Query gi|254780789|ref|YP_003065202.1| hypothetical protein CLIBASIA_03400 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 192 No_of_seqs 121 out of 1003 Neff 5.7 Searched_HMMs 23785 Date Mon May 30 13:21:16 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780789.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1ib8_A Conserved protein SP14. 100.0 3.9E-42 0 282.1 16.4 151 19-175 8-161 (164) 2 3bw1_A SMX4 protein, U6 snRNA- 85.6 0.5 2.1E-05 25.5 3.0 47 94-147 3-50 (96) 3 2rm4_A CG6311-PB, DM EDC3; enh 84.0 1.5 6.5E-05 22.5 5.0 61 110-173 8-70 (103) 4 1ycy_A Conserved hypothetical 83.8 1.5 6.2E-05 22.6 4.8 59 105-168 7-65 (71) 5 1y96_A Gemin6, SIP2, GEM-assoc 83.5 2.3 9.8E-05 21.4 5.8 74 104-185 7-84 (86) 6 3cw1_G Small nuclear ribonucle 82.8 1.2 5.1E-05 23.1 4.0 37 106-146 6-43 (76) 7 2vc8_A Enhancer of mRNA-decapp 82.1 2.4 0.0001 21.2 5.3 60 111-173 6-67 (84) 8 2hbp_A Cytoskeleton assembly c 78.4 0.52 2.2E-05 25.4 0.9 63 117-188 5-67 (68) 9 1n9r_A SMF, small nuclear ribo 76.8 2.9 0.00012 20.8 4.4 37 109-148 26-63 (93) 10 1ljo_A Archaeal SM-like protei 76.4 2.7 0.00011 21.0 4.1 38 107-147 8-46 (77) 11 3fb9_A Uncharacterized protein 76.2 4 0.00017 19.9 8.5 68 106-173 17-85 (90) 12 3cw1_F Small nuclear ribonucle 76.0 3.3 0.00014 20.4 4.5 41 103-147 5-46 (86) 13 2ckk_A KIN17; beta barrel, rib 75.9 2.3 9.7E-05 21.4 3.6 51 113-169 73-125 (127) 14 3cw1_A Small nuclear ribonucle 74.5 4.4 0.00019 19.6 5.4 39 104-146 4-43 (174) 15 1h64_1 SnRNP SM-like protein; 73.9 3.2 0.00014 20.5 4.0 41 100-147 3-44 (75) 16 2e70_A Transcription elongatio 71.6 3.3 0.00014 20.4 3.6 50 109-168 16-65 (71) 17 1nz9_A Transcription antitermi 71.3 5.2 0.00022 19.2 4.5 50 113-170 7-58 (58) 18 1mgq_A SM-like protein; LSM, R 69.5 5 0.00021 19.3 4.1 49 92-147 4-55 (83) 19 1i8f_A Putative snRNP SM-like 69.4 4.5 0.00019 19.6 3.9 38 106-147 13-51 (81) 20 1d3b_B Protein (small nuclear 67.9 4.9 0.00021 19.3 3.8 35 109-147 9-44 (91) 21 1i4k_A Putative snRNP SM-like 66.9 5.1 0.00021 19.2 3.7 40 101-147 4-44 (77) 22 1d3b_A Protein (small nuclear 63.1 7.2 0.0003 18.3 3.9 35 109-147 10-45 (75) 23 1th7_A SnRNP-2, small nuclear 58.1 9.4 0.0004 17.6 6.4 36 108-147 13-49 (81) 24 2ej9_A Putative biotin ligase; 57.9 9.5 0.0004 17.6 4.3 42 103-148 181-222 (237) 25 2e6z_A Transcription elongatio 54.7 9.9 0.00042 17.4 3.5 49 113-169 10-58 (59) 26 3cw1_D Small nuclear ribonucle 52.9 11 0.00048 17.1 3.9 38 102-146 6-44 (126) 27 3cw1_E Small nuclear ribonucle 52.5 9.2 0.00039 17.6 3.0 40 107-146 19-59 (92) 28 2fwk_A U6 snRNA-associated SM- 50.8 7.4 0.00031 18.2 2.3 35 109-147 33-68 (121) 29 1bia_A BIRA bifunctional prote 40.7 18 0.00074 15.9 3.9 44 98-146 257-300 (321) 30 2jvv_A Transcription antitermi 40.1 18 0.00076 15.8 3.9 50 113-170 130-181 (181) 31 2dgb_A Hypothetical protein PU 39.7 18 0.00077 15.8 5.6 69 18-96 13-81 (84) 32 1m5q_A SMAP3, small nuclear ri 39.2 19 0.00078 15.7 5.3 58 107-169 3-61 (130) 33 2pt7_G HP1451, hypothetical pr 36.6 20 0.00086 15.5 4.3 68 22-94 4-78 (152) 34 3bpp_A 1510-N membrane proteas 34.4 22 0.00093 15.3 4.8 56 49-111 7-62 (230) 35 1b34_A Protein (small nuclear 31.5 25 0.001 14.9 3.7 36 107-146 5-41 (119) 36 2eay_A Biotin [acetyl-COA-carb 29.1 27 0.0011 14.7 3.8 46 98-149 172-217 (233) 37 1tt9_A Formimidoyltransferase- 27.6 24 0.001 15.1 1.8 60 37-97 69-131 (541) 38 2f5g_A Transposase, putative; 24.5 33 0.0014 14.2 8.4 102 6-115 18-127 (133) 39 1msc_A Bacteriophage MS2 coat 24.1 22 0.00094 15.2 1.2 26 64-89 96-121 (129) 40 1gtd_A MTH169; synthetase, FGA 23.5 34 0.0014 14.1 5.6 69 18-95 12-80 (85) 41 2vjv_A Transposase ORFA; DNA-b 23.1 35 0.0015 14.0 8.8 103 6-116 26-138 (159) 42 1dpg_A G6PD, glucose 6-phospha 22.2 36 0.0015 13.9 3.9 39 51-90 140-179 (485) 43 1c1y_B Proto-onkogene serine/t 22.0 37 0.0016 13.9 2.8 53 63-121 21-76 (77) 44 1wwj_A Circadian clock protein 20.4 40 0.0017 13.7 3.1 44 49-99 6-49 (105) 45 2bh9_A G6PD, glucose-6-phospha 20.1 40 0.0017 13.6 4.0 34 52-86 138-171 (489) No 1 >1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1 Probab=100.00 E-value=3.9e-42 Score=282.10 Aligned_cols=151 Identities=26% Similarity=0.490 Sum_probs=138.4 Q ss_pred CCHHHHHHHHHHHHHHHCCCEEEEEEEEC-CCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCC--CCCCCCCCEEEEE Q ss_conf 12799999999999974797799999954-99868999996587787899999999998752021--1356765079997 Q gi|254780789|r 19 MGLAGDISSVIQPVIEEMSFRSVQISLLE-EKNLLLQIFVERDDGNMTLRDCEELSQAISPILDV--ENIIEGHYRLEVS 95 (192) Q Consensus 19 ~~i~~~i~~li~p~v~~lG~eLv~v~~~~-~~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~--~d~i~~~Y~LEVS 95 (192) ..+.+.|+++++|+++ .||+||+|++.+ +++++||||||+++| |++|||+.+||.|++.||+ +|+++++|+|||| T Consensus 8 ~~i~e~i~~li~p~~~-~g~eL~die~~~~~~~~~lrI~ID~~~g-v~iddC~~vSr~i~~~LD~~~~d~i~~~Y~LEVS 85 (164) T 1ib8_A 8 ATIVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEG-ITLNDTADLTEMISPVLDTIKPDPFPEQYFLEIT 85 (164) T ss_dssp HHHHHHHHHHHHHHHC-SSSEEEEEEEEEETTEEEEEEEEECSSC-CCHHHHHHHHHHHGGGTTTCCSCCCCSCEEEEEE T ss_pred HHHHHHHHHHHHHHHH-CCCEEEEEEEEECCCCEEEEEEEECCCC-CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEE T ss_conf 9999999999899986-6988999999908996799999999999-4589999999999987535446667875799996 Q ss_pred ECCCCCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEEHHHHHHCCEECC Q ss_conf 27887744578999987105688987226688078999985126975999963554567777269976887651725046 Q gi|254780789|r 96 SPGIDRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEKDMNELQIAISFDSLLSARLIVT 175 (192) Q Consensus 96 SPGidRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k~~~~~~v~ip~~~I~kAkLv~~ 175 (192) |||++|||++++||+||+|+.|+|+|+.+.+|+++|+|+|.+++++.++|.+..+.. ..+++|||++|++|||++. T Consensus 86 SPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~i~l~~~~~~~----~~~~~I~~~~I~ka~l~ve 161 (164) T 1ib8_A 86 SPGLERPLKTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDELTMEYMDKTR----KKTVQIPYSLVSKARLAVK 161 (164) T ss_dssp CCSSSSCCSSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTEEEEEEECSSC----EEEEEECSSCCSSCEEECS T ss_pred CCCCCCCCCCHHHHHHHCCCEEEEEEECCCCCCEEEEEEEEEEECCEEEEEEECCCC----CEEEEEEHHHCCEEEEEEE T ss_conf 699885437979999865957999996476993899999999749989999923777----6599970698146999999 No 2 >3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, homomeric, octamer, cytoplasm; 2.50A {Saccharomyces cerevisiae} Probab=85.57 E-value=0.5 Score=25.52 Aligned_cols=47 Identities=11% Similarity=0.105 Sum_probs=35.1 Q ss_pred EEECCCCCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 972788774457899998710568898722668807899998512697-599996 Q gi|254780789|r 94 VSSPGIDRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 94 VSSPGidRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) .++.+++.||.. .+.++|+.|.|++++ | +.|.|+|.++|.. .++|.. T Consensus 3 ~~~~~me~Pl~l---L~~~l~k~V~V~lkd---g-~~~~G~L~~~D~~mNlvL~d 50 (96) T 3bw1_A 3 HHHHHMETPLDL---LKLNLDERVYIKLRG---A-RTLVGTLQAFDSHCNIVLSD 50 (96) T ss_dssp ---CCCCCHHHH---HGGGTTSEEEEEEGG---G-CEEEEEEEEECTTCCEEEEE T ss_pred CCCCCCCCHHHH---HHHHCCCEEEEEECC---C-CEEEEEEEEECCCCCEEEEE T ss_conf 521132387999---998789849999869---9-79999999997857779740 No 3 >2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster} Probab=84.03 E-value=1.5 Score=22.47 Aligned_cols=61 Identities=16% Similarity=0.157 Sum_probs=47.7 Q ss_pred HHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCC--CCCCCEEEEEHHHHHHCCEE Q ss_conf 98710568898722668807899998512697599996355456--77772699768876517250 Q gi|254780789|r 110 LRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEK--DMNELQIAISFDSLLSARLI 173 (192) Q Consensus 110 ~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k--~~~~~~v~ip~~~I~kAkLv 173 (192) +.|+|..|.+++.+ +.-.|.|.+..++...|+|...-+... +..-.++++.-.+|..-+|+ T Consensus 8 e~~IG~~VSi~C~d---~lgvyQG~I~~vs~q~Itl~~af~NGvPlk~~~~eVTLsa~DI~~LkiI 70 (103) T 2rm4_A 8 QDWIGCAVSIACDE---VLGVFQGLIKQISAEEITIVRAFRNGVPLRKQNAEVVLKCTDIRSIDLI 70 (103) T ss_dssp GGGTTCEEEEEECT---TTCEEEEEEEEEETTEEEEEEEEETTEECSCSSSCEEEETTTEEEEEEE T ss_pred CCCEEEEEEEEECC---CCCEEEEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEEHHHCCCCEEE T ss_conf 25020799999779---8737878999843444897323247876556883489882432110265 No 4 >1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4 Probab=83.75 E-value=1.5 Score=22.60 Aligned_cols=59 Identities=19% Similarity=0.289 Sum_probs=39.4 Q ss_pred CHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEEHHHHH Q ss_conf 7899998710568898722668807899998512697599996355456777726997688765 Q gi|254780789|r 105 RKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEKDMNELQIAISFDSLL 168 (192) Q Consensus 105 ~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k~~~~~~v~ip~~~I~ 168 (192) ..+-.++|.|++|.|. +++...|+|+|..++++.+.+..--... ....+.+-+..++|. T Consensus 7 LdktL~~WKg~kvAv~----vg~ehSFtGiledFDeEviLL~dV~D~~-GNk~k~liv~idDin 65 (71) T 1ycy_A 7 LEKVLKEWKGHKVAVS----VGGDHSFTGTLEDFDEEVILLKDVVDVI-GNRGKQMLIGLEDIN 65 (71) T ss_dssp HHHHHHHHTTSEEEEE----EC----CEEEEEEECSSEEEEEEEEETT-EEEEEEEEEEGGGEE T ss_pred HHHHHHHHCCCEEEEE----ECCCCEEEEEHHHCCCCEEEHHHHHHHH-CCCCCEEEEEECCCE T ss_conf 9999998479679999----6685215666545586367511568885-655231589853623 No 5 >1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Probab=83.49 E-value=2.3 Score=21.37 Aligned_cols=74 Identities=14% Similarity=0.087 Sum_probs=48.6 Q ss_pred CCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEE--EE-EECCCCCCCCCCCEEEEEHHHHHHCCEECC-HHHH Q ss_conf 5789999871056889872266880789999851269759--99-963554567777269976887651725046-9999 Q gi|254780789|r 104 VRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGF--FL-EKEKRGEKDMNELQIAISFDSLLSARLIVT-DELL 179 (192) Q Consensus 104 ~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i--~l-~~~~~~~k~~~~~~v~ip~~~I~kAkLv~~-d~l~ 179 (192) +.|.+|+.|++++|+|++.+ .+.+.|..-.+|.-.. .| ...+.+ ......|+=-+|+...++-+ ++.. T Consensus 7 ~sP~~~~~yv~keV~vt~~d----~~~~~GwVyTvDPVS~SIVL~~~~e~~----~~~~~vVmGHAVk~Vevv~~~~~~~ 78 (86) T 1y96_A 7 KGPLEWQDYIYKEVRVTASE----KNEYKGWVLTTDPVSANIVLVNFLEDG----SMSVTGIMGHAVQTVETMNEGDHRV 78 (86) T ss_dssp SCHHHHHHTTTCEEEEEETT----TEEEEEEEEEECTTTCCEEEEEECTTS----CEEEEEECGGGEEEEEEEECCCHHH T ss_pred CCHHHHHHHHCCEEEEEECC----CCEEEEEEEEECCCCCEEEEEECCCCC----CCCEEEEECCCEEEEEEEECCCHHH T ss_conf 79899998639789999825----987987999968874179996121047----6317999445044899982786999 Q ss_pred HHHHHC Q ss_conf 999960 Q gi|254780789|r 180 RASLNN 185 (192) Q Consensus 180 ~~~~~~ 185 (192) ++-|.+ T Consensus 79 ~e~L~~ 84 (86) T 1y96_A 79 REKLMH 84 (86) T ss_dssp HHHHHT T ss_pred HHHHHH T ss_conf 999985 No 6 >3cw1_G Small nuclear ribonucleoprotein G; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=82.75 E-value=1.2 Score=23.13 Aligned_cols=37 Identities=5% Similarity=0.202 Sum_probs=28.8 Q ss_pred HHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEE Q ss_conf 899998710568898722668807899998512697-59999 Q gi|254780789|r 106 KSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLE 146 (192) Q Consensus 106 ~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~ 146 (192) |-+.++++|+.|.|++++ | +.|.|+|.++|.. .+.|. T Consensus 6 p~~L~~~l~k~V~V~l~~---g-r~~~G~L~~~D~~mNlvL~ 43 (76) T 3cw1_G 6 PPELKKFMDKKLSLKLNG---G-RHVQGILRGFDPFMNLVID 43 (76) T ss_pred CHHHHHHCCCCEEEEECC---C-CEEEEEEEEECCCCCEEEC T ss_conf 747998669919999889---9-1999999999772358980 No 7 >2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens} Probab=82.07 E-value=2.4 Score=21.23 Aligned_cols=60 Identities=8% Similarity=0.149 Sum_probs=48.2 Q ss_pred HHHCCEEEEEEECCCCCEEEEEEEEEECC--CCEEEEEECCCCCCCCCCCEEEEEHHHHHHCCEE Q ss_conf 87105688987226688078999985126--9759999635545677772699768876517250 Q gi|254780789|r 111 RWNGHVVACEIVLSSGDKQKLIGKIMGTS--ETGFFLEKEKRGEKDMNELQIAISFDSLLSARLI 173 (192) Q Consensus 111 r~~G~~VkV~l~~~~~g~k~~~G~L~~v~--~~~i~l~~~~~~~k~~~~~~v~ip~~~I~kAkLv 173 (192) .|+|+.|.|.... +.-.|.|.+..++ +..|+|...=....+....++++.-.+|..-+|+ T Consensus 6 ~~iG~~VSI~C~~---~lGvyQG~I~~v~~t~q~ItL~kaf~NGvp~~~~EVTl~a~DI~~Lkii 67 (84) T 2vc8_A 6 DWLGSIVSINCGD---SLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKIL 67 (84) T ss_dssp TTTTCEEEEECCT---TTCEEEEEEEEEETTTTEEEEEEEEETTEECSSSEEEEEGGGCSEEEEE T ss_pred CCCCEEEEEEECC---CCCEEEEEEEEECCCCCEEEEEHHHHCCCCCCCCEEEEEEHHCCCCEEE T ss_conf 1155489998579---8647888998825877679980263488878885599980322131389 No 8 >2hbp_A Cytoskeleton assembly control protein SLA1; SHD1, NPFX(1,2)D, endocytosis, protein binding; NMR {Saccharomyces cerevisiae} Probab=78.41 E-value=0.52 Score=25.44 Aligned_cols=63 Identities=19% Similarity=0.288 Sum_probs=45.6 Q ss_pred EEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEEHHHHHHCCEECCHHHHHHHHHCCCC Q ss_conf 889872266880789999851269759999635545677772699768876517250469999999960796 Q gi|254780789|r 117 VACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEKDMNELQIAISFDSLLSARLIVTDELLRASLNNYGS 188 (192) Q Consensus 117 VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k~~~~~~v~ip~~~I~kAkLv~~d~l~~~~~~~~~~ 188 (192) .++++ -..|+-++.+.+.++.++.|.|... +...+.+|++..+.+-+.+-+++.++++..+++ T Consensus 5 ~R~WT--d~~G~~~veA~fv~~~~~~V~L~~~-------~G~~i~vpl~~LS~~Dq~yve~~~~~sl~~~k~ 67 (68) T 2hbp_A 5 SRLWV--DRSGTFKVDAEFIGCAKGKIHLHKA-------NGVKIAVAADKLSNEDLAYVEKITGFSLEKFKA 67 (68) T ss_dssp SEEEE--BSSSCCEEEEEEEEEETTEEEEECT-------TSCEEEEETTSBCHHHHHHHHHHHSCCCGGGCC T ss_pred EEEEE--ECCCCEEEEEEEEEEECCEEEEEEC-------CCEEEEEEHHHCCHHHHHHHHHHHCCCCHHHCC T ss_conf 06879--4899989999999961999999975-------997999474997998999999986376122226 No 9 >1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Probab=76.82 E-value=2.9 Score=20.75 Aligned_cols=37 Identities=14% Similarity=0.199 Sum_probs=28.9 Q ss_pred HHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEEC Q ss_conf 998710568898722668807899998512697-5999963 Q gi|254780789|r 109 FLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEKE 148 (192) Q Consensus 109 f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~~ 148 (192) .+.++|+.|.|+|+ .+...+.|+|.++|+- .+.|... T Consensus 26 L~~~igk~V~V~Lk---~ng~~~~G~L~~~D~~mNlvL~d~ 63 (93) T 1n9r_A 26 LKGLVNHRVGVKLK---FNSTEYRGTLVSTDNYFNLQLNEA 63 (93) T ss_dssp CGGGTTSEEEEEES---STTEEEEEEEEECCTTTCEEEEEE T ss_pred HHHHCCCEEEEEEE---CCCEEEEEEEEEECCCCCEEEEEE T ss_conf 98738986999994---299999999999848980599159 No 10 >1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown function; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Probab=76.40 E-value=2.7 Score=20.98 Aligned_cols=38 Identities=21% Similarity=0.523 Sum_probs=29.4 Q ss_pred HHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 99998710568898722668807899998512697-599996 Q gi|254780789|r 107 SDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 107 ~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) ...+.++|+.|.|+++ +|+..+.|+|.++|.. .+.|.. T Consensus 8 ~~L~~~~~~~V~V~Lk---~~~~~~~G~L~~~D~~mNivL~~ 46 (77) T 1ljo_A 8 QMVKSMVGKIIRVEMK---GEENQLVGKLEGVDDYMNLYLTN 46 (77) T ss_dssp HHHHHTTTSEEEEEET---TCSSEEEEEEEEECTTCCEEEEE T ss_pred HHHHHHCCCEEEEEEE---CCCEEEEEEEEEECCCCCEEEEE T ss_conf 9998748997999996---89899999999995868879988 No 11 >3fb9_A Uncharacterized protein; unknown function, structural genomics, MCSG, PSI2, protein structure initiative; 1.80A {Streptococcus pneumoniae TIGR4} Probab=76.17 E-value=4 Score=19.89 Aligned_cols=68 Identities=16% Similarity=0.304 Sum_probs=48.4 Q ss_pred HHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCC-CCCCCCCEEEEEHHHHHHCCEE Q ss_conf 8999987105688987226688078999985126975999963554-5677772699768876517250 Q gi|254780789|r 106 KSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRG-EKDMNELQIAISFDSLLSARLI 173 (192) Q Consensus 106 ~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~-~k~~~~~~v~ip~~~I~kAkLv 173 (192) .+....++|+.|.++....=.....-.|+|.++=..-+++.++... ........++..|.+|---+.. T Consensus 17 K~~l~~~iG~~V~l~an~GRkK~~~r~GvL~etYPSvFvV~ld~~~~~~~~~~~rvSYSYsDvLT~~V~ 85 (90) T 3fb9_A 17 KEEIKAHEGQVVEMTLENGRKRQKNRLGKLIEVYPSLFIVEFGDVEGDKQVNVYVESFTYSDILTEKNL 85 (90) T ss_dssp HHHHHHTTTSEEEEEECCSSSCCSCEEEEEEEECSSEEEEEESCSTTSCCSSCEEEEEEHHHHHTTSEE T ss_pred HHHHHHHCCCEEEEEECCCCCCEEEEEEEEEEECCCEEEEEECCCCCCCCCCEEEEEEEEEEEECCCEE T ss_conf 999997279889999638951279999999541562899997265677567548998886202316189 No 12 >3cw1_F Small nuclear ribonucleoprotein F; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=75.95 E-value=3.3 Score=20.42 Aligned_cols=41 Identities=12% Similarity=0.121 Sum_probs=29.4 Q ss_pred CCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 457899998710568898722668807899998512697-599996 Q gi|254780789|r 103 MVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 103 L~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) +.-..-.+.++|+.|.|+|++ .+.+.|+|.++|+. .++|.. T Consensus 5 i~P~~~L~~~~~~~V~V~Lk~----g~~~~G~L~~~D~~mNlvL~~ 46 (86) T 3cw1_F 5 LNPKPFLNGLTGKPVMVKLKW----GMEYKGYLVSVDGYMNMQLAN 46 (86) T ss_pred CCHHHHHHHHCCCEEEEEECC----CCEEEEEEEECCCCCEEEEEE T ss_conf 587999987289779999989----959999999846886079910 No 13 >2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens} Probab=75.89 E-value=2.3 Score=21.40 Aligned_cols=51 Identities=10% Similarity=0.055 Sum_probs=33.4 Q ss_pred HCCEEEEEEECCCCCEEEEEEEEEECCCCE--EEEEECCCCCCCCCCCEEEEEHHHHHH Q ss_conf 105688987226688078999985126975--999963554567777269976887651 Q gi|254780789|r 113 NGHVVACEIVLSSGDKQKLIGKIMGTSETG--FFLEKEKRGEKDMNELQIAISFDSLLS 169 (192) Q Consensus 113 ~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~--i~l~~~~~~~k~~~~~~v~ip~~~I~k 169 (192) .|..|.| +..+..|. .|+|.+.+.+. +.+.++.. .........+||++|.+ T Consensus 73 ~g~~V~V-v~G~~rG~---~g~L~~id~~~~~~~v~l~~~--~~~~~~v~~~~yddick 125 (127) T 2ckk_A 73 PGKRILV-LNGGYRGN---EGTLESINEKTFSATIVIETG--PLKGRRVEGIQYEDISK 125 (127) T ss_dssp TTCEEEE-CSSTTTTC---EEEEEEEEGGGTEEEEEECSS--TTTTCEEEEEEGGGEEE T ss_pred CCCEEEE-EECCCCCC---EEEEEEEECCCCEEEEEECCC--CCCCCEEEECCHHHHHC T ss_conf 9997999-84676785---899999934368899997158--87675897248899740 No 14 >3cw1_A Small nuclear ribonucleoprotein-associated proteins B and B; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=74.49 E-value=4.4 Score=19.62 Aligned_cols=39 Identities=15% Similarity=0.212 Sum_probs=28.0 Q ss_pred CCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEE Q ss_conf 57899998710568898722668807899998512697-59999 Q gi|254780789|r 104 VRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLE 146 (192) Q Consensus 104 ~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~ 146 (192) .+......|+++.|+|++++ | +.|.|+|.++|.. +++|. T Consensus 4 ~k~skL~~~InkrVrV~l~D---G-R~~vG~L~afD~~mNLVL~ 43 (174) T 3cw1_A 4 GKSSKMLQHIDYRMRCILQD---G-RIFIGTFKAFDKHMNLILC 43 (174) T ss_pred CCHHHHHHHCCCEEEEEEEC---C-EEEEEEEEEECCCCCEEEC T ss_conf 73168998669979999809---9-4999999997674667624 No 15 >1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Probab=73.94 E-value=3.2 Score=20.46 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=30.3 Q ss_pred CCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 774457899998710568898722668807899998512697-599996 Q gi|254780789|r 100 DRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 100 dRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) ++||. -.+.++|+.|.|++++ .+.+.|+|.++|.. .+.|.. T Consensus 3 ~~Pl~---lL~~~~~~~V~V~lk~----g~~~~G~L~~~D~~mNlvL~~ 44 (75) T 1h64_1 3 ERPLD---VIHRSLDKDVLVILKK----GFEFRGRLIGYDIHLNVVLAD 44 (75) T ss_dssp CCHHH---HHHTTTTSEEEEEETT----SEEEEEEEEEECTTCCEEEEE T ss_pred CCCHH---HHHHHCCCEEEEEECC----CCEEEEEEEEECCCCCEEEEE T ss_conf 63379---9998689979999959----989999999997999879856 No 16 >2e70_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=71.64 E-value=3.3 Score=20.41 Aligned_cols=50 Identities=16% Similarity=0.075 Sum_probs=38.2 Q ss_pred HHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEEHHHHH Q ss_conf 998710568898722668807899998512697599996355456777726997688765 Q gi|254780789|r 109 FLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEKDMNELQIAISFDSLL 168 (192) Q Consensus 109 f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k~~~~~~v~ip~~~I~ 168 (192) ..+++|+.|+|+ ..|..| +.|++..++++.+.+++.... ..+++|-+.+. T Consensus 16 ~d~liGktV~I~-~GpyKG---~~G~Vkd~t~~~~rVELhs~~------K~V~V~r~~l~ 65 (71) T 2e70_A 16 DNELIGQTVRIS-QGPYKG---YIGVVKDATESTARVELHSTC------QTISVDRQRLT 65 (71) T ss_dssp TTSSTTSEEEEC-SSTTTT---CEEEEEEECSSCEEEEESSSC------CEEEECTTTEE T ss_pred CCCCCCCEEEEE-ECCCCC---EEEEEEECCCCEEEEEEECCC------EEEEEEHHHEE T ss_conf 733358888996-637688---689999652887999981587------69998988804 No 17 >1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4 Probab=71.29 E-value=5.2 Score=19.20 Aligned_cols=50 Identities=16% Similarity=0.241 Sum_probs=36.7 Q ss_pred HCCEEEEEEECCCCCEEEEEEEEEECCC--CEEEEEECCCCCCCCCCCEEEEEHHHHHHC Q ss_conf 1056889872266880789999851269--759999635545677772699768876517 Q gi|254780789|r 113 NGHVVACEIVLSSGDKQKLIGKIMGTSE--TGFFLEKEKRGEKDMNELQIAISFDSLLSA 170 (192) Q Consensus 113 ~G~~VkV~l~~~~~g~k~~~G~L~~v~~--~~i~l~~~~~~~k~~~~~~v~ip~~~I~kA 170 (192) .|..|+| +..|..| |.|++.+++. ..+.+.++--++ +..+++++++|.|| T Consensus 7 ~Gd~V~V-~~GpF~g---~~g~V~~i~~~~~rv~Vll~ifGr----~t~vel~~~~veKA 58 (58) T 1nz9_A 7 EGDQVRV-VSGPFAD---FTGTVTEINPERGKVKVMVTIFGR----ETPVELDFSQVVKA 58 (58) T ss_dssp TTCEEEE-CSGGGTT---CEEEEEEEETTTTEEEEEEESSSS----EEEEEECGGGEEEC T ss_pred CCCEEEE-ECCCCCC---CEEEEEEECCCCCEEEEEEEECCC----CCEEEECHHHEECC T ss_conf 9999999-0368999---899999991889999999994499----82373698998709 No 18 >1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Probab=69.50 E-value=5 Score=19.29 Aligned_cols=49 Identities=20% Similarity=0.307 Sum_probs=34.1 Q ss_pred EEEEECCC--CCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 99972788--774457899998710568898722668807899998512697-599996 Q gi|254780789|r 92 LEVSSPGI--DRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 92 LEVSSPGi--dRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) +++||+=. .+||.. .++++|+.|.|+|+ +| +.+.|+|.++|.. .+.|.. T Consensus 4 ~~~~~~~~~~~~Pl~~---L~~~~~k~V~V~Lk---~g-~~~~G~L~~~D~~mNlvL~~ 55 (83) T 1mgq_A 4 IDVSSQRVNVQRPLDA---LGNSLNSPVIIKLK---GD-REFRGVLKSFDLHMNLVLND 55 (83) T ss_dssp ------CCCTTCTTHH---HHHTTTSEEEEEET---TT-EEEEEEEEEECTTCCEEEEE T ss_pred EECCCCCCCCCCCHHH---HHHHCCCEEEEEEC---CC-CEEEEEEEEECCCCCEEEEE T ss_conf 5324310135588899---99858997999987---99-99999999998999879845 No 19 >1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet in the heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Probab=69.38 E-value=4.5 Score=19.57 Aligned_cols=38 Identities=13% Similarity=0.190 Sum_probs=29.3 Q ss_pred HHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 899998710568898722668807899998512697-599996 Q gi|254780789|r 106 KSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 106 ~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) ..-.++++|+.|.|+|++ | +.+.|+|.++|.. .+.|.. T Consensus 13 ~~~L~~~l~k~V~V~lk~---g-~~~~G~L~~~D~~~NlvL~~ 51 (81) T 1i8f_A 13 GATLQDSIGKQVLVKLRD---S-HEIRGILRSFDQHVNLLLED 51 (81) T ss_dssp HHHHHTTTTSEEEEEEGG---G-EEEEEEEEEECTTCCEEEEE T ss_pred HHHHHHHCCCEEEEEECC---C-CEEEEEEEEECCCCCEEECC T ss_conf 899998679979999889---9-59999999975756688637 No 20 >1d3b_B Protein (small nuclear ribonucleoprotein associated protein B); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Probab=67.86 E-value=4.9 Score=19.33 Aligned_cols=35 Identities=17% Similarity=0.291 Sum_probs=27.0 Q ss_pred HHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 998710568898722668807899998512697-599996 Q gi|254780789|r 109 FLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 109 f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) ..+|+|+.|.|++. +.+.|.|+|.++|.. .+.|.. T Consensus 9 L~~~i~k~v~V~l~----dgR~~~G~L~~~D~~~NlVL~~ 44 (91) T 1d3b_B 9 MLQHIDYRMRCILQ----DGRIFIGTFKAFDKHMNLILCD 44 (91) T ss_dssp CGGGTTSEEEEEET----TCCEEEEEEEECCTTCCEEEEE T ss_pred HHHHCCCEEEEEEC----CCCEEEEEEEEECCCCCEEEEC T ss_conf 89865997999987----9959999999998756888506 No 21 >1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Probab=66.93 E-value=5.1 Score=19.24 Aligned_cols=40 Identities=18% Similarity=0.164 Sum_probs=29.1 Q ss_pred CCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 74457899998710568898722668807899998512697-599996 Q gi|254780789|r 101 RPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 101 RpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) |||.. ...++|+.|.|++++ | +.+.|+|.++|.. .+.|.. T Consensus 4 ~Pl~~---L~~~~~k~V~V~lk~---g-~~~~G~L~~~D~~mNlvL~d 44 (77) T 1i4k_A 4 RPLDV---LNRSLKSPVIVRLKG---G-REFRGTLDGYDIHMNLVLLD 44 (77) T ss_dssp CHHHH---HHTTTTSEEEEEETT---S-CEEEEEEEEECTTCCEEEEE T ss_pred CHHHH---HHHHCCCEEEEEECC---C-CEEEEEEEEECCCCCEEEEE T ss_conf 65999---998589979999989---9-79999999997999769821 No 22 >1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus erythematosus, SLE; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Probab=63.07 E-value=7.2 Score=18.30 Aligned_cols=35 Identities=20% Similarity=0.421 Sum_probs=27.1 Q ss_pred HHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 998710568898722668807899998512697-599996 Q gi|254780789|r 109 FLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 109 f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) .+..+|+.|.|+|++ ...+.|+|.++|+. .+.|.. T Consensus 10 L~~~~g~~V~VeLk~----g~~~~G~L~~~D~~mNl~L~d 45 (75) T 1d3b_A 10 LHEAEGHIVTCETNT----GEVYRGKLIEAEDNMNCQMSN 45 (75) T ss_dssp HHHTTTSEEEEEETT----SCEEEEEEEEECTTCCEEEEE T ss_pred HHHCCCCEEEEEECC----CCEEEEEEEEECCCEEEEEEE T ss_conf 976689989999999----829999999886873899989 No 23 >1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Probab=58.05 E-value=9.4 Score=17.58 Aligned_cols=36 Identities=8% Similarity=0.129 Sum_probs=27.6 Q ss_pred HHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 9998710568898722668807899998512697-599996 Q gi|254780789|r 108 DFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 108 ~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) -...++|+.|.|+|++ | +.+.|+|.++|.. .+.|.. T Consensus 13 ~L~~~l~~~V~V~l~~---g-~~~~G~L~~~D~~mNlvL~~ 49 (81) T 1th7_A 13 VLAESLNNLVLVKLKG---N-KEVRGMLRSYDQHMNLVLSD 49 (81) T ss_dssp HHHHHTTSEEEEEETT---T-EEEEEEEEEECTTCCEEEEE T ss_pred HHHHHCCCEEEEEECC---C-CEEEEEEEEECCCCCEEECE T ss_conf 9998779959999889---9-69999999995878439840 No 24 >2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii} Probab=57.89 E-value=9.5 Score=17.56 Aligned_cols=42 Identities=17% Similarity=0.251 Sum_probs=30.2 Q ss_pred CCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEEC Q ss_conf 4578999987105688987226688078999985126975999963 Q gi|254780789|r 103 MVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKE 148 (192) Q Consensus 103 L~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~ 148 (192) +...+++..+.|+.|++.+. +.+.+.|++.++++++..+..+ T Consensus 181 ~~~~~~~~~~~g~~v~v~~~----~~~~~~G~~~gI~~~G~Ll~~~ 222 (237) T 2ej9_A 181 LKKYKKYSITIGKQVKILLS----NNEIITGKVYDIDFDGIVLGTE 222 (237) T ss_dssp HHHHHHHBSSTTCEEEEEET----TSCEEEEEEEEECSSEEEEEET T ss_pred HHHHHHHHHHCCCEEEEEEC----CCEEEEEEEEEECCCCCEEEEC T ss_conf 99999877667998999979----9919999999999998299979 No 25 >2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=54.71 E-value=9.9 Score=17.43 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=35.0 Q ss_pred HCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEEHHHHHH Q ss_conf 105688987226688078999985126975999963554567777269976887651 Q gi|254780789|r 113 NGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEKRGEKDMNELQIAISFDSLLS 169 (192) Q Consensus 113 ~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~k~~~~~~v~ip~~~I~k 169 (192) .|-.|.|-- ..++...|++.+++++.|++..+...- ...+++|-.+.+| T Consensus 10 ~GD~VeV~~----GEl~~l~G~V~~v~~d~Vti~p~~~~L----~~~l~fp~~~LrK 58 (59) T 2e6z_A 10 PGDNVEVCE----GELINLQGKILSVDGNKITIMPKHEDL----KDMLEFPAQELRK 58 (59) T ss_dssp TTSEEEECS----STTTTCEEEECCCBTTEEEEEECCSSC----CSCEEEETTTEEE T ss_pred CCCEEEEEC----CEECCCEEEEEEECCCEEEEEECCCCC----CCCEEECHHHCCC T ss_conf 999899922----676377999999729999997774035----8507607898734 No 26 >3cw1_D Small nuclear ribonucleoprotein SM D3; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=52.91 E-value=11 Score=17.05 Aligned_cols=38 Identities=21% Similarity=0.437 Sum_probs=28.3 Q ss_pred CCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEE Q ss_conf 4457899998710568898722668807899998512697-59999 Q gi|254780789|r 102 PMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLE 146 (192) Q Consensus 102 pL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~ 146 (192) ||+. ....+|+.|.|+|+. ...+.|+|.++|+. .++|. T Consensus 6 Pl~l---L~~~~g~~V~VeLKn----g~~~~G~L~~~D~~MN~~L~ 44 (126) T 3cw1_D 6 PIKV---LHEAEGHIVTCETNT----GEVYRGKLIEAEDNMNCQMS 44 (126) T ss_pred HHHH---HHHHCCCEEEEEECC----CCEEEEEEEEECCCEEEEEE T ss_conf 7999---997179989999899----84999999977285489997 No 27 >3cw1_E Small nuclear ribonucleoprotein E; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, zinc finger, RNA recognition motif; 5.49A {Homo sapiens} Probab=52.50 E-value=9.2 Score=17.64 Aligned_cols=40 Identities=18% Similarity=0.256 Sum_probs=26.2 Q ss_pred HHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEE Q ss_conf 99998710568898722668807899998512697-59999 Q gi|254780789|r 107 SDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLE 146 (192) Q Consensus 107 ~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~ 146 (192) .-..+|..+.+.|+..-...+.+++.|+|.++|+- .++|. T Consensus 19 ~~l~k~l~~~~~v~V~v~~~~~~~i~G~L~g~D~~mNlvL~ 59 (92) T 3cw1_E 19 NLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLD 59 (92) T ss_pred HHHHHHHHHCCCEEEEEEECCCEEEEEEEEEEECCCEEEEE T ss_conf 99999997278879999976991999999998034179981 No 28 >2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 Probab=50.82 E-value=7.4 Score=18.23 Aligned_cols=35 Identities=14% Similarity=0.215 Sum_probs=27.1 Q ss_pred HHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEE Q ss_conf 998710568898722668807899998512697-599996 Q gi|254780789|r 109 FLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEK 147 (192) Q Consensus 109 f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~ 147 (192) ..+++|+.|.|+|++ .+.|.|+|.++|.. .+.|.. T Consensus 33 L~~~lgk~V~V~lkd----gr~~~G~L~~fD~~mNLvL~d 68 (121) T 2fwk_A 33 IDKCIGNRIYVVMKG----DKEFSGVLRGFDEYVNMVLDD 68 (121) T ss_dssp HHHTBTSBCEEEETT----TEEECCEEEEECTTCCEEEES T ss_pred HHHHCCCEEEEEECC----CCEEEEEEEEECCCCCEEEEE T ss_conf 998779879999879----989999999997768857852 No 29 >1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A* Probab=40.70 E-value=18 Score=15.87 Aligned_cols=44 Identities=18% Similarity=0.253 Sum_probs=29.9 Q ss_pred CCCCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEE Q ss_conf 8877445789999871056889872266880789999851269759999 Q gi|254780789|r 98 GIDRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLE 146 (192) Q Consensus 98 GidRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~ 146 (192) |...-+...+.+..+.|+.|.|.. +.+.+.|+..++++++-.+- T Consensus 257 g~~~~~~~~~~~~~~~gk~V~v~~-----~~~~~~G~~~gId~~G~Liv 300 (321) T 1bia_A 257 GLAPYLSRWEKLDNFINRPVKLII-----GDKEIFGISRGIDKQGALLL 300 (321) T ss_dssp TTGGGHHHHHHHBTTTTSEEEEEE-----TTEEEEEEEEEECTTSCEEE T ss_pred CHHHHHHHHHHHHCCCCCEEEEEE-----CCEEEEEEEEEECCCCEEEE T ss_conf 969999999986332498699997-----99799999999998985999 No 30 >2jvv_A Transcription antitermination protein NUSG; transcription factor, transcription regulation, transcription termination; NMR {Escherichia coli} PDB: 2k06_A 2kvq_G Probab=40.13 E-value=18 Score=15.81 Aligned_cols=50 Identities=14% Similarity=0.141 Sum_probs=35.7 Q ss_pred HCCEEEEEEECCCCCEEEEEEEEEECCC--CEEEEEECCCCCCCCCCCEEEEEHHHHHHC Q ss_conf 1056889872266880789999851269--759999635545677772699768876517 Q gi|254780789|r 113 NGHVVACEIVLSSGDKQKLIGKIMGTSE--TGFFLEKEKRGEKDMNELQIAISFDSLLSA 170 (192) Q Consensus 113 ~G~~VkV~l~~~~~g~k~~~G~L~~v~~--~~i~l~~~~~~~k~~~~~~v~ip~~~I~kA 170 (192) .|..|+| ...|..| |.|.+..++. ..+.+.++-=+ ....+++++++|.+| T Consensus 130 ~Gd~V~I-~~GPf~g---~~g~v~~v~~~k~r~~V~l~i~G----r~~~v~v~~~~v~ka 181 (181) T 2jvv_A 130 PGEMVRV-NDGPFAD---FNGVVEEVDYEKSRLKVSVSIFG----RATPVELDFSQVEKA 181 (181) T ss_dssp TTEEEEE-CSSTTTT---EEEEEEEEETTTTEEEEEEEETT----EEEEEEECTTTEEEC T ss_pred CCCEEEE-ECCCCCC---CEEEEEEEECCCCEEEEEEEECC----CCEEEEECHHHEEEC T ss_conf 7988999-1368999---68999998077899999999679----956899878998809 No 31 >2dgb_A Hypothetical protein PURS; purine, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Thermus thermophilus} PDB: 2cuw_A Probab=39.69 E-value=18 Score=15.77 Aligned_cols=69 Identities=19% Similarity=0.342 Sum_probs=43.9 Q ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE Q ss_conf 4127999999999999747977999999549986899999658778789999999999875202113567650799972 Q gi|254780789|r 18 DMGLAGDISSVIQPVIEEMSFRSVQISLLEEKNLLLQIFVERDDGNMTLRDCEELSQAISPILDVENIIEGHYRLEVSS 96 (192) Q Consensus 18 ~~~i~~~i~~li~p~v~~lG~eLv~v~~~~~~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEVSS 96 (192) ++++-+.=-+.+...+..+||.+-+|.+- +.+.+.++..+ -+++...-+.+...| .+|+-+.|..||.+ T Consensus 13 K~gVlDPqG~aI~~aL~~lG~~v~~vr~G----K~iel~i~~~~----~e~a~~~~~~~~klL--aNpvIE~y~i~v~e 81 (84) T 2dgb_A 13 KKGILDPQGRAVEGVLKDLGHPVEEVRVG----KVLEIVFPAEN----LLEAEEKAKAMGALL--ANPVMEVYALEALK 81 (84) T ss_dssp CTTSCCHHHHHHHHHHHHTTCCCSEEEEE----EEEEEEEECSS----HHHHHHHHHHHHHHH--SCTTTEEEEEEEEE T ss_pred CCCCCCCHHHHHHHHHHHCCCCCCEEEEE----EEEEEEECCCC----HHHHHHHHHHHHHHC--CCCCEEEEEEEEEE T ss_conf 99772817999999999759985438976----69999985899----899999999998874--99734789999973 No 32 >1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Probab=39.21 E-value=19 Score=15.73 Aligned_cols=58 Identities=9% Similarity=0.135 Sum_probs=35.6 Q ss_pred HHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEEECCCCCCCCCCCEEEEEHHHHHH Q ss_conf 99998710568898722668807899998512697-5999963554567777269976887651 Q gi|254780789|r 107 SDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLEKEKRGEKDMNELQIAISFDSLLS 169 (192) Q Consensus 107 ~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~~~~~~~k~~~~~~v~ip~~~I~k 169 (192) ..+..++|+.|.|+|++ .+.+.|+|.++|+. .+.|......... .-..+-|-=+.|.. T Consensus 3 ~~L~~ligk~V~V~Lkn----G~~~~G~L~~~D~~mNlvL~~a~~~~~~-k~~~v~IRG~~I~~ 61 (130) T 1m5q_A 3 AELNNLLGREVQVVLSN----GEVYKGVLHAVDNQLNIVLANASNKAGE-KFNRVFIMYRYIVH 61 (130) T ss_dssp HHHHHTTTSEEEEEETT----SCEEEEEEEEECTTCCEEEEEEECTTCC-EEEEEEECGGGEEE T ss_pred HHHHHHCCCEEEEEECC----CCEEEEEEEEECCCCEEEEEEEEECCCC-CCCEEEEECCCEEE T ss_conf 78887379879999989----9699999988669866899678986788-44449992783899 No 33 >2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolase/protein binding complex; 2.40A {Helicobacter pylori 26695} Probab=36.55 E-value=20 Score=15.47 Aligned_cols=68 Identities=12% Similarity=0.117 Sum_probs=46.3 Q ss_pred HHHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEECCCC-------CCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEE Q ss_conf 99999999999974797799999954998689999965877-------87899999999998752021135676507999 Q gi|254780789|r 22 AGDISSVIQPVIEEMSFRSVQISLLEEKNLLLQIFVERDDG-------NMTLRDCEELSQAISPILDVENIIEGHYRLEV 94 (192) Q Consensus 22 ~~~i~~li~p~v~~lG~eLv~v~~~~~~~~~LrI~ID~~dg-------~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEV 94 (192) .+.+.+.++.+++.+|+++--+++....+.++.+-++.++- |=+|+...-+.+.+-..- . +...+|+| T Consensus 4 i~evke~Le~lL~~mg~~~~~~~v~~~~~~~i~i~i~g~d~~~LIGk~G~tL~AlQ~L~~~~vn~~--~---~~~v~lDi 78 (152) T 2pt7_G 4 LHEIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPT--Y---GYSIRLEI 78 (152) T ss_dssp HHHHHHHHHHHTTTTTCCEEEEEEEEEETTEEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHH--H---SCEEEEEE T ss_pred HHHHHHHHHHHHHHCCCCCEEEEEEECCCCEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHHHHC--C---CEEEEEEH T ss_conf 999999999999977997269998633797799997687355463779643799999999998525--7---91699858 No 34 >3bpp_A 1510-N membrane protease; specific for A stomatin homolog, archaea, thermostable, catalytic DYAD, hydrolase; 2.30A {Pyrococcus horikoshii} PDB: 2deo_A Probab=34.41 E-value=22 Score=15.25 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=35.3 Q ss_pred CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCHHHHHH Q ss_conf 986899999658778789999999999875202113567650799972788774457899998 Q gi|254780789|r 49 KNLLLQIFVERDDGNMTLRDCEELSQAISPILDVENIIEGHYRLEVSSPGIDRPMVRKSDFLR 111 (192) Q Consensus 49 ~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEVSSPGidRpL~~~~~f~r 111 (192) ++.+..|-| +|.|+-..+..+.+.+...-|. + ...-.|.|.|||-. +.-...=+.. T Consensus 7 ~~~V~vi~i---~G~I~~~~~~~i~~~l~~a~~~-~--~kaivL~IdSPGG~-v~~~~~I~~~ 62 (230) T 3bpp_A 7 KNIVYVAQI---KGQITSYTYDQFDRYITIAEQD-N--AEAIIIELDTPGGR-ADAMMNIVQR 62 (230) T ss_dssp CSEEEEEEE---ESSBCHHHHHHHHHHHHHHHHT-T--CSEEEEEEEBSCBC-HHHHHHHHHH T ss_pred CCEEEEEEE---EEEECHHHHHHHHHHHHHHHHC-C--CCEEEEEEECCCCC-HHHHHHHHHH T ss_conf 897999998---7688869999999999999768-9--98699998598818-9999999999 No 35 >1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemic lupus erythematosus, SLE; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 3cw1_B Probab=31.45 E-value=25 Score=14.95 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=26.8 Q ss_pred HHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCC-EEEEE Q ss_conf 99998710568898722668807899998512697-59999 Q gi|254780789|r 107 SDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSET-GFFLE 146 (192) Q Consensus 107 ~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~-~i~l~ 146 (192) +=+++..|+.|.|+|++ | ..+.|+|.++|+. .+.|. T Consensus 5 ~fL~kl~g~~VtVELKn---G-~~~~G~L~~vD~~MNl~L~ 41 (119) T 1b34_A 5 RFLMKLSHETVTIELKN---G-TQVHGTITGVDVSMNTHLK 41 (119) T ss_dssp HHHHTCTTCEEEEEETT---C-CEEEEEEEEECTTCCEEEE T ss_pred HHHHHCCCCEEEEEECC---C-CEEEEEEEEECCCEEEEEE T ss_conf 99986699869999889---9-6999999998598869998 No 36 >2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A* Probab=29.10 E-value=27 Score=14.70 Aligned_cols=46 Identities=22% Similarity=0.203 Sum_probs=29.4 Q ss_pred CCCCCCCCHHHHHHHHCCEEEEEEECCCCCEEEEEEEEEECCCCEEEEEECC Q ss_conf 8877445789999871056889872266880789999851269759999635 Q gi|254780789|r 98 GIDRPMVRKSDFLRWNGHVVACEIVLSSGDKQKLIGKIMGTSETGFFLEKEK 149 (192) Q Consensus 98 GidRpL~~~~~f~r~~G~~VkV~l~~~~~g~k~~~G~L~~v~~~~i~l~~~~ 149 (192) |.+.-+....++-.++|+.|.|. +...+.|++.++++++-.+-... T Consensus 172 ~~~~i~~~~~~~~~~~gq~V~v~------~~~~i~G~~~GId~~G~Lil~~~ 217 (233) T 2eay_A 172 SFKEFKGKIESKMLYLGEEVKLL------GEGKITGKLVGLSEKGGALILTE 217 (233) T ss_dssp CGGGTHHHHHHHBTTTTSEEEET------TEEEEEEEEEEECTTSCEEEEET T ss_pred CHHHHHHHHHHHHHHCCCEEEEC------CCCEEEEEEEEECCCCCEEEEEC T ss_conf 88999999999985479889996------69989999999989997899989 No 37 >1tt9_A Formimidoyltransferase-cyclodeaminase (formiminotransferase- cyclodeaminase) (FTCD)...; hepatitis autoantigen, intermediate channeling; 3.42A {Rattus norvegicus} PDB: 2pfd_A Probab=27.61 E-value=24 Score=15.06 Aligned_cols=60 Identities=8% Similarity=0.076 Sum_probs=34.1 Q ss_pred CCEEEEEEEECCCCCEE---EEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEC Q ss_conf 97799999954998689---99996587787899999999998752021135676507999727 Q gi|254780789|r 37 SFRSVQISLLEEKNLLL---QIFVERDDGNMTLRDCEELSQAISPILDVENIIEGHYRLEVSSP 97 (192) Q Consensus 37 G~eLv~v~~~~~~~~~L---rI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEVSSP 97 (192) -+++.|++.+.+.++.+ -+.--.|=+++|+++|..+++.+...+-.+--+|- |.-+-+.+ T Consensus 69 A~~~IDm~~H~G~HPR~GavDv~pf~Pl~~~t~eec~~~A~~~~~~i~~~l~vPv-flYg~aa~ 131 (541) T 1tt9_A 69 ASQLIDMRKHKGEHPRMGALDVCPFIPVRGVSMDECVLCAKAFGQRLAEELNVPV-YLYGEAAQ 131 (541) T ss_pred HHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCE-EEEHHHCC T ss_conf 9985575557787998984252311228999999999999999999986269876-85253148 No 38 >2f5g_A Transposase, putative; dimer, stem-loop binding, gene regulation; 1.70A {Sulfolobus solfataricus} SCOP: d.58.57.1 PDB: 2f4f_A 2ec2_A Probab=24.54 E-value=33 Score=14.19 Aligned_cols=102 Identities=11% Similarity=0.146 Sum_probs=65.1 Q ss_pred HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHH-HCCC- Q ss_conf 01133376100141279999999999997479779999995499868999996587787899999999998752-0211- Q gi|254780789|r 6 FLHSKYEPRIFGDMGLAGDISSVIQPVIEEMSFRSVQISLLEEKNLLLQIFVERDDGNMTLRDCEELSQAISPI-LDVE- 83 (192) Q Consensus 6 ~~~~~~~~r~~~~~~i~~~i~~li~p~v~~lG~eLv~v~~~~~~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~-LD~~- 83 (192) .++++|-...+.. .+.+++.+++..+++..|++++.+++...- +-+++.-+- .+++.++...=+..|.. +-.+ T Consensus 18 V~~tKyR~~vl~~-ei~~~l~~~i~~i~~~~~~~i~~~~~~~DH---VHllv~~~p-~~svs~~v~~lKg~Ssr~i~~~~ 92 (133) T 2f5g_A 18 VWIPKHRRNTLVN-EIAEYTKEVLKSIAEELGCEIIALEVMPDH---IHLFVNCPP-RYAPSYLANYFKGKSARLILKKF 92 (133) T ss_dssp EECBSSCTTCSCH-HHHHHHHHHHHHHHHHHTCEEEEEEEETTE---EEEEEECCT-TSCHHHHHHHHHHHHHHHHHHHC T ss_pred EEEECCCCHHCCH-HHHHHHHHHHHHHHHHCCCEEEEEEECCCE---EEEEEECCC-CCCHHHHHHHHHHHHHHHHHHHC T ss_conf 9933464233287-899999999999998649278998752997---999995189-77999999985346579999978 Q ss_pred ------CCCCCCCEEEEEECCCCCCCCCHHHHHHHHCC Q ss_conf ------35676507999727887744578999987105 Q gi|254780789|r 84 ------NIIEGHYRLEVSSPGIDRPMVRKSDFLRWNGH 115 (192) Q Consensus 84 ------d~i~~~Y~LEVSSPGidRpL~~~~~f~r~~G~ 115 (192) ..-...|. ++|-|- ..+-..++|.++.+. T Consensus 93 p~l~~~~~W~~gy~--~~svg~-~~~~~i~~YI~~Q~~ 127 (133) T 2f5g_A 93 PQLNKGKLWTRSYF--VATAGN-VSSEVIKKYIEEQWR 127 (133) T ss_dssp GGGCSSCSBCSCEE--EEEEBC-CCHHHHHHHHHHHHH T ss_pred CCCCCCCCCCCCEE--EEECCC-CCHHHHHHHHHHHCC T ss_conf 13237875468727--981689-999999999997283 No 39 >1msc_A Bacteriophage MS2 coat protein; translation repressor, viral protein; 2.00A {Enterobacterio phage MS2} SCOP: d.85.1.1 PDB: 2bu1_A* 1u1y_A 1zdi_A 1zdj_A 1zdk_A 1zdh_A* 2c4q_A* 2c4y_A* 2c4z_A* 2c50_A 2c51_A 2iz8_A 2iz9_A* 2izm_A 2izn_A 2ms2_A 5msf_A 6msf_A 7msf_A 1aq3_A ... Probab=24.07 E-value=22 Score=15.23 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=20.3 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 78999999999987520211356765 Q gi|254780789|r 64 MTLRDCEELSQAISPILDVENIIEGH 89 (192) Q Consensus 64 i~iddC~~vSr~i~~~LD~~d~i~~~ 89 (192) -+-|||+-+++++...|..-+||+++ T Consensus 96 at~dd~~li~kal~glfk~gnpia~a 121 (129) T 1msc_A 96 ATNSDCELIVKAMQGLLKDGNPIPSA 121 (129) T ss_dssp CCHHHHHHHHHHHHHHTCTTSHHHHH T ss_pred ECCCCHHHHHHHHHHHHHCCCCHHHH T ss_conf 61886312799856675059863787 No 40 >1gtd_A MTH169; synthetase, FGAM synthetase, purine synthesis pathway, PSI, protein structure initiative, NESG; 2.56A {Methanobacterium thermoautotrophicum} SCOP: d.284.1.1 Probab=23.45 E-value=34 Score=14.06 Aligned_cols=69 Identities=12% Similarity=0.257 Sum_probs=41.1 Q ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEE Q ss_conf 412799999999999974797799999954998689999965877878999999999987520211356765079997 Q gi|254780789|r 18 DMGLAGDISSVIQPVIEEMSFRSVQISLLEEKNLLLQIFVERDDGNMTLRDCEELSQAISPILDVENIIEGHYRLEVS 95 (192) Q Consensus 18 ~~~i~~~i~~li~p~v~~lG~eLv~v~~~~~~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEVS 95 (192) ++++-+.--+.+...+..+||.+-+|... + .+.+.++.+ +-+.+..--..+...| -.+|+-+.|..++. T Consensus 12 K~gVlDPqG~av~~aL~~lG~~v~~vr~g--K--~~~l~~~~~----~~e~a~~~v~~~c~~l-LaNpvIE~y~i~i~ 80 (85) T 1gtd_A 12 KKGMLNPEAATIERALALLGYEVEDTDTT--D--VITFTMDED----SLEAVEREVEDMCQRL-LCNPVIHDYDVSIN 80 (85) T ss_dssp CTTSCCHHHHHHHHHHHHHTCCCEEEEEE--E--EEEEEECCS----CHHHHHHHHHHHHHHT-TCCTTTEEEEEEEE T ss_pred CCCCCCCHHHHHHHHHHHCCCCCCEEEEE--E--EEEEEECCC----CHHHHHHHHHHHHHHH-CCCCCEEEEEEEEE T ss_conf 99870837999999999759963048998--8--999997789----9899999999999986-39866578999999 No 41 >2vjv_A Transposase ORFA; DNA-binding protein, protein-DNA complex, HUH motif, DNA stem loop, transposition; 1.90A {Helicobacter pylori} SCOP: d.58.57.1 PDB: 2vhg_A 2vic_A 2vju_A 2vih_A 2a6m_A 2a6o_A Probab=23.15 E-value=35 Score=14.02 Aligned_cols=103 Identities=11% Similarity=0.223 Sum_probs=66.5 Q ss_pred HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHH-----HHHHH Q ss_conf 0113337610014127999999999999747977999999549986899999658778789999999999-----87520 Q gi|254780789|r 6 FLHSKYEPRIFGDMGLAGDISSVIQPVIEEMSFRSVQISLLEEKNLLLQIFVERDDGNMTLRDCEELSQA-----ISPIL 80 (192) Q Consensus 6 ~~~~~~~~r~~~~~~i~~~i~~li~p~v~~lG~eLv~v~~~~~~~~~LrI~ID~~dg~i~iddC~~vSr~-----i~~~L 80 (192) .++++|-..++.. .+.+++.+++..+++..|++++.+++...- +-++++-+- .+++-++...=+. |-..+ T Consensus 26 V~~tKyR~~vl~~-~v~~~l~~~i~~i~~~~~~~i~~~~~~~DH---VHllv~~~p-~~sis~~v~~lKg~SSr~l~k~f 100 (159) T 2vjv_A 26 VWCPKYRRKVLVG-AVEMRLKEIIQEVAKELRVEIIEMQTDKDH---IHILADIDP-SFGVMKFIKTAKGRSSRILRQEF 100 (159) T ss_dssp EECBGGGCCCCSH-HHHHHHHHHHHHHHHHTTCEEEEEEEETTE---EEEEEECCT-TTCHHHHHHHHHHHHHHHHHHHC T ss_pred EEEECCCCHHCCH-HHHHHHHHHHHHHHHHCCCCEEECCCCCCE---EEEEEECCC-CCCHHHHHHHHHHHHHHHHHHHH T ss_conf 9930566432487-899999999999998609804662436982---799996188-74268999988608899999998 Q ss_pred C----CCC-CCCCCCEEEEEECCCCCCCCCHHHHHHHHCCE Q ss_conf 2----113-56765079997278877445789999871056 Q gi|254780789|r 81 D----VEN-IIEGHYRLEVSSPGIDRPMVRKSDFLRWNGHV 116 (192) Q Consensus 81 D----~~d-~i~~~Y~LEVSSPGidRpL~~~~~f~r~~G~~ 116 (192) . ... +-...|. |+|-|- ..+-..++|..+.+.. T Consensus 101 p~l~~~~~~~Ws~gYf--~~SvG~-~~~e~Ik~YI~nQ~~~ 138 (159) T 2vjv_A 101 NHLKTKLPTLWTNSCF--ISTVGG-APLNVVKQYIENQQNS 138 (159) T ss_dssp HHHHHSCSCSBCSCEE--EEEECS-SCHHHHHHHHTC---- T ss_pred HHHHHHHCCCCCCCEE--EEECCC-CCHHHHHHHHHHHCCC T ss_conf 6777766064689778--992189-9899999999960520 No 42 >1dpg_A G6PD, glucose 6-phosphate dehydrogenase; oxidoreductase, NADP/NAD, glucose metabolism, oxidoreductase (CHOH(D) - NAD(P)); 2.00A {Leuconostoc mesenteroides} SCOP: c.2.1.3 d.81.1.5 PDB: 1e7y_A* 1e7m_A* 1h93_A 1h94_A* 1h9a_A* 1e77_A* 1h9b_A 2dpg_A* Probab=22.20 E-value=36 Score=13.90 Aligned_cols=39 Identities=18% Similarity=0.346 Sum_probs=31.8 Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCC-CCCC Q ss_conf 689999965877878999999999987520211356-7650 Q gi|254780789|r 51 LLLQIFVERDDGNMTLRDCEELSQAISPILDVENII-EGHY 90 (192) Q Consensus 51 ~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i-~~~Y 90 (192) ..-||.+++|-| -+++.|..+++.|...++++.++ -++| T Consensus 140 ~~~RvviEKPfG-~dl~Sa~~Ln~~l~~~f~E~qIyRIDHY 179 (485) T 1dpg_A 140 GYNRLMIEKPFG-TSYDTAAELQNDLENAFDDNQLFRIDHY 179 (485) T ss_dssp SCEEEEECSCCC-SSHHHHHHHHHHHTTTCCGGGEEECCGG T ss_pred CCEEEEEECCCC-CCCCCHHHHHHHHHHHCCHHHHCCCHHH T ss_conf 753578624775-7731689999999976297760351122 No 43 >1c1y_B Proto-onkogene serine/threonine protein kinase RAF-1; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: d.15.1.5 PDB: 1gua_B* 1rfa_A 3kud_B* 3kuc_B* Probab=21.96 E-value=37 Score=13.87 Aligned_cols=53 Identities=21% Similarity=0.344 Sum_probs=38.4 Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCC---CEEEEEECCCCCCCCCHHHHHHHHCCEEEEEE Q ss_conf 878999999999987520211356765---07999727887744578999987105688987 Q gi|254780789|r 63 NMTLRDCEELSQAISPILDVENIIEGH---YRLEVSSPGIDRPMVRKSDFLRWNGHVVACEI 121 (192) Q Consensus 63 ~i~iddC~~vSr~i~~~LD~~d~i~~~---Y~LEVSSPGidRpL~~~~~f~r~~G~~VkV~l 121 (192) |.++.|| ++..|+.-.+-.+. |.+...+.|-+.|+--..|-....|+.+.|++ T Consensus 21 G~tlrd~------L~k~l~kRgl~~~~c~V~~~~~~~~g~~~~l~~d~d~s~L~g~El~Ve~ 76 (77) T 1c1y_B 21 GMSLHDC------LMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDF 76 (77) T ss_dssp TCBHHHH------HHHHHHTTTCCGGGEEEEEEEGGGSSEEEEECTTSBGGGGTTCEEEEEE T ss_pred CCCHHHH------HHHHHHHCCCCHHHEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEE T ss_conf 9899999------9999987599967889998424457887410247620111587799996 No 44 >1wwj_A Circadian clock protein KAIB; 1.90A {Synechocystis SP} PDB: 1r5p_A 2qke_A 1vgl_A Probab=20.38 E-value=40 Score=13.67 Aligned_cols=44 Identities=20% Similarity=0.330 Sum_probs=29.2 Q ss_pred CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCC Q ss_conf 986899999658778789999999999875202113567650799972788 Q gi|254780789|r 49 KNLLLQIFVERDDGNMTLRDCEELSQAISPILDVENIIEGHYRLEVSSPGI 99 (192) Q Consensus 49 ~~~~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i~~~Y~LEVSSPGi 99 (192) +.++|+.|+.+.. .-+.....++.+.+... .++.|.|||--..- T Consensus 6 ~~y~L~LyVaG~t-p~S~~ai~nl~~ice~~------l~g~y~LeVIDv~~ 49 (105) T 1wwj_A 6 KTYVLKLYVAGNT-PNSVRALKMLKNILEQE------FQGVYALKVIDVLK 49 (105) T ss_dssp EEEEEEEEESSCC-HHHHHHHHHHHHHHHHH------HTTSEEEEEEETTT T ss_pred CCEEEEEEEECCC-HHHHHHHHHHHHHHHHH------CCCCEEEEEEECCC T ss_conf 6369999980898-37899999999999986------69967999987333 No 45 >2bh9_A G6PD, glucose-6-phosphate 1-dehydrogenase; oxidoreductase, oxidoreductase (CHOH(D)-NADP), carbohydrate metabolism, glucose metabolism; HET: NAP; 2.5A {Homo sapiens} PDB: 2bhl_A* 1qki_A* Probab=20.08 E-value=40 Score=13.63 Aligned_cols=34 Identities=29% Similarity=0.427 Sum_probs=29.3 Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCC Q ss_conf 89999965877878999999999987520211356 Q gi|254780789|r 52 LLQIFVERDDGNMTLRDCEELSQAISPILDVENII 86 (192) Q Consensus 52 ~LrI~ID~~dg~i~iddC~~vSr~i~~~LD~~d~i 86 (192) ..||.+++|=| -+++.+..+++.|...++++.++ T Consensus 138 ~~RvVvEKPFG-~Dl~SA~~ln~~l~~~f~E~qIy 171 (489) T 2bh9_A 138 WNRIIVEKPFG-RDLQSSDRLSNHISSLFREDQIY 171 (489) T ss_dssp CEEEEECSCSC-SSHHHHHHHHHHHTTTSCGGGEE T ss_pred CCEEEEECCCC-CCHHHHHHHHHHHHHHCCCHHHC T ss_conf 71488845877-86688999999999756913320 Done!