Query gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62] Match_columns 354 No_of_seqs 197 out of 4149 Neff 8.4 Searched_HMMs 23785 Date Mon May 30 10:29:49 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780406.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3dh3_A Ribosomal large subunit 100.0 0 0 459.8 20.5 231 11-248 4-236 (290) 2 1ksk_A Ribosomal small subunit 100.0 0 0 418.5 18.9 232 12-245 2-234 (234) 3 1vio_A Ribosomal small subunit 100.0 0 0 373.5 20.2 232 13-247 2-235 (243) 4 2gml_A Ribosomal large subunit 100.0 0 0 353.0 11.5 174 70-249 11-184 (237) 5 2olw_A Ribosomal large subunit 100.0 1.5E-44 0 298.9 14.0 186 50-238 17-217 (217) 6 2oml_A Ribosomal large subunit 100.0 4.7E-42 0 283.3 14.1 167 70-238 8-189 (189) 7 1v9f_A Ribosomal large subunit 100.0 2.1E-33 8.7E-38 228.9 3.2 215 6-222 9-254 (325) 8 1v9k_A Ribosomal large subunit 99.7 5.8E-19 2.4E-23 137.9 3.6 146 68-214 4-166 (228) 9 2i82_A Ribosomal large subunit 99.7 4.5E-18 1.9E-22 132.3 4.4 145 69-213 15-174 (217) 10 1p9k_A ORF, hypothetical prote 99.4 1.9E-14 8.1E-19 109.4 0.3 58 12-69 19-77 (79) 11 2k6p_A Uncharacterized protein 98.8 1.8E-10 7.7E-15 84.3 -1.3 75 14-89 1-90 (92) 12 1dm9_A Hypothetical 15.5 KD pr 98.8 1.2E-08 5.2E-13 72.8 6.8 54 9-63 4-58 (133) 13 2vqe_D 30S ribosomal protein S 98.4 8E-07 3.3E-11 61.4 6.6 53 14-66 99-152 (209) 14 3hp7_A Hemolysin, putative; st 98.4 1.6E-07 6.7E-12 65.8 3.0 56 12-67 5-63 (291) 15 2aus_C Pseudouridine synthase; 98.3 6.9E-06 2.9E-10 55.5 9.7 146 72-227 45-212 (334) 16 1c05_A Ribosomal protein S4 de 98.3 1.8E-06 7.6E-11 59.2 6.7 52 14-65 51-103 (159) 17 3ofo_D 30S ribosomal protein S 98.1 2.1E-06 9E-11 58.7 4.0 53 14-66 95-148 (205) 18 3bbn_D Ribosomal protein S4; s 98.1 1.4E-06 5.7E-11 60.0 2.7 53 14-66 89-142 (201) 19 1r3e_A TRNA pseudouridine synt 98.1 5.3E-05 2.2E-09 50.0 10.6 161 73-246 3-220 (309) 20 2apo_A Probable tRNA pseudouri 98.0 3.2E-05 1.4E-09 51.3 9.4 145 73-227 66-232 (357) 21 1k8w_A TRNA pseudouridine synt 98.0 2.1E-05 8.7E-10 52.5 8.3 153 62-227 17-225 (327) 22 2cqj_A BRMS2, U3 small nucleol 97.9 7.9E-06 3.3E-10 55.2 3.5 55 10-64 4-61 (71) 23 1sgv_A TRNA pseudouridine synt 97.8 0.00024 1E-08 45.8 10.6 146 72-227 5-211 (316) 24 3jyv_D 40S ribosomal protein S 97.5 2.3E-05 9.6E-10 52.2 2.0 49 14-62 102-151 (158) 25 1s1h_D 40S ribosomal protein S 97.4 7.8E-05 3.3E-09 48.9 3.4 53 10-62 85-138 (179) 26 1h3f_A Tyrosyl-tRNA synthetase 97.1 0.0015 6.5E-08 40.7 7.5 13 26-38 23-35 (432) 27 2jan_A Tyrosyl-tRNA synthetase 96.9 0.00068 2.9E-08 43.0 4.0 47 13-59 355-402 (432) 28 1jil_A Tyrrs, tyrosyl-tRNA syn 96.4 0.00045 1.9E-08 44.1 0.0 13 123-135 120-132 (420) 29 2ts1_A Tyrosyl-tRNA synthetase 96.3 0.00048 2E-08 43.9 0.0 12 123-134 119-130 (419) 30 3kbg_A 30S ribosomal protein S 95.9 0.024 9.9E-07 33.3 6.9 53 12-64 6-60 (213) 31 2exu_A Transcription initiatio 87.1 0.84 3.5E-05 23.5 4.8 76 114-202 42-118 (200) 32 3hvz_A Uncharacterized protein 62.3 4.3 0.00018 19.0 2.7 23 39-62 43-65 (78) 33 2kmm_A Guanosine-3',5'-BIS(dip 58.6 5.4 0.00023 18.4 2.6 23 39-62 38-60 (73) 34 3h7h_A Transcription elongatio 58.3 8.5 0.00036 17.2 3.8 50 116-165 58-109 (120) 35 3gmg_A Uncharacterized protein 36.7 17 0.00073 15.2 2.4 31 39-69 68-102 (170) 36 2qjl_A URM1, ubiquitin-related 32.0 22 0.00093 14.6 3.0 49 14-62 35-92 (99) 37 3fm8_A Kinesin-like protein KI 30.9 23 0.00097 14.4 4.1 10 34-43 14-23 (124) 38 2k9x_A Tburm1, uncharacterized 29.9 14 0.00059 15.8 1.0 23 40-62 70-95 (110) 39 2bj7_A Nickel responsive regul 29.9 24 0.001 14.3 2.3 19 14-32 16-34 (138) 40 2kl0_A Putative thiamin biosyn 27.9 25 0.0011 14.2 2.0 40 15-62 16-58 (73) 41 1rws_A Hypothetical protein PF 27.7 14 0.00061 15.7 0.7 43 11-62 28-70 (77) 42 2g1e_A Hypothetical protein TA 26.7 25 0.0011 14.2 1.9 27 36-62 54-83 (90) 43 2q5w_D Molybdopterin convertin 25.9 28 0.0012 13.9 3.0 24 38-62 47-70 (77) 44 1vjk_A Molybdopterin convertin 25.6 25 0.001 14.2 1.6 23 39-62 69-91 (98) 45 1ryj_A Unknown; beta/alpha pro 25.6 28 0.0012 13.9 2.8 45 9-62 19-63 (70) 46 2z0t_A Putative uncharacterize 24.6 13 0.00053 16.1 -0.0 36 30-65 10-45 (109) 47 3dwg_C 9.5 kDa culture filtrat 24.4 30 0.0013 13.7 2.7 24 39-62 60-86 (93) 48 2jqj_A DNA damage response pro 23.1 32 0.0013 13.6 3.3 16 106-123 37-52 (151) 49 2v9v_A Selenocysteine-specific 22.7 32 0.0014 13.5 2.0 21 32-52 111-131 (135) 50 1xne_A Hypothetical protein PF 22.2 17 0.00071 15.3 0.3 36 30-65 11-46 (113) 51 1v8c_A MOAD related protein; r 21.6 34 0.0014 13.4 2.9 24 39-62 54-80 (168) 52 2wvf_A Hpnikr, putative nickel 21.2 35 0.0015 13.3 2.3 36 186-225 105-140 (148) 53 2hza_A Nickel-responsive regul 20.1 37 0.0015 13.2 2.9 19 14-32 14-32 (133) No 1 >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} Probab=100.00 E-value=0 Score=459.78 Aligned_cols=231 Identities=27% Similarity=0.402 Sum_probs=210.9 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCC--CEEEEECCCCCEEEECC Q ss_conf 7734478899988687789999999869869999992406878079997999998922556--43896027875156314 Q gi|254780406|r 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--RTRLWLYHKPIGLVTTH 88 (354) Q Consensus 11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~--~~~~~~~~KP~g~~~~~ 88 (354) ++++|||||||++|+||||+|++||++|+|+|||++|+ ++++|.++|.|.|||+++.+.+ ...||++|||.+++|+. T Consensus 4 ~~~iRL~K~La~~g~~SRr~ae~lI~~GrV~VNGkvv~-~~~kV~~~D~I~vdg~~~~~~~~~~~~~i~~~kp~~~~~~~ 82 (290) T 3dh3_A 4 DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTT 82 (290) T ss_dssp CCCEEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEEECCCCGGGCCEEEEEECTTCBCCC T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHCCEEEECCEECC-CCCCCCCCCEEEECCEECCCCCCCCEEEEEECCCCCEECCC T ss_conf 88725999998778842999999997796998999957-98897999989999998444356525999707987423354 Q ss_pred CCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCC Q ss_conf 43333644210110234320026655433232022236764100012344574047752112455646788874000008 Q gi|254780406|r 89 SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168 (354) Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~ 168 (354) .+.. ..+++++ .....+|++|||||+||||||||||||+|+++|+||+++|+++|+|+|.++++++.+..|..|+.++ T Consensus 83 ~~~~-~~~~~~l-~~~~~rl~~VGRLD~dTsGLLLlTnDg~l~~~L~~p~~~i~k~Y~v~v~g~i~~~~l~~l~~Gv~~~ 160 (290) T 3dh3_A 83 EDGE-RDNIVDF-VNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160 (290) T ss_dssp CSSC-TTBHHHH-HTCSSCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGCCCEEEEEEESSCCCHHHHHHHHTCCBCS T ss_pred CCCC-CCCHHHH-CCCCCCEEECCCCCCCCCCEEEEECCCHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHCCCEEE T ss_conf 5677-7754441-1355523561346888875499955958999986022267626899993679999999997387531 Q ss_pred CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHH Q ss_conf 76750343036402688079999995184289999999839868688975870545187554748867999998753210 Q gi|254780406|r 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248 (354) Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~~~~ 248 (354) ++.+.++.+.. ..++|++|+|.||+|||||+||+++||+|++|+||+||+|+|++|++|+||+|+++||.+|+... T Consensus 161 ~~~~~~~~~~~----~~~~~l~i~l~eGr~rqIRr~~~~iG~~V~~L~R~~~G~~~l~~L~~G~~r~l~~~ei~~l~~~~ 236 (290) T 3dh3_A 161 GTVTKKCKVKK----EAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLI 236 (290) T ss_dssp SSBCCCCEEEE----CSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTC T ss_pred EEEEEEEEEEE----CCCCEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHH T ss_conf 15732124552----36715899925886799999999869979798999989987389899774899999999999876 No 2 >1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Probab=100.00 E-value=0 Score=418.48 Aligned_cols=232 Identities=25% Similarity=0.403 Sum_probs=210.2 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCC Q ss_conf 73447889998868778999999986986999999240687807999799999892255643896027875156314433 Q gi|254780406|r 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91 (354) Q Consensus 12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~ 91 (354) +.||||||||++|.||||+|++||++|+|+|||++|++++++|.++|.|.|||+++..+++..||++|||+|++|+..+. T Consensus 2 ~~iRLdk~Ls~~~~~SR~~a~~lI~~G~V~VNg~~v~~~~~~V~~~d~I~v~~~~i~~~~~~~~ivlnKP~G~~~~~~~~ 81 (234) T 1ksk_A 2 SHMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDP 81 (234) T ss_dssp CCEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETTEEECCCCCCCEEEEEECTTCBSSSSCS T ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEECCCCCCCCCCCCEEEECCCEEEECCCCEEEEEECCCCCCCCCCCC T ss_conf 75229999987789689999999988959999999567885817766688503145204574799998999867666455 Q ss_pred CCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE Q ss_conf 33644210110234320026655433232022236764100012344574047752112455646788874000008767 Q gi|254780406|r 92 DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171 (354) Q Consensus 92 ~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~ 171 (354) ....++.........++++|||||++||||||||||+++++.|++|..+++++|++.|.++++.+.+..+..|+.+++.. T Consensus 82 ~~~~~~~~l~~~~~~~~~~V~RLD~dTsGLll~t~d~~~~~~l~~~~~~i~k~Y~~~v~g~~~~~~~~~l~~~v~~~~~~ 161 (234) T 1ksk_A 82 DHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEK 161 (234) T ss_dssp SSCBGGGGCCCTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSCCCTTHHHHHHHCCCCTTCS T ss_pred CCCEEEECCCCCCCCEEEECCCCCCCCCCEEEECCCHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHEEEEECCCE T ss_conf 43144301345445507650225888865487505867888775552288579960557888776754542156757955 Q ss_pred EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCCCEEECCHHHHHHHH Q ss_conf 503430364026880799999951842899999998398686889758705451-87554748867999998753 Q gi|254780406|r 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245 (354) Q Consensus 172 ~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G~~r~l~~~e~~~l~ 245 (354) .......+... .++|++|+|.|||+||||+||+++||+|.+|+|++||+++| ++|++|+||+||++||..|+ T Consensus 162 ~~~~~~~~~~~--~~~~l~i~l~tGR~hQIR~h~~~~G~pV~~L~Ri~~G~~~L~~~L~~G~~r~Lt~~Ei~~l~ 234 (234) T 1ksk_A 162 DLTKPAVLEVI--TPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV 234 (234) T ss_dssp SCCCCCEEEEE--ETTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHTTCC T ss_pred EEEEEEEEECC--CCCEEEEEEECCCHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCCCEEECCHHHHHHHC T ss_conf 45656785215--99589999824973899999998699798999999876614898999653799999999659 No 3 >1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Probab=100.00 E-value=0 Score=373.45 Aligned_cols=232 Identities=25% Similarity=0.388 Sum_probs=207.6 Q ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCC Q ss_conf 34478899988687789999999869869999992406878079997999998922556438960278751563144333 Q gi|254780406|r 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92 (354) Q Consensus 13 ~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~ 92 (354) .||||||||..+.|||++|+++|++|+|+|||++|+.++++|.++|.|.++++++...++..|+++|||+|++|+..... T Consensus 2 ~mRLdkfLs~~~~~SR~~a~~lI~~G~V~VNG~~v~~~~~~v~~~d~V~~~~~~i~~~e~~~~~vvnKP~G~~~~~~~~~ 81 (243) T 1vio_A 2 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSNDDGD 81 (243) T ss_dssp CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETTEECCSSCCCCEEEEEECTTCBSSCCC-- T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCEEEEECCCEEEEEECCCCCCCCCCCCC T ss_conf 56899999987785899999999789099999990549968488787995486577603514999977998511123322 Q ss_pred CCCCCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE Q ss_conf 36442101102-34320026655433232022236764100012344574047752112455646788874000008767 Q gi|254780406|r 93 GRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171 (354) Q Consensus 93 ~~~~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~ 171 (354) ..++++.+.. ...++++|||||++||||||||+|+.+++.++.+..+++++|.|+|.+++..+.+..+..++.+++.. T Consensus 82 -~~~v~~~~~~~~~~~~~~VhRLDr~TSGlll~ak~~~~~~~~~~~~~~~~~~y~v~v~~~~~~~~~~~l~~~v~~~g~~ 160 (243) T 1vio_A 82 -YPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEK 160 (243) T ss_dssp -CCBGGGGSCTTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEESSCCCTTHHHHHHHCCCCTTCS T ss_pred -CEEEEEECCCCCCCCEEEEEECCCCCCCCEEEECCHHHHHHHHHHCCCCEEEEEEEECCCCCHHHHHHHHCCEEECCCC T ss_conf -2048761244557856354445888787065502846633221120387289999995355166899985545607902 Q ss_pred EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CCCCCCEEECCHHHHHHHHHH Q ss_conf 5034303640268807999999518428999999983986868897587054518-755474886799999875321 Q gi|254780406|r 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247 (354) Q Consensus 172 ~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L~~G~~r~l~~~e~~~l~~~ 247 (354) .......+. ....+|++|+|.|||+||||+||+++|++|++|+|++||++.|+ +|++|+||+|++.||..|+.. T Consensus 161 ~~~~~~~~~--~~~~~~l~v~l~TGRtHQIR~hl~~lG~PIi~l~Ri~~g~~~l~~~L~~G~~r~l~~~Ei~~l~~~ 235 (243) T 1vio_A 161 EPTKPAKLE--ILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVEG 235 (243) T ss_dssp SCCCCCEEE--ECSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHHHTC-- T ss_pred CEEEEEEEE--CCCCCEEEEECCCCCCHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCCCEEECCHHHHHHHHHC T ss_conf 206888763--168836999857896459999999869969798999989744699999976369999999999857 No 4 >2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Probab=100.00 E-value=0 Score=352.97 Aligned_cols=174 Identities=24% Similarity=0.394 Sum_probs=160.6 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE Q ss_conf 56438960278751563144333364421011023432002665543323202223676410001234457404775211 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v 149 (354) -.+..||+||||+|++||..|+. +++++++++. ..++++|||||+||||||||||||+|+++|+||+++|+|+|+|+| T Consensus 11 g~D~vyillNKP~G~v~t~~d~~-r~tv~dll~~-~~rl~~VGRLD~dtsGLLLlTnDg~l~~~L~~p~~~i~K~Y~v~v 88 (237) T 2gml_A 11 GSDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH-SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTV 88 (237) T ss_dssp --CCCEEEEEECTTCBCCSSSSC-SSBHHHHSCC-SSCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHHHSCEEEEEEE T ss_pred CCCEEEEEEECCCCEEECCCCCC-CCCCHHHCCC-CCCEEECCCCCCCCCCCEEEECCHHHHHHHHCCCCCCEEEEEEEE T ss_conf 75139999989997696558999-9971653366-455314046788887748994687798986289876516998885 Q ss_pred CCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCC Q ss_conf 24556467888740000087675034303640268807999999518428999999983986868897587054518755 Q gi|254780406|r 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229 (354) Q Consensus 150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~ 229 (354) +++++++.+..|..|+.++++.+.++.+... .++|++|+|.||+|||||+||+++|++|++|+||+||+|.|++|+ T Consensus 89 ~g~i~~~~l~~l~~Gv~l~~~~~~~~~~~~~----~~~~~~i~l~eGrnrqIRrm~~~lG~~V~~L~Ri~iG~l~L~~L~ 164 (237) T 2gml_A 89 DKPITEEFIRGMSAGVPILGTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIP 164 (237) T ss_dssp SSCCCHHHHHHHSSCCEETTEECCCCEEEEE----ETTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEEEETTEECTTCC T ss_pred CCCCCHHHHHHHHCCCEECCEEEECCCCCCC----CCEEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCC T ss_conf 3689999999998298531225001001356----764999996678779999999987997858899998998868989 Q ss_pred CCCEEECCHHHHHHHHHHHH Q ss_conf 47488679999987532100 Q gi|254780406|r 230 AGSTREVSKKILREQLGPHL 249 (354) Q Consensus 230 ~G~~r~l~~~e~~~l~~~~~ 249 (354) +|+||+|+++||..|+.+.. T Consensus 165 ~G~~r~L~~~Ei~~L~~~~~ 184 (237) T 2gml_A 165 LGEWRDLTDDELIDLFKLIE 184 (237) T ss_dssp TTCEEECCHHHHHHHHTTST T ss_pred CCCEEECCHHHHHHHHHHHH T ss_conf 97738999999999998764 No 5 >2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Probab=100.00 E-value=1.5e-44 Score=298.86 Aligned_cols=186 Identities=28% Similarity=0.465 Sum_probs=165.2 Q ss_pred CCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCC Q ss_conf 68780799979999989225564389602787515631443333644210110234320026655433232022236764 Q gi|254780406|r 50 AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129 (354) Q Consensus 50 ~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~ 129 (354) ...+|...+.+.+++..... ++..||++|||+|++|+..|+.++.+++++++. .++++|||||++||||||||+|++ T Consensus 17 ~~~~v~~~~~~~~~~~~~~~-~~~~~iv~NKP~G~l~~~~d~~~~~tl~~~l~~--~~l~~VhRLDrdTSGLll~akd~~ 93 (217) T 2olw_A 17 RNHQVKRFSSQRSTRRKPEN-QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGA 93 (217) T ss_dssp ---------------------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCCC--CSCEESSCCCTTCEEEEEEESCHH T ss_pred CCCCCEECCCCCCCCCCCCC-CCCEEEEEECCCCEEECCCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCEEEEECCHH T ss_conf 55221044652135568888-999899998999848747799889768996684--583487557867788189827767 Q ss_pred CCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEE---------------CCCCEEEEEEEEE Q ss_conf 1000123445740477521124556467888740000087675034303640---------------2688079999995 Q gi|254780406|r 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------------QKGSNAWVTVGLR 194 (354) Q Consensus 130 l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~---------------~~~~~~~~~v~l~ 194 (354) ++++|+++...++|+|++.|.|.++++....+..|+.+.+....++...... .....+|++++|. T Consensus 94 ~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~i~l~ 173 (217) T 2olw_A 94 LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLY 173 (217) T ss_dssp HHHHHHCTTCCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CCSSCEEEEEEEES T ss_pred HHHHHCCCCCEEEEEEEEEEECCCCHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEECCCCEEEEEEEEE T ss_conf 87653268761568999999347999999998769823786033316999526644230113688621576068999962 Q ss_pred ECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCH Q ss_conf 18428999999983986868897587054518755474886799 Q gi|254780406|r 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238 (354) Q Consensus 195 eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~ 238 (354) |||+||||+||+++||+|.+|+|++||+|.|++|++|+||+||. T Consensus 174 tGRtHQIR~hl~~lG~pI~~L~Ri~~G~~~l~~L~~G~~r~lte 217 (217) T 2olw_A 174 EGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 217 (217) T ss_dssp CCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECC- T ss_pred CCCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCC T ss_conf 48549999999986997989899999998617889988087979 No 6 >2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Probab=100.00 E-value=4.7e-42 Score=283.29 Aligned_cols=167 Identities=31% Similarity=0.535 Sum_probs=151.6 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE Q ss_conf 56438960278751563144333364421011023432002665543323202223676410001234457404775211 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v 149 (354) .++..||++|||+|++|+..|+.++.++++++.. .++++|||||++||||||||+|++++++|+++...++|+|++.| T Consensus 8 ~~~~~~iivnKP~G~~~~~~~~~~~~~l~~~l~~--~~~~~vhRLDr~TSGLll~a~~~~~~~~l~~~~~~i~K~Y~a~v 85 (189) T 2oml_A 8 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQV 85 (189) T ss_dssp CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCCC--SSCEESSCCCTTCEEEEEEESCHHHHHHHHSTTSCCCEEEEEEE T ss_pred CCCCEEEEEECCCCCEECCCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCCEEEECCCHHHHHHCCCCCCEEEEEEEEE T ss_conf 8998899999999838317799999768896672--47537634587778808983373035554257653678999999 Q ss_pred CCCCCHHHHHHHHHHHHCCCEEEECCCEEEE---------------ECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE Q ss_conf 2455646788874000008767503430364---------------0268807999999518428999999983986868 Q gi|254780406|r 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 (354) Q Consensus 150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~---------------~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~ 214 (354) .|.++++....+.+|+...+....+...... ......+|++|+|.|||+||||+||+++||+|++ T Consensus 86 ~g~~~~~~~~~l~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~v~l~tGR~HQIR~hl~~iG~pI~~ 165 (189) T 2oml_A 86 EGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLR 165 (189) T ss_dssp ESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CTTSCEEEEEEEESCCCTTHHHHHHHHTTCCEEE T ss_pred ECCCCHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEECCCCEEEEEEECCCCHHHHHHHHHHCCCEEEE T ss_conf 53799899999864983468622320689953566522046689986236514899995158749999999986997978 Q ss_pred EEEEEECCEECCCCCCCCEEECCH Q ss_conf 897587054518755474886799 Q gi|254780406|r 215 LIRISYGPFQLGTLLAGSTREVSK 238 (354) Q Consensus 215 L~Rv~~G~~~l~~L~~G~~r~l~~ 238 (354) |+|++||+|+|++|++|+||+||. T Consensus 166 l~R~~~G~~~l~~L~~G~~R~Lte 189 (189) T 2oml_A 166 LIRYAMGDYSLDNLANGEWREVTD 189 (189) T ss_dssp EEEEEETTEECTTCCTTCEEECCC T ss_pred EEEEEECCEECCCCCCCCEEECCC T ss_conf 899999998617889988287979 No 7 >1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Probab=99.97 E-value=2.1e-33 Score=228.89 Aligned_cols=215 Identities=20% Similarity=0.188 Sum_probs=168.1 Q ss_pred CCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC-------------CCCC Q ss_conf 4466677344788999886-8778999999986986999999240687807999799999892-------------2556 Q gi|254780406|r 6 IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-------------RKAE 71 (354) Q Consensus 6 ~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i-------------~~~~ 71 (354) .++++..++||++||+... ..||+.++++|+.|.|+|||++++.++++|..+|.|.++.... ..++ T Consensus 9 tV~~~~~G~RLD~~L~~~~~~~sr~~i~k~i~~g~V~vNg~~~~k~~~~l~~gD~I~i~~~~~~~~~~~~~~~~~~ilye 88 (325) T 1v9f_A 9 TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYE 88 (325) T ss_dssp -------------------------------------------------------------------CCCCCCCCCEEEE T ss_pred EECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCCCCCCEEEE T ss_conf 98977588679999998668779999999998699899999937854165699999982676665446755688607996 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECCC------CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE Q ss_conf 438960278751563144333364421011023------43200266554332320222367641000123--4457404 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~------~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k 143 (354) +..++++|||.|+.|+........++.+.+... ...+++|+|||++|||||||+.+.+.+..|.. ....+.| T Consensus 89 d~~~ivvnKP~Gl~~~p~~~~~~~tl~~~~~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~K 168 (325) T 1v9f_A 89 DEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITR 168 (325) T ss_dssp CSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEE T ss_pred ECCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCCEEEEEECCHHHHHHHHHHHHCEEEE T ss_conf 08899998999872589999888749999998634313776521665789887426997400057899988764070205 Q ss_pred EEEEEECCCCCHHHHHHH---------HHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE Q ss_conf 775211245564678887---------40000087675034303640268807999999518428999999983986868 Q gi|254780406|r 144 VYRVRFHGQVDQDKLNLL---------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 (354) Q Consensus 144 ~Y~v~v~~~~~~~~~~~~---------~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~ 214 (354) +|++.|.|.+........ .......++......+.+.......+++++.+.+||+||||.+|+++|++| T Consensus 169 ~Y~A~v~G~~~~~~~~~~~~~~~~~~~~~~~v~~~gk~a~T~~~~~~~~~~~slv~~~~~TGRtHQIRvHla~lG~PI-- 246 (325) T 1v9f_A 169 EYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPL-- 246 (325) T ss_dssp EEEEEEESCCCCCEEEECCEEECSSCTTCEEECTTSBCCEEEEEEEEECSSEEEEEEEESCCCTTHHHHHHHHTTCCB-- T ss_pred EEEEEEECCCCCCCCEECCCCCCCCCCCEEEECCCCEEEEEEEEEEEECCCCEEEEEEECCCCCHHHHHHHHHCCCCE-- T ss_conf 899999764276650504432377776279978898035899997442388446899978888679999999859937-- Q ss_pred EEEEEECC Q ss_conf 89758705 Q gi|254780406|r 215 LIRISYGP 222 (354) Q Consensus 215 L~Rv~~G~ 222 (354) |.-..||. T Consensus 247 lGD~~YG~ 254 (325) T 1v9f_A 247 VGDPVYGG 254 (325) T ss_dssp TTCTTTTC T ss_pred ECCCCCCC T ss_conf 58613487 No 8 >1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Probab=99.74 E-value=5.8e-19 Score=137.87 Aligned_cols=146 Identities=16% Similarity=0.162 Sum_probs=105.4 Q ss_pred CCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEEC---CCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCE Q ss_conf 25564389602787515631443333644210110---2343200266554332320222367641000123--445740 Q gi|254780406|r 68 RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWL 142 (354) Q Consensus 68 ~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~---~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~ 142 (354) ..+|+..++++|||.|+.|+........++ ..+. .....+.+|+|||++|||||||+.+...+..|.. ....+. T Consensus 4 IlyED~~ilvvnKP~gl~vh~~~~~~~~~~-~~l~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~~a~~~l~~~f~~r~v~ 82 (228) T 1v9k_A 4 IMYEDDHILVLNKPSGTAVHGGSGLSFGVI-EGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQ 82 (228) T ss_dssp EEEECSSEEEEEECTTSCSSCCSSSBCCHH-HHHHHHSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSE T ss_pred EEEECCCEEEEECCCCCCCCCCCCCCCHHH-HHHHHHCCCCCCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHCCEE T ss_conf 999789999999899986489989962699-9999867788756667307987623389865688899999999738333 Q ss_pred EEEEEEECCCCCHHHHHHHH--------HH----HHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC Q ss_conf 47752112455646788874--------00----0008767503430364026880799999951842899999998398 Q gi|254780406|r 143 RVYRVRFHGQVDQDKLNLLK--------KG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210 (354) Q Consensus 143 k~Y~v~v~~~~~~~~~~~~~--------~g----~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~ 210 (354) |+|++.|.|.+......... .+ ....++......+.+.......+++++.+.+||+||||.+|+++|+ T Consensus 83 K~Y~a~v~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gk~a~T~~~~~~~~~~~slv~~~~~TGRtHQIRvHla~lG~ 162 (228) T 1v9k_A 83 KDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGH 162 (228) T ss_dssp EEEEEEEESCCCTTCCEECCCEEEEECTTSCEEEEECTTSBCCCEEEEEEEECSSEEEEEEEESSCCTTHHHHHHHHTTC T ss_pred EEEECCCCCCCCCCCCEEECCEECCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCEEEEEEECCCCHHHHHHHHHHCCC T ss_conf 68700227863223560420201133334037888579982232676542034886799999586838999999874797 Q ss_pred EEEE Q ss_conf 6868 Q gi|254780406|r 211 KVNR 214 (354) Q Consensus 211 ~V~~ 214 (354) +++. T Consensus 163 PIvG 166 (228) T 1v9k_A 163 PIAF 166 (228) T ss_dssp CBTT T ss_pred EEEC T ss_conf 4836 No 9 >2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Probab=99.71 E-value=4.5e-18 Score=132.30 Aligned_cols=145 Identities=14% Similarity=0.165 Sum_probs=101.4 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCCCCEE-ECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCC--CCCCCCCEEEE Q ss_conf 55643896027875156314433336442101-1023432002665543323202223676410001--23445740477 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~-~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l--~~p~~~~~k~Y 145 (354) .+|+..++++|||.|+.|+............. .......+.+|+|||++||||+|++.+.+.+..| +.....+.|.| T Consensus 15 lyed~~~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlvl~Ak~~~~~~~l~~~~~~~~v~K~Y 94 (217) T 2i82_A 15 LYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQY 94 (217) T ss_dssp EEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCTTCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEE T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEEECHHHHHHHHHHHHCCEEEEEE T ss_conf 99789999999999982569988776048999875037864315457875214799950205578999998659351599 Q ss_pred EEEECCCCCHHHHHHHH-----------HH-HHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE Q ss_conf 52112455646788874-----------00-0008767503430364026880799999951842899999998398686 Q gi|254780406|r 146 RVRFHGQVDQDKLNLLK-----------KG-IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213 (354) Q Consensus 146 ~v~v~~~~~~~~~~~~~-----------~g-~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~ 213 (354) ++.|.|.+......... .. ....+.................+++++.+.+||.||||.+|+++|++++ T Consensus 95 ~a~v~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~TGR~HQIRvHla~ig~PIv 174 (217) T 2i82_A 95 VARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPIL 174 (217) T ss_dssp EEEEESCCSSSEEEEECCEEECGGGTTCEEECTTTCBCCEEEEEEEEEETTTEEEEEEEESSCCTTHHHHHHHHTTCCBT T ss_pred EEEECCCCCCCCCEEEEEEEECCCCCCCEEEEECCCCCCCEEEEEEEEECCCCEEEEEEECCCCCHHHHHHHHHCCCCCC T ss_conf 78751433566436975452014567413565037863315899987511331477999898984799999997698261 No 10 >1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} SCOP: d.66.1.6 Probab=99.40 E-value=1.9e-14 Score=109.40 Aligned_cols=58 Identities=17% Similarity=0.310 Sum_probs=54.8 Q ss_pred CCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 734478899988687-7899999998698699999924068780799979999989225 Q gi|254780406|r 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 12 ~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) ..+||+|||+.+|+| ||++|++||.+|+|+|||++++.++++|.++|.|+|||++|.. T Consensus 19 ~~irL~k~L~~~g~~~Sr~eAk~lI~~G~V~VNG~~v~~p~~~v~~gD~V~vdg~~i~i 77 (79) T 1p9k_A 19 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV 77 (79) T ss_dssp SCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETTEEEEE T ss_pred CCEEHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCEEEEE T ss_conf 71979999987788368999999998499798999927788798999999999999999 No 11 >2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Probab=98.82 E-value=1.8e-10 Score=84.35 Aligned_cols=75 Identities=24% Similarity=0.302 Sum_probs=60.3 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC-----------EEC---CCCCCEEEEEC Q ss_conf 4478899988687-78999999986986999999240687807999799999-----------892---25564389602 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----------VPL---RKAERTRLWLY 78 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg-----------~~i---~~~~~~~~~~~ 78 (354) +||||||+.++++ ||..|+++|.+|.|+|||++++ ++++|..+|.|+|.- .++ .++++..+++. T Consensus 1 mRlDk~L~~~~~~~SRs~~~~lI~~G~V~vng~~~k-~s~~V~~Gd~i~i~~~~~~~~~~v~~i~~~~~i~~ED~~l~ii 79 (92) T 2k6p_A 1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYIA 79 (92) T ss_dssp CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECC-TTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSEE T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEE-ECCEECCCCEEEEEECCCCEEEEEEECCCCCCCCHHHHCCCEE T ss_conf 977899987377379999999998892897999975-2368279999999838970799999788657985255182698 Q ss_pred CCCCEEEECCC Q ss_conf 78751563144 Q gi|254780406|r 79 HKPIGLVTTHS 89 (354) Q Consensus 79 ~KP~g~~~~~~ 89 (354) |||+|+-.+.. T Consensus 80 ~K~~~le~~~~ 90 (92) T 2k6p_A 80 PKTKELEHHHH 90 (92) T ss_dssp ECCCC------ T ss_pred CCHHCCCCCCC T ss_conf 06004634445 No 12 >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} SCOP: d.66.1.3 PDB: 3bbu_A Probab=98.77 E-value=1.2e-08 Score=72.81 Aligned_cols=54 Identities=19% Similarity=0.148 Sum_probs=48.8 Q ss_pred CCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEEC Q ss_conf 667734478899988687-7899999998698699999924068780799979999 Q gi|254780406|r 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63 (354) Q Consensus 9 ~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vd 63 (354) +..+.+||||||..+.++ ||..|.++|..|.|+|||++++ +++.|.++|.|.|. T Consensus 4 ~~~~~mRlD~~L~~~r~~KtRs~A~~~i~~G~V~vNg~~~K-~s~~v~~gD~i~i~ 58 (133) T 1dm9_A 4 KPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLR 58 (133) T ss_dssp -CTTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEE T ss_pred CCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEEE T ss_conf 88886863899987162504999999998694798996467-66668899989998 No 13 >2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Probab=98.35 E-value=8e-07 Score=61.44 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=49.7 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-+|-++|++ |+++|.+||..|.|.|||+.|+.|++.|.++|.|.|..+. T Consensus 99 ~RlD~vv~r~g~a~s~~~ARQ~v~Hghv~vng~~v~ips~~~k~gd~i~~~~k~ 152 (209) T 2vqe_D 99 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKS 152 (209) T ss_dssp TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGGG T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHCCEECCCEEECCCCEECCCCCEEEECCCC T ss_conf 988999983475179999999987307321997973588682799999861021 No 14 >3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} Probab=98.35 E-value=1.6e-07 Score=65.82 Aligned_cols=56 Identities=18% Similarity=0.348 Sum_probs=50.3 Q ss_pred CCHHHHHHHHHCCC-CCHHHHHHHHHCCCE--EECCEECCCCCEEECCCCEEEECCEEC Q ss_conf 73447889998868-778999999986986--999999240687807999799999892 Q gi|254780406|r 12 TPQRVSKVIARAGI-ASRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGVPL 67 (354) Q Consensus 12 ~~~RL~K~la~~g~-~SRr~a~~lI~~G~V--~Vng~~v~~~~~~v~~~d~v~vdg~~i 67 (354) ..+|||++|-..|+ -||.+|..+|.+|.| +|||++++.+++.|.+++.|+|.++.. T Consensus 5 ~k~RLD~~Lv~~gl~~SR~~A~~lI~~G~V~~~Vng~~v~Kps~~v~~~~~i~v~~~~~ 63 (291) T 3hp7_A 5 PKERVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTELKLKGEKL 63 (291) T ss_dssp CEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETTCCC T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEECCCC T ss_conf 17679999997848114999999998599524209989468867879999899947876 No 15 >2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A Probab=98.27 E-value=6.9e-06 Score=55.54 Aligned_cols=146 Identities=19% Similarity=0.208 Sum_probs=89.5 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE-- Q ss_conf 438960278751563144333364421011023432002665543323202223676410001234457404775211-- Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-- 149 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v-- 149 (354) ..-++++|||.|+.++..=..-+.. + ...++...|-||-..+|+|++.-.. +.++..--.+..|+|.+++ T Consensus 45 ~~G~l~i~KP~g~tS~~~v~~~k~~----~--~~~KvGH~GTLDP~AsGvL~i~ig~--aTk~~~~~~~~~K~Y~~~~~l 116 (334) T 2aus_C 45 QYGVINLDKPPGPTSHEVVAWIKRI----L--NLEKAGHGGTLDPKVSGVLPVALER--ATRVVQALLPAGKEYVALMHL 116 (334) T ss_dssp HTEEEEEEECSSSCHHHHHHHHHHH----T--TCSCEEESSCCCTTCEEEEEEEEGG--GGGGGGGGTTCCEEEEEEEEE T ss_pred CCCEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCCCCEEEEEEEE T ss_conf 7708999569989989999999987----3--6121379999999773789999878--986869875698189999984 Q ss_pred CCCCCHHHHHHHHHHHHCCCEEEEC-----------C---CEEEEECCCCEEEEEEEEEECCHHHHHHHHHHC------C Q ss_conf 2455646788874000008767503-----------4---303640268807999999518428999999983------9 Q gi|254780406|r 150 HGQVDQDKLNLLKKGIVIQGICYGD-----------M---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF------N 209 (354) Q Consensus 150 ~~~~~~~~~~~~~~g~~~~~~~~~~-----------~---~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~------g 209 (354) .+.++.+.+......+.-+-.+..| . .+.+..-......++|....|-| ||-++..+ + T Consensus 117 ~~~~~~~~i~~~l~~f~G~i~Q~PP~~SA~K~~~R~v~I~~~ell~~~~~~~~f~v~cs~GTY--IRSL~~Dig~~Lg~~ 194 (334) T 2aus_C 117 HGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEILEIDGRDVLFRVGVEAGTY--IRSLIHHIGLALGVG 194 (334) T ss_dssp SSCCCHHHHHHHHHHTSEEEECC------------EEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHSSC T ss_pred CCCCHHHHHHHHHHCCCEEEEECCCHHHHCCCCCCCCEEEEEEEEECCCCEEEEEEEEECCCC--HHHHHHHHHHHHCCC T ss_conf 221017799976403622288779646523002555147899998437982899999607813--899999999885988 Q ss_pred CEEEEEEEEEECCEECCC Q ss_conf 868688975870545187 Q gi|254780406|r 210 WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 210 ~~V~~L~Rv~~G~~~l~~ 227 (354) -.+..|.|+++|+|.+++ T Consensus 195 a~l~~L~Rt~~G~f~~~~ 212 (334) T 2aus_C 195 AHMAELRRTRSGPFKEDE 212 (334) T ss_dssp EEEEEEEEEEETTEESST T ss_pred CEEEEEEEEEECCCCHHH T ss_conf 485131625664735899 No 16 >1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Probab=98.26 E-value=1.8e-06 Score=59.18 Aligned_cols=52 Identities=21% Similarity=0.415 Sum_probs=48.6 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE Q ss_conf 4478899988687-789999999869869999992406878079997999998 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~ 65 (354) .|||-++-++|++ |+++|.+||..|.|.|||+.|+.|++.|.++|.|++..+ T Consensus 51 ~RLDnvvyR~gfa~t~~~ARQlv~Hghi~VNgk~v~ipS~~vk~gD~I~~~~k 103 (159) T 1c05_A 51 SRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREK 103 (159) T ss_dssp HBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTEECCCSSCBCCTTCEEEECGG T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHCCEEECCEEEEECCEECCCCCEEEECCC T ss_conf 86567720477527999999999803707024798525677489989873210 No 17 >3ofo_D 30S ribosomal protein S4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ... Probab=98.09 E-value=2.1e-06 Score=58.74 Aligned_cols=53 Identities=23% Similarity=0.449 Sum_probs=49.4 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|++ |+..|.+||..|.|.|||+.|+.|++.|.++|.|.|..+. T Consensus 95 ~RLDnvvyR~gfa~t~~~ARQlV~Hghi~VNgk~v~ips~~~k~gd~i~v~eks 148 (205) T 3ofo_D 95 GRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKA 148 (205) T ss_dssp HBHHHHHHTTTSCSSHHHHHHHHHTTCEESSSSBCCSTTCBCCTTCEEEECSSS T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEEECCCCCCCCCCCEEEHHHHH T ss_conf 877789860662047999998886088650997863787253699897531335 No 18 >3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=98.07 E-value=1.4e-06 Score=59.96 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=49.1 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|+| |+.+|.+||..|.|.|||+.|+.|++.|.++|.|.|..+. T Consensus 89 ~RLDnvvyR~gfa~t~~~ARQlV~Hghi~VNgk~v~ipSy~vk~GD~I~v~eks 142 (201) T 3bbn_D 89 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQ 142 (201) T ss_dssp SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSST T ss_pred HHHHHHHHHCCCCCCHHHHCCEEECCCEEECCEEECCCCEECCCCCEEEECHHH T ss_conf 876788750552157776130473278487798977998782799989973222 No 19 >1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Probab=98.05 E-value=5.3e-05 Score=49.95 Aligned_cols=161 Identities=16% Similarity=0.146 Sum_probs=95.3 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC- Q ss_conf 3896027875156314433336442101102343200266554332320222367641000123445740477521124- Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG- 151 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~- 151 (354) .-++++|||.|+.++..=..-+.. + ...++...|.||-..+|+|++.-.. +.++..--....|+|.+++.- T Consensus 3 nG~l~v~KP~g~tS~~vv~~vr~~----l--~~kkvGH~GTLDP~AtGvL~i~~g~--aTk~~~~~~~~~K~Y~~~~~lG 74 (309) T 1r3e_A 3 HGILVAYKPKGPTSHDVVDEVRKK----L--KTRKVGHGGTLDPFACGVLIIGVNQ--GTRILEFYKDLKKVYWVKMRLG 74 (309) T ss_dssp CEEEEEEECSSSCHHHHHHHHHHH----T--TCSCEEESSCCCTTCEEEEEEEEGG--GGGGGGGGTTSCEEEEEEEEET T ss_pred CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHHHCCCEEEEEEEEE T ss_conf 669999779989989999999998----6--8897876856797461379999887--7624477612275547999993 Q ss_pred ------------------CCCHHHHHHHHHHH--------------HCCCEE-----------------EECCCEEEEEC Q ss_conf ------------------55646788874000--------------008767-----------------50343036402 Q gi|254780406|r 152 ------------------QVDQDKLNLLKKGI--------------VIQGIC-----------------YGDMQVTLDTQ 182 (354) Q Consensus 152 ------------------~~~~~~~~~~~~g~--------------~~~~~~-----------------~~~~~~~~~~~ 182 (354) .++.+.+......+ .+.+.. +....+.+..- T Consensus 75 ~~TdT~D~~G~v~~~~~~~~~~~~i~~~l~~f~G~~~Q~PP~ySAvKv~Gkr~Y~lAR~g~~~~~~~r~v~i~~~~~~~~ 154 (309) T 1r3e_A 75 LITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNI 154 (309) T ss_dssp EEESSSBTTSCEEEECCCCCCHHHHHHHHHSSSEEEEECCCSSSSCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEE T ss_pred EECCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHCCCHHHHHHHHCCCCCCCCCCEEEEEEEEEECC T ss_conf 42367687887764146665499999999963160200684667643266312368765876567764699999876044 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC-CCCCCEEECCHHHHHHHHH Q ss_conf 688079999995184289999999839------868688975870545187-5547488679999987532 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~-L~~G~~r~l~~~e~~~l~~ 246 (354) ......++|.-..|-| ||-+..-+| -.+..|.|+++|+|.+.+ +..-+ +..+++...+- T Consensus 155 ~~~~~~~~v~cs~GTY--IRsL~~dig~~Lg~~a~~~~LrRt~~G~f~~~~a~~l~~---~~~~~~~~~l~ 220 (309) T 1r3e_A 155 EGRDVSFRVEVSPGTY--IRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFE---AAPEEIENRII 220 (309) T ss_dssp ETTEEEEEEEECTTCC--HHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGCBCTTT---SCHHHHHHHCE T ss_pred CCCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEECCCCCCCHHHHCCHHH---HCHHHCCCCCC T ss_conf 4426999999899837--999999997751995898158980578954677447988---58233156324 No 20 >2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Probab=98.04 E-value=3.2e-05 Score=51.31 Aligned_cols=145 Identities=17% Similarity=0.127 Sum_probs=89.8 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC-- Q ss_conf 389602787515631443333644210110234320026655433232022236764100012344574047752112-- Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-- 150 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~-- 150 (354) .-++++|||.|..++..-..-+. .+ ...+....|-||-..+|+|++.-.. +.++..--..-.|+|.+.+. T Consensus 66 ~G~l~idKP~G~TS~~vv~~vkk----~l--~~kK~GH~GTLDP~AtGvL~i~ig~--aTKl~~~~~~~~K~Y~~~~~lg 137 (357) T 2apo_A 66 YGVVVVDKPRGPTSHEVSTWVKK----IL--NLDKAGHGGTLDPKVTGVLPVALER--ATKTIPMWHIPPKEYVCLMHLH 137 (357) T ss_dssp TEEEEEEECSSSCHHHHHHHHHH----HT--TCSCEEESSCCCTTCEEEEEEEEGG--GGGGGGGTTSSCEEEEEEEEES T ss_pred CCEEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCEEEEEEECH--HHCCCHHHCCCCEEEEEEEEEE T ss_conf 96899978999998999999999----84--8882577867897672069999885--6430645437980999999972 Q ss_pred CCCCHHHHHHHHHHHHCCCEEEECC--------------CEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC------C Q ss_conf 4556467888740000087675034--------------3036402688079999995184289999999839------8 Q gi|254780406|r 151 GQVDQDKLNLLKKGIVIQGICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN------W 210 (354) Q Consensus 151 ~~~~~~~~~~~~~g~~~~~~~~~~~--------------~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~ 210 (354) ...+.+.+.+....+.-.-.+..|. .+.+..-+.....|+|.-.-|-| ||.++..+| - T Consensus 138 ~~t~~~di~~~l~~F~G~i~Q~PP~~SAvKr~~R~~~Iy~l~ll~~~~~~~~f~V~Cs~GTY--IRsLa~DlG~~Lg~~a 215 (357) T 2apo_A 138 RDASEEDILRVFKEFTGRIYQRPPLKAAVKRRLRIRKIHELELLDKDGKDVLFRVKCQSGTY--IRKLCEDIGEALGTSA 215 (357) T ss_dssp SCCCHHHHHHHHHHHSEEEECC-----------CEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHTTSCE T ss_pred ECCCCHHHHHHHHHCCCCEEECCCCHHHCCCCCCCCEEEEEEEECCCCCEEEEEEEECCCEE--HHHHHHHHHHHHCCCE T ss_conf 22441779999986786162069915640024453079999874157886899999568636--8999999999839968 Q ss_pred EEEEEEEEEECCEECCC Q ss_conf 68688975870545187 Q gi|254780406|r 211 KVNRLIRISYGPFQLGT 227 (354) Q Consensus 211 ~V~~L~Rv~~G~~~l~~ 227 (354) .+..|.|+++|+|.+++ T Consensus 216 ~m~~LrRt~~G~F~~~~ 232 (357) T 2apo_A 216 HMQELRRTKSGCFEEKD 232 (357) T ss_dssp EEEEEEEEEETTEEGGG T ss_pred EEEECCCCCCCCCCHHH T ss_conf 98315874028868798 No 21 >1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Probab=98.04 E-value=2.1e-05 Score=52.52 Aligned_cols=153 Identities=15% Similarity=0.146 Sum_probs=89.3 Q ss_pred ECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCC Q ss_conf 99989225564389602787515631443333644210110234320026655433232022236764100012344574 Q gi|254780406|r 62 VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141 (354) Q Consensus 62 vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~ 141 (354) +.|+.... .-++++|||.|+.++..=..-+.. -...++...|.||-..+|+|++.-.- +.+|..--... T Consensus 17 ~~~~~~~~---nG~l~i~Kp~g~tS~~~v~~~r~~------l~~kKvGH~GTLDP~AtGvL~v~~G~--aTKl~~~~~~~ 85 (327) T 1k8w_A 17 IEGRHMDI---NGVLLLDKPQGMSSNDALQKVKRI------YNANRAGHTGALDPLATGMLPICLGE--ATKFSQYLLDS 85 (327) T ss_dssp -----CCC---CEEEEEEECTTCCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEGG--GGGGTHHHHTS T ss_pred CCCCCCCC---CEEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCC T ss_conf 45888885---469999689989989999999998------58985877865798560139999787--87488887789 Q ss_pred EEEEEEEECCC-------------------CCHHHHHHHHHHHHCCCEEEECC--------------------------- Q ss_conf 04775211245-------------------56467888740000087675034--------------------------- Q gi|254780406|r 142 LRVYRVRFHGQ-------------------VDQDKLNLLKKGIVIQGICYGDM--------------------------- 175 (354) Q Consensus 142 ~k~Y~v~v~~~-------------------~~~~~~~~~~~g~~~~~~~~~~~--------------------------- 175 (354) .|+|.+++.-- ++.+.++.....+.-.-.+..|. T Consensus 86 ~K~Y~~~~~lG~~TdT~D~~G~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~Y~lAR~g~~v~~~~r~ 165 (327) T 1k8w_A 86 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARP 165 (327) T ss_dssp CEEEEEEEEETEEESSSBTTSCEEEECCCCCCHHHHHHHHHTTSEEEEECCCSSSCCEETTEEHHHHHHTTCCCCCCCEE T ss_pred CCCEEEEEEECCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCEEECCCHHHHHHCCCHHHHHHHHHCCCCCCCCCE T ss_conf 87328999987757654468967542378511999999999737777874861121000474189999746665568601 Q ss_pred ----CEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf ----3036402688079999995184289999999839------868688975870545187 Q gi|254780406|r 176 ----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 176 ----~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .+.+..-+.....++|.-..|-| ||-++.-+| -.+..|.|+++|+|.+++ T Consensus 166 v~I~~i~~~~~~~~~~~~~v~cs~GTY--IRsLa~DiG~~Lg~~a~l~~LrRt~~G~f~~~~ 225 (327) T 1k8w_A 166 ITVYELLFIRHEGNELELEIHCSKGTY--IRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVER 225 (327) T ss_dssp EEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHTSCEEEEEEEEEEETTCCGGG T ss_pred EEEEEEEEEECCCCEEEEEEEECCCHH--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCCHH T ss_conf 145348997415888999999658369--999999987650894898378988887818121 No 22 >2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Probab=97.86 E-value=7.9e-06 Score=55.16 Aligned_cols=55 Identities=16% Similarity=0.207 Sum_probs=49.0 Q ss_pred CCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCC--CEEEECC Q ss_conf 67734478899988687-7899999998698699999924068780799--9799999 Q gi|254780406|r 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDG 64 (354) Q Consensus 10 ~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~--d~v~vdg 64 (354) ....-|||-+|.+.|++ |+.+|.+||..|.|.|||++|+.|++.|..+ |.|++.. T Consensus 4 ~~~~RRLd~il~r~~fa~S~~~ARqlI~HghI~Vng~~V~~Ps~lV~~~~Ed~It~~~ 61 (71) T 2cqj_A 4 GSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVD 61 (71) T ss_dssp SCCEEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESC T ss_pred CHHHCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCCCEEEEEC T ss_conf 0323013789988265378999999976695999999965797695389887699967 No 23 >1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} SCOP: b.122.1.1 d.265.1.2 Probab=97.82 E-value=0.00024 Score=45.83 Aligned_cols=146 Identities=17% Similarity=0.186 Sum_probs=80.8 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC Q ss_conf 43896027875156314433336442101102343200266554332320222367641000123445740477521124 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~ 151 (354) ..-++++|||.|+.++..=..-+.. -...++...|.||-..+|||++--. -+.+++.--....|+|.+++.- T Consensus 5 ~~G~l~i~KP~G~TS~~~v~~vk~~------~~~~KvGH~GTLDP~AsGvL~i~vG--~aTKl~~~~~~~~K~Y~~~~~l 76 (316) T 1sgv_A 5 GPGIVVIDKPAGMTSHDVVGRCRRI------FATRRVGHAGTLDPMATGVLVIGIE--RATKILGLLTAAPKSYAATIRL 76 (316) T ss_dssp CSEEEEEEECTTCCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEG--GGGGGGGGTTTSCEEEEEEEEE T ss_pred CCEEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCEEEEEEEEC--HHHHHHHHHHCCCEEEEEEEEE T ss_conf 9889999779999989999999998------5878456487789756334999978--7884779985186489999997 Q ss_pred C--------------------CCHHHHHHHHHHH--------------HCCCEEE--------------ECCCE---EEE Q ss_conf 5--------------------5646788874000--------------0087675--------------03430---364 Q gi|254780406|r 152 Q--------------------VDQDKLNLLKKGI--------------VIQGICY--------------GDMQV---TLD 180 (354) Q Consensus 152 ~--------------------~~~~~~~~~~~g~--------------~~~~~~~--------------~~~~~---~~~ 180 (354) - ++.+.++.....+ .+++... ++..+ .+. T Consensus 77 G~~TdT~D~~G~v~~~~~~~~~~~e~i~~~L~~f~G~i~Q~PP~ySAiKv~GkraYelAR~G~~v~~~~r~v~I~~i~l~ 156 (316) T 1sgv_A 77 GQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELL 156 (316) T ss_dssp TEEETTSBTTSCEEEECCCTTCCHHHHHHHHHHTCEEC----------------------------CCCCCCEEEEEEEE T ss_pred CCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCCCHHHHHHCCCCCCCCCCCEEEEEEEEE T ss_conf 76457778777477664157799999999998658715542866663012784087898758865456444279899999 Q ss_pred EC--CCC--EEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 02--688--079999995184289999999839------868688975870545187 Q gi|254780406|r 181 TQ--KGS--NAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 181 ~~--~~~--~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .- ... ...++|+-..|-| ||-+...+| -.+..|.|+++|+|.+++ T Consensus 157 ~~~~~~~~p~~~~~v~Cs~GTY--IRsLa~DiG~~Lgt~A~~~~LrRt~~G~F~~~~ 211 (316) T 1sgv_A 157 AARRRDQLIDIDVEIDCSSGTY--IRALARDLGDALGVGGHVTALRRTRVGRFELDQ 211 (316) T ss_dssp EEEEETTEEEEEEEEEESCCTT--HHHHHHHHHHHHTSCEEEEEEEEEEETTEEGGG T ss_pred EECCCCCCCEEEEEEEECCCCH--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 7316677705899999789507--999999999986998798689977785788898 No 24 >3jyv_D 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} Probab=97.55 E-value=2.3e-05 Score=52.25 Aligned_cols=49 Identities=16% Similarity=0.278 Sum_probs=43.0 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 4478899988687-789999999869869999992406878079997999 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -||+-++...|+| |..+|.+||..|-|.|||++|+.|++.|..+|...| T Consensus 102 RRLd~vv~r~g~a~s~~~ARqlI~HGHI~Vng~~V~iPSy~V~~~~Ed~I 151 (158) T 3jyv_D 102 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHI 151 (158) T ss_dssp HBHHHHHHHHTSSSSTTTTTHHHHTSCEEESSCCCSCTTCBCCSSSCEEE T ss_pred HHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEECCCCCEE T ss_conf 76888999957779989998766788899999996379738425985669 No 25 >1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1 Probab=97.42 E-value=7.8e-05 Score=48.89 Aligned_cols=53 Identities=17% Similarity=0.304 Sum_probs=46.1 Q ss_pred CCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 67734478899988687-789999999869869999992406878079997999 Q gi|254780406|r 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 10 ~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) +.-.-||+-++.++|+| |..+|.+||..|.|.|||++|+.|++.|..++...| T Consensus 85 ~~lerRL~~~v~r~~~a~s~~~Arq~I~hghi~v~~~~v~~Ps~~v~~~~E~~i 138 (179) T 1s1h_D 85 DFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHI 138 (179) T ss_dssp SSGGGBHHHHHHHHTSSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCB T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCEEEECCCCCEE T ss_conf 999888999999936668899999997547635899895248658415884537 No 26 >1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Probab=97.15 E-value=0.0015 Score=40.74 Aligned_cols=13 Identities=8% Similarity=0.130 Sum_probs=8.1 Q ss_pred CCHHHHHHHHHCC Q ss_conf 7789999999869 Q gi|254780406|r 26 ASRREVERMIAQQ 38 (354) Q Consensus 26 ~SRr~a~~lI~~G 38 (354) ++.++..+++.+| T Consensus 23 ~~~eel~~~l~~~ 35 (432) T 1h3f_A 23 VPEEELLAKLKEG 35 (432) T ss_dssp ETHHHHHHHHHTC T ss_pred CCHHHHHHHHHCC T ss_conf 5989999999649 No 27 >2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Probab=96.92 E-value=0.00068 Score=42.97 Aligned_cols=47 Identities=23% Similarity=0.396 Sum_probs=35.1 Q ss_pred CHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCE Q ss_conf 34478899988687-789999999869869999992406878079997 Q gi|254780406|r 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59 (354) Q Consensus 13 ~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~ 59 (354) +.-|-.+|..+|+| |++||.+||.+|-|+|||+.|+++.+.+...|. T Consensus 355 ~~~l~dLLv~~gL~~SksEARRLI~qGgV~IN~~kI~d~~~~l~~~d~ 402 (432) T 2jan_A 355 PDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF 402 (432) T ss_dssp CCSHHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS T ss_pred CCCHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHH T ss_conf 676999999828977899999999919899899981694331378781 No 28 >1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Probab=96.38 E-value=0.00045 Score=44.12 Aligned_cols=13 Identities=15% Similarity=0.245 Sum_probs=5.8 Q ss_pred EECCCCCCCCCCC Q ss_conf 2236764100012 Q gi|254780406|r 123 LLTNDGGLARVLE 135 (354) Q Consensus 123 llTndg~l~~~l~ 135 (354) .+.|+.+|-.++. T Consensus 120 ~iv~N~~W~~~~~ 132 (420) T 1jil_A 120 VLVNNRDWLGQIS 132 (420) T ss_dssp EEEETHHHHTTCC T ss_pred EEECCHHHHCCCC T ss_conf 9954468655563 No 29 >2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Probab=96.34 E-value=0.00048 Score=43.91 Aligned_cols=12 Identities=17% Similarity=0.075 Sum_probs=6.0 Q ss_pred EECCCCCCCCCC Q ss_conf 223676410001 Q gi|254780406|r 123 LLTNDGGLARVL 134 (354) Q Consensus 123 llTndg~l~~~l 134 (354) .+-|+.+|-..+ T Consensus 119 ~iv~N~~W~~~~ 130 (419) T 2ts1_A 119 KIKNNYDWIGPL 130 (419) T ss_dssp EEEETHHHHTTC T ss_pred EEEECHHHHCCC T ss_conf 998807850762 No 30 >3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Probab=95.90 E-value=0.024 Score=33.28 Aligned_cols=53 Identities=26% Similarity=0.340 Sum_probs=41.9 Q ss_pred CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 734478899988-6-8778999999986986999999240687807999799999 Q gi|254780406|r 12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) +++=|.=+|-+. + --+.|||...+.+|.|.|||++.++..+.|---|+|++.+ T Consensus 6 ~siPL~iiLRd~Lk~A~t~rEak~Il~~~~V~VDGkvr~d~k~PvGlmDVisi~~ 60 (213) T 3kbg_A 6 QSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFMDVIEING 60 (213) T ss_dssp SCEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEETT T ss_pred CCCCEEHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECC T ss_conf 2665405531353412657999999868938989999644899874378999789 No 31 >2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae} Probab=87.10 E-value=0.84 Score=23.52 Aligned_cols=76 Identities=21% Similarity=0.290 Sum_probs=56.5 Q ss_pred CCCCCCCEEEECC-CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEE Q ss_conf 5433232022236-764100012344574047752112455646788874000008767503430364026880799999 Q gi|254780406|r 114 LDINTEGLLLLTN-DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192 (354) Q Consensus 114 LD~~t~GLlllTn-dg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 192 (354) .-.+.+|++.+.+ +..|+-+.+.-...+.-.|.+.|.|.+.++.++.|.. |+|- + ..++.+-+.|- T Consensus 42 tS~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAl~V~g~lp~~i~~~l~~--------y~~r----d-~s~~~sIw~Vr 108 (200) T 2exu_A 42 TSPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIKVDGRLPAEVVELLPH--------YKPR----D-GSGSATIWGVR 108 (200) T ss_dssp EESCEEEEEEESCTTTCHHHHHTTCTTSCSEEEEEEECSCCCHHHHTTCTT--------CCCT----T-SCSCCCEEEEE T ss_pred CCCCCCEEEEEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHH--------CCCC----C-CCCCCCEEEEE T ss_conf 676713189996852739999857877789737999517499889999997--------2789----8-87887579997 Q ss_pred EEECCHHHHH Q ss_conf 9518428999 Q gi|254780406|r 193 LREGKNREIK 202 (354) Q Consensus 193 l~eGr~~qIr 202 (354) -+.|+-++|- T Consensus 109 c~~GkErevv 118 (200) T 2exu_A 109 CRPGKEKELI 118 (200) T ss_dssp ECTTCHHHHH T ss_pred CCCCCHHHHH T ss_conf 5787179999 No 32 >3hvz_A Uncharacterized protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.20A {Clostridium leptum dsm 753} Probab=62.30 E-value=4.3 Score=19.01 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=18.1 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+.+. +.+.+..+|+|++ T Consensus 43 ~akING~~v~-l~~~L~~GD~VeI 65 (78) T 3hvz_A 43 GAKVDGRIVP-IDYKVKTGEIIDV 65 (78) T ss_dssp EEEETTEEEC-TTCBCCTTCBEEE T ss_pred EEEECCEECC-CCCCCCCCCEEEE T ss_conf 2699999999-9887699999999 No 33 >2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis} Probab=58.58 E-value=5.4 Score=18.42 Aligned_cols=23 Identities=35% Similarity=0.358 Sum_probs=19.0 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+.+. +.+.+..+|+|++ T Consensus 38 ~A~ING~~~~-L~~~L~~GD~VeI 60 (73) T 2kmm_A 38 GAKVNHKLVP-LSYVLNSGDQVEV 60 (73) T ss_dssp EEEETTEECC-TTCBCCSSSBEEE T ss_pred EEEECCEECC-CCCCCCCCCEEEE T ss_conf 6788999999-8888589999999 No 34 >3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, metal-binding, nucleus, repressor, transcription regulation, zinc; 1.55A {Homo sapiens} Probab=58.33 E-value=8.5 Score=17.18 Aligned_cols=50 Identities=20% Similarity=0.276 Sum_probs=40.1 Q ss_pred CCCCCEEEECCC-CCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHH-HH Q ss_conf 332320222367-641000123445740477521124556467888740-00 Q gi|254780406|r 116 INTEGLLLLTND-GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GI 165 (354) Q Consensus 116 ~~t~GLlllTnd-g~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~-g~ 165 (354) .+.+|++-+.+. ..|+-+.+.-...+.-.|.|.|.|.+.++.+..|.. |+ T Consensus 58 ~~F~G~Ial~~P~~SWVArw~ri~~~vpG~YAv~V~g~Lp~~i~~~le~~gi 109 (120) T 3h7h_A 58 SSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGV 109 (120) T ss_dssp SCEEEEEEESCGGGCHHHHHTTCTTSCSEEEEEEECCCCCHHHHHHHHHTTC T ss_pred CCCCEEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHCCC T ss_conf 6633379995684238999864567789748988458599899999998398 No 35 >3gmg_A Uncharacterized protein RV1825/MT1873; structural genomics, unknown function, cell membrane, membrane, transmembrane, PSI-2; 1.50A {Mycobacterium tuberculosis} Probab=36.71 E-value=17 Score=15.23 Aligned_cols=31 Identities=16% Similarity=0.118 Sum_probs=16.3 Q ss_pred CEEECCE----ECCCCCEEECCCCEEEECCEECCC Q ss_conf 8699999----924068780799979999989225 Q gi|254780406|r 39 RVKVNGI----LLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 39 ~V~Vng~----~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) -|.|||+ .+..-..-...+..|.|||+++.+ T Consensus 68 AIsINgq~~~vRi~~~S~Ir~~g~~i~Vng~~i~~ 102 (170) T 3gmg_A 68 AIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSP 102 (170) T ss_dssp EEEEECSSCEEECCTTCCEEEETTEEEETTEEECS T ss_pred EEEECCCCCCEEEEEEEEEEECCCEEEECCEEECC T ss_conf 79987974317997557999049989999999369 No 36 >2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A Probab=31.96 E-value=22 Score=14.57 Aligned_cols=49 Identities=16% Similarity=0.109 Sum_probs=32.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCC------EEECCEECCC---CCEEECCCCEEEE Q ss_conf 44788999886877899999998698------6999999240---6878079997999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVERMIAQQR------VKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~lI~~G~------V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .-|-.+|+..-...+++..-+.+.|. |.|||+-+.. +.+.+.++|.|.+ T Consensus 35 ~~Ll~~L~~~~~~~~~~~~~~~~~~~lr~~i~v~vN~~di~~l~gl~t~l~~gD~V~i 92 (99) T 2qjl_A 35 GDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISF 92 (99) T ss_dssp HHHHHHHHHHTCSSGGGHHHHEETTEECTTEEEEETTEEGGGGTGGGCBCCTTCEEEE T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCCCCCEEEEECCCEEEECCCCCCCCCCCCEEEE T ss_conf 9999999987553225554330135644527999899263505786748699799999 No 37 >3fm8_A Kinesin-like protein KIF13B; kinesin, GAP, GTPase activation, structural genomics consortium, SGC, ATP-binding, coiled coil, cytoplasm, cytoskeleton; 2.30A {Homo sapiens} PDB: 3mdb_A* Probab=30.85 E-value=23 Score=14.45 Aligned_cols=10 Identities=30% Similarity=0.355 Sum_probs=4.0 Q ss_pred HHHCCCEEEC Q ss_conf 9986986999 Q gi|254780406|r 34 MIAQQRVKVN 43 (354) Q Consensus 34 lI~~G~V~Vn 43 (354) +.+++-|+|+ T Consensus 14 ~~~~~gi~~~ 23 (124) T 3fm8_A 14 LYFQGGIKVG 23 (124) T ss_dssp ---------- T ss_pred HHHHCCEEEC T ss_conf 9973886407 No 38 >2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} Probab=29.85 E-value=14 Score=15.82 Aligned_cols=23 Identities=26% Similarity=0.148 Sum_probs=13.1 Q ss_pred EEECCEECCC---CCEEECCCCEEEE Q ss_conf 6999999240---6878079997999 Q gi|254780406|r 40 VKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) |.|||+-+.. +.+.+.++|.|.+ T Consensus 70 VlVNg~~i~~l~gldt~L~dgDeV~~ 95 (110) T 2k9x_A 70 VLVNSCDAEVVGGMDYVLNDGDTVEF 95 (110) T ss_dssp EEESSSBHHHHTSSCCCCCSSCEEEE T ss_pred EEECCEECCCCCCCCCCCCCCCEEEE T ss_conf 99999284368886638399699999 No 39 >2bj7_A Nickel responsive regulator; transcription, repressor, NIKR, DNA- binding, metal-binding, transcription regulation; HET: PG4; 2.1A {Pyrococcus horikoshii} SCOP: a.43.1.3 d.58.18.4 PDB: 2bj1_A 2bj3_A* 2bj8_A* 2bj9_A* Probab=29.85 E-value=24 Score=14.34 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=13.1 Q ss_pred HHHHHHHHHCCCCCHHHHH Q ss_conf 4478899988687789999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVE 32 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~ 32 (354) +.|++++...|+.||++|- T Consensus 16 ~~lD~~v~~~Gy~sRSe~I 34 (138) T 2bj7_A 16 EKFDQIIEEIGYENRSEAI 34 (138) T ss_dssp HHHHHHHHHHTCSSHHHHH T ss_pred HHHHHHHHHCCCCCHHHHH T ss_conf 9999999980999689999 No 40 >2kl0_A Putative thiamin biosynthesis THis; structural genomics, PSI-2, protein structure initiative, N structural genomics consortium, NESG; NMR {Rhodopseudomonas palustris} Probab=27.94 E-value=25 Score=14.18 Aligned_cols=40 Identities=20% Similarity=0.260 Sum_probs=22.9 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCC---CCEEECCCCEEEE Q ss_conf 47889998868778999999986986999999240---6878079997999 Q gi|254780406|r 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 15 RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) -|..+|...++-.. .=-|-|||++|.. ..+.+..+|+|++ T Consensus 16 tl~~lL~~~~~~~~--------~vAV~vN~~iVpr~~~~~~~L~egD~IEI 58 (73) T 2kl0_A 16 SVAALMTELDCTGG--------HFAVALNYDVVPRGKWDETPVTAGDEIEI 58 (73) T ss_dssp BHHHHHHHTTCCSS--------SCEEEESSSEECHHHHTTCBCCTTCEEEE T ss_pred HHHHHHHHCCCCCC--------EEEEEECCEECCHHHCCCCCCCCCCEEEE T ss_conf 49999997599987--------29999899992889938221899899999 No 41 >1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} SCOP: d.15.3.2 PDB: 1sf0_A Probab=27.66 E-value=14 Score=15.72 Aligned_cols=43 Identities=23% Similarity=0.322 Sum_probs=29.0 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 7734478899988687789999999869869999992406878079997999 Q gi|254780406|r 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) .++..+..+|...++-. +.=-|.|||+.+. ....+.++|.|.+ T Consensus 28 ~~~~tv~dlL~~L~~~~--------~~v~VavNg~~v~-~d~~l~dgDeV~i 70 (77) T 1rws_A 28 REGMKVRDILRAVGFNT--------ESAIAKVNGKVVL-EDDEVKDGDFVEV 70 (77) T ss_dssp CSSCCHHHHHHTTTCSS--------CSSCEEETTEEEC-SSSCCCSSCCCBC T ss_pred CCCCCHHHHHHHCCCCC--------CCEEEEECCEECC-CCCCCCCCCEEEE T ss_conf 99897999998869997--------7489998999968-9848799999999 No 42 >2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A Probab=26.70 E-value=25 Score=14.17 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=18.4 Q ss_pred HCCCEEECCEECCC---CCEEECCCCEEEE Q ss_conf 86986999999240---6878079997999 Q gi|254780406|r 36 AQQRVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 36 ~~G~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) ..=.|.|||+.+.. +.+.+.++|.|.+ T Consensus 54 ~~v~v~vNg~~i~~~~~~~t~l~dgDeV~i 83 (90) T 2g1e_A 54 KNVIILVNGNNITSMKGLDTEIKDDDKIDL 83 (90) T ss_dssp TTCEEEESSSBGGGTCSSSCBCCTTCEEEE T ss_pred HEEEEEECCEEECCCCCCCCCCCCCCEEEE T ss_conf 207998858870444565653799999999 No 43 >2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B* Probab=25.93 E-value=28 Score=13.91 Aligned_cols=24 Identities=17% Similarity=0.253 Sum_probs=19.2 Q ss_pred CCEEECCEECCCCCEEECCCCEEEE Q ss_conf 9869999992406878079997999 Q gi|254780406|r 38 QRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 38 G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) =+|.||++.+. ..+.+.++|.|.+ T Consensus 47 ~~vavN~~~~~-~~~~l~dgDeVa~ 70 (77) T 2q5w_D 47 FQVAVNEEFVQ-KSDFIQPNDTVAL 70 (77) T ss_dssp CEEEETTEEEC-TTSEECTTCEEEE T ss_pred EEEEECCEECC-CCCEECCCCEEEE T ss_conf 99998997979-9953099799999 No 44 >1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1 Probab=25.59 E-value=25 Score=14.24 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=13.6 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) .|.|||+.+. ..+.+.++|.|.+ T Consensus 69 ~v~vN~~~~~-~d~~L~dgDeVai 91 (98) T 1vjk_A 69 NIAVNGRYVS-WDEELKDGDVVGV 91 (98) T ss_dssp EEEETTBCCC-TTCBCCTTCEEEE T ss_pred EEEECCEECC-CCCCCCCCCEEEE T ss_conf 9998889969-9978099899999 No 45 >1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2 Probab=25.56 E-value=28 Score=13.87 Aligned_cols=45 Identities=31% Similarity=0.437 Sum_probs=28.6 Q ss_pred CCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 667734478899988687789999999869869999992406878079997999 Q gi|254780406|r 9 ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 9 ~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) |.+.+-++.-+|-..-+- |+.=-|+.||+.|.+ ..++..+|.+++ T Consensus 19 E~~~p~~IkDiL~~lEip--------ieTvVvK~NG~~Vie-eeei~dgDeiei 63 (70) T 1ryj_A 19 ESGAPRRIKDVLGELEIP--------IETVVVKKNGQIVID-EEEIFDGDIIEV 63 (70) T ss_dssp EESSCCBHHHHHHHTTCC--------TTTEEEEETTEECCT-TSBCCTTCEEEE T ss_pred HCCCCHHHHHHHCCCCCC--------CEEEEEECCCCEEEC-HHHCCCCCEEEE T ss_conf 437872588873144565--------169998128838821-544158987999 No 46 >2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A Probab=24.62 E-value=13 Score=16.09 Aligned_cols=36 Identities=22% Similarity=0.312 Sum_probs=29.1 Q ss_pred HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE Q ss_conf 999999869869999992406878079997999998 Q gi|254780406|r 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65 (354) Q Consensus 30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~ 65 (354) .--.+|++|.=+|-+.+...--.++.++|.|.+.++ T Consensus 10 ~~f~~I~~G~KtiE~Rl~d~k~~~ik~GD~I~F~n~ 45 (109) T 2z0t_A 10 EYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEGG 45 (109) T ss_dssp HHHHHHHTTSCCEEEEECCTTGGGCCTTCEEEEGGG T ss_pred HHHHHHHCCCCEEEEEECHHHHHHCCCCCEEEEECC T ss_conf 168998769988999804266872899999999689 No 47 >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 Probab=24.38 E-value=30 Score=13.73 Aligned_cols=24 Identities=17% Similarity=0.199 Sum_probs=15.7 Q ss_pred CEEECCEECCC---CCEEECCCCEEEE Q ss_conf 86999999240---6878079997999 Q gi|254780406|r 39 RVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .|.|||+.+.. +.+.|.++|.|.+ T Consensus 60 ~v~vn~~~i~~~~~~~~~l~~gdeV~i 86 (93) T 3dwg_C 60 NIYVNDEDVRFSGGLATAIADGDSVTI 86 (93) T ss_dssp EEEETTEEGGGTTGGGCBCCTTCEEEE T ss_pred EEEECCHHHCCCCCCCCCCCCCCEEEE T ss_conf 999887110033575664899999999 No 48 >2jqj_A DNA damage response protein kinase DUN1; protein/phosphopeptide, cell cycle; HET: DNA; NMR {Saccharomyces cerevisiae} PDB: 2jql_A* Probab=23.05 E-value=32 Score=13.57 Aligned_cols=16 Identities=25% Similarity=0.493 Sum_probs=8.0 Q ss_pred CCEECCCCCCCCCCCEEE Q ss_conf 320026655433232022 Q gi|254780406|r 106 SRVISVGRLDINTEGLLL 123 (354) Q Consensus 106 ~~~~~vgRLD~~t~GLll 123 (354) ...+.|||-. .+-+.| T Consensus 37 ~~~~~IGR~~--~~di~l 52 (151) T 2jqj_A 37 RNVTTIGRSR--SCDVIL 52 (151) T ss_dssp CSCEEEESST--TSSEEC T ss_pred CCCEEECCCC--CCCEEE T ss_conf 9818973887--889997 No 49 >2v9v_A Selenocysteine-specific elongation factor; transcription, protein conformational change, transcription elongation factor SELB; 1.10A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 Probab=22.73 E-value=32 Score=13.53 Aligned_cols=21 Identities=14% Similarity=0.158 Sum_probs=8.3 Q ss_pred HHHHHCCCEEECCEECCCCCE Q ss_conf 999986986999999240687 Q gi|254780406|r 32 ERMIAQQRVKVNGILLERAAV 52 (354) Q Consensus 32 ~~lI~~G~V~Vng~~v~~~~~ 52 (354) +.||++|.+.++|..|.-+++ T Consensus 111 ~~l~~~g~i~~~g~~v~l~~f 131 (135) T 2v9v_A 111 EEWSREGRLQLAANTVALAGF 131 (135) T ss_dssp HHHHHTTSEEECSSEEEETTC T ss_pred HHHHHCCCEEEECCEEECCCC T ss_conf 999978987976999988997 No 50 >1xne_A Hypothetical protein PF0469; GFT structural genomics, protein structure initiative, PSI, NESG, PFR14, alpha and beta protein; NMR {Pyrococcus furiosus dsm 3638} SCOP: b.122.1.6 Probab=22.21 E-value=17 Score=15.28 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=29.9 Q ss_pred HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE Q ss_conf 999999869869999992406878079997999998 Q gi|254780406|r 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65 (354) Q Consensus 30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~ 65 (354) .--.+|++|.=+|-+.+.+.--.++.++|.|.+++. T Consensus 11 ~~f~~I~~G~KtiE~Rl~d~k~~~ik~GD~I~F~~~ 46 (113) T 1xne_A 11 EYLEMVKSGKKRIEVRVAYPQLKDIKRGDKIIFNDL 46 (113) T ss_dssp HHHHHHHHTCCCEEECCCTTTTTTCCTTCEEEETTT T ss_pred CHHHHHHCCCCEEEEEECHHHHHHCCCCCEEEEECE T ss_conf 458999769977999825177860899999999010 No 51 >1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} SCOP: d.15.3.1 d.129.5.1 Probab=21.61 E-value=34 Score=13.38 Aligned_cols=24 Identities=8% Similarity=0.122 Sum_probs=17.5 Q ss_pred CEEECCEECCC---CCEEECCCCEEEE Q ss_conf 86999999240---6878079997999 Q gi|254780406|r 39 RVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .|.|||+.+.. +.+.+.++|.|.+ T Consensus 54 ~V~VNge~I~~~~g~dt~L~dgDEVai 80 (168) T 1v8c_A 54 SVFLEGRDVRYLQGLSTPLSPGATLDL 80 (168) T ss_dssp EEEETTEEGGGTTGGGCBCCTTCEEEE T ss_pred EEEECCEEECCCCCCCCCCCCCCEEEE T ss_conf 999847663145688855699999999 No 52 >2wvf_A Hpnikr, putative nickel-responsive regulator; transcription factor, transcription regulation, RHH, DNA-binding, transcription, metal-binding; 1.60A {Helicobacter pylori} PDB: 2wvc_A 2ca9_A 2cad_A* 2caj_A 2wvd_A 2wve_A* 2wvb_A Probab=21.22 E-value=35 Score=13.33 Aligned_cols=36 Identities=11% Similarity=0.140 Sum_probs=19.3 Q ss_pred EEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 0799999951842899999998398686889758705451 Q gi|254780406|r 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 186 ~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) +..+++.+.+|.-.+|+.+...+.. ++-|.+|.|.+ T Consensus 105 ~~ClEvi~v~G~~~~I~~l~~~l~~----~kGV~~~kL~~ 140 (148) T 2wvf_A 105 HNCLETIILQGNSFEIQRLQLEIGG----LRGVKFAKLTK 140 (148) T ss_dssp SEEEEEEEEEECHHHHHHHHHHHHT----STTEEEEEEEE T ss_pred CCEEEEEEEEECHHHHHHHHHHHHC----CCCEEEEEEEE T ss_conf 8238999998359999999999864----58857899898 No 53 >2hza_A Nickel-responsive regulator; nickel-binding, ribbon-helix-helix, transcription factor, metal binding protein; HET: 3CM; 2.10A {Escherichia coli} SCOP: a.43.1.3 d.58.18.4 PDB: 1q5v_A* 2hzv_A 3od2_A* Probab=20.09 E-value=37 Score=13.18 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=11.5 Q ss_pred HHHHHHHHHCCCCCHHHHH Q ss_conf 4478899988687789999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVE 32 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~ 32 (354) +.|++++...|+-||++|- T Consensus 14 ~~lD~~v~~~gy~nRSeaI 32 (133) T 2hza_A 14 ETLDSLSQRRGYNNRSEAI 32 (133) T ss_dssp HHHHHHHHHTTCCSHHHHH T ss_pred HHHHHHHHHCCCCCHHHHH T ss_conf 9999999982998688999 Done!