Query gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 227 No_of_seqs 132 out of 1311 Neff 6.6 Searched_HMMs 23785 Date Tue May 24 08:23:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780255.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3i1m_C 30S ribosomal protein S 100.0 0 0 534.7 15.8 214 1-215 1-214 (233) 2 2vqe_C 30S ribosomal protein S 100.0 0 0 509.3 15.7 215 1-215 1-215 (239) 3 3ofo_C 30S ribosomal protein S 100.0 0 0 509.9 14.1 206 2-207 1-206 (206) 4 3bbn_C Ribosomal protein S3; s 100.0 0 0 496.0 11.1 207 1-207 1-218 (218) 5 2zkq_c 40S ribosomal protein S 100.0 0 0 386.8 13.5 185 20-205 2-191 (243) 6 1wh9_A 40S ribosomal protein S 99.6 2.9E-16 1.2E-20 112.7 7.3 78 37-114 10-90 (92) 7 2pt7_G HP1451, hypothetical pr 95.5 0.022 9.3E-07 32.5 5.6 107 37-143 5-125 (152) 8 3gku_A Probable RNA-binding pr 94.1 0.025 1E-06 32.2 2.8 103 38-140 65-187 (225) 9 1wf3_A GTP-binding protein; GT 83.5 2.1 8.9E-05 21.0 7.7 83 37-119 195-294 (301) 10 3af5_A Putative uncharacterize 81.7 2.5 0.00011 20.6 13.5 108 40-158 86-198 (651) 11 2xr1_A Cleavage and polyadenyl 78.0 3.3 0.00014 19.9 11.6 107 41-158 82-193 (640) 12 2cxc_A NUSA; transcription ter 74.7 1.9 8.1E-05 21.2 3.0 44 49-92 23-66 (144) 13 1we8_A Tudor and KH domain con 60.9 2.7 0.00011 20.4 1.4 41 52-92 5-45 (104) 14 2hh2_A KH-type splicing regula 59.0 5.2 0.00022 18.7 2.6 29 63-91 8-36 (107) 15 3iev_A GTP-binding protein ERA 57.8 9.1 0.00038 17.4 5.6 52 67-118 243-303 (308) 16 2hh3_A KH-type splicing regula 55.2 5.2 0.00022 18.8 2.1 32 61-92 10-41 (106) 17 1dtj_A RNA-binding neurooncolo 53.0 5.7 0.00024 18.5 2.0 29 64-92 5-33 (76) 18 1zzk_A Heterogeneous nuclear r 52.5 8.7 0.00037 17.5 2.9 29 64-92 9-37 (82) 19 1ec6_A RNA-binding protein NOV 50.8 4.4 0.00018 19.2 1.1 30 63-92 4-33 (87) 20 2axy_A Poly(RC)-binding protei 45.2 6.1 0.00026 18.4 1.1 29 64-92 7-35 (73) 21 1j4w_A FUSE binding protein; s 44.3 6.4 0.00027 18.2 1.1 29 64-92 5-33 (174) 22 1ega_A Protein (GTP-binding pr 42.6 16 0.00068 15.9 7.6 84 34-117 193-293 (301) 23 3krm_A Insulin-like growth fac 41.9 10 0.00043 17.0 1.9 29 64-92 5-33 (163) 24 2jzx_A Poly(RC)-binding protei 41.0 7.7 0.00032 17.8 1.1 29 64-92 7-35 (160) 25 1j5k_A Heterogeneous nuclear r 39.4 8.5 0.00036 17.5 1.1 29 64-92 16-44 (89) 26 3ej9_B Beta-subunit of trans-3 39.4 6.8 0.00029 18.1 0.7 17 150-167 49-65 (70) 27 2anr_A Neuro-oncological ventr 38.2 9.1 0.00038 17.4 1.1 29 64-92 8-36 (178) 28 1vig_A Vigilin; RNA-binding pr 37.9 8.7 0.00037 17.5 1.0 30 63-92 6-35 (71) 29 1x4n_A FAR upstream element bi 37.5 9.6 0.0004 17.2 1.2 30 63-92 16-45 (92) 30 1x4m_A FAR upstream element bi 37.4 8 0.00033 17.7 0.7 29 64-92 17-45 (94) 31 1tua_A Hypothetical protein AP 36.8 9 0.00038 17.4 0.9 29 64-92 6-34 (191) 32 1wvn_A Poly(RC)-binding protei 36.5 14 0.00059 16.3 1.9 29 64-92 8-36 (82) 33 2ctl_A Vigilin; K homology typ 36.0 9.1 0.00038 17.4 0.9 29 64-92 19-47 (97) 34 2opv_A KHSRP protein; KH domai 36.0 11 0.00048 16.8 1.4 29 64-92 16-44 (85) 35 2p2r_A Poly(RC)-binding protei 33.6 12 0.0005 16.7 1.1 30 63-92 6-35 (76) 36 2jvz_A KH type-splicing, FAR u 29.9 16 0.00068 15.9 1.3 27 65-91 5-31 (164) 37 2qnd_A FMR1 protein; KH domain 28.9 9.6 0.00041 17.2 0.0 28 65-92 7-34 (144) 38 2cte_A Vigilin; K homology typ 28.4 14 0.00057 16.4 0.7 29 64-92 19-47 (94) 39 2ctm_A Vigilin; K homology typ 28.2 14 0.00057 16.3 0.7 29 64-92 19-47 (95) 40 2ctj_A Vigilin; K homology typ 27.6 14 0.00057 16.3 0.6 28 64-91 19-46 (95) 41 2ctf_A Vigilin; K homology typ 27.1 16 0.00065 16.0 0.8 28 65-92 30-57 (102) 42 2ctk_A Vigilin; K homology typ 25.4 12 0.00051 16.6 0.0 29 64-92 19-47 (104) 43 2cpq_A FragIle X mental retard 24.0 10 0.00042 17.1 -0.6 28 64-91 17-44 (91) 44 2dgr_A Ring finger and KH doma 22.1 37 0.0015 13.9 2.7 28 65-92 13-40 (83) 45 2asb_A Transcription elongatio 21.8 37 0.0016 13.8 2.9 56 38-93 84-148 (251) 46 2e3u_A PH-DIM2P, hypothetical 20.2 17 0.00073 15.7 -0.0 29 65-93 37-65 (219) No 1 >3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3kc4_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* ... Probab=100.00 E-value=0 Score=534.70 Aligned_cols=214 Identities=51% Similarity=0.860 Sum_probs=207.9 Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCC Q ss_conf 98645785266503206215670273125799998999999999877422642215532588518999973741001356 Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKK 80 (227) Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkk 80 (227) |||||||+|||||++++|+|.|||++++|+++|+||++||+||.+++.++|+++++|+|+++.+.|.||+++|+.++|++ T Consensus 1 MGQKvnP~gfRlgi~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~~~~agis~i~I~rt~~~~~I~I~~~~Pg~iig~k 80 (233) T 3i1m_C 1 MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKK 80 (233) T ss_dssp -CCCCCTTTTTTTSSCCCSBCCCCCHHHHHHHHHHHHHHHHHHHHHTGGGTEEEEEBCCCSSCBCCEEEESCHHHHHCST T ss_pred CCCCCCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCEEECCC T ss_conf 97987980311132479741787893334799889999999999987761443010574366469999934886487265 Q ss_pred CHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCC Q ss_conf 53489989876403587057879981375533778799999998759636899999999853238855999970367864 Q gi|254780255|r 81 GTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGA 160 (227) Q Consensus 81 g~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~ 160 (227) |.++++|+..|++.++.+++|++.++++|+++|.++|++||++||+|++||++++++++++|++||+||||+|||||||| T Consensus 81 g~~i~~l~~~l~~~~~~~~~i~V~evk~p~l~A~~iA~~Ia~~Lekr~~fRr~~~~~~~~~~~~gakGikI~isGRL~Ga 160 (233) T 3i1m_C 81 GEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGA 160 (233) T ss_dssp THHHHHHHHHHHHHHTSCBCCEEEECSSGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTCCSEEEEEEESSTTSC T ss_pred CHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHH T ss_conf 35689999999984287316999994480034689999999999851357789999999998769967899981454402 Q ss_pred CCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCC Q ss_conf 2221578752553245200003056899995382667999973288537721134 Q gi|254780255|r 161 ELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTI 215 (227) Q Consensus 161 e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~~~~ 215 (227) ||||+|||++|+|||||++|+|||++++|+|+||+||||||||.+|+++ ++... T Consensus 161 e~Ar~e~~~~G~vpl~tl~a~Idy~~~~a~T~yGv~GVKVwI~~~~~~~-~~~~~ 214 (233) T 3i1m_C 161 EIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILG-GMAAV 214 (233) T ss_dssp SSCCCCBCCEECCCTTCSSSEEEEEEECCEETTEECEEEEEEEEECC-------- T ss_pred HHHEEEEEECCCCCCCCCCCCEEEEEEEEECCCEEEEEEEEEECCCCCC-CCCCC T ss_conf 3111323536632356755406999999984886289999997786568-74344 No 2 >2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Probab=100.00 E-value=0 Score=509.32 Aligned_cols=215 Identities=47% Similarity=0.789 Sum_probs=209.3 Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCC Q ss_conf 98645785266503206215670273125799998999999999877422642215532588518999973741001356 Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKK 80 (227) Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkk 80 (227) |||||||+|||||++++|+|.|||++++|+++|+||++||+||+++|.++|+++++|+|+++.+.|+||+++|+.++|++ T Consensus 1 MGQKvnP~g~RLgi~k~w~S~Wya~~k~Y~~~L~eD~~IR~yl~k~l~~agis~i~I~r~~~~~~I~I~~~~p~~iig~k 80 (239) T 2vqe_C 1 MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRG 80 (239) T ss_dssp -CCCCCTTTTTTTSSCCCSBCCCCCTTTHHHHHHHHHHHHHHHHTTTTTTCEEEECBCBSSSCBCCEEEESCGGGTSCSS T ss_pred CCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCEECCCC T ss_conf 97988981520154689863484791355799999999999999762552445310463267459999935875220255 Q ss_pred CHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCC Q ss_conf 53489989876403587057879981375533778799999998759636899999999853238855999970367864 Q gi|254780255|r 81 GTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGA 160 (227) Q Consensus 81 g~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~ 160 (227) |..++++...++++++.+++|++.++.+|+++|.++|++||++||+|++||++++++++++|++||+|++|+|||||||+ T Consensus 81 g~~i~~l~~~l~k~~~~~~~i~v~~v~~p~l~a~~iA~~ia~~Le~r~~frr~~~~~l~~~~~~gakG~kI~iSGRl~g~ 160 (239) T 2vqe_C 81 GERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGA 160 (239) T ss_dssp SSHHHHHHHHHHHHSTTCCCCEEEECSCTTSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCSEEEEEECSCTTTC T ss_pred CHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHH T ss_conf 42578999999997489659999991275520589999999999704044999999999875548757999963653633 Q ss_pred CCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCC Q ss_conf 2221578752553245200003056899995382667999973288537721134 Q gi|254780255|r 161 ELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTI 215 (227) Q Consensus 161 e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~~~~ 215 (227) ||||+||+++|+|||||++++|||++++|+|+||+||||||||.+|+.+++.... T Consensus 161 e~ar~e~~~~G~vpl~t~~~~Idy~~~~a~Tk~Gi~GVKVwI~~~~~~~~~~~~~ 215 (239) T 2vqe_C 161 EQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKA 215 (239) T ss_dssp SSCCCBCCEEECCCTTCGGGCEEEEEECCBCSSCBCCEEEEEECCCC-------- T ss_pred HCEEEEEEECCEEECCCCCCCEEEEEEEEEECCEEEEEEEEEECCCCCCCCCCCC T ss_conf 2027899856299887546616999999980887189999998887478877655 No 3 >3ofo_C 30S ribosomal protein S3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 2gyb_C 2gy9_C* 3fih_C* 2wwl_C 3ofp_C Probab=100.00 E-value=0 Score=509.87 Aligned_cols=206 Identities=53% Similarity=0.879 Sum_probs=204.1 Q ss_pred CCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCC Q ss_conf 86457852665032062156702731257999989999999998774226422155325885189999737410013565 Q gi|254780255|r 2 GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKG 81 (227) Q Consensus 2 GQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg 81 (227) ||||||+|||||++++|+|.|||++++|+++|+||++||+||++++.++|+++++|+|+++.+.|+||+++|+.++|++| T Consensus 1 GQKvnP~gfRlgi~k~w~S~Wfa~~k~Y~~~l~eD~~IR~~i~k~l~~agis~i~I~rt~~~~~I~I~~~~p~~iig~~g 80 (206) T 3ofo_C 1 GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKG 80 (206) T ss_dssp CCCCCTTTTTTTSSCCCSBCCCCCHHHHHHHHHHHTTTHHHHHHHTTTTTEEEEEBCCCSSCBCCEEEESSHHHHHCGGG T ss_pred CCCCCCCCEEECCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCEEEEEEECCCCHHHCCCH T ss_conf 99879814300104798657878834347998999999999998877614431479965883799999547611113641 Q ss_pred HHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCC Q ss_conf 34899898764035870578799813755337787999999987596368999999998532388559999703678642 Q gi|254780255|r 82 TDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAE 161 (227) Q Consensus 82 ~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e 161 (227) .++++|++.|++.++.++++++.++++|+++|.++|++||++||+|++|||+++++++++|++||+||||+|||||+|+| T Consensus 81 ~~i~~l~~~l~~~~~~~~~i~v~ev~~p~l~A~~iA~~Ia~~Lekr~~fRr~~~~~~~~~~~~gakG~kI~isGrl~G~e 160 (206) T 3ofo_C 81 EDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAE 160 (206) T ss_dssp HHHHHHHHHHHHHHTSCBCCBCCCCSCGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTSCSEEEEEEESSTTSCS T ss_pred HHHHHHHHHHHHHCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCC T ss_conf 67999999999850983479999943810558999999999997361289999999999998599668999813436554 Q ss_pred CCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCC Q ss_conf 2215787525532452000030568999953826679999732885 Q gi|254780255|r 162 LSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207 (227) Q Consensus 162 ~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~ 207 (227) |||+|||++|+|||||++|+|||++++|+|+||+||||||||++|+ T Consensus 161 ~Ar~e~~~~G~v~l~t~~~~idy~~~~a~t~~G~~GvkVwI~~~e~ 206 (206) T 3ofo_C 161 IARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEI 206 (206) T ss_dssp SCCCCEEECSCCCTTCSSSEECCEEEEEEETTEEEEEEEEEEEECC T ss_pred CCCEEEEEECEEECCCCCCCEEEEEEEEECCCEEEEEEEEEECCCC T ss_conf 5414999726526687343217999999848712899999978999 No 4 >3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=100.00 E-value=0 Score=496.03 Aligned_cols=207 Identities=35% Similarity=0.637 Sum_probs=199.1 Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHH--------CCCCCEEEEECCCCCEEEEEECC Q ss_conf 9864578526650320621567027312579999899999999987742--------26422155325885189999737 Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQ--------AGVAKILIERTHKNCRIIVYSAR 72 (227) Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~--------agis~i~I~Rt~~~i~I~I~~~k 72 (227) |||||||+|||||++++|+|.|||++++|+++|+||++||+||.++++. +++++++|+|+++.+.+++|+++ T Consensus 1 MGQKvnP~g~RLgi~~~w~S~Wfa~~k~Y~~~l~eD~~IR~~i~~~~~~~~~~~~~~~~is~I~I~r~~~~~~i~i~~~~ 80 (218) T 3bbn_C 1 MGQKINPLGFRLGTTQSHYSLWFSQPKNYAEGLQEDQKIRDCIKNYVQKNTKTSSGVEGIARIEIQKRIDLIQVIIHMGF 80 (218) T ss_dssp CCCCCCTTTSSTTTTSCCSBCCCCCTTSSHHHHHHHHHHHHHHHSCCSSSSCCTTTTTCEEEEEBCBSSSCBCCEEEESC T ss_pred CCCCCCCEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCEEEEEEECC T ss_conf 97988974132033579742793682154798887999999999999987553220352578998614775179999436 Q ss_pred CCCCCCCCCHHHHHHHHHHHCCC---CCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEE Q ss_conf 41001356534899898764035---870578799813755337787999999987596368999999998532388559 Q gi|254780255|r 73 PGLIIGKKGTDIEKIRKKLSNMT---NSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGV 149 (227) Q Consensus 73 P~~iiGkkg~~i~~l~~~L~~~~---~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGi 149 (227) |+.++|+.+..+++++..+++++ +.++.+++.+++.|+++|.++|++||.|||+|++|||+|+++++.+|++||+|| T Consensus 81 p~~vig~~~~~~~~l~~~~~k~~~~~~~~i~i~~~ev~~p~~~a~~iA~~ia~qLe~r~~frr~~k~~~~~~~~~g~kGi 160 (218) T 3bbn_C 81 PKLLIENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGI 160 (218) T ss_dssp TTTTSCSSSCTTHHHHHHHHHHSCSSCCCCCCCEEECSCTTTSHHHHHHHSTTTTTTTCCHHHHHTHHHHHHHTTCCSEE T ss_pred CCEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCEE T ss_conf 64010355224899999999985345761899999941720358999999999998120688999999988743479879 Q ss_pred EEEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCC Q ss_conf 9997036786422215787525532452000030568999953826679999732885 Q gi|254780255|r 150 KVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207 (227) Q Consensus 150 kI~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~ 207 (227) ||+||||||||||||+||+++|+|||||++|+|||++++|+|+||+||||||||.+|. T Consensus 161 kI~isGRl~Gae~Ar~e~~~~G~vpl~t~~~~Idy~~~~a~T~~Gi~GvKVWi~~~~~ 218 (218) T 3bbn_C 161 QIQIAGRIDGKEIARIEWIREGRVPLQTIRAKIDYCAYTVRTIYGVLGIKIWIFMGEE 218 (218) T ss_dssp EEECCSCCTTCSSCCCCEEEEECCCSSCSTTCCBCCEEECCCSSCCCEEEEEEECCC- T ss_pred EEEEECCCCHHHHCEEEEEEECCCCCCCCCCCCEEEEEEEECCCCEEEEEEEEECCCC T ss_conf 9999024775651004678845210776301127999999759850899999983899 No 5 >2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C 3jyv_C* Probab=100.00 E-value=0 Score=386.75 Aligned_cols=185 Identities=21% Similarity=0.304 Sum_probs=177.9 Q ss_pred EEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC--- Q ss_conf 56702731257999989999999998774226422155325885189999737410013565348998987640358--- Q gi|254780255|r 20 SRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN--- 96 (227) Q Consensus 20 S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~--- 96 (227) +.|.+.++.|.....++.+||+||.+.|.++||++++|+|+++.+.|+||+++||++||++|..+++|++.|++.|+ T Consensus 2 ~~~~s~kkkfv~~~~~~~~irefl~k~l~~aGis~ieI~Rt~~~~~I~I~t~rPg~vIGrkG~~i~~L~~~L~k~~~~~~ 81 (243) T 2zkq_c 2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPE 81 (243) T ss_dssp CBCCCCTTTHHHHHHHHHHHHHHHHHHTCTTTEEEEECBEETTEECCEEEESCHHHHHCGGGHHHHHHHHHHHHHSCTTT T ss_pred CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHHHHHHHHHCCCC T ss_conf 42576666999813289999999999887677444999987882899999189963755775789999999999837678 Q ss_pred CEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCC- Q ss_conf 7057879981375533778799999998759636899999999853238855999970367864222157875255324- Q gi|254780255|r 97 SEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPL- 175 (227) Q Consensus 97 ~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl- 175 (227) .++.|++.+|.+|++||+++|++||+|||+|++|||+++++++++|++||+||+|+|||||+| ||||+|||++|+||| T Consensus 82 ~~i~i~v~ev~~p~l~A~l~A~~ia~qLe~r~~fRra~~~~i~~~m~aGAkGikI~iSGrL~g-e~AR~e~~~eG~vp~s 160 (243) T 2zkq_c 82 GSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHS 160 (243) T ss_dssp CCCCCEEEECSCGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHSSCSEEEEEECSSGGG-SSCCCBCCEEESSHHH T ss_pred CEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCH-HHHHHHHHHCCCCCCC T ss_conf 728999997578431869999999999865722899999999998765986359999436446-7652556436853227 Q ss_pred -CCEEEECEEEEEEEEECCCEEEEEEEEEEC Q ss_conf -520000305689999538266799997328 Q gi|254780255|r 176 -QTLRAHIDYGTAVAETAYGSCGIKVYVSLR 205 (227) Q Consensus 176 -~t~~a~idy~~~~a~T~~G~~GvKVwi~~~ 205 (227) ||++++|||++++|+|+||++|||||||++ T Consensus 161 g~t~r~~IDya~~~a~t~~GiiGVKVwI~~~ 191 (243) T 2zkq_c 161 GDPVNYYVDTAVRHVLLRQGVLGIKVKIMLP 191 (243) T ss_dssp HSSTTCCEEEEEECCCCSSCCCCEEEEEECC T ss_pred CCCCCCEEEEEEEEEECCCEEEEEEEEEECC T ss_conf 9600100358999996587269999999568 No 6 >1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Probab=99.64 E-value=2.9e-16 Score=112.66 Aligned_cols=78 Identities=18% Similarity=0.347 Sum_probs=72.6 Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC---CEEEEEEEEECCCCCCH Q ss_conf 999999998774226422155325885189999737410013565348998987640358---70578799813755337 Q gi|254780255|r 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN---SEIHLSVNEVPKPEINA 113 (227) Q Consensus 37 ~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~---~~v~i~v~ei~~p~~~A 113 (227) -+||+||.+.|.+|||++|+|+|+++.+.|+||+++||+|||++|.++++|++.|++.|+ .++.|++.+|.+-.++| T Consensus 10 aeIre~l~k~l~~AGis~IeIeR~~~~i~I~I~tarPG~vIGrkG~~I~~L~~~L~k~~~~~~~~i~l~ae~Ia~r~l~p 89 (92) T 1wh9_A 10 AELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGSGP 89 (92) T ss_dssp HHHHHHHHHHTTTTTEEEEEEEECSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCCCTTSEEEEEEECCCSCCCS T ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCEECCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHCCCCC T ss_conf 99999999988768736599998799179999978976242347553999999999997899982899851543257885 Q ss_pred H Q ss_conf 7 Q gi|254780255|r 114 T 114 (227) Q Consensus 114 ~ 114 (227) . T Consensus 90 ~ 90 (92) T 1wh9_A 90 S 90 (92) T ss_dssp C T ss_pred C T ss_conf 4 No 7 >2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolase/protein binding complex; 2.40A {Helicobacter pylori 26695} Probab=95.55 E-value=0.022 Score=32.45 Aligned_cols=107 Identities=15% Similarity=0.089 Sum_probs=68.8 Q ss_pred HHHHHHHHHHHHHCCCCC--EEEEE-CCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC----CEEEEEEEEEC-C Q ss_conf 999999998774226422--15532-5885189999737410013565348998987640358----70578799813-7 Q gi|254780255|r 37 LKIREYLQCHLKQAGVAK--ILIER-THKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN----SEIHLSVNEVP-K 108 (227) Q Consensus 37 ~~IR~fi~k~l~~agis~--i~I~R-t~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~----~~v~i~v~ei~-~ 108 (227) -.+++|++..|...|+.- +++.. ....+.+.|.....+++||++|..++.|+..+....+ ..+.+++.... + T Consensus 5 ~evke~Le~lL~~mg~~~~~~~v~~~~~~~i~i~i~g~d~~~LIGk~G~tL~AlQ~L~~~~vn~~~~~~v~lDi~~YR~r 84 (152) T 2pt7_G 5 HEIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPTYGYSIRLEISTFLQN 84 (152) T ss_dssp HHHHHHHHHHTTTTTCCEEEEEEEEEETTEEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHHHSCEEEEEETTHHHH T ss_pred HHHHHHHHHHHHHCCCCCEEEEEEECCCCEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH T ss_conf 99999999999977997269998633797799997687355463779643799999999998525791699858888999 Q ss_pred CCCCHHHHHHHHHHHHHC-CC----H-HHHHHHHHHHHHHH Q ss_conf 553377879999999875-96----3-68999999998532 Q gi|254780255|r 109 PEINATLIAQSIAQQLER-RV----V-FRRAMKRAVQSAMR 143 (227) Q Consensus 109 p~~~A~~iA~~Ia~~Lek-r~----~-fRr~~k~~i~~~~k 143 (227) -+-.-.-+|..+|.+..+ +- | =|+++..+++.... T Consensus 85 R~e~L~~lA~~~A~kV~~tGr~~m~p~erriih~al~~~r~ 125 (152) T 2pt7_G 85 QEKVMDTQLQSVIMTVHEVGKGQMKAPDGVLTYIALKKLRK 125 (152) T ss_dssp HHHHHHHHHHHHHHHHHHTSCEEEECCSTTHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH T ss_conf 99999999999999999989899997006499999999887 No 8 >3gku_A Probable RNA-binding protein; APC21302, structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940} Probab=94.14 E-value=0.025 Score=32.19 Aligned_cols=103 Identities=22% Similarity=0.363 Sum_probs=66.9 Q ss_pred HHHHHHHHHHHHCCCC-CEEEEE--CCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCC----CCE--EEEEEEEEC- Q ss_conf 9999999877422642-215532--588518999973741001356534899898764035----870--578799813- Q gi|254780255|r 38 KIREYLQCHLKQAGVA-KILIER--THKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMT----NSE--IHLSVNEVP- 107 (227) Q Consensus 38 ~IR~fi~k~l~~agis-~i~I~R--t~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~----~~~--v~i~v~ei~- 107 (227) ...+|++..+...|+. .+.++. ....+.|.|.+..++++||++|..++.|+..+.... +.. +.+++.... T Consensus 65 ~a~~~Le~ll~~mg~~~~v~v~~~~~~~~i~i~i~g~d~g~LIGk~G~tL~aLQ~L~~~~v~~~~~~~~~V~lDi~~YR~ 144 (225) T 3gku_A 65 KAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRE 144 (225) T ss_dssp HHHHHHHHHHHHTTCCCEEEEEEETTTTEEEEEEECHHHHHCSTTHHHHHHHHHHHHHHHHHHTCSSCCEEEEESTTHHH T ss_pred HHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHH T ss_conf 89999999999759981489999447608999960662322314797106899999999998744873599985798999 Q ss_pred CCCCCHHHHHHHHHHHHHC-CC---------HHHHHHHHHHHH Q ss_conf 7553377879999999875-96---------368999999998 Q gi|254780255|r 108 KPEINATLIAQSIAQQLER-RV---------VFRRAMKRAVQS 140 (227) Q Consensus 108 ~p~~~A~~iA~~Ia~~Lek-r~---------~fRr~~k~~i~~ 140 (227) +-+-.-.-+|..+|.+..+ +. .-||++..+++. T Consensus 145 rR~e~L~~lA~~~a~kv~~tgk~v~L~PM~~~ERRiIH~~L~~ 187 (225) T 3gku_A 145 RRKETLETLAKNIAYKVKRTKRSVSLEPMNPYERRIIHAALQN 187 (225) T ss_dssp HHHHHHHHHHHHHHHHHHHHCSCEECCCCCHHHHHHHHHHTTT T ss_pred HHHHHHHHHHHHHHHHHHHHCCEEECCCCCHHHHHHHHHHHHC T ss_conf 9999999999999999984296787489986889999999841 No 9 >1wf3_A GTP-binding protein; GTPase, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus HB8} SCOP: c.37.1.8 d.52.3.1 Probab=83.53 E-value=2.1 Score=21.00 Aligned_cols=83 Identities=22% Similarity=0.342 Sum_probs=52.3 Q ss_pred HHHHHHHHHHHHHCC--CCCEEEE----ECCC--CCEEEEEECCCC---CCCCCCCHHHHHHH----HHHHCCCCCEEEE Q ss_conf 999999998774226--4221553----2588--518999973741---00135653489989----8764035870578 Q gi|254780255|r 37 LKIREYLQCHLKQAG--VAKILIE----RTHK--NCRIIVYSARPG---LIIGKKGTDIEKIR----KKLSNMTNSEIHL 101 (227) Q Consensus 37 ~~IR~fi~k~l~~ag--is~i~I~----Rt~~--~i~I~I~~~kP~---~iiGkkg~~i~~l~----~~L~~~~~~~v~i 101 (227) -.||+-+..++.+.= -..++|+ +..+ .+...|++.++. ++||++|+.|+++. +.|+++|+.++.+ T Consensus 195 EiiRe~i~~~l~~EiPy~~~v~i~~~~e~~~~~~~I~~~I~v~~~sqK~IviGk~G~~ik~I~~~ar~~le~~~~~kv~L 274 (301) T 1wf3_A 195 EILREEAMKRLWHEVPYAVATKVEEVAERENGVLYIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL 274 (301) T ss_dssp HHHHHHHHHTCCTTHHHHCEEEEEEEEEETTTEEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE T ss_pred HHHHHHHHHHCCCCCCCEEEEEEEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEE T ss_conf 99999998751433797679999988881388438999999867875307983784169999999999999996897699 Q ss_pred EE--EEECCCCCCHHHHHHH Q ss_conf 79--9813755337787999 Q gi|254780255|r 102 SV--NEVPKPEINATLIAQS 119 (227) Q Consensus 102 ~v--~ei~~p~~~A~~iA~~ 119 (227) .+ .--+++--+..++.+. T Consensus 275 ~l~VkV~~~W~~~~~~l~~~ 294 (301) T 1wf3_A 275 DLEVKVYPDWRKDPEALREL 294 (301) T ss_dssp EEEEEECTTGGGCHHHHHHH T ss_pred EEEEEECCCCCCCHHHHHHC T ss_conf 99999888846598999867 No 10 >3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp family, KH domain, ribonuclease, ME beta-lactamase superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB: 3af6_A* Probab=81.66 E-value=2.5 Score=20.58 Aligned_cols=108 Identities=20% Similarity=0.367 Sum_probs=64.7 Q ss_pred HHHHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHH Q ss_conf 999998774-2264221553258851899997374100135653489989876403587057879981375533778799 Q gi|254780255|r 40 REYLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQ 118 (227) Q Consensus 40 R~fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~ 118 (227) ++.|....+ .|||..+.-. +..-.|+|.+.+||+++|+.|+.++++++..-.. ..-+..|-+....+ + T Consensus 86 ~~~i~~~~~~~~~~~~~~f~--~~~~~v~~~~~~p~~~~~~~~~~~~~~~~~~~w~--------~~~~~~~~~~s~~~-~ 154 (651) T 3af5_A 86 EKLIFEIVPKEAEITNIAFD--PSVGEVLIEAKKPGLVIGKNGETLRLITQKVKWA--------PKVVRTPPLQSQTI-Y 154 (651) T ss_dssp HHHHHHHSCGGGCCCEEEEE--TTTTEEEEEESSTTTTSCTTSHHHHHHHHHHCSE--------EEEEECCSSCCHHH-H T ss_pred HHHHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCE--------EEEEECCCCCCHHH-H T ss_conf 99999758976671258974--8972799996797468647626899999974985--------68986799972789-9 Q ss_pred HHHHHHHCCCHHHHH-HHHHHHHHHH---CCCCEEEEEEECCCC Q ss_conf 999998759636899-9999998532---388559999703678 Q gi|254780255|r 119 SIAQQLERRVVFRRA-MKRAVQSAMR---FGADGVKVIASGRLN 158 (227) Q Consensus 119 ~Ia~~Lekr~~fRr~-~k~~i~~~~k---~g~kGikI~isGRl~ 158 (227) .|..-|..-..+|+- +++.=.++.+ ..-..++|..=|=.+ T Consensus 155 ~~~~~~~~~~~~r~~~l~~~g~~i~~~~~~~~~~vrit~LGG~~ 198 (651) T 3af5_A 155 SIRQILQTESKDRRKFLRQVGRNIYRKPEYKSRWIRITGLGGFR 198 (651) T ss_dssp HHHHHHHHCHHHHHHHHHHHHHHHTSSSCCCCSCEEEEEEECSS T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCC T ss_conf 99999997189999999985687368987899827999936888 No 11 >2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei} Probab=77.97 E-value=3.3 Score=19.88 Aligned_cols=107 Identities=20% Similarity=0.347 Sum_probs=65.1 Q ss_pred HHHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHH Q ss_conf 99998774-22642215532588518999973741001356534899898764035870578799813755337787999 Q gi|254780255|r 41 EYLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQS 119 (227) Q Consensus 41 ~fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~ 119 (227) +.|....+ .|||+.+... +..-.|+|.+.+||+++|+.|..++++++..-. ...-+..|-+....+ +. T Consensus 82 ~~i~~~~~~~~~~~~~~~~--~~~~~v~~~~~~p~~~~~~~~~~~~~~~~~~~w--------~~~~~~~~~~~s~~~-~~ 150 (640) T 2xr1_A 82 SIIEEVVPKESVISSYYFD--PDSGEVIIEAEKPGLVIGKHGATLREITKQIGW--------IPKVVRTPPIKSRTV-KN 150 (640) T ss_dssp HHHHHHSCGGGCEEEEEEC--TTTSEEEEEESSHHHHHCSSSHHHHHHHHHHCS--------EEEEEECCSSCCHHH-HH T ss_pred HHHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCEEEECCCCHHHHHHHHHHCC--------EEEEEECCCCCCHHH-HH T ss_conf 9999758965683058973--897389999679755656773579999997598--------368997799972789-99 Q ss_pred HHHHHHCCCHHHHH-HHHHHHHHHH---CCCCEEEEEEECCCC Q ss_conf 99998759636899-9999998532---388559999703678 Q gi|254780255|r 120 IAQQLERRVVFRRA-MKRAVQSAMR---FGADGVKVIASGRLN 158 (227) Q Consensus 120 Ia~~Lekr~~fRr~-~k~~i~~~~k---~g~kGikI~isGRl~ 158 (227) |..-|..-...|+- +++.=.++-+ .+-.-++|..=|=.+ T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~irit~LGG~~ 193 (640) T 2xr1_A 151 IREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALGGCK 193 (640) T ss_dssp HHHHHHHTHHHHHHHHHHHHHHHTSCCCCSCCCCEEEEEECSS T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCC T ss_conf 9999998499999999986786279987899808999947888 No 12 >2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A Probab=74.67 E-value=1.9 Score=21.25 Aligned_cols=44 Identities=18% Similarity=0.346 Sum_probs=32.8 Q ss_pred HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 22642215532588518999973741001356534899898764 Q gi|254780255|r 49 QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 49 ~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ++-..+|.+.-..+.+.+.+....-|.+||++|++|++|++... T Consensus 23 ~~~~~~c~~~d~~~~iifvVp~~~vG~iIGkgG~~Ik~i~e~tg 66 (144) T 2cxc_A 23 GVTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALG 66 (144) T ss_dssp SCCEEEEEEEGGGTEEEEEECTTCHHHHHCGGGHHHHHHHHHHS T ss_pred CCCEEEEEEECCCCEEEEEECCCHHHHEECCCCHHHHHHHHHHC T ss_conf 98536899937999899998867242415878189999999719 No 13 >1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Probab=60.87 E-value=2.7 Score=20.38 Aligned_cols=41 Identities=32% Similarity=0.317 Sum_probs=31.3 Q ss_pred CCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 42215532588518999973741001356534899898764 Q gi|254780255|r 52 VAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 52 is~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) -+.+..+.++-...+.|-...-+.|||++|.+|++|++.-. T Consensus 5 s~~~~~~~~~v~~~i~IP~~~vg~iIG~~G~~I~~I~~~tg 45 (104) T 1we8_A 5 SSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASG 45 (104) T ss_dssp CCCCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHC T ss_pred CCCCCCCCCCEEEEEEECHHHCCEEECCCCHHHHHHHHHHC T ss_conf 88866899988999998967638219969719997468759 No 14 >2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Probab=58.98 E-value=5.2 Score=18.74 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=24.5 Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHH Q ss_conf 51899997374100135653489989876 Q gi|254780255|r 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227) Q Consensus 63 ~i~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227) .+.+.|-...-|.|||++|..|++|++.- T Consensus 8 ~i~~~VP~~~vG~IIGk~G~~Ik~i~~~t 36 (107) T 2hh2_A 8 EMTFSIPTHKCGLVIGRGGENVKAINQQT 36 (107) T ss_dssp CEEEEEEGGGTTTTSTTTTCHHHHHHHHS T ss_pred EEEEEECHHHCCEEECCCCHHHHHHHHHC T ss_conf 59999896661645898984898323315 No 15 >3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome assembly, GTP-binding; HET: GNP; 1.90A {Aquifex aeolicus} Probab=57.79 E-value=9.1 Score=17.35 Aligned_cols=52 Identities=27% Similarity=0.418 Sum_probs=25.8 Q ss_pred EEEECCCC---CCCCCCCHHHHHH----HHHHHCCCCCEEEEE--EEEECCCCCCHHHHHH Q ss_conf 99973741---0013565348998----987640358705787--9981375533778799 Q gi|254780255|r 67 IVYSARPG---LIIGKKGTDIEKI----RKKLSNMTNSEIHLS--VNEVPKPEINATLIAQ 118 (227) Q Consensus 67 ~I~~~kP~---~iiGkkg~~i~~l----~~~L~~~~~~~v~i~--v~ei~~p~~~A~~iA~ 118 (227) .|++.+.. +++|++|+.|+++ +..|+++++.++.+. |.--+++-.++.++.+ T Consensus 243 ~i~v~k~s~k~iiiG~~G~~ik~I~~~ar~~l~~~~~~~v~L~l~VkV~~~W~~~~~~l~~ 303 (308) T 3iev_A 243 EIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRL 303 (308) T ss_dssp EEEESSGGGHHHHHCGGGHHHHHHHHHHHHHHHHHHTSCEEEEEEEEECTTGGGCHHHHHH T ss_pred EEEECCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCHHHHHH T ss_conf 9986163501278768725799999999999999809987999999989883359899997 No 16 >2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Probab=55.17 E-value=5.2 Score=18.78 Aligned_cols=32 Identities=25% Similarity=0.388 Sum_probs=26.8 Q ss_pred CCCCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 88518999973741001356534899898764 Q gi|254780255|r 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 61 ~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ...+.|.|-...-+.|||++|..|++|++.-. T Consensus 10 ~~~~ei~VP~~~vG~IIGk~G~~Ik~I~~~tg 41 (106) T 2hh3_A 10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAG 41 (106) T ss_dssp --CEEEEEETTTHHHHHTTTTHHHHHHHHHHT T ss_pred CCEEEEEECHHHCCEEECCCCCHHHHHHHHCC T ss_conf 86299997866578438999802589998679 No 17 >1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Probab=53.02 E-value=5.7 Score=18.54 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=24.3 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +.+.|-...-|.+||++|..|+++++.-. T Consensus 5 v~i~VP~~~vg~iIGk~G~~Ik~I~~~tg 33 (76) T 1dtj_A 5 VEMAVPENLVGAILGKGGKTLVEYQELTG 33 (76) T ss_dssp EEEEEETTTHHHHHCSTTHHHHHHHHHHC T ss_pred EEEEECHHHCCEEECCCCHHHHHHHHHHC T ss_conf 99996977503128989747999999879 No 18 >1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Probab=52.53 E-value=8.7 Score=17.45 Aligned_cols=29 Identities=31% Similarity=0.511 Sum_probs=24.3 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..|.|-...-|.|||++|..|+++++.-. T Consensus 9 ~~i~VP~~~vg~iIGk~G~~I~~I~~~tg 37 (82) T 1zzk_A 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESG 37 (82) T ss_dssp EEEEEETTTGGGGTCGGGHHHHHHHHHHC T ss_pred EEEEECHHHCCCEECCCCHHHHHHHHHHC T ss_conf 99999867505018979723899999739 No 19 >1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Probab=50.81 E-value=4.4 Score=19.18 Aligned_cols=30 Identities=23% Similarity=0.285 Sum_probs=24.9 Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 518999973741001356534899898764 Q gi|254780255|r 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 63 ~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) -++|.|-...-|.|||++|..|+++++.-. T Consensus 4 ~vei~VP~~~vg~iIGk~G~~Ik~I~~~tg 33 (87) T 1ec6_A 4 LVEIAVPENLVGAILGKGGKTLVEYQELTG 33 (87) T ss_dssp EEEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEEECHHHCCEEECCCCHHHHHHHHHHC T ss_conf 999993974446369969868999999879 No 20 >2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein/DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A Probab=45.16 E-value=6.1 Score=18.36 Aligned_cols=29 Identities=34% Similarity=0.634 Sum_probs=24.2 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +.+.+-...-|.+||++|..+++|++.-. T Consensus 7 ~~i~ip~~~~g~iIG~~G~~I~~I~~~tg 35 (73) T 2axy_A 7 IRLLMHGKEVGSIIGKKGESVKKMREESG 35 (73) T ss_dssp EEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEECHHHEEEEECCCCHHHHHHHHHCC T ss_conf 99998866723589999834999999709 No 21 >1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Probab=44.26 E-value=6.4 Score=18.23 Aligned_cols=29 Identities=24% Similarity=0.446 Sum_probs=22.3 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +++.|-...-|.|||++|..|++|++.-. T Consensus 5 i~v~IP~~~vG~IIGk~G~~Ik~i~~~tg 33 (174) T 1j4w_A 5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAG 33 (174) T ss_dssp EEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEECHHHHCEEECCCCHHHHHHHHHHC T ss_conf 99994724503579999979999999879 No 22 >1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X Probab=42.59 E-value=16 Score=15.93 Aligned_cols=84 Identities=24% Similarity=0.278 Sum_probs=50.8 Q ss_pred HHHHHHHHHHHHHHHHCCCC--CEEEE----ECCCC--CEEEEEECCCC---CCCCCCCHHHHHHH----HHHHCCCCCE Q ss_conf 98999999999877422642--21553----25885--18999973741---00135653489989----8764035870 Q gi|254780255|r 34 HEDLKIREYLQCHLKQAGVA--KILIE----RTHKN--CRIIVYSARPG---LIIGKKGTDIEKIR----KKLSNMTNSE 98 (227) Q Consensus 34 ~eD~~IR~fi~k~l~~agis--~i~I~----Rt~~~--i~I~I~~~kP~---~iiGkkg~~i~~l~----~~L~~~~~~~ 98 (227) ...-.+|+.+...+++.=-- .++++ +.... +...|++.++. +++|++|..++++. ..|+++++.+ T Consensus 193 ~~~EiiRe~i~~~l~~EiPy~~~v~~~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~G~~iK~I~~~ar~~l~~~~~~~ 272 (301) T 1ega_A 193 MASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAP 272 (301) T ss_dssp HHHHHHHHHHHHHHGGGCCTTEEEEEEEEECCSSCSEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHTTSC T ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 15887676652024555210357888999862688489999999964894689992898418999999999999995999 Q ss_pred EEE--EEEEECCCCCCHHHHH Q ss_conf 578--7998137553377879 Q gi|254780255|r 99 IHL--SVNEVPKPEINATLIA 117 (227) Q Consensus 99 v~i--~v~ei~~p~~~A~~iA 117 (227) +.+ .|.--+++.-++..+. T Consensus 273 V~L~l~Vkv~~~w~~~~~~l~ 293 (301) T 1ega_A 273 VHLELWVKVKSGWADDERALR 293 (301) T ss_dssp EEEEEEEEETTCCCHHHHHHT T ss_pred EEEEEEEEECCCCCCCHHHHH T ss_conf 699999997489565889998 No 23 >3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Probab=41.85 E-value=10 Score=17.04 Aligned_cols=29 Identities=31% Similarity=0.543 Sum_probs=20.9 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +.|.|=...-|+|||++|..|+++.+.-. T Consensus 5 i~i~IP~~~vg~vIGk~G~~Ik~I~~~tg 33 (163) T 3krm_A 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFAS 33 (163) T ss_dssp EEEEEEGGGHHHHHCGGGHHHHHHHHHHT T ss_pred EEEEECHHHHCEEECCCCHHHHHHHHHHC T ss_conf 99997757705118999877999999859 No 24 >2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, cytoplasm, DNA-binding, nucleus, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Homo sapiens} Probab=40.99 E-value=7.7 Score=17.76 Aligned_cols=29 Identities=34% Similarity=0.634 Sum_probs=21.5 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .++.+.+..-|.|||++|..|++|++.-. T Consensus 7 ~ri~vp~~~vg~vIGk~G~~Ik~I~~~tg 35 (160) T 2jzx_A 7 IRLLMHGKEVGSIIGKKGESVKKMREESG 35 (160) T ss_dssp EEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEECHHHHCEEECCCCHHHHHHHHHHC T ss_conf 99998456712237888778999999879 No 25 >1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Probab=39.41 E-value=8.5 Score=17.54 Aligned_cols=29 Identities=31% Similarity=0.511 Sum_probs=23.0 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..+.|-...-+.|||++|..|++|++.-. T Consensus 16 ~~i~VP~~~vg~iIG~~G~~I~~I~~~sg 44 (89) T 1j5k_A 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESG 44 (89) T ss_dssp EEEEEEHHHHHHHHCGGGHHHHHHHHHTC T ss_pred EEEEECHHHCCEEECCCCCCHHHHHHHHC T ss_conf 99999977567279989842489999749 No 26 >3ej9_B Beta-subunit of trans-3-chloroacrylic acid dehalogenase; CAAD, isomerase, hydrolase; 1.50A {Pseudomonas pavonaceae} PDB: 3ej7_B 3ej3_B 1s0y_B Probab=39.40 E-value=6.8 Score=18.07 Aligned_cols=17 Identities=41% Similarity=0.610 Sum_probs=12.6 Q ss_pred EEEEECCCCCCCCCEEEE Q ss_conf 999703678642221578 Q gi|254780255|r 150 KVIASGRLNGAELSRTEC 167 (227) Q Consensus 150 kI~isGRl~G~e~Ar~e~ 167 (227) -+.+|||++| |-|.+|. T Consensus 49 n~sis~ri~g-eaaster 65 (70) T 3ej9_B 49 NMSISGRIHG-EAASTER 65 (70) T ss_dssp GEESTTCCTT-C------ T ss_pred CCCEEEEECC-CCCCCCC T ss_conf 2634203325-1103344 No 27 >2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein/RNA complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Probab=38.22 E-value=9.1 Score=17.36 Aligned_cols=29 Identities=31% Similarity=0.529 Sum_probs=23.1 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +++.+-...-|.|||++|..|++|++... T Consensus 8 ~r~~vP~~~~g~IIGk~G~~Ik~i~~~tg 36 (178) T 2anr_A 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETG 36 (178) T ss_dssp EEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEECHHHHCEEECCCCHHHHHHHHHHC T ss_conf 99998867724179989877999999879 No 28 >1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Probab=37.92 E-value=8.7 Score=17.46 Aligned_cols=30 Identities=23% Similarity=0.392 Sum_probs=23.7 Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 518999973741001356534899898764 Q gi|254780255|r 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 63 ~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .+.|.|-...-+.+||++|..|+++++.-. T Consensus 6 ~~~i~Vp~~~~~~iIG~~G~~I~~I~~~t~ 35 (71) T 1vig_A 6 YVEINIDHKFHRHLIGKSGANINRIKDQYK 35 (71) T ss_dssp EEEEEECSSHHHHHTCSSCCHHHHHHHHTC T ss_pred EEEEEECHHHHHHCCCCCCHHHHHHHHHHC T ss_conf 999999988752328999901999999849 No 29 >1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Probab=37.46 E-value=9.6 Score=17.23 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=24.4 Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 518999973741001356534899898764 Q gi|254780255|r 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 63 ~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ...+.|-...-+.|||++|..|++|++.-. T Consensus 16 t~~i~ip~~~vg~iIGk~G~~I~~I~~~tg 45 (92) T 1x4n_A 16 TEEYKVPDGMVGFIIGRGGEQISRIQQESG 45 (92) T ss_dssp EEEEEEEHHHHHHHHCSSSHHHHHHHHHSC T ss_pred EEEEEECHHHCCCEECCCCHHHHHHHHHHC T ss_conf 999999978648038989726999999729 No 30 >1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Probab=37.41 E-value=8 Score=17.69 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=23.7 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .+|.|-...-+.|||++|..|++|++.-. T Consensus 17 ~~i~Vp~~~~g~iIG~~G~~Ik~I~~~tg 45 (94) T 1x4m_A 17 QEIMIPASKAGLVIGKGGETIKQLQERAG 45 (94) T ss_dssp EEEEECHHHHHHHSCSSSSHHHHHHHHHT T ss_pred EEEEECHHHHCCEECCCCHHHHHHHHHCC T ss_conf 99997867400009959733799999809 No 31 >1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Probab=36.75 E-value=9 Score=17.37 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=16.0 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +.|.|=..+-|.|||++|..|++|++... T Consensus 6 ~~V~IP~~~vG~IIGk~G~~Ik~I~~~tg 34 (191) T 1tua_A 6 IYVKVKPERLGAVIGPRGEVKAEIMRRTG 34 (191) T ss_dssp EEEECCGGGHHHHHCGGGHHHHHHHHHHT T ss_pred EEEECCHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 89878978731334955889999999979 No 32 >1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Probab=36.51 E-value=14 Score=16.27 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=23.9 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..+.|-...-+.|||++|..|+++++.-. T Consensus 8 ~~v~VP~~~vg~iIG~~G~~i~~I~~~tg 36 (82) T 1wvn_A 8 HELTIPNNLIGCIIGRQGANINEIRQMSG 36 (82) T ss_dssp EEEEEEGGGHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHHC T ss_conf 99998865446289989983999999739 No 33 >2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=36.05 E-value=9.1 Score=17.36 Aligned_cols=29 Identities=31% Similarity=0.362 Sum_probs=23.4 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) +.|.|-...-+.|||++|..|++|++.-. T Consensus 19 ~~i~Vp~~~~~~iIG~~G~~I~~I~~~tg 47 (97) T 2ctl_A 19 LSVTVDPKYHPKIIGRKGAVITQIRLEHD 47 (97) T ss_dssp EEEECCTTTHHHHSCSSSCHHHHHHHHHT T ss_pred EEEEECHHHHHHCCCCCCCCHHHHHHHHC T ss_conf 99999989983527989730999999869 No 34 >2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Probab=36.05 E-value=11 Score=16.78 Aligned_cols=29 Identities=28% Similarity=0.645 Sum_probs=23.6 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .++.|-...-++|||++|..|++++..-. T Consensus 16 ~~v~Vp~~~vg~iIGk~G~~Ik~I~~~sg 44 (85) T 2opv_A 16 QEIMIPAGKAGLVIGKGGETIKQLQERAG 44 (85) T ss_dssp EEEEECTTTHHHHHTTTTHHHHHHHHHHT T ss_pred EEEEECHHHCCEEECCCCHHHHHHHHHCC T ss_conf 99996977637239989737999999809 No 35 >2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Probab=33.61 E-value=12 Score=16.68 Aligned_cols=30 Identities=27% Similarity=0.476 Sum_probs=23.8 Q ss_pred CCEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 518999973741001356534899898764 Q gi|254780255|r 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 63 ~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ...+.|-...-+.|||++|.+|++|++.-. T Consensus 6 s~~i~VP~~~vg~iIGk~G~~i~~i~~~sg 35 (76) T 2p2r_A 6 SHELTIPNDLIGCIIGRQGAKINEIRQMSG 35 (76) T ss_dssp EEEEEEEHHHHHHHHCGGGHHHHHHHHHHC T ss_pred EEEEEECHHHCCEEECCCCHHHHHHHHHHC T ss_conf 899998977538169989818999999759 No 36 >2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Probab=29.88 E-value=16 Score=15.89 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=17.1 Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHH Q ss_conf 899997374100135653489989876 Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227) Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227) .+.+-...-|.|||++|..|++|++.- T Consensus 5 ~iliP~~~vg~iIGk~G~~I~~i~~~t 31 (164) T 2jvz_A 5 EIMIPAGKAGLVIGKGGETIKQLQERA 31 (164) T ss_dssp EEEECTTCHHHHTCTTTHHHHHHHHTS T ss_pred EEECCHHHCCEEECCCCHHHHHHHHHH T ss_conf 998475670746889987899999997 No 37 >2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I KH domains, fragIle X mental retardation protein, RNA binding protein; 1.90A {Homo sapiens} PDB: 2fmr_A Probab=28.89 E-value=9.6 Score=17.21 Aligned_cols=28 Identities=36% Similarity=0.532 Sum_probs=20.8 Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 8999973741001356534899898764 Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .+.+-...-|.+||++|.+|+++++... T Consensus 7 ~~~vp~~~vg~iIGk~G~~Ik~i~~~tg 34 (144) T 2qnd_A 7 QFIVREDLMGLAIGTHGANIQQARKVPG 34 (144) T ss_dssp EEECCGGGHHHHHCGGGHHHHHHHTSTT T ss_pred EEEECHHHHHHCCCCCHHHHHHHHHHCC T ss_conf 9999978873557956288999999719 No 38 >2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=28.40 E-value=14 Score=16.35 Aligned_cols=29 Identities=17% Similarity=0.426 Sum_probs=23.1 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..|.|-...-++|||++|..|+++++.-. T Consensus 19 ~~v~Ip~~~~~~iIG~~G~~I~~I~~~tg 47 (94) T 2cte_A 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTA 47 (94) T ss_dssp EEEECCTTTHHHHHCSSSCHHHHHHHHTT T ss_pred EEEEECHHHHHHCCCCCCHHHHHHHHHHC T ss_conf 99999989881516979651999999859 No 39 >2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=28.17 E-value=14 Score=16.33 Aligned_cols=29 Identities=24% Similarity=0.319 Sum_probs=23.5 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..+.|-...-++|||++|..|++|++.-. T Consensus 19 ~~i~Ip~~~~~~iIG~~G~~I~~I~~~t~ 47 (95) T 2ctm_A 19 EDVPLDHRVHARIIGARGKAIRKIMDEFK 47 (95) T ss_dssp EEEECCTTTHHHHHCSSSCHHHHHHHHHT T ss_pred EEEEECHHHHHHHHCCCCHHHHHHHHHHC T ss_conf 99999989985741889633999999859 No 40 >2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=27.58 E-value=14 Score=16.35 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=21.6 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHH Q ss_conf 1899997374100135653489989876 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227) ..|.|-...-++|||++|..|++|++.. T Consensus 19 ~~i~Vp~~~~~~iIG~~G~~i~~I~~~~ 46 (95) T 2ctj_A 19 VEVSIPAKLHNSLIGTKGRLIRSIMEEC 46 (95) T ss_dssp EEEECCHHHHHHHHCSSSHHHHHHHHHH T ss_pred EEEEECHHHHHHCCCCCCCCHHHHHHHC T ss_conf 9999898998560788984099999983 No 41 >2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=27.09 E-value=16 Score=16.02 Aligned_cols=28 Identities=32% Similarity=0.491 Sum_probs=21.4 Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 8999973741001356534899898764 Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .|.+-....++|||++|..|++|.+.-. T Consensus 30 ~i~vP~~~h~~IIG~~G~~Ir~i~~~~g 57 (102) T 2ctf_A 30 SVAAPSWLHRFIIGKKGQNLAKITQQMP 57 (102) T ss_dssp EEECCSTTHHHHHTTTTCHHHHHHHHCS T ss_pred EEECCHHHHHHEECCCCHHHHHHHHHCC T ss_conf 9981888882406899446999999849 No 42 >2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=25.41 E-value=12 Score=16.63 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=22.3 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18999973741001356534899898764 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) ..+.|-...-+.|||++|.+|++|++.-. T Consensus 19 ~~i~VP~~~~~~iIG~~G~~I~~I~~~t~ 47 (104) T 2ctk_A 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFE 47 (104) T ss_dssp EEEECCHHHHHHHHCSSSHHHHHHHHHTC T ss_pred EEEEECHHHHHHCCCCCCHHHHHHHHHHC T ss_conf 99999989995615899633999999809 No 43 >2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Probab=24.05 E-value=10 Score=17.12 Aligned_cols=28 Identities=32% Similarity=0.478 Sum_probs=21.9 Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHH Q ss_conf 1899997374100135653489989876 Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227) Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227) ..|.|-...-+++||++|.+|+++++.- T Consensus 17 ~ev~Vp~~~vg~vIG~gG~~I~~I~~~t 44 (91) T 2cpq_A 17 EEFVVREDLMGLAIGTHGSNIQQARKVP 44 (91) T ss_dssp EEEECCHHHHHHHHTTTTHHHHHHHTST T ss_pred EEEEECHHHHHHCCCCCCHHHHHHHHHH T ss_conf 9999997773320798966699999971 No 44 >2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=22.09 E-value=37 Score=13.87 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=21.9 Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHH Q ss_conf 8999973741001356534899898764 Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227) Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227) .+.|-...-++|||++|..|++|++... T Consensus 13 ~i~Vp~~~~g~iIG~~G~~i~~I~~~tg 40 (83) T 2dgr_A 13 QVRVPYRVVGLVVGPKGATIKRIQQRTH 40 (83) T ss_dssp EEECCHHHHHHHHTTTTSSHHHHHHHTT T ss_pred EEEECHHHHCCEECCCCHHHHHHHHHHC T ss_conf 9999968627348888538999999889 No 45 >2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A Probab=21.78 E-value=37 Score=13.83 Aligned_cols=56 Identities=21% Similarity=0.402 Sum_probs=38.3 Q ss_pred HHHHHHHHHHHHC--CCCC-EEEEECC-CCCEEEEEECCCC-----CCCCCCCHHHHHHHHHHHC Q ss_conf 9999999877422--6422-1553258-8518999973741-----0013565348998987640 Q gi|254780255|r 38 KIREYLQCHLKQA--GVAK-ILIERTH-KNCRIIVYSARPG-----LIIGKKGTDIEKIRKKLSN 93 (227) Q Consensus 38 ~IR~fi~k~l~~a--gis~-i~I~Rt~-~~i~I~I~~~kP~-----~iiGkkg~~i~~l~~~L~~ 93 (227) ++++.|+...+.. |+.. ..|-|-| ...+|-+++..|+ ..+|.+|..++.+.+.|.. T Consensus 84 ~v~~Lfe~EVPEI~~G~VeIk~IaR~pG~RtKIAV~s~d~~iDpvGacVG~~GsRI~~I~~eL~g 148 (251) T 2asb_A 84 LVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSG 148 (251) T ss_dssp HHHHHHHHHCHHHHTTSEEEEEEEEETTTEEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTT T ss_pred HHHHHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEEECCCCCCCEEEEEECCCCHHHHHHHHHCC T ss_conf 99999996407741896899998317886237999924898350236750575089999998679 No 46 >2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii OT3} PDB: 3aev_B Probab=20.25 E-value=17 Score=15.74 Aligned_cols=29 Identities=28% Similarity=0.457 Sum_probs=22.8 Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHHC Q ss_conf 89999737410013565348998987640 Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSN 93 (227) Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~~ 93 (227) .|.|-..+-|.|||++|..|++|++...- T Consensus 37 ~v~IP~~~vG~IIGkgG~~Ik~Iqe~tg~ 65 (219) T 2e3u_A 37 YVKIPKDRIAVLIGKKGQTKKEIEKRTKT 65 (219) T ss_dssp EEECCHHHHHHHHCGGGHHHHHHHHHHTE T ss_pred EEECCHHHHHHHHCCCHHHHHHHHHHHCC T ss_conf 99668787334227753899999999665 Done!