Query gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus str. psy62] Match_columns 340 No_of_seqs 150 out of 5691 Neff 7.1 Searched_HMMs 33803 Date Wed Jun 1 15:26:29 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780610.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 0 463.5 14.9 311 9-339 2-313 (325) 2 >1v9k_A Ribosomal large subuni 100.0 0 0 378.6 14.1 226 90-340 2-227 (228) 3 >2i82_A Ribosomal large subuni 100.0 0 0 344.3 12.1 208 87-327 9-216 (217) 4 >2gml_A Ribosomal large subuni 100.0 0 0 330.5 9.1 212 87-339 4-223 (237) 5 >3dh3_A Ribosomal large subuni 100.0 0 0 317.6 6.1 205 94-339 1-213 (227) 6 >2oml_A Ribosomal large subuni 100.0 0 0 293.9 7.2 183 88-308 2-185 (189) 7 >1ksk_A Ribosomal small subuni 100.0 1.6E-42 0 272.8 7.0 171 94-315 2-172 (176) 8 >1vio_A Ribosomal small subuni 100.0 5.6E-42 0 269.6 7.7 184 93-316 1-184 (186) 9 >2olw_A Ribosomal large subuni 99.9 5.7E-24 1.7E-28 162.2 4.1 100 39-171 2-101 (119) 10 >1dm9_A Hypothetical 15.5 KD p 99.9 8.8E-24 2.6E-28 161.1 2.6 124 15-163 1-131 (133) 11 >2olw_A Ribosomal large subuni 99.8 4.6E-21 1.4E-25 144.9 3.1 96 179-279 1-97 (98) 12 >2k6p_A Uncharacterized protei 99.8 7.5E-21 2.2E-25 143.6 -0.1 90 23-114 1-91 (92) 13 >3dh3_A Ribosomal large subuni 99.0 2.8E-10 8.3E-15 80.6 5.2 57 18-77 2-58 (63) 14 >1p9k_A ORF, hypothetical prot 98.9 2E-10 6E-15 81.5 0.8 71 4-75 2-72 (79) 15 >1ksk_A Ribosomal small subuni 98.9 5.5E-09 1.6E-13 72.9 6.4 53 21-75 2-54 (58) 16 >1vio_A Ribosomal small subuni 98.8 8.5E-09 2.5E-13 71.8 6.4 52 22-75 2-53 (57) 17 >2vqe_D 30S ribosomal protein 98.4 6.4E-07 1.9E-11 60.6 6.6 51 24-75 1-51 (94) 18 >3hp7_A Hemolysin, putative; s 98.4 2.6E-07 7.8E-12 62.9 3.4 58 17-75 1-60 (65) 19 >1h3f_A Tyrosyl-tRNA synthetas 98.2 8.6E-06 2.5E-10 53.9 7.4 66 9-75 3-71 (83) 20 >3i1m_D 30S ribosomal protein 98.1 1.3E-06 3.9E-11 58.8 3.1 52 24-76 1-52 (94) 21 >3bbn_D Ribosomal protein S4; 98.1 1.4E-06 4.2E-11 58.5 2.5 54 21-75 6-59 (120) 22 >1s1h_D 40S ribosomal protein 98.0 7.4E-06 2.2E-10 54.3 4.4 55 20-75 6-60 (99) 23 >2cqj_A BRMS2, U3 small nucleo 97.8 1.4E-05 4.2E-10 52.6 3.2 55 19-74 4-60 (71) 24 >2aus_C Pseudouridine synthase 96.9 0.00048 1.4E-08 43.5 2.6 84 95-202 14-97 (215) 25 >2apo_A Probable tRNA pseudour 96.9 0.0007 2.1E-08 42.5 2.9 85 94-202 13-97 (216) 26 >2jan_A Tyrosyl-tRNA synthetas 96.8 0.0016 4.6E-08 40.4 4.1 51 19-70 8-58 (88) 27 >3kbg_A 30S ribosomal protein 95.0 0.059 1.8E-06 31.0 5.7 70 22-103 7-76 (81) 28 >1sgv_A TRNA pseudouridine syn 94.6 0.032 9.6E-07 32.6 3.5 55 94-164 3-57 (87) 29 >1k8w_A TRNA pseudouridine syn 94.4 0.039 1.2E-06 32.1 3.5 55 94-164 22-76 (108) 30 >1jil_A Tyrrs, tyrosyl-tRNA sy 94.3 0.0091 2.7E-07 35.9 0.0 52 19-71 103-154 (174) 31 >1r3e_A TRNA pseudouridine syn 94.1 0.043 1.3E-06 31.8 3.2 52 97-164 3-54 (92) 32 >2ts1_A Tyrosyl-tRNA synthetas 93.1 0.02 5.8E-07 33.9 0.0 51 20-71 104-154 (174) 33 >1c05_A Ribosomal protein S4 d 92.9 0.095 2.8E-06 29.8 3.3 25 50-74 1-25 (83) 34 >1fm0_D Molybdopterin converti 72.1 6.5 0.00019 18.9 4.7 51 22-76 25-77 (81) 35 >2q5w_D Molybdopterin converti 63.1 10 0.0003 17.8 4.0 28 48-76 46-73 (77) 36 >1vjk_A Molybdopterin converti 47.9 12 0.00036 17.3 2.2 26 50-76 69-94 (98) 37 >2hj1_A Hypothetical protein; 46.2 2.7 8.1E-05 21.1 -1.3 69 4-79 6-88 (97) 38 >1v8c_A MOAD related protein; 44.0 21 0.00061 15.9 3.0 60 11-76 15-83 (84) 39 >2ff4_A Probable regulatory pr 41.8 23 0.00067 15.7 3.3 23 50-73 60-82 (99) 40 >2rk0_A Glyoxalase/bleomycin r 39.2 25 0.00073 15.4 3.8 46 257-329 19-64 (69) 41 >1rws_A Hypothetical protein P 38.5 12 0.00036 17.2 1.1 62 3-75 4-72 (77) 42 >2qjl_A URM1, ubiquitin-relate 37.6 26 0.00077 15.3 3.1 48 27-76 39-95 (99) 43 >1vc3_B L-aspartate-alpha-deca 36.1 14 0.00043 16.8 1.1 41 18-74 24-64 (96) 44 >1c05_A Ribosomal protein S4 d 34.6 29 0.00087 15.0 2.6 27 22-49 29-55 (55) 45 >3gqs_A Adenylate cyclase-like 32.8 31 0.00093 14.8 2.7 10 152-161 23-32 (106) 46 >3dwg_C 9.5 kDa culture filtra 32.6 32 0.00094 14.8 3.1 26 51-76 61-89 (93) 47 >2k9x_A Tburm1, uncharacterize 30.9 25 0.00075 15.4 1.7 27 51-77 70-99 (110) 48 >1wgk_A Riken cDNA 2900073H19 30.7 34 0.001 14.6 2.6 27 50-76 75-104 (114) 49 >2g1e_A Hypothetical protein T 30.1 29 0.00087 15.0 1.9 27 50-76 57-86 (90) 50 >2c45_A Aspartate 1-decarboxyl 29.6 25 0.00075 15.4 1.5 22 48-73 66-87 (139) 51 >2wyh_A Alpha-mannosidase; hyd 28.9 37 0.0011 14.4 2.6 29 22-53 35-65 (72) 52 >1wv3_A Similar to DNA segrega 28.9 37 0.0011 14.4 3.3 26 48-73 54-79 (158) 53 >1pqh_A Aspartate 1-decarboxyl 27.4 21 0.00063 15.8 0.8 15 93-107 55-69 (143) 54 >3huh_A Virulence protein STM3 25.9 41 0.0012 14.1 3.7 49 258-330 21-71 (75) 55 >1wxq_A GTP-binding protein; s 25.9 19 0.00056 16.1 0.3 25 50-75 54-78 (81) 56 >2z0t_A Putative uncharacteriz 23.0 47 0.0014 13.7 2.4 35 41-75 10-44 (109) 57 >3cuz_A MSA, malate synthase A 22.4 20 0.0006 15.9 -0.1 23 37-59 54-76 (134) 58 >2pbt_A AP4A hydrolase; nudix 21.0 35 0.001 14.5 0.9 42 91-132 9-51 (134) 59 >3cux_A Malate synthase; TIM b 20.5 29 0.00084 15.1 0.3 23 37-59 54-77 (134) 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=463.50 Aligned_cols=311 Identities=38% Similarity=0.580 Sum_probs=256.2 Q ss_pred CCEEE-EEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHH Q ss_conf 62499-99571136875789999871768898999999985990499899328675804898899970560111102332 Q gi|254780610|r 9 SSIKI-SLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQEN 87 (340) Q Consensus 9 ~~~~~-~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~ 87 (340) +-|++ ++|+++++|+|||+||++.++ ++||+.++++|++|.|+|||+++..+++.+..++.+.............+.. T Consensus 2 ~~~~~~~~v~~~~~g~rl~~~L~~~~~-~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (325) T 1v9f_A 2 QRVQLTATVSENQLGQRLDQALAEMFP-DYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQD 80 (325) T ss_dssp ---------------------------------------------------------------------------CCCCC T ss_pred CEEEEEEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCC T ss_conf 748999998976488669999998668-6799999999986998999999178320625898997325433222333344 Q ss_pred HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH Q ss_conf 22221014402789962401110456787542100222222102443344443643244443323240572120357888 Q gi|254780610|r 88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQK 167 (340) Q Consensus 88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~ 167 (340) .++.|||||++++|+|||+|++|||+++...+|+...+....... .....+++|||||++|||+||+|||..+++. T Consensus 81 ~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~ 156 (325) T 1v9f_A 81 IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTR 156 (325) T ss_dssp CCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG----GGSGGGGBCCCCCTTCEEEEEEESSHHHHHH T ss_pred CCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCC----CCCCCEEEEECCCCCCCCCEEEECCHHHHHH T ss_conf 541125101105787078886548987778886323211344433----3334214653258898651466402588999 Q ss_pred HHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCE Q ss_conf 89999972113221334454320243323321100134344433221234445555530000122210112566775001 Q gi|254780610|r 168 LSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSL 247 (340) Q Consensus 168 l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~sl 247 (340) |.++|. .+.+.|+|+|+|.|.+..+.+.+..+........ .......+++|.|+|.+... ...+|+ T Consensus 157 l~~~~~----~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~a~~~~~~~~~-----~~~~sl 222 (325) T 1v9f_A 157 LVESLQ----RREITREYEAVAIGHMTAGGTVDEPISRHPTKRT-----HMAVHPMGKPAVTHYRIMEH-----FRVHTR 222 (325) T ss_dssp HHHHHH----TTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT-----CEEECTTSBCCEEEEEEEEE-----CSSEEE T ss_pred HHHHHH----CCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC-----EEEECCCCCEEEEEEEEEEE-----CCCCEE T ss_conf 998750----1210124234301354745662355335766653-----05876887157899898653-----388457 Q ss_pred EEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCC Q ss_conf 23443115899999999870978604154477554443345701355440798044321000424688976899984997 Q gi|254780610|r 248 LKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIP 327 (340) Q Consensus 248 v~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP 327 (340) ++|+|.|||+||||+|||++|||||||.+||........ .............+++|||+.|+|.||.+++.++|+||+| T Consensus 223 ~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~-l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P 301 (325) T 1v9f_A 223 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG-ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP 301 (325) T ss_dssp EEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT-CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC T ss_pred EEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH T ss_conf 999977883179999999839976687778985545443-3166777651586434653705857789998899991797 Q ss_pred HHHHHHHHHHHC Q ss_conf 899999998851 Q gi|254780610|r 328 EDMLTVIRKLNE 339 (340) Q Consensus 328 ~~~~~~l~~L~~ 339 (340) ++|..+|++|+. T Consensus 302 ~~f~~~l~~l~~ 313 (325) T 1v9f_A 302 QDMVELIEVMRA 313 (325) T ss_dssp HHHHHHHHHHHH T ss_pred HHHHHHHHHHHH T ss_conf 999999999730 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=378.58 Aligned_cols=226 Identities=31% Similarity=0.422 Sum_probs=188.4 Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH Q ss_conf 22101440278996240111045678754210022222210244334444364324444332324057212035788889 Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS 169 (340) Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~ 169 (340) +.|||||++|+|+|||+||+|||++++...|+.+.+..+... .++++|||||++|||+||+|||..+++.++ T Consensus 2 ~~Iiyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~--------~~~~~vhRLD~~TSGlll~ak~~~~a~~l~ 73 (228) T 1v9k_A 2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA--------RFLELVHRLDRDTSGVLLVAKKRSALRSLH 73 (228) T ss_dssp CCEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHSTTC--------SCCEESSCCCTTCEEEEEEESSHHHHHHHH T ss_pred CEEEEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCC--------CCCCEEEECCCCCCCEEEEECCHHHHHHHH T ss_conf 989996899999999999863899899536999999867787--------653166404643221367523579999999 Q ss_pred HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEE Q ss_conf 99997211322133445432024332332110013434443322123444555553000012221011256677500123 Q gi|254780610|r 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249 (340) Q Consensus 170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~ 249 (340) ++|. ++.+.|+|+|+|.|.++...+.+..++.......... ........+.|.++|.+... ....++++ T Consensus 74 ~~~~----~~~v~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~ 142 (228) T 1v9k_A 74 EQLR----EKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGER--IVRVSQEGKPSETRFKVEER-----YAFATLVR 142 (228) T ss_dssp HHHH----TTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCE--EEEECTTSBCCCEEEEEEEE-----CSSEEEEE T ss_pred HHHH----HHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCEE--EEECCCCCCCCCEEECHHHH-----CCCCEEEE T ss_conf 9987----4034543210346864223575223300001101015--55207888422155005553-----58737999 Q ss_pred EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHH Q ss_conf 44311589999999987097860415447755444334570135544079804432100042468897689998499789 Q gi|254780610|r 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED 329 (340) Q Consensus 250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~ 329 (340) ++|.|||+||||+||+++||||+||.+||....... ........++++|||++|+|+||.|++.+.|+||+|++ T Consensus 143 ~~~~tGR~HQIR~h~a~~g~PIvgD~~Y~~~~~~~~------~~~~~~~~~~~~Lha~~l~f~~p~~~~~~~~~ap~P~~ 216 (228) T 1v9k_A 143 CSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQ------LTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEG 216 (228) T ss_dssp EEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHHHH------HHHTTCCCCSCCEEEEEEEEECTTTCCEEEEECCCCHH T ss_pred EEECCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHH------HHHHCCCCCHHHHHCCCCEEECCCCCCEEEEEECCHHH T ss_conf 994757357888888854972135774130000023------33202686237887150392879999889999178699 Q ss_pred HHHHHHHHHCC Q ss_conf 99999988519 Q gi|254780610|r 330 MLTVIRKLNEK 340 (340) Q Consensus 330 ~~~~l~~L~~~ 340 (340) |.++|++|+++ T Consensus 217 ~~~~l~~~~~~ 227 (228) T 1v9k_A 217 LKRCLQKXRNA 227 (228) T ss_dssp HHHHHHHHHHC T ss_pred HHHHHHHHHHC T ss_conf 99999998737 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=344.32 Aligned_cols=208 Identities=31% Similarity=0.439 Sum_probs=172.1 Q ss_pred HHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH Q ss_conf 22222101440278996240111045678754210022222210244334444364324444332324057212035788 Q gi|254780610|r 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQ 166 (340) Q Consensus 87 ~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~ 166 (340) ..+++|||||++|+|+|||+||+||++++....++...+...... ++++|||||++|||+||+||+.++++ T Consensus 9 ~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~~~~~~~---------~l~~vhRLD~~TSGllllak~~~~~~ 79 (217) T 2i82_A 9 EPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYP---------QAESVHRLDXATSGVIVVALTKAAER 79 (217) T ss_dssp SSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCT---------TCEESSCCCTTCEEEEEEESSHHHHH T ss_pred CCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCC---------CCCCCCCCCCCCCEEEEEEECHHHHH T ss_conf 999529997998999999999825799887760389997644103---------32223455542101589860317777 Q ss_pred HHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC Q ss_conf 88999997211322133445432024332332110013434443322123444555553000012221011256677500 Q gi|254780610|r 167 KLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS 246 (340) Q Consensus 167 ~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s 246 (340) .|+++|. .+.+.|+|+|++.|.+...++.+..+............ ......++.+.+.|.++. ....+| T Consensus 80 ~l~~~~~----~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~-----~~~~~s 148 (217) T 2i82_A 80 ELKRQFR----EREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQK--VCYETGKPAQTEYEVVEY-----AADNTA 148 (217) T ss_dssp HHHHHHH----TTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEE--ECTTTCBCCEEEEEEEEE-----ETTTEE T ss_pred HHHHHHH----HCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCE--ECCCCCCCCCCEECCCCC-----CCCCCE T ss_conf 8898765----14010368988615446664067410123224332200--012247630010101111-----233104 Q ss_pred EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCC Q ss_conf 12344311589999999987097860415447755444334570135544079804432100042468897689998499 Q gi|254780610|r 247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI 326 (340) Q Consensus 247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~apl 326 (340) +++|+|.|||+||||+||+++||||+||.+||..... ...+|++|||++|+|+||.|||.+.|+||+ T Consensus 149 ~~~~~~~TGr~HQIR~h~a~lg~PIlgD~~Yg~~~~~-------------~~~~~~~Lha~~l~f~~p~~ge~~~~~~p~ 215 (217) T 2i82_A 149 RVVLKPITGRSHQLRVHXLALGHPILGDRFYASPEAR-------------AXAPRLLLHAEXLTITHPAYGNSXTFKAPA 215 (217) T ss_dssp EEEEEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHH-------------HTCSSCCEEEEEEEEECTTTCCEEEEECCC T ss_pred EEEEEECCCCHHHHHHHHHHHCCEEECCCCCCCHHHC-------------CCCCCHHHHCCCCEEECCCCCCEEEEECCC T ss_conf 7889850262378999999719768167676885563-------------688466676276788998999889997899 Q ss_pred C Q ss_conf 7 Q gi|254780610|r 327 P 327 (340) Q Consensus 327 P 327 (340) | T Consensus 216 P 216 (217) T 2i82_A 216 D 216 (217) T ss_dssp C T ss_pred C T ss_conf 9 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=330.54 Aligned_cols=212 Identities=15% Similarity=0.044 Sum_probs=163.7 Q ss_pred HHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH Q ss_conf 22222101440278996240111045678754210022222210244334444364324444332324057212035788 Q gi|254780610|r 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQ 166 (340) Q Consensus 87 ~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~ 166 (340) +.++.|||||++|+|||||+|++||+++.... ++.+.+. ...++++|||||++||||||||++.+++. T Consensus 4 ~~~~~ii~ed~~~ivvnKP~G~~~~~~~~~~~-~~~~~l~-----------~~~~~~~vhRLD~~TSGlll~a~~~~~~~ 71 (237) T 2gml_A 4 SHHHHHHGSDLVLIALNKPVGIVSTTEDGERD-NIVDFVN-----------HSKRVFPIGRLDKDSQGLIFLTNHGDLVN 71 (237) T ss_dssp ---------CCCEEEEEECTTCBCCSSSSCSS-BHHHHSC-----------CSSCCEEESCCCTTCEEEEEEESCHHHHH T ss_pred CCCCCCCCCCEEEEEEECCCCEEECCCCCCCC-CCHHHCC-----------CCCCEEECCCCCCCCCCCEEEECCHHHHH T ss_conf 55555568523999997999389722899999-7442157-----------64561141246888888589841668888 Q ss_pred HHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC Q ss_conf 88999997211322133445432024332332110013434443322123444555553000012221011256677500 Q gi|254780610|r 167 KLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS 246 (340) Q Consensus 167 ~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s 246 (340) .+..++. .+.|+|+|+|.|.+..+.+.+..+.... .+.+.+... ....+.+ T Consensus 72 ~~~~~~~------~i~K~Y~a~v~G~~~~~~~~~~~~~~~~------------------~~~~~~~~~-----~~~~~~~ 122 (237) T 2gml_A 72 KILRAGN------DHEKEYLVTVDKPITEEFIRGXSAGVPI------------------LGTVTKKCK-----VKKEAPF 122 (237) T ss_dssp HHHHHHH------HSCEEEEEEESSCCCHHHHHHHSSCCEE------------------TTEECCCCE-----EEEEETT T ss_pred HHHHHCC------CCCEEEEEEECCCCCHHHHHHHHCCCEE------------------CCEEEECHH-----HCCCCCE T ss_conf 8765313------5514887785267999999999759887------------------775742000-----0356654 Q ss_pred EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCC--------HHHHHHCCCCCHHHHHCEEEEECCCCCC Q ss_conf 12344311589999999987097860415447755444334570--------1355440798044321000424688976 Q gi|254780610|r 247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNN--------NAKSAILSLARQALHAHSLSFSHPRNNQ 318 (340) Q Consensus 247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~--------~~~~~~~~~~r~~LHA~~l~f~hP~t~~ 318 (340) ++++.|.|||+||||+||+++||||+||.+||...........+ ..........+++|||++|.|.||.|++ T Consensus 123 ~v~~~~~tGR~HQIR~h~~~~G~pI~gD~~y~~~~~~~~~l~~g~~~~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~t~e 202 (237) T 2gml_A 123 VFRITLVQGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAG 202 (237) T ss_dssp EEEEEECCCSTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHTTSTTCC--------------- T ss_pred EEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEEECCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC T ss_conf 99999816886199999998699766699999888880897997838999999999998763345666886667887666 Q ss_pred EEEEECCCCHHHHHHHHHHHC Q ss_conf 899984997899999998851 Q gi|254780610|r 319 DMDFQVPIPEDMLTVIRKLNE 339 (340) Q Consensus 319 ~~~f~aplP~~~~~~l~~L~~ 339 (340) .+.|+||+|++|.++++.|.. T Consensus 203 ~~~~~~p~p~~~~~~~~~l~~ 223 (237) T 2gml_A 203 IKRPVVKXEKTAEKGGRPASN 223 (237) T ss_dssp --------------------- T ss_pred CCCCCCCCCCCCCCCCCCCCC T ss_conf 678877777777888898889 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=317.64 Aligned_cols=205 Identities=16% Similarity=0.065 Sum_probs=160.2 Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999 Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340) Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340) -||++|+|||||+||+||+++++.. |+.+.+..+ .++.+|||||++|||||||||+.+++..+..++ T Consensus 1 aEd~~~ivinKP~Gl~~~~~~~~~~-~l~~~l~~~-----------~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~- 67 (227) T 3dh3_A 1 AEDLVLIALNKPVGIVSTTEDGERD-NIVDFVNHS-----------KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAG- 67 (227) T ss_dssp GGGCCEEEEEECTTCBCCCCSSCTT-BHHHHHTCS-----------SCCEESSCCCTTCEEEEEEESCTTHHHHHHCGG- T ss_pred CCCEEEEECCCCCCEEECCCCCCCC-CCHHHCCCC-----------CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHH- T ss_conf 2311356436665212033347777-501101344-----------431224656767631489943987998887631- Q ss_pred HHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEEC Q ss_conf 72113221334454320243323321100134344433221234445555530000122210112566775001234431 Q gi|254780610|r 174 DHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLE 253 (340) Q Consensus 174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~ 253 (340) ++++|+|+|+|.|.+.++.+.+..++.... ..+.+.+.. ....++++++.+. T Consensus 68 -----~~i~K~Y~a~v~G~~~~~~~~~~~~~~~~~------------------~~~~~~~~~-----~~~~~~~~~~~~~ 119 (227) T 3dh3_A 68 -----NDHEKEYLVTVDKPITEEFIRGMSAGVPIL------------------GTVTKKCKV-----KKEAPFVFRITLV 119 (227) T ss_dssp -----GCCCEEEEEEESSCCCHHHHHHHHTCCBCS------------------SSBCCCCEE-----EECSSSEEEEEES T ss_pred -----CCCCCCCCEEECCCCCHHHHHHHHCCCEEC------------------CEEEEEEEE-----EECCCCEEEEEEC T ss_conf -----244322112760579999999997599845------------------657442577-----5226725899925 Q ss_pred HHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCC--------HHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECC Q ss_conf 1589999999987097860415447755444334570--------13554407980443210004246889768999849 Q gi|254780610|r 254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNN--------NAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP 325 (340) Q Consensus 254 TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~--------~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~ap 325 (340) |||+||||+||+++||||+||.+||.+.........+ ..........+++|||+++.|+||.+++.++|+|| T Consensus 120 tGr~hQIR~h~a~~g~pI~gd~~y~~~~~~l~~l~~g~~r~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~~~e~~~~~ap 199 (227) T 3dh3_A 120 QGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVK 199 (227) T ss_dssp CCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTCCCCSSCC------------------- T ss_pred CCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 88525999999987996766999998787748979977388999999999987632456678876678877666788777 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 97899999998851 Q gi|254780610|r 326 IPEDMLTVIRKLNE 339 (340) Q Consensus 326 lP~~~~~~l~~L~~ 339 (340) +|++|..++++|++ T Consensus 200 ~p~~~~~~~~~l~~ 213 (227) T 3dh3_A 200 MEKTAEKGGRPASN 213 (227) T ss_dssp -------------- T ss_pred CCCCCCCCCCCCCC T ss_conf 77787888998889 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=0 Score=293.86 Aligned_cols=183 Identities=23% Similarity=0.192 Sum_probs=149.6 Q ss_pred HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH Q ss_conf 22221014402789962401110456787542100222222102443344443643244443323240572120357888 Q gi|254780610|r 88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQK 167 (340) Q Consensus 88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~ 167 (340) .+++|||||++++|||||+|++|||++++...++..++. ..++++|||||++|||+||||++.+++.. T Consensus 2 ~~~~vl~ed~~~ivinKP~g~~~~~~~~~~~~~~~~~l~------------~~~l~~vhRLD~~tsGlll~a~~~~~~~~ 69 (189) T 2oml_A 2 TRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP------------VQGVYAAGRLDRDSEGLLVLTNNGALQAR 69 (189) T ss_dssp ------CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC------------CSSCEESSCCCTTCEEEEEEESCHHHHHH T ss_pred CCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCHHHHCC------------CCCCEECCCCCCCCCCEEEEECCCHHHHH T ss_conf 865778899889999899983860779988865889637------------12534731026120007999325302221 Q ss_pred HHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCEECCCCCEEECCCCCCCCC Q ss_conf 899999721132213344543202433233211001343444332212-3444555553000012221011256677500 Q gi|254780610|r 168 LSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRA-VKGIDDKTADSAITHYQTIEIYNKNSNFAVS 246 (340) Q Consensus 168 l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~-~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s 246 (340) +..+| +.+.|+|+|+|.|.+.++.+++..++.....+..+.. ........++.+.+.|.++. .....+ T Consensus 70 l~~~~------~~i~k~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~ 138 (189) T 2oml_A 70 LTQPG------KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER-----KSIPTS 138 (189) T ss_dssp HHSTT------SCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-C-----TTSCEE T ss_pred CCCCC------EEEEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEE-----EECCCC T ss_conf 03123------0377899999932799899999864945078515765799953566410245578887-----405650 Q ss_pred EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCE Q ss_conf 12344311589999999987097860415447755444334570135544079804432100 Q gi|254780610|r 247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHS 308 (340) Q Consensus 247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~ 308 (340) +++++|.|||+||||+||+++||||+||.+||.+.. .+.|+.||||+ T Consensus 139 ~~~~~l~tGr~hQIR~hl~~lg~pIvgD~~Y~~~~~---------------~~~~l~l~~~R 185 (189) T 2oml_A 139 WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDY---------------SLDNLANGEWR 185 (189) T ss_dssp EEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTE---------------ECTTCCTTCEE T ss_pred EEEEEEECCCHHHHHHHHHHCCCEEEEEEEEEECCE---------------ECCCCCCCCCE T ss_conf 799999459779999999986996989899999998---------------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=1.6e-42 Score=272.79 Aligned_cols=171 Identities=17% Similarity=0.132 Sum_probs=129.0 Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999 Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340) Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340) |||++++|||||+||+||++++.... +.+.+..+. ..++++|||||++|||||+|||+..++..+..+ T Consensus 2 Yed~~~ivvnKP~gl~~~~~~~~~~~-~~~~l~~~~---------~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~~-- 69 (176) T 1ksk_A 2 QHGPRYFXLNKPQGYVCSTDDPDHPT-VLYFLDEPV---------AWKLHAAGRLDIDTTGLVLXTDDGQWSHRITSP-- 69 (176) T ss_dssp CCCCCEEEEEECTTCBSSSSCSSSCB-GGGGCCCTT---------GGGCEESSCCCTTCEEEEEEESCHHHHHHHHCT-- T ss_pred CCCCEEEEEECCCCCCCCCCCCCCCC-CCCCCCCCC---------CCCEEEECCCCCCCCCEEEEECCHHHHHHHHHH-- T ss_conf 57857999989998505665554431-000012444---------563656013885557558860586888877554-- Q ss_pred HHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEEC Q ss_conf 72113221334454320243323321100134344433221234445555530000122210112566775001234431 Q gi|254780610|r 174 DHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLE 253 (340) Q Consensus 174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~ 253 (340) .+.+.|+|+|+|.|.+......+..... ...+..+.+.+...+ ....|++++.|. T Consensus 70 ----~~~~~k~y~~~v~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~------~~~~s~~~~~~~ 124 (176) T 1ksk_A 70 ----RHHCEKTYLVTLESPVADDTAEQFAKGV---------------QLHNEKDLTKPAVLE------VITPTQVRLTIS 124 (176) T ss_dssp ----TSCCCEEEEEEESSCCCTTHHHHHHHCC---------------CCTTCSSCCCCCEEE------EEETTEEEEEES T ss_pred ----HCCCCEEEEECCCCCCCHHHHHHHHEEE---------------EECCCEEEEEEEEEE------CCCCCEEEEEEC T ss_conf ----2388479984467888878977753025---------------638957555346840------379968999963 Q ss_pred HHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCC Q ss_conf 15899999999870978604154477554443345701355440798044321000424688 Q gi|254780610|r 254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPR 315 (340) Q Consensus 254 TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~ 315 (340) |||+||||+||+++||||+||.+||...... ..|++||||++-|.++. T Consensus 125 tGr~HQIR~h~~~~g~pI~gD~~Y~~~~~~~--------------~~~l~l~~~r~l~~~e~ 172 (176) T 1ksk_A 125 EGRYHQVKRXFAAVGNHVVELHRERIGGITL--------------DADLAPGEYRPLTEEEI 172 (176) T ss_dssp CCCTTHHHHHHHHTTCCEEEEEEEEETTEEC--------------CTTCCTTCEEECCHHHH T ss_pred CCCHHHHHHHHHHCCCEEEEEEEEEECCCCC--------------CCCCCCCCEEECCHHHH T ss_conf 5983999999998799798999999886504--------------79899975159999999 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=5.6e-42 Score=269.56 Aligned_cols=184 Identities=16% Similarity=0.184 Sum_probs=134.5 Q ss_pred CCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH Q ss_conf 01440278996240111045678754210022222210244334444364324444332324057212035788889999 Q gi|254780610|r 93 LYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQF 172 (340) Q Consensus 93 lyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f 172 (340) .|||++++|||||+|++||++++... ++.+.+..+.. .++.+|||||++||||||||||..++..+..+| T Consensus 1 ~yed~~~ivinKP~gl~~~~~~~~~~-~~~~~l~~~~~---------~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~ 70 (186) T 1vio_A 1 WIEEGQYFMLNKPQGCVCSNDDGDYP-TIYQFFDYPLA---------GKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPK 70 (186) T ss_dssp SSCCCCEEEEEECTTCBSSCCC--CC-BGGGGSCTTGG---------GGCEESSCCCTTCEEEEEEESCHHHHHHHHCTT T ss_pred CCCCCEEEEEECCCCCCCCCCCCCCE-EEEEEECCCCC---------CEEEECCCCCCCCCCEEEEECCCCCCCCCCCCC T ss_conf 22221035540258864333443201-45420024533---------136540212401221378741775320001112 Q ss_pred HHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEE Q ss_conf 97211322133445432024332332110013434443322123444555553000012221011256677500123443 Q gi|254780610|r 173 VDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHL 252 (340) Q Consensus 173 ~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~ 252 (340) ..++|+|+|+|.|.+..+...+....... .+. ........ ......++++++| T Consensus 71 ------~~~~k~y~~~v~g~~~~~~~~~~~~~~~~---------------~~~-~~~~~~~~-----~~~~~~~~~~~~~ 123 (186) T 1vio_A 71 ------HHCEKTYLVTLADPVEENYSAACAEGILL---------------RGE-KEPTKPAK-----LEILDDYNVNLTI 123 (186) T ss_dssp ------SCCCEEEEEEESSCCCTTHHHHHHHCCCC---------------TTC-SSCCCCCE-----EEECSSSEEEEEE T ss_pred ------CCCCEEEEEEEEEECCHHHHHHHHCCEEC---------------CCC-CCCEEEEE-----ECCCCCCEEEEEE T ss_conf ------45520112599851204478898536561---------------683-01023322-----0135684489885 Q ss_pred CHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCC Q ss_conf 1158999999998709786041544775544433457013554407980443210004246889 Q gi|254780610|r 253 ETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRN 316 (340) Q Consensus 253 ~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t 316 (340) .|||+||||+||+++||||+||.+||.+.......+.. .....+.++.||+..+.|.||.+ T Consensus 124 ~tGr~hQIR~h~a~lg~pIvgD~~yg~~~~~~~~~l~~---g~~r~l~~~~l~~~~l~~~~~~~ 184 (186) T 1vio_A 124 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEE---GEYRPLTQSEIEKLVEGGSHHHH 184 (186) T ss_dssp SCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCT---TCEEECCHHHHHHTC-------- T ss_pred CCCCCHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCC---CCEEECCHHHHHHHHHCCCCCCC T ss_conf 05760799999998599793889999887247999999---76259999999999957986545 No 9 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217) Probab=99.89 E-value=5.7e-24 Score=162.24 Aligned_cols=100 Identities=19% Similarity=0.173 Sum_probs=81.6 Q ss_pred HHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCC Q ss_conf 89999999859904998993286758048988999705601111023322222101440278996240111045678754 Q gi|254780610|r 39 RSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWT 118 (340) Q Consensus 39 R~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~ 118 (340) |++++++|++|.|+|||+++++++. + .+. ...|+|||++++|+|||+|++|||+.+... T Consensus 2 Rr~~~~~i~~G~V~Vng~~v~~~d~-i------~~~--------------~~~I~yed~~~ivvnKP~g~~~~~~~~~~~ 60 (119) T 2olw_A 2 RQFIISENTMQKTSFRNHQVKRFSS-Q------RST--------------RRKPENQPTRVILFNKPYDVLPQFTDEAGR 60 (119) T ss_dssp --------------------------------------------------------CCCCEEEEEECTTBCSCSSCCTTS T ss_pred CEEEECCCEEECCCCCCCCCCCCCC-C------CCC--------------CCCCCCCCCEEEEEECCCCEEEECCCCCCC T ss_conf 5367068714212255422120554-0------035--------------568878998899998999959707799888 Q ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH Q ss_conf 21002222221024433444436432444433232405721203578888999 Q gi|254780610|r 119 GTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQ 171 (340) Q Consensus 119 ~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~ 171 (340) +|+.+.+. ..++++|||||++|||+|+|||+..+++.|.++ T Consensus 61 ~tl~~~~~------------~~~l~~vhRLDr~TSGLll~ak~~~~~~~L~~~ 101 (119) T 2olw_A 61 KTLKEFIP------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP 101 (119) T ss_dssp BCGGGTCC------------CCSCEESSCCCTTCEEEEEEESCHHHHHHHHCT T ss_pred CCHHHHCC------------CCCCEECCCCCCCEEEEEEEECCCHHHHHHHHC T ss_conf 76889657------------126347531143120069984360565453110 No 10 >>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} (A:) Probab=99.88 E-value=8.8e-24 Score=161.12 Aligned_cols=124 Identities=19% Similarity=0.218 Sum_probs=98.9 Q ss_pred EECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHC-------CHHHHH Q ss_conf 9571136875789999871768898999999985990499899328675804898899970560111-------102332 Q gi|254780610|r 15 LLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKL-------NIAQEN 87 (340) Q Consensus 15 ~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~-------~~~~~~ 87 (340) +|+++++|+|||+||++.++ .+||+++++||+.|+|+|||++++ +++++..||.+.+........ ...... T Consensus 1 iv~~~~~g~RLDk~L~~~~~-~~sR~~a~~li~~G~V~VNG~~~~-~s~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~~~ 78 (133) T 1dm9_A 1 MKEKPAVEVRLDKWLWAARF-YKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQGNDERTVIVKAITEQRRPA 78 (133) T ss_dssp ----CTTCCBHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEEETTEEEEEEECEEESCCCCH T ss_pred CCCCCCCCEEHHHHHHHCCC-CCCHHHHHHHHHCCEEEECCEECC-CCCEECCCCEEEEEECCEEEEEEEEEEEECCCCC T ss_conf 99887764629999987867-168999999998691888999734-5856159998999879986589999876225673 Q ss_pred HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH Q ss_conf 2222101440278996240111045678754210022222210244334444364324444332324057212035 Q gi|254780610|r 88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDL 163 (340) Q Consensus 88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~ 163 (340) .++.++|||++.+++|||+|+.+|+.... .++++|||||+.|||.|+++++.. T Consensus 79 ~~~~~~~ed~~~~v~~kp~~~~~~~~~~~-----------------------~r~~~vgRLDk~~t~~ll~l~~dg 131 (133) T 1dm9_A 79 SEAALLYEETAESVEKREKMALARKLNAL-----------------------TMPHPDRRPDKKERRDLLRFKHGD 131 (133) T ss_dssp HHHGGGEEECHHHHHHHHHHHHHHHHHHT-----------------------C----------------------- T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHCCC-----------------------CCCCCCCCCCHHHHHHHHHHHCCC T ss_conf 03566632368871134577776652245-----------------------578899786859999999875589 No 11 >>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200) Probab=99.81 E-value=4.6e-21 Score=144.89 Aligned_cols=96 Identities=24% Similarity=0.186 Sum_probs=72.6 Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHH Q ss_conf 221334454320243323321100134344433-2212344455555300001222101125667750012344311589 Q gi|254780610|r 179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNR-LRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRT 257 (340) Q Consensus 179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~-~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRt 257 (340) ++|+|+|+|+|.|.++++.+.+........... ....+.......++.|.|.|+++.. ...+|++++.|.|||+ T Consensus 1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~-----~~~~s~~~i~l~tGr~ 75 (98) T 2olw_A 1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERK-----SIPTSWLKITLYEGRN 75 (98) T ss_dssp CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CC-----SSCEEEEEEEESCCCT T ss_pred CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEE-----CCCCEEEEEEEECCCH T ss_conf 22215899999456888999998659365785357756999535544331010477742-----1550589999915975 Q ss_pred HHHHHHHHHHCCEEECCCCCCC Q ss_conf 9999999870978604154477 Q gi|254780610|r 258 HQIRVHMAHKGNPLIGDPLYGK 279 (340) Q Consensus 258 HQIRvhla~lG~PIvGD~~YG~ 279 (340) ||||+||+++||||+||.+||. T Consensus 76 HQIR~~la~~g~pI~gd~ry~~ 97 (98) T 2olw_A 76 RQVRRMTAHVGFPTLRLIRYAM 97 (98) T ss_dssp THHHHHHHHTTCCEEEEEEEEE T ss_pred HHHHHHHHHCCCEEEEEEEEEE T ss_conf 9999999985997989899999 No 12 >>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:) Probab=99.79 E-value=7.5e-21 Score=143.63 Aligned_cols=90 Identities=20% Similarity=0.211 Sum_probs=78.5 Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCH-HCCHHHHHHHHHHCCCCCEEEE Q ss_conf 757899998717688989999999859904998993286758048988999705601-1110233222221014402789 Q gi|254780610|r 23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQ-KLNIAQENIPLDILYEDDDIIV 101 (340) Q Consensus 23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~-~~~~~~~~~~~~IlyED~~llv 101 (340) +|||+||.+.++ ..||++++++|++|+|+|||+++. ++++|..||.|.+...... .....+...++.|+|||++++| T Consensus 1 mRLD~~L~~~~~-~~sr~~~~k~i~~g~I~VNg~~~~-~~~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~i~yed~~~lv 78 (92) T 2k6p_A 1 MRIDKFLQSVGL-VKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYI 78 (92) T ss_dssp CBHHHHSTTTTS-CCCCCSSCCHHHHTCCEETTEECC-TTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSE T ss_pred CCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEEE-ECCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCHHHHCCCE T ss_conf 967899987277-159999999998997998989986-624718999999984896368999978865898645506159 Q ss_pred EECCCHHHCCCCC Q ss_conf 9624011104567 Q gi|254780610|r 102 INKPAGLVVHPAP 114 (340) Q Consensus 102 inKPaGl~vhp~~ 114 (340) +|||+||+|||+. T Consensus 79 inKpagl~~hp~~ 91 (92) T 2k6p_A 79 APKTKELEHHHHH 91 (92) T ss_dssp EECCCC------- T ss_pred EECHHCCCCCCCC T ss_conf 8063216244457 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=2.8e-10 Score=80.64 Aligned_cols=57 Identities=21% Similarity=0.260 Sum_probs=50.3 Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECC Q ss_conf 113687578999987176889899999998599049989932867580489889997056 Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPA 77 (340) Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~ 77 (340) .+++++|||+||+... .+||+.++++|++|.|+|||++++ ++++|..||.|.+..+. T Consensus 2 ~~~~~~RLDk~La~~~--~~SR~~~~~li~~G~V~Vng~~vk-~~~~v~~~d~I~v~~~~ 58 (63) T 3dh3_A 2 LPDSSVRLNKYISESG--ICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQL 58 (63) T ss_dssp --CCCEEHHHHHHTTT--SSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEE T ss_pred CCCCCCCHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEE T ss_conf 7988704999998778--851999999998793898999947-88896999989999999 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=98.92 E-value=2e-10 Score=81.47 Aligned_cols=71 Identities=17% Similarity=0.131 Sum_probs=62.1 Q ss_pred CCHHCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 511016249999571136875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 4 TLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 4 ~~~~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) +|.+--......+.....++|||+||.+... ..||++++++|..|.|+|||++++++++.|.+||.|.+.. T Consensus 2 ~m~~~~~~~~~~~~~~~~~~RLd~~L~~~~~-~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~ 72 (79) T 1p9k_A 2 SMIHRMSNMATFSLGKHPHVELCDLLKLEGW-SESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 72 (79) T ss_dssp CCCCSSCCCCEEECCSCSCCCHHHHHHHHTS-CSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETT T ss_pred CHHHCCCCCCEEECCCCCCEEHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC T ss_conf 5100014771386499971979999987788-3689999999984997989999277887989999999999 No 15 >>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58) Probab=98.86 E-value=5.5e-09 Score=72.92 Aligned_cols=53 Identities=21% Similarity=0.368 Sum_probs=48.8 Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 6875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) ..+|||+||++.. .+||++++++|+.|.|+|||++++++++.+.+||.|.+.- T Consensus 2 ~~~RLDk~L~~~~--~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~g 54 (58) T 1ksk_A 2 SHXRLDKFIAQQL--GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDG 54 (58) T ss_dssp CCEEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETT T ss_pred CCCHHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEEE T ss_conf 8400999998778--9689999999988929999999466885807867699721 No 16 >>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57) Probab=98.82 E-value=8.5e-09 Score=71.83 Aligned_cols=52 Identities=21% Similarity=0.340 Sum_probs=48.1 Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) .+|||+||++.. .+||++++++|++|.|+|||++++++++.+.+||.|.+.- T Consensus 2 ~~RLDk~L~~~~--~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~g 53 (57) T 1vio_A 2 SLRLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFED 53 (57) T ss_dssp CEEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETT T ss_pred CHHHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEEE T ss_conf 558999999877--8589999999987978999999154895868878787620 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=98.42 E-value=6.4e-07 Score=60.65 Aligned_cols=51 Identities=27% Similarity=0.401 Sum_probs=45.3 Q ss_pred CHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 5789999871768898999999985990499899328675804898899970 Q gi|254780610|r 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) |||+||.+.-. .-||.+++++|..|+|.|||++++.|++.+.+||.|.+.. T Consensus 1 RLD~~l~r~~~-~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~ 51 (94) T 2vqe_D 1 RLDNVVYRLGF-AVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAE 51 (94) T ss_dssp BHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECG T ss_pred HHHHHHHHCCC-HHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHH T ss_conf 99999985352-0028988899870684508879975367852886001211 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=98.36 E-value=2.6e-07 Score=62.94 Aligned_cols=58 Identities=21% Similarity=0.242 Sum_probs=50.1 Q ss_pred CHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCE--EECCEEECCCCCEECCCCEEEEEE Q ss_conf 71136875789999871768898999999985990--499899328675804898899970 Q gi|254780610|r 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFI--SINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 17 ~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V--~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) ++....+|||++|.+.-. .-||++++++|..|.| +|||+++.+|++.+.+||.|.+.- T Consensus 1 s~~~~~~RLD~~L~~~g~-~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~~ 60 (65) T 3hp7_A 1 SNAXPKERVDVLAYKQGL-FETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLKG 60 (65) T ss_dssp --CCCEEEHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETT T ss_pred CCCCCHHHHHHHHHHCCC-CCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEEC T ss_conf 996508899999998758-124999999998599423209989568867879999899807 No 19 >>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432) Probab=98.15 E-value=8.6e-06 Score=53.92 Aligned_cols=66 Identities=17% Similarity=0.103 Sum_probs=54.9 Q ss_pred CCEEEEEECHHHC---CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 6249999571136---875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 9 SSIKISLLSDSTA---EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 9 ~~~~~~~V~~~~~---g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) ..|..+.++.++. +.|||.+|.+.= -.-|+++++++|+.|.|+|||++++.+++.+..||.+.+.. T Consensus 3 e~~p~~~i~~~~~~~~~~rl~~~l~~~g-l~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~~ 71 (83) T 1h3f_A 3 EEIPEVTIPASELKEGRIWVARLFTLAG-LTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQR 71 (83) T ss_dssp CCSCEEEECGGGCBTTEEEHHHHHHHTT-SSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEEE T ss_pred CCCCCEEECHHHHCCCCCCHHHHHHHCC-CCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE T ss_conf 5798157438783258634999999849-86778999999985998989998248770215898089984 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=98.14 E-value=1.3e-06 Score=58.77 Aligned_cols=52 Identities=23% Similarity=0.218 Sum_probs=46.2 Q ss_pred CHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEEC Q ss_conf 57899998717688989999999859904998993286758048988999705 Q gi|254780610|r 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 (340) Q Consensus 24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340) |||.||-+.- -.-|+.+++++|..|.|+|||+++..|++.|++||.|.+... T Consensus 1 RLD~~l~r~g-fa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~ 52 (94) T 3i1m_D 1 RLDNVVYRMG-FGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREK 52 (94) T ss_dssp STTHHHHTTT-SCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSS T ss_pred HHHHHHHHCC-HHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCC T ss_conf 8888866031-254099999999850376088799763177058977886232 No 21 >>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201) Probab=98.10 E-value=1.4e-06 Score=58.55 Aligned_cols=54 Identities=20% Similarity=0.206 Sum_probs=47.1 Q ss_pred CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 6875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) -++|||.+|-+.- -.-|+.+++++|..|.|+|||++++.|++.+++||.|.+.. T Consensus 6 LE~RLD~~l~R~g-fa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~ 59 (120) T 3bbn_D 6 LEMRLDNILFRLG-MAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARD 59 (120) T ss_dssp HHSBTTTTTTTTT-SSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECS T ss_pred HHHHHHHEEEECC-CCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCC T ss_conf 9875310355057-33576888899987513615489816572546166300100 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=97.98 E-value=7.4e-06 Score=54.31 Aligned_cols=55 Identities=16% Similarity=0.068 Sum_probs=48.2 Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 36875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) --.+|||..|-+.- -.-|+.+++++|..|.|.|||++++.|++.|++||.|.+.. T Consensus 6 ~LErRLD~il~R~g-fa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~ 60 (99) T 1s1h_D 6 FLERRLQTQVYKLG-LAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDF 60 (99) T ss_dssp SGGGBHHHHHHHHT-SSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCS T ss_pred HHHHHHHHHHHHHC-CCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEE T ss_conf 88750788999815-65889999999873772589999876246840587560556 No 23 >>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Probab=97.80 E-value=1.4e-05 Score=52.59 Aligned_cols=55 Identities=13% Similarity=0.079 Sum_probs=46.3 Q ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCC--CEEEEE Q ss_conf 13687578999987176889899999998599049989932867580489--889997 Q gi|254780610|r 19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPG--DSFLIT 74 (340) Q Consensus 19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~g--d~I~i~ 74 (340) +...+|||.+|.+.-. .-|+.+++++|..|.|+|||++++.|++.|..| |.|.+. T Consensus 4 ~~lerRLd~~l~~~g~-a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~ 60 (71) T 2cqj_A 4 GSSGRRLPTVLLKLRM-AQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWV 60 (71) T ss_dssp SCCEEEHHHHHHHTTC-SSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEES T ss_pred HHHHCCHHHHHHHHCC-CCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEE T ss_conf 3444126899998055-27899999999849899899995569858358998869984 No 24 >>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A (C:31-245) Probab=96.94 E-value=0.00048 Score=43.51 Aligned_cols=84 Identities=20% Similarity=0.240 Sum_probs=53.8 Q ss_pred CCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHH Q ss_conf 44027899624011104567875421002222221024433444436432444433232405721203578888999997 Q gi|254780610|r 95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVD 174 (340) Q Consensus 95 ED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~ 174 (340) .-+.+|++|||.|+.+| .+++.+...+.. .+.+-..-||-..||+++++-+... .+.+.|. T Consensus 14 ~~~G~l~~~KP~g~tS~--------~vv~~ik~~~~~--------~kvGh~GTLDp~atGvl~i~vg~aT--kl~~~~~- 74 (215) T 2aus_C 14 IQYGVINLDKPPGPTSH--------EVVAWIKRILNL--------EKAGHGGTLDPKVSGVLPVALERAT--RVVQALL- 74 (215) T ss_dssp HHTEEEEEEECSSSCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG--GGGGGGT- T ss_pred HCCCEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCCEEEEECHHH--HHHHHHC- T ss_conf 47838999579989999--------999999987183--------4257898789865034767873899--8999974- Q ss_pred HCCCCCEEEEEEEEEECCCCCCCCCCCC Q ss_conf 2113221334454320243323321100 Q gi|254780610|r 175 HGKSTRLKRAYYAMVWGIPLPDSGIINA 202 (340) Q Consensus 175 ~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~ 202 (340) .-.|+|.|.+..-...++..++. T Consensus 75 -----~~~K~Y~~~~~~g~~t~t~d~~~ 97 (215) T 2aus_C 75 -----PAGKEYVALMHLHGDVPEDKIRA 97 (215) T ss_dssp -----TCCEEEEEEEEESSCCCHHHHHH T ss_pred -----CCCCEEEEEEEECCCCCCCHHHE T ss_conf -----58859999988723444440013 No 25 >>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=96.87 E-value=0.0007 Score=42.52 Aligned_cols=85 Identities=19% Similarity=0.171 Sum_probs=52.9 Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357888899999 Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV 173 (340) Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~ 173 (340) |--+.|+++|||+|+.+|. +++.+.+.+.. .+.+-...||-..||+|+++-+... .+...| T Consensus 13 ~~~~G~l~i~KP~g~tS~~--------vv~~~k~~~~~--------~kvgh~GtLDp~a~GvLiv~ig~~T--kl~~~~- 73 (216) T 2apo_A 13 LIKYGVVVVDKPRGPTSHE--------VSTWVKKILNL--------DKAGHGGTLDPKVTGVLPVALERAT--KTIPMW- 73 (216) T ss_dssp HHHTEEEEEEECSSSCHHH--------HHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG--GGGGGT- T ss_pred HHCCCEEEEECCCCCCHHH--------HHHHHHHHHCC--------CCCCCCCCCCCCCCCCHHHEECHHH--HHHHHH- T ss_conf 8549989997999899899--------99999998487--------7357787789634365532118653--221775- Q ss_pred HHCCCCCEEEEEEEEEECCCCCCCCCCCC Q ss_conf 72113221334454320243323321100 Q gi|254780610|r 174 DHGKSTRLKRAYYAMVWGIPLPDSGIINA 202 (340) Q Consensus 174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~ 202 (340) ..-.|+|.|.+.=-...++..++. T Consensus 74 -----~~~~K~Y~~~~~lG~~Tdt~di~~ 97 (216) T 2apo_A 74 -----HIPPKEYVCLMHLHRDASEEDILR 97 (216) T ss_dssp -----TSSCEEEEEEEEESSCCCHHHHHH T ss_pred -----CCCCCEEEEEEEEEECCCCCHHHH T ss_conf -----058827999999831243214999 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=96.76 E-value=0.0016 Score=40.44 Aligned_cols=51 Identities=20% Similarity=0.113 Sum_probs=41.3 Q ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCE Q ss_conf 1368757899998717688989999999859904998993286758048988 Q gi|254780610|r 19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDS 70 (340) Q Consensus 19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~ 70 (340) -+.+.+|..+|...-. .-|++.++++|++|.|+|||+++++++..+.++|. T Consensus 8 ~~~~~~i~~lL~~~gl-~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~ 58 (88) T 2jan_A 8 PGSPDGIVDLLVASGL-SASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF 58 (88) T ss_dssp SSSCCSHHHHHHHHTS-CSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS T ss_pred CCCCCCHHHHHHHCCC-CCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHH T ss_conf 5787779999998288-67899999999939999899981694330278782 No 27 >>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} (A:1-81) Probab=95.03 E-value=0.059 Score=31.04 Aligned_cols=70 Identities=16% Similarity=0.216 Sum_probs=52.9 Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEE Q ss_conf 87578999987176889899999998599049989932867580489889997056011110233222221014402789 Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIV 101 (340) Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llv 101 (340) +.-|--||...|.-..+.+-+++.+.+|.|.|||++.++..+.+-.-|.|++.-+ .+.++|....-++ T Consensus 7 siPL~i~LRd~Lk~A~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~~e------------~yRvl~d~kgr~~ 74 (81) T 3kbg_A 7 SVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEINGE------------SYRVVYNDQGALV 74 (81) T ss_dssp CEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEETTE------------EEEEEECTTSCEE T ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECCC------------EEEEEECCCCEEE T ss_conf 5654378644645226589999998679389899996238998870679997997------------7999985897399 Q ss_pred EE Q ss_conf 96 Q gi|254780610|r 102 IN 103 (340) Q Consensus 102 in 103 (340) +. T Consensus 75 l~ 76 (81) T 3kbg_A 75 LX 76 (81) T ss_dssp EE T ss_pred EE T ss_conf 99 No 28 >>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=94.64 E-value=0.032 Score=32.60 Aligned_cols=55 Identities=31% Similarity=0.438 Sum_probs=37.8 Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357 Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA 164 (340) Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a 164 (340) |.-+.++++|||.|+.+| .+++.+...+.. .+.+-..-||-..||+|+++-+... T Consensus 3 ~~~~Gil~idKP~G~TS~--------~vv~~iKk~l~~--------kKVGH~GTLDP~AtGvLiv~iG~aT 57 (87) T 1sgv_A 3 ATGPGIVVIDKPAGMTSH--------DVVGRCRRIFAT--------RRVGHAGTLDPMATGVLVIGIERAT 57 (87) T ss_dssp CCCSEEEEEEECTTCCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG T ss_pred CCCCEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH T ss_conf 889889999769989989--------999999998488--------8556387889736423999989676 No 29 >>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=94.41 E-value=0.039 Score=32.09 Aligned_cols=55 Identities=16% Similarity=0.356 Sum_probs=37.9 Q ss_pred CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH Q ss_conf 14402789962401110456787542100222222102443344443643244443323240572120357 Q gi|254780610|r 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA 164 (340) Q Consensus 94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a 164 (340) ++-+.|+++|||.|+.++ .+++.+...+.. .+.|-..-||-..||||+++-...+ T Consensus 22 ~~~~Gil~idKP~G~TS~--------~vV~~vkk~l~~--------kKVGH~GTLDP~AtGvLiv~iG~aT 76 (108) T 1k8w_A 22 MDINGVLLLDKPQGMSSN--------DALQKVKRIYNA--------NRAGHTGALDPLATGMLPICLGEAT 76 (108) T ss_dssp CCCCEEEEEEECTTCCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG T ss_pred CCCCEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH T ss_conf 885369998479989989--------999999998589--------9687686579746135999988888 No 30 >>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420) Probab=94.27 E-value=0.0091 Score=35.89 Aligned_cols=52 Identities=25% Similarity=0.209 Sum_probs=39.8 Q ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEE Q ss_conf 13687578999987176889899999998599049989932867580489889 Q gi|254780610|r 19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71 (340) Q Consensus 19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I 71 (340) ...+.+|...|.+.- -.-|++.++++|.+|.|+|||++++++++.+..+|.+ T Consensus 103 ~~~~~~l~~lL~~~~-l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~ 154 (174) T 1jil_A 103 SNDTTNIVEVLIETG-ISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI 154 (174) T ss_dssp ----------------------------------------------------- T ss_pred CCCCCCHHHHHHHCC-CCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCC T ss_conf 588878999999838-8467999999998499899999813844400775704 No 31 >>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=94.13 E-value=0.043 Score=31.85 Aligned_cols=52 Identities=25% Similarity=0.378 Sum_probs=36.1 Q ss_pred CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH Q ss_conf 02789962401110456787542100222222102443344443643244443323240572120357 Q gi|254780610|r 97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA 164 (340) Q Consensus 97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a 164 (340) +.++.+|||.|+.+| .++..+.+.+.. .+.+-..-||-..||+|+++-+... T Consensus 3 nGil~idKP~G~TS~--------~vV~~iKk~l~~--------kKVGH~GTLDP~AtGvLii~iG~aT 54 (92) T 1r3e_A 3 HGILVAYKPKGPTSH--------DVVDEVRKKLKT--------RKVGHGGTLDPFACGVLIIGVNQGT 54 (92) T ss_dssp CEEEEEEECSSSCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG T ss_pred CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH T ss_conf 559999669989989--------999999998688--------8787785679746446999988675 No 32 >>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419) Probab=93.09 E-value=0.02 Score=33.91 Aligned_cols=51 Identities=16% Similarity=0.109 Sum_probs=36.9 Q ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEE Q ss_conf 3687578999987176889899999998599049989932867580489889 Q gi|254780610|r 20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71 (340) Q Consensus 20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I 71 (340) ..+.++-..|...-. .-|++.++++|.+|.|+|||++++++++.+...+.+ T Consensus 104 ~~~~~l~~lL~~~gl-~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~ 154 (174) T 2ts1_A 104 GGDVPLVELLVSAGI-SPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL 154 (174) T ss_dssp ---------------------------------------------------- T ss_pred CCCCCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCC T ss_conf 799769999998598-677899999998699898999823842201775714 No 33 >>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159) Probab=92.86 E-value=0.095 Score=29.80 Aligned_cols=25 Identities=24% Similarity=0.503 Sum_probs=23.2 Q ss_pred CEEECCEEECCCCCEECCCCEEEEE Q ss_conf 9049989932867580489889997 Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLIT 74 (340) Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340) +|.|||+++.-|++.+++||.|.+. T Consensus 1 Hi~VNgkkVdIPSy~~k~gD~I~ik 25 (83) T 1c05_A 1 HILVDGSRVNIPSYRVKPGQTIAVR 25 (83) T ss_dssp CEEETTEECCCSSCBCCTTCEEEEC T ss_pred CEECCCEEEEECCEEECCCCEEEEC T ss_conf 6360436998434162178487502 No 34 >>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:) Probab=72.13 E-value=6.5 Score=18.86 Aligned_cols=51 Identities=12% Similarity=0.194 Sum_probs=33.6 Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCC--CEEECCEEECCCCCEECCCCEEEEEEC Q ss_conf 8757899998717688989999999859--904998993286758048988999705 Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNG--FISINGMVSKNPNRKVVPGDSFLITVP 76 (340) Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G--~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340) +..+... .+.|...++ .++..+... .|.|||+.+. .++.+..||+|.+..| T Consensus 25 ~~tv~~l-~~~L~~~~p--~~~~~l~~~~~~v~vn~~~v~-~~~~l~~gdeVai~PP 77 (81) T 1fm0_D 25 FPTVEAL-RQHMAAQSD--RWALALEDGKLLAAVNQTLVS-FDHPLTDGDEVAFFPP 77 (81) T ss_dssp CSBHHHH-HHHHHTTCH--HHHHHHCCTTCEEEETTEECC-TTCBCCTTCEEEEECC T ss_pred CCCHHHH-HHHHHHHCC--HHHHHHCCCCEEEECCCEECC-CCCCCCCCCEEEEECC T ss_conf 9999999-999987682--488862789589972845979-9978599999999699 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=63.12 E-value=10 Score=17.75 Aligned_cols=28 Identities=14% Similarity=0.255 Sum_probs=23.1 Q ss_pred CCCEEECCEEECCCCCEECCCCEEEEEEC Q ss_conf 59904998993286758048988999705 Q gi|254780610|r 48 NGFISINGMVSKNPNRKVVPGDSFLITVP 76 (340) Q Consensus 48 ~G~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340) .-.|.|||+.+. .++.|+.||+|.+..| T Consensus 46 ~~~v~vN~~~v~-~~~~l~dgDeVai~PP 73 (77) T 2q5w_D 46 KFQVAVNEEFVQ-KSDFIQPNDTVALIPP 73 (77) T ss_dssp CCEEEETTEEEC-TTSEECTTCEEEEECS T ss_pred HHHHHCCCEECC-CCCCCCCCCEEEEECC T ss_conf 313410880768-8867099899999799 No 36 >>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:) Probab=47.88 E-value=12 Score=17.27 Aligned_cols=26 Identities=23% Similarity=0.293 Sum_probs=21.2 Q ss_pred CEEECCEEECCCCCEECCCCEEEEEEC Q ss_conf 904998993286758048988999705 Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLITVP 76 (340) Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~~~ 76 (340) .|.|||+.+. .++.|..||+|.+..| T Consensus 69 ~v~vN~~~v~-~~~~l~dgdeV~i~PP 94 (98) T 1vjk_A 69 NIAVNGRYVS-WDEELKDGDVVGVFPP 94 (98) T ss_dssp EEEETTBCCC-TTCBCCTTCEEEEESC T ss_pred EEEECCEECC-CCCCCCCCCEEEEECC T ss_conf 9986788869-8978199999999798 No 37 >>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative; 2.10A {Haemophilus influenzae 86-028np} (A:) Probab=46.22 E-value=2.7 Score=21.11 Aligned_cols=69 Identities=14% Similarity=0.106 Sum_probs=41.5 Q ss_pred CCHHCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHH--------------HHCCCEEECCEEECCCCCEECCCC Q ss_conf 511016249999571136875789999871768898999999--------------985990499899328675804898 Q gi|254780610|r 4 TLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKIL--------------ILNGFISINGMVSKNPNRKVVPGD 69 (340) Q Consensus 4 ~~~~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kl--------------i~~G~V~vnG~~~~~~~~~l~~gd 69 (340) .|++.+.|++.++.+.-..+.+- .-.++.+.+ +.++ +....+-|=|+.+ ..++.|+.|| T Consensus 6 ~m~~~~~i~VeV~YA~p~~q~~~---~l~v~~GtT---v~~Ai~~SGil~~fPeidl~~~~vGIfgk~v-~~d~~L~~GD 78 (97) T 2hj1_A 6 HHHSLNQINIEIAYAFPERYYLK---SFQVDEGIT---VQTAITQSGILSQFPEIDLSTNKIGIFSRPI-KLTDVLKEGD 78 (97) T ss_dssp -----CEEEEEEEEEETTEEEEE---EEEEETTCB---HHHHHHHHTHHHHCTTCCTTTSEEEEEECSC-CTTCBCCTTC T ss_pred CCCCCCEEEEEEEEECCCEEEEE---EEECCCCCC---HHHHHHHCCCHHHCCCCCCCCCCEEEECCCC-CCCCCCCCCC T ss_conf 53411536999999879957999---998799893---9999987593545966470106155689385-8877178999 Q ss_pred EEEEEECCCH Q ss_conf 8999705601 Q gi|254780610|r 70 SFLITVPAAQ 79 (340) Q Consensus 70 ~I~i~~~~~~ 79 (340) +|.++.|-.- T Consensus 79 RVEIYRPL~~ 88 (97) T 2hj1_A 79 RIEIYRPLLA 88 (97) T ss_dssp EEEECCCCC- T ss_pred EEEEECCCCC T ss_conf 9999456555 No 38 >>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84) Probab=44.05 E-value=21 Score=15.87 Aligned_cols=60 Identities=13% Similarity=0.148 Sum_probs=35.0 Q ss_pred EEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCC------CEEECCEEEC---CCCCEECCCCEEEEEEC Q ss_conf 499995711368757899998717688989999999859------9049989932---86758048988999705 Q gi|254780610|r 11 IKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNG------FISINGMVSK---NPNRKVVPGDSFLITVP 76 (340) Q Consensus 11 ~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G------~V~vnG~~~~---~~~~~l~~gd~I~i~~~ 76 (340) .....|+....+.=|+ .|.++++ .+ .+.++..| .|.|||+.++ ..++.|..||+|.+..| T Consensus 15 ~~~~~v~~~Tv~~ll~-~L~~~~p-~~----~~~l~~~g~~~~~v~i~vNg~~i~~~~~~~t~l~dgDeVai~PP 83 (84) T 1v8c_A 15 KSQLELPGATVGEVLE-NLVRAYP-AL----KEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPP 83 (84) T ss_dssp CSEEECCCSBHHHHHH-HHHHHCG-GG----HHHHEETTEECTTCEEEETTEEGGGTTGGGCBCCTTCEEEEECS T ss_pred CEEEEECCCCHHHHHH-HHHHHCC-CC----HHHCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCEEEEECC T ss_conf 9079957899999999-9985786-30----22003443510138999878774145788868699999999699 No 39 >>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=41.78 E-value=23 Score=15.66 Aligned_cols=23 Identities=13% Similarity=0.118 Sum_probs=10.4 Q ss_pred CEEECCEEECCCCCEECCCCEEEE Q ss_conf 904998993286758048988999 Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLI 73 (340) Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i 73 (340) .++|||+++. ..+.|..||.|.+ T Consensus 60 g~~vng~~v~-~~~~L~~Gd~i~i 82 (99) T 2ff4_A 60 GVHVQHERIR-SAVTLNDGDHIRI 82 (99) T ss_dssp CCEETTEECS-SEEEECTTCEEEE T ss_pred CEEECCEECC-CCEECCCCCEEEE T ss_conf 8579999987-8567899999999 No 40 >>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=39.17 E-value=25 Score=15.42 Aligned_cols=46 Identities=11% Similarity=0.131 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHH Q ss_conf 9999999987097860415447755444334570135544079804432100042468897689998499789 Q gi|254780610|r 257 THQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED 329 (340) Q Consensus 257 tHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~ 329 (340) --+++.+|...|.+|.+-.-.|. .++|-|..| +|-.+++.++-|.. T Consensus 19 l~~~~~~L~~~gv~~~~~~~~g~--------------------------~~siyf~DP-dG~~iEl~~~~p~~ 64 (69) T 2rk0_A 19 LDVLEERLAKAGAAFTPTQELPF--------------------------GWILAFRDA-DNIALEAXLGREGH 64 (69) T ss_dssp HHHHHHHHHHHTCCBCCCEEETT--------------------------EEEEEEECT-TCCEEEEEEECTTS T ss_pred HHHHHHHHHHCCCEECCCCCCCC--------------------------EEEEEEECC-CCCEEEEEECCCCC T ss_conf 99999999978986478661798--------------------------499999999-99989999999855 No 41 >>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:) Probab=38.54 E-value=12 Score=17.23 Aligned_cols=62 Identities=16% Similarity=0.271 Sum_probs=36.6 Q ss_pred CCCHHCCCEEEEEEC-------HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 651101624999957-------1136875789999871768898999999985990499899328675804898899970 Q gi|254780610|r 3 QTLDNCSSIKISLLS-------DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 3 ~~~~~~~~~~~~~V~-------~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) +.+.....|++.+.- +-..+..+..+| ..| +++.. .=.|.+||+.+. .++.|+.||.|.+.. T Consensus 4 ~~~~~~~mm~i~v~~~~~~~~~~~~~~~Tv~~ll-~~L--~l~~~-------~v~v~vNg~~v~-~~~~L~dgD~v~i~~ 72 (77) T 1rws_A 4 HHHHGSKMIKVKVIGRNIEKEIEWREGMKVRDIL-RAV--GFNTE-------SAIAKVNGKVVL-EDDEVKDGDFVEVIP 72 (77) T ss_dssp ------CCCCCBSTTCCCCCCCCCCSSCCHHHHH-HTT--TCSSC-------SSCEEETTEEEC-SSSCCCSSCCCBCSC T ss_pred CCCCCCEEEEEEEECCCCEEEEECCCCCCHHHHH-HHH--CCCCH-------HHHEEECCEECC-CCCCCCCCCEEEEEE T ss_conf 5667875999999625606899879969999999-980--99830-------101559999969-972869999999990 No 42 >>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:) Probab=37.62 E-value=26 Score=15.27 Aligned_cols=48 Identities=17% Similarity=0.160 Sum_probs=29.1 Q ss_pred HHHHHHCCCCCCHHHHHHHHHCC------CEEECCEEEC---CCCCEECCCCEEEEEEC Q ss_conf 99998717688989999999859------9049989932---86758048988999705 Q gi|254780610|r 27 RWLATSLKEQFSRSYVKILILNG------FISINGMVSK---NPNRKVVPGDSFLITVP 76 (340) Q Consensus 27 ~~L~~~l~~~~sR~~i~kli~~G------~V~vnG~~~~---~~~~~l~~gd~I~i~~~ 76 (340) ..|..+++ .. +..+.-.-..| .|.|||+-++ ..++.|+.||+|.+..+ T Consensus 39 ~~l~~~~p-~~-~~~~~~~~~~~~~~~~~~v~vNg~~i~~~~~~~t~L~~gDeV~i~pp 95 (99) T 2qjl_A 39 DHIVSTMI-NN-PNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTST 95 (99) T ss_dssp HHHHHHTC-SS-GGGHHHHEETTEECTTEEEEETTEEGGGGTGGGCBCCTTCEEEEEEC T ss_pred HHHHHHCC-CC-HHHHHHHCCCCCEEEEEEEEECCCEEECCCCCCCCCCCCCEEEEECC T ss_conf 99998745-53-03433112345423228999879587817887758599799999678 No 43 >>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=36.09 E-value=14 Score=16.81 Aligned_cols=41 Identities=32% Similarity=0.513 Sum_probs=22.7 Q ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE Q ss_conf 113687578999987176889899999998599049989932867580489889997 Q gi|254780610|r 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT 74 (340) Q Consensus 18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~ 74 (340) .-+.|.|+.+|...- .+ -+|.|.+||.- .+.+++||.|.+. T Consensus 24 Nv~NG~Rf~TY~I~G-----~~-------GSg~I~lNGAA----Arl~~~GD~vII~ 64 (96) T 1vc3_B 24 DITNGARLTTYALPG-----ER-------GSGVIGINGAA----AHLVKPGDLVILV 64 (96) T ss_dssp ETTTCCEEEEECEEE-----CT-------TTTCEEEEGGG----GGTCCTTCEEEEE T ss_pred ECCCCCEEEEEEEEC-----CC-------CCCEEEECCHH----HEECCCCCEEEEE T ss_conf 998994898799963-----67-------66879855856----4235999999999 No 44 >>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:22-76) Probab=34.55 E-value=29 Score=14.97 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=19.4 Q ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHCC Q ss_conf 8757899998717688989999999859 Q gi|254780610|r 22 EGRIDRWLATSLKEQFSRSYVKILILNG 49 (340) Q Consensus 22 g~RLD~~L~~~l~~~~sR~~i~kli~~G 49 (340) ++|||..+-+. .-.-|+.+++++|..| T Consensus 29 E~RLD~vvyR~-gfa~S~~~ARQlV~HG 55 (55) T 1c05_A 29 ESRLDNLVYRL-GLARTRRQARQLVTHG 55 (55) T ss_dssp HHBHHHHHHHT-TSCSSHHHHHHHHHTT T ss_pred HHHHHHHHCCC-CCCCCHHHHHHHHHHC T ss_conf 98754541157-7437888899888735 No 45 >>3gqs_A Adenylate cyclase-like protein; FHA domain, structural genomics, PSI-2, protein structure initiative; 2.20A {Chlamydia trachomatis D} (A:) Probab=32.78 E-value=31 Score=14.80 Aligned_cols=10 Identities=10% Similarity=0.282 Sum_probs=3.6 Q ss_pred CCCEEEEECC Q ss_conf 3240572120 Q gi|254780610|r 152 TTGVMVVAKN 161 (340) Q Consensus 152 TSGlll~Ak~ 161 (340) +++...+++. T Consensus 23 ~~~~~~IGR~ 32 (106) T 3gqs_A 23 SGKTYIVGSD 32 (106) T ss_dssp TTCEEEEESC T ss_pred CCCEEEEEEC T ss_conf 9983998188 No 46 >>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=32.58 E-value=32 Score=14.78 Aligned_cols=26 Identities=23% Similarity=0.202 Sum_probs=20.6 Q ss_pred EEECCEEECC---CCCEECCCCEEEEEEC Q ss_conf 0499899328---6758048988999705 Q gi|254780610|r 51 ISINGMVSKN---PNRKVVPGDSFLITVP 76 (340) Q Consensus 51 V~vnG~~~~~---~~~~l~~gd~I~i~~~ 76 (340) |.|||+.+.. .++.|..||+|.+..| T Consensus 61 v~vNg~~v~~~~~~~t~l~~gDeV~ilPp 89 (93) T 3dwg_C 61 IYVNDEDVRFSGGLATAIADGDSVTILPA 89 (93) T ss_dssp EEETTEEGGGTTGGGCBCCTTCEEEEEEC T ss_pred EEECCEEECCCCCCCCCCCCCCEEEEECC T ss_conf 99857451001476663799899999688 No 47 >>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:) Probab=30.92 E-value=25 Score=15.37 Aligned_cols=27 Identities=11% Similarity=0.135 Sum_probs=20.3 Q ss_pred EEECCEEEC---CCCCEECCCCEEEEEECC Q ss_conf 049989932---867580489889997056 Q gi|254780610|r 51 ISINGMVSK---NPNRKVVPGDSFLITVPA 77 (340) Q Consensus 51 V~vnG~~~~---~~~~~l~~gd~I~i~~~~ 77 (340) |.|||+.+. ..++.|+.||.|.+..|- T Consensus 70 v~VN~~~v~~~~~~~t~L~~gDeV~ilppv 99 (110) T 2k9x_A 70 VLVNSCDAEVVGGMDYVLNDGDTVEFISTL 99 (110) T ss_dssp EEESSSBHHHHTSSCCCCCSSCEEEEEECC T ss_pred EEECCCEEECCCCCCCCCCCCCEEEEECCC T ss_conf 998895624388856485997999997888 No 48 >>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:) Probab=30.72 E-value=34 Score=14.59 Aligned_cols=27 Identities=19% Similarity=0.196 Sum_probs=19.5 Q ss_pred CEEECCEEEC---CCCCEECCCCEEEEEEC Q ss_conf 9049989932---86758048988999705 Q gi|254780610|r 50 FISINGMVSK---NPNRKVVPGDSFLITVP 76 (340) Q Consensus 50 ~V~vnG~~~~---~~~~~l~~gd~I~i~~~ 76 (340) .|.|||+.+. ..++.|+.||.|.+..+ T Consensus 75 ~v~vN~~~v~~~~~~~t~l~~gDeV~i~Pp 104 (114) T 1wgk_A 75 LVLINDADWELLGELDYQLQDQDSILFIST 104 (114) T ss_dssp EEEESSSBHHHHCTTTCBCCSSEEEEEEEC T ss_pred EEEECCCEEEECCCCCCCCCCCCEEEEECC T ss_conf 999758424605686637699799999788 No 49 >>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:) Probab=30.07 E-value=29 Score=14.97 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=20.9 Q ss_pred CEEECCEEECC---CCCEECCCCEEEEEEC Q ss_conf 90499899328---6758048988999705 Q gi|254780610|r 50 FISINGMVSKN---PNRKVVPGDSFLITVP 76 (340) Q Consensus 50 ~V~vnG~~~~~---~~~~l~~gd~I~i~~~ 76 (340) .|.|||+.++. .++.|+.||+|.+..+ T Consensus 57 ~v~vNg~~v~~~~~~~t~l~~gD~V~ilPp 86 (90) T 2g1e_A 57 IILVNGNNITSMKGLDTEIKDDDKIDLFPP 86 (90) T ss_dssp EEEESSSBGGGTCSSSCBCCTTCEEEEECC T ss_pred EEEEECCCCCCCCCCCCCCCCCCEEEEECC T ss_conf 457703000234465653799999999688 No 50 >>2c45_A Aspartate 1-decarboxylase precursor; double-PSI beta barrel, lyase, zymogen, pantothenate biosynthesis, pyruvate; 2.99A {Mycobacterium tuberculosis} (A:) Probab=29.63 E-value=25 Score=15.37 Aligned_cols=22 Identities=41% Similarity=0.726 Sum_probs=9.6 Q ss_pred CCCEEECCEEECCCCCEECCCCEEEE Q ss_conf 59904998993286758048988999 Q gi|254780610|r 48 NGFISINGMVSKNPNRKVVPGDSFLI 73 (340) Q Consensus 48 ~G~V~vnG~~~~~~~~~l~~gd~I~i 73 (340) +|.|.+||.- .+.+++||.|.+ T Consensus 66 Sg~I~lNGAA----Ar~~~~GD~vII 87 (139) T 2c45_A 66 SGVIGINGAA----AHLVHPGDLVIL 87 (139) T ss_dssp TTCEEEESST----TTTSCTTCEEEE T ss_pred CCEEEECCHH----HEECCCCCEEEE T ss_conf 7448754834----403488999999 No 51 >>2wyh_A Alpha-mannosidase; hydrolase, glycosidase, glycoside hydrolase; 1.90A {Streptococcus pyogenes} PDB: 2wyi_A* (A:41-112) Probab=28.94 E-value=37 Score=14.41 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=21.0 Q ss_pred CCC--HHHHHHHHCCCCCCHHHHHHHHHCCCEEE Q ss_conf 875--78999987176889899999998599049 Q gi|254780610|r 22 EGR--IDRWLATSLKEQFSRSYVKILILNGFISI 53 (340) Q Consensus 22 g~R--LD~~L~~~l~~~~sR~~i~kli~~G~V~v 53 (340) ||. ||.||.-+ |. -+.+++++|++|++.| T Consensus 35 GQt~ileDYL~~~-Pe--~~eri~klv~~grL~i 65 (72) T 2wyh_A 35 GQTIILDDYLKVR-PE--REPEIRQAIASGKLRI 65 (72) T ss_dssp TBTHHHHHHHHHC-GG--GHHHHHHHHHTTSEEC T ss_pred CHHHHHHHHHHCC-HH--HHHHHHHHHHCCCEEE T ss_conf 1899999998659-99--9999999998698848 No 52 >>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238) Probab=28.92 E-value=37 Score=14.41 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=15.8 Q ss_pred CCCEEECCEEECCCCCEECCCCEEEE Q ss_conf 59904998993286758048988999 Q gi|254780610|r 48 NGFISINGMVSKNPNRKVVPGDSFLI 73 (340) Q Consensus 48 ~G~V~vnG~~~~~~~~~l~~gd~I~i 73 (340) +|-+.+||+++....+.|+.||+|.+ T Consensus 54 ngt~~~n~~~~~~~~~~L~~Gd~i~i 79 (158) T 1wv3_A 54 NTDVYINYELQEQLTNKAYIGDHIYV 79 (158) T ss_dssp TCCEEETTEECCSSEEEEETTCEEEE T ss_pred CCCEEECCEEEECCEEECCCCCEEEE T ss_conf 98699878997255043048999999 No 53 >>1pqh_A Aspartate 1-decarboxylase; pyruvoyl dependent decarboxylase, protein SELF-processing, lyase; 1.29A {Escherichia coli} (A:) Probab=27.40 E-value=21 Score=15.82 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=10.8 Q ss_pred CCCCCEEEEEECCCH Q ss_conf 014402789962401 Q gi|254780610|r 93 LYEDDDIIVINKPAG 107 (340) Q Consensus 93 lyED~~llvinKPaG 107 (340) |.+-+.+.|+|.-.| T Consensus 55 i~~~E~V~V~Nv~NG 69 (143) T 1pqh_A 55 ILENEAIDIWNVTNG 69 (143) T ss_dssp CCTTCEEEEEETTTC T ss_pred CCCCCEEEEEECCCC T ss_conf 988988999999999 No 54 >>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=25.95 E-value=41 Score=14.08 Aligned_cols=49 Identities=10% Similarity=0.209 Sum_probs=35.8 Q ss_pred HHHHHHHHHHCCEEECCC--CCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHHH Q ss_conf 999999987097860415--4477554443345701355440798044321000424688976899984997899 Q gi|254780610|r 258 HQIRVHMAHKGNPLIGDP--LYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDM 330 (340) Q Consensus 258 HQIRvhla~lG~PIvGD~--~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~~ 330 (340) .+...||++.|.+|++.. .+|.... ..++-|..| .|-.++|.++.|..- T Consensus 21 d~~~~~L~~~Gv~i~~~p~~~~~~~~~-----------------------~~siYf~DP-dG~~iEl~~~~~~~~ 71 (75) T 3huh_A 21 NDVVSEILQAGISIVEGPVERTGATGE-----------------------IMSIYIRDP-DGNLIEISQYVEGHH 71 (75) T ss_dssp HHHHHHHHHTTCCCSEEEEEEEETTEE-----------------------EEEEEEECT-TCCEEEEEEC----- T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCC-----------------------EEEEEEECC-CCCEEEEEEECCCCC T ss_conf 899999987186522387332268886-----------------------899999999-999899988889876 No 55 >>1wxq_A GTP-binding protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.60A {Pyrococcus horikoshii OT3} (A:317-397) Probab=25.87 E-value=19 Score=16.13 Aligned_cols=25 Identities=8% Similarity=-0.078 Sum_probs=15.4 Q ss_pred CEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 90499899328675804898899970 Q gi|254780610|r 50 FISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 50 ~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) .+++||+++ ..++.|..||.|.+.. T Consensus 54 ~~~~~g~~v-~~d~~L~dgDvV~Iit 78 (81) T 1wxq_A 54 INARTKRRV-GEDYELQFNDIVKIVS 78 (81) T ss_dssp EETTTCSBC-CTTCCCCTTEEEEEEE T ss_pred EECCCCEEE-CCCCEECCCCEEEEEE T ss_conf 866776285-6984856898899995 No 56 >>2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A (A:) Probab=23.02 E-value=47 Score=13.75 Aligned_cols=35 Identities=26% Similarity=0.337 Sum_probs=27.3 Q ss_pred HHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE Q ss_conf 99999985990499899328675804898899970 Q gi|254780610|r 41 YVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 (340) Q Consensus 41 ~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~ 75 (340) ..-.+|++|.=+|-++.....-..++.||.|.+.- T Consensus 10 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~n 44 (109) T 2z0t_A 10 EYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEG 44 (109) T ss_dssp HHHHHHHTTSCCEEEEECCTTGGGCCTTCEEEEGG T ss_pred HHHHHHHCCCCEEEEECCHHHHHHCCCCCEEEEEC T ss_conf 05799876998899982776786289999999947 No 57 >>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=22.41 E-value=20 Score=15.94 Aligned_cols=23 Identities=22% Similarity=0.079 Sum_probs=15.9 Q ss_pred CCHHHHHHHHHCCCEEECCEEEC Q ss_conf 89899999998599049989932 Q gi|254780610|r 37 FSRSYVKILILNGFISINGMVSK 59 (340) Q Consensus 37 ~sR~~i~kli~~G~V~vnG~~~~ 59 (340) +||+|+-+|++.|...-||++++ T Consensus 54 ISR~QlWQWi~hg~~l~dG~~vt 76 (134) T 3cuz_A 54 ISRTSIWQWIHHQKTLSNGKPVT 76 (134) T ss_dssp HHHHHHHHHHHTTCBCTTSCBCC T ss_pred HHHHHHHHHHHCCCCCCCCCCCC T ss_conf 99999999997677778884726 No 58 >>2pbt_A AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A* (A:) Probab=20.95 E-value=35 Score=14.49 Aligned_cols=42 Identities=12% Similarity=0.292 Sum_probs=32.9 Q ss_pred HHCCCCCEEEEEECCCHHHCCCCCCCCC-CCCHHHHHHHHCCC Q ss_conf 2101440278996240111045678754-21002222221024 Q gi|254780610|r 91 DILYEDDDIIVINKPAGLVVHPAPGNWT-GTLVNALLYHCHNN 132 (340) Q Consensus 91 ~IlyED~~llvinKPaGl~vhp~~~~~~-~tl~~~l~~~~~~~ 132 (340) -|++.|+.+|++....|.-..|++.... .|..+++.+.+.++ T Consensus 9 ~vv~~~~~vLl~~r~~g~w~~PgG~ie~gE~~~~aa~REl~EE 51 (134) T 2pbt_A 9 GVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEE 51 (134) T ss_dssp EEEEETTEEEEEECTTSCEECCEEECCTTCCHHHHHHHHHHHH T ss_pred EEEEECCEEEEEEECCCCEECCEEEECCCCCHHHHHHHHHHHE T ss_conf 9999899999999579988998715479989999975532120 No 59 >>3cux_A Malate synthase; TIM barrel, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.70A {Bacillus anthracis} (A:395-528) Probab=20.54 E-value=29 Score=15.05 Aligned_cols=23 Identities=22% Similarity=0.049 Sum_probs=13.5 Q ss_pred CCHHHHHHHHHCCCEEE-CCEEEC Q ss_conf 89899999998599049-989932 Q gi|254780610|r 37 FSRSYVKILILNGFISI-NGMVSK 59 (340) Q Consensus 37 ~sR~~i~kli~~G~V~v-nG~~~~ 59 (340) +||+|+-+||+.|.++. ||++++ T Consensus 54 ISR~QiWQWi~hg~~~~ddG~~vt 77 (134) T 3cux_A 54 ISRAQVWQWIRHEGGKLNDGRNIT 77 (134) T ss_dssp HHHHHHHHHHHCTTCBCTTSCBCC T ss_pred HHHHHHHHHHHCCCEECCCCCCCC T ss_conf 999999999972681446764427 Done!