7 1.2 3.4E-05 23.6 8.0 66 159-226 72-145 (145) 32 >2v9k_A Uncharacterized protei 87.8 1.9 5.5E-05 22.3 7.4 81 142-224 2-114 (120) 33 >1sgv_A TRNA pseudouridine syn 81.3 0.3 8.8E-06 27.3 -0.3 47 72-126 5-53 (87) 34 >1r3e_A TRNA pseudouridine syn 79.7 0.37 1.1E-05 26.7 -0.3 46 74-127 4-51 (92) 35 >1k8w_A TRNA pseudouridine syn 78.9 0.4 1.2E-05 26.5 -0.3 48 71-126 23-72 (108) 36 >2exu_A Transcription initiati 72.9 3 8.8E-05 21.0 2.8 47 115-161 43-90 (91) 37 >1c05_A Ribosomal protein S4 d 64.7 7.2 0.00021 18.6 3.4 25 14-38 30-55 (55) 38 >3gmg_A Uncharacterized protei 47.4 13 0.00039 16.9 2.4 31 39-69 68-102 (170) 39 >1tke_A Threonyl-tRNA syntheta 46.2 14 0.00041 16.8 2.3 23 39-62 37-59 (63) 40 >2r9q_A AGR_C_764P, 2'-deoxycy 44.6 20 0.00059 15.8 3.0 39 23-61 10-52 (174) 41 >2kmm_A Guanosine-3',5'-BIS(di 44.3 18 0.00052 16.1 2.6 23 39-62 38-60 (73) 42 >2z0t_A Putative uncharacteriz 38.1 7.7 0.00023 18.4 -0.0 39 30-68 10-48 (109) 43 >2q5w_D Molybdopterin converti 36.9 26 0.00077 15.1 3.0 25 37-62 46-70 (77) 44 >1qf6_A THRRS, threonyl-tRNA s 36.2 14 0.00041 16.8 1.1 23 39-62 37-59 (63) 45 >1fm0_D Molybdopterin converti 34.8 28 0.00083 14.9 3.7 30 32-62 44-74 (81) 46 >1rws_A Hypothetical protein P 34.4 13 0.0004 16.9 0.7 43 11-62 28-70 (77) 47 >1wv3_A Similar to DNA segrega 32.3 31 0.00092 14.6 6.2 39 37-75 54-92 (158) 48 >2qjl_A URM1, ubiquitin-relate 31.5 32 0.00094 14.5 2.7 24 39-62 66-92 (99) 49 >3dwg_C 9.5 kDa culture filtra 31.5 32 0.00094 14.5 2.7 24 39-62 60-86 (93) 50 >2g1e_A Hypothetical protein T 31.4 24 0.00071 15.3 1.6 26 37-62 55-83 (90) 51 >3hvz_A Uncharacterized protei 30.6 33 0.00098 14.4 2.7 22 40-62 44-65 (78) 52 >3h7h_A Transcription elongati 30.2 34 0.00099 14.4 2.5 39 114-152 56-95 (95) 53 >1vjk_A Molybdopterin converti 30.1 27 0.0008 15.0 1.7 24 38-62 68-91 (98) 54 >1nyr_A Threonyl-tRNA syntheta 28.6 21 0.00062 15.7 0.9 23 39-62 39-61 (65) 55 >2ff4_A Probable regulatory pr 27.0 38 0.0011 14.0 4.0 30 38-68 59-88 (99) 56 >1xne_A Hypothetical protein P 25.6 17 0.0005 16.3 -0.0 39 30-68 11-49 (113) 57 >1wwt_A Threonyl-tRNA syntheta 25.1 31 0.00092 14.6 1.3 22 40-62 49-70 (88) 58 >1h6l_A 3-phytase; hydrolase, 24.7 42 0.0012 13.8 3.1 33 96-129 53-86 (196) 59 >1v8c_A MOAD related protein; 23.6 44 0.0013 13.6 2.9 24 39-62 54-80 (84) 60 >1mio_A Nitrogenase molybdenum 23.2 45 0.0013 13.6 2.6 24 192-215 37-60 (107) 61 >2k9x_A Tburm1, uncharacterize 22.0 31 0.00093 14.6 0.8 23 40-62 70-95 (110) 62 >3f7f_A Nucleoporin NUP120; nu 22.0 40 0.0012 13.9 1.3 37 97-134 18-54 (56) 63 >1wln_A Afadin; beta sandwich, 20.7 50 0.0015 13.3 2.6 10 107-116 36-45 (120) 64 >1wgk_A Riken cDNA 2900073H19 20.3 28 0.00084 14.8 0.3 12 140-151 69-80 (114) No 1 >>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:) Probab=100.00 E-value=7.8e-41 Score=276.59 Aligned_cols=244 Identities=17% Similarity=0.103 Sum_probs=203.4 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE------------- Q ss_conf 986534466677344788999886-877899999998698699999924068780799979999989------------- Q gi|254780406|r 1 MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------------- 66 (354) Q Consensus 1 ~~~~~~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~------------- 66 (354) |+....+.++..++||++||+..+ .|||++++++|++|+|+|||+.+..+...+...+.+.+.... T Consensus 4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (325) T 1v9f_A 4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPL 83 (325) T ss_dssp ------------------------------------------------------------------------CCCCCCCC T ss_pred EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCCCCC T ss_conf 89999989764886699999986686799999999986998999999178320625898997325433222333344541 Q ss_pred CCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC------CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--C Q ss_conf 2255643896027875156314433336442101102------3432002665543323202223676410001234--4 Q gi|254780406|r 67 LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138 (354) Q Consensus 67 i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~ 138 (354) ...+++..|+++|||.|+.|+..+.....++...+.. ....+++|||||++||||||||++++++++|..+ . T Consensus 84 ~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~ 163 (325) T 1v9f_A 84 DIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQR 163 (325) T ss_dssp CEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHT T ss_pred CEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHC T ss_conf 12510110578707888654898777888632321134443333342146532588986514664025889999987501 Q ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHCC---------CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC Q ss_conf 574047752112455646788874000008---------76750343036402688079999995184289999999839 Q gi|254780406|r 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209 (354) Q Consensus 139 ~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~---------~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g 209 (354) ..+.|+|++.|.|.+..+............ .+......+.+.......+++++.+.|||+||||+||+++| T Consensus 164 ~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~sl~~~~~~TGR~HQIR~hla~~G 243 (325) T 1v9f_A 164 REITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHIT 243 (325) T ss_dssp TCSEEEEEEEEESCCCCCEEEECCEEECSSCTTCEEECTTSBCCEEEEEEEEECSSEEEEEEEESCCCTTHHHHHHHHTT T ss_pred CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHC T ss_conf 21012423430135474566235533576665305876887157899898653388457999977883179999999839 Q ss_pred CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHH Q ss_conf 86868897587054518755474886799999875 Q gi|254780406|r 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244 (354) Q Consensus 210 ~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l 244 (354) ++|+.+++.++|++.+++|+.|+|++++..+...| T Consensus 244 ~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~L 278 (325) T 1v9f_A 244 HPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQAL 278 (325) T ss_dssp CCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSE T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHH T ss_conf 97668777898554544331667776515864346 No 2 >>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:) Probab=100.00 E-value=5.9e-33 Score=226.99 Aligned_cols=181 Identities=24% Similarity=0.389 Sum_probs=160.9 Q ss_pred EEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCC Q ss_conf 99999892255643896027875156314433336442101102343200266554332320222367641000123445 Q gi|254780406|r 60 IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139 (354) Q Consensus 60 v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~ 139 (354) |.||+++-..+++..|+++|||+|+.|+..+.. ..++++.+... .++++|||||++||||||||+|++.+++++.+.. T Consensus 1 v~~~~~~~ii~ed~~~ivvnKP~G~~~~~~~~~-~~~~~~~l~~~-~~~~~vhRLD~~TSGlll~a~~~~~~~~~~~~~~ 78 (237) T 2gml_A 1 MGSSHHHHHHGSDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNHS-KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGN 78 (237) T ss_dssp ------------CCCEEEEEECTTCBCCSSSSC-SSBHHHHSCCS-SCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHH T ss_pred CCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC-CCCCHHHCCCC-CCEEECCCCCCCCCCCEEEECCHHHHHHHHHHCC T ss_conf 985555555685239999979993897228999-99744215764-5611412468888885898416688888765313 Q ss_pred CCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEE Q ss_conf 74047752112455646788874000008767503430364026880799999951842899999998398686889758 Q gi|254780406|r 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219 (354) Q Consensus 140 ~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~ 219 (354) .++|+|++.|.|.+..+.......+..........+... ....+++++.+.+||+||||.||+++|++|+++++++ T Consensus 79 ~i~K~Y~a~v~G~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~v~~~~~tGR~HQIR~h~~~~G~pI~gD~~y~ 154 (237) T 2gml_A 79 DHEKEYLVTVDKPITEEFIRGXSAGVPILGTVTKKCKVK----KEAPFVFRITLVQGLNRQIRRXCEHFGYEVKKLERTR 154 (237) T ss_dssp HSCEEEEEEESSCCCHHHHHHHSSCCEETTEECCCCEEE----EEETTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEEE T ss_pred CCCEEEEEEECCCCCHHHHHHHHCCCEECCEEEECHHHC----CCCCEEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEE T ss_conf 551488778526799999999975988777574200003----5665499999816886199999998699766699999 Q ss_pred ECCEECCCCCCCCEEECCHHHHHHHHH Q ss_conf 705451875547488679999987532 Q gi|254780406|r 220 YGPFQLGTLLAGSTREVSKKILREQLG 246 (354) Q Consensus 220 ~G~~~l~~L~~G~~r~l~~~e~~~l~~ 246 (354) ++++.+++|++|+|++|+..|+..+.. T Consensus 155 ~~~~~~~~l~~g~~~~l~~~e~~~~~~ 181 (237) T 2gml_A 155 IXNVSLSGIPLGEWRDLTDDELIDLFK 181 (237) T ss_dssp ETTEECTTCCTTCEEECCHHHHHHHHT T ss_pred ECCEEECCCCCCCEEECCHHHHHHHHH T ss_conf 888880897997838999999999998 No 3 >>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234) Probab=100.00 E-value=2.1e-32 Score=223.47 Aligned_cols=174 Identities=24% Similarity=0.368 Sum_probs=158.9 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE Q ss_conf 56438960278751563144333364421011023432002665543323202223676410001234457404775211 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v 149 (354) ||+..++++|||.|+.|+..+.....++.........++++|||||++|||||+||+|++.+.++.+....++|+|.+.| T Consensus 2 Yed~~~ivvnKP~gl~~~~~~~~~~~~~~~l~~~~~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~~~~~~~k~y~~~v 81 (176) T 1ksk_A 2 QHGPRYFXLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLXTDDGQWSHRITSPRHHCEKTYLVTL 81 (176) T ss_dssp CCCCCEEEEEECTTCBSSSSCSSSCBGGGGCCCTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEE T ss_pred CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCHHHHHHHHHHHCCCCEEEEECC T ss_conf 57857999989998505665554431000012444563656013885557558860586888877554238847998446 Q ss_pred CCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CC Q ss_conf 24556467888740000087675034303640268807999999518428999999983986868897587054518-75 Q gi|254780406|r 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL 228 (354) Q Consensus 150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L 228 (354) .+.+..........++..+........... .....+|+++.+.+||+||||+||+++|++|..+.+.++|++.+. .| T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~s~~~~~~~tGr~HQIR~h~~~~g~pI~gD~~Y~~~~~~~~~~l 159 (176) T 1ksk_A 82 ESPVADDTAEQFAKGVQLHNEKDLTKPAVL--EVITPTQVRLTISEGRYHQVKRXFAAVGNHVVELHRERIGGITLDADL 159 (176) T ss_dssp SSCCCTTHHHHHHHCCCCTTCSSCCCCCEE--EEEETTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTC T ss_pred CCCCCHHHHHHHHEEEEECCCEEEEEEEEE--ECCCCCEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCC T ss_conf 788887897775302563895755534684--037996899996359839999999987997989999998865047989 Q ss_pred CCCCEEECCHHHHHHHH Q ss_conf 54748867999998753 Q gi|254780406|r 229 LAGSTREVSKKILREQL 245 (354) Q Consensus 229 ~~G~~r~l~~~e~~~l~ 245 (354) +.|+||+|+++|++.|| T Consensus 160 ~l~~~r~l~~~e~~~ll 176 (176) T 1ksk_A 160 APGEYRPLTEEEIASVV 176 (176) T ss_dssp CTTCEEECCHHHHTTCC T ss_pred CCCCEEECCHHHHHHHC T ss_conf 99751599999999659 No 4 >>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:64-290) Probab=99.97 E-value=1.4e-31 Score=218.34 Aligned_cols=170 Identities=25% Similarity=0.425 Sum_probs=151.1 Q ss_pred CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC Q ss_conf 64389602787515631443333644210110234320026655433232022236764100012344574047752112 Q gi|254780406|r 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150 (354) Q Consensus 71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~ 150 (354) |+..+|++|||.|+.|+..+.. ..++.+.+... .++++|||||++||||||||+|+++++.|+++...++|+|++.|. T Consensus 2 Ed~~~ivinKP~Gl~~~~~~~~-~~~l~~~l~~~-~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~ 79 (227) T 3dh3_A 2 EDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNHS-KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVD 79 (227) T ss_dssp GGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTCS-SCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGCCCEEEEEEES T ss_pred CCEEEEECCCCCCEEECCCCCC-CCCCHHHCCCC-CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCEEEC T ss_conf 3113564366652120333477-77501101344-431224656767631489943987998887631244322112760 Q ss_pred CCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC Q ss_conf 45564678887400000876750343036402688079999995184289999999839868688975870545187554 Q gi|254780406|r 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230 (354) Q Consensus 151 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~ 230 (354) |.++.+....+..+..........+. ......+|+++.+.+|++||||+||+++|++|+.+.++++|++.|.+|+. T Consensus 80 G~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~tGr~hQIR~h~a~~g~pI~gd~~y~~~~~~l~~l~~ 155 (227) T 3dh3_A 80 KPITEEFIRGMSAGVPILGTVTKKCK----VKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPL 155 (227) T ss_dssp SCCCHHHHHHHHTCCBCSSSBCCCCE----EEECSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCT T ss_pred CCCCHHHHHHHHCCCEECCEEEEEEE----EEECCCCEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC T ss_conf 57999999999759984565744257----75226725899925885259999999879967669999987877489799 Q ss_pred CCEEECCHHHHHHHHH Q ss_conf 7488679999987532 Q gi|254780406|r 231 GSTREVSKKILREQLG 246 (354) Q Consensus 231 G~~r~l~~~e~~~l~~ 246 (354) |+||+|+..|+..+.. T Consensus 156 g~~r~l~~~e~~~~~~ 171 (227) T 3dh3_A 156 GEWRDLTDDELIDLFK 171 (227) T ss_dssp TCEEECCHHHHHHHHH T ss_pred CCEEECCHHHHHHHHH T ss_conf 7738899999999998 No 5 >>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:) Probab=99.97 E-value=5e-31 Score=214.82 Aligned_cols=168 Identities=30% Similarity=0.527 Sum_probs=149.3 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEE Q ss_conf 55643896027875156314433336442101102343200266554332320222367641000123445740477521 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~ 148 (354) .+++..|+++|||.|+.|+..+.....++...+.. .++++|||||++|+||||||+|+++++.|+.+...+.|+|.+. T Consensus 7 l~ed~~~ivinKP~g~~~~~~~~~~~~~~~~~l~~--~~l~~vhRLD~~tsGlll~a~~~~~~~~l~~~~~~i~k~Y~a~ 84 (189) T 2oml_A 7 ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQ 84 (189) T ss_dssp -CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCCC--SSCEESSCCCTTCEEEEEEESCHHHHHHHHSTTSCCCEEEEEE T ss_pred CCCCCEEEEEECCCCEEEECCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCEEEEECCCHHHHHCCCCCEEEEEEEEEE T ss_conf 88998899998999838607799888658896371--2534731026120007999325302221031230377899999 Q ss_pred ECCCCCHHHHHHHHHHHHCCCEEEEC---------------CCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE Q ss_conf 12455646788874000008767503---------------430364026880799999951842899999998398686 Q gi|254780406|r 149 FHGQVDQDKLNLLKKGIVIQGICYGD---------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213 (354) Q Consensus 149 v~~~~~~~~~~~~~~g~~~~~~~~~~---------------~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~ 213 (354) |.+.+..+....+..+....+..... ..+.........+++.+++.+||+||||+||+++|++|. T Consensus 85 v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~tGr~hQIR~hl~~lg~pIv 164 (189) T 2oml_A 85 VEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 164 (189) T ss_dssp EESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CTTSCEEEEEEEESCCCTTHHHHHHHHTTCCEE T ss_pred EECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEEEECCCCEEEEEEECCCHHHHHHHHHHCCCEEE T ss_conf 93279989999986494507851576579995356641024557888740565079999945977999999998699698 Q ss_pred EEEEEEECCEECCCCCCCCEEECCH Q ss_conf 8897587054518755474886799 Q gi|254780406|r 214 RLIRISYGPFQLGTLLAGSTREVSK 238 (354) Q Consensus 214 ~L~Rv~~G~~~l~~L~~G~~r~l~~ 238 (354) .+.++++|++.+++|++|+||+||. T Consensus 165 gD~~Y~~~~~~~~~l~l~~~R~lt~ 189 (189) T 2oml_A 165 RLIRYAMGDYSLDNLANGEWREVTD 189 (189) T ss_dssp EEEEEEETTEECTTCCTTCEEECCC T ss_pred EEEEEEECCEECCCCCCCCCEECCC T ss_conf 9899999998507889988377979 No 6 >>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243) Probab=99.97 E-value=1.3e-30 Score=212.17 Aligned_cols=178 Identities=24% Similarity=0.333 Sum_probs=161.3 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEE Q ss_conf 55643896027875156314433336442101102343200266554332320222367641000123445740477521 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~ 148 (354) .+|+..||++|||.|+.|+..+.....++.........++++|+|||++||||||||+|++.+.+++.+...++|+|.+. T Consensus 1 ~yed~~~ivinKP~gl~~~~~~~~~~~~~~~l~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~k~y~~~ 80 (186) T 1vio_A 1 WIEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVT 80 (186) T ss_dssp SSCCCCEEEEEECTTCBSSCCC--CCBGGGGSCTTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEE T ss_pred CCCCCEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCCEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEEEE T ss_conf 22221035540258864333443201454200245331365402124012213787417753200011124552011259 Q ss_pred ECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-C Q ss_conf 124556467888740000087675034303640268807999999518428999999983986868897587054518-7 Q gi|254780406|r 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-T 227 (354) Q Consensus 149 v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~ 227 (354) |.+.+..+.......++...+.......... .....+++++.+.+||+||||+||+++|++|.+.+++++|++.++ . T Consensus 81 v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~tGr~hQIR~h~a~lg~pIvgD~~yg~~~~~~~~~ 158 (186) T 1vio_A 81 LADPVEENYSAACAEGILLRGEKEPTKPAKL--EILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDES 158 (186) T ss_dssp ESSCCCTTHHHHHHHCCCCTTCSSCCCCCEE--EECSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTT T ss_pred EEEECCHHHHHHHHCCEECCCCCCCEEEEEE--CCCCCCEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEECCCCCCCC T ss_conf 9851204478898536561683010233220--13568448988505760799999998599793889999887247999 Q ss_pred CCCCCEEECCHHHHHHHHHHH Q ss_conf 554748867999998753210 Q gi|254780406|r 228 LLAGSTREVSKKILREQLGPH 248 (354) Q Consensus 228 L~~G~~r~l~~~e~~~l~~~~ 248 (354) |+.|+||+|++.|+..+.... T Consensus 159 l~~g~~r~l~~~~l~~~~l~~ 179 (186) T 1vio_A 159 LEEGEYRPLTQSEIEKLVEGG 179 (186) T ss_dssp CCTTCEEECCHHHHHHTC--- T ss_pred CCCCCEEECCHHHHHHHHHCC T ss_conf 999762599999999999579 No 7 >>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:) Probab=99.91 E-value=8.4e-27 Score=188.22 Aligned_cols=172 Identities=14% Similarity=0.074 Sum_probs=140.2 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEE Q ss_conf 556438960278751563144333364421011023--432002665543323202223676410001234--4574047 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~ 144 (354) .+++..|+++|||.|+.|+..+.....++++.+... ..++++|||||++||||||+|+|+++++.|.++ ...+.|+ T Consensus 5 iyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~a~~l~~~~~~~~v~K~ 84 (228) T 1v9k_A 5 XYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKD 84 (228) T ss_dssp EEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEE T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCC T ss_conf 99689999999999986389989953699999986778765316640464322136752357999999999874034543 Q ss_pred EEEEECCCCCHHHHHHHHHHHHCC------------CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEE Q ss_conf 752112455646788874000008------------76750343036402688079999995184289999999839868 Q gi|254780406|r 145 YRVRFHGQVDQDKLNLLKKGIVIQ------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212 (354) Q Consensus 145 Y~v~v~~~~~~~~~~~~~~g~~~~------------~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V 212 (354) |++.|.+.++.........+.... +.......+.........+++++.+.+||+||||.||+++|++| T Consensus 85 Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGR~HQIR~h~a~~g~PI 164 (228) T 1v9k_A 85 YLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPI 164 (228) T ss_dssp EEEEEESCCCTTCCEECCCEEEEECTTSCEEEEECTTSBCCCEEEEEEEECSSEEEEEEEESSCCTTHHHHHHHHTTCCB T ss_pred CCCCCCCCCCCCCCCCCCCHHHCCCCCCEEEEECCCCCCCCCEEECHHHHCCCCEEEEEEECCCCHHHHHHHHHHCCCCC T ss_conf 21034686422357522330000110101555207888422155005553587379999947573578888888549721 Q ss_pred EEEEEEEECCEECCCCCCCC---EEECCHHH Q ss_conf 68897587054518755474---88679999 Q gi|254780406|r 213 NRLIRISYGPFQLGTLLAGS---TREVSKKI 240 (354) Q Consensus 213 ~~L~Rv~~G~~~l~~L~~G~---~r~l~~~e 240 (354) ++.++..++.+.+..++.|+ |+.|...+ T Consensus 165 vgD~~Y~~~~~~~~~~~~~~~~~~~~Lha~~ 195 (228) T 1v9k_A 165 AFDDRYGDREFDRQLTEAGTGLNRLFLHAAA 195 (228) T ss_dssp TTCTTTSCHHHHHHHHHTTCCCCSCCEEEEE T ss_pred CCCCCCCCCHHHHHHHHHCCCCCHHHHHCCC T ss_conf 3577413000002333202686237887150 No 8 >>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:) Probab=99.88 E-value=6.8e-25 Score=176.20 Aligned_cols=169 Identities=13% Similarity=0.068 Sum_probs=128.5 Q ss_pred CCEEEECCEECC-CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCC Q ss_conf 997999998922-55643896027875156314433336442101102-3432002665543323202223676410001 Q gi|254780406|r 57 TDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL 134 (354) Q Consensus 57 ~d~v~vdg~~i~-~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l 134 (354) +|.+.+++..+. .+++..|+++|||.|+.|+..+.....++...+.. ...++++|||||++||||||||+|+++++.| T Consensus 2 ~~~~~~~~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGllllak~~~~~~~l 81 (217) T 2i82_A 2 ENYNPPQEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAESVHRLDXATSGVIVVALTKAAEREL 81 (217) T ss_dssp CCCCCCCSSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCTTCEESSCCCTTCEEEEEEESSHHHHHHH T ss_pred CCCCCCCCCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECHHHHHHH T ss_conf 88894989995299979989999999998257998877603899976441033222345554210158986031777788 Q ss_pred CCC--CCCCEEEEEEEECCCCCHHHHHHHHHHH------------HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHH Q ss_conf 234--4574047752112455646788874000------------00876750343036402688079999995184289 Q gi|254780406|r 135 ELP--STQWLRVYRVRFHGQVDQDKLNLLKKGI------------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200 (354) Q Consensus 135 ~~p--~~~~~k~Y~v~v~~~~~~~~~~~~~~g~------------~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~q 200 (354) .++ ...+.|.|.+.+.+.+............ ...+.......+.........+++++.+.+||+|| T Consensus 82 ~~~~~~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~TGr~HQ 161 (217) T 2i82_A 82 KRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQ 161 (217) T ss_dssp HHHHHTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEEECTTTCBCCEEEEEEEEEETTTEEEEEEEESSCCTTH T ss_pred HHHHHHCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCEECCCCCCCCCCEECCCCCCCCCCEEEEEEECCCCHHH T ss_conf 98765140103689886154466640674101232243322000122476300101011112331047889850262378 Q ss_pred HHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 9999998398686889758705451 Q gi|254780406|r 201 IKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 201 Irr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) ||+||+++|++|.+..+...+.+.+ T Consensus 162 IR~h~a~lg~PIlgD~~Yg~~~~~~ 186 (217) T 2i82_A 162 LRVHXLALGHPILGDRFYASPEARA 186 (217) T ss_dssp HHHHHHHTTCCBTTCTTTSCHHHHH T ss_pred HHHHHHHHCCEEECCCCCCCHHHCC T ss_conf 9999997197681676768855636 No 9 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217) Probab=99.79 E-value=1.2e-20 Score=149.39 Aligned_cols=102 Identities=27% Similarity=0.419 Sum_probs=91.8 Q ss_pred HHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCC Q ss_conf 89999999869869999992406878079997999998922556438960278751563144333364421011023432 Q gi|254780406|r 28 RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107 (354) Q Consensus 28 Rr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~ 107 (354) ||+++++|++|+|+|||++|+ ++|.|.++|..|.+ ++..|+++|||.|+.|+..+.....++.+.+.. .+ T Consensus 2 Rr~~~~~i~~G~V~Vng~~v~-------~~d~i~~~~~~I~y-ed~~~ivvnKP~g~~~~~~~~~~~~tl~~~~~~--~~ 71 (119) T 2olw_A 2 RQFIISENTMQKTSFRNHQVK-------RFSSQRSTRRKPEN-QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QG 71 (119) T ss_dssp -------------------------------------------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCCC--CS T ss_pred CEEEECCCEEECCCCCCCCCC-------CCCCCCCCCCCCCC-CCCEEEEEECCCCEEEECCCCCCCCCHHHHCCC--CC T ss_conf 536706871421225542212-------05540035568878-998899998999959707799888768896571--26 Q ss_pred EECCCCCCCCCCCEEEECCCCCCCCCCCCCCC Q ss_conf 00266554332320222367641000123445 Q gi|254780406|r 108 VISVGRLDINTEGLLLLTNDGGLARVLELPST 139 (354) Q Consensus 108 ~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~ 139 (354) +++|||||++||||||||+|+++++.|++|+- T Consensus 72 l~~vhRLDr~TSGLll~ak~~~~~~~L~~~~~ 103 (119) T 2olw_A 72 VYAAGRLDRDSEGLLVLTNNGALQARLTQPGD 103 (119) T ss_dssp CEESSCCCTTCEEEEEEESCHHHHHHHHCTTT T ss_pred CEECCCCCCCEEEEEEEECCCHHHHHHHHCCC T ss_conf 34753114312006998436056545311038 No 10 >>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} (A:) Probab=99.77 E-value=1.5e-19 Score=142.56 Aligned_cols=122 Identities=13% Similarity=0.060 Sum_probs=91.3 Q ss_pred CCCCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE--CCEECCCCCCEEEEECCCCC Q ss_conf 446667734478899988687-789999999869869999992406878079997999--99892255643896027875 Q gi|254780406|r 6 IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYHKPI 82 (354) Q Consensus 6 ~~~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v--dg~~i~~~~~~~~~~~~KP~ 82 (354) ++++...++||||||+.+++| ||++|++||+.|+|+|||++++ ++++|.++|.|.| ++...... ...+...+++. T Consensus 1 iv~~~~~g~RLDk~L~~~~~~~sR~~a~~li~~G~V~VNG~~~~-~s~~v~~gD~i~i~~~~~~~~~~-~~~~~~~~~~~ 78 (133) T 1dm9_A 1 MKEKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQGNDERTVI-VKAITEQRRPA 78 (133) T ss_dssp ----CTTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEEETTEEEEEE-ECEEESCCCCH T ss_pred CCCCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEECC-CCCEECCCCEEEEEECCEEEEEE-EEEEEECCCCC T ss_conf 99887764629999987867168999999998691888999734-58561599989998799865899-99876225673 Q ss_pred EEEECCCCCC-----CCCCCCEEE-CCCCCCEECCCCCCC-CCCCEEEECCCCC Q ss_conf 1563144333-----364421011-023432002665543-3232022236764 Q gi|254780406|r 83 GLVTTHSDPD-----GRSTVFDNL-PSIFSRVISVGRLDI-NTEGLLLLTNDGG 129 (354) Q Consensus 83 g~~~~~~~~~-----~~~~~~~~~-~~~~~~~~~vgRLD~-~t~GLlllTndg~ 129 (354) +..+...... ..+..+..+ .....++++|||||+ +|+|||+|||||. T Consensus 79 ~~~~~~~ed~~~~v~~kp~~~~~~~~~~~~r~~~vgRLDk~~t~~ll~l~~dgs 132 (133) T 1dm9_A 79 SEAALLYEETAESVEKREKMALARKLNALTMPHPDRRPDKKERRDLLRFKHGDS 132 (133) T ss_dssp HHHGGGEEECHHHHHHHHHHHHHHHHHHTC------------------------ T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCC T ss_conf 035666323688711345777766522455788997868599999998755899 No 11 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200) Probab=99.53 E-value=6e-14 Score=107.28 Aligned_cols=83 Identities=24% Similarity=0.445 Sum_probs=74.7 Q ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEE---------------EECCCCEEEEEEEEEECCHHHHHH Q ss_conf 57404775211245564678887400000876750343036---------------402688079999995184289999 Q gi|254780406|r 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKK 203 (354) Q Consensus 139 ~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~---------------~~~~~~~~~~~v~l~eGr~~qIrr 203 (354) ..|+|+|++.|.|+++++.+..+..|+.+.+....++.+.. .......+|++++|.|||+||||+ T Consensus 1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~~~~~s~~~i~l~tGr~HQIR~ 80 (98) T 2olw_A 1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRR 80 (98) T ss_dssp CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CCSSCEEEEEEEESCCCTTHHHH T ss_pred CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEECCCCEEEEEEEECCCHHHHHH T ss_conf 22215899999456888999998659365785357756999535544331010477742155058999991597599999 Q ss_pred HHHHCCCEEEEEEEEEEC Q ss_conf 999839868688975870 Q gi|254780406|r 204 VFEFFNWKVNRLIRISYG 221 (354) Q Consensus 204 ~~~~~g~~V~~L~Rv~~G 221 (354) ||+++|++|..++|++|| T Consensus 81 ~la~~g~pI~gd~ry~~G 98 (98) T 2olw_A 81 MTAHVGFPTLRLIRYAMG 98 (98) T ss_dssp HHHHTTCCEEEEEEEEET T ss_pred HHHHCCCEEEEEEEEEEC T ss_conf 999859979898999999 No 12 >>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57) Probab=99.50 E-value=2.7e-14 Score=109.41 Aligned_cols=56 Identities=27% Similarity=0.367 Sum_probs=54.3 Q ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 34478899988687789999999869869999992406878079997999998922 Q gi|254780406|r 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 13 ~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) ++|||||||++|+|||++|++||++|+|+|||+++++++++|+++|.|.|||++|. T Consensus 2 ~~RLDk~L~~~~~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~g~~it 57 (57) T 1vio_A 2 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLT 57 (57) T ss_dssp CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETTEECC T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEEECCCC T ss_conf 55899999987785899999999879789999991548958688787876203222 No 13 >>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58) Probab=99.49 E-value=4.5e-14 Score=108.06 Aligned_cols=57 Identities=32% Similarity=0.438 Sum_probs=54.9 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 734478899988687789999999869869999992406878079997999998922 Q gi|254780406|r 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) +.+|||||||+.++|||++|++||.+|+|+|||++|++++++|+++|.|+|||++|. T Consensus 2 ~~~RLDk~L~~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~g~~it 58 (58) T 1ksk_A 2 SHXRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLA 58 (58) T ss_dssp CCEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETTEEEC T ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEEEEEEE T ss_conf 840099999877896899999999889299999994668858078676997210565 No 14 >>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:1-63) Probab=99.43 E-value=3.8e-13 Score=102.23 Aligned_cols=61 Identities=33% Similarity=0.423 Sum_probs=56.7 Q ss_pred CCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCC Q ss_conf 67734478899988687789999999869869999992406878079997999998922556 Q gi|254780406|r 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71 (354) Q Consensus 10 ~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~ 71 (354) ...++|||||||+.|+|||++|++||++|+|+|||++|+ ++++|.++|.|+|+++++.+.+ T Consensus 3 ~~~~~RLDk~La~~~~~SR~~~~~li~~G~V~Vng~~vk-~~~~v~~~d~I~v~~~~~~~~e 63 (63) T 3dh3_A 3 PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPRE 63 (63) T ss_dssp -CCCEEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEEECCCC T ss_pred CCCCCCHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEEEEEEE T ss_conf 988704999998778851999999998793898999947-8889699998999999921120 No 15 >>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} (A:) Probab=99.22 E-value=1.5e-12 Score=98.47 Aligned_cols=65 Identities=15% Similarity=0.271 Sum_probs=59.9 Q ss_pred CCCCCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 3446667734478899988687-7899999998698699999924068780799979999989225 Q gi|254780406|r 5 NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 5 ~~~~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) ........++||++||+.+++| ||++|++||.+|.|+|||++++.++++|.++|.|+|+++++.+ T Consensus 12 ~~~~~~~~~~RLd~~L~~~~~~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~~~~~~ 77 (79) T 1p9k_A 12 TFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV 77 (79) T ss_dssp EEECCSCSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETTEEEEE T ss_pred EEECCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCEEEEE T ss_conf 386499971979999987788368999999998499798999927788798999999999999999 No 16 >>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65) Probab=99.17 E-value=1.3e-11 Score=92.55 Aligned_cols=62 Identities=18% Similarity=0.324 Sum_probs=57.2 Q ss_pred CCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCE--EECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 6667734478899988687-78999999986986--99999924068780799979999989225 Q gi|254780406|r 8 QENFTPQRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 8 ~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V--~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) ++....+|||++|+.+|+| ||++|++||..|.| +|||++|+.|++.|.++|.|.|+++++.+ T Consensus 1 s~~~~~~RLD~~L~~~g~~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~~~~~~y 65 (65) T 3hp7_A 1 SNAXPKERVDVLAYKQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLKGEKLRY 65 (65) T ss_dssp --CCCEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETTCCCCS T ss_pred CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEECCCCCC T ss_conf 99650889999999875812499999999859942320998956886787999989980777664 No 17 >>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:) Probab=99.06 E-value=1.1e-11 Score=93.12 Aligned_cols=76 Identities=22% Similarity=0.238 Sum_probs=65.0 Q ss_pred HHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC----EE---------C-CCCCCEEEEEC Q ss_conf 44788999886-8778999999986986999999240687807999799999----89---------2-25564389602 Q gi|254780406|r 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VP---------L-RKAERTRLWLY 78 (354) Q Consensus 14 ~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg----~~---------i-~~~~~~~~~~~ 78 (354) +||++||+..+ .+||+.+.++|+.|.|+|||+++. +++.|..+|.|++.. .+ + ..+++..|+++ T Consensus 1 mRLD~~L~~~~~~~sr~~~~k~i~~g~I~VNg~~~~-~~~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~i~yed~~~lvi 79 (92) T 2k6p_A 1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYIA 79 (92) T ss_dssp CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECC-TTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSEE T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEE-ECCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCHHHHCCCEE T ss_conf 967899987277159999999998997998989986-6247189999999848963689999788658986455061598 Q ss_pred CCCCEEEECCCC Q ss_conf 787515631443 Q gi|254780406|r 79 HKPIGLVTTHSD 90 (354) Q Consensus 79 ~KP~g~~~~~~~ 90 (354) |||+|++++... T Consensus 80 nKpagl~~hp~~ 91 (92) T 2k6p_A 80 PKTKELEHHHHH 91 (92) T ss_dssp ECCCC------- T ss_pred ECHHCCCCCCCC T ss_conf 063216244457 No 18 >>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (D:100-193) Probab=98.83 E-value=7.8e-09 Score=75.04 Aligned_cols=53 Identities=28% Similarity=0.449 Sum_probs=49.8 Q ss_pred HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC Q ss_conf 478899988687-78999999986986999999240687807999799999892 Q gi|254780406|r 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 (354) Q Consensus 15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i 67 (354) |||++|.++|+| ||.+|.++|..|.|.|||++|+.|++.|.++|.|++.+... T Consensus 1 RLD~~l~r~~~~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~~~~ 54 (94) T 2vqe_D 1 RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSR 54 (94) T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGGGT T ss_pred HHHHHHHHCCCHHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHHHHH T ss_conf 999999853520028988899870684508879975367852886001211010 No 19 >>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=98.51 E-value=7e-08 Score=69.07 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=49.8 Q ss_pred CCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEECCEE Q ss_conf 7734478899988687-789999999869869999992406878079--9979999989 Q gi|254780406|r 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVP 66 (354) Q Consensus 11 ~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vdg~~ 66 (354) .-..|||.+|.++|++ ||.+|.+||..|.|+|||++|+.|++.|.+ +|.|++.++. T Consensus 5 ~lerRLd~~l~~~g~a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~~~~ 63 (71) T 2cqj_A 5 SSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSS 63 (71) T ss_dssp CCEEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESCCS T ss_pred HHHCCHHHHHHHHCCCCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEECCC T ss_conf 44412689999805527899999999849899899995569858358998869984688 No 20 >>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432) Probab=98.46 E-value=3.9e-07 Score=64.36 Aligned_cols=52 Identities=19% Similarity=0.320 Sum_probs=48.1 Q ss_pred CCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEEC Q ss_conf 734478899988687-7899999998698699999924068780799979999 Q gi|254780406|r 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63 (354) Q Consensus 12 ~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vd 63 (354) ...||+++|..+|+| |+++|.++|.+|-|+|||+.|+++++.|.++|.|.|. T Consensus 18 ~~~rl~~~l~~~gl~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~ 70 (83) T 1h3f_A 18 GRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQ 70 (83) T ss_dssp TEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEE T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE T ss_conf 86349999998498677899999998599898999824877021589808998 No 21 >>3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... (D:97-190) Probab=98.39 E-value=1.8e-07 Score=66.41 Aligned_cols=51 Identities=24% Similarity=0.472 Sum_probs=48.2 Q ss_pred HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE Q ss_conf 478899988687-789999999869869999992406878079997999998 Q gi|254780406|r 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65 (354) Q Consensus 15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~ 65 (354) |||.+|.++|++ ||.+|.+||..|.|.|||++|+.|++.|.++|.|+|..+ T Consensus 1 RLD~~l~r~gfa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~ 52 (94) T 3i1m_D 1 RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREK 52 (94) T ss_dssp STTHHHHTTTSCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSS T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCC T ss_conf 8888866031254099999999850376088799763177058977886232 No 22 >>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} (A:345-432) Probab=98.35 E-value=2e-07 Score=66.24 Aligned_cols=70 Identities=20% Similarity=0.281 Sum_probs=58.8 Q ss_pred CCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEEC Q ss_conf 667734478899988687-7899999998698699999924068780799979999989225564389602 Q gi|254780406|r 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78 (354) Q Consensus 9 ~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~ 78 (354) +=..+++|.++|..+|+| |+++|.++|.+|-|+|||+.++++...+.++|.+.-+.-.|..-+..++++. T Consensus 7 ~~~~~~~i~~lL~~~gl~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~i~~~~~~lr~GKK~~~~i~ 77 (88) T 2jan_A 7 KPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVLRRGKRSIAGVE 77 (88) T ss_dssp CSSSCCSHHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGSBTTTEEEEESSSSCEEEEE T ss_pred CCCCCCCHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHHCCCCEEEEEECCCCEEEEE T ss_conf 35787779999998288678999999999399998999816943302787822798899997670289999 No 23 >>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201) Probab=98.30 E-value=3e-07 Score=65.03 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=49.7 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-+|.++|++ |+.+|.+||..|.|.|||++|+.|++.|.++|.|++..+. T Consensus 8 ~RLD~~l~R~gfa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~~~ 61 (120) T 3bbn_D 8 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQ 61 (120) T ss_dssp SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSST T ss_pred HHHHHEEEECCCCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCCHH T ss_conf 753103550573357688889998751361548981657254616630010013 No 24 >>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A (C:31-245) Probab=98.24 E-value=9.8e-06 Score=55.53 Aligned_cols=157 Identities=17% Similarity=0.135 Sum_probs=97.8 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||.|+.++..-...+.. ....++...|-||-..+|+|++.-. -+.+|..--....|+|.+++..- T Consensus 16 ~G~l~~~KP~g~tS~~vv~~ik~~------~~~~kvGh~GTLDp~atGvl~i~vg--~aTkl~~~~~~~~K~Y~~~~~~g 87 (215) T 2aus_C 16 YGVINLDKPPGPTSHEVVAWIKRI------LNLEKAGHGGTLDPKVSGVLPVALE--RATRVVQALLPAGKEYVALMHLH 87 (215) T ss_dssp TEEEEEEECSSSCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEG--GGGGGGGGGTTCCEEEEEEEEES T ss_pred CCEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCCEEEEEC--HHHHHHHHHCCCCCEEEEEEEEC T ss_conf 838999579989999999999987------1834257898789865034767873--89989999745885999998872 Q ss_pred CCHHHHHHHHHHHHCCCE----------------EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------ Q ss_conf 564678887400000876----------------7503430364026880799999951842899999998398------ Q gi|254780406|r 153 VDQDKLNLLKKGIVIQGI----------------CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------ 210 (354) Q Consensus 153 ~~~~~~~~~~~g~~~~~~----------------~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------ 210 (354) ...+..+.-..-..+.+. ...-.......-+.....++|....|-| ||-++..+|. T Consensus 88 ~~t~t~d~~~~~~~~~g~~~Q~pP~~SA~k~~g~r~y~~ar~g~~~~~p~~~~~v~cs~GTY--IRsL~~Dig~~Lg~~a 165 (215) T 2aus_C 88 GDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEILEIDGRDVLFRVGVEAGTY--IRSLIHHIGLALGVGA 165 (215) T ss_dssp SCCCHHHHHHHHHHTSEEEECC------------EEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHSSCE T ss_pred CCCCCCHHHEEECCCEEEEEECCCHHHHHHCCCCCEEEEEEEEEECCCCEEEEEEEECCCCE--EEHHHHHHHHHHCCCC T ss_conf 34444400133023214488888845631014654067899986226733899999549937--5038999766650152 Q ss_pred EEEEEEEEEECCEECCC-CCCCCEEECCHHHHHHHHH Q ss_conf 68688975870545187-5547488679999987532 Q gi|254780406|r 211 KVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246 (354) Q Consensus 211 ~V~~L~Rv~~G~~~l~~-L~~G~~r~l~~~e~~~l~~ 246 (354) .+..|.|+++|+|.+++ | ++-+||.++.. T Consensus 166 ~l~~L~Rt~~G~F~l~~al-------~~l~~l~~~~~ 195 (215) T 2aus_C 166 HMAELRRTRSGPFKEDETL-------VTLHDLVDYYH 195 (215) T ss_dssp EEEEEEEEEETTEESSTTE-------ECHHHHHHHHH T ss_pred EEEEEEEEEECCCCHHHHH-------HHHHHHHHHHH T ss_conf 1414796445686889975-------44999998999 No 25 >>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} (D:81-179) Probab=98.09 E-value=2.2e-06 Score=59.58 Aligned_cols=54 Identities=19% Similarity=0.294 Sum_probs=49.6 Q ss_pred CHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 34478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 13 ~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) ..|||-+|.++|++ |+.+|.++|..|.|.|||++|+.|++.|.++|.|.|..+. T Consensus 8 ErRLD~il~R~gfa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~~~ 62 (99) T 1s1h_D 8 ERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP 62 (99) T ss_dssp GGBHHHHHHHHTSSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCSSC T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEEEC T ss_conf 7507889998156588999999987377258999987624684058756055606 No 26 >>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} (A:51-266) Probab=97.93 E-value=0.00011 Score=48.88 Aligned_cols=156 Identities=16% Similarity=0.085 Sum_probs=94.3 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||.|+.++..=...+.. ....++...|.||-..+|+|++--. -+.++..--....|+|.+++.-- T Consensus 16 ~G~l~i~KP~g~tS~~vv~~~k~~------~~~~kvgh~GtLDp~a~GvLiv~ig--~~Tkl~~~~~~~~K~Y~~~~~lG 87 (216) T 2apo_A 16 YGVVVVDKPRGPTSHEVSTWVKKI------LNLDKAGHGGTLDPKVTGVLPVALE--RATKTIPMWHIPPKEYVCLMHLH 87 (216) T ss_dssp TEEEEEEECSSSCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEG--GGGGGGGGTTSSCEEEEEEEEES T ss_pred CCEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCCHHHEEC--HHHHHHHHHCCCCCEEEEEEEEE T ss_conf 998999799989989999999998------4877357787789634365532118--65322177505882799999983 Q ss_pred C--CHHHHHHHHHHHH--------------CCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------ Q ss_conf 5--6467888740000--------------08767503430364026880799999951842899999998398------ Q gi|254780406|r 153 V--DQDKLNLLKKGIV--------------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------ 210 (354) Q Consensus 153 ~--~~~~~~~~~~g~~--------------~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------ 210 (354) . +.+.++.....+. +.+....-....-..-+.....++|....|-| ||.++..+|. T Consensus 88 ~~Tdt~di~~~l~~f~g~~~q~pp~~Savk~~g~~ayelar~g~~~~~p~~~~~v~cs~GtY--IRsL~~Dlg~~Lg~~a 165 (216) T 2apo_A 88 RDASEEDILRVFKEFTGRIYQRPPLKAAVKRRLRIRKIHELELLDKDGKDVLFRVKCQSGTY--IRKLCEDIGEALGTSA 165 (216) T ss_dssp SCCCHHHHHHHHHHHSEEEECC-----------CEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHTTSCE T ss_pred ECCCCCHHHHHHHHCCCCEEECCCCHHHCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCC--HHHHHHHHHHHCCCCE T ss_conf 12432149999985376043248614310134445279999986258884899999658816--7999999998605447 Q ss_pred EEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHH Q ss_conf 68688975870545187554748867999998753 Q gi|254780406|r 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245 (354) Q Consensus 211 ~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~ 245 (354) .+..|.|+++|+|.+++- ++-++|.+.. T Consensus 166 ~~~~LrRt~~G~f~~~~a-------~~l~~l~~~~ 193 (216) T 2apo_A 166 HMQELRRTKSGCFEEKDA-------VYLQDLLDAY 193 (216) T ss_dssp EEEEEEEEEETTEEGGGC-------BCHHHHHHHH T ss_pred EEEECCCCCCCCCCCCCC-------CCHHHHHHHH T ss_conf 883053655699062334-------7899999878 No 27 >>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420) Probab=97.38 E-value=2.9e-05 Score=52.53 Aligned_cols=69 Identities=14% Similarity=0.274 Sum_probs=53.6 Q ss_pred CCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEE Q ss_conf 667734478899988687-789999999869869999992406878079997999998922556438960 Q gi|254780406|r 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77 (354) Q Consensus 9 ~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~ 77 (354) .....++|..+|..+|+| |+++|.++|.+|-|+|||++|+++.+.+..+|.+.-..-.|...+..++++ T Consensus 102 ~~~~~~~l~~lL~~~~l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~~~~~~ilr~GKk~~~~i 171 (174) T 1jil_A 102 LSNDTTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKIDGEFTIIRRGKKKYFMV 171 (174) T ss_dssp ---------------------------------------------------------------------- T ss_pred ECCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCCCCCEEEEEECCCCEEEE T ss_conf 1588878999999838846799999999849989999981384440077570489789999558747999 No 28 >>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419) Probab=96.97 E-value=0.00013 Score=48.38 Aligned_cols=64 Identities=17% Similarity=0.234 Sum_probs=48.0 Q ss_pred CCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCE Q ss_conf 677344788999886-8778999999986986999999240687807999799999892255643 Q gi|254780406|r 10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73 (354) Q Consensus 10 ~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~ 73 (354) .....+|..+|..+| ..|+++|.++|.+|-|+|||+.|+++...+...|.+.=..-.|...+.. T Consensus 103 ~~~~~~l~~lL~~~gl~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~~~~~~ilr~GKk~ 167 (174) T 2ts1_A 103 EGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRRGKKK 167 (174) T ss_dssp ----------------------------------------------------------------- T ss_pred CCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCCCCCEEEEEECCCC T ss_conf 57997699999985986778999999986998989998238422017757148978999957954 No 29 >>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} (A:1-81) Probab=95.98 E-value=0.012 Score=36.04 Aligned_cols=42 Identities=31% Similarity=0.424 Sum_probs=38.3 Q ss_pred CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC Q ss_conf 778999999986986999999240687807999799999892 Q gi|254780406|r 26 ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 (354) Q Consensus 26 ~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i 67 (354) -+.|||...|.+|.|+|||++.++..+.|---|+|++.|+-. T Consensus 22 ~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~~e~y 63 (81) T 3kbg_A 22 DKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEINGESY 63 (81) T ss_dssp TCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEETTEEE T ss_pred CCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECCCEE T ss_conf 658999999867938989999623899887067999799779 No 30 >>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159) Probab=91.52 E-value=0.16 Score=29.00 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=23.9 Q ss_pred EEECCEECCCCCEEECCCCEEEECCE Q ss_conf 69999992406878079997999998 Q gi|254780406|r 40 VKVNGILLERAAVNVMSTDHIEVDGV 65 (354) Q Consensus 40 V~Vng~~v~~~~~~v~~~d~v~vdg~ 65 (354) |.|||+.|.-|++.+.++|.|+|..+ T Consensus 2 i~VNgkkVdIPSy~~k~gD~I~ik~k 27 (83) T 1c05_A 2 ILVDGSRVNIPSYRVKPGQTIAVREK 27 (83) T ss_dssp EEETTEECCCSSCBCCTTCEEEECGG T ss_pred EECCCEEEEECCEEECCCCEEEECCC T ss_conf 36043699843416217848750200 No 31 >>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:80-224) Probab=90.68 E-value=1.2 Score=23.61 Aligned_cols=66 Identities=12% Similarity=0.208 Sum_probs=42.5 Q ss_pred HHHHHHHHCCCEEEE--CCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECC Q ss_conf 887400000876750--3430364026880799999951842899999998398------6868897587054518 Q gi|254780406|r 159 NLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLG 226 (354) Q Consensus 159 ~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~ 226 (354) +-.++|..++-..-. --.+.+..-.....++++.-..|-+ ||.++..+|. .+..|.|+++|+|.|+ T Consensus 72 elAr~G~~~~~~~r~v~I~~~~l~~~~~p~~~~~v~cs~GTY--IRsL~~dig~~Lg~~a~~~~L~Rt~~G~f~l~ 145 (145) T 1k8w_A 72 EYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTY--IRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVE 145 (145) T ss_dssp HHHHTTCCCCCCCEEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHTSCEEEEEEEEEEETTCCGG T ss_pred HHHHHCCCCCCCCEEEEEEEEEEEECCCCEEEEEEEECCCHH--HHHHHHHHHHHCCCCEEEEEEEEEEECCCCCH T ss_conf 999756655578366465127984133548999999678458--99999998765089589837898888783803 No 32 >>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domain, lyase; HET: EPE; 2.0A {Homo sapiens} (A:411-530) Probab=87.82 E-value=1.9 Score=22.30 Aligned_cols=81 Identities=9% Similarity=0.012 Sum_probs=50.1 Q ss_pred EEEEEEEEC--CCCCHHHHHHHHHHHHCCCEEEECCC----------------EEEEECCCCEEEEEEEEEECCHHHHHH Q ss_conf 047752112--45564678887400000876750343----------------036402688079999995184289999 Q gi|254780406|r 142 LRVYRVRFH--GQVDQDKLNLLKKGIVIQGICYGDMQ----------------VTLDTQKGSNAWVTVGLREGKNREIKK 203 (354) Q Consensus 142 ~k~Y~v~v~--~~~~~~~~~~~~~g~~~~~~~~~~~~----------------~~~~~~~~~~~~~~v~l~eGr~~qIrr 203 (354) .|+|.+++. ..++.+.++....-....=.+..|+. +.+..-......++|....|-+ ||. T Consensus 2 ~K~Y~a~v~~g~~~~~edi~~~l~~f~g~i~Q~pP~~SA~K~~gk~R~~~I~~~~~~~~~~~~~~l~i~~s~GtY--IR~ 79 (120) T 2v9k_A 2 TKTYSALIWTNKAIQKKDIEFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYVDEHHFRLHLKTQAGTY--IKE 79 (120) T ss_dssp CEEEEEEEEESSCCCHHHHGGGGGCCSEEEEEECCGGGTTTSCCCEEEEEEEEEEEEEEETTEEEEEEEECTTCC--HHH T ss_pred CEEEEEEEEECCCCCHHHHHHHHHCCCCEEEECCCCHHHHCCCCCCEEEEEEEEEEEEECCCEEEEEEEECCCCE--EEE T ss_conf 548999998479888899999872689668813740632105788504699999979943958999999507975--454 Q ss_pred HHH--------HCC------CEEEEEEEEEECCEE Q ss_conf 999--------839------868688975870545 Q gi|254780406|r 204 VFE--------FFN------WKVNRLIRISYGPFQ 224 (354) Q Consensus 204 ~~~--------~~g------~~V~~L~Rv~~G~~~ 224 (354) ++. .+| ..+..|.|+++|++. T Consensus 80 l~~~d~grt~pdlg~~lg~~~~~~~L~R~~vg~~~ 114 (120) T 2v9k_A 80 FVHGDFGRTKPNIGSLMNVTADILELDVESVDVDW 114 (120) T ss_dssp HHHCTTTTEESCHHHHHTSCEEEEEEEEEEECCCC T ss_pred EEECCCCCCCCCHHHHHCCCCEEEEEEEEEEEECC T ss_conf 26179998677879984897569993751487158 No 33 >>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} (A:1-60,A:206-232) Probab=81.27 E-value=0.3 Score=27.30 Aligned_cols=47 Identities=21% Similarity=0.299 Sum_probs=32.7 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECC Q ss_conf 43896027875156314433336442101102--34320026655433232022236 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN 126 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTn 126 (354) ..-++++|||.|+.++.. ...+.. ...++...|-||-..+|+|++.- T Consensus 5 ~~Gil~idKP~G~TS~~v--------v~~iKk~l~~kKVGH~GTLDP~AtGvLiv~i 53 (87) T 1sgv_A 5 GPGIVVIDKPAGMTSHDV--------VGRCRRIFATRRVGHAGTLDPMATGVLVIGI 53 (87) T ss_dssp CSEEEEEEECTTCCHHHH--------HHHHHHHTTCSCEEESSCCCTTCEEEEEEEE T ss_pred CCEEEEEECCCCCCHHHH--------HHHHHHHHCCCCCCCCCCCCCCCEEEEEEEE T ss_conf 988999976998998999--------9999998488855638788973642399998 No 34 >>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} (A:1-57,A:190-224) Probab=79.75 E-value=0.37 Score=26.73 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=31.9 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECCC Q ss_conf 896027875156314433336442101102--343200266554332320222367 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTND 127 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTnd 127 (354) -++++|||.|+.++..- ..+.. ...+....|-||-..+|+|++.-. T Consensus 4 Gil~idKP~G~TS~~vV--------~~iKk~l~~kKVGH~GTLDP~AtGvLii~iG 51 (92) T 1r3e_A 4 GILVAYKPKGPTSHDVV--------DEVRKKLKTRKVGHGGTLDPFACGVLIIGVN 51 (92) T ss_dssp EEEEEEECSSSCHHHHH--------HHHHHHTTCSCEEESSCCCTTCEEEEEEEEG T ss_pred EEEEEECCCCCCHHHHH--------HHHHHHHCCCCCCCCCCCCCCCEEEEEEEEC T ss_conf 59999669989989999--------9999986888787785679746446999988 No 35 >>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:1-79,A:225-253) Probab=78.88 E-value=0.4 Score=26.51 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=33.1 Q ss_pred CCEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECC Q ss_conf 643896027875156314433336442101102--34320026655433232022236 Q gi|254780406|r 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN 126 (354) Q Consensus 71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTn 126 (354) ...-++++|||.|+.++.. ...+.. ...++...|-||-..+|||++.- T Consensus 23 ~~~Gil~idKP~G~TS~~v--------V~~vkk~l~~kKVGH~GTLDP~AtGvLiv~i 72 (108) T 1k8w_A 23 DINGVLLLDKPQGMSSNDA--------LQKVKRIYNANRAGHTGALDPLATGMLPICL 72 (108) T ss_dssp CCCEEEEEEECTTCCHHHH--------HHHHHHHTTCSCEEESSCCCTTCEEEEEEEE T ss_pred CCCEEEEEECCCCCCHHHH--------HHHHHHHHCCCCCCCCCCCCCCCEEEEEEEE T ss_conf 8536999847998998999--------9999998589968768657974613599998 No 36 >>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae} (A:1-91) Probab=72.90 E-value=3 Score=21.01 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=38.9 Q ss_pred CCCCCCEEEECC-CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHH Q ss_conf 433232022236-76410001234457404775211245564678887 Q gi|254780406|r 115 DINTEGLLLLTN-DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161 (354) Q Consensus 115 D~~t~GLlllTn-dg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~ 161 (354) -.+.+|++.+.+ +-.|+-+.+.-...+.-.|.+.|.+.+.++.+..| T Consensus 43 T~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAi~V~g~lp~~i~~~l 90 (91) T 2exu_A 43 SPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIKVDGRLPAEVVELL 90 (91) T ss_dssp ESCEEEEEEESCTTTCHHHHHTTCTTSCSEEEEEEECSCCCHHHHTTC T ss_pred CCCCCCEEEEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHH T ss_conf 726164899967627399998578877886589995375877799999 No 37 >>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:22-76) Probab=64.67 E-value=7.2 Score=18.59 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=22.4 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCC Q ss_conf 4478899988687-789999999869 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQ 38 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G 38 (354) .|||-++-++|++ |+.+|.++|..| T Consensus 30 ~RLD~vvyR~gfa~S~~~ARQlV~HG 55 (55) T 1c05_A 30 SRLDNLVYRLGLARTRRQARQLVTHG 55 (55) T ss_dssp HBHHHHHHHTTSCSSHHHHHHHHHTT T ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHC T ss_conf 87545411577437888899888735 No 38 >>3gmg_A Uncharacterized protein RV1825/MT1873; structural genomics, unknown function, cell membrane, membrane, transmembrane, PSI-2; 1.50A {Mycobacterium tuberculosis} (A:) Probab=47.37 E-value=13 Score=16.90 Aligned_cols=31 Identities=16% Similarity=0.118 Sum_probs=22.7 Q ss_pred CEEECCE----ECCCCCEEECCCCEEEECCEECCC Q ss_conf 8699999----924068780799979999989225 Q gi|254780406|r 39 RVKVNGI----LLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 39 ~V~Vng~----~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) -|.|||+ .+.....-...+..|.|||.++.+ T Consensus 68 AIsINgq~~~vRi~~~S~Ir~~G~~i~V~g~~i~~ 102 (170) T 3gmg_A 68 AIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSP 102 (170) T ss_dssp EEEEECSSCEEECCTTCCEEEETTEEEETTEEECS T ss_pred EEEECCCCCCEEEEEEEEEEECCCEEEECCEEECC T ss_conf 79986875436994205999249989999999369 No 39 >>1tke_A Threonyl-tRNA synthetase; ligase; 1.46A {Escherichia coli} (A:1-63) Probab=46.24 E-value=14 Score=16.78 Aligned_cols=23 Identities=22% Similarity=0.312 Sum_probs=19.1 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+++ ++.+.+..++.|++ T Consensus 37 ~a~vng~l~-dL~~~l~~d~~ve~ 59 (63) T 1tke_A 37 AGRVNGELV-DACDLIENDAQLSI 59 (63) T ss_dssp EEEETTEEE-ETTCCBCSCEEEEE T ss_pred EEEECCEEE-CCCCCCCCCCEEEE T ss_conf 999999996-38844178758999 No 40 >>2r9q_A AGR_C_764P, 2'-deoxycytidine 5'-triphosphate deaminase; structural genomics, MCSG, PSI-2, protein structure initiative; 2.20A {Agrobacterium tumefaciens str} (A:1-174) Probab=44.58 E-value=20 Score=15.81 Aligned_cols=39 Identities=13% Similarity=0.225 Sum_probs=26.3 Q ss_pred CCCCCHHHHHHHHHCCCEEECC----EECCCCCEEECCCCEEE Q ss_conf 8687789999999869869999----99240687807999799 Q gi|254780406|r 23 AGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDHIE 61 (354) Q Consensus 23 ~g~~SRr~a~~lI~~G~V~Vng----~~v~~~~~~v~~~d~v~ 61 (354) .++.|-++.+++|++|.+.++= +.+...++.+..++.+. T Consensus 10 ~~iLsd~~I~~~~~~~~l~~~~~~~~~~v~~~s~Dl~l~~~~~ 52 (174) T 2r9q_A 10 TGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAY 52 (174) T ss_dssp SEECCHHHHHHHHHHTSEEESSCCCTTCBCSSCEEEEBCSEEE T ss_pred CEECCHHHHHHHHHCCCEEECCCCCHHHCCCCEEEEECCCEEE T ss_conf 8678799999998779806079999677788469943586899 No 41 >>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis} (A:) Probab=44.29 E-value=18 Score=16.12 Aligned_cols=23 Identities=35% Similarity=0.352 Sum_probs=19.1 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -.+|||+.+ ++.+.+..++.|++ T Consensus 38 ~A~vng~l~-dL~~~l~~~~~ve~ 60 (73) T 2kmm_A 38 GAKVNHKLV-PLSYVLNSGDQVEV 60 (73) T ss_dssp EEEETTEEC-CTTCBCCSSSBEEE T ss_pred EEEECCEEC-CCCCCCCCCCEEEE T ss_conf 998898599-88879589999999 No 42 >>2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A (A:) Probab=38.09 E-value=7.7 Score=18.40 Aligned_cols=39 Identities=23% Similarity=0.340 Sum_probs=32.8 Q ss_pred HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 999999869869999992406878079997999998922 Q gi|254780406|r 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) +--.+|++|.=+|-+.+...--.++.++|.|.+.++.+. T Consensus 10 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~n~~l~ 48 (109) T 2z0t_A 10 EYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEGGKLK 48 (109) T ss_dssp HHHHHHHTTSCCEEEEECCTTGGGCCTTCEEEEGGGTEE T ss_pred HHHHHHHCCCCEEEEECCHHHHHHCCCCCEEEEECCEEE T ss_conf 057998769988999827767862899999999478389 No 43 >>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B* (D:) Probab=36.89 E-value=26 Score=15.06 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=20.9 Q ss_pred CCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 69869999992406878079997999 Q gi|254780406|r 37 QQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 37 ~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) .-.|.|||+.+. ..+.+..+|.|.+ T Consensus 46 ~~~v~vN~~~v~-~~~~l~dgDeVai 70 (77) T 2q5w_D 46 KFQVAVNEEFVQ-KSDFIQPNDTVAL 70 (77) T ss_dssp CCEEEETTEEEC-TTSEECTTCEEEE T ss_pred HHHHHCCCEECC-CCCCCCCCCEEEE T ss_conf 313410880768-8867099899999 No 44 >>1qf6_A THRRS, threonyl-tRNA synthetase; tRNA(Thr), AMP, zinc, mRNA, aminoacylation, translational regulation, protein/RNA, ligase/RNA complex; HET: H2U AET G7M 5MU PSU AMP; 2.90A {Escherichia coli} (A:1-63) Probab=36.20 E-value=14 Score=16.78 Aligned_cols=23 Identities=22% Similarity=0.312 Sum_probs=18.0 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+++ ++.+.+..++.|++ T Consensus 37 ~a~vng~l~-dL~~~l~~d~~ve~ 59 (63) T 1qf6_A 37 AGRVNGELV-DACDLIENDAQLSI 59 (63) T ss_dssp EEEETTEEE-ETTSCBCSCEECCE T ss_pred EEEECCEEE-ECCCCCCCCCEEEE T ss_conf 999999998-57851799988998 No 45 >>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:) Probab=34.79 E-value=28 Score=14.86 Aligned_cols=30 Identities=13% Similarity=0.072 Sum_probs=22.8 Q ss_pred HHHHHC-CCEEECCEECCCCCEEECCCCEEEE Q ss_conf 999986-9869999992406878079997999 Q gi|254780406|r 32 ERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 32 ~~lI~~-G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) +.++.. -+|.|||+.+. ..+.+.++|.|.+ T Consensus 44 ~~l~~~~~~v~vn~~~v~-~~~~l~~gdeVai 74 (81) T 1fm0_D 44 LALEDGKLLAAVNQTLVS-FDHPLTDGDEVAF 74 (81) T ss_dssp HHHCCTTCEEEETTEECC-TTCBCCTTCEEEE T ss_pred HHHCCCCEEEECCCEECC-CCCCCCCCCEEEE T ss_conf 862789589972845979-9978599999999 No 46 >>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:) Probab=34.43 E-value=13 Score=16.88 Aligned_cols=43 Identities=23% Similarity=0.322 Sum_probs=30.3 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 7734478899988687789999999869869999992406878079997999 Q gi|254780406|r 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) ..+.-+..+|...++-. ..=-|.|||+++. +.+.+.++|.|.+ T Consensus 28 ~~~~Tv~~ll~~L~l~~--------~~v~v~vNg~~v~-~~~~L~dgD~v~i 70 (77) T 1rws_A 28 REGMKVRDILRAVGFNT--------ESAIAKVNGKVVL-EDDEVKDGDFVEV 70 (77) T ss_dssp CSSCCHHHHHHTTTCSS--------CSSCEEETTEEEC-SSSCCCSSCCCBC T ss_pred CCCCCHHHHHHHHCCCC--------HHHHEEECCEECC-CCCCCCCCCEEEE T ss_conf 99699999999809983--------0101559999969-9728699999999 No 47 >>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238) Probab=32.30 E-value=31 Score=14.60 Aligned_cols=39 Identities=26% Similarity=0.199 Sum_probs=29.3 Q ss_pred CCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEE Q ss_conf 698699999924068780799979999989225564389 Q gi|254780406|r 37 QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75 (354) Q Consensus 37 ~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~ 75 (354) +|-+.+||+++....+.+..+|.|.|.+..+.+.....- T Consensus 54 ngt~~~n~~~~~~~~~~L~~Gd~i~iG~~~~~~~~~~~~ 92 (158) T 1wv3_A 54 NTDVYINYELQEQLTNKAYIGDHIYVEGIWLEVQADGLN 92 (158) T ss_dssp TCCEEETTEECCSSEEEEETTCEEEETTEEEEECSSEEE T ss_pred CCCEEECCEEEECCEEECCCCCEEEECCEEEEEECCCEE T ss_conf 986998789972550430489999999899999742179 No 48 >>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:) Probab=31.53 E-value=32 Score=14.52 Aligned_cols=24 Identities=17% Similarity=0.003 Sum_probs=18.1 Q ss_pred CEEECCEECCC---CCEEECCCCEEEE Q ss_conf 86999999240---6878079997999 Q gi|254780406|r 39 RVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .|.|||+.+.. +.+.+.++|.|.+ T Consensus 66 ~v~vNg~~i~~~~~~~t~L~~gDeV~i 92 (99) T 2qjl_A 66 ITLINDTDWELEGEKDYILEDGDIISF 92 (99) T ss_dssp EEEETTEEGGGGTGGGCBCCTTCEEEE T ss_pred EEEECCCEEECCCCCCCCCCCCCEEEE T ss_conf 999879587817887758599799999 No 49 >>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis H37RV} PDB: 3dwm_A (C:) Probab=31.52 E-value=32 Score=14.52 Aligned_cols=24 Identities=17% Similarity=0.231 Sum_probs=18.9 Q ss_pred CEEECCEECCCC---CEEECCCCEEEE Q ss_conf 869999992406---878079997999 Q gi|254780406|r 39 RVKVNGILLERA---AVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~---~~~v~~~d~v~v 62 (354) .|.|||+.+... .+.+.++|.|.+ T Consensus 60 ~v~vNg~~v~~~~~~~t~l~~gDeV~i 86 (93) T 3dwg_C 60 NIYVNDEDVRFSGGLATAIADGDSVTI 86 (93) T ss_dssp EEEETTEEGGGTTGGGCBCCTTCEEEE T ss_pred EEEECCEEECCCCCCCCCCCCCCEEEE T ss_conf 999857451001476663799899999 No 50 >>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:) Probab=31.38 E-value=24 Score=15.31 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=20.0 Q ss_pred CCCEEECCEECCC---CCEEECCCCEEEE Q ss_conf 6986999999240---6878079997999 Q gi|254780406|r 37 QQRVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 37 ~G~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .=.|.|||+.+.. +.+.+.++|.|.+ T Consensus 55 ~v~v~vNg~~v~~~~~~~t~l~~gD~V~i 83 (90) T 2g1e_A 55 NVIILVNGNNITSMKGLDTEIKDDDKIDL 83 (90) T ss_dssp TCEEEESSSBGGGTCSSSCBCCTTCEEEE T ss_pred HEEEEEECCCCCCCCCCCCCCCCCCEEEE T ss_conf 50457703000234465653799999999 No 51 >>3hvz_A Uncharacterized protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.20A {Clostridium leptum dsm 753} (A:) Probab=30.55 E-value=33 Score=14.42 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=17.9 Q ss_pred EEECCEECCCCCEEECCCCEEEE Q ss_conf 69999992406878079997999 Q gi|254780406|r 40 VKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~~~~~v~~~d~v~v 62 (354) ..|||+.+ ++.+.+..++.|++ T Consensus 44 a~vng~l~-dL~~~l~~~~~vei 65 (78) T 3hvz_A 44 AKVDGRIV-PIDYKVKTGEIIDV 65 (78) T ss_dssp EEETTEEE-CTTCBCCTTCBEEE T ss_pred EEECCEEC-CCCCCCCCCCEEEE T ss_conf 79999999-99888589999999 No 52 >>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, metal-binding, nucleus, repressor, transcription regulation, zinc; 1.55A {Homo sapiens} (A:1-95) Probab=30.16 E-value=34 Score=14.38 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=31.3 Q ss_pred CCCCCCCEEEECC-CCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 5433232022236-76410001234457404775211245 Q gi|254780406|r 114 LDINTEGLLLLTN-DGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 114 LD~~t~GLlllTn-dg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) +-.+.+|++.+.+ +..|+-+.+.-...+.-.|.+.|.++ T Consensus 56 tT~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAi~V~g~ 95 (95) T 3h7h_A 56 TSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGR 95 (95) T ss_dssp EESCEEEEEEESCGGGCHHHHHTTCTTSCSEEEEEEECCC T ss_pred CCCCCCEEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCC T ss_conf 4666333799956842389998645677897489884585 No 53 >>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:) Probab=30.09 E-value=27 Score=14.97 Aligned_cols=24 Identities=21% Similarity=0.254 Sum_probs=16.8 Q ss_pred CCEEECCEECCCCCEEECCCCEEEE Q ss_conf 9869999992406878079997999 Q gi|254780406|r 38 QRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 38 G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) =.|.|||+.+. ..+.+..+|.|.+ T Consensus 68 ~~v~vN~~~v~-~~~~l~dgdeV~i 91 (98) T 1vjk_A 68 VNIAVNGRYVS-WDEELKDGDVVGV 91 (98) T ss_dssp BEEEETTBCCC-TTCBCCTTCEEEE T ss_pred EEEEECCEECC-CCCCCCCCCEEEE T ss_conf 79986788869-8978199999999 No 54 >>1nyr_A Threonyl-tRNA synthetase 1; ATP, threonine, ligase; HET: ATP; 2.80A {Staphylococcus aureus} (A:1-65) Probab=28.61 E-value=21 Score=15.67 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=17.6 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+++ ++.+.+..++.|++ T Consensus 39 aA~vng~lv-dL~~~l~~d~~ve~ 61 (65) T 1nyr_A 39 AGKFNGQLV-DLTKPLETDGSIEI 61 (65) T ss_dssp EEEETTEEE-CTTSCCCSCBCCCE T ss_pred EEEECCEEE-CCCCCCCCCCEEEE T ss_conf 999999996-27851799988999 No 55 >>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, transcription; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis H37RV} (A:290-388) Probab=27.03 E-value=38 Score=14.03 Aligned_cols=30 Identities=23% Similarity=0.270 Sum_probs=16.5 Q ss_pred CCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 9869999992406878079997999998922 Q gi|254780406|r 38 QRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 38 G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) .-|.|||+.+.. .+.+.++|.|.|.+..+. T Consensus 59 ~g~~vng~~v~~-~~~L~~Gd~i~iG~~~~~ 88 (99) T 2ff4_A 59 NGVHVQHERIRS-AVTLNDGDHIRICDHEFT 88 (99) T ss_dssp SCCEETTEECSS-EEEECTTCEEEETTEEEE T ss_pred CCEEECCEECCC-CEECCCCCEEEECCEEEE T ss_conf 785799999878-567899999999789999 No 56 >>1xne_A Hypothetical protein PF0469; GFT structural genomics, protein structure initiative, PSI, NESG, PFR14, alpha and beta protein; NMR {Pyrococcus furiosus dsm 3638} (A:) Probab=25.61 E-value=17 Score=16.25 Aligned_cols=39 Identities=10% Similarity=0.089 Sum_probs=32.2 Q ss_pred HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 999999869869999992406878079997999998922 Q gi|254780406|r 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) +--.+|++|.=+|-+.+...--.++.++|.|.+++.... T Consensus 11 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~~~l~v 49 (113) T 1xne_A 11 EYLEMVKSGKKRIEVRVAYPQLKDIKRGDKIIFNDLIPA 49 (113) T ss_dssp HHHHHHHHTCCCEEECCCTTTTTTCCTTCEEEETTTEEE T ss_pred CHHHHHHCCCCEEEEEECCHHHHHCCCCCEEEEECCEEE T ss_conf 248998769977999825267861899999999301899 No 57 >>1wwt_A Threonyl-tRNA synthetase, cytoplasmic; TGS domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ligase; NMR {Homo sapiens} (A:) Probab=25.13 E-value=31 Score=14.58 Aligned_cols=22 Identities=18% Similarity=0.231 Sum_probs=11.5 Q ss_pred EEECCEECCCCCEEECCCCEEEE Q ss_conf 69999992406878079997999 Q gi|254780406|r 40 VKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~~~~~v~~~d~v~v 62 (354) ..|||+.+ ++.+.+..++.|++ T Consensus 49 a~vng~l~-dL~~~l~~d~~ve~ 70 (88) T 1wwt_A 49 AKVNNVVW-DLDRPLEEDCTLEL 70 (88) T ss_dssp EEESSSEE-CSSSCCCSSEEEEE T ss_pred ECCCCEEE-EEEEECCCCCEEEE T ss_conf 13298787-50178189999999 No 58 >>1h6l_A 3-phytase; hydrolase, phosphatase, propeller, phosphate; 1.8A {Bacillus amyloliquefaciens} (A:1-69,A:227-353) Probab=24.71 E-value=42 Score=13.77 Aligned_cols=33 Identities=27% Similarity=0.462 Sum_probs=22.9 Q ss_pred CCCEEECCCCCCEECCCCCCCCCCCEEEECC-CCC Q ss_conf 4210110234320026655433232022236-764 Q gi|254780406|r 96 TVFDNLPSIFSRVISVGRLDINTEGLLLLTN-DGG 129 (354) Q Consensus 96 ~~~~~~~~~~~~~~~vgRLD~~t~GLlllTn-dg~ 129 (354) .+++ |....-..+++|||-.|.|||-|+.. +++ T Consensus 53 ~vyd-l~G~~~q~~~~G~l~aDvEGltly~~~~~~ 86 (196) T 1h6l_A 53 AVYS-LEGKMLHSYHTGKLTPDIEGLTIYYAADGK 86 (196) T ss_dssp EEEE-TTCCEEEECCSSCCCSCEEEEEEEECGGGC T ss_pred EEEC-CCCCEEEECCCCCCCCCCCCCEEEECCCCC T ss_conf 9987-898788863678733582113578756897 No 59 >>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84) Probab=23.57 E-value=44 Score=13.63 Aligned_cols=24 Identities=8% Similarity=0.122 Sum_probs=18.4 Q ss_pred CEEECCEECCC---CCEEECCCCEEEE Q ss_conf 86999999240---6878079997999 Q gi|254780406|r 39 RVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .|.|||+-+.. +.+.+.++|.|.+ T Consensus 54 ~i~vNg~~i~~~~~~~t~l~dgDeVai 80 (84) T 1v8c_A 54 SVFLEGRDVRYLQGLSTPLSPGATLDL 80 (84) T ss_dssp EEEETTEEGGGTTGGGCBCCTTCEEEE T ss_pred EEEECCEEECCCCCCCCCCCCCCEEEE T ss_conf 999878774145788868699999999 No 60 >>1mio_A Nitrogenase molybdenum iron protein (alpha chain); HET: HCA CFM CLP; 3.00A {Clostridium pasteurianum} (A:47-68,A:201-285) Probab=23.24 E-value=45 Score=13.59 Aligned_cols=24 Identities=25% Similarity=0.299 Sum_probs=19.7 Q ss_pred EEEECCHHHHHHHHHHCCCEEEEE Q ss_conf 995184289999999839868688 Q gi|254780406|r 192 GLREGKNREIKKVFEFFNWKVNRL 215 (354) Q Consensus 192 ~l~eGr~~qIrr~~~~~g~~V~~L 215 (354) ....|-..+|++||+.+|++|..+ T Consensus 37 ~~~~~D~~EIkrlL~~~Gi~vn~~ 60 (107) T 1mio_A 37 YNIGGDAWEMDRVLEKIGYHVNAT 60 (107) T ss_dssp CCBTSHHHHHHHHHHHHTCEEEEE T ss_pred CCCCCCHHHHHHHHHHCCCCEEEE T ss_conf 877214999999999859945897 No 61 >>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:) Probab=22.02 E-value=31 Score=14.57 Aligned_cols=23 Identities=26% Similarity=0.148 Sum_probs=14.4 Q ss_pred EEECCEECCC---CCEEECCCCEEEE Q ss_conf 6999999240---6878079997999 Q gi|254780406|r 40 VKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) |.|||+.+.. +.+.+.++|.|.+ T Consensus 70 v~VN~~~v~~~~~~~t~L~~gDeV~i 95 (110) T 2k9x_A 70 VLVNSCDAEVVGGMDYVLNDGDTVEF 95 (110) T ss_dssp EEESSSBHHHHTSSCCCCCSSCEEEE T ss_pred EEECCCEEECCCCCCCCCCCCCEEEE T ss_conf 99889562438885648599799999 No 62 >>3f7f_A Nucleoporin NUP120; nuclear pore complex, macromolecular assembly, membrane coat, nucleocytoplasmic transport, beta-propeller; 2.60A {Saccharomyces cerevisiae} PDB: 3h7n_A 3hxr_A (A:270-325) Probab=21.95 E-value=40 Score=13.88 Aligned_cols=37 Identities=22% Similarity=0.375 Sum_probs=27.9 Q ss_pred CCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCC Q ss_conf 21011023432002665543323202223676410001 Q gi|254780406|r 97 VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134 (354) Q Consensus 97 ~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l 134 (354) +.-++|.. .-+|-+|-|+.|++|-|-+|--+-+...| T Consensus 18 L~v~LPf~-NG~F~~gtL~v~~sg~l~~t~k~~i~tNL 54 (56) T 3f7f_A 18 LVTLLPLE-NGLFQMGTLLVDSSGILTYTFQNNIPTNL 54 (56) T ss_dssp EEEEETTT-TCEEEEEEEEC-----CEEECCCEEECCC T ss_pred EEEECCCC-CCCEEEEEECCCCCCCCCCCCCCCCCCCC T ss_conf 99975567-87489999634776631245678789877 No 63 >>1wln_A Afadin; beta sandwich, FHA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Probab=20.74 E-value=50 Score=13.27 Aligned_cols=10 Identities=30% Similarity=0.378 Sum_probs=4.1 Q ss_pred CEECCCCCCC Q ss_conf 2002665543 Q gi|254780406|r 107 RVISVGRLDI 116 (354) Q Consensus 107 ~~~~vgRLD~ 116 (354) ..+.|||-.. T Consensus 36 ~~~~IGR~~~ 45 (120) T 1wln_A 36 SVTEVGTEKF 45 (120) T ss_dssp EEEECSSSCC T ss_pred CCEEECCCCC T ss_conf 8389858878 No 64 >>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:) Probab=20.29 E-value=28 Score=14.84 Aligned_cols=12 Identities=8% Similarity=-0.225 Sum_probs=4.0 Q ss_pred CCEEEEEEEECC Q ss_conf 740477521124 Q gi|254780406|r 140 QWLRVYRVRFHG 151 (354) Q Consensus 140 ~~~k~Y~v~v~~ 151 (354) .+..-+.|-|++ T Consensus 69 ~~~~~i~v~vN~ 80 (114) T 1wgk_A 69 SVRPGILVLIND 80 (114) T ss_dssp SCCSSEEEEESS T ss_pred CCCEEEEEEECC T ss_conf 850558999758 Done!