Query gi|254780913|ref|YP_003065326.1| cold shock protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 78 No_of_seqs 112 out of 2159 Neff 6.0 Searched_HMMs 39220 Date Mon May 30 00:39:50 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780913.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK09937 stationary phase/star 99.9 1.2E-25 3E-30 164.2 8.4 72 2-78 1-72 (74) 2 COG1278 CspC Cold shock protei 99.9 5.7E-25 1.5E-29 160.3 7.7 67 2-73 1-67 (67) 3 PRK10354 major cold shock prot 99.9 3.9E-24 9.9E-29 155.7 7.7 67 2-73 4-70 (70) 4 PRK10943 cold shock-like prote 99.9 4.2E-24 1.1E-28 155.5 7.7 67 2-73 3-69 (69) 5 PRK09890 cold shock protein Cs 99.9 4.2E-24 1.1E-28 155.5 7.2 67 2-73 4-70 (70) 6 PRK09507 cspE cold shock prote 99.9 7.5E-24 1.9E-28 154.1 7.8 67 2-73 3-69 (69) 7 LOAD_cold consensus 99.9 2.2E-23 5.6E-28 151.5 8.0 66 2-72 1-66 (67) 8 pfam00313 CSD 'Cold-shock' DNA 99.9 1.6E-22 4.1E-27 146.6 8.4 66 3-73 1-66 (66) 9 smart00357 CSP Cold shock prot 99.8 1.7E-20 4.3E-25 135.4 7.7 64 4-73 1-64 (64) 10 cd04458 CSP_CDS Cold-Shock Pro 99.8 2.7E-20 6.9E-25 134.2 7.7 65 3-72 1-65 (65) 11 TIGR02381 cspD cold shock doma 99.7 1.3E-16 3.4E-21 113.6 6.9 67 2-73 1-67 (68) 12 KOG3070 consensus 99.5 2E-14 5E-19 101.5 4.2 64 3-71 57-124 (235) 13 pfam08206 OB_RNB Ribonuclease 97.8 4.9E-05 1.2E-09 49.1 5.1 53 12-72 6-58 (58) 14 PRK11642 exoribonuclease R; Pr 97.7 9.9E-05 2.5E-09 47.4 6.0 65 3-77 85-149 (813) 15 PRK05054 exoribonuclease II; P 96.9 0.0022 5.7E-08 39.8 5.6 60 3-75 22-81 (644) 16 TIGR02063 RNase_R ribonuclease 96.3 0.0084 2.1E-07 36.6 5.1 67 4-77 76-149 (755) 17 pfam07497 Rho_RNA_bind Rho ter 96.0 0.0087 2.2E-07 36.5 3.8 58 13-73 11-71 (78) 18 cd04459 Rho_CSD Rho_CSD: Rho p 95.7 0.013 3.4E-07 35.4 3.9 52 13-67 9-62 (68) 19 PRK09376 rho transcription ter 94.7 0.036 9.1E-07 33.1 3.5 59 13-74 60-121 (416) 20 PRK08059 general stress protei 94.3 0.13 3.3E-06 29.9 5.7 69 3-77 10-82 (119) 21 TIGR02062 RNase_B exoribonucle 92.9 0.23 5.9E-06 28.6 4.9 59 3-74 22-80 (664) 22 TIGR00717 rpsA ribosomal prote 92.3 0.55 1.4E-05 26.4 6.2 70 2-76 203-276 (534) 23 PRK12608 transcription termina 92.2 0.18 4.6E-06 29.2 3.7 56 13-73 26-83 (379) 24 PRK07400 30S ribosomal protein 91.0 0.73 1.9E-05 25.7 5.8 66 3-75 200-269 (314) 25 COG1158 Rho Transcription term 90.2 0.27 6.9E-06 28.2 2.9 51 13-67 62-115 (422) 26 cd04472 S1_PNPase S1_PNPase: P 90.0 0.86 2.2E-05 25.4 5.4 57 2-64 3-63 (68) 27 PRK12678 transcription termina 90.0 0.2 5.2E-06 28.9 2.1 48 5-58 293-340 (667) 28 cd05692 S1_RPS1_repeat_hs4 S1_ 88.8 1.3 3.3E-05 24.4 5.5 57 2-64 3-63 (69) 29 pfam00575 S1 S1 RNA binding do 88.2 1.1 2.7E-05 24.9 4.8 55 2-62 7-65 (74) 30 cd00164 S1_like S1_like: Ribos 87.9 1.3 3.3E-05 24.4 5.1 52 4-61 2-57 (65) 31 cd05691 S1_RPS1_repeat_ec6 S1_ 87.7 1.8 4.5E-05 23.6 5.6 66 2-73 3-72 (73) 32 COG1098 VacB Predicted RNA bin 87.1 0.68 1.7E-05 25.9 3.3 57 15-76 18-79 (129) 33 cd04465 S1_RPS1_repeat_ec2_hs2 86.9 1.3 3.4E-05 24.3 4.6 52 3-62 4-58 (67) 34 COG0557 VacB Exoribonuclease R 86.6 0.86 2.2E-05 25.4 3.5 65 4-76 71-136 (706) 35 TIGR00358 3_prime_RNase VacB a 86.3 0.39 9.9E-06 27.3 1.7 64 3-75 19-83 (684) 36 PRK00087 4-hydroxy-3-methylbut 84.9 2.6 6.6E-05 22.7 5.3 63 4-73 570-637 (670) 37 PRK07252 hypothetical protein; 84.8 1.6 4.2E-05 23.8 4.3 67 3-75 7-77 (120) 38 PRK08582 hypothetical protein; 83.6 3.4 8.7E-05 22.0 5.5 63 3-73 9-76 (139) 39 PRK07899 rpsA 30S ribosomal pr 83.5 3.9 0.0001 21.7 5.7 51 3-61 212-267 (484) 40 smart00316 S1 Ribosomal protei 83.3 3 7.5E-05 22.4 5.0 54 3-62 6-63 (72) 41 PRK11824 polynucleotide phosph 82.7 3.8 9.7E-05 21.8 5.4 58 3-66 625-686 (694) 42 TIGR03591 polynuc_phos polyrib 82.7 4.3 0.00011 21.5 5.7 57 3-65 622-682 (684) 43 cd05684 S1_DHX8_helicase S1_DH 82.4 4.5 0.00011 21.4 7.1 68 3-76 4-77 (79) 44 cd04473 S1_RecJ_like S1_RecJ_l 81.6 4.8 0.00012 21.2 6.2 52 3-64 20-71 (77) 45 cd05689 S1_RPS1_repeat_ec4 S1_ 81.0 4.2 0.00011 21.5 5.1 54 3-62 7-65 (72) 46 PRK06676 rpsA 30S ribosomal pr 80.8 3.7 9.4E-05 21.8 4.8 13 46-58 322-334 (390) 47 PRK05807 hypothetical protein; 80.4 4.9 0.00013 21.1 5.3 60 3-71 9-73 (136) 48 cd05686 S1_pNO40 S1_pNO40: pNO 79.9 5 0.00013 21.1 5.2 56 3-64 7-67 (73) 49 PRK12269 bifunctional cytidyla 78.3 6.2 0.00016 20.6 6.3 33 27-59 687-724 (863) 50 PRK13806 rpsA 30S ribosomal pr 78.0 5.6 0.00014 20.8 5.0 49 4-58 206-258 (489) 51 cd05688 S1_RPS1_repeat_ec3 S1_ 77.5 6.5 0.00017 20.4 5.9 52 3-61 5-60 (68) 52 cd05708 S1_Rrp5_repeat_sc12 S1 76.1 7.2 0.00018 20.2 6.0 55 2-62 5-64 (77) 53 cd05685 S1_Tex S1_Tex: The C-t 75.5 7.5 0.00019 20.1 5.9 54 2-61 3-60 (68) 54 COG4776 Rnb Exoribonuclease II 73.8 5 0.00013 21.1 3.8 54 3-69 22-75 (645) 55 cd05690 S1_RPS1_repeat_ec5 S1_ 72.9 7.8 0.0002 20.0 4.6 52 3-61 4-61 (69) 56 cd04453 S1_RNase_E S1_RNase_E: 69.5 10 0.00027 19.3 5.9 58 3-64 11-75 (88) 57 cd04452 S1_IF2_alpha S1_IF2_al 68.3 11 0.00028 19.2 5.1 57 3-64 7-69 (76) 58 cd05697 S1_Rrp5_repeat_hs5 S1_ 67.3 12 0.0003 19.0 4.7 56 1-62 2-61 (69) 59 PRK11637 hypothetical protein; 67.2 12 0.00029 19.1 4.5 51 3-54 322-373 (404) 60 TIGR01622 SF-CC1 splicing fact 66.4 2.2 5.6E-05 23.1 0.7 10 13-22 276-285 (531) 61 PRK03987 translation initiatio 65.0 11 0.00029 19.1 4.1 54 4-62 13-71 (262) 62 KOG0125 consensus 63.6 3 7.8E-05 22.3 1.0 18 9-26 129-148 (376) 63 cd05698 S1_Rrp5_repeat_hs6_sc5 56.6 18 0.00047 17.9 5.1 56 1-62 2-61 (70) 64 COG1093 SUI2 Translation initi 56.5 8.5 0.00022 19.8 2.3 53 5-62 17-74 (269) 65 cd05702 S1_Rrp5_repeat_hs11_sc 54.2 19 0.00047 17.9 3.7 54 3-63 4-63 (70) 66 cd04461 S1_Rrp5_repeat_hs8_sc7 50.9 23 0.00058 17.4 5.4 54 2-61 17-74 (83) 67 COG0539 RpsA Ribosomal protein 47.6 26 0.00066 17.1 5.0 13 46-58 236-248 (541) 68 pfam11604 CusF_Ec Copper bindi 46.9 19 0.00048 17.9 2.7 20 42-61 39-58 (61) 69 COG2190 NagE Phosphotransferas 45.4 28 0.00072 16.9 4.7 45 4-53 50-100 (156) 70 KOG0149 consensus 44.9 10 0.00026 19.4 1.1 13 10-22 50-62 (247) 71 TIGR01661 ELAV_HUD_SF ELAV/HuD 42.9 9.5 0.00024 19.5 0.7 11 11-21 392-402 (436) 72 COG1185 Pnp Polyribonucleotide 41.2 33 0.00084 16.5 4.8 59 3-67 623-685 (692) 73 PTZ00162 RNA polymerase II sub 41.0 33 0.00084 16.5 4.1 41 15-59 94-148 (170) 74 PRK09838 periplasmic copper-bi 40.7 33 0.00085 16.5 6.8 69 2-72 43-112 (114) 75 cd05707 S1_Rrp5_repeat_sc11 S1 40.5 34 0.00086 16.5 4.3 57 1-64 2-64 (68) 76 cd02787 MopB_CT_ydeP The MopB_ 38.3 27 0.00068 17.0 2.4 29 28-59 30-58 (112) 77 pfam04225 OapA Opacity-associa 38.2 37 0.00094 16.3 3.2 27 42-71 39-65 (85) 78 pfam01551 Peptidase_M23 Peptid 35.6 40 0.001 16.0 3.8 51 3-54 20-71 (96) 79 cd04485 DnaE_OBF DnaE_OBF: A s 35.6 40 0.001 16.0 4.2 67 7-75 9-79 (84) 80 cd00210 PTS_IIA_glc PTS_IIA, P 34.5 42 0.0011 15.9 4.7 45 4-53 43-93 (124) 81 COG1095 RPB7 DNA-directed RNA 33.4 24 0.0006 17.3 1.5 46 13-62 92-152 (183) 82 pfam00358 PTS_EIIA_1 phosphoen 32.1 46 0.0012 15.7 5.0 45 4-53 48-98 (133) 83 COG5569 Uncharacterized conser 29.4 46 0.0012 15.7 2.5 41 29-71 52-107 (108) 84 COG2996 Predicted RNA-bindinin 29.1 52 0.0013 15.4 6.3 54 12-71 15-68 (287) 85 KOG0291 consensus 29.1 52 0.0013 15.4 4.2 61 3-63 370-447 (893) 86 TIGR01645 half-pint poly-U bin 27.9 17 0.00044 18.1 0.1 11 12-22 281-291 (791) 87 TIGR02997 Sig70-cyanoRpoD RNA 26.8 20 0.00052 17.7 0.2 15 7-21 152-166 (336) 88 cd04460 S1_RpoE S1_RpoE: RpoE, 26.2 59 0.0015 15.1 3.4 42 14-59 11-67 (99) 89 KOG4208 consensus 25.9 60 0.0015 15.1 2.6 19 5-23 75-101 (214) 90 TIGR01371 met_syn_B12ind 5-met 25.0 29 0.00073 16.8 0.8 28 7-38 119-146 (778) 91 TIGR01628 PABP-1234 polyadenyl 24.2 30 0.00076 16.8 0.7 10 13-22 128-137 (860) 92 TIGR02375 pseudoazurin pseudoa 23.9 55 0.0014 15.3 2.0 32 42-77 18-50 (123) 93 TIGR02408 ectoine_ThpD ectoine 23.1 38 0.00096 16.2 1.0 12 28-39 104-115 (278) 94 KOG0407 consensus 23.0 52 0.0013 15.4 1.8 36 29-67 26-62 (139) 95 pfam06523 DUF1106 Protein of u 22.8 69 0.0018 14.7 4.8 56 3-58 33-89 (91) 96 PRK07135 dnaE DNA polymerase I 22.6 70 0.0018 14.7 4.1 50 12-64 927-976 (987) 97 TIGR02712 urea_carbox urea car 22.5 68 0.0017 14.8 2.3 34 19-55 726-762 (1226) 98 COG4942 Membrane-bound metallo 22.4 71 0.0018 14.7 2.8 51 3-53 338-388 (420) 99 KOG3074 consensus 21.9 72 0.0018 14.6 2.6 28 11-42 185-212 (263) 100 KOG0109 consensus 21.6 46 0.0012 15.7 1.3 20 4-23 26-45 (346) 101 TIGR02383 Hfq RNA chaperone Hf 21.3 42 0.0011 15.9 1.0 29 3-38 28-56 (61) 102 KOG4246 consensus 20.9 5.5 0.00014 20.8 -3.6 50 15-75 159-209 (1194) 103 cd04471 S1_RNase_R S1_RNase_R: 20.4 78 0.002 14.4 5.8 52 4-61 6-73 (83) No 1 >PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional Probab=99.93 E-value=1.2e-25 Score=164.15 Aligned_cols=72 Identities=35% Similarity=0.660 Sum_probs=65.9 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCCC Q ss_conf 87762775146887465885488778837999950002358844689988999999869997111059996357889 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN 78 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~~ 78 (78) |++|+|||||.+||||||+|| ++++|||||+|+|+..|+++|.+||+|+|++.+++++ ++|.+|..++.++. T Consensus 1 M~~G~VKwFn~~KGyGFI~~d---~gg~DvFvH~s~i~~~G~~~L~~G~~V~f~v~~g~kG--~~A~~V~~ve~~~a 72 (74) T PRK09937 1 MEKGTVKWFNNAKGFGFICPE---GGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG--NHASVIVPVEVEAA 72 (74) T ss_pred CCCCEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEECCCCCC T ss_conf 998379788389971886207---9995599985882315884249999999999989998--51567588576667 No 2 >COG1278 CspC Cold shock proteins [Transcription] Probab=99.91 E-value=5.7e-25 Score=160.32 Aligned_cols=67 Identities=45% Similarity=0.830 Sum_probs=61.3 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) |.+|+|||||+.||||||+|| +|++|||||+|+|+..|+++|.+||+|+|++++++++ ++|.||+.+ T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~---~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg--p~A~nv~~~ 67 (67) T COG1278 1 MATGTVKWFNATKGFGFITPE---DGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG--PSAANVRAL 67 (67) T ss_pred CCCCEEEEEECCCCCEEECCC---CCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCC--CCEEEEEEC T ss_conf 986168885089863370789---9985779980125127886557998899999528999--722678829 No 3 >PRK10354 major cold shock protein; Provisional Probab=99.90 E-value=3.9e-24 Score=155.68 Aligned_cols=67 Identities=39% Similarity=0.720 Sum_probs=61.2 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) ..+|+|||||.+||||||+|| ++++|||||+|+|+.+++++|.+||+|+|++++++++ ++|.||+.| T Consensus 4 ~~tG~VKwFn~~KGyGFI~~d---~g~~DvFvH~s~l~~~g~~~L~~Gq~V~f~~~~g~kG--~~A~nV~~l 70 (70) T PRK10354 4 KMTGIVKWFNADKGFGFITPD---DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG--PAAGNVTSL 70 (70) T ss_pred CEEEEEEEEECCCCEEEEECC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC T ss_conf 507999987099985998427---9984299985891704897259999999999979998--620777859 No 4 >PRK10943 cold shock-like protein CspC; Provisional Probab=99.90 E-value=4.2e-24 Score=155.49 Aligned_cols=67 Identities=37% Similarity=0.728 Sum_probs=61.3 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) +.+|+|||||++||||||+|+ |+++|||||+|+|+..++++|.+||+|+|++.+++++ ++|+||+.| T Consensus 3 ~~~G~VKwFn~~kGfGFI~~~---dg~~DvFvH~s~i~~~g~~~L~eGq~V~f~~~~g~kG--~~A~~V~~i 69 (69) T PRK10943 3 KIKGQVKWFNESKGFGFITPA---DGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG--PAAVNVTAI 69 (69) T ss_pred CEEEEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CCCEEEEEC T ss_conf 378899998399986998617---9983099993882716883239999999999979998--631887969 No 5 >PRK09890 cold shock protein CspG; Provisional Probab=99.90 E-value=4.2e-24 Score=155.46 Aligned_cols=67 Identities=37% Similarity=0.676 Sum_probs=61.2 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) +.+|+|||||.+||||||+|| |+++|||||+|+|+..++++|.+||+|+|++.+++++ ++|.||..| T Consensus 4 ~~tG~VKwFn~~KGyGFI~~d---dg~~DvFvH~s~i~~~~~~~L~~Gq~V~f~v~~g~kG--~~A~~V~~L 70 (70) T PRK09890 4 KMTGLVKWFNADKGFGFITPD---DGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG--PAAANVVTL 70 (70) T ss_pred CEEEEEEEECCCCCEEEECCC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CCCEEEEEC T ss_conf 506999988399986997038---9994299986892726883329999999999979998--611438879 No 6 >PRK09507 cspE cold shock protein CspE; Reviewed Probab=99.90 E-value=7.5e-24 Score=154.09 Aligned_cols=67 Identities=40% Similarity=0.757 Sum_probs=61.1 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) +.+|+|||||++||||||+|| |+++|||||+|+|+..++++|.+||+|+|++.+++++ ++|.||..| T Consensus 3 ~i~G~VKwF~~~kGyGFI~~~---dG~~DvFvH~s~i~~~g~~~L~~Gq~V~f~v~~~~kG--~~A~~V~~l 69 (69) T PRK09507 3 KIKGNVKWFNESKGFGFITPE---DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG--PSAANVIAL 69 (69) T ss_pred CEEEEEEEEECCCCEEEEECC---CCCCCEEEEHHHCCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC T ss_conf 478899998399987999707---9983299990770525786169999999999969999--851888979 No 7 >LOAD_cold consensus Probab=99.89 E-value=2.2e-23 Score=151.46 Aligned_cols=66 Identities=47% Similarity=0.891 Sum_probs=60.7 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE Q ss_conf 87762775146887465885488778837999950002358844689988999999869997111059996 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL 72 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~ 72 (78) |.+|+|||||.+||||||+|| ++++|||+|+|+|+..+++.|.+||+|+|++.+++++ ++|+||++ T Consensus 1 M~~G~VK~f~~~kGfGFI~~~---~g~~DvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~kG--~~A~~V~l 66 (67) T LOAD_cold 1 MVKGTVKWFNVKKGFGFITPE---DGGEDVFVHQSAIQGDGFRSLTEGQEVEFDIVEGPKG--PQAANVVL 66 (67) T ss_pred CCCEEEEEEECCCCCEEEEEC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEC T ss_conf 998699999899994788757---9982189994781404786479999999999989999--67688989 No 8 >pfam00313 CSD 'Cold-shock' DNA-binding domain. Probab=99.88 E-value=1.6e-22 Score=146.64 Aligned_cols=66 Identities=44% Similarity=0.827 Sum_probs=60.2 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 77627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) .+|+|||||++||||||+|+ ++++|||+|+|+|+..+++.|.+|++|+|++.+++++ ++|.||++| T Consensus 1 ~tG~VK~f~~~kGfGFI~~~---~~~~DiFvH~s~l~~~~~~~L~~G~~V~f~v~~~~kG--~~A~nV~~i 66 (66) T pfam00313 1 MTGTVKWFNAKKGFGFITPE---DGDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEGTKG--PQAANVTLL 66 (66) T ss_pred CCEEEEEEECCCCEEEEEEC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC T ss_conf 94899999599996999978---9984699992681214786179999999999979998--663899989 No 9 >smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor. Probab=99.83 E-value=1.7e-20 Score=135.39 Aligned_cols=64 Identities=44% Similarity=0.848 Sum_probs=57.3 Q ss_pred CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 7627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) +|+||||| ||||||+|+ ++++|||||+|+|+ .+++.|.+||+|+|++.+++.+++++|.||+.| T Consensus 1 tG~Vk~f~--kGfGFI~~~---~g~~DvFvH~s~i~-~~~~~l~~Gd~V~f~v~~~~~~~~~~A~~v~~l 64 (64) T smart00357 1 TGVVKWFN--KGFGFIRPD---DGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPRGGGKPEAENVVKL 64 (64) T ss_pred CCEEEEEE--CCEEEEEEC---CCCCCEEEEHHHHC-CCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEC T ss_conf 94796982--844888618---99940999869954-677744758789999998899998441898979 No 10 >cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription. Probab=99.82 E-value=2.7e-20 Score=134.23 Aligned_cols=65 Identities=40% Similarity=0.848 Sum_probs=58.1 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE Q ss_conf 7762775146887465885488778837999950002358844689988999999869997111059996 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL 72 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~ 72 (78) .+|+|||||.+||||||+++ ++++|||||+|+|+..+++.|.+|++|+|++.+++++ ++|.+|++ T Consensus 1 ~~G~Vk~f~~~kGfGFI~~~---~~~~diF~H~s~~~~~~~~~l~~G~~V~f~~~~~~~g--~~A~~v~~ 65 (65) T cd04458 1 VTGTVKWFDDEKGFGFITPD---DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG--PQAVNVRL 65 (65) T ss_pred CEEEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEC T ss_conf 93899999799996999957---9982299995892434697479898999999989899--76899899 No 11 >TIGR02381 cspD cold shock domain protein CspD; InterPro: IPR012751 This entry represents what appears to be a phylogenetically distinct clade, containing Escherichia coli CspD (P24245 from SWISSPROT) and related proteobacterial proteins within the larger family of cold shock domain proteins. The gene symbol cspD may have been used independently for other subfamilies of cold shock domain proteins, such as for Bacillus subtilis CspD. These proteins typically are shorter than 70 amino acids. In Escherichia coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication . ; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription DNA-dependent, 0006950 response to stress, 0005737 cytoplasm. Probab=99.67 E-value=1.3e-16 Score=113.61 Aligned_cols=67 Identities=34% Similarity=0.691 Sum_probs=59.1 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 877627751468874658854887788379999500023588446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) |..|+|||||..||||||.+++ ...|||.|+|.|+.+||++|+.||.|.|++.+.+++ ..|..|..+ T Consensus 1 m~~G~vkWfnn~kGfGfi~~~~---~~~d~fahys~i~~dGy~~lk~Gq~v~f~~~~~~~G--~~a~~~~~~ 67 (68) T TIGR02381 1 MEIGIVKWFNNAKGFGFISAEG---KDEDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGEKG--AHATKIVPI 67 (68) T ss_pred CCCCCEEECCCCCCEEEEECCC---CCCCEEEEEEEEECCCCEEECCCCEEEEEEEECCCC--CCEEEEEEE T ss_conf 9744045301665203541478---776223211100014430001474368986207888--410266760 No 12 >KOG3070 consensus Probab=99.49 E-value=2e-14 Score=101.50 Aligned_cols=64 Identities=39% Similarity=0.812 Sum_probs=54.8 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCC----CCCCCCCCCCEEEEEEEECCCCCCCCCEEEE Q ss_conf 77627751468874658854887788379999500023----5884468998899999986999711105999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVAS----AGLFNLTEGQLVTYDYVQNDANGKYSAENLK 71 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~----~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~ 71 (78) .+|+|||||..+|||||+++ |+++|||||+|+|.+ .++++|.+++.|+|++++...+ ..|+++. T Consensus 57 ~~G~~kwfnv~~G~gFi~~~---d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g--~~a~~vt 124 (235) T KOG3070 57 VKGTVKWFNVGKGYGFITRD---DGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG--TEAANVT 124 (235) T ss_pred CCCCCEEEECCCCCCEECCC---CCCCCEEEEEEEEECCCCCCCHHHCCCCCCCCCEECCCCCC--CEEEEEC T ss_conf 35864048636786300146---78886347864000145330011125688756100015765--3266623 No 13 >pfam08206 OB_RNB Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. Probab=97.75 E-value=4.9e-05 Score=49.06 Aligned_cols=53 Identities=23% Similarity=0.534 Sum_probs=41.1 Q ss_pred CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE Q ss_conf 6887465885488778837999950002358844689988999999869997111059996 Q gi|254780913|r 12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL 72 (78) Q Consensus 12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~ 72 (78) ..+||||+.||+ .++|||+....+.. .-.|++|..++....+++|+.+.-|++ T Consensus 6 ~~~GfGFv~~d~---~~~DifI~~~~l~~-----A~~GD~V~v~v~~~~~~~r~eG~vv~I 58 (58) T pfam08206 6 HKKGFGFLIPDD---EEDDIFIPPEQMKK-----AMHGDRVLVRITKGDRRGRREGRIVRI 58 (58) T ss_pred CCCCEEEEEECC---CCCCEEECHHHHCC-----CCCCCEEEEEEECCCCCCCCCEEEEEC T ss_conf 389009998689---98899999899745-----659999999995388899836999989 No 14 >PRK11642 exoribonuclease R; Provisional Probab=97.71 E-value=9.9e-05 Score=47.35 Aligned_cols=65 Identities=23% Similarity=0.450 Sum_probs=49.1 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCC Q ss_conf 776277514688746588548877883799995000235884468998899999986999711105999635788 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSS 77 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~ 77 (78) .+|+|.- ..+||||+.+|+ +++|||++-+.+.. .-.|++|.-.+...+++|++.+..|++|+.+. T Consensus 85 v~G~v~~--~~~GfgFv~~e~---~~eDifI~~~~l~~-----a~~GDrVlvr~~~~~r~gr~Eg~Vv~IleR~~ 149 (813) T PRK11642 85 LKGTVIG--HRDGYGFLRVEG---RKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLVPKT 149 (813) T ss_pred EEEEEEE--CCCCCEEEECCC---CCCCEEECHHHHCC-----CCCCCEEEEEEECCCCCCCCCEEEEEEEECCC T ss_conf 6899998--888777887079---87770008467432-----67999999998247788986179999995188 No 15 >PRK05054 exoribonuclease II; Provisional Probab=96.93 E-value=0.0022 Score=39.81 Aligned_cols=60 Identities=20% Similarity=0.362 Sum_probs=41.3 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCC Q ss_conf 7762775146887465885488778837999950002358844689988999999869997111059996357 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPK 75 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~ 75 (78) .+|+|+- ..|||||+.+| +++|||++-+.+.. .-.|++|...+... ++|..|.-++++.. T Consensus 22 v~G~~~~--~~~GfGFv~~d----~~~difI~~~~~~~-----a~~GD~V~v~v~~~--~~r~~~~~~~iv~r 81 (644) T PRK05054 22 VEGVVKA--TEKGFGFLEVD----AKKSYFIPPPQMKK-----VMHGDRIIAVIHTE--KERESAEPEELIEP 81 (644) T ss_pred EEEEEEE--ECCCCEEEEEC----CCCCEEECHHHHHH-----CCCCCEEEEEEEEC--CCCCEEEEEEEEEE T ss_conf 8999999--48963898508----98657699899944-----78999999999854--99846789999995 No 16 >TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity. Probab=96.31 E-value=0.0084 Score=36.58 Aligned_cols=67 Identities=19% Similarity=0.512 Sum_probs=48.1 Q ss_pred CCEEEEEECCCCEEEEEECCCC--CCCCEEEEEEEECCCCCCCCCCC--CCEEEEEEEECCCC--C-CCCCEEEEECCCC Q ss_conf 7627751468874658854887--78837999950002358844689--98899999986999--7-1110599963578 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEGST--ESGDDVFLHRSAVASAGLFNLTE--GQLVTYDYVQNDAN--G-KYSAENLKLVPKS 76 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~~~--d~g~DvFvH~s~i~~~g~~~l~~--G~~V~F~i~~~~~~--g-k~~A~~v~~i~~~ 76 (78) +|++. -..+||||+.|+++. +...|+|++.+.+.. .-. ||+|.+.+....+. | +.-|..+++|..+ T Consensus 76 ~G~~~--~~~~GfgF~~~~~~~~~~~~~d~~~~~~~~~~-----a~~G~gD~V~~~~~~~~~~~~~~~~eg~v~kil~r~ 148 (755) T TIGR02063 76 KGTVI--AHRDGFGFLRPEDDKYDEDEEDIFIPPEELNG-----AMHGLGDRVLVKITGKEDEKKGDRAEGRVIKILERA 148 (755) T ss_pred EEEEE--ECCCCCEEEEECCCCCCCCCCCEEECHHHHHH-----HHCCCCCEEEEEEECCCCCCCCCCCCEEEEEEECCC T ss_conf 99999--63765137885045576556511107588866-----434899789999603643458798525899996088 Q ss_pred C Q ss_conf 8 Q gi|254780913|r 77 S 77 (78) Q Consensus 77 ~ 77 (78) . T Consensus 149 ~ 149 (755) T TIGR02063 149 N 149 (755) T ss_pred C T ss_conf 7 No 17 >pfam07497 Rho_RNA_bind Rho termination factor, RNA-binding domain. The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. Probab=95.97 E-value=0.0087 Score=36.48 Aligned_cols=58 Identities=16% Similarity=0.365 Sum_probs=39.1 Q ss_pred CCCEEEEEE--CCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCC-CCEEEEEC Q ss_conf 887465885--48877883799995000235884468998899999986999711-10599963 Q gi|254780913|r 13 DKGYGFITP--EGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKY-SAENLKLV 73 (78) Q Consensus 13 ~kGfGFI~~--d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~-~A~~v~~i 73 (78) ..|||||.. .+...+-.||||+.|.|+..+ |+.|+.|+=.+..-..+-|+ +...|..+ T Consensus 11 ~dGyGFLR~~~~~y~~~~~DvyVs~~~Irrf~---LR~GD~V~G~vR~p~~~ek~~aL~~V~~V 71 (78) T pfam07497 11 PDGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTIEGKIRPPKEGERYFALLKVETI 71 (78) T ss_pred CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEEECCCCCCCCEEEEEEEEE T ss_conf 89837947786587999888788999998719---98888999998799989875210689758 No 18 >cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer. Probab=95.71 E-value=0.013 Score=35.44 Aligned_cols=52 Identities=23% Similarity=0.433 Sum_probs=36.5 Q ss_pred CCCEEEEEECCC--CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCC Q ss_conf 887465885488--7788379999500023588446899889999998699971110 Q gi|254780913|r 13 DKGYGFITPEGS--TESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSA 67 (78) Q Consensus 13 ~kGfGFI~~d~~--~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A 67 (78) ..||||+...+. ..+..||||+.+.|+..+ |+.|+.|+=.+..-..+-|+-| T Consensus 9 ~dGyGFLR~~~~ny~~~~~DvyVs~~~Irrf~---LR~GD~V~G~vR~p~~~Eky~a 62 (68) T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPKEGERYFA 62 (68) T ss_pred CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEEECCCCCCCCCC T ss_conf 89828967898778899888789999997739---9889999997779998886410 No 19 >PRK09376 rho transcription termination factor Rho; Provisional Probab=94.71 E-value=0.036 Score=33.06 Aligned_cols=59 Identities=19% Similarity=0.357 Sum_probs=39.4 Q ss_pred CCCEEEEEE--CCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCC-CCEEEEECC Q ss_conf 887465885--48877883799995000235884468998899999986999711-105999635 Q gi|254780913|r 13 DKGYGFITP--EGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKY-SAENLKLVP 74 (78) Q Consensus 13 ~kGfGFI~~--d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~-~A~~v~~i~ 74 (78) ..||||+.. .+..-+-.||||..|.|+..+ |+.|+.|+-.+..-..+-|+ +...|..+. T Consensus 60 ~dGyGFLR~~~~nylp~~dDiYVS~sqIrrf~---LR~GD~V~G~vR~pke~Ery~aLl~V~~VN 121 (416) T PRK09376 60 PDGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVN 121 (416) T ss_pred CCCCEEEECCCCCCCCCCCCEEECHHHHHHHC---CCCCCEEEEEEECCCCCCCCCCEEEEEECC T ss_conf 89865705787688899888336899999809---988888999886898888774337763228 No 20 >PRK08059 general stress protein 13; Validated Probab=94.34 E-value=0.13 Score=29.91 Aligned_cols=69 Identities=13% Similarity=0.144 Sum_probs=47.0 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCC Q ss_conf 77627751468874658854887788379999500023588----4468998899999986999711105999635788 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSS 77 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~ 77 (78) .+|+|+-..+ ||..+.- +++-+-|+|+|.|...-. ..+..||.|.+.+..-+...+-.+..++.+.+.| T Consensus 10 v~G~V~~I~~---fG~FV~l---~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~ri~LSlK~l~~~P 82 (119) T PRK08059 10 VTGKVTGIQD---YGAFVAL---DEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHGKISLSIRATEEAP 82 (119) T ss_pred EEEEEEEEEC---EEEEEEE---ECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEECCCCCCCC T ss_conf 9999999974---0489999---43953788878824566679999705899899999999899999987503576483 No 21 >TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process. Probab=92.85 E-value=0.23 Score=28.56 Aligned_cols=59 Identities=20% Similarity=0.405 Sum_probs=41.8 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECC Q ss_conf 776277514688746588548877883799995000235884468998899999986999711105999635 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVP 74 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~ 74 (78) ..|+||- .+|||||+..|. .+-+| |..-..+.+-=||+|.=.|.. + +-|.+|+==.||+ T Consensus 22 ~EGvvKa--tdkgFGFLEvDa----kksYF-----ipPp~MKkvMHGDki~A~i~~-e-~drE~AEPe~LiE 80 (664) T TIGR02062 22 VEGVVKA--TDKGFGFLEVDA----KKSYF-----IPPPSMKKVMHGDKIVAVIKK-E-KDREVAEPEELIE 80 (664) T ss_pred CCEEEEE--CCCCCCCEEEEC----CCCCC-----CCCCCCCCCCCCCEEEEEEEE-C-CCCCCCCCHHHHH T ss_conf 2316841--466752047607----64323-----786767841348827999973-5-8712148434310 No 22 >TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome. Probab=92.26 E-value=0.55 Score=26.45 Aligned_cols=70 Identities=23% Similarity=0.241 Sum_probs=50.1 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECC----CCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC Q ss_conf 87762775146887465885488778837999950002----3588446899889999998699971110599963578 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVA----SAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS 76 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~----~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~ 76 (78) ...|.||-+.+-.|-=||.. +|-|=|+|++++. ......+..||.|+-.+..-|+.-+.-+..++-+.+- T Consensus 203 ~v~GvVk~iT~fGGv~Fvdl-----gg~dGLLH~~d~sWkr~~~P~e~~~~G~~~~Vkv~~~D~~~~Ri~LsLK~~~~d 276 (534) T TIGR00717 203 VVKGVVKNITDFGGVAFVDL-----GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKKRISLSLKQLKED 276 (534) T ss_pred EEEEEEEEECCCCCEEEEEC-----CCEEECCCHHHCCCCCCCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCC T ss_conf 76108888889874999981-----643320350121478878834640079889999996526576077871205888 No 23 >PRK12608 transcription termination factor Rho; Provisional Probab=92.22 E-value=0.18 Score=29.16 Aligned_cols=56 Identities=25% Similarity=0.389 Sum_probs=37.1 Q ss_pred CCCEEEEEEC--CCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 8874658854--887788379999500023588446899889999998699971110599963 Q gi|254780913|r 13 DKGYGFITPE--GSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 13 ~kGfGFI~~d--~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) ..||||+-.. +...+-.||||..|.|+..+ |+.|+.|+=.+.. ++.|. +...|.-+ T Consensus 26 ~dGyGFLR~~~~nYlp~pdDiYVS~sqIrrf~---LR~GD~V~G~iR~-p~~ge-aL~~V~~V 83 (379) T PRK12608 26 GKGFGFLRSPERNYLPSPDDVYVSPALIRRFG---LRTGDLVEGVIRA-PREKE-TLVRIDSV 83 (379) T ss_pred CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEECC-CCCCH-HHEEEHHC T ss_conf 89975835898788999988100999997549---9999989998638-99874-20414523 No 24 >PRK07400 30S ribosomal protein S1; Reviewed Probab=91.05 E-value=0.73 Score=25.74 Aligned_cols=66 Identities=15% Similarity=0.142 Sum_probs=33.7 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCC Q ss_conf 77627751468874658854887788379999500023588----44689988999999869997111059996357 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPK 75 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~ 75 (78) .+|+|+-.. -||....- +|-|=|+|+|.|.-... ..++.||.|+..+..-++..+--+..++.+.+ T Consensus 200 v~G~V~~I~---~fGaFVdi----gGvdGLlHiSeiSw~rv~~p~dv~kvGd~V~vkVi~iD~e~~rIsLSiK~l~~ 269 (314) T PRK07400 200 VVGTVRGIK---PYGAFIDI----GGVSGLLHISEISHEHIETPHSVFNVNDQMKVMIIDLDAERGRISLSTKQLEP 269 (314) T ss_pred EEEEEEEEE---CEEEEEEE----CCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEHHHCCC T ss_conf 999999996---40889997----89189998146165444898782679999999999973889889977666555 No 25 >COG1158 Rho Transcription termination factor [Transcription] Probab=90.18 E-value=0.27 Score=28.16 Aligned_cols=51 Identities=24% Similarity=0.438 Sum_probs=36.0 Q ss_pred CCCEEEEEECC--CCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCC Q ss_conf 88746588548--8778837999950002358844689988999999869997-1110 Q gi|254780913|r 13 DKGYGFITPEG--STESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSA 67 (78) Q Consensus 13 ~kGfGFI~~d~--~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A 67 (78) .-||||+.... ...+..||||.-|.|+..+ |+.|+.|+=.+.. ++.| |+-| T Consensus 62 ~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~-Pke~Ery~a 115 (422) T COG1158 62 PDGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRP-PKEGERYFA 115 (422) T ss_pred CCCCCEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEECC-CCCCCCEEE T ss_conf 67742440576455789776678789986506---7668877666448-876430000 No 26 >cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. Probab=90.03 E-value=0.86 Score=25.37 Aligned_cols=57 Identities=19% Similarity=0.300 Sum_probs=39.4 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC Q ss_conf 877627751468874658854887788379999500023588----446899889999998699971 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk 64 (78) ..+|+|+-.-+ ||....- ..+.+=++|+|.|...-. ..++.||.|+..+..-+.++| T Consensus 3 iv~G~V~~i~~---fG~FV~l---~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~r 63 (68) T cd04472 3 IYEGKVVKIKD---FGAFVEI---LPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGR 63 (68) T ss_pred EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCC T ss_conf 99999999973---2999995---7996248886893456546988907899999999999999997 No 27 >PRK12678 transcription termination factor Rho; Provisional Probab=89.98 E-value=0.2 Score=28.87 Aligned_cols=48 Identities=23% Similarity=0.432 Sum_probs=37.1 Q ss_pred CEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEE Q ss_conf 627751468874658854887788379999500023588446899889999998 Q gi|254780913|r 5 GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQ 58 (78) Q Consensus 5 G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~ 58 (78) |.+--.| ||||+-..+..-+-.||||..|.|+..+ |+.|+.|.=.+.. T Consensus 293 Gildi~d---~y~FlRt~~ylp~~~DvYvs~~qir~~~---Lr~GD~v~G~vr~ 340 (667) T PRK12678 293 GILDVLD---NYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRRGDAITGAVRA 340 (667) T ss_pred EEEEEEE---CCEEEECCCCCCCCCCEEECHHHHHHHC---CCCCCEEEEEECC T ss_conf 1789740---6116634898899877547899998719---9988987872018 No 28 >cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=88.81 E-value=1.3 Score=24.39 Aligned_cols=57 Identities=26% Similarity=0.386 Sum_probs=39.0 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC Q ss_conf 877627751468874658854887788379999500023588----446899889999998699971 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk 64 (78) ..+|+|+---+ ||....- ..|.+=|+|+|.+..... ..+..||.|+..+..-+.++| T Consensus 3 vv~G~V~~I~~---fGaFV~l---~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id~~~r 63 (69) T cd05692 3 VVEGTVTRLKP---FGAFVEL---GGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63 (69) T ss_pred EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCC T ss_conf 99999999985---3899996---8998899996983456557988917899999999999999996 No 29 >pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Probab=88.21 E-value=1.1 Score=24.86 Aligned_cols=55 Identities=18% Similarity=0.181 Sum_probs=39.3 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCCC Q ss_conf 8776277514688746588548877883799995000235----884468998899999986999 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~~ 62 (78) ..+|+|+-.++ ||....- ..+-+-|+|.|.+... ....+..||.|.+.+..-+.. T Consensus 7 iv~G~V~~i~~---~G~fV~l---~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~ 65 (74) T pfam00575 7 VVKGTVTRVTK---GGAFVDL---GNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKE 65 (74) T ss_pred EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECC T ss_conf 99999999987---7599997---89979999844613655567768305999999999999999 No 30 >cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Probab=87.91 E-value=1.3 Score=24.37 Aligned_cols=52 Identities=17% Similarity=0.230 Sum_probs=37.6 Q ss_pred CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCC Q ss_conf 76277514688746588548877883799995000235----88446899889999998699 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~ 61 (78) +|+|+... .||..... ..+.+.|+|.|.+... ....+..||.|.+.+..-+. T Consensus 2 ~G~V~~i~---~~G~fV~~---~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~ 57 (65) T cd00164 2 TGKVVSIT---KFGVFVEL---EDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP 57 (65) T ss_pred EEEEEEEE---CCEEEEEE---CCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEEC T ss_conf 89999997---84599998---9871788988891676535951098599999999999989 No 31 >cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=87.69 E-value=1.8 Score=23.63 Aligned_cols=66 Identities=15% Similarity=0.185 Sum_probs=43.4 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 87762775146887465885488778837999950002358----8446899889999998699971110599963 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) ..+|+|+--.+ .|. |+..+ .+-+-|+|.|.+.... ...+..||.|...+..-++..+.-...++.+ T Consensus 3 iV~G~V~~i~~-~G~-fV~l~----~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~ri~LSiKal 72 (73) T cd05691 3 IVTGKVTEVDA-KGA-TVKLG----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73) T ss_pred EEEEEEEEEEC-CCE-EEEEC----CCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCCEEEEEEEEC T ss_conf 99999999977-868-99928----996999998997821132925438999999999999978899998674245 No 32 >COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Probab=87.13 E-value=0.68 Score=25.91 Aligned_cols=57 Identities=32% Similarity=0.437 Sum_probs=36.8 Q ss_pred CEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC Q ss_conf 746-5885488778837999950002358----8446899889999998699971110599963578 Q gi|254780913|r 15 GYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS 76 (78) Q Consensus 15 GfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~ 76 (78) -|| |+..++ |.-=+||+|.|...= ...|.+||.|.-.+.--+..|+.. ..|+-+.+. T Consensus 18 ~yGAFV~l~~----g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKis-LSIr~~~e~ 79 (129) T COG1098 18 PYGAFVELEG----GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKIS-LSIRKLEEE 79 (129) T ss_pred ECCEEEEECC----CCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCC-EEHHHHHHC T ss_conf 4334898239----9731488357544367739988427887999997214689703-356876647 No 33 >cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=86.92 E-value=1.3 Score=24.32 Aligned_cols=52 Identities=25% Similarity=0.323 Sum_probs=36.4 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC---CCCCCCCCEEEEEEEECCCC Q ss_conf 7762775146887465885488778837999950002358---84468998899999986999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG---LFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g---~~~l~~G~~V~F~i~~~~~~ 62 (78) .+|+|+-.+ || |||+.- +|-..|++.|.+...- ...+ .|+.++|.+.+-++. T Consensus 4 v~g~I~~~~--kG-G~~v~~----~gv~~FiP~Sq~~~~~~~~~~~~-vG~~i~~~Ii~~d~~ 58 (67) T cd04465 4 VEGKVTEKV--KG-GLIVDI----EGVRAFLPASQVDLRPVEDLDEY-VGKELKFKIIEIDRE 58 (67) T ss_pred EEEEEEEEE--CC-CEEEEE----CCEEEEEECHHCCCCCCCCHHHH-CCCEEEEEEEEEECC T ss_conf 999999998--57-199999----99999988025255456896897-899899999999278 No 34 >COG0557 VacB Exoribonuclease R [Transcription] Probab=86.58 E-value=0.86 Score=25.36 Aligned_cols=65 Identities=23% Similarity=0.566 Sum_probs=43.6 Q ss_pred CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC-CCCEEEEECCCC Q ss_conf 7627751468874658854887788379999500023588446899889999998699971-110599963578 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK-YSAENLKLVPKS 76 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk-~~A~~v~~i~~~ 76 (78) .|++.+ ..+||||+.++.. ....|+|+-...+ .....|++|..++.+.++.++ +.|..+++++.+ T Consensus 71 ~~~~~~--~~~gf~f~~~~~~-~~~~d~~v~~~~~-----~~a~~gD~V~v~~~~~~~~~~~~~~~v~~il~r~ 136 (706) T COG0557 71 EGIVEA--SAKGFGFLSPDDS-KDADDIFVPKDPL-----NRALHGDRVLVELLPSDKRGRFKEAAVVRILERA 136 (706) T ss_pred HCEEEC--CCCCCCEECCCCC-CCCCCEEECCHHH-----HHCCCCCEEEEEECCCCCCCCCCEEEEEHHHHHH T ss_conf 026521--3567742313667-7866578643555-----3201699899996765566666226866255553 No 35 >TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus influenzae is designated exoribonuclease II (Rnb) . Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process. Probab=86.34 E-value=0.39 Score=27.27 Aligned_cols=64 Identities=25% Similarity=0.472 Sum_probs=45.6 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCCEEEEECCC Q ss_conf 7762775146887465885488778837999950002358844689988999999869997-111059996357 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSAENLKLVPK 75 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A~~v~~i~~ 75 (78) .+|+++- ..+||||+.++. +...++|+|.+.+.. ...|+.|.+.....+..+ +..|.-++++.. T Consensus 19 ~~g~~~~--~~~~~gf~~~~~--~~~~~~~~~~~~~~~-----~~~gd~~~~~~~~~~~~~d~~~~~~~~~~~~ 83 (684) T TIGR00358 19 VKGVVKG--HNKGFGFLRPDD--GDKKDYFIPPPQLKG-----ALHGDLVLACPLGKPEKGDRREAEPVRLLEP 83 (684) T ss_pred HCCEEEE--CCCCCEEEEECC--CCCCEEEECCHHHHH-----HHCCCEEEEEECCCCCCCCHHHHHHHHHHHH T ss_conf 2100220--456530133316--775236645334312-----1045424675336664432011257778777 No 36 >PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Probab=84.92 E-value=2.6 Score=22.67 Aligned_cols=63 Identities=25% Similarity=0.296 Sum_probs=28.7 Q ss_pred CCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 76277514688746-5885488778837999950002358----8446899889999998699971110599963 Q gi|254780913|r 4 RGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 4 ~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) +|+|+... -|| |+..+ .|-|=|+|+|.+.... -..++.||.|+..+..-+...|--...++-+ T Consensus 570 ~g~V~~i~---~fGaFVel~----~gveGlih~sels~~~~~~~~~~~~~Gd~v~~kIl~id~~~krisLSiK~~ 637 (670) T PRK00087 570 LGKVVRIA---PFGAFVELE----PGVDGLVHISEISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 637 (670) T ss_pred EEEEEEEE---CCEEEEEEC----CCCEEEEEHHHCCCCCCCCHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHC T ss_conf 99999996---770799957----997899898994843248977748999989999999837778899784653 No 37 >PRK07252 hypothetical protein; Provisional Probab=84.83 E-value=1.6 Score=23.81 Aligned_cols=67 Identities=19% Similarity=0.238 Sum_probs=41.7 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEECCC Q ss_conf 7762775146887465885488778837999950002358----844689988999999869997111059996357 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLVPK 75 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~ 75 (78) .+|+|+--- -||..+.- +++.+=|+|+|.|...- ...+..||.|...+..-+...+--...++-+.+ T Consensus 7 v~G~V~~I~---~fGaFV~l---~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~rIsLSiK~l~e 77 (120) T PRK07252 7 LKGTITGIK---PYGAFVAL---ENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTKKASLSMRTLEE 77 (120) T ss_pred EEEEEEEEE---CCEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEECCHHHHCC T ss_conf 999999997---54579995---799578888666010200499994789999999999986899988613633224 No 38 >PRK08582 hypothetical protein; Provisional Probab=83.62 E-value=3.4 Score=22.03 Aligned_cols=63 Identities=22% Similarity=0.346 Sum_probs=41.4 Q ss_pred CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEEC Q ss_conf 776277514688746-58854887788379999500023588----446899889999998699971110599963 Q gi|254780913|r 3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLV 73 (78) Q Consensus 3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i 73 (78) .+|+|+--- -|| ||.. .++.+-++|+|.|...-. ..|..||.|.-.+..-+..||. ...|+-+ T Consensus 9 v~G~V~~I~---~fGaFV~l----~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~~gKI-~LSiK~~ 76 (139) T PRK08582 9 LQGKVTGIT---NFGAFVEL----PEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVEDDGKI-GLSIKKA 76 (139) T ss_pred EEEEEEEEE---CCEEEEEE----CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE-EEEHHHC T ss_conf 999998996---41789995----69966788736625665689999578999999999988899970-5165554 No 39 >PRK07899 rpsA 30S ribosomal protein S1; Reviewed Probab=83.50 E-value=3.9 Score=21.67 Aligned_cols=51 Identities=22% Similarity=0.304 Sum_probs=26.1 Q ss_pred CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC Q ss_conf 776277514688746-5885488778837999950002358----8446899889999998699 Q gi|254780913|r 3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~ 61 (78) .+|+||.. .-|| ||.. ||-|=++|+|.|.-.. ...+..||.|+..+..-++ T Consensus 212 veG~Vk~I---t~fGAFVDL-----GGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~ 267 (484) T PRK07899 212 RKGVVSSI---VNFGAFVDL-----GGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDL 267 (484) T ss_pred EEEEEEEE---CCCEEEEEE-----CCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECC T ss_conf 99999982---164689995-----572378981340356779989957799879999987747 No 40 >smart00316 S1 Ribosomal protein S1-like RNA-binding domain. Probab=83.28 E-value=3 Score=22.37 Aligned_cols=54 Identities=17% Similarity=0.206 Sum_probs=39.0 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCCC Q ss_conf 776277514688746588548877883799995000235----884468998899999986999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~~ 62 (78) .+|+|.-.++ +|++..- .++-+-|+|.|.+... ....+..|+.|.+.+..-+.. T Consensus 6 v~g~V~~v~~---~g~~v~i---~~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~ 63 (72) T smart00316 6 VEGTVTEITP---FGAFVDL---GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEE 63 (72) T ss_pred EEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECC T ss_conf 9999999978---7399997---69989999807505555478468363898999999999999 No 41 >PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Probab=82.73 E-value=3.8 Score=21.75 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=40.3 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCC Q ss_conf 77627751468874658854887788379999500023588----44689988999999869997111 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYS 66 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~ 66 (78) .+|+|+.--+ ||-.+-- -.|+|-++|+|.|..... ..|++||.|...+..-+++||.. T Consensus 625 y~g~V~~i~~---fGafve~---~pg~~GLlHiSel~~~rv~~v~d~~~~Gd~i~Vk~~~id~~Gri~ 686 (694) T PRK11824 625 YEGKVVRIVD---FGAFVEI---LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKRGRIR 686 (694) T ss_pred EEEEEEEEEE---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEE T ss_conf 9999999984---4189996---799806888002465234686451168988999999898999866 No 42 >TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). Probab=82.68 E-value=4.3 Score=21.47 Aligned_cols=57 Identities=23% Similarity=0.316 Sum_probs=39.6 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCC Q ss_conf 77627751468874658854887788379999500023588----4468998899999986999711 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKY 65 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~ 65 (78) .+|+|+--- -||-.+-- -.|+|=++|+|.|..... ..|++||.|...+..-+++||. T Consensus 622 y~g~V~~i~---~fGafve~---~pg~~GLlHiSel~~~rv~~v~dv~~~Gd~i~Vk~~~id~~Gri 682 (684) T TIGR03591 622 YEGKVVRIM---DFGAFVEI---LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRI 682 (684) T ss_pred EEEEEEEEE---ECEEEEEE---CCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCC T ss_conf 999999998---44089996---79981478700136534468645216898899999978899982 No 43 >cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. Probab=82.40 E-value=4.5 Score=21.36 Aligned_cols=68 Identities=22% Similarity=0.328 Sum_probs=43.7 Q ss_pred CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC-----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC Q ss_conf 776277514688746-58854887788379999500023588-----446899889999998699971110599963578 Q gi|254780913|r 3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL-----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS 76 (78) Q Consensus 3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~-----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~ 76 (78) .+|+|+..- -|| ||..++ ...+.|=++|+|.|...+. ..++.||.|...+..-++ +| -...++-+.+. T Consensus 4 ~~G~V~~i~---~fGaFV~l~~-~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~-~k-i~LS~K~~~~~ 77 (79) T cd05684 4 YKGKVTSIM---DFGCFVQLEG-LKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQN-GK-ISLSMKDVDQD 77 (79) T ss_pred EEEEEEEEE---EEEEEEEEEC-CCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEEC-CE-EEEEEEECCCC T ss_conf 999998997---5339999967-889806789956815755558988936799999999999869-98-88722613467 No 44 >cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair. Probab=81.62 E-value=4.8 Score=21.19 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=36.6 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC Q ss_conf 77627751468874658854887788379999500023588446899889999998699971 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk 64 (78) .+|+|...- -||--..- ..+.+=++|+|.+.. .+++|+.|.-.+..-+++|| T Consensus 20 y~G~V~~v~---~fGaFV~l---~~~~~GLiHiS~l~~----~~~vGD~V~VkV~~I~~~Gk 71 (77) T cd04473 20 YKGKVNGVA---KYGVFVDL---NDHVRGLIHRSNLLR----DYEVGDEVIVQVTDIPENGN 71 (77) T ss_pred EEEEEEEEE---ECCEEEEC---CCCCEEEEEEHHCCC----CCCCCCEEEEEEEEECCCCC T ss_conf 999998896---62889992---699879689316668----78999999999999999997 No 45 >cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=80.96 E-value=4.2 Score=21.49 Aligned_cols=54 Identities=19% Similarity=0.185 Sum_probs=36.2 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC-----CCCCCCCCCEEEEEEEECCCC Q ss_conf 776277514688746588548877883799995000235-----884468998899999986999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA-----GLFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~-----g~~~l~~G~~V~F~i~~~~~~ 62 (78) .+|+|+--. -||.... -+.|-|=++|+|.|.-. ....++.||.|++.+.+-++. T Consensus 7 v~G~V~~It---~fG~FV~---i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e 65 (72) T cd05689 7 LFGKVTNLT---DYGCFVE---LEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEE 65 (72) T ss_pred EEEEEEEEE---CCEEEEE---ECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECC T ss_conf 999998994---7623999---6699389999766316546679636038999999999999599 No 46 >PRK06676 rpsA 30S ribosomal protein S1; Reviewed Probab=80.81 E-value=3.7 Score=21.84 Aligned_cols=13 Identities=38% Similarity=0.496 Sum_probs=4.8 Q ss_pred CCCCCEEEEEEEE Q ss_conf 6899889999998 Q gi|254780913|r 46 LTEGQLVTYDYVQ 58 (78) Q Consensus 46 l~~G~~V~F~i~~ 58 (78) ++.||.|...+.. T Consensus 322 ~~~Gd~V~~~Vl~ 334 (390) T PRK06676 322 LEEGQEVKVKVLE 334 (390) T ss_pred CCCCCEEEEEEEE T ss_conf 7899999999999 No 47 >PRK05807 hypothetical protein; Provisional Probab=80.40 E-value=4.9 Score=21.13 Aligned_cols=60 Identities=28% Similarity=0.411 Sum_probs=40.1 Q ss_pred CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEE Q ss_conf 776277514688746-58854887788379999500023588----4468998899999986999711105999 Q gi|254780913|r 3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLK 71 (78) Q Consensus 3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~ 71 (78) .+|+|+-.- -|| ||..+ |.+=+||+|.|...-. ..|.+||.|...+..-+.+||. ...++ T Consensus 9 v~G~V~~I~---~fGaFV~l~-----g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD~~gkI-~LSiK 73 (136) T PRK05807 9 LEGTVVNIT---NFGAFVEVE-----GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKI-SLSIK 73 (136) T ss_pred EEEEEEEEE---CCEEEEEEC-----CEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCC-EEEHH T ss_conf 999999997---244799978-----927689856707764369999678999999999998999981-43322 No 48 >cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis. Probab=79.91 E-value=5 Score=21.09 Aligned_cols=56 Identities=20% Similarity=0.355 Sum_probs=37.3 Q ss_pred CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC Q ss_conf 776277514688746-58854887788379999500023588----446899889999998699971 Q gi|254780913|r 3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk 64 (78) .+|+|+.-- -|| ||..++. +.|=++|+|.|...-. ..|+.||.|.-.+..-+.++| T Consensus 7 ~~G~V~~i~---~fGAFV~i~g~---~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id~~~k 67 (73) T cd05686 7 FKGEVASVT---EYGAFVKIPGC---RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDK 67 (73) T ss_pred EEEEEEEEE---ECCEEEEECCC---CCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC T ss_conf 999998997---53239990898---84355995605412028999955799999999998868998 No 49 >PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Probab=78.29 E-value=6.2 Score=20.57 Aligned_cols=33 Identities=21% Similarity=0.250 Sum_probs=15.3 Q ss_pred CCCEEEEEEEECCC--C---CCCCCCCCCEEEEEEEEC Q ss_conf 88379999500023--5---884468998899999986 Q gi|254780913|r 27 SGDDVFLHRSAVAS--A---GLFNLTEGQLVTYDYVQN 59 (78) Q Consensus 27 ~g~DvFvH~s~i~~--~---g~~~l~~G~~V~F~i~~~ 59 (78) ++-|-|+|.|+|.= . ..+..+.|+.|++.+..- T Consensus 687 ~gIDGlvH~sDlSW~~~~~~~~~~~kkGd~ve~kVL~I 724 (863) T PRK12269 687 EGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIEC 724 (863) T ss_pred CCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEE T ss_conf 99367898210676787726566257898799999997 No 50 >PRK13806 rpsA 30S ribosomal protein S1; Provisional Probab=78.03 E-value=5.6 Score=20.82 Aligned_cols=49 Identities=16% Similarity=0.259 Sum_probs=19.7 Q ss_pred CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEE Q ss_conf 762775146887465885488778837999950002358----8446899889999998 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQ 58 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~ 58 (78) +|+|+-..+ ||-.+.- ..|-|-|+|+|.|.-.. ...+..||.|...+.. T Consensus 206 ~G~V~~i~~---~GaFVdl---~~GvdGllHiSeiSw~rv~~p~~~~~vGd~v~vkVl~ 258 (489) T PRK13806 206 EGTVTRLAP---FGAFVEI---APGVEGMVHISELSWSRVQQADEAVSVGDRVRVKVLG 258 (489) T ss_pred CEEEEEECC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEE T ss_conf 429999757---5389993---7980799983555865668888945169889999999 No 51 >cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=77.52 E-value=6.5 Score=20.44 Aligned_cols=52 Identities=21% Similarity=0.246 Sum_probs=35.8 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCC Q ss_conf 77627751468874658854887788379999500023588----446899889999998699 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~ 61 (78) .+|+|+-.. -||....- + +-+-|+|+|.|..... ..++.||.|...+..-++ T Consensus 5 v~g~V~~i~---~fG~FV~l---~-gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~ 60 (68) T cd05688 5 VEGTVKSIT---DFGAFVDL---G-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60 (68) T ss_pred EEEEEEEEE---CCEEEEEE---C-CEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEEC T ss_conf 999999995---63889997---9-98999984364666668988914799999999999999 No 52 >cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=76.09 E-value=7.2 Score=20.21 Aligned_cols=55 Identities=18% Similarity=0.306 Sum_probs=36.8 Q ss_pred CCCCEEEEEECCCCEEEEE-ECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCC Q ss_conf 8776277514688746588-54887788379999500023588----4468998899999986999 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFIT-PEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~-~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~ 62 (78) ..+|+|+--. -||... .++ .+-+=|+|+|.|..... ..++.||.|...+.+-+.. T Consensus 5 ~v~G~V~~i~---~fG~FV~l~g---~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e 64 (77) T cd05708 5 KIDGTVRRVE---DYGVFIDIDG---TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAE 64 (77) T ss_pred EEEEEEEEEE---CEEEEEEECC---CCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECC T ss_conf 9999999996---4178999678---9807998878817565689889168999999999999899 No 53 >cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Probab=75.50 E-value=7.5 Score=20.12 Aligned_cols=54 Identities=19% Similarity=0.210 Sum_probs=36.8 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC Q ss_conf 87762775146887465885488778837999950002358----8446899889999998699 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~ 61 (78) ..+|+|+-.. -||-... ...+-|=++|+|.|.... ...++.||.|...+..-+. T Consensus 3 iv~G~V~~i~---~fG~FV~---l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~ 60 (68) T cd05685 3 VLEGVVTNVT---DFGAFVD---IGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60 (68) T ss_pred EEEEEEEEEE---CEEEEEE---ECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEEC T ss_conf 9999999996---5289999---14997899981897678767986857999999999999989 No 54 >COG4776 Rnb Exoribonuclease II [Transcription] Probab=73.80 E-value=5 Score=21.07 Aligned_cols=54 Identities=20% Similarity=0.370 Sum_probs=35.5 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEE Q ss_conf 7762775146887465885488778837999950002358844689988999999869997111059 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAEN 69 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~ 69 (78) ..|+||- .+|||||+..| ..+-+|+---. .+.+.-|+++.--+... +-|.+|+- T Consensus 22 vEGvVK~--tekgfGFLEvD----~qkSYFIpPp~-----MKkvMHGDkIiA~i~te--~erE~aEP 75 (645) T COG4776 22 VEGVVKA--TEKGFGFLEVD----AQKSYFIPPPQ-----MKKVMHGDKIIAVIHTE--KERESAEP 75 (645) T ss_pred CCEEEEE--CCCCCEEEEEC----CCCCCCCCCHH-----HHHHCCCCEEEEEEEEC--CCCCCCCH T ss_conf 0105740--45641028875----76540138878-----86521567589998742--74010586 No 55 >cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=72.87 E-value=7.8 Score=20.01 Aligned_cols=52 Identities=23% Similarity=0.244 Sum_probs=35.6 Q ss_pred CCCEEEEEECCCCEEE-EEECCCCCCCCEEEEEEEECCCC-----CCCCCCCCCEEEEEEEECCC Q ss_conf 7762775146887465-88548877883799995000235-----88446899889999998699 Q gi|254780913|r 3 HRGSIKWYNPDKGYGF-ITPEGSTESGDDVFLHRSAVASA-----GLFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 3 ~~G~VKwfn~~kGfGF-I~~d~~~d~g~DvFvH~s~i~~~-----g~~~l~~G~~V~F~i~~~~~ 61 (78) .+|+|+-.- -||. |.. +++-|=++|+|.+.-. ....++.||.|+..+..-+. T Consensus 4 v~G~V~~i~---~fG~FV~l----~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~ 61 (69) T cd05690 4 VSGKIKSIT---DFGIFVGL----DGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDV 61 (69) T ss_pred EEEEEEEEC---CCEEEEEE----CCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEEC T ss_conf 999999991---31899997----69965999948824566667976825899999999999979 No 56 >cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th Probab=69.48 E-value=10 Score=19.31 Aligned_cols=58 Identities=28% Similarity=0.271 Sum_probs=42.2 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC-------CCCCCCCCEEEEEEEECCCCCC Q ss_conf 7762775146887465885488778837999950002358-------8446899889999998699971 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG-------LFNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g-------~~~l~~G~~V~F~i~~~~~~gk 64 (78) ..|+|+-..+.=.==||... .+++-|+|++++.... -..|.+||.|-.++...+.+.| T Consensus 11 Y~GkV~~v~p~i~AAFVdiG----~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~K 75 (88) T cd04453 11 YLGRVKKIVPGLQAAFVDIG----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTK 75 (88) T ss_pred EEEEEEEECCCCCEEEEECC----CCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCC T ss_conf 99999886668748999658----986899990345723513578877837799999999976687997 No 57 >cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c Probab=68.29 E-value=11 Score=19.16 Aligned_cols=57 Identities=11% Similarity=0.023 Sum_probs=38.0 Q ss_pred CCCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCC-CCC Q ss_conf 77627751468874658-854887788379999500023588----446899889999998699-971 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDA-NGK 64 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~-~gk 64 (78) .+|+|+--. -||.. ..+. -+|.+=|+|+|.|...-. ..++.||.|...+..-++ +++ T Consensus 7 v~G~V~~i~---~~GafV~l~e--~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~~ 69 (76) T cd04452 7 VVVTVKSIA---DMGAYVSLLE--YGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGY 69 (76) T ss_pred EEEEEEEEE---CCEEEEEECC--CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE T ss_conf 999999997---3469999733--69919999979968451159999558999999999999789999 No 58 >cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=67.30 E-value=12 Score=19.05 Aligned_cols=56 Identities=13% Similarity=0.112 Sum_probs=38.4 Q ss_pred CCCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC Q ss_conf 987762775146887465885488778837999950002358----84468998899999986999 Q gi|254780913|r 1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 1 mm~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~ 62 (78) +..+|+|+... -||.... -.++-|=++|.|.+.... ......||.|.+.+..-+.. T Consensus 2 ~iv~G~V~~i~---~fG~fV~---l~~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~ 61 (69) T cd05697 2 QVVKGTIRKLR---PSGIFVK---LSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPE 61 (69) T ss_pred CEEEEEEEEEC---CCEEEEE---ECCCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECC T ss_conf 99999999973---8427999---579906998789908652069889089999999999999488 No 59 >PRK11637 hypothetical protein; Provisional Probab=67.15 E-value=12 Score=19.07 Aligned_cols=51 Identities=14% Similarity=0.176 Sum_probs=34.6 Q ss_pred CCCEEEEEECCCCEEEEE-ECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEE Q ss_conf 776277514688746588-5488778837999950002358844689988999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFIT-PEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTY 54 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~-~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F 54 (78) ..|+|.+=+.-+|||-++ .|+ .++=--++-|.|.|...--..+..||.+-. T Consensus 322 ~~G~Vv~a~~~~gyG~~ViIdH-G~g~~TlYah~s~l~v~~Gq~V~~Gq~Ig~ 373 (404) T PRK11637 322 ADGRVILADWLQGYGLVVVVEH-GKGDMSLYGYNQSALVSVGAQVRAGQPIAL 373 (404) T ss_pred CCEEEEEEEECCCCCCEEEEEC-CCCCEEECCCCCCCCCCCCCEECCCCEEEE T ss_conf 1769999114088885799986-994657152889588899799899996987 No 60 >TIGR01622 SF-CC1 splicing factor, CC1-like family; InterPro: IPR006509 These sequences represent a subfamily of RNA splicing factors including the Pad-1 protein (Neurospora crassa), CAPER (mouse) and CC1.3 (human). All are characterised by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 human paralogs, two) RNA recognition domains. These splicing factors are closely related to the U2AF splicing factor family (IPR006529 from INTERPRO). ; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus. Probab=66.41 E-value=2.2 Score=23.10 Aligned_cols=10 Identities=60% Similarity=1.075 Sum_probs=7.7 Q ss_pred CCCEEEEEEC Q ss_conf 8874658854 Q gi|254780913|r 13 DKGYGFITPE 22 (78) Q Consensus 13 ~kGfGFI~~d 22 (78) .||||||+-- T Consensus 276 SkGyGFiqF~ 285 (531) T TIGR01622 276 SKGYGFIQFR 285 (531) T ss_pred CCCCCEEEEC T ss_conf 3254005511 No 61 >PRK03987 translation initiation factor IF-2 subunit alpha; Validated Probab=64.96 E-value=11 Score=19.08 Aligned_cols=54 Identities=30% Similarity=0.370 Sum_probs=35.2 Q ss_pred CCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC Q ss_conf 7627751468874658-85488778837999950002358----84468998899999986999 Q gi|254780913|r 4 RGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~ 62 (78) .|+|+--. -||.. ..+. -+|.+-|+|+|.|...- ...|++||.|...+..-++. T Consensus 13 ~~~V~~i~---~~Ga~v~l~e--y~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~ 71 (262) T PRK03987 13 VGTVKEVK---DFGAFVTLDE--YPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPK 71 (262) T ss_pred EEEEEEEE---CCEEEEEECC--CCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCC T ss_conf 99999995---6679999356--59931678879834677519998515898899999988387 No 62 >KOG0125 consensus Probab=63.59 E-value=3 Score=22.30 Aligned_cols=18 Identities=39% Similarity=0.861 Sum_probs=12.7 Q ss_pred EEEC--CCCEEEEEECCCCC Q ss_conf 5146--88746588548877 Q gi|254780913|r 9 WYNP--DKGYGFITPEGSTE 26 (78) Q Consensus 9 wfn~--~kGfGFI~~d~~~d 26 (78) -||+ .|||||+|-|...| T Consensus 129 IfNERGSKGFGFVTmen~~d 148 (376) T KOG0125 129 IFNERGSKGFGFVTMENPAD 148 (376) T ss_pred EECCCCCCCCCEEEECCHHH T ss_conf 86367777523487228246 No 63 >cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=56.59 E-value=18 Score=17.93 Aligned_cols=56 Identities=21% Similarity=0.230 Sum_probs=38.3 Q ss_pred CCCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCC Q ss_conf 9877627751468874658854887788379999500023588----4468998899999986999 Q gi|254780913|r 1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 1 mm~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~ 62 (78) |..+|+|+-.. -||-+..- .++-+-|+|.|.+..... ..+..||.|...+..-+.. T Consensus 2 ~vv~G~V~~i~---~~G~fV~~---~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~ 61 (70) T cd05698 2 LKTHGTIVKVK---PNGCIVSF---YNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE 61 (70) T ss_pred CEEEEEEEEEE---CCCEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECC T ss_conf 99999999998---17189994---89969998989928320289899377999999999998089 No 64 >COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Probab=56.53 E-value=8.5 Score=19.79 Aligned_cols=53 Identities=30% Similarity=0.422 Sum_probs=36.1 Q ss_pred CEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC Q ss_conf 6277514688746-5885488778837999950002358----84468998899999986999 Q gi|254780913|r 5 GSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 5 G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~ 62 (78) |+|+- -..|| |+..|. -+|.+-|+|+|.+...- ...+++||+|-+.+..-+++ T Consensus 17 ~tV~~---V~~~GA~v~L~E--Y~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~ 74 (269) T COG1093 17 GTVKQ---VADYGAYVELDE--YPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPK 74 (269) T ss_pred EEEEE---EECCCCEEEEEC--CCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCC T ss_conf 99998---604642798420--59962267789987789988999861698699999888687 No 65 >cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=54.18 E-value=19 Score=17.92 Aligned_cols=54 Identities=13% Similarity=0.055 Sum_probs=34.9 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCC------CCCCCCCCCCEEEEEEEECCCCC Q ss_conf 77627751468874658854887788379999500023------58844689988999999869997 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVAS------AGLFNLTEGQLVTYDYVQNDANG 63 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~------~g~~~l~~G~~V~F~i~~~~~~g 63 (78) .+|+|+.-. .||....- .++-.=++|+|.+-. .....+++||.|+..+.- -+.. T Consensus 4 v~g~V~sik---~~~l~V~L---~d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG-~~d~ 63 (70) T cd05702 4 VKAKVKSVK---PTQLNVQL---ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIG-GHDA 63 (70) T ss_pred EEEEEEEEE---CCEEEEEE---CCCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEE-EECC T ss_conf 999999994---67089996---899577898455213555556946856899999999997-6546 No 66 >cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=50.95 E-value=23 Score=17.41 Aligned_cols=54 Identities=24% Similarity=0.297 Sum_probs=37.3 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC Q ss_conf 87762775146887465885488778837999950002358----8446899889999998699 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~ 61 (78) ..+|+|+...+ ||..+.- .++-+=|+|.|.+.... ...+..||.|...+..-+. T Consensus 17 iv~G~V~~i~~---~G~FV~l---~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~ 74 (83) T cd04461 17 VVHGYVRNITP---YGVFVEF---LGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83) T ss_pred EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEEC T ss_conf 99999999927---8199995---6994899899996864226989945599999999999958 No 67 >COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Probab=47.61 E-value=26 Score=17.10 Aligned_cols=13 Identities=15% Similarity=0.253 Sum_probs=5.1 Q ss_pred CCCCCEEEEEEEE Q ss_conf 6899889999998 Q gi|254780913|r 46 LTEGQLVTYDYVQ 58 (78) Q Consensus 46 l~~G~~V~F~i~~ 58 (78) ++.||.|...+.. T Consensus 236 vkvGd~VkvkVi~ 248 (541) T COG0539 236 VKVGDEVKVKVIS 248 (541) T ss_pred CCCCCEEEEEEEE T ss_conf 3569889999999 No 68 >pfam11604 CusF_Ec Copper binding periplasmic protein CusF. CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein. Probab=46.93 E-value=19 Score=17.89 Aligned_cols=20 Identities=25% Similarity=0.529 Sum_probs=15.7 Q ss_pred CCCCCCCCCEEEEEEEECCC Q ss_conf 88446899889999998699 Q gi|254780913|r 42 GLFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 42 g~~~l~~G~~V~F~i~~~~~ 61 (78) -+..|.+|++|.|++.+... T Consensus 39 ~l~~l~~G~~V~F~~~~~~~ 58 (61) T pfam11604 39 DLAGLKPGDKVRFEFEKGDD 58 (61) T ss_pred HHHCCCCCCEEEEEEEECCC T ss_conf 87449999989999997889 No 69 >COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism] Probab=45.37 E-value=28 Score=16.90 Aligned_cols=45 Identities=20% Similarity=0.434 Sum_probs=30.0 Q ss_pred CCEE-EEEECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE Q ss_conf 7627-75146887465885488778837999950----00235884-468998899 Q gi|254780913|r 4 RGSI-KWYNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT 53 (78) Q Consensus 4 ~G~V-Kwfn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~ 53 (78) .|+| .-|...-.||+.+ +.|-++++|+- .|...|+. .+++||+|. T Consensus 50 dG~v~~iFpTkHAigi~t-----~~GvEiLiHiGiDTV~L~GegF~~~v~~Gd~Vk 100 (156) T COG2190 50 DGTVVLIFPTKHAIGIET-----DEGVEILIHIGIDTVKLNGEGFESLVKEGDKVK 100 (156) T ss_pred CCEEEEEEECCCEEEEEC-----CCCCEEEEEECEEEEEECCCCEEEEEECCCEEC T ss_conf 858999851784799983-----899599999564058688932478750799881 No 70 >KOG0149 consensus Probab=44.91 E-value=10 Score=19.38 Aligned_cols=13 Identities=46% Similarity=0.807 Sum_probs=9.8 Q ss_pred EECCCCEEEEEEC Q ss_conf 1468874658854 Q gi|254780913|r 10 YNPDKGYGFITPE 22 (78) Q Consensus 10 fn~~kGfGFI~~d 22 (78) =...|||||+|-- T Consensus 50 t~rskGyGfVTf~ 62 (247) T KOG0149 50 TGRSKGYGFVTFR 62 (247) T ss_pred CCCCCCEEEEEEE T ss_conf 7642324568861 No 71 >TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548 These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding. Probab=42.90 E-value=9.5 Score=19.54 Aligned_cols=11 Identities=55% Similarity=1.011 Sum_probs=5.6 Q ss_pred ECCCCEEEEEE Q ss_conf 46887465885 Q gi|254780913|r 11 NPDKGYGFITP 21 (78) Q Consensus 11 n~~kGfGFI~~ 21 (78) |.=|||||++= T Consensus 392 n~CKGygFVsM 402 (436) T TIGR01661 392 NKCKGYGFVSM 402 (436) T ss_pred CCCCCCEEEEC T ss_conf 85121123524 No 72 >COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Probab=41.22 E-value=33 Score=16.53 Aligned_cols=59 Identities=22% Similarity=0.277 Sum_probs=41.4 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCC Q ss_conf 7762775146887465885488778837999950002358----8446899889999998699971110 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSA 67 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A 67 (78) ..|+|+.-.+ ||--+- --.|+|-++|+|.+.... -..|++||.|...+..-++.||... T Consensus 623 y~G~V~ri~~---fGaFv~---l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692) T COG1185 623 YEGTVVRIVD---FGAFVE---LLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692) T ss_pred EEEEEEEEEE---CCEEEE---ECCCCCEEEEEHHHHHHHHHCCCCEEECCCEEEEEEEEECCCCCCCC T ss_conf 9988999864---125898---33896206874353345553204535448659999963366677032 No 73 >PTZ00162 RNA polymerase II subunit 7; Provisional Probab=40.97 E-value=33 Score=16.51 Aligned_cols=41 Identities=20% Similarity=0.366 Sum_probs=27.3 Q ss_pred CEEEEEECCCCCCCCEEEEEEEECCCC--------------CCCCCCCCCEEEEEEEEC Q ss_conf 746588548877883799995000235--------------884468998899999986 Q gi|254780913|r 15 GYGFITPEGSTESGDDVFLHRSAVASA--------------GLFNLTEGQLVTYDYVQN 59 (78) Q Consensus 15 GfGFI~~d~~~d~g~DvFvH~s~i~~~--------------g~~~l~~G~~V~F~i~~~ 59 (78) -|||...-++ -|+|+|.|.+..+ .-+.|+.|+.|.+.++-. T Consensus 94 ~~G~fv~~GP----l~~fv~~s~i~~d~~yd~~~~~~~~~~~~~~i~kgd~VR~rIvg~ 148 (170) T PTZ00162 94 KLGFFAQAGP----LKIFVSRTAIPPNFVYDSDSAYPCFSDGTISIKPQSEVRLRLQGI 148 (170) T ss_pred CCEEEEEECC----EEEEEEHHHCCCCCEECCCCCCCEECCCCCEECCCCEEEEEEEEE T ss_conf 4079999128----089989899998648978998604827883888899999999998 No 74 >PRK09838 periplasmic copper-binding protein; Provisional Probab=40.70 E-value=33 Score=16.48 Aligned_cols=69 Identities=13% Similarity=0.177 Sum_probs=36.7 Q ss_pred CCCCEEEEEECCCCEEEEEECCC-CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE Q ss_conf 87762775146887465885488-778837999950002358844689988999999869997111059996 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGS-TESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL 72 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~-~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~ 72 (78) +-+|+|+-.|.+.|-=-|.-+-- +-+-+-.=.-+..-...-+..|++|++|.|+.++. ++.+.-.+|++ T Consensus 43 ~~~G~V~~ID~~~~kVTI~H~pI~aL~WPaMTM~F~v~~~~~l~~lk~Gd~V~F~Fvq~--G~~~~l~~I~~ 112 (114) T PRK09838 43 SATGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQ--GNLSLLQDIKV 112 (114) T ss_pred EEEEEEEEEECCCCEEEEECCCCCCCCCCCCEEEEECCCHHHHHCCCCCCEEEEEEEEE--CCEEEEEEEEE T ss_conf 73479999826799799825861306998635763338956760599999899999963--99779999886 No 75 >cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=40.48 E-value=34 Score=16.46 Aligned_cols=57 Identities=32% Similarity=0.343 Sum_probs=37.5 Q ss_pred CCCCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCC-CCC Q ss_conf 98776277514688746-588548877883799995000235----88446899889999998699-971 Q gi|254780913|r 1 MVHRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDA-NGK 64 (78) Q Consensus 1 mm~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~-~gk 64 (78) |..+|+||.-. -|| |+... .+.|-++|+|.|... -...+..||.|.-.+..-+. .+| T Consensus 2 ~~v~G~V~~i~---~~G~FV~l~----~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~r 64 (68) T cd05707 2 DVVRGFVKNIA---NNGVFVTLG----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGR 64 (68) T ss_pred CEEEEEEEEEC---CCCEEEEEC----CCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCCE T ss_conf 99899999803---640799917----9967999959917235649989179999999999998287586 No 76 >cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=38.26 E-value=27 Score=17.02 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=22.2 Q ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEEEC Q ss_conf 83799995000235884468998899999986 Q gi|254780913|r 28 GDDVFLHRSAVASAGLFNLTEGQLVTYDYVQN 59 (78) Q Consensus 28 g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~ 59 (78) ...||+|-.+++..| |++|++|...-..+ T Consensus 30 R~vVfMNp~D~~~lG---l~~Gd~V~l~S~~g 58 (112) T cd02787 30 RDVVFMNPDDIARLG---LKAGDRVDLESAFG 58 (112) T ss_pred EEEEEECHHHHHHCC---CCCCCEEEEEEECC T ss_conf 259998899999829---99999999998538 No 77 >pfam04225 OapA Opacity-associated protein A LysM-like domain. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This is a LysM-like domain. Probab=38.15 E-value=37 Score=16.25 Aligned_cols=27 Identities=30% Similarity=0.425 Sum_probs=19.8 Q ss_pred CCCCCCCCCEEEEEEEECCCCCCCCCEEEE Q ss_conf 884468998899999986999711105999 Q gi|254780913|r 42 GLFNLTEGQLVTYDYVQNDANGKYSAENLK 71 (78) Q Consensus 42 g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~ 71 (78) .+..|++||.|+|.+- ..|+.++..|. T Consensus 39 ~Ls~Lk~Gq~v~~~~n---~~G~l~~L~i~ 65 (85) T pfam04225 39 PLSNIKSGQLVRIKLN---AQGRVDELQIE 65 (85) T ss_pred CHHHCCCCCEEEEEEC---CCCCEEEEEEE T ss_conf 0544589999999999---99988999981 No 78 >pfam01551 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. Probab=35.62 E-value=40 Score=16.02 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=31.7 Q ss_pred CCCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEE Q ss_conf 77627751468874658-85488778837999950002358844689988999 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTY 54 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F 54 (78) ..|+|..-...++||-. ..+. .++-.-+|.|.+.+.-.--..+++||.+-. T Consensus 20 ~~G~V~~~~~~~~~G~~v~i~h-~~g~~~~Y~hl~~~~V~~G~~V~~G~~IG~ 71 (96) T pfam01551 20 ADGVVVFAGYLGGYGNLVIIDH-GNGYETLYAHLSKILVKVGQRVKAGQVIGT 71 (96) T ss_pred ECEEEEEEEECCCCCEEEEEEE-CCCCEEEECCCEEEEECCCCCHHHCCEEEE T ss_conf 3679999898399885999993-898769983644677958989013999998 No 79 >cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis. Probab=35.61 E-value=40 Score=16.02 Aligned_cols=67 Identities=16% Similarity=0.159 Sum_probs=39.7 Q ss_pred EEEEECCCC--EEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCC--CCCCCEEEEECCC Q ss_conf 775146887--46588548877883799995000235884468998899999986999--7111059996357 Q gi|254780913|r 7 IKWYNPDKG--YGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDAN--GKYSAENLKLVPK 75 (78) Q Consensus 7 VKwfn~~kG--fGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~--gk~~A~~v~~i~~ 75 (78) +|..-..+| |+|++.++. .|.-|+-+--..+.... ..|.+++.|-+...-..+. -+..|.++..+.+ T Consensus 9 ~k~~~tk~G~~~a~~tleD~-~g~~e~~~F~~~~~~~~-~~l~~~~~v~i~g~v~~~~~~~~l~~~~i~~l~~ 79 (84) T cd04485 9 VRRRRTKKGKRMAFVTLEDL-TGSIEVVVFPETYEKYR-DLLKEDALLLVEGKVERRDGGLRLIAERIEDLED 79 (84) T ss_pred EEEEECCCCCEEEEEEEECC-CCCEEEEECHHHHHHHH-HHHCCCCEEEEEEEEEEECCEEEEEEEEEEEHHH T ss_conf 89985579998999999437-87499999699999988-8744698899999999969989999999467899 No 80 >cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. Probab=34.47 E-value=42 Score=15.91 Aligned_cols=45 Identities=24% Similarity=0.474 Sum_probs=29.1 Q ss_pred CCEEEE-EECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE Q ss_conf 762775-146887465885488778837999950----00235884-468998899 Q gi|254780913|r 4 RGSIKW-YNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT 53 (78) Q Consensus 4 ~G~VKw-fn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~ 53 (78) .|+|.. |...-.||+-+. +|-+|++|+- .|...|+. .+++||+|. T Consensus 43 ~G~V~~v~~T~HAigi~t~-----~G~evLiHiGiDTV~L~G~gF~~~v~~Gd~V~ 93 (124) T cd00210 43 DGTIVQIFPTKHAIGIESD-----SGVEILIHIGIDTVKLNGEGFTSHVEEGQRVK 93 (124) T ss_pred CEEEEEECCCCCEEEEEEC-----CCCEEEEEEEECCCCCCCCCEEEEECCCCEEC T ss_conf 9799998678969999968-----99899999730420148953189974889998 No 81 >COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Probab=33.35 E-value=24 Score=17.32 Aligned_cols=46 Identities=20% Similarity=0.114 Sum_probs=29.5 Q ss_pred CCCEEEEEECCCCCCCCEEEEEEEECCCC---------------CCCCCCCCCEEEEEEEECCCC Q ss_conf 88746588548877883799995000235---------------884468998899999986999 Q gi|254780913|r 13 DKGYGFITPEGSTESGDDVFLHRSAVASA---------------GLFNLTEGQLVTYDYVQNDAN 62 (78) Q Consensus 13 ~kGfGFI~~d~~~d~g~DvFvH~s~i~~~---------------g~~~l~~G~~V~F~i~~~~~~ 62 (78) ..-||+-+.=+ --|.|+|.|.|-.. .-+.+..|+.|.+.|+-.... T Consensus 92 ~~~~G~fV~ig----p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~ 152 (183) T COG1095 92 VVEFGAFVRIG----PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLK 152 (183) T ss_pred EEECCEEEEEC----CCCCCCCHHHCCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEECC T ss_conf 96144699963----62221138666575325275554124036515884198899999996146 No 82 >pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1. Probab=32.12 E-value=46 Score=15.69 Aligned_cols=45 Identities=20% Similarity=0.437 Sum_probs=28.8 Q ss_pred CCEEEE-EECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE Q ss_conf 762775-146887465885488778837999950----00235884-468998899 Q gi|254780913|r 4 RGSIKW-YNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT 53 (78) Q Consensus 4 ~G~VKw-fn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~ 53 (78) .|+|.. |...-.||+-+. +|-++++|+- .|...|+. .+++||+|. T Consensus 48 ~G~V~~v~~T~HAigi~~~-----~G~eiLiHiGiDTV~L~G~gF~~~v~~Gd~V~ 98 (133) T pfam00358 48 DGTIVQIFPTKHAIGIESD-----GGVEILIHVGIDTVKLNGEGFESHVEEGDRVK 98 (133) T ss_pred CEEEEEECCCCCEEEEEEC-----CCCEEEEEECCCCEECCCCCEEEEECCCCEEC T ss_conf 9799998689979999968-----99899999864522338963189975899998 No 83 >COG5569 Uncharacterized conserved protein [Function unknown] Probab=29.43 E-value=46 Score=15.69 Aligned_cols=41 Identities=32% Similarity=0.536 Sum_probs=26.3 Q ss_pred CEEEEEEEECCC---------------CCCCCCCCCCEEEEEEEECCCCCCCCCEEEE Q ss_conf 379999500023---------------5884468998899999986999711105999 Q gi|254780913|r 29 DDVFLHRSAVAS---------------AGLFNLTEGQLVTYDYVQNDANGKYSAENLK 71 (78) Q Consensus 29 ~DvFvH~s~i~~---------------~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~ 71 (78) +.|=+|.-.|.. .-+..|++|+.|+|..+. .+|++-..+|+ T Consensus 52 kKVTl~He~i~~l~mp~MTM~F~Vkd~a~ls~lKeGdkV~fvfer--v~gk~tv~qvk 107 (108) T COG5569 52 KKVTLHHEPIKNLNMPAMTMVFRVKDQAKLSGLKEGDKVEFVFER--VNGKLTVQQVK 107 (108) T ss_pred CEEEEECCCHHHCCCCCEEEEEEECCHHHHHCCCCCCCEEEEEEE--ECCEEEEEEEC T ss_conf 567886251533799640799996557776434567727889875--38978888705 No 84 >COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Probab=29.09 E-value=52 Score=15.39 Aligned_cols=54 Identities=20% Similarity=0.250 Sum_probs=32.7 Q ss_pred CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEE Q ss_conf 688746588548877883799995000235884468998899999986999711105999 Q gi|254780913|r 12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLK 71 (78) Q Consensus 12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~ 71 (78) ....||.--.. ..++..|++|.+.... ..+..|+.|++=+ -.+..+++.|.-.. T Consensus 15 ~~~~~g~fL~~--~~~~~~ilL~k~~~~~---~e~evGdev~vFi-Y~D~~~rl~aTt~~ 68 (287) T COG2996 15 EFSDFGYFLDA--GEDGTTILLPKSEPEE---DELEVGDEVTVFI-YVDSEDRLIATTRE 68 (287) T ss_pred EEECEEEEEEC--CCCCEEEECCCCCCCC---CCCCCCCEEEEEE-EECCCCCEEHEEEC T ss_conf 85221489966--8886078625667767---8511376899999-98887763010104 No 85 >KOG0291 consensus Probab=29.06 E-value=52 Score=15.39 Aligned_cols=61 Identities=20% Similarity=0.337 Sum_probs=34.5 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEE-------C---------C-CCCCCCCCCCCEEEEEEEECCCCC Q ss_conf 77627751468874658854887788379999500-------0---------2-358844689988999999869997 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSA-------V---------A-SAGLFNLTEGQLVTYDYVQNDANG 63 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~-------i---------~-~~g~~~l~~G~~V~F~i~~~~~~g 63 (78) .-|+||-||...||=|+|-+....+-.-+-+|++. | + -..+|+...-.+++|..+-.++.| T Consensus 370 eDgKVKvWn~~SgfC~vTFteHts~Vt~v~f~~~g~~llssSLDGtVRAwDlkRYrNfRTft~P~p~QfscvavD~sG 447 (893) T KOG0291 370 EDGKVKVWNTQSGFCFVTFTEHTSGVTAVQFTARGNVLLSSSLDGTVRAWDLKRYRNFRTFTSPEPIQFSCVAVDPSG 447 (893) T ss_pred CCCCEEEEECCCCEEEEEECCCCCCEEEEEEEECCCEEEEEECCCEEEEEEECCCCEEEEECCCCCEEEEEEEECCCC T ss_conf 778378985368638999525887447999996287899962387178434103320243127886036688875888 No 86 >TIGR01645 half-pint poly-U binding splicing factor, half-pint family; InterPro: IPR006532 The proteins contain three RNA recognition motifs and have been characterised as poly-pyrimidine tract binding proteins associated with RNA splicing factors , , . In the case of PUF60, in complex with p54, and in the presence of U2AF, it facilitates association of U2 snRNP with pre-mRNA . . Probab=27.89 E-value=17 Score=18.06 Aligned_cols=11 Identities=55% Similarity=0.969 Sum_probs=7.4 Q ss_pred CCCCEEEEEEC Q ss_conf 68874658854 Q gi|254780913|r 12 PDKGYGFITPE 22 (78) Q Consensus 12 ~~kGfGFI~~d 22 (78) .-||||||..+ T Consensus 281 ~HkGfGFiEf~ 291 (791) T TIGR01645 281 KHKGFGFIEFE 291 (791) T ss_pred CCCCCCCHHHH T ss_conf 85431000110 No 87 >TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. Probab=26.79 E-value=20 Score=17.70 Aligned_cols=15 Identities=33% Similarity=0.806 Sum_probs=11.1 Q ss_pred EEEEECCCCEEEEEE Q ss_conf 775146887465885 Q gi|254780913|r 7 IKWYNPDKGYGFITP 21 (78) Q Consensus 7 VKwfn~~kGfGFI~~ 21 (78) |==|||+|||=|=|. T Consensus 152 VEKFDPtrGYKFSTY 166 (336) T TIGR02997 152 VEKFDPTRGYKFSTY 166 (336) T ss_pred CCCCCCCCCCCCCCH T ss_conf 233577778863301 No 88 >cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core. Probab=26.23 E-value=59 Score=15.10 Aligned_cols=42 Identities=24% Similarity=0.246 Sum_probs=25.5 Q ss_pred CCEEEEEECCCCCCCCEEEEEEEECCCCCC---------------CCCCCCCEEEEEEEEC Q ss_conf 874658854887788379999500023588---------------4468998899999986 Q gi|254780913|r 14 KGYGFITPEGSTESGDDVFLHRSAVASAGL---------------FNLTEGQLVTYDYVQN 59 (78) Q Consensus 14 kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~---------------~~l~~G~~V~F~i~~~ 59 (78) ..||+-+.-++ -|=++|+|.|..+-+ +.++.||.|.-.+..- T Consensus 11 t~fG~FV~L~~----ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V 67 (99) T cd04460 11 VDFGAFVRIGP----VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAV 67 (99) T ss_pred EECCEEEEECC----CEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEE T ss_conf 82566999328----1068993675784399812446898512786984799999999998 No 89 >KOG4208 consensus Probab=25.85 E-value=60 Score=15.06 Aligned_cols=19 Identities=32% Similarity=0.730 Sum_probs=13.3 Q ss_pred CEEEEEEC--------CCCEEEEEECC Q ss_conf 62775146--------88746588548 Q gi|254780913|r 5 GSIKWYNP--------DKGYGFITPEG 23 (78) Q Consensus 5 G~VKwfn~--------~kGfGFI~~d~ 23 (78) |+|+.|-. .|||+||.-+. T Consensus 75 g~v~r~rlsRnkrTGNSKgYAFVEFEs 101 (214) T KOG4208 75 GTVTRFRLSRNKRTGNSKGYAFVEFES 101 (214) T ss_pred CEEEEEEEECCCCCCCCCCEEEEEECC T ss_conf 836999842244467767537887356 No 90 >TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process. Probab=25.04 E-value=29 Score=16.85 Aligned_cols=28 Identities=32% Similarity=0.631 Sum_probs=19.2 Q ss_pred EEEEECCCCEEEEEECCCCCCCCEEEEEEEEC Q ss_conf 77514688746588548877883799995000 Q gi|254780913|r 7 IKWYNPDKGYGFITPEGSTESGDDVFLHRSAV 38 (78) Q Consensus 7 VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i 38 (78) +||||. .|=+|+|+-.. ...+-++.+.+ T Consensus 119 tKWFnT--NYHYiVPE~~~--~~~F~L~~~k~ 146 (778) T TIGR01371 119 TKWFNT--NYHYIVPELSP--ATEFKLTSNKP 146 (778) T ss_pred ECCCCC--CCCEEECCCCC--CCEEEECCCHH T ss_conf 224367--74303113589--74143240005 No 91 >TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family; InterPro: IPR006515 These eukaryotic proteins recognize the poly-A of mRNA and consist of four tandem RNA recognition domains at the N terminus followed by a PABP-specific domain at the C terminus. The protein is involved in the transport of mRNAs from the nucleus to the cytoplasm . There are four paralogs in Homo sapiens which are expressed in testis , platelets (Q13310 from SWISSPROT ), broadly expressed (P11940 from SWISSPROT ) and of unknown tissue range (Q15097 from SWISSPROT). ; GO: 0003723 RNA binding. Probab=24.19 E-value=30 Score=16.77 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=5.2 Q ss_pred CCCEEEEEEC Q ss_conf 8874658854 Q gi|254780913|r 13 DKGYGFITPE 22 (78) Q Consensus 13 ~kGfGFI~~d 22 (78) .||||||.-+ T Consensus 128 SrGYgFV~fE 137 (860) T TIGR01628 128 SRGYGFVHFE 137 (860) T ss_pred CCCCCEEECC T ss_conf 0354134023 No 92 >TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745 Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding. Probab=23.89 E-value=55 Score=15.28 Aligned_cols=32 Identities=22% Similarity=0.497 Sum_probs=20.3 Q ss_pred CCCCCCCCCEEEEEEEECCCCCCCCCEEE-EECCCCC Q ss_conf 88446899889999998699971110599-9635788 Q gi|254780913|r 42 GLFNLTEGQLVTYDYVQNDANGKYSAENL-KLVPKSS 77 (78) Q Consensus 42 g~~~l~~G~~V~F~i~~~~~~gk~~A~~v-~~i~~~~ 77 (78) .+-.+.+||.|.| +..+++ ..+..| ..+|+++ T Consensus 18 A~i~a~pGDtv~F--vPtDKG--HNve~iKgm~P~GA 50 (123) T TIGR02375 18 AYIKAAPGDTVTF--VPTDKG--HNVETIKGMIPEGA 50 (123) T ss_pred CEEEECCCCEEEE--ECCCCC--CCHHCCCCCCCCCH T ss_conf 3366538976877--528887--67000023365221 No 93 >TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774 Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups. Probab=23.06 E-value=38 Score=16.20 Aligned_cols=12 Identities=42% Similarity=0.944 Sum_probs=8.9 Q ss_pred CCEEEEEEEECC Q ss_conf 837999950002 Q gi|254780913|r 28 GDDVFLHRSAVA 39 (78) Q Consensus 28 g~DvFvH~s~i~ 39 (78) |.|||||+|=|- T Consensus 104 GSdVYvHQsRiN 115 (278) T TIGR02408 104 GSDVYVHQSRIN 115 (278) T ss_pred CCCEEEEEEEEC T ss_conf 561244321100 No 94 >KOG0407 consensus Probab=22.99 E-value=52 Score=15.42 Aligned_cols=36 Identities=28% Similarity=0.521 Sum_probs=22.0 Q ss_pred CEEEEEEEECCCCC-CCCCCCCCEEEEEEEECCCCCCCCC Q ss_conf 37999950002358-8446899889999998699971110 Q gi|254780913|r 29 DDVFLHRSAVASAG-LFNLTEGQLVTYDYVQNDANGKYSA 67 (78) Q Consensus 29 ~DvFvH~s~i~~~g-~~~l~~G~~V~F~i~~~~~~gk~~A 67 (78) .|-|||++++.... +-.+.-|.+|.-+ .+...+++| T Consensus 26 ndtfvhitdlsg~eti~rvtggmkvkad---rdesspyaa 62 (139) T KOG0407 26 NDTFVHVTDLSGKETIVRVTGGMKVKAD---RDESSPYAA 62 (139) T ss_pred CCCEEEEECCCCCEEEEEEECCEEEECC---CCCCCHHHH T ss_conf 6616998615785688985076278604---566886899 No 95 >pfam06523 DUF1106 Protein of unknown function (DUF1106). This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown. Probab=22.82 E-value=69 Score=14.72 Aligned_cols=56 Identities=14% Similarity=0.261 Sum_probs=37.9 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEE-EEEECCCCCCCCCCCCCEEEEEEEE Q ss_conf 7762775146887465885488778837999-9500023588446899889999998 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFL-HRSAVASAGLFNLTEGQLVTYDYVQ 58 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFv-H~s~i~~~g~~~l~~G~~V~F~i~~ 58 (78) .+|.|--+.-.+|-=++...-..+...-||+ |.....-+.++.+-+.+.++|.++- T Consensus 33 lrgivlt~kcs~g~iylsi~~~pnnr~hiflyhkk~yi~dklkeifpde~iefsiey 89 (91) T pfam06523 33 LRGIVLTFKCSKGIIYLSIKVNPNNRKHIFLYHKKDYIFDKLKEIFPDEAIEFSIEY 89 (91) T ss_pred EEEEEEEEEECCCEEEEEEEECCCCCCEEEEEEECCHHHHHHHHHCCCCCEEEEEEE T ss_conf 023899999469689999996899863489996042577779875899763899984 No 96 >PRK07135 dnaE DNA polymerase III DnaE; Validated Probab=22.64 E-value=70 Score=14.70 Aligned_cols=50 Identities=12% Similarity=0.169 Sum_probs=36.9 Q ss_pred CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC Q ss_conf 68874658854887788379999500023588446899889999998699971 Q gi|254780913|r 12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk 64 (78) ..+++.|++.++ ..+.-+++|--..+.+ ++.|+.|+.+.+.+.-..++|. T Consensus 927 ~~~~~af~~l~D-~tg~~e~~vf~~~~ek--yr~l~~g~~~~~~v~~~~~~~~ 976 (987) T PRK07135 927 KNKEYKKVIFAD-DTVEIKIFVNDNNLEK--YRLLKTGKIYEVIIFFKKPGGN 976 (987) T ss_pred CCCCEEEEEEEC-CCCCEEEEECHHHHHH--HHCCCCCCEEEEEEEEECCCCC T ss_conf 897579999986-8865899986899998--7626469879999999658984 No 97 >TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084 Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea.. Probab=22.52 E-value=68 Score=14.78 Aligned_cols=34 Identities=29% Similarity=0.517 Sum_probs=24.2 Q ss_pred EEECCCCCCCCEEEEEEEECCCCC---CCCCCCCCEEEEE Q ss_conf 885488778837999950002358---8446899889999 Q gi|254780913|r 19 ITPEGSTESGDDVFLHRSAVASAG---LFNLTEGQLVTYD 55 (78) Q Consensus 19 I~~d~~~d~g~DvFvH~s~i~~~g---~~~l~~G~~V~F~ 55 (78) |+||+++=|| ||=--.|..+. .-=|++||+|.|. T Consensus 726 LgpDGPSLGG---FVCpAvv~~AELWK~GQlKPGD~vrF~ 762 (1226) T TIGR02712 726 LGPDGPSLGG---FVCPAVVAEAELWKVGQLKPGDTVRFV 762 (1226) T ss_pred ECCCCCCCCC---CCCCEEECCCCEECCCEECCCCEEEEE T ss_conf 0775786767---114238312452413433688816887 No 98 >COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning] Probab=22.37 E-value=71 Score=14.67 Aligned_cols=51 Identities=10% Similarity=0.157 Sum_probs=29.0 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEE Q ss_conf 776277514688746588548877883799995000235884468998899 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVT 53 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~ 53 (78) .-|+|-+=+.-+|||-++.-+..+|---|+-+...|....-..+..|+.|- T Consensus 338 AdG~VvyA~~l~GYG~vvIldhG~gy~slyg~~~~i~v~~G~~V~AGepIa 388 (420) T COG4942 338 ADGRVVYADWLRGYGLVVILDHGGGYHSLYGGNQSILVNPGQFVKAGEPIA 388 (420) T ss_pred CCCEEEECHHHCCCCEEEEEECCCCCEEEECCCCEEEECCCCEEECCCCHH T ss_conf 695699543325675699997488537886166422106897755697153 No 99 >KOG3074 consensus Probab=21.93 E-value=72 Score=14.62 Aligned_cols=28 Identities=29% Similarity=0.330 Sum_probs=19.8 Q ss_pred ECCCCEEEEEECCCCCCCCEEEEEEEECCCCC Q ss_conf 46887465885488778837999950002358 Q gi|254780913|r 11 NPDKGYGFITPEGSTESGDDVFLHRSAVASAG 42 (78) Q Consensus 11 n~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g 42 (78) -+.|+|+|+.= . +..-+|+.+|.|+..+ T Consensus 185 vDnk~F~Fd~G--~--N~~G~f~riSEVk~n~ 212 (263) T KOG3074 185 VDNKRFLFDVG--K--NKRGVFVRISEVKSNG 212 (263) T ss_pred EECCEEEEECC--C--CCCCCEEEEEEECCCC T ss_conf 71450687437--7--8755257888742788 No 100 >KOG0109 consensus Probab=21.60 E-value=46 Score=15.68 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=15.0 Q ss_pred CCEEEEEECCCCEEEEEECC Q ss_conf 76277514688746588548 Q gi|254780913|r 4 RGSIKWYNPDKGYGFITPEG 23 (78) Q Consensus 4 ~G~VKwfn~~kGfGFI~~d~ 23 (78) -|+|---|-.|.|||+..++ T Consensus 26 ygkVlECDIvKNYgFVHiEd 45 (346) T KOG0109 26 YGKVLECDIVKNYGFVHIED 45 (346) T ss_pred HCCEEEEEEECCCCEEEEEC T ss_conf 17467632450311378403 No 101 >TIGR02383 Hfq RNA chaperone Hfq; InterPro: IPR005001 This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see ). The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication. The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11 kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the beta-4 strand in one molecule dimerises with the beta-5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure . The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands .; GO: 0003723 RNA binding, 0006355 regulation of transcription DNA-dependent. Probab=21.31 E-value=42 Score=15.92 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=16.5 Q ss_pred CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEEC Q ss_conf 776277514688746588548877883799995000 Q gi|254780913|r 3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAV 38 (78) Q Consensus 3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i 38 (78) .+|.|+|||. |-+.- ..+|+-=+|..=|| T Consensus 28 l~G~i~sFD~-----FtVlL--~~~g~Q~LiYKHAI 56 (61) T TIGR02383 28 LKGVIKSFDN-----FTVLL--ESQGKQQLIYKHAI 56 (61) T ss_pred CCCEEEEECC-----EEEEE--CCCCEEEEEEEEEE T ss_conf 0518997221-----79987--20992688997666 No 102 >KOG4246 consensus Probab=20.87 E-value=5.5 Score=20.85 Aligned_cols=50 Identities=24% Similarity=0.406 Sum_probs=29.4 Q ss_pred CEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCCEEEEECCC Q ss_conf 7465885488778837999950002358844689988999999869997-111059996357 Q gi|254780913|r 15 GYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSAENLKLVPK 75 (78) Q Consensus 15 GfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A~~v~~i~~ 75 (78) -||||- .||||..|+++.. ....|++|--+.-.++.-. |+.|..|+.++. T Consensus 159 tygfVD--------~dvffQls~~~g~---hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~~ 209 (1194) T KOG4246 159 TYGFVD--------QDVFFQLSKMQGL---HPSVGDAVNVEADYNPSMPFKWNAQRIQHLGG 209 (1194) T ss_pred CCCCCC--------HHHHHHHHHHHCC---CCCCCCCEEEECCCCCCCCCCCCHHHHHHCCC T ss_conf 324410--------7889999887067---87511000132256888874401799875045 No 103 >cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA. Probab=20.36 E-value=78 Score=14.43 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=30.0 Q ss_pred CCEEEEEECCCCEEE-EEECCCCCCCCEEEEEEEECCCCC---------------CCCCCCCCEEEEEEEECCC Q ss_conf 762775146887465-885488778837999950002358---------------8446899889999998699 Q gi|254780913|r 4 RGSIKWYNPDKGYGF-ITPEGSTESGDDVFLHRSAVASAG---------------LFNLTEGQLVTYDYVQNDA 61 (78) Q Consensus 4 ~G~VKwfn~~kGfGF-I~~d~~~d~g~DvFvH~s~i~~~g---------------~~~l~~G~~V~F~i~~~~~ 61 (78) +|+|.-.+ -||+ +..+. .+-|=|+|.|.|...- -+.+.-||+|.-.+..-+. T Consensus 6 ~g~I~~v~---~~GiFV~l~~---~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~ 73 (83) T cd04471 6 DGVISGVT---SFGLFVELDN---LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDL 73 (83) T ss_pred EEEEEEEE---EEEEEEEEEC---CCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEEC T ss_conf 99999898---3069999828---87399998221456722447402189813477599789999999999943 Done!