Query gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter asiaticus str. psy62] Match_columns 346 No_of_seqs 165 out of 5456 Neff 7.1 Searched_HMMs 33803 Date Wed Jun 1 15:31:39 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780608.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 0 0 453.2 9.8 300 7-328 4-317 (325) 2 >1v9k_A Ribosomal large subuni 100.0 0 0 368.3 9.5 219 99-323 2-225 (228) 3 >2i82_A Ribosomal large subuni 100.0 0 0 341.4 9.9 208 95-312 8-216 (217) 4 >2gml_A Ribosomal large subuni 100.0 0 0 329.6 3.5 205 97-328 5-227 (237) 5 >3dh3_A Ribosomal large subuni 100.0 0 0 317.7 4.7 197 104-327 2-216 (227) 6 >2oml_A Ribosomal large subuni 100.0 2E-43 0 293.5 5.9 184 97-294 2-185 (189) 7 >1ksk_A Ribosomal small subuni 100.0 1.2E-40 4.2E-45 275.8 5.1 170 103-300 2-171 (176) 8 >1vio_A Ribosomal small subuni 100.0 1.6E-39 4.8E-44 268.9 6.3 178 103-303 2-185 (186) 9 >1dm9_A Hypothetical 15.5 KD p 99.9 1.4E-23 4.1E-28 168.4 0.4 131 11-165 1-131 (133) 10 >2olw_A Ribosomal large subuni 99.9 1.3E-22 3.8E-27 162.3 4.2 100 34-173 2-101 (119) 11 >2olw_A Ribosomal large subuni 99.8 6.4E-21 1.9E-25 151.6 1.7 96 177-273 1-96 (98) 12 >2k6p_A Uncharacterized protei 99.8 3.8E-20 1.1E-24 146.7 1.5 91 19-123 1-91 (92) 13 >3dh3_A Ribosomal large subuni 99.0 2.9E-10 8.6E-15 84.4 5.2 54 15-69 3-56 (63) 14 >1p9k_A ORF, hypothetical prot 98.9 4.7E-10 1.4E-14 83.1 2.1 69 1-69 3-72 (79) 15 >1ksk_A Ribosomal small subuni 98.6 8.2E-08 2.4E-12 68.9 5.6 51 17-68 2-53 (58) 16 >1vio_A Ribosomal small subuni 98.5 1.3E-07 3.9E-12 67.6 5.4 50 18-68 2-52 (57) 17 >2vqe_D 30S ribosomal protein 98.1 1E-05 3E-10 55.7 6.8 50 20-70 1-52 (94) 18 >3hp7_A Hemolysin, putative; s 98.1 2.2E-06 6.6E-11 59.9 3.2 55 14-68 2-59 (65) 19 >3bbn_D Ribosomal protein S4; 97.9 1.1E-05 3.2E-10 55.6 3.9 53 19-71 8-61 (120) 20 >3i1m_D 30S ribosomal protein 97.9 7.3E-06 2.2E-10 56.6 3.1 53 20-72 1-54 (94) 21 >1h3f_A Tyrosyl-tRNA synthetas 97.6 0.00026 7.6E-09 46.9 6.9 62 7-68 5-70 (83) 22 >1s1h_D 40S ribosomal protein 97.5 0.00011 3.3E-09 49.2 4.6 51 19-69 9-60 (99) 23 >2cqj_A BRMS2, U3 small nucleo 97.3 0.00021 6.1E-09 47.5 3.5 52 18-69 7-61 (71) 24 >2apo_A Probable tRNA pseudour 96.5 0.002 6E-08 41.2 2.9 71 105-188 15-85 (216) 25 >2aus_C Pseudouridine synthase 96.4 0.0025 7.4E-08 40.7 3.0 83 105-200 15-97 (215) 26 >2jan_A Tyrosyl-tRNA synthetas 95.8 0.011 3.2E-07 36.6 4.1 50 15-64 8-58 (88) 27 >1sgv_A TRNA pseudouridine syn 92.5 0.057 1.7E-06 32.1 1.7 53 105-166 5-57 (87) 28 >1k8w_A TRNA pseudouridine syn 92.1 0.068 2E-06 31.6 1.7 55 103-166 22-76 (108) 29 >1r3e_A TRNA pseudouridine syn 92.0 0.071 2.1E-06 31.5 1.8 59 106-175 3-61 (92) 30 >1c05_A Ribosomal protein S4 d 91.4 0.16 4.8E-06 29.2 3.0 25 45-69 1-26 (83) 31 >1jil_A Tyrrs, tyrosyl-tRNA sy 91.1 0.046 1.4E-06 32.7 0.0 53 13-65 101-154 (174) 32 >3kbg_A 30S ribosomal protein 90.4 0.42 1.2E-05 26.6 4.4 53 16-68 5-59 (81) 33 >2ts1_A Tyrosyl-tRNA synthetas 89.1 0.086 2.5E-06 31.0 0.0 50 16-65 104-154 (174) 34 >1fm0_D Molybdopterin converti 84.0 1.6 4.7E-05 23.0 4.2 53 17-71 24-78 (81) 35 >2q5w_D Molybdopterin converti 83.7 1.4 4.3E-05 23.2 3.9 44 21-71 31-74 (77) 36 >1vjk_A Molybdopterin converti 71.6 2.9 8.7E-05 21.3 2.6 51 21-71 42-95 (98) 37 >2eh0_A KLP, kinesin-like prot 65.8 4.5 0.00013 20.1 2.5 22 46-67 82-103 (130) 38 >2g1e_A Hypothetical protein T 65.3 8.2 0.00024 18.5 3.8 53 18-71 24-87 (90) 39 >2g1l_A Kinesin-like protein K 64.9 6.2 0.00018 19.2 3.1 22 46-67 73-94 (104) 40 >1rws_A Hypothetical protein P 64.7 2.7 8E-05 21.5 1.2 46 16-70 28-73 (77) 41 >1wln_A Afadin; beta sandwich, 64.4 4.7 0.00014 20.0 2.4 10 101-110 64-73 (120) 42 >1wgk_A Riken cDNA 2900073H19 63.1 5.3 0.00016 19.7 2.5 61 11-71 35-105 (114) 43 >2ff4_A Probable regulatory pr 62.1 7 0.00021 18.9 2.9 25 44-68 59-83 (99) 44 >1v8c_A MOAD related protein; 59.0 10 0.0003 17.9 3.3 46 21-70 28-83 (84) 45 >3els_A PRE-mRNA leakage prote 56.6 11 0.00033 17.6 3.2 18 155-172 70-87 (158) 46 >1tyg_B YJBS; alpha beta barre 54.7 12 0.00035 17.5 3.0 59 2-69 15-82 (87) 47 >2hj1_A Hypothetical protein; 52.3 8.5 0.00025 18.4 2.0 38 26-70 48-85 (97) 48 >1wxq_A GTP-binding protein; s 49.8 4.8 0.00014 19.9 0.4 24 45-68 54-77 (81) 49 >2qjl_A URM1, ubiquitin-relate 49.6 16 0.00048 16.6 3.1 53 17-70 30-95 (99) 50 >3dwg_C 9.5 kDa culture filtra 48.6 17 0.00051 16.4 3.1 27 45-71 60-90 (93) 51 >3huh_A Virulence protein STM3 46.2 19 0.00057 16.1 3.6 50 252-315 20-71 (75) 52 >2rk0_A Glyoxalase/bleomycin r 45.6 20 0.00059 16.1 3.5 45 252-313 19-63 (69) 53 >1wwt_A Threonyl-tRNA syntheta 40.3 24 0.00071 15.5 5.3 61 1-68 5-71 (88) 54 >3hvz_A Uncharacterized protei 39.5 23 0.00067 15.7 2.5 60 2-68 2-66 (78) 55 >2k9x_A Tburm1, uncharacterize 36.3 16 0.00048 16.6 1.4 56 17-72 33-100 (110) 56 >2eki_A DRG 1, developmentally 31.3 28 0.00083 15.1 1.9 16 52-67 69-84 (93) 57 >3ct8_A Protein BH2160, putati 31.3 33 0.00098 14.6 4.8 47 252-310 21-67 (67) 58 >2exd_A NFED short homolog; me 30.8 34 0.001 14.6 2.4 27 42-68 29-57 (80) 59 >2csw_A Ubiquitin ligase prote 29.3 35 0.001 14.5 2.1 10 156-165 36-45 (145) 60 >3ey7_A Biphenyl-2,3-DIOL 1,2- 27.4 39 0.0011 14.2 3.5 45 253-311 19-65 (67) 61 >1vc3_B L-aspartate-alpha-deca 26.3 34 0.001 14.5 1.7 48 9-70 19-66 (96) 62 >1yj5_C 5' polynucleotide kina 26.3 41 0.0012 14.1 2.3 22 46-67 72-95 (143) 63 >1wv3_A Similar to DNA segrega 26.2 41 0.0012 14.1 2.6 27 43-69 54-81 (158) 64 >2k5p_A THis protein, thiamine 26.1 41 0.0012 14.1 2.5 46 17-70 16-65 (78) 65 >1tke_A Threonyl-tRNA syntheta 26.1 41 0.0012 14.1 2.5 45 16-67 15-59 (63) 66 >1f0z_A THis protein; ubiquiti 24.8 42 0.0012 14.0 1.9 44 17-69 14-61 (66) 67 >3kt9_A Aprataxin; FHA domain, 24.7 43 0.0013 13.9 2.8 24 45-68 65-90 (102) 68 >3elx_A Ileal bIle acid-bindin 23.2 46 0.0014 13.7 5.7 48 1-53 1-51 (138) 69 >2kmm_A Guanosine-3',5'-BIS(di 22.9 47 0.0014 13.7 3.3 45 17-68 17-61 (73) 70 >2hd9_A UPF0310 protein PH1033 22.2 48 0.0014 13.7 1.8 42 32-73 8-49 (145) 71 >3cuz_A MSA, malate synthase A 21.8 24 0.00072 15.5 0.2 27 31-57 53-79 (134) 72 >1qf6_A THRRS, threonyl-tRNA s 21.7 41 0.0012 14.1 1.3 45 16-67 15-59 (63) 73 >1nki_A Probable fosfomycin re 20.8 52 0.0015 13.4 4.7 61 245-323 9-70 (77) No 1 >>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:) Probab=100.00 E-value=0 Score=453.24 Aligned_cols=300 Identities=25% Similarity=0.368 Sum_probs=235.6 Q ss_pred EEE-EEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCC-CCEEEEECCCCCCCCCCCCCCCC Q ss_conf 049-9984113686689999987678898999999984990388788451121179-98899935655422233222234 Q gi|254780608|r 7 VQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKIL 84 (346) Q Consensus 7 ~~~-~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~-GD~I~i~~~~~~~~~~~~~~~~~ 84 (346) |++ ++|+++++|+|||+||++.++++||+.++++|++|+|+|||+++...+.+.. ++.+........ T Consensus 4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~----------- 72 (325) T 1v9f_A 4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEE----------- 72 (325) T ss_dssp -------------------------------------------------------------------------------- T ss_pred EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCC----------- T ss_conf 899999897648866999999866867999999999869989999991783206258989973254332----------- Q ss_pred CCCCCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCC--CCCCCCCCCCCCCCCCCCCEEEEE Q ss_conf 55433432223454307861785688417653112235785332-332011011--111001333544534222404621 Q gi|254780608|r 85 DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVA 161 (346) Q Consensus 85 ~~~~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~--~~~~~~~~lVHRLDr~TSGlll~A 161 (346) .........+..|||||++++|+|||+|++|||+.+.... +...+.... ......+++|||||++||||||+| T Consensus 73 ----~~~~~~~~~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~A 148 (325) T 1v9f_A 73 ----EARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVA 148 (325) T ss_dssp -------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEE T ss_pred ----CCCCCCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEE T ss_conf ----2233334454112510110578707888654898777888632321134443333342146532588986514664 Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCC Q ss_conf 23101222102333322111200013456541000000012234655432111335555555303430101343202442 Q gi|254780608|r 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241 (346) Q Consensus 162 K~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~s 241 (346) ||..+++.|+.+|+.+.+.|+|+|+|.|.+....+.+..+........ .......++.|.|+|.+..... .+| T Consensus 149 k~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~a~~~~~~~~~~~-~~s 221 (325) T 1v9f_A 149 KTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRT------HMAVHPMGKPAVTHYRIMEHFR-VHT 221 (325) T ss_dssp SSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT------CEEECTTSBCCEEEEEEEEECS-SEE T ss_pred CCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC------EEEECCCCCEEEEEEEEEEECC-CCE T ss_conf 025889999987501210124234301354745662355335766653------0587688715789989865338-845 Q ss_pred EEEEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCH--------HCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCC Q ss_conf 04578612378999999996398000464446652210--------001344624131100043758896-499983997 Q gi|254780608|r 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312 (346) Q Consensus 242 lv~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~--------~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP 312 (346) +++|+|.|||+||||+||+++||||+||.+||...... .......+++|||+.++|+||.++ .+.|+||+| T Consensus 222 l~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P 301 (325) T 1v9f_A 222 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP 301 (325) T ss_dssp EEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC T ss_pred EEEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH T ss_conf 79999778831799999998399766877789855454433166777651586434653705857789998899991797 Q ss_pred HHHHHHHHHHCCCCCC Q ss_conf 8999999980898752 Q gi|254780608|r 313 AHMVKTWDSLGFKYDR 328 (346) Q Consensus 313 ~~f~~~l~~l~~~~d~ 328 (346) ++|..+|+.|+++.+. T Consensus 302 ~~f~~~l~~l~~~~~~ 317 (325) T 1v9f_A 302 QDMVELIEVMRADFEE 317 (325) T ss_dssp HHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999997307765 No 2 >>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:) Probab=100.00 E-value=0 Score=368.29 Aligned_cols=219 Identities=33% Similarity=0.518 Sum_probs=179.4 Q ss_pred CEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCC Q ss_conf 307861785688417653112235785332-3320110111110013335445342224046212310122210233332 Q gi|254780608|r 99 SILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177 (346) Q Consensus 99 ~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~ 177 (346) +.|||||++|+|||||+|++|||+.+.... +..++... ....++.+|||||++||||||+|||..+++.|+.+|+++ T Consensus 2 ~~Iiyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~--~~~~~~~~vhRLD~~TSGlll~ak~~~~a~~l~~~~~~~ 79 (228) T 1v9k_A 2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 79 (228) T ss_dssp CCEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHS--TTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTT T ss_pred CEEEEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHC--CCCCCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHH T ss_conf 989996899999999999863899899536999999867--787653166404643221367523579999999998740 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHH Q ss_conf 21112000134565410000000122346554321113355555553034301013432024420457861237899999 Q gi|254780608|r 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257 (346) Q Consensus 178 ~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRv 257 (346) .+.|+|+|+|.|.+....+.+..++......... .......+.+.|.++|.+....+ .+++++++|.|||+||||+ T Consensus 80 ~v~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~tGR~HQIR~ 155 (228) T 1v9k_A 80 GXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE---RIVRVSQEGKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRV 155 (228) T ss_dssp CSEEEEEEEEESCCCTTCCEECCCEEEEECTTSC---EEEEECTTSBCCCEEEEEEEECS-SEEEEEEEESSCCTTHHHH T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCE---EEEECCCCCCCCCEEECHHHHCC-CCEEEEEEECCCCHHHHHH T ss_conf 3454321034686422357522330000110101---55520788842215500555358-7379999947573578888 Q ss_pred HHHHCCCCEECCCCCCCCCCCHH---CCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHHHHHHHHHC Q ss_conf 99963980004644466522100---013446241311000437588964-9998399789999999808 Q gi|254780608|r 258 HALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323 (346) Q Consensus 258 hl~~~g~PivGD~~Yg~~~~~~~---~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f~~~l~~l~ 323 (346) ||+++||||+||.+||....... ......+++|||++|+|+||.+++ +.|+||+|++|.++|+.|. T Consensus 156 h~a~~g~PIvgD~~Y~~~~~~~~~~~~~~~~~~~~Lha~~l~f~~p~~~~~~~~~ap~P~~~~~~l~~~~ 225 (228) T 1v9k_A 156 HTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEGLKRCLQKXR 225 (228) T ss_dssp HHHHTTCCBTTCTTTSCHHHHHHHHHTTCCCCSCCEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH T ss_pred HHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHCCCCEEECCCCCCEEEEEECCHHHHHHHHHHHH T ss_conf 8885497213577413000002333202686237887150392879999889999178699999999987 No 3 >>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:) Probab=100.00 E-value=0 Score=341.44 Aligned_cols=208 Identities=30% Similarity=0.404 Sum_probs=170.7 Q ss_pred CCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCC Q ss_conf 34543078617856884176531122357853323320110111110013335445342224046212310122210233 Q gi|254780608|r 95 DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174 (346) Q Consensus 95 ~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f 174 (346) ......|||||++++|||||+|++|||+.+........+. ......++.+|||||++||||||+||+.++++.|+.+| T Consensus 8 ~~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~--~~~~~~~l~~vhRLD~~TSGllllak~~~~~~~l~~~~ 85 (217) T 2i82_A 8 QEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTR--IQRDYPQAESVHRLDXATSGVIVVALTKAAERELKRQF 85 (217) T ss_dssp CSSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHH--HHHHCTTCEESSCCCTTCEEEEEEESSHHHHHHHHHHH T ss_pred CCCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHH--HHHHCCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHHH T ss_conf 8999529997998999999999825799887760389997--64410332223455542101589860317777889876 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHH Q ss_conf 33221112000134565410000000122346554321113355555553034301013432024420457861237899 Q gi|254780608|r 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254 (346) Q Consensus 175 ~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQ 254 (346) .++.+.|+|+|++.|.+....+.+..+............ .....+++.+.+.|.++... ..+|+++|+|.|||+|| T Consensus 86 ~~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-~~~s~~~~~~~TGr~HQ 161 (217) T 2i82_A 86 REREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQK---VCYETGKPAQTEYEVVEYAA-DNTARVVLKPITGRSHQ 161 (217) T ss_dssp HTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEE---ECTTTCBCCEEEEEEEEEET-TTEEEEEEEESSCCTTH T ss_pred HHCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCE---ECCCCCCCCCCEECCCCCCC-CCCEEEEEEECCCCHHH T ss_conf 514010368988615446664067410123224332200---01224763001010111123-31047889850262378 Q ss_pred HHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCC Q ss_conf 99999963980004644466522100013446241311000437588964-99983997 Q gi|254780608|r 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312 (346) Q Consensus 255 IRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP 312 (346) ||+||+++||||+||.+||...... ...|++|||++|+|+||.+++ +.|.||+| T Consensus 162 IR~h~a~lg~PIlgD~~Yg~~~~~~----~~~~~~Lha~~l~f~~p~~ge~~~~~~p~P 216 (217) T 2i82_A 162 LRVHXLALGHPILGDRFYASPEARA----XAPRLLLHAEXLTITHPAYGNSXTFKAPAD 216 (217) T ss_dssp HHHHHHHTTCCBTTCTTTSCHHHHH----TCSSCCEEEEEEEEECTTTCCEEEEECCCC T ss_pred HHHHHHHHCCEEECCCCCCCHHHCC----CCCCHHHHCCCCEEECCCCCCEEEEECCCC T ss_conf 9999997197681676768855636----884666762767889989998899978999 No 4 >>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:) Probab=100.00 E-value=0 Score=329.60 Aligned_cols=205 Identities=12% Similarity=-0.003 Sum_probs=161.7 Q ss_pred CCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCC Q ss_conf 54307861785688417653112235785332332011011111001333544534222404621231012221023333 Q gi|254780608|r 97 LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176 (346) Q Consensus 97 ~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~ 176 (346) .+..|||||+++||||||+|++|||+.....++...+.. ..++++|||||++||||||||++.+++..+.. .. T Consensus 5 ~~~~ii~ed~~~ivvnKP~G~~~~~~~~~~~~~~~~l~~-----~~~~~~vhRLD~~TSGlll~a~~~~~~~~~~~--~~ 77 (237) T 2gml_A 5 HHHHHHGSDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AG 77 (237) T ss_dssp --------CCCEEEEEECTTCBCCSSSSCSSBHHHHSCC-----SSCCEEESCCCTTCEEEEEEESCHHHHHHHHH--HH T ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCCCCCCCHHHCCC-----CCCEEECCCCCCCCCCCEEEECCHHHHHHHHH--HC T ss_conf 555556852399999799938972289999974421576-----45611412468888885898416688888765--31 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH Q ss_conf 22111200013456541000000012234655432111335555555303430101343202442045786123789999 Q gi|254780608|r 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256 (346) Q Consensus 177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR 256 (346) +.+.|+|+|+|.|.+....+.+..+.... .+.+.+...... .++++++++|.|||+|||| T Consensus 78 ~~i~K~Y~a~v~G~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~-~~~~~v~~~~~tGR~HQIR 137 (237) T 2gml_A 78 NDHEKEYLVTVDKPITEEFIRGXSAGVPI-------------------LGTVTKKCKVKK-EAPFVFRITLVQGLNRQIR 137 (237) T ss_dssp HHSCEEEEEEESSCCCHHHHHHHSSCCEE-------------------TTEECCCCEEEE-EETTEEEEEECCCSTTHHH T ss_pred CCCCEEEEEEECCCCCHHHHHHHHCCCEE-------------------CCEEEECHHHCC-CCCEEEEEEEECCCCHHHH T ss_conf 35514887785267999999999759887-------------------775742000035-6654999998168861999 Q ss_pred HHHHHCCCCEECCCCCCCCCCCH-----------------HCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHHHHH Q ss_conf 99996398000464446652210-----------------001344624131100043758896-499983997899999 Q gi|254780608|r 257 VHALHMGCPIVGDHKYCANFKGN-----------------FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318 (346) Q Consensus 257 vhl~~~g~PivGD~~Yg~~~~~~-----------------~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f~~~ 318 (346) +||+++||||+||.+||...... .......+++|||++++|+||.++ ++.|+||+|++|.++ T Consensus 138 ~h~~~~G~pI~gD~~y~~~~~~~~~l~~g~~~~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~t~e~~~~~~p~p~~~~~~ 217 (237) T 2gml_A 138 RXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKXEKTAEKG 217 (237) T ss_dssp HHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHTTSTTCC------------------------------ T ss_pred HHHHHCCCEEEEEEEEEECCEEECCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 99998699766699999888880897997838999999999998763345666886667887666678877777777888 Q ss_pred HHHHCCCCCC Q ss_conf 9980898752 Q gi|254780608|r 319 WDSLGFKYDR 328 (346) Q Consensus 319 l~~l~~~~d~ 328 (346) ++.|++.-+. T Consensus 218 ~~~l~~~~~~ 227 (237) T 2gml_A 218 GRPASNGKRF 227 (237) T ss_dssp ---------- T ss_pred CCCCCCCCCC T ss_conf 8988899898 No 5 >>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=100.00 E-value=0 Score=317.68 Aligned_cols=197 Identities=13% Similarity=0.024 Sum_probs=160.3 Q ss_pred ECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCC Q ss_conf 17856884176531122357853323320110111110013335445342224046212310122210233332211120 Q gi|254780608|r 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183 (346) Q Consensus 104 ED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y 183 (346) ||+++||||||+||+|||+++...++.+++..+ .++.+|||||++|||||||||+.+++..++.+ .+.++|+| T Consensus 2 Ed~~~ivinKP~Gl~~~~~~~~~~~l~~~l~~~-----~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y 74 (227) T 3dh3_A 2 EDLVLIALNKPVGIVSTTEDGERDNIVDFVNHS-----KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRA--GNDHEKEY 74 (227) T ss_dssp GGCCEEEEEECTTCBCCCCSSCTTBHHHHHTCS-----SCCEESSCCCTTCEEEEEEESCTTHHHHHHCG--GGCCCEEE T ss_pred CCEEEEECCCCCCEEECCCCCCCCCCHHHCCCC-----CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHH--HCCCCCCC T ss_conf 311356436665212033347777501101344-----43122465676763148994398799888763--12443221 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCC Q ss_conf 00134565410000000122346554321113355555553034301013432024420457861237899999999639 Q gi|254780608|r 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263 (346) Q Consensus 184 ~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g 263 (346) +|+|.|.+....+.+..+.... ...+.+.+.... ..++++++.+.|||+||||+||+++| T Consensus 75 ~a~v~G~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~-~~~~~~~~~~~tGr~hQIR~h~a~~g 134 (227) T 3dh3_A 75 LVTVDKPITEEFIRGMSAGVPI-------------------LGTVTKKCKVKK-EAPFVFRITLVQGLNRQIRRMCEHFG 134 (227) T ss_dssp EEEESSCCCHHHHHHHHTCCBC-------------------SSSBCCCCEEEE-CSSSEEEEEESCCCTTHHHHHHHHTT T ss_pred CEEECCCCCHHHHHHHHCCCEE-------------------CCEEEEEEEEEE-CCCCEEEEEECCCCCHHHHHHHHHCC T ss_conf 1276057999999999759984-------------------565744257752-26725899925885259999999879 Q ss_pred CCEECCCCCCCCCCCH-----------------HCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHHHHHHHHHCCC Q ss_conf 8000464446652210-----------------0013446241311000437588964-999839978999999980898 Q gi|254780608|r 264 CPIVGDHKYCANFKGN-----------------FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325 (346) Q Consensus 264 ~PivGD~~Yg~~~~~~-----------------~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f~~~l~~l~~~ 325 (346) |||+||.+||...... .......+++|||+++.|+||.+++ ++|+||+|++|.++++.|+.. T Consensus 135 ~pI~gd~~y~~~~~~l~~l~~g~~r~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~~~e~~~~~ap~p~~~~~~~~~l~~~ 214 (227) T 3dh3_A 135 YEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNG 214 (227) T ss_dssp CCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTCCCCSSCC---------------------------------- T ss_pred CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 96766999998787748979977388999999999987632456678876678877666788777777878889988899 Q ss_pred CC Q ss_conf 75 Q gi|254780608|r 326 YD 327 (346) Q Consensus 326 ~d 327 (346) .+ T Consensus 215 ~~ 216 (227) T 3dh3_A 215 KR 216 (227) T ss_dssp -- T ss_pred CC T ss_conf 99 No 6 >>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:) Probab=100.00 E-value=2e-43 Score=293.51 Aligned_cols=184 Identities=20% Similarity=0.177 Sum_probs=149.1 Q ss_pred CCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCC Q ss_conf 54307861785688417653112235785332332011011111001333544534222404621231012221023333 Q gi|254780608|r 97 LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176 (346) Q Consensus 97 ~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~ 176 (346) .+..|||||++++|||||+|++|||+++..... +..+. ....+.+|||||++|||||||||+.+++..|..+| T Consensus 2 ~~~~vl~ed~~~ivinKP~g~~~~~~~~~~~~~---~~~~l--~~~~l~~vhRLD~~tsGlll~a~~~~~~~~l~~~~-- 74 (189) T 2oml_A 2 TRRKPENQPTRVILFNKPYDVLPQFTDEAGRKT---LKEFI--PVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPG-- 74 (189) T ss_dssp ------CCCCCEEEEEECTTBCSCSSCCTTCBC---GGGTC--CCSSCEESSCCCTTCEEEEEEESCHHHHHHHHSTT-- T ss_pred CCCCCCCCCCEEEEEECCCCEEEECCCCCCCCC---HHHHC--CCCCCEECCCCCCCCCCEEEEECCCHHHHHCCCCC-- T ss_conf 865778899889999899983860779988865---88963--71253473102612000799932530222103123-- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH Q ss_conf 22111200013456541000000012234655432111335555555303430101343202442045786123789999 Q gi|254780608|r 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256 (346) Q Consensus 177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR 256 (346) +.+.|+|+|+|.|.+....+.+..+....................+++.+.+.|.++... ..++++++.|.|||+|||| T Consensus 75 ~~i~k~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~tGr~hQIR 153 (189) T 2oml_A 75 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKS-IPTSWLKITLYEGRNRQVR 153 (189) T ss_dssp SCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CTT-SCEEEEEEEESCCCTTHHH T ss_pred EEEEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEEEE-CCCCEEEEEEECCCHHHHH T ss_conf 037789999993279989999986494507851576579995356641024557888740-5650799999459779999 Q ss_pred HHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHH Q ss_conf 99996398000464446652210001344624131100 Q gi|254780608|r 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294 (346) Q Consensus 257 vhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~ 294 (346) +||+++||||+||.+||.... ...+++||||+ T Consensus 154 ~hl~~lg~pIvgD~~Y~~~~~------~~~~l~l~~~R 185 (189) T 2oml_A 154 RMTAHVGFPTLRLIRYAMGDY------SLDNLANGEWR 185 (189) T ss_dssp HHHHHTTCCEEEEEEEEETTE------ECTTCCTTCEE T ss_pred HHHHHCCCEEEEEEEEEECCE------ECCCCCCCCCE T ss_conf 999986996989899999998------50788998837 No 7 >>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234) Probab=100.00 E-value=1.2e-40 Score=275.83 Aligned_cols=170 Identities=14% Similarity=0.112 Sum_probs=133.4 Q ss_pred EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCC Q ss_conf 61785688417653112235785332332011011111001333544534222404621231012221023333221112 Q gi|254780608|r 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182 (346) Q Consensus 103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~ 182 (346) |||+++||||||+|++|||+.+....+.+.+. .....++++|||||++|||||||||+.+++..+.. ..+.+.|+ T Consensus 2 Yed~~~ivvnKP~gl~~~~~~~~~~~~~~~l~---~~~~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~--~~~~~~k~ 76 (176) T 1ksk_A 2 QHGPRYFXLNKPQGYVCSTDDPDHPTVLYFLD---EPVAWKLHAAGRLDIDTTGLVLXTDDGQWSHRITS--PRHHCEKT 76 (176) T ss_dssp CCCCCEEEEEECTTCBSSSSCSSSCBGGGGCC---CTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEE T ss_pred CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCC---CCCCCCEEEECCCCCCCCCEEEEECCHHHHHHHHH--HHCCCCEE T ss_conf 57857999989998505665554431000012---44456365601388555755886058688887755--42388479 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC Q ss_conf 00013456541000000012234655432111335555555303430101343202442045786123789999999963 Q gi|254780608|r 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262 (346) Q Consensus 183 Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~ 262 (346) |+|+|.|.++.....+..... ..+...+.|.+..... ..+|+++|.|.|||+||||+||+++ T Consensus 77 y~~~v~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~--~~~s~~~~~~~tGr~HQIR~h~~~~ 138 (176) T 1ksk_A 77 YLVTLESPVADDTAEQFAKGV----------------QLHNEKDLTKPAVLEV--ITPTQVRLTISEGRYHQVKRXFAAV 138 (176) T ss_dssp EEEEESSCCCTTHHHHHHHCC----------------CCTTCSSCCCCCEEEE--EETTEEEEEESCCCTTHHHHHHHHT T ss_pred EEECCCCCCCHHHHHHHHEEE----------------EECCCEEEEEEEEEEC--CCCCEEEEEECCCCHHHHHHHHHHC T ss_conf 984467888878977753025----------------6389575553468403--7996899996359839999999987 Q ss_pred CCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECC Q ss_conf 98000464446652210001344624131100043758 Q gi|254780608|r 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300 (346) Q Consensus 263 g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp 300 (346) ||||+||.+||.... ....+++||||++-|+++ T Consensus 139 g~pI~gD~~Y~~~~~-----~~~~~l~l~~~r~l~~~e 171 (176) T 1ksk_A 139 GNHVVELHRERIGGI-----TLDADLAPGEYRPLTEEE 171 (176) T ss_dssp TCCEEEEEEEEETTE-----ECCTTCCTTCEEECCHHH T ss_pred CCEEEEEEEEEECCC-----CCCCCCCCCCEEECCHHH T ss_conf 997989999998865-----047989997515999999 No 8 >>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243) Probab=100.00 E-value=1.6e-39 Score=268.86 Aligned_cols=178 Identities=15% Similarity=0.112 Sum_probs=134.8 Q ss_pred EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCC Q ss_conf 61785688417653112235785332332011011111001333544534222404621231012221023333221112 Q gi|254780608|r 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182 (346) Q Consensus 103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~ 182 (346) |||+++||||||+|++|||+.+...++...+. .....++.+|||||++||||||||||.+++..+..++ +.++|+ T Consensus 2 yed~~~ivinKP~gl~~~~~~~~~~~~~~~l~---~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~--~~~~k~ 76 (186) T 1vio_A 2 IEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFD---YPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPK--HHCEKT 76 (186) T ss_dssp SCCCCEEEEEECTTCBSSCCC--CCBGGGGSC---TTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTT--SCCCEE T ss_pred CCCCEEEEEECCCCCCCCCCCCCCEEEEEEEC---CCCCCEEEECCCCCCCCCCEEEEECCCCCCCCCCCCC--CCCCEE T ss_conf 22210355402588643334432014542002---4533136540212401221378741775320001112--455201 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC Q ss_conf 00013456541000000012234655432111335555555303430101343202442045786123789999999963 Q gi|254780608|r 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262 (346) Q Consensus 183 Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~ 262 (346) |+|+|.|.+......+........ +. ......+... ...+++++++|.|||+||||+||+++ T Consensus 77 y~~~v~g~~~~~~~~~~~~~~~~~---------------~~--~~~~~~~~~~-~~~~~~~~~~~~tGr~hQIR~h~a~l 138 (186) T 1vio_A 77 YLVTLADPVEENYSAACAEGILLR---------------GE--KEPTKPAKLE-ILDDYNVNLTISEGRYHQVKRMFAAL 138 (186) T ss_dssp EEEEESSCCCTTHHHHHHHCCCCT---------------TC--SSCCCCCEEE-ECSSSEEEEEESCCCTTHHHHHHHHT T ss_pred EEEEEEEECCHHHHHHHHCCEECC---------------CC--CCCEEEEEEC-CCCCCEEEEEECCCCCHHHHHHHHHC T ss_conf 125998512044788985365616---------------83--0102332201-35684489885057607999999985 Q ss_pred CCCEECCCCCCCCCCCH--H----CCCCCCCHHHHHHHHEEECCCCC Q ss_conf 98000464446652210--0----01344624131100043758896 Q gi|254780608|r 263 GCPIVGDHKYCANFKGN--F----TSPIQNKLYLHARYMDLPHPEGG 303 (346) Q Consensus 263 g~PivGD~~Yg~~~~~~--~----~~~~~~r~~LHa~~l~f~hp~~~ 303 (346) ||||+||.+||...... . ......++.||++.+.|.||.+. T Consensus 139 g~pIvgD~~yg~~~~~~~~~l~~g~~r~l~~~~l~~~~l~~~~~~~~ 185 (186) T 1vio_A 139 GNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVEGGSHHHHH 185 (186) T ss_dssp TCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHHHTC--------- T ss_pred CCEEEEEEEEEECCCCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCC T ss_conf 99793889999887247999999762599999999999579865457 No 9 >>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=99.86 E-value=1.4e-23 Score=168.36 Aligned_cols=131 Identities=15% Similarity=0.162 Sum_probs=101.9 Q ss_pred EECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCC Q ss_conf 98411368668999998767889899999998499038878845112117998899935655422233222234554334 Q gi|254780608|r 11 VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90 (346) Q Consensus 11 ~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~ 90 (346) +|+++++|||||+||++..+++||+.+++||++|+|+|||++++++++|+.||.|.+.............. . T Consensus 1 iv~~~~~g~RLDk~L~~~~~~~sR~~a~~li~~G~V~VNG~~~~~s~~v~~gD~i~i~~~~~~~~~~~~~~--------~ 72 (133) T 1dm9_A 1 MKEKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAI--------T 72 (133) T ss_dssp ----CTTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCTTCBCCTTCEEEEEETTEEEEEEECEE--------E T ss_pred CCCCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEECCCCCEECCCCEEEEEECCEEEEEEEEEE--------E T ss_conf 99887764629999987867168999999998691888999734585615999899987998658999987--------6 Q ss_pred CCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCC Q ss_conf 322234543078617856884176531122357853323320110111110013335445342224046212310 Q gi|254780608|r 91 TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165 (346) Q Consensus 91 ~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~ 165 (346) ..........++|||++.+++|||+|+.+||.. ...++++|||||+.|||.|+++++.- T Consensus 73 ~~~~~~~~~~~~~ed~~~~v~~kp~~~~~~~~~----------------~~~r~~~vgRLDk~~t~~ll~l~~dg 131 (133) T 1dm9_A 73 EQRRPASEAALLYEETAESVEKREKMALARKLN----------------ALTMPHPDRRPDKKERRDLLRFKHGD 131 (133) T ss_dssp SCCCCHHHHGGGEEECHHHHHHHHHHHHHHHHH----------------HTC----------------------- T ss_pred ECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHC----------------CCCCCCCCCCCCHHHHHHHHHHHCCC T ss_conf 225673035666323688711345777766522----------------45578899786859999999875589 No 10 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217) Probab=99.86 E-value=1.3e-22 Score=162.27 Aligned_cols=100 Identities=20% Similarity=0.187 Sum_probs=79.4 Q ss_pred HHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEEECC Q ss_conf 89999999849903887884511211799889993565542223322223455433432223454307861785688417 Q gi|254780608|r 34 FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113 (346) Q Consensus 34 r~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiyED~~livinK 113 (346) |++++++|++|.|+|||++++.++. |.++ ...|+|||++++|+|| T Consensus 2 Rr~~~~~i~~G~V~Vng~~v~~~d~------i~~~-----------------------------~~~I~yed~~~ivvnK 46 (119) T 2olw_A 2 RQFIISENTMQKTSFRNHQVKRFSS------QRST-----------------------------RRKPENQPTRVILFNK 46 (119) T ss_dssp ----------------------------------------------------------------------CCCCEEEEEE T ss_pred CEEEECCCEEECCCCCCCCCCCCCC------CCCC-----------------------------CCCCCCCCCEEEEEEC T ss_conf 5367068714212255422120554------0035-----------------------------5688789988999989 Q ss_pred CCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCC Q ss_conf 653112235785332332011011111001333544534222404621231012221023 Q gi|254780608|r 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173 (346) Q Consensus 114 PaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~ 173 (346) |+|++|||+.+...+ .+..+ ....++++|||||++|||||+|||+..+++.|+.+ T Consensus 47 P~g~~~~~~~~~~~~---tl~~~--~~~~~l~~vhRLDr~TSGLll~ak~~~~~~~L~~~ 101 (119) T 2olw_A 47 PYDVLPQFTDEAGRK---TLKEF--IPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP 101 (119) T ss_dssp CTTBCSCSSCCTTSB---CGGGT--CCCCSCEESSCCCTTCEEEEEEESCHHHHHHHHCT T ss_pred CCCEEEECCCCCCCC---CHHHH--CCCCCCEECCCCCCCEEEEEEEECCCHHHHHHHHC T ss_conf 999597077998887---68896--57126347531143120069984360565453110 No 11 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200) Probab=99.80 E-value=6.4e-21 Score=151.58 Aligned_cols=96 Identities=20% Similarity=0.165 Sum_probs=74.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH Q ss_conf 22111200013456541000000012234655432111335555555303430101343202442045786123789999 Q gi|254780608|r 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256 (346) Q Consensus 177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR 256 (346) |.|.|+|+|+|.|.++.....+.......................+++.|+|.|.++...+ .+|++++.|.|||+|||| T Consensus 1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~~~-~~s~~~i~l~tGr~HQIR 79 (98) T 2olw_A 1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSI-PTSWLKITLYEGRNRQVR 79 (98) T ss_dssp CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CCSS-CEEEEEEEESCCCTTHHH T ss_pred CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEECC-CCEEEEEEEECCCHHHHH T ss_conf 2221589999945688899999865936578535775699953554433101047774215-505899999159759999 Q ss_pred HHHHHCCCCEECCCCCC Q ss_conf 99996398000464446 Q gi|254780608|r 257 VHALHMGCPIVGDHKYC 273 (346) Q Consensus 257 vhl~~~g~PivGD~~Yg 273 (346) +||+++||||+||.+|| T Consensus 80 ~~la~~g~pI~gd~ry~ 96 (98) T 2olw_A 80 RMTAHVGFPTLRLIRYA 96 (98) T ss_dssp HHHHHTTCCEEEEEEEE T ss_pred HHHHHCCCEEEEEEEEE T ss_conf 99998599798989999 No 12 >>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:) Probab=99.77 E-value=3.8e-20 Score=146.69 Aligned_cols=91 Identities=13% Similarity=0.136 Sum_probs=76.4 Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 66899999876788989999999849903887884511211799889993565542223322223455433432223454 Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98 (346) Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (346) ||||+||++.+++.||+++++++++|.|+|||++++++++|+.||+|++......... .......+ T Consensus 1 mRLD~~L~~~~~~~sr~~~~k~i~~g~I~VNg~~~~~~~~v~~gD~i~i~~~~~~~~~--------------~~~~~~~~ 66 (92) T 2k6p_A 1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAKASKEVKAGDTISLHYLKGIEEY--------------TILQIPAL 66 (92) T ss_dssp CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECCTTCBCCTTCEEEECCSSCCEEE--------------EECCCCCC T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEEECCCCCCCCEEEEEECCCCEEE--------------EEEECCCC T ss_conf 9678999872771599999999989979989899866247189999999848963689--------------99978865 Q ss_pred CEEEEECCCEEEECCCCCCEEECCC Q ss_conf 3078617856884176531122357 Q gi|254780608|r 99 SILLYEDSKIYVFNKPAGISVQGGS 123 (346) Q Consensus 99 ~~IiyED~~livinKPaGl~vhp~~ 123 (346) ..|+|||++++|+|||||++|||+. T Consensus 67 ~~i~yed~~~lvinKpagl~~hp~~ 91 (92) T 2k6p_A 67 KNVPRKDTHLYIAPKTKELEHHHHH 91 (92) T ss_dssp SCCCSSSTTSSEEECCCC------- T ss_pred CCCCHHHHCCCEEECHHCCCCCCCC T ss_conf 8986455061598063216244457 No 13 >>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=99.03 E-value=2.9e-10 Score=84.37 Aligned_cols=54 Identities=17% Similarity=0.401 Sum_probs=50.1 Q ss_pred HHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEEC Q ss_conf 1368668999998767889899999998499038878845112117998899935 Q gi|254780608|r 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69 (346) Q Consensus 15 ~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~ 69 (346) +++++|||+||+..+ +.||++++++|++|.|+|||++++++++|..||.|.+.. T Consensus 3 ~~~~~RLDk~La~~~-~~SR~~~~~li~~G~V~Vng~~vk~~~~v~~~d~I~v~~ 56 (63) T 3dh3_A 3 PDSSVRLNKYISESG-ICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNG 56 (63) T ss_dssp -CCCEEHHHHHHTTT-SSCHHHHHHHHHTTCEEETTEECCTTCEECTTCCEEETT T ss_pred CCCCCCHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCEEEECC T ss_conf 988704999998778-851999999998793898999947888969999899999 No 14 >>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=98.90 E-value=4.7e-10 Score=83.07 Aligned_cols=69 Identities=17% Similarity=0.063 Sum_probs=60.1 Q ss_pred CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC Q ss_conf 97668304999841136866899999876788989999999849903887884-5112117998899935 Q gi|254780608|r 1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69 (346) Q Consensus 1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~ 69 (346) |+-|+.....++.....++|||+||++.....||++++++|..|.|+|||+++ +++++|..||.|.+.. T Consensus 3 m~~~~~~~~~~~~~~~~~~RLd~~L~~~~~~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~ 72 (79) T 1p9k_A 3 MIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 72 (79) T ss_dssp CCCSSCCCCEEECCSCSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETT T ss_pred HHHCCCCCCEEECCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC T ss_conf 1000147713864999719799999877883689999999984997989999277887989999999999 No 15 >>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58) Probab=98.58 E-value=8.2e-08 Score=68.91 Aligned_cols=51 Identities=18% Similarity=0.254 Sum_probs=46.7 Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE Q ss_conf 6866899999876788989999999849903887884-511211799889993 Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68 (346) Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~ 68 (346) ..+|||+||++.. ..||++++++|+.|.|+|||+++ ++++.|..||.|.+. T Consensus 2 ~~~RLDk~L~~~~-~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~ 53 (58) T 1ksk_A 2 SHXRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYD 53 (58) T ss_dssp CCEEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEET T ss_pred CCCHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEE T ss_conf 8400999998778-968999999998892999999946688580786769972 No 16 >>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57) Probab=98.53 E-value=1.3e-07 Score=67.60 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=46.1 Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE Q ss_conf 866899999876788989999999849903887884-511211799889993 Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68 (346) Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~ 68 (346) .+|||+||++.. ..||++++++|++|+|+|||+++ ++++.|..||.|.+. T Consensus 2 ~~RLDk~L~~~~-~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~ 52 (57) T 1vio_A 2 SLRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFE 52 (57) T ss_dssp CEEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEET T ss_pred CHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEE T ss_conf 558999999877-858999999998797899999915489586887878762 No 17 >>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=98.09 E-value=1e-05 Score=55.71 Aligned_cols=50 Identities=20% Similarity=0.424 Sum_probs=43.9 Q ss_pred CHHHHHHHH-CCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC Q ss_conf 689999987-67889899999998499038878845-1121179988999356 Q gi|254780608|r 20 RLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70 (346) Q Consensus 20 RLd~~L~~~-~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~ 70 (346) |||.||.+. | ..|+.+++++|..|.|+|||++++ +++.|+.||.|++... T Consensus 1 RLD~~l~r~~~-~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~~ 52 (94) T 2vqe_D 1 RLDNVVYRLGF-AVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK 52 (94) T ss_dssp BHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGG T ss_pred HHHHHHHHCCC-HHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHHH T ss_conf 99999985352-00289888998706845088799753678528860012110 No 18 >>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65) Probab=98.08 E-value=2.2e-06 Score=59.87 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=47.8 Q ss_pred HHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCC--EECCEEE-CCCCCCCCCCEEEEE Q ss_conf 113686689999987678898999999984990--3887884-511211799889993 Q gi|254780608|r 14 NDEENMRLDRWFKNHYPHINFVNLQKILRSGQV--RVDKKRV-KFNNRIQSGQVVRIP 68 (346) Q Consensus 14 ~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V--~VNG~~v-k~~~~v~~GD~I~i~ 68 (346) +....+|||++|.+.--..||++++++|.+|.| .|||+++ +|++.|..||.|.|. T Consensus 2 ~~~~~~RLD~~L~~~g~~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~ 59 (65) T 3hp7_A 2 NAXPKERVDVLAYKQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLK 59 (65) T ss_dssp -CCCEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEET T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEE T ss_conf 9650889999999875812499999999859942320998956886787999989980 No 19 >>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201) Probab=97.90 E-value=1.1e-05 Score=55.57 Aligned_cols=53 Identities=13% Similarity=0.088 Sum_probs=44.4 Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCC Q ss_conf 66899999876788989999999849903887884-511211799889993565 Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71 (346) Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~ 71 (346) +|||.++-+.-=.-|+.+++++|.+|.|.|||+++ ++++.|+.||.|.+.+.. 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 20 >>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=97.90 E-value=7.3e-06 Score=56.60 Aligned_cols=53 Identities=15% Similarity=0.129 Sum_probs=44.4 Q ss_pred CHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCC Q ss_conf 6899999876788989999999849903887884-5112117998899935655 Q gi|254780608|r 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72 (346) Q Consensus 20 RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~ 72 (346) |||.+|-+.-=.-|+.+++++|..|.|+|||+++ +|++.|+.||+|.+..... T Consensus 1 RLD~~l~r~gfa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~~~ 54 (94) T 3i1m_D 1 RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAK 54 (94) T ss_dssp STTHHHHTTTSCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSSSC T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCCHH T ss_conf 888886603125409999999985037608879976317705897788623232 No 21 >>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432) Probab=97.57 E-value=0.00026 Score=46.87 Aligned_cols=62 Identities=10% Similarity=0.120 Sum_probs=50.0 Q ss_pred EEEEEECHHHC---CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE Q ss_conf 04999841136---866899999876788989999999849903887884-511211799889993 Q gi|254780608|r 7 VQYVVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68 (346) Q Consensus 7 ~~~~~V~~~~~---g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~ 68 (346) +..+.++.++. ++|||.+|.+.==.-|+++.+++|+.|.|+|||+++ ++++.|..||.+.+. T Consensus 5 ~p~~~i~~~~~~~~~~rl~~~l~~~gl~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~ 70 (83) T 1h3f_A 5 IPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQ 70 (83) T ss_dssp SCEEEECGGGCBTTEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEE T ss_pred CCCEEECHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE T ss_conf 981574387832586349999998498677899999998599898999824877021589808998 No 22 >>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=97.53 E-value=0.00011 Score=49.15 Aligned_cols=51 Identities=12% Similarity=-0.007 Sum_probs=43.9 Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC Q ss_conf 66899999876788989999999849903887884-5112117998899935 Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69 (346) Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~ 69 (346) +|||.++-+.-=.-|+.+++++|..|.|+|||+++ .|++.|+.||.|.+.. T Consensus 9 rRLD~il~R~gfa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~ 60 (99) T 1s1h_D 9 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDF 60 (99) T ss_dssp GBHHHHHHHHTSSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCS T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEE T ss_conf 5078899981565889999999873772589999876246840587560556 No 23 >>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=97.29 E-value=0.00021 Score=47.48 Aligned_cols=52 Identities=15% Similarity=0.082 Sum_probs=42.9 Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCC--CEEEEEC Q ss_conf 866899999876788989999999849903887884-511211799--8899935 Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG--QVVRIPP 69 (346) Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~G--D~I~i~~ 69 (346) -+|||.+|.+.-=.-|+.+++++|..|.|+|||+++ +|++.|+.| |.|.+.+ T Consensus 7 erRLd~~l~~~g~a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~~ 61 (71) T 2cqj_A 7 GRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVD 61 (71) T ss_dssp EEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESC T ss_pred HCCHHHHHHHHCCCCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEEC T ss_conf 4126899998055278999999998498998999955698583589988699846 No 24 >>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=96.45 E-value=0.002 Score=41.20 Aligned_cols=71 Identities=24% Similarity=0.310 Sum_probs=46.5 Q ss_pred CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC Q ss_conf 78568841765311223578533233201101111100133354453422240462123101222102333322111200 Q gi|254780608|r 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184 (346) Q Consensus 105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~ 184 (346) -+.|++||||+|+.+|. +.+.+.... ...+.+-.+.||-..||+|+++-++.+ +.+..+ ....|+|. T Consensus 15 ~~G~l~i~KP~g~tS~~-------vv~~~k~~~--~~~kvgh~GtLDp~a~GvLiv~ig~~T-kl~~~~---~~~~K~Y~ 81 (216) T 2apo_A 15 KYGVVVVDKPRGPTSHE-------VSTWVKKIL--NLDKAGHGGTLDPKVTGVLPVALERAT-KTIPMW---HIPPKEYV 81 (216) T ss_dssp HTEEEEEEECSSSCHHH-------HHHHHHHHT--TCSCEEESSCCCTTCEEEEEEEEGGGG-GGGGGT---TSSCEEEE T ss_pred CCCEEEEECCCCCCHHH-------HHHHHHHHH--CCCCCCCCCCCCCCCCCCHHHEECHHH-HHHHHH---CCCCCEEE T ss_conf 49989997999899899-------999999984--877357787789634365532118653-221775---05882799 Q ss_pred CCCC Q ss_conf 0134 Q gi|254780608|r 185 SLVW 188 (346) Q Consensus 185 Aiv~ 188 (346) |.+. T Consensus 82 ~~~~ 85 (216) T 2apo_A 82 CLMH 85 (216) T ss_dssp EEEE T ss_pred EEEE T ss_conf 9999 No 25 >>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=96.38 E-value=0.0025 Score=40.65 Aligned_cols=83 Identities=22% Similarity=0.272 Sum_probs=50.5 Q ss_pred CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC Q ss_conf 78568841765311223578533233201101111100133354453422240462123101222102333322111200 Q gi|254780608|r 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184 (346) Q Consensus 105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~ 184 (346) -+.+|++|||.|+.+|- +...+..... ..+.+-.+-||-..||+++++-.+.+ +.+ ..| ..-.|+|. T Consensus 15 ~~G~l~~~KP~g~tS~~-------vv~~ik~~~~--~~kvGh~GTLDp~atGvl~i~vg~aT-kl~-~~~--~~~~K~Y~ 81 (215) T 2aus_C 15 QYGVINLDKPPGPTSHE-------VVAWIKRILN--LEKAGHGGTLDPKVSGVLPVALERAT-RVV-QAL--LPAGKEYV 81 (215) T ss_dssp HTEEEEEEECSSSCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG-GGG-GGG--TTCCEEEE T ss_pred CCCEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCCEEEEECHHH-HHH-HHH--CCCCCEEE T ss_conf 78389995799899999-------9999998718--34257898789865034767873899-899-997--45885999 Q ss_pred CCCCCCCCCCCCCCCC Q ss_conf 0134565410000000 Q gi|254780608|r 185 SLVWGIPKNKKECIAN 200 (346) Q Consensus 185 Aiv~G~~~~~~~~i~~ 200 (346) |.+..-...+..-++. T Consensus 82 ~~~~~g~~t~t~d~~~ 97 (215) T 2aus_C 82 ALMHLHGDVPEDKIRA 97 (215) T ss_dssp EEEEESSCCCHHHHHH T ss_pred EEEEECCCCCCCHHHE T ss_conf 9988723444440013 No 26 >>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=95.82 E-value=0.011 Score=36.61 Aligned_cols=50 Identities=14% Similarity=0.016 Sum_probs=39.4 Q ss_pred HHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCE Q ss_conf 1368668999998767889899999998499038878845-1121179988 Q gi|254780608|r 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64 (346) Q Consensus 15 ~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~ 64 (346) -.+|++|..+|...=-..|++..+++|++|.|+|||+++. ++..+..+|. T Consensus 8 ~~~~~~i~~lL~~~gl~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~ 58 (88) T 2jan_A 8 PGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF 58 (88) T ss_dssp SSSCCSHHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS T ss_pred CCCCCCHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHH T ss_conf 578777999999828867899999999939999899981694330278782 No 27 >>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=92.49 E-value=0.057 Score=32.08 Aligned_cols=53 Identities=26% Similarity=0.426 Sum_probs=36.8 Q ss_pred CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCH Q ss_conf 78568841765311223578533233201101111100133354453422240462123101 Q gi|254780608|r 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166 (346) Q Consensus 105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a 166 (346) -+.|++||||.|+.+|. +...+....+ ..+.+-..-||-..||+|+++-.+.+ T Consensus 5 ~~Gil~idKP~G~TS~~-------vv~~iKk~l~--~kKVGH~GTLDP~AtGvLiv~iG~aT 57 (87) T 1sgv_A 5 GPGIVVIDKPAGMTSHD-------VVGRCRRIFA--TRRVGHAGTLDPMATGVLVIGIERAT 57 (87) T ss_dssp CSEEEEEEECTTCCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG T ss_pred CCEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH T ss_conf 98899997699899899-------9999999848--88556387889736423999989676 No 28 >>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=92.08 E-value=0.068 Score=31.61 Aligned_cols=55 Identities=20% Similarity=0.298 Sum_probs=37.5 Q ss_pred EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCH Q ss_conf 6178568841765311223578533233201101111100133354453422240462123101 Q gi|254780608|r 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166 (346) Q Consensus 103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a 166 (346) ++-+.|++||||.|+.+|. +...+....+ ..+.+-..-||-..||||+++-.+.+ T Consensus 22 ~~~~Gil~idKP~G~TS~~-------vV~~vkk~l~--~kKVGH~GTLDP~AtGvLiv~iG~aT 76 (108) T 1k8w_A 22 MDINGVLLLDKPQGMSSND-------ALQKVKRIYN--ANRAGHTGALDPLATGMLPICLGEAT 76 (108) T ss_dssp CCCCEEEEEEECTTCCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG T ss_pred CCCCEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH T ss_conf 8853699984799899899-------9999999858--99687686579746135999988888 No 29 >>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=92.05 E-value=0.071 Score=31.47 Aligned_cols=59 Identities=20% Similarity=0.283 Sum_probs=38.0 Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCC Q ss_conf 8568841765311223578533233201101111100133354453422240462123101222102333 Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175 (346) Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~ 175 (346) +.|+.+|||.|+.+|- +...+....+ ..+.+-..-||-..||+|+++-++.+ .|.++.+ T Consensus 3 nGil~idKP~G~TS~~-------vV~~iKk~l~--~kKVGH~GTLDP~AtGvLii~iG~aT--KL~~~~~ 61 (92) T 1r3e_A 3 HGILVAYKPKGPTSHD-------VVDEVRKKLK--TRKVGHGGTLDPFACGVLIIGVNQGT--RILELVR 61 (92) T ss_dssp CEEEEEEECSSSCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG--GGGEEEE T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH--HHHEEEE T ss_conf 5599996699899899-------9999999868--88787785679746446999988675--3323898 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=91.40 E-value=0.16 Score=29.22 Aligned_cols=25 Identities=28% Similarity=0.494 Sum_probs=22.0 Q ss_pred CCEECCEEEC-CCCCCCCCCEEEEEC Q ss_conf 9038878845-112117998899935 Q gi|254780608|r 45 QVRVDKKRVK-FNNRIQSGQVVRIPP 69 (346) Q Consensus 45 ~V~VNG~~vk-~~~~v~~GD~I~i~~ 69 (346) .|.|||+++. |++.+++||+|.+.. T Consensus 1 Hi~VNgkkVdIPSy~~k~gD~I~ik~ 26 (83) T 1c05_A 1 HILVDGSRVNIPSYRVKPGQTIAVRE 26 (83) T ss_dssp CEEETTEECCCSSCBCCTTCEEEECG T ss_pred CEECCCEEEEECCEEECCCCEEEECC T ss_conf 63604369984341621784875020 No 31 >>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420) Probab=91.13 E-value=0.046 Score=32.66 Aligned_cols=53 Identities=6% Similarity=0.073 Sum_probs=39.4 Q ss_pred CHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEE Q ss_conf 411368668999998767889899999998499038878845-11211799889 Q gi|254780608|r 13 ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65 (346) Q Consensus 13 ~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I 65 (346) +....+.+|...|.+.--.-|++.++++|.+|.|+|||++++ +++.+..+|.+ T Consensus 101 ~~~~~~~~l~~lL~~~~l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~ 154 (174) T 1jil_A 101 TLSNDTTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI 154 (174) T ss_dssp ------------------------------------------------------ T ss_pred EECCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCC T ss_conf 715888789999998388467999999998499899999813844400775704 No 32 >>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=90.41 E-value=0.42 Score=26.60 Aligned_cols=53 Identities=21% Similarity=0.258 Sum_probs=42.8 Q ss_pred HCCCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEE Q ss_conf 36866899999876788-9899999998499038878845-11211799889993 Q gi|254780608|r 16 EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68 (346) Q Consensus 16 ~~g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~ 68 (346) ..++.|--||.+.++.. +...+++.+.+|.|.|||++.+ ..+.+-.-|+|+|+ T Consensus 5 ~~siPL~i~LRd~Lk~A~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~ 59 (81) T 3kbg_A 5 DQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEIN 59 (81) T ss_dssp CSCEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEET T ss_pred CCCCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEEC T ss_conf 1256543786446452265899999986793898999962389988706799979 No 33 >>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419) Probab=89.09 E-value=0.086 Score=30.96 Aligned_cols=50 Identities=8% Similarity=0.106 Sum_probs=34.9 Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEE Q ss_conf 368668999998767889899999998499038878845-11211799889 Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65 (346) Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I 65 (346) ..+.++..+|...--.-|++..+++|++|.|+|||++++ +++.+...|.+ T Consensus 104 ~~~~~l~~lL~~~gl~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~ 154 (174) T 2ts1_A 104 GGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL 154 (174) T ss_dssp --------------------------------------------------- T ss_pred CCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCC T ss_conf 799769999998598677899999998699898999823842201775714 No 34 >>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:) Probab=84.03 E-value=1.6 Score=22.97 Aligned_cols=53 Identities=13% Similarity=0.183 Sum_probs=33.7 Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHC--CCCEECCEEECCCCCCCCCCEEEEECCC Q ss_conf 686689999987678898999999984--9903887884511211799889993565 Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRS--GQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346) Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~--G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346) .+..+...+...-..++ .++..+.. -.|.|||+.+..++.|+.||+|.+.|+. T Consensus 24 ~~~tv~~l~~~L~~~~p--~~~~~l~~~~~~v~vn~~~v~~~~~l~~gdeVai~PPv 78 (81) T 1fm0_D 24 DFPTVEALRQHMAAQSD--RWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPV 78 (81) T ss_dssp CCSBHHHHHHHHHTTCH--HHHHHHCCTTCEEEETTEECCTTCBCCTTCEEEEECCC T ss_pred CCCCHHHHHHHHHHHCC--HHHHHHCCCCEEEECCCEECCCCCCCCCCCEEEEECCC T ss_conf 99999999999987682--48886278958997284597999785999999996997 No 35 >>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=83.70 E-value=1.4 Score=23.22 Aligned_cols=44 Identities=27% Similarity=0.417 Sum_probs=31.4 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC Q ss_conf 899999876788989999999849903887884511211799889993565 Q gi|254780608|r 21 LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346) Q Consensus 21 Ld~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346) |-..|.+++|.+-. +.-.|.|||+.++.++.|+.||.|.+.|+. T Consensus 31 l~~~L~~~~~~~~~-------~~~~v~vN~~~v~~~~~l~dgDeVai~PPv 74 (77) T 2q5w_D 31 FEDLLFERYPQINN-------KKFQVAVNEEFVQKSDFIQPNDTVALIPPV 74 (77) T ss_dssp HHHHHHHHCGGGTT-------CCCEEEETTEEECTTSEECTTCEEEEECSC T ss_pred HHHHHHHHCCCCCC-------HHHHHHCCCEECCCCCCCCCCCEEEEECCC T ss_conf 99999987785511-------331341088076888670998999997998 No 36 >>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:) Probab=71.60 E-value=2.9 Score=21.28 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=31.1 Q ss_pred HHHHHHHHCCCCCHHHH---HHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC Q ss_conf 89999987678898999---9999849903887884511211799889993565 Q gi|254780608|r 21 LDRWFKNHYPHINFVNL---QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346) Q Consensus 21 Ld~~L~~~~~~~sr~~~---~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346) |-..|..++|.+....+ ..+...=.|.|||+.+..++.|+.||+|.+.|+. T Consensus 42 l~~~L~~~~p~l~~~l~~~~~~~~~~~~v~vN~~~v~~~~~l~dgdeV~i~PPv 95 (98) T 1vjk_A 42 LIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDGDVVGVFPPV 95 (98) T ss_dssp HHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTTCBCCTTCEEEEESCC T ss_pred HHHHHHHHCCHHHHHHHHHCCCCCCCEEEEECCEECCCCCCCCCCCEEEEECCC T ss_conf 999999867067888641101456547998678886989781999999997987 No 37 >>2eh0_A KLP, kinesin-like protein KIF1B; FHA domain, KIAA0591, KIAA1448, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=65.83 E-value=4.5 Score=20.10 Aligned_cols=22 Identities=27% Similarity=0.379 Sum_probs=8.2 Q ss_pred CEECCEEECCCCCCCCCCEEEE Q ss_conf 0388788451121179988999 Q gi|254780608|r 46 VRVDKKRVKFNNRIQSGQVVRI 67 (346) Q Consensus 46 V~VNG~~vk~~~~v~~GD~I~i 67 (346) +.|||.++.....|+.||+|++ T Consensus 82 t~vNg~~i~~~~~L~~GD~i~i 103 (130) T 2eh0_A 82 TYVNGKRVSQPVQLRSGNRIIM 103 (130) T ss_dssp EEETTEECCSCEECCTTCBCEE T ss_pred EEECCEECCCCEECCCCCEEEE T ss_conf 6999969465278799999998 No 38 >>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:) Probab=65.34 E-value=8.2 Score=18.47 Aligned_cols=53 Identities=8% Similarity=0.142 Sum_probs=30.7 Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHH-C-----C-CCEECCEEEC----CCCCCCCCCEEEEECCC Q ss_conf 8668999998767889899999998-4-----9-9038878845----11211799889993565 Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILR-S-----G-QVRVDKKRVK----FNNRIQSGQVVRIPPVI 71 (346) Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir-~-----G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~ 71 (346) +..+..++......++.... +++. . + .|.|||+.+. .++.|+.||+|.+.|+. T Consensus 24 ~~Tv~~ll~~L~~~~p~~~~-~l~~~~~~~~~~v~v~vNg~~v~~~~~~~t~l~~gD~V~ilPpv 87 (90) T 2g1e_A 24 ISKISELLERLKVEYGSEFT-KQMYDGNNLFKNVIILVNGNNITSMKGLDTEIKDDDKIDLFPPV 87 (90) T ss_dssp CCBHHHHHHHHHHHSCHHHH-HHHCCSSCSTTTCEEEESSSBGGGTCSSSCBCCTTCEEEEECCT T ss_pred CCCHHHHHHHHHHHHHHHHH-HHHHHHHCHHHHEEEEEECCCCCCCCCCCCCCCCCCEEEEECCC T ss_conf 99899999999967427899-99850102333504577030002344656537999999996888 No 39 >>2g1l_A Kinesin-like protein KIF1C; transport, FHA domain, structural genomics consortium, SGC, transport protein; 2.60A {Homo sapiens} (A:) Probab=64.89 E-value=6.2 Score=19.22 Aligned_cols=22 Identities=23% Similarity=0.196 Sum_probs=9.1 Q ss_pred CEECCEEECCCCCCCCCCEEEE Q ss_conf 0388788451121179988999 Q gi|254780608|r 46 VRVDKKRVKFNNRIQSGQVVRI 67 (346) Q Consensus 46 V~VNG~~vk~~~~v~~GD~I~i 67 (346) +.|||++++....|+.||+|.+ T Consensus 73 t~vNg~~i~~~~~L~~gD~i~i 94 (104) T 2g1l_A 73 TYVNGKLVTEPLVLKSGNRIVM 94 (104) T ss_dssp EEETTEECCSCEECCTTCEEEE T ss_pred CEECCEECCCCEECCCCCEEEE T ss_conf 0899878024269999999998 No 40 >>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:) Probab=64.75 E-value=2.7 Score=21.52 Aligned_cols=46 Identities=24% Similarity=0.378 Sum_probs=34.5 Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC Q ss_conf 3686689999987678898999999984990388788451121179988999356 Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346) Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346) .++..+..+|... +++.. .=.|.+||..+..++.|+.||.|.|.++ T Consensus 28 ~~~~Tv~~ll~~L--~l~~~-------~v~v~vNg~~v~~~~~L~dgD~v~i~~~ 73 (77) T 1rws_A 28 REGMKVRDILRAV--GFNTE-------SAIAKVNGKVVLEDDEVKDGDFVEVIPV 73 (77) T ss_dssp CSSCCHHHHHHTT--TCSSC-------SSCEEETTEEECSSSCCCSSCCCBCSCC T ss_pred CCCCCHHHHHHHH--CCCCH-------HHHEEECCEECCCCCCCCCCCEEEEEEC T ss_conf 9969999999980--99830-------1015599999699728699999999904 No 41 >>1wln_A Afadin; beta sandwich, FHA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Probab=64.41 E-value=4.7 Score=20.01 Aligned_cols=10 Identities=30% Similarity=0.245 Sum_probs=3.3 Q ss_pred EEEECCCEEE Q ss_conf 7861785688 Q gi|254780608|r 101 LLYEDSKIYV 110 (346) Q Consensus 101 IiyED~~liv 110 (346) |.|+++.+.+ T Consensus 64 I~~~~~~~~i 73 (120) T 1wln_A 64 LTNMDGVVTV 73 (120) T ss_dssp EEESSSCEEE T ss_pred EEECCCCCEE T ss_conf 9972464489 No 42 >>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:) Probab=63.12 E-value=5.3 Score=19.67 Aligned_cols=61 Identities=13% Similarity=0.243 Sum_probs=34.2 Q ss_pred EECHHHCCCCHH---HHHHHHCCCCCHHHHHH--HHHCC-CCEECCEEEC----CCCCCCCCCEEEEECCC Q ss_conf 984113686689---99998767889899999--99849-9038878845----11211799889993565 Q gi|254780608|r 11 VVENDEENMRLD---RWFKNHYPHINFVNLQK--ILRSG-QVRVDKKRVK----FNNRIQSGQVVRIPPVI 71 (346) Q Consensus 11 ~V~~~~~g~RLd---~~L~~~~~~~sr~~~~~--lir~G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~ 71 (346) .++....+..+. .+|..++|.+.....-. -++.+ .|.|||+.+. .++.|+.||.|.+.|+. T Consensus 35 ~~~~~~~~~Tv~~ll~~L~~~~p~l~~~l~d~~~~~~~~i~v~vN~~~v~~~~~~~t~l~~gDeV~i~Ppv 105 (114) T 1wgk_A 35 ALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWELLGELDYQLQDQDSILFISTL 105 (114) T ss_dssp EECCCSSCCBHHHHHHHHTTTTCCSCHHHHCCSSSCCSSEEEEESSSBHHHHCTTTCBCCSSEEEEEEECS T ss_pred EECCCCCCCCHHHHHHHHHHHCCCCCHHHHCCCCCCCEEEEEEECCCEEEECCCCCCCCCCCCEEEEECCC T ss_conf 70799987569999999998767522345314788505589997584246056866376997999997888 No 43 >>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=62.14 E-value=7 Score=18.89 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=16.5 Q ss_pred CCCEECCEEECCCCCCCCCCEEEEE Q ss_conf 9903887884511211799889993 Q gi|254780608|r 44 GQVRVDKKRVKFNNRIQSGQVVRIP 68 (346) Q Consensus 44 G~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346) ..+.|||+++.....|+.||.|.|. T Consensus 59 ~g~~vng~~v~~~~~L~~Gd~i~iG 83 (99) T 2ff4_A 59 NGVHVQHERIRSAVTLNDGDHIRIC 83 (99) T ss_dssp SCCEETTEECSSEEEECTTCEEEET T ss_pred CCEEECCEECCCCEECCCCCEEEEC T ss_conf 7857999998785678999999997 No 44 >>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84) Probab=58.96 E-value=10 Score=17.89 Aligned_cols=46 Identities=13% Similarity=0.372 Sum_probs=29.7 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCC------CCEECCEEEC----CCCCCCCCCEEEEECC Q ss_conf 899999876788989999999849------9038878845----1121179988999356 Q gi|254780608|r 21 LDRWFKNHYPHINFVNLQKILRSG------QVRVDKKRVK----FNNRIQSGQVVRIPPV 70 (346) Q Consensus 21 Ld~~L~~~~~~~sr~~~~~lir~G------~V~VNG~~vk----~~~~v~~GD~I~i~~~ 70 (346) |-..|...+|++. ..++..| .|.|||+.++ .++.|+.||.|.+.|+ T Consensus 28 ll~~L~~~~p~~~----~~l~~~g~~~~~v~i~vNg~~i~~~~~~~t~l~dgDeVai~PP 83 (84) T 1v8c_A 28 VLENLVRAYPALK----EELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPP 83 (84) T ss_dssp HHHHHHHHCGGGH----HHHEETTEECTTCEEEETTEEGGGTTGGGCBCCTTCEEEEECS T ss_pred HHHHHHHHCCCCH----HHCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCEEEEECC T ss_conf 9999985786302----2003443510138999878774145788868699999999699 No 45 >>3els_A PRE-mRNA leakage protein 1; intrinsically unstructured domain, forkhead-associated domain (FHA) domain, PRE-mRNA retention and splicing; 1.80A {Saccharomyces cerevisiae} (A:) Probab=56.64 E-value=11 Score=17.63 Aligned_cols=18 Identities=11% Similarity=-0.010 Sum_probs=7.9 Q ss_pred CCEEEEECCCCHHHHHCC Q ss_conf 240462123101222102 Q gi|254780608|r 155 SGILVVARTRAAAQHLTE 172 (346) Q Consensus 155 SGlll~AK~~~a~~~l~~ 172 (346) .+-+++.++..+--.|.. T Consensus 70 ~~~~~iGR~~~~di~l~~ 87 (158) T 3els_A 70 TDLDDRTEIVVADIGIPE 87 (158) T ss_dssp ------CCCCCCSEEECC T ss_pred CCCCCCCCCCCCCEECCC T ss_conf 532244775210377799 No 46 >>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, biosynthetic protein; 3.15A {Bacillus subtilis} (B:) Probab=54.65 E-value=12 Score=17.49 Aligned_cols=59 Identities=7% Similarity=0.018 Sum_probs=36.0 Q ss_pred CCCCCEEEEEECHH---H--CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEEC Q ss_conf 76683049998411---3--686689999987678898999999984990388788451----12117998899935 Q gi|254780608|r 2 SLMTYVQYVVVEND---E--ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPP 69 (346) Q Consensus 2 ~~M~~~~~~~V~~~---~--~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~ 69 (346) .-|+.+-.++|... . ++..|..+|... +++.. .=.|-|||..+.. ++.|+.||.|+|.. T Consensus 15 ~~~~~~m~I~vNG~~~~~~~e~~tl~~lL~~l--~~~~~-------~vaV~vN~~iVpr~~w~~~~L~~gD~IEIi~ 82 (87) T 1tyg_B 15 GHIGGRHMLQLNGKDVKWKKDTGTIQDLLASY--QLENK-------IVIVERNKEIIGKERYHEVELCDRDVIEIVH 82 (87) T ss_dssp -------CEEETTEEECCSSSCCBHHHHHHHT--TCTTS-------CCEEEETTEEECGGGTTTSBCCSSSEEEEEE T ss_pred CCCCCEEEEEECCEEEECCCCCCCHHHHHHHC--CCCCC-------EEEEEECCEECCHHHCCHHCCCCCCEEEEEE T ss_conf 55388599999998988688886499999875--99988-------1999989998786787530599979999998 No 47 >>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative; 2.10A {Haemophilus influenzae 86-028np} (A:) Probab=52.29 E-value=8.5 Score=18.39 Aligned_cols=38 Identities=13% Similarity=0.420 Sum_probs=27.4 Q ss_pred HHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC Q ss_conf 987678898999999984990388788451121179988999356 Q gi|254780608|r 26 KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346) Q Consensus 26 ~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346) .+.||++.. ....|=|=|+.++.++.|+.||+|+|+-+ T Consensus 48 l~~fPeidl-------~~~~vGIfgk~v~~d~~L~~GDRVEIYRP 85 (97) T 2hj1_A 48 LSQFPEIDL-------STNKIGIFSRPIKLTDVLKEGDRIEIYRP 85 (97) T ss_dssp HHHCTTCCT-------TTSEEEEEECSCCTTCBCCTTCEEEECCC T ss_pred HHHCCCCCC-------CCCCEEEECCCCCCCCCCCCCCEEEEECC T ss_conf 545966470-------10615568938588771789999999456 No 48 >>1wxq_A GTP-binding protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.60A {Pyrococcus horikoshii OT3} (A:317-397) Probab=49.76 E-value=4.8 Score=19.95 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=20.6 Q ss_pred CCEECCEEECCCCCCCCCCEEEEE Q ss_conf 903887884511211799889993 Q gi|254780608|r 45 QVRVDKKRVKFNNRIQSGQVVRIP 68 (346) Q Consensus 45 ~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346) .+.+||+++..++.|+.||+|+|- T Consensus 54 ~~~~~g~~v~~d~~L~dgDvV~Ii 77 (81) T 1wxq_A 54 INARTKRRVGEDYELQFNDIVKIV 77 (81) T ss_dssp EETTTCSBCCTTCCCCTTEEEEEE T ss_pred EECCCCEEECCCCEECCCCEEEEE T ss_conf 866776285698485689889999 No 49 >>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:) Probab=49.61 E-value=16 Score=16.60 Aligned_cols=53 Identities=2% Similarity=0.081 Sum_probs=32.2 Q ss_pred CCCCHHH---HHHHHCCCCCHHHHHHHHHCC------CCEECCEEEC----CCCCCCCCCEEEEECC Q ss_conf 6866899---999876788989999999849------9038878845----1121179988999356 Q gi|254780608|r 17 ENMRLDR---WFKNHYPHINFVNLQKILRSG------QVRVDKKRVK----FNNRIQSGQVVRIPPV 70 (346) Q Consensus 17 ~g~RLd~---~L~~~~~~~sr~~~~~lir~G------~V~VNG~~vk----~~~~v~~GD~I~i~~~ 70 (346) .|..+.. .|.+++|...+. +.-....| .|.|||+.++ .++.|+.||.|.+.|+ T Consensus 30 ~~~Tv~~li~~l~~~~p~~~~~-~~~~~~~~~~~~~~~v~vNg~~i~~~~~~~t~L~~gDeV~i~pp 95 (99) T 2qjl_A 30 DPVTVGDLIDHIVSTMINNPND-VSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTST 95 (99) T ss_dssp SCCBHHHHHHHHHHHTCSSGGG-HHHHEETTEECTTEEEEETTEEGGGGTGGGCBCCTTCEEEEEEC T ss_pred CCCCHHHHHHHHHHHCCCCHHH-HHHHCCCCCEEEEEEEEECCCEEECCCCCCCCCCCCCEEEEECC T ss_conf 8888999999999874553034-33112345423228999879587817887758599799999678 No 50 >>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=48.63 E-value=17 Score=16.43 Aligned_cols=27 Identities=26% Similarity=0.534 Sum_probs=21.2 Q ss_pred CCEECCEEEC----CCCCCCCCCEEEEECCC Q ss_conf 9038878845----11211799889993565 Q gi|254780608|r 45 QVRVDKKRVK----FNNRIQSGQVVRIPPVI 71 (346) Q Consensus 45 ~V~VNG~~vk----~~~~v~~GD~I~i~~~~ 71 (346) .|.|||..+. .++.|+.||+|.+.|+. T Consensus 60 ~v~vNg~~v~~~~~~~t~l~~gDeV~ilPpv 90 (93) T 3dwg_C 60 NIYVNDEDVRFSGGLATAIADGDSVTILPAV 90 (93) T ss_dssp EEEETTEEGGGTTGGGCBCCTTCEEEEEECC T ss_pred EEEECCEEECCCCCCCCCCCCCCEEEEECCC T ss_conf 9998574510014766637998999996888 No 51 >>3huh_A Virulence protein STM3117; structural genomics, nysgrc, target 13955A1BCT15P1, dioxygenase, PSI-2, protein structure initiative; 1.50A {Salmonella enterica subsp} PDB: 3hnq_A (A:78-152) Probab=46.22 E-value=19 Score=16.12 Aligned_cols=50 Identities=18% Similarity=0.265 Sum_probs=37.7 Q ss_pred HHHHHHHHHHCCCCEECCC--CCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCHHH Q ss_conf 8999999996398000464--446652210001344624131100043758896499983997899 Q gi|254780608|r 252 THQLRVHALHMGCPIVGDH--KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315 (346) Q Consensus 252 ~HQIRvhl~~~g~PivGD~--~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~~f 315 (346) -.+...||...|.+|.+.+ .+|.... .+++-|..|++..+++.++.|..- T Consensus 20 ~d~~~~~L~~~Gv~i~~~p~~~~~~~~~--------------~~siYf~DPdG~~iEl~~~~~~~~ 71 (75) T 3huh_A 20 INDVVSEILQAGISIVEGPVERTGATGE--------------IMSIYIRDPDGNLIEISQYVEGHH 71 (75) T ss_dssp HHHHHHHHHHTTCCCSEEEEEEEETTEE--------------EEEEEEECTTCCEEEEEEC----- T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCC--------------EEEEEEECCCCCEEEEEEECCCCC T ss_conf 7899999987186522387332268886--------------899999999999899988889876 No 52 >>2rk0_A Glyoxalase/bleomycin resistance protein/dioxygenase domain; 11002Z, glyoxylase, PSI-II, newyork structural genomix research consortium (nysgrc); 2.04A {Frankia SP} (A:68-136) Probab=45.62 E-value=20 Score=16.06 Aligned_cols=45 Identities=7% Similarity=0.020 Sum_probs=36.0 Q ss_pred HHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCH Q ss_conf 89999999963980004644466522100013446241311000437588964999839978 Q gi|254780608|r 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313 (346) Q Consensus 252 ~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~ 313 (346) --+++.+|...|.++.+-.-.|. .+++.|..|.+..+++.++-|. T Consensus 19 l~~~~~~L~~~gv~~~~~~~~g~-----------------~~siyf~DPdG~~iEl~~~~p~ 63 (69) T 2rk0_A 19 LDVLEERLAKAGAAFTPTQELPF-----------------GWILAFRDADNIALEAXLGREG 63 (69) T ss_dssp HHHHHHHHHHHTCCBCCCEEETT-----------------EEEEEEECTTCCEEEEEEECTT T ss_pred HHHHHHHHHHCCCEECCCCCCCC-----------------EEEEEEECCCCCEEEEEECCCC T ss_conf 99999999978986478661798-----------------4999999999998999999985 No 53 >>1wwt_A Threonyl-tRNA synthetase, cytoplasmic; TGS domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ligase; NMR {Homo sapiens} (A:) Probab=40.33 E-value=24 Score=15.55 Aligned_cols=61 Identities=7% Similarity=-0.097 Sum_probs=41.5 Q ss_pred CCCCCCEEEEEECHH-----H-CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE Q ss_conf 976683049998411-----3-6866899999876788989999999849903887884511211799889993 Q gi|254780608|r 1 MSLMTYVQYVVVEND-----E-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68 (346) Q Consensus 1 ~~~M~~~~~~~V~~~-----~-~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346) +++|+.+=.++.+.. . .|..+..|.....+.+.+. .=..+|||+.+..++.|..++.|++- T Consensus 5 ~~~~~~~I~V~lpdg~~~~~~~~gtT~~dia~~i~~~~~~~-------~vaa~vng~l~dL~~~l~~d~~ve~i 71 (88) T 1wwt_A 5 SSGDSKPIKVTLPDGKQVDAESWKTTPYQIACGISQGLADN-------TVIAKVNNVVWDLDRPLEEDCTLELL 71 (88) T ss_dssp CCCSCCEEEEECTTSCEEEEETTTCCHHHHHHHSSTTTGGG-------CCCEEESSSEECSSSCCCSSEEEEEC T ss_pred CCCCCCCEEEECCCCCEEECCCCCCCHHHHHHHHCHHHHHH-------HHEECCCCEEEEEEEECCCCCEEEEE T ss_conf 55788757999799998971289977999999877778888-------87313298787501781899999999 No 54 >>3hvz_A Uncharacterized protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.20A {Clostridium leptum dsm 753} (A:) Probab=39.52 E-value=23 Score=15.70 Aligned_cols=60 Identities=10% Similarity=0.140 Sum_probs=37.6 Q ss_pred CCCCCEEEEEECHH-----HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE Q ss_conf 76683049998411-----36866899999876788989999999849903887884511211799889993 Q gi|254780608|r 2 SLMTYVQYVVVEND-----EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68 (346) Q Consensus 2 ~~M~~~~~~~V~~~-----~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346) +||+.+=+++.+.. ..|.+.-.+.....+ ....+ .=..+|||+.+..++.|+.|+.|++- T Consensus 2 ~l~~~~I~V~lpdG~~~~~~~g~T~~diA~~i~~----~l~~~---~v~a~vng~l~dL~~~l~~~~~veii 66 (78) T 3hvz_A 2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHS----AVGNR---XIGAKVDGRIVPIDYKVKTGEIIDVL 66 (78) T ss_dssp ----CEEEEECTTSCEEEEETTCBHHHHHHHHCH----HHHHT---EEEEEETTEEECTTCBCCTTCBEEEE T ss_pred CCCCCEEEEECCCCCEEECCCCCCHHHHHHHHHH----HHHHH---EEEEEECCEECCCCCCCCCCCEEEEE T ss_conf 8778768998999976879999958898998700----36532---00379999999998885899999999 No 55 >>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:) Probab=36.28 E-value=16 Score=16.62 Aligned_cols=56 Identities=20% Similarity=0.270 Sum_probs=32.1 Q ss_pred CCCCHHHHH---HHHCCCCCHHHHH----HHHHCC-CCEECCEEEC----CCCCCCCCCEEEEECCCC Q ss_conf 686689999---9876788989999----999849-9038878845----112117998899935655 Q gi|254780608|r 17 ENMRLDRWF---KNHYPHINFVNLQ----KILRSG-QVRVDKKRVK----FNNRIQSGQVVRIPPVIN 72 (346) Q Consensus 17 ~g~RLd~~L---~~~~~~~sr~~~~----~lir~G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~~ 72 (346) .|..+..++ .+.+|.+.+.... .-++.+ .|.|||+.+. .++.|+.||.|.+.|+.- T Consensus 33 ~~~Tv~~ll~~L~~~~p~~~~~l~~~~~~~~~r~~i~v~VN~~~v~~~~~~~t~L~~gDeV~ilppvs 100 (110) T 2k9x_A 33 TGTNLNGLVQLLKTNYVKERPDLLVDQTGQTLRPGILVLVNSCDAEVVGGMDYVLNDGDTVEFISTLH 100 (110) T ss_dssp GGCCHHHHHHHHTTTTCCSCHHHHBCSSSSSBCTTEEEEESSSBHHHHTSSCCCCCSSCEEEEEECCC T ss_pred CCCCHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCEEEEECCCC T ss_conf 99869999999998767303440244556650111899988956243888564859979999978887 No 56 >>2eki_A DRG 1, developmentally-regulated GTP-binding protein 1; protein NEDD3, neural precursor cell expressed developmentally DOWN-regulated protein 3; NMR {Homo sapiens} (A:) Probab=31.31 E-value=28 Score=15.11 Aligned_cols=16 Identities=19% Similarity=0.459 Sum_probs=7.3 Q ss_pred EECCCCCCCCCCEEEE Q ss_conf 8451121179988999 Q gi|254780608|r 52 RVKFNNRIQSGQVVRI 67 (346) Q Consensus 52 ~vk~~~~v~~GD~I~i 67 (346) ++-.++.|+.||+|+| T Consensus 69 ~vgl~~~L~dgDvV~I 84 (93) T 2eki_A 69 KVGKDHTLEDEDVIQI 84 (93) T ss_dssp EECSSCCCCSSEEECE T ss_pred CCCCCCEECCCCEEEE T ss_conf 6787628069999999 No 57 >>3ct8_A Protein BH2160, putative glyoxalase; NP_243026.1, glyoxalase/bleomycin resistance protein/dioxygenase superfamily, structural genomics; HET: UNL; 2.10A {Bacillus halodurans c-125} (A:80-146) Probab=31.30 E-value=33 Score=14.64 Aligned_cols=47 Identities=17% Similarity=0.127 Sum_probs=34.6 Q ss_pred HHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECC Q ss_conf 89999999963980004644466522100013446241311000437588964999839 Q gi|254780608|r 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310 (346) Q Consensus 252 ~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~ap 310 (346) -.++..++...|.+|++.+....... -..+.+.|..|++.++++.|| T Consensus 21 Vd~~~~~l~~~G~~i~~~p~~~~~~~------------~~~~~~~~~DPDG~~iEi~~P 67 (67) T 3ct8_A 21 VDELTQKLKERGDPILYEDRHPFAGG------------PNHYAVFCEDPNRIKVEIVAP 67 (67) T ss_dssp HHHHHHHHHHHTCCBCCTTTTTCTTC------------TTCCEEEEECTTCCEEEEECC T ss_pred HHHHHHHHHHCCCEEECCCCCCCCCC------------CCEEEEEEECCCCCEEEEEEC T ss_conf 89998889875977835998762689------------967999999899999999969 No 58 >>2exd_A NFED short homolog; membrane protein; NMR {Pyrococcus horikoshii OT3} (A:) Probab=30.75 E-value=34 Score=14.58 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=21.0 Q ss_pred HCCCCEECCEE--ECCCCCCCCCCEEEEE Q ss_conf 84990388788--4511211799889993 Q gi|254780608|r 42 RSGQVRVDKKR--VKFNNRIQSGQVVRIP 68 (346) Q Consensus 42 r~G~V~VNG~~--vk~~~~v~~GD~I~i~ 68 (346) ..|.|+++|.. +.....+..||.|+|- T Consensus 29 ~~G~V~v~G~~W~A~s~~~i~~G~~V~V~ 57 (80) T 2exd_A 29 DHYLVEVEGDKWIAYSDEKLSLGDRVMVV 57 (80) T ss_dssp TCEEEEETTEEEEECCSSCCCTTCEEEEE T ss_pred CCEEEEECCEEEEEEECCCCCCCCEEEEE T ss_conf 98999999989999979964899999999 No 59 >>2csw_A Ubiquitin ligase protein RNF8; 11-stranded beta sandwich, ring finger protein 8, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=29.28 E-value=35 Score=14.53 Aligned_cols=10 Identities=20% Similarity=0.066 Sum_probs=3.4 Q ss_pred CEEEEECCCC Q ss_conf 4046212310 Q gi|254780608|r 156 GILVVARTRA 165 (346) Q Consensus 156 Glll~AK~~~ 165 (346) +.++|.+... T Consensus 36 ~~~~iGR~~~ 45 (145) T 2csw_A 36 CEVTVGRGFG 45 (145) T ss_dssp CCEEEESSTT T ss_pred CEEEEECCCC T ss_conf 7499837999 No 60 >>3ey7_A Biphenyl-2,3-DIOL 1,2-dioxygenase III-related protein; integron cassette protein mobIle metagenome structural genomics, oxidoreductase, PSI-2; HET: MSE; 1.60A {Vibrio cholerae} PDB: 3ey8_A* (A:67-133) Probab=27.35 E-value=39 Score=14.21 Aligned_cols=45 Identities=13% Similarity=0.138 Sum_probs=33.6 Q ss_pred HHHHHHHHHCCCCEECCCC--CCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCC Q ss_conf 9999999963980004644--4665221000134462413110004375889649998399 Q gi|254780608|r 253 HQLRVHALHMGCPIVGDHK--YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311 (346) Q Consensus 253 HQIRvhl~~~g~PivGD~~--Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~apl 311 (346) -.+..||.+.|.+|.+++. +|.... ..++.|..|++..++|.++. T Consensus 19 d~~~~~L~~~Gv~i~~~p~~~~~~~g~--------------~~siYf~DPdG~~iEl~~~p 65 (67) T 3ey7_A 19 SDAXKHVEDQGVTIXEGPVKRTGAQGA--------------ITSFYFRDPDGNLIEVSTYS 65 (67) T ss_dssp HHHHHHHHHTTCCCCEEEEEEEETTEE--------------EEEEEEECTTCCEEEEEESC T ss_pred HHHHHHHHHCCCCEECCCCCCCCCCCC--------------EEEEEEECCCCCEEEEEECC T ss_conf 899999997597400287232278886--------------89999999999999989776 No 61 >>1vc3_B L-aspartate-alpha-decarboxylase heavy chain; tetramer, pyruvoyl group, riken structural genomics/proteomics initiative, RSGI; 1.50A {Thermus thermophilus} PDB: 2eeo_B (B:) Probab=26.30 E-value=34 Score=14.54 Aligned_cols=48 Identities=15% Similarity=0.171 Sum_probs=29.8 Q ss_pred EEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC Q ss_conf 99984113686689999987678898999999984990388788451121179988999356 Q gi|254780608|r 9 YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346) Q Consensus 9 ~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346) .+-|-.-..|.|+..|...-- + -+|.|.+||..+ ..++.||+|.|-.+ T Consensus 19 ~V~V~Nv~NG~Rf~TY~I~G~----~-------GSg~I~lNGAAA---rl~~~GD~vII~sy 66 (96) T 1vc3_B 19 QVDIYDITNGARLTTYALPGE----R-------GSGVIGINGAAA---HLVKPGDLVILVAY 66 (96) T ss_dssp EEEEEETTTCCEEEEECEEEC----T-------TTTCEEEEGGGG---GTCCTTCEEEEEEE T ss_pred EEEEEECCCCCEEEEEEEECC----C-------CCCEEEECCHHH---EECCCCCEEEEEEC T ss_conf 899999989948987999636----7-------668798558564---23599999999987 No 62 >>1yj5_C 5' polynucleotide kinase-3' phosphatase FHA domain; beta sandwich, P-loop, transferase; 2.80A {Mus musculus} (C:) Probab=26.28 E-value=41 Score=14.09 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=11.5 Q ss_pred CEECCEEECCC--CCCCCCCEEEE Q ss_conf 03887884511--21179988999 Q gi|254780608|r 46 VRVDKKRVKFN--NRIQSGQVVRI 67 (346) Q Consensus 46 V~VNG~~vk~~--~~v~~GD~I~i 67 (346) +.|||+++... +.|+.||+|.| T Consensus 72 t~vNg~~i~~~~~~~L~~Gd~i~i 95 (143) T 1yj5_C 72 STVGVHELKPGLSGSLSLGDVLYL 95 (143) T ss_dssp CEETTEECCTTCEEEECTTCEEES T ss_pred CEECCEECCCCEEEECCCCCEEEE T ss_conf 378548804763898479999999 No 63 >>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238) Probab=26.19 E-value=41 Score=14.08 Aligned_cols=27 Identities=11% Similarity=0.208 Sum_probs=20.2 Q ss_pred CCCCEECCEEEC-CCCCCCCCCEEEEEC Q ss_conf 499038878845-112117998899935 Q gi|254780608|r 43 SGQVRVDKKRVK-FNNRIQSGQVVRIPP 69 (346) Q Consensus 43 ~G~V~VNG~~vk-~~~~v~~GD~I~i~~ 69 (346) +|-+.+||+.+. ....|+.||+|.|.. T Consensus 54 ngt~~~n~~~~~~~~~~L~~Gd~i~iG~ 81 (158) T 1wv3_A 54 NTDVYINYELQEQLTNKAYIGDHIYVEG 81 (158) T ss_dssp TCCEEETTEECCSSEEEEETTCEEEETT T ss_pred CCCEEECCEEEECCEEECCCCCEEEECC T ss_conf 9869987899725504304899999998 No 64 >>2k5p_A THis protein, thiamine-biosynthesis protein; NESG, GMR137, structural genomics, PSI-2, protein structure initiative; NMR {Geobacter metallireducens gs-15} PDB: 3cwi_A (A:) Probab=26.10 E-value=41 Score=14.07 Aligned_cols=46 Identities=9% Similarity=0.169 Sum_probs=30.6 Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEECC Q ss_conf 686689999987678898999999984990388788451----121179988999356 Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPPV 70 (346) Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~~ 70 (346) .+..|..+|... +++.. +.=.|-+||+.+.. ++.|+.||.|.|... T Consensus 16 ~~~tl~~lL~~l--~~~~~------~~iaV~vN~~iVpr~~w~~~~L~~gD~IeIi~~ 65 (78) T 2k5p_A 16 ESLNVTELLSAL--KVAQA------EYVTVELNGEVLEREAFDATTVKDGDAVEFLYF 65 (78) T ss_dssp SCEEHHHHHHHH--TCSCT------TTCCEEETTEECCTTHHHHCEECSSBCEEECCC T ss_pred CCCCHHHHHHHC--CCCCC------CEEEEEECCEEECHHHHCCCCCCCCCEEEEEEE T ss_conf 998099999877--99889------879999899994778918044899799999958 No 65 >>1tke_A Threonyl-tRNA synthetase; ligase; 1.46A {Escherichia coli} (A:1-63) Probab=26.10 E-value=41 Score=14.07 Aligned_cols=45 Identities=13% Similarity=-0.001 Sum_probs=31.4 Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEE Q ss_conf 3686689999987678898999999984990388788451121179988999 Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67 (346) Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i 67 (346) ..|..+-.+.....+ +..++ .=..+|||+.+..++.|..++.|++ T Consensus 15 ~~g~T~~dia~~i~~----~~~~~---~v~a~vng~l~dL~~~l~~d~~ve~ 59 (63) T 1tke_A 15 DHAVSPMDVALDIGP----GLAKA---CIAGRVNGELVDACDLIENDAQLSI 59 (63) T ss_dssp SSCBCHHHHHHHHCH----HHHHH---CCEEEETTEEEETTCCBCSCEEEEE T ss_pred CCCCCHHHHHHHHCC----CHHHH---EEEEEECCEEECCCCCCCCCCEEEE T ss_conf 899999999998670----01544---6999999999638844178758999 No 66 >>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} (A:) Probab=24.80 E-value=42 Score=14.00 Aligned_cols=44 Identities=7% Similarity=0.141 Sum_probs=28.2 Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEEC Q ss_conf 686689999987678898999999984990388788451----12117998899935 Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPP 69 (346) Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~ 69 (346) +++.|..+|... ++... .=.|-+||..+.. ++.++.||.|.|.. T Consensus 14 ~~~tl~~lL~~~--~~~~~-------~vav~vN~~iv~k~~~~~~~l~~gD~ieiv~ 61 (66) T 1f0z_A 14 AGQTVHELLEQL--DQRQA-------GAALAINQQIVPREQWAQHIVQDGDQILLFQ 61 (66) T ss_dssp TTCCHHHHHHHH--TCCCS-------SEEEEETTEEECHHHHTTCCCCTTEEECEEE T ss_pred CCCCHHHHHHHC--CCCCC-------CEEEEECCEECCHHHCCCCCCCCCCEEEEEE T ss_conf 999999999876--99998-------1999999999387882813489989999997 No 67 >>3kt9_A Aprataxin; FHA domain, beta sandwich, beta sheet, AMP hydrolase, alternative splicing, disease mutation, DNA damage, DNA repair, DNA-binding; 1.65A {Homo sapiens} (A:) Probab=24.69 E-value=43 Score=13.91 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=14.6 Q ss_pred CCEECCEEECC--CCCCCCCCEEEEE Q ss_conf 90388788451--1211799889993 Q gi|254780608|r 45 QVRVDKKRVKF--NNRIQSGQVVRIP 68 (346) Q Consensus 45 ~V~VNG~~vk~--~~~v~~GD~I~i~ 68 (346) .+.|||+++.+ ...|+.||.|++. T Consensus 65 gt~vng~~l~~~~~~~L~~gd~I~iG 90 (102) T 3kt9_A 65 PTSIDSVVIGKDQEVKLQPGQVLHMV 90 (102) T ss_dssp CCEETTEECCBTCEEEECTTCCEEEE T ss_pred CEEECCEEECCCCCCCCCCCCEEEEE T ss_conf 75899899468976164899999990 No 68 >>3elx_A Ileal bIle acid-binding protein; ileal bIle acid-bindign protein, zebrafish, cholic acid, X- RAY structure, lipid-binding, transport; 1.60A {Danio rerio} PDB: 3elz_A* 3em0_A* (A:) Probab=23.25 E-value=46 Score=13.73 Aligned_cols=48 Identities=13% Similarity=-0.034 Sum_probs=33.0 Q ss_pred CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCC---CCEECCEEE Q ss_conf 97668304999841136866899999876788989999999849---903887884 Q gi|254780608|r 1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSG---QVRVDKKRV 53 (346) Q Consensus 1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G---~V~VNG~~v 53 (346) |++|.........+.++ .|.||... ++|....+.+-... .|..||... T Consensus 1 Ms~~~f~Gtwkl~~sEN---fd~~Lk~l--GV~~~~Rk~a~~~kp~~~I~~~Gd~~ 51 (138) T 3elx_A 1 MRGSAFNGKWETESQEG---YEPFCKLI--GIPDDVIAKGRDFKLVTEIVQNGDDF 51 (138) T ss_dssp --CCTTCEEEEEEEEES---HHHHHHHT--TCCHHHHHHTTTCCCEEEEEEETTEE T ss_pred CCCCCCEEEEEEEEEEC---HHHHHHHH--CCCHHHHHHHHCCCCEEEEEEECCEE T ss_conf 97762207999984219---99999884--99999998876179769999909989 No 69 >>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis} (A:) Probab=22.88 E-value=47 Score=13.69 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=30.4 Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE Q ss_conf 6866899999876788989999999849903887884511211799889993 Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68 (346) Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346) .|..+-.+.....+.+.+ + .=..+|||+.+..++.|..|+.|++- T Consensus 17 ~GtT~~dia~~i~~~l~~----~---~v~A~vng~l~dL~~~l~~~~~ve~i 61 (73) T 2kmm_A 17 QGATALDFAYSLHSDLGD----H---CIGAKVNHKLVPLSYVLNSGDQVEVL 61 (73) T ss_dssp TTCBHHHHHHHHCSHHHH----T---EEEEEETTEECCTTCBCCSSSBEEEE T ss_pred CCCCHHHHHHHHCCCHHH----E---EEEEEECCEECCCCCCCCCCCEEEEE T ss_conf 999631048774845023----6---89998898599888795899999999 No 70 >>2hd9_A UPF0310 protein PH1033; structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: CIT; 1.35A {Pyrococcus horikoshii OT3} (A:) Probab=22.21 E-value=48 Score=13.66 Aligned_cols=42 Identities=24% Similarity=0.148 Sum_probs=32.8 Q ss_pred CCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCC Q ss_conf 898999999984990388788451121179988999356554 Q gi|254780608|r 32 INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73 (346) Q Consensus 32 ~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~ 73 (346) .|+..++.....|-..++..+..+-.++++||.|.+..+... T Consensus 8 ~s~e~~~~~~~~g~~~v~~gk~~~l~rikpGD~li~Y~~~~~ 49 (145) T 2hd9_A 8 TNRENWEVIKRHNVWGVPKKHKNTLSRVKPGDKLVIYVRQEK 49 (145) T ss_dssp ECHHHHHHHHHHCEEEECGGGHHHHTTCCTTCEEEEEECCEE T ss_pred CCHHHHHHHHHCCEEECCCCCHHHHHHCCCCCEEEEEECCCC T ss_conf 799999999968888525765537861788887999955424 No 71 >>3cuz_A MSA, malate synthase A; TIM barrel, cytoplasm, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.04A {Escherichia coli} PDB: 3cv1_A 3cv2_A* (A:399-532) Probab=21.77 E-value=24 Score=15.48 Aligned_cols=27 Identities=11% Similarity=0.047 Sum_probs=20.2 Q ss_pred CCCHHHHHHHHHCCCCEECCEEECCCC Q ss_conf 889899999998499038878845112 Q gi|254780608|r 31 HINFVNLQKILRSGQVRVDKKRVKFNN 57 (346) Q Consensus 31 ~~sr~~~~~lir~G~V~VNG~~vk~~~ 57 (346) .+||+++=+|++.|...-||+++.... T Consensus 53 EISR~QlWQWi~hg~~l~dG~~vt~~~ 79 (134) T 3cuz_A 53 EISRTSIWQWIHHQKTLSNGKPVTKAL 79 (134) T ss_dssp HHHHHHHHHHHHTTCBCTTSCBCCHHH T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHH T ss_conf 999999999997677778884726999 No 72 >>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=21.74 E-value=41 Score=14.07 Aligned_cols=45 Identities=13% Similarity=-0.001 Sum_probs=30.9 Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEE Q ss_conf 3686689999987678898999999984990388788451121179988999 Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67 (346) Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i 67 (346) ..|..+-.+.....+ +..++ .=..+|||+.+..++.|..++.|++ T Consensus 15 ~~g~T~~dia~~i~~----~~~~~---~v~a~vng~l~dL~~~l~~d~~ve~ 59 (63) T 1qf6_A 15 DHAVSPMDVALDIGP----GLAKA---CIAGRVNGELVDACDLIENDAQLSI 59 (63) T ss_dssp SSCBCHHHHHHHHCH----HHHHH---CSEEEETTEEEETTSCBCSCEECCE T ss_pred CCCCCHHHHHHHHCH----HHHHH---EEEEEECCEEEECCCCCCCCCEEEE T ss_conf 899999999998653----12435---6999999999857851799988998 No 73 >>1nki_A Probable fosfomycin resistance protein; potassium binding loop, manganese binding, transferase; 0.95A {Pseudomonas aeruginosa PAO1} (A:59-135) Probab=20.82 E-value=52 Score=13.43 Aligned_cols=61 Identities=8% Similarity=0.016 Sum_probs=42.2 Q ss_pred EEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCHH-HHHHHHHHC Q ss_conf 7861237899999999639800046444665221000134462413110004375889649998399789-999999808 Q gi|254780608|r 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH-MVKTWDSLG 323 (346) Q Consensus 245 ~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~~-f~~~l~~l~ 323 (346) +..-+.--.+++.+|...|.|+.....=+ ..++.|..|.+..+++.+.-|.. .......++ T Consensus 9 F~v~~~~~~~~~~~L~~~Gv~v~~~~~~~------------------~~siYf~DPdG~~iEl~~~~~~~~~~~~~~~~~ 70 (77) T 1nki_A 9 FGIAAADFARFAAQLRAHGVREWKQNRSE------------------GDSFYFLDPDGHRLEAHVGDLRSRLAACRQAPY 70 (77) T ss_dssp EEECHHHHHHHHHHHHHTTCCEEECCCSS------------------SCEEEEECTTCCEEEEESCCHHHHHHHHHHSCC T ss_pred ECCCHHHHHHHHHHHHHCCCCEECCCCCC------------------EEEEEEECCCCCEEEEEECCHHHCCCCCCCCCC T ss_conf 12558899999999998899472489887------------------479999999999999998971341200446882 Done!