Query gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 129 No_of_seqs 107 out of 1080 Neff 5.7 Searched_HMMs 39220 Date Mon May 23 23:52:55 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780238.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05309 30S ribosomal protein 100.0 0 0 319.3 15.9 122 7-128 5-126 (126) 2 PTZ00129 40S ribosomal protein 100.0 1.4E-45 0 299.3 14.6 128 1-128 10-146 (150) 3 COG0100 RpsK Ribosomal protein 100.0 5.6E-45 0 296.3 14.7 129 1-129 1-129 (129) 4 TIGR03632 bact_S11 30S ribosom 100.0 9.8E-45 0 294.6 14.5 108 19-126 1-108 (108) 5 pfam00411 Ribosomal_S11 Riboso 100.0 1.3E-44 0 293.9 14.9 109 19-127 1-109 (109) 6 PRK09607 rps11p 30S ribosomal 100.0 4.9E-44 0 290.4 14.6 116 13-128 1-125 (129) 7 CHL00041 rps11 ribosomal prote 100.0 5.1E-43 0 284.1 14.9 114 8-121 3-116 (116) 8 KOG0408 consensus 100.0 3.4E-39 8.7E-44 260.7 13.6 120 8-129 71-190 (190) 9 TIGR03628 arch_S11P archaeal r 100.0 1.4E-37 3.5E-42 250.9 13.8 104 18-121 2-114 (114) 10 KOG0407 consensus 99.9 9E-23 2.3E-27 160.2 11.6 114 15-128 13-135 (139) 11 PTZ00090 40S ribosomal protein 99.2 4.3E-11 1.1E-15 88.7 6.2 109 20-129 101-214 (214) 12 cd00432 Ribosomal_L18_L5e Ribo 97.6 0.001 2.6E-08 43.6 9.9 88 18-105 11-103 (103) 13 CHL00139 rpl18 ribosomal prote 97.3 0.0033 8.4E-08 40.5 9.0 87 18-106 15-108 (109) 14 PRK05593 rplR 50S ribosomal pr 97.2 0.0039 9.9E-08 40.1 8.7 86 17-106 24-114 (115) 15 pfam00861 Ribosomal_L18p Ribos 97.0 0.0057 1.4E-07 39.1 8.1 90 17-106 22-118 (119) 16 PRK08569 rpl18p 50S ribosomal 95.8 0.099 2.5E-06 31.5 8.6 100 20-129 34-143 (193) 17 COG0256 RplR Ribosomal protein 95.8 0.12 3.1E-06 31.0 9.0 90 18-107 29-125 (125) 18 TIGR00060 L18_bact ribosomal p 93.7 0.51 1.3E-05 27.1 7.8 89 19-107 25-118 (118) 19 cd05313 NAD_bind_2_Glu_DH NAD( 87.9 1.5 3.8E-05 24.3 5.3 67 52-119 10-76 (254) 20 cd01076 NAD_bind_1_Glu_DH NAD( 87.5 1.6 4.1E-05 24.1 5.3 65 51-116 2-66 (227) 21 pfam00208 ELFV_dehydrog Glutam 85.0 2 5.2E-05 23.4 4.8 67 53-119 4-70 (237) 22 TIGR01418 PEP_synth phosphoeno 84.4 1.1 2.7E-05 25.2 3.1 58 48-106 685-749 (877) 23 PTZ00079 NADP-specific glutama 82.8 4.3 0.00011 21.5 5.7 77 37-119 214-290 (469) 24 PRK09414 glutamate dehydrogena 81.7 4.8 0.00012 21.2 5.9 76 38-119 192-267 (446) 25 cd05211 NAD_bind_Glu_Leu_Phe_V 69.6 10 0.00026 19.2 5.0 56 63-119 6-61 (217) 26 pfam00044 Gp_dh_N Glyceraldehy 57.1 13 0.00034 18.5 3.3 16 75-92 108-123 (150) 27 smart00846 Gp_dh_N Glyceraldeh 56.4 12 0.00032 18.6 3.1 16 75-92 108-123 (149) 28 PTZ00032 60S ribosomal protein 55.9 18 0.00046 17.6 8.9 87 20-106 107-210 (211) 29 pfam07733 DNA_pol3_alpha Bacte 50.0 13 0.00034 18.4 2.4 46 63-119 40-85 (381) 30 PRK08356 hypothetical protein; 48.8 23 0.0006 17.0 4.5 27 83-111 96-122 (195) 31 TIGR00423 TIGR00423 conserved 48.7 13 0.00033 18.5 2.1 58 28-92 5-65 (331) 32 PRK07012 consensus 45.5 15 0.00039 18.1 2.1 23 23-45 997-1023(1173) 33 COG0334 GdhA Glutamate dehydro 43.7 28 0.00071 16.5 5.9 65 54-119 181-245 (411) 34 PRK08744 consensus 43.6 18 0.00046 17.6 2.2 11 30-40 1044-1054(1195) 35 PRK08957 consensus 42.8 16 0.00041 18.0 1.9 17 24-40 1005-1024(1159) 36 PRK09532 DNA polymerase III su 42.6 17 0.00044 17.8 2.0 12 101-112 195-206 (874) 37 PRK07279 dnaE DNA polymerase I 41.2 14 0.00035 18.4 1.3 10 30-39 908-917 (1033) 38 PRK08444 hypothetical protein; 41.2 19 0.00048 17.5 2.0 68 28-102 49-124 (353) 39 pfam08901 DUF1847 Protein of u 39.6 32 0.00083 16.1 3.6 54 58-111 34-88 (157) 40 PRK06658 consensus 39.2 19 0.00048 17.5 1.8 22 23-44 992-1018(1145) 41 TIGR01534 GAPDH-I glyceraldehy 38.2 33 0.00083 16.1 2.9 32 83-115 1-40 (366) 42 PRK06115 dihydrolipoamide dehy 37.0 32 0.00081 16.1 2.7 45 63-108 182-233 (466) 43 PRK09074 consensus 36.7 18 0.00047 17.6 1.4 18 23-40 1001-1021(1149) 44 PRK07374 dnaE DNA polymerase I 36.6 26 0.00067 16.6 2.2 11 102-112 198-208 (1171) 45 PRK05673 dnaE DNA polymerase I 36.3 30 0.00076 16.3 2.4 22 23-44 993-1019(1143) 46 PTZ00069 60S ribosomal protein 35.4 38 0.00097 15.7 9.0 105 11-125 41-183 (300) 47 pfam00728 Glyco_hydro_20 Glyco 35.3 38 0.00097 15.7 5.3 73 26-100 31-103 (335) 48 PRK06292 dihydrolipoamide dehy 34.5 39 0.001 15.6 3.0 26 63-89 177-202 (460) 49 PRK06245 cofG FO synthase subu 34.5 39 0.001 15.6 3.9 55 28-88 12-66 (336) 50 PRK06826 dnaE DNA polymerase I 33.9 29 0.00073 16.4 2.0 10 31-40 1021-1030(1157) 51 PRK06920 dnaE DNA polymerase I 32.9 21 0.00054 17.2 1.2 16 25-40 959-977 (1107) 52 PRK07135 dnaE DNA polymerase I 32.3 22 0.00057 17.1 1.3 27 90-119 289-315 (987) 53 PRK05802 hypothetical protein; 31.7 44 0.0011 15.3 5.3 40 80-119 174-214 (328) 54 PRK08010 pyridine nucleotide-d 31.2 44 0.0011 15.2 2.8 44 64-108 167-217 (441) 55 PRK05898 dnaE DNA polymerase I 31.1 31 0.0008 16.2 1.8 27 90-119 292-318 (971) 56 COG4782 Uncharacterized protei 29.9 47 0.0012 15.1 5.6 74 26-101 124-210 (377) 57 TIGR03550 F420_cofG 7,8-dideme 29.5 37 0.00095 15.7 2.0 57 28-91 4-63 (322) 58 PRK05249 soluble pyridine nucl 29.1 48 0.0012 15.0 2.8 42 66-108 187-235 (465) 59 TIGR03551 F420_cofH 7,8-dideme 25.0 45 0.0011 15.2 1.7 58 28-92 39-99 (343) 60 TIGR01438 TGR thioredoxin and 24.6 58 0.0015 14.5 4.9 23 63-86 196-218 (513) 61 TIGR02183 GRXA Glutaredoxin, G 23.5 61 0.0016 14.4 3.0 34 58-91 9-44 (86) 62 COG4911 Uncharacterized conser 23.2 62 0.0016 14.4 2.7 51 14-64 68-119 (123) 63 PRK08013 hypothetical protein; 23.1 62 0.0016 14.3 4.1 10 92-101 165-174 (400) 64 PRK01259 ribose-phosphate pyro 22.9 63 0.0016 14.3 6.6 59 66-126 223-282 (309) 65 TIGR02684 dnstrm_HI1420 probab 22.3 41 0.0011 15.4 1.1 38 64-104 33-70 (91) 66 TIGR02530 flg_new flagellar op 21.9 64 0.0016 14.3 2.1 21 19-39 78-98 (113) 67 KOG4120 consensus 21.6 25 0.00064 16.7 -0.1 69 51-119 118-202 (426) 68 pfam05990 DUF900 Alpha/beta hy 21.5 67 0.0017 14.2 3.2 78 21-101 23-113 (230) 69 pfam01019 G_glu_transpept Gamm 21.5 67 0.0017 14.1 3.3 22 26-47 320-341 (506) 70 smart00300 ChSh Chromo Shadow 21.4 67 0.0017 14.1 3.2 41 30-76 11-51 (61) No 1 >PRK05309 30S ribosomal protein S11; Validated Probab=100.00 E-value=0 Score=319.35 Aligned_cols=122 Identities=57% Similarity=0.926 Sum_probs=118.6 Q ss_pred CCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE Q ss_conf 43343001225218999917987799997089988997404443557754335203789999999999986981999999 Q gi|254780238|r 7 RIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKV 86 (129) Q Consensus 7 ~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i 86 (129) +.+++.++.++.||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|++ T Consensus 5 ~~~~~~k~~i~~GivhI~ss~NNTiitlTD~~Gn~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~Gi~~v~V~i 84 (126) T PRK05309 5 KVRKKVKKNVSSGVAHIHATFNNTIVTITDRQGNAISWASAGGSGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFV 84 (126) T ss_pred CCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEE T ss_conf 55655361377608999944798899998399999999807750258876566669999999999999972971999999 Q ss_pred ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC Q ss_conf 779986788877876369369999963889888868888678 Q gi|254780238|r 87 SGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR 128 (129) Q Consensus 87 kG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR 128 (129) +|+|+||+++|++|+.+||+|.+|+|+||+|||||||||+|| T Consensus 85 kG~G~GR~~air~L~~~gikI~~I~D~TpiphnGcRp~K~RR 126 (126) T PRK05309 85 KGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKRRR 126 (126) T ss_pred ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC T ss_conf 778833899999998789889999989999978989899998 No 2 >PTZ00129 40S ribosomal protein S14; Provisional Probab=100.00 E-value=1.4e-45 Score=299.31 Aligned_cols=128 Identities=34% Similarity=0.511 Sum_probs=119.7 Q ss_pred CCCCCCCCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 98876443343001225218999917987799997089988997404443557754-33520378999999999998698 Q gi|254780238|r 1 MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSR-KNSPFAAQVATDDCSAKAQNHGM 79 (129) Q Consensus 1 m~~~~~~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~k-k~t~~Aa~~~a~~~~~~~~~~gi 79 (129) |++.+.+...+.++.+++|++||++||||||||+||+.|+.+.|+|+|.++||+.+ |+||||||+++++++++++++|| T Consensus 10 ~~~~~~~~~~~~~~~~v~GvaHI~ASfNNTIVtvTD~~G~~t~~~sSGg~~~k~~r~ksTPyAAq~AAe~aa~~a~e~Gi 89 (150) T PTZ00129 10 VPETPTTLGPQVKGEHVFGVAHVFASFNDTFIHITDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDAAARAKELGI 89 (150) T ss_pred CCCCCEECCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEEECCCCEEECCCCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 63154003772236537799999824587189987399998999968972685787778879999999999999998198 Q ss_pred CEEEEEEEC--------CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC Q ss_conf 199999977--------9986788877876369369999963889888868888678 Q gi|254780238|r 80 SSLEVKVSG--------LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR 128 (129) Q Consensus 80 ~~v~v~ikG--------~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR 128 (129) +.|+|+++| ||+||+++||+|+.+||+|.+|+|+||+|||||||||+|| T Consensus 90 ~~v~V~vrg~Gg~~~k~PGpGresAIRaL~~~Gl~I~~I~DVTPiPHnGcRppk~RR 146 (150) T PTZ00129 90 TAVHVKLRATGGTRSKTPGPGAQSALRSLARSGLKIGRIEDVTPIPTDSTRRKCGRR 146 (150) T ss_pred CEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC T ss_conf 189999982478767889864667789987479889898877999999989899877 No 3 >COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=5.6e-45 Score=296.29 Aligned_cols=129 Identities=53% Similarity=0.882 Sum_probs=121.2 Q ss_pred CCCCCCCCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 98876443343001225218999917987799997089988997404443557754335203789999999999986981 Q gi|254780238|r 1 MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMS 80 (129) Q Consensus 1 m~~~~~~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~ 80 (129) |++.....+++.++.+..|++||++||||||||+||+.||.++|.|+|.+|||+++++||||||++++.+++.++++|++ T Consensus 1 ~~~~~~~~~~~~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~ 80 (129) T COG0100 1 MAKAKARKKKKVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIK 80 (129) T ss_pred CCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEECCCCCCEEEEEECCCCEECCCCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf 97533343300012321315899726788589740789988999704762474788888689999999999999970854 Q ss_pred EEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC Q ss_conf 9999997799867888778763693699999638898888688886789 Q gi|254780238|r 81 SLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129 (129) Q Consensus 81 ~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi 129 (129) .|+|+++|||+||+++||+|+..|++|.+|.|+||+|||||||||.||+ T Consensus 81 ~v~v~vkgpG~GreaAiraL~~ag~~i~~I~DvTPiphnG~Rppk~RR~ 129 (129) T COG0100 81 SVEVKVKGPGPGREAAIRALAAAGLKITRIEDVTPIPHNGCRPPKRRRV 129 (129) T ss_pred EEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC T ss_conf 7999996899758999999987365587888868778899789887789 No 4 >TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected. Probab=100.00 E-value=9.8e-45 Score=294.63 Aligned_cols=108 Identities=56% Similarity=0.957 Sum_probs=107.0 Q ss_pred EEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHH Q ss_conf 18999917987799997089988997404443557754335203789999999999986981999999779986788877 Q gi|254780238|r 19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR 98 (129) Q Consensus 19 GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik 98 (129) ||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|+++|+|+||+++|| T Consensus 1 Gi~hI~~s~NNTiit~Td~~Gn~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~V~ikG~G~Gr~~air 80 (108) T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGAGRESAIR 80 (108) T ss_pred CEEEEEECCCCEEEEEECCCCCEEEEEECCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHH T ss_conf 98999935787899998799999999947733327765588899999999999999970961999999689974799999 Q ss_pred HHHHCCCEEEEEEECCCCCCCCCCCCCC Q ss_conf 8763693699999638898888688886 Q gi|254780238|r 99 ALRAIGFTIVSICDVTMIAHNGCRPRKR 126 (129) Q Consensus 99 ~l~~~glkI~~I~D~T~ip~nGcRp~K~ 126 (129) +|..+||+|.+|+|+||+|||||||||+ T Consensus 81 ~l~~~glkI~~I~D~TpiphnGcRp~Kk 108 (108) T TIGR03632 81 ALQAAGLEVTSIKDVTPIPHNGCRPPKR 108 (108) T ss_pred HHHHCCCEEEEEEECCCCCCCCCCCCCC T ss_conf 9998898899999889999899898989 No 5 >pfam00411 Ribosomal_S11 Ribosomal protein S11. Probab=100.00 E-value=1.3e-44 Score=293.87 Aligned_cols=109 Identities=51% Similarity=0.849 Sum_probs=108.2 Q ss_pred EEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHH Q ss_conf 18999917987799997089988997404443557754335203789999999999986981999999779986788877 Q gi|254780238|r 19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR 98 (129) Q Consensus 19 GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik 98 (129) ||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|+++|+|+||++++| T Consensus 1 Givhi~~t~NNTiitlTD~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~air 80 (109) T pfam00411 1 GIAHIQASFNNTIVTVTDVIGRVVSWSSAGGCGFKGSRKSTPYAAQTAAENAAKIAKEQGIKALEVKIKGPGPGRESALR 80 (109) T ss_pred CEEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHH T ss_conf 97999925788899998599899999957876558887689899999999999999981985999999889987899999 Q ss_pred HHHHCCCEEEEEEECCCCCCCCCCCCCCC Q ss_conf 87636936999996388988886888867 Q gi|254780238|r 99 ALRAIGFTIVSICDVTMIAHNGCRPRKRR 127 (129) Q Consensus 99 ~l~~~glkI~~I~D~T~ip~nGcRp~K~R 127 (129) +|+.+||+|.+|+|+||+|||||||||+| T Consensus 81 ~l~~~gl~I~~I~D~TpiphnGcRp~K~R 109 (109) T pfam00411 81 ALARSGLRIGRIRDVTPIPHNGCRPPKKR 109 (109) T ss_pred HHHHCCCEEEEEEECCCCCCCCCCCCCCC T ss_conf 99877998999998599998996989899 No 6 >PRK09607 rps11p 30S ribosomal protein S11P; Reviewed Probab=100.00 E-value=4.9e-44 Score=290.37 Aligned_cols=116 Identities=40% Similarity=0.524 Sum_probs=111.2 Q ss_pred EEECCCEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECC-- Q ss_conf 012252189999179877999970899-88997404443557754335203789999999999986981999999779-- Q gi|254780238|r 13 RKNIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGL-- 89 (129) Q Consensus 13 ~~~i~~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~-- 89 (129) ++++++||+||++||||||||+||++| +++.|+|+|+++|++++|+||||||+++|.++++++++||+.|+|+++|+ T Consensus 1 krk~~~GivhI~asfNNTivtvTD~~G~~~~~~ssgg~~~k~~~kK~Tp~AAq~aae~~~~~a~~~Gi~~v~V~vkG~G~ 80 (129) T PRK09607 1 QRKEKWGIAHIYASFNNTIITITDLTGAETIAKVSGGMVVKADRDEPSPYAAMQAAFRAAELAKDKGITGVHIKVRAPGG 80 (129) T ss_pred CCCCEEEEEEEEECCCCEEEEEECCCCCEEEEEECCCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCC T ss_conf 98540489999936898599998599996999947763004888768989999999999999997698589999983787 Q ss_pred ------CCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC Q ss_conf ------986788877876369369999963889888868888678 Q gi|254780238|r 90 ------GAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR 128 (129) Q Consensus 90 ------G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR 128 (129) ||||+++||+|+..||+|.+|.|+||+|||||||||+|| T Consensus 81 ~~~k~pGpGr~~air~l~~~Gl~I~~I~DvTpiPhNGcRp~K~RR 125 (129) T PRK09607 81 NGSKTPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRR 125 (129) T ss_pred CCCCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCC T ss_conf 776788842899999998689789898870989989989899877 No 7 >CHL00041 rps11 ribosomal protein S11 Probab=100.00 E-value=5.1e-43 Score=284.10 Aligned_cols=114 Identities=44% Similarity=0.753 Sum_probs=111.8 Q ss_pred CCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE Q ss_conf 33430012252189999179877999970899889974044435577543352037899999999999869819999997 Q gi|254780238|r 8 IRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS 87 (129) Q Consensus 8 ~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik 87 (129) ..+|.+++++.|++||++|+|||||||||++||+++|+|+|++||||++|+||||||+++|.++++++++||+.|+|+++ T Consensus 3 ~~kk~k~~~~~Gi~hI~~t~NNTiitlTD~~Gn~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~a~~~Gi~~v~v~vk 82 (116) T CHL00041 3 GSRKSKRKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGRRKGTPFAAQTAAENAIRTVIDQGMKRAEVMIK 82 (116) T ss_pred CCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEE T ss_conf 65555555866799999447988999984999999998077311588876898899999999999999739849999997 Q ss_pred CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC Q ss_conf 7998678887787636936999996388988886 Q gi|254780238|r 88 GLGAGRDSALRALRAIGFTIVSICDVTMIAHNGC 121 (129) Q Consensus 88 G~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGc 121 (129) |+|+||+++||+|+..||+|++|+|+||+||||| T Consensus 83 G~G~GR~~aik~l~~~glkI~~I~D~TpiphNGC 116 (116) T CHL00041 83 GPGLGRDTALRAIRRSGLKLSSIRDVTPMPHNGC 116 (116) T ss_pred CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC T ss_conf 8884589999999878988999998999999998 No 8 >KOG0408 consensus Probab=100.00 E-value=3.4e-39 Score=260.70 Aligned_cols=120 Identities=45% Similarity=0.744 Sum_probs=115.9 Q ss_pred CCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE Q ss_conf 33430012252189999179877999970899889974044435577543352037899999999999869819999997 Q gi|254780238|r 8 IRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS 87 (129) Q Consensus 8 ~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik 87 (129) ...+..+++| ++||++|+|||+||+||.+|.++.|+|||.+||+|++|+|++|||.++..+...++++|++.++|.+| T Consensus 71 ~~g~~f~eiP--i~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrntrkgT~iAaQtaavaa~~r~v~~G~~~vrV~Vk 148 (190) T KOG0408 71 FSGKNFREIP--IIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTRKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVK 148 (190) T ss_pred CCCCCCCCCC--EEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEEE T ss_conf 4786213054--68998537870899980688489885024201235666885067777789999999716369999984 Q ss_pred CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC Q ss_conf 799867888778763693699999638898888688886789 Q gi|254780238|r 88 GLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129 (129) Q Consensus 88 G~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi 129 (129) |+||||.+++++|...|+.|++|+|.||+|||||||+|+||| T Consensus 149 GlGpGRmsa~kgl~m~Gl~vvsItD~Tp~~~ng~RPrK~Rrl 190 (190) T KOG0408 149 GLGPGRMSALKGLRMGGLLVVSITDNTPMPHNGCRPRKKRRL 190 (190) T ss_pred CCCCCHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCC T ss_conf 588647888765521556999960688688789996412469 No 9 >TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria. Probab=100.00 E-value=1.4e-37 Score=250.90 Aligned_cols=104 Identities=44% Similarity=0.582 Sum_probs=101.4 Q ss_pred CEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC-------- Q ss_conf 2189999179877999970899-8899740444355775433520378999999999998698199999977-------- Q gi|254780238|r 18 SGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG-------- 88 (129) Q Consensus 18 ~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG-------- 88 (129) +||+||++||||||||+||++| +++.|+|+|+++|++++|+||||||+++|.++++++++||+.|+|+++| T Consensus 2 ~Gi~hI~atfNNTiitvTD~~G~~~~~~ssgg~~~~~~~~K~Tp~AAq~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~ 81 (114) T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114) T ss_pred CEEEEEECCCCCEEEEEECCCCCEEEEEECCCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC T ss_conf 47999991689859999859999799996687465188877888999999999999999869849999999478787778 Q ss_pred CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC Q ss_conf 998678887787636936999996388988886 Q gi|254780238|r 89 LGAGRDSALRALRAIGFTIVSICDVTMIAHNGC 121 (129) Q Consensus 89 ~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGc 121 (129) +|||||++||+|+..||+|.+|.|+||+||||. T Consensus 82 pGpGresAiral~~~Gl~I~~I~DvTPiPHNGt 114 (114) T TIGR03628 82 PGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114 (114) T ss_pred CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC T ss_conf 986289999999868979999898799998988 No 10 >KOG0407 consensus Probab=99.89 E-value=9e-23 Score=160.21 Aligned_cols=114 Identities=36% Similarity=0.512 Sum_probs=107.4 Q ss_pred ECCCEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC----- Q ss_conf 2252189999179877999970899-8899740444355775433520378999999999998698199999977----- Q gi|254780238|r 15 NIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG----- 88 (129) Q Consensus 15 ~i~~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG----- 88 (129) ..+.|++||++|||+||+++||+.| ++|...++||--....+.++||||+++++.++.+|+++||+.+++++++ T Consensus 13 ~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klratgg~k 92 (139) T KOG0407 13 EQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTK 92 (139) T ss_pred CEEEEEEEEEEECCCCEEEEECCCCCEEEEEEECCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEEEEECCCCC T ss_conf 41335667664136616998615785688985076278604566886899998779999987628058999998238866 Q ss_pred ---CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC Q ss_conf ---9986788877876369369999963889888868888678 Q gi|254780238|r 89 ---LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR 128 (129) Q Consensus 89 ---~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR 128 (129) +|||.++++|+|..+|++|-+|+|+||+|-.-.|.+.-|| T Consensus 93 tktpgpgaqsalralar~gmrigriedvtpip~d~trrkggrr 135 (139) T KOG0407 93 TKTPGPGAQSALRALARSGMRIGRIEDVTPIPSDSTRRKGGRR 135 (139) T ss_pred CCCCCCCHHHHHHHHHHHCCEEEEECCCCCCCCCCHHHCCCCC T ss_conf 6888963789999999715602101125558862011115745 No 11 >PTZ00090 40S ribosomal protein S11; Provisional Probab=99.18 E-value=4.3e-11 Score=88.73 Aligned_cols=109 Identities=22% Similarity=0.325 Sum_probs=97.6 Q ss_pred EEEEEECCCCEEEEEECCCC--CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHH Q ss_conf 89999179877999970899--8899740444355775433520378999999999998698199999977998678887 Q gi|254780238|r 20 RAHVVSTFNNTRITITDPHG--NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSAL 97 (129) Q Consensus 20 iihI~~t~NNTiitlTd~~G--n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~i 97 (129) .+-++.|+||.+.++.+..- .+++.+-+|.+||......+.-.|+..+|.++++|+.+|+..++|.++-+- --+.++ T Consensus 101 ~~V~ttsKNNvhaqvvNkS~nyrTvfgsfAGnVG~~K~~qq~~kcAyRIGeniAkKcrRLGif~vdvkFRrim-Rve~vl 179 (214) T PTZ00090 101 MLVLTTSKNNVHAQLVNRSKNYKTVFGSFAGNVGFTKKLQQSERCAYRIGENIAKKCKRLGIFAVDVKFRRIM-RVETVL 179 (214) T ss_pred EEEEECCCCCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEHHHHHHH-HHHHHH T ss_conf 9999805774440110044440256531154210678876300689999889999988728221104689999-999999 Q ss_pred HHHHHCCCEEEEEEECCCCCC---CCCCCCCCCCC Q ss_conf 787636936999996388988---88688886789 Q gi|254780238|r 98 RALRAIGFTIVSICDVTMIAH---NGCRPRKRRRI 129 (129) Q Consensus 98 k~l~~~glkI~~I~D~T~ip~---nGcRp~K~RRi 129 (129) .++...||.|..|....++|- |..||+++||| T Consensus 180 qa~~a~~l~v~q~iheprlpk~g~n~~~pr~rrrv 214 (214) T PTZ00090 180 QAFYANGLQVTQLIHEPRLPKTGLNSVRPRRRRRV 214 (214) T ss_pred HHHHHCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC T ss_conf 99997376246552377788667665684302469 No 12 >cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified. Probab=97.60 E-value=0.001 Score=43.64 Aligned_cols=88 Identities=19% Similarity=0.197 Sum_probs=69.1 Q ss_pred CEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CH Q ss_conf 218999917987799997089-98899740444355775--433520378999999999998698199999977998-67 Q gi|254780238|r 18 SGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSGS--RKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA-GR 93 (129) Q Consensus 18 ~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg~--kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~-GR 93 (129) ...+.|+.|.+|+.+++.|.. +.+++.+|+-...+++. ......||+.+++.+++++++.|+..+..-..|+-. || T Consensus 11 ~pRl~V~~Snk~i~aqiid~~~~~tl~sasT~~~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vvfDrg~~~yhgr 90 (103) T cd00432 11 RPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRYHGR 90 (103) T ss_pred CCEEEEEEECCEEEEEEEECCCCCEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHH T ss_conf 98899998189389999985999599999714065531236886299999999999999998799889986799976379 Q ss_pred -HHHHHHHHHCCC Q ss_conf -888778763693 Q gi|254780238|r 94 -DSALRALRAIGF 105 (129) Q Consensus 94 -~~~ik~l~~~gl 105 (129) .+++.++...|| T Consensus 91 v~a~a~~~re~Gl 103 (103) T cd00432 91 VKALAKGAREGGL 103 (103) T ss_pred HHHHHHHHHHCCC T ss_conf 9999999998589 No 13 >CHL00139 rpl18 ribosomal protein L18; Validated Probab=97.25 E-value=0.0033 Score=40.52 Aligned_cols=87 Identities=21% Similarity=0.247 Sum_probs=63.9 Q ss_pred CEEEEEEECCCCEEEEEE-CCCCCEEEEECCCCCCCCCCCC--CCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC--- Q ss_conf 218999917987799997-0899889974044435577543--3520378999999999998698199999977998--- Q gi|254780238|r 18 SGRAHVVSTFNNTRITIT-DPHGNTIAWSSPKVVGFSGSRK--NSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA--- 91 (129) Q Consensus 18 ~GiihI~~t~NNTiitlT-d~~Gn~i~~~S~G~~gfkg~kk--~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~--- 91 (129) ...+.|+-|.+|...++. |..|.+|+.+|+=...++...+ ++-.||..+++.+++++++.||..| ++=+| |. T Consensus 15 rpRL~V~rSnkhiyaQiIDD~~g~tl~saST~~k~~~~~~~~~~n~e~A~~vG~~ia~~a~~~gI~~V-vFDRg-gy~YH 92 (109) T CHL00139 15 RPRLSVFRSNKHIYAQIIDDTNGKTLVSCSTLDPDVKSNLSIGSTCDASKLVGQKLAKKSLKKGITKV-VFDRG-GKLYH 92 (109) T ss_pred CCEEEEEECCCEEEEEEEECCCCCEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCH T ss_conf 88899997088189999987999899996233677765514786699999999999999998799999-98589-98422 Q ss_pred CHH-HHHHHHHHCCCE Q ss_conf 678-887787636936 Q gi|254780238|r 92 GRD-SALRALRAIGFT 106 (129) Q Consensus 92 GR~-~~ik~l~~~glk 106 (129) ||- ++--++...||+ T Consensus 93 GrVkalAd~aRe~GLk 108 (109) T CHL00139 93 GRIKALAEAAREAGLQ 108 (109) T ss_pred HHHHHHHHHHHHCCCC T ss_conf 1999999999984898 No 14 >PRK05593 rplR 50S ribosomal protein L18; Reviewed Probab=97.17 E-value=0.0039 Score=40.07 Aligned_cols=86 Identities=23% Similarity=0.240 Sum_probs=62.9 Q ss_pred CCEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC---C Q ss_conf 5218999917987799997089-98899740444355775433520378999999999998698199999977998---6 Q gi|254780238|r 17 VSGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA---G 92 (129) Q Consensus 17 ~~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~---G 92 (129) ....+.|+-|.+|..+.|.|.. |.+|+.+|+=...+++ ++.-.+|..+++.+++++.+.||+.| ++=+| |. | T Consensus 24 ~rpRL~VfrSnkhiyaQiIDD~~~~tl~saST~~k~~~~--~~n~~~A~~vG~~ia~~a~~~~I~~v-~FDR~-g~~YHG 99 (115) T PRK05593 24 ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDLKA--GGNKEAAKKVGKLIAERAKAKGIKQV-VFDRG-GYKYHG 99 (115) T ss_pred CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCCHHHHC--CCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCCH T ss_conf 986799996088279999986999799997414244416--88499999999999999998799889-98189-984223 Q ss_pred HHHH-HHHHHHCCCE Q ss_conf 7888-7787636936 Q gi|254780238|r 93 RDSA-LRALRAIGFT 106 (129) Q Consensus 93 R~~~-ik~l~~~glk 106 (129) |-.+ --++...||+ T Consensus 100 rvkalAd~aRe~Gl~ 114 (115) T PRK05593 100 RVKALADAAREAGLK 114 (115) T ss_pred HHHHHHHHHHHCCCC T ss_conf 999999999984899 No 15 >pfam00861 Ribosomal_L18p Ribosomal L18p/L5e family. This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of the rat 60S ribosomal protein L5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding. Probab=96.98 E-value=0.0057 Score=39.07 Aligned_cols=90 Identities=19% Similarity=0.165 Sum_probs=64.1 Q ss_pred CCEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCC----CCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC Q ss_conf 5218999917987799997089-9889974044435577----5433520378999999999998698199999977998 Q gi|254780238|r 17 VSGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSG----SRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA 91 (129) Q Consensus 17 ~~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg----~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~ 91 (129) ....+.|+-|..|+.+.+.|.. +.++..+|+=...++. ...+.-.||..+++.+++++++.|+..|..--.|+=. T Consensus 22 ~rpRL~V~rSNkhiyaQiIdd~~~~tl~saSt~~k~lkk~~~k~~~~n~~aA~~vG~~ia~ka~~~gi~~v~fDR~g~~y 101 (119) T pfam00861 22 ERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKKYGLKGGGNNTAAAYLVGLLLAKRALKKGIAVVVFDRGGYTY 101 (119) T ss_pred CCCEEEEEEECCEEEEEEEECCCCCEEEEEECCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC T ss_conf 99889999968948999998689988999973405677734446776499999999999999998799889983899844 Q ss_pred -CH-HHHHHHHHHCCCE Q ss_conf -67-8887787636936 Q gi|254780238|r 92 -GR-DSALRALRAIGFT 106 (129) Q Consensus 92 -GR-~~~ik~l~~~glk 106 (129) || .++..++...||+ T Consensus 102 hGrvka~A~~aRe~Gl~ 118 (119) T pfam00861 102 HGRVFALAKGAREAGLN 118 (119) T ss_pred HHHHHHHHHHHHHCCCC T ss_conf 59999999999983888 No 16 >PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed Probab=95.81 E-value=0.099 Score=31.48 Aligned_cols=100 Identities=25% Similarity=0.306 Sum_probs=73.2 Q ss_pred EEEEEECCCCEEEEEEC--CCCC-EEEEECCC---CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--ECC-- Q ss_conf 89999179877999970--8998-89974044---43557754335203789999999999986981999999--779-- Q gi|254780238|r 20 RAHVVSTFNNTRITITD--PHGN-TIAWSSPK---VVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKV--SGL-- 89 (129) Q Consensus 20 iihI~~t~NNTiitlTd--~~Gn-~i~~~S~G---~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i--kG~-- 89 (129) .+-|..|.+++++.+.. +.|+ +++.+.+- ..|.++..+++| ||+.++-.++.++.+.|+.+..+-+ .-+ T Consensus 34 R~VVR~TN~~ii~Qiv~~~~~GD~v~~sa~s~eL~kyG~k~~~~N~p-AaYltGlL~gkral~~G~~eaiLDiGL~~~t~ 112 (193) T PRK08569 34 RLVVRKTNKHVIAQIVKYDPKGDRTLASAHSKELAKYGWKGDTGNTP-AAYLTGLLAGKKALKAGVEEAVLDIGLHRPTK 112 (193) T ss_pred EEEEEECCCCEEEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCCCCH-HHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC T ss_conf 59999738847999998607898999997652375568478877208-99998999999999749763798405664655 Q ss_pred CCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC Q ss_conf 9867888778763693699999638898888688886789 Q gi|254780238|r 90 GAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129 (129) Q Consensus 90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi 129 (129) |.---+++|+....|+. |||+--+-|..-|| T Consensus 113 G~rvfaalKGavDaGl~---------IPh~e~~fP~~dRi 143 (193) T PRK08569 113 GSRVFAALKGAVDAGLE---------VPHGEEVLPDEDRI 143 (193) T ss_pred CCCHHHHHHCCCCCCCC---------CCCCCCCCCCHHHC T ss_conf 62068866323245611---------67987768863231 No 17 >COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis] Probab=95.78 E-value=0.12 Score=30.95 Aligned_cols=90 Identities=18% Similarity=0.145 Sum_probs=66.0 Q ss_pred CEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCC--C--CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC- Q ss_conf 2189999179877999970899-889974044435577--5--433520378999999999998698199999977998- Q gi|254780238|r 18 SGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSG--S--RKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA- 91 (129) Q Consensus 18 ~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg--~--kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~- 91 (129) ...+.|+-|.+|.++.+.|... -++..+|+=...+++ . ..+.-.||..+++.+++++++.|++.+.+=..|+=+ T Consensus 29 rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g~~yh 108 (125) T COG0256 29 RPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYKYH 108 (125) T ss_pred CCEEEEEEECCCEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCC T ss_conf 95799998089389999974899669998713677764032578987899999999999999985995899838988651 Q ss_pred CH-HHHHHHHHHCCCEE Q ss_conf 67-88877876369369 Q gi|254780238|r 92 GR-DSALRALRAIGFTI 107 (129) Q Consensus 92 GR-~~~ik~l~~~glkI 107 (129) || .++..+....||++ T Consensus 109 gRV~Ala~~AreaGL~f 125 (125) T COG0256 109 GRVAALADGAREAGLEF 125 (125) T ss_pred HHHHHHHHHHHHCCCCC T ss_conf 19999999999729679 No 18 >TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389 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 , . This is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=93.72 E-value=0.51 Score=27.13 Aligned_cols=89 Identities=19% Similarity=0.168 Sum_probs=62.2 Q ss_pred EEEEEEECCCCEEEEEECCCCC-EEEEECCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CHH Q ss_conf 1899991798779999708998-8997404443557--75433520378999999999998698199999977998-678 Q gi|254780238|r 19 GRAHVVSTFNNTRITITDPHGN-TIAWSSPKVVGFS--GSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA-GRD 94 (129) Q Consensus 19 GiihI~~t~NNTiitlTd~~Gn-~i~~~S~G~~gfk--g~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~-GR~ 94 (129) ..+.|+-|.++....+-|..++ ||..+|+=....+ =.-.++..+|..+++.+|+++.++||..|.-==.|+=+ ||- T Consensus 25 prl~VfrS~~hiYAQvIDd~~~~tlas~Stl~~~l~~~~~~~~n~~~a~~vG~~~A~rl~~kgi~~vvFDR~G~~YHGrv 104 (118) T TIGR00060 25 PRLVVFRSNRHIYAQVIDDVKQVTLASASTLEKKLKEQLKSTGNKDAAKKVGKLVAERLIKKGINDVVFDRGGYKYHGRV 104 (118) T ss_pred CEEEEEEECCCEEEEEEECCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHH T ss_conf 36899861681789999858884787315566887765103789889999999999999972772268526996223389 Q ss_pred HHHH-HHHHCCCEE Q ss_conf 8877-876369369 Q gi|254780238|r 95 SALR-ALRAIGFTI 107 (129) Q Consensus 95 ~~ik-~l~~~glkI 107 (129) +++- ++...||++ T Consensus 105 ~ALAeaaRE~Gl~f 118 (118) T TIGR00060 105 AALAEAAREAGLNF 118 (118) T ss_pred HHHHHHHHHHCCCC T ss_conf 99999999700359 No 19 >cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t Probab=87.91 E-value=1.5 Score=24.30 Aligned_cols=67 Identities=15% Similarity=0.158 Sum_probs=51.2 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 57754335203789999999999986981999999779986788877876369369999963889888 Q gi|254780238|r 52 FSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 52 fkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) -.|+...|-+-...+++.+++.. ...++...|.+.|||.--..+-+-|...|.+|+-|.|.+.--|| T Consensus 10 s~gR~eATG~Gv~~~~~~~~~~~-~~~l~g~~vaIQGfGnVG~~aA~~l~e~GakvVaVsD~~G~i~~ 76 (254) T cd05313 10 SLIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAISGSGNVAQYAAEKLLELGAKVVTLSDSKGYVYD 76 (254) T ss_pred CCCCCCEEHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC T ss_conf 86877501088999999999967-96958999999897799999999999779979999857850887 No 20 >cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids Probab=87.54 E-value=1.6 Score=24.09 Aligned_cols=65 Identities=23% Similarity=0.311 Sum_probs=51.0 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCC Q ss_conf 557754335203789999999999986981999999779986788877876369369999963889 Q gi|254780238|r 51 GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMI 116 (129) Q Consensus 51 gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~i 116 (129) |-.++...|-|-...+.+.+++.. ..+++...|.+.|||.=-..+.+-|...|-+|+.|.|.+.. T Consensus 2 Gs~gR~eATG~Gv~~~~~~~l~~~-~~~l~g~~v~IqG~GnVG~~~a~~L~~~Gakvv~vsD~~G~ 66 (227) T cd01076 2 GSLGREEATGRGVAYATREALKKL-GIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDSDGT 66 (227) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCE T ss_conf 999997332889999999999976-98978999999898899999999999879959999847873 No 21 >pfam00208 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. Probab=84.96 E-value=2 Score=23.45 Aligned_cols=67 Identities=16% Similarity=0.245 Sum_probs=49.2 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 7754335203789999999999986981999999779986788877876369369999963889888 Q gi|254780238|r 53 SGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 53 kg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) .|+...|-|-...+.+.+++..-.-.++...|.+.|||.=-..+.+-|...|.+|+.+.|.+..-|| T Consensus 4 ~gR~eATg~Gv~~~~~~~~~~~~~~~l~g~~v~IqGfGnVG~~~a~~l~~~GakvvavsD~~G~i~~ 70 (237) T pfam00208 4 LGRPEATGYGVVYFVEEALKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVAVSDSSGYIYD 70 (237) T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC T ss_conf 9998341899999999999974999878999999898899999999999879969999828767999 No 22 >TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319 This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis. Probab=84.39 E-value=1.1 Score=25.19 Aligned_cols=58 Identities=16% Similarity=0.346 Sum_probs=41.9 Q ss_pred CCCCCCCCCCCCC--CH-HHHHHHHHHHHHH-HCCCCEEEEEE---ECCCCCHHHHHHHHHHCCCE Q ss_conf 4435577543352--03-7899999999999-86981999999---77998678887787636936 Q gi|254780238|r 48 KVVGFSGSRKNSP--FA-AQVATDDCSAKAQ-NHGMSSLEVKV---SGLGAGRDSALRALRAIGFT 106 (129) Q Consensus 48 G~~gfkg~kk~t~--~A-a~~~a~~~~~~~~-~~gi~~v~v~i---kG~G~GR~~~ik~l~~~glk 106 (129) -|+||+|++|--. |. |+.+=-++.++++ ++|+++|.|.| |-+--|+. ++..|...||+ T Consensus 685 PMlG~RGasRY~s~~y~eaF~lE~~A~k~VR~eMGLtNV~vMiPFvRT~~E~~r-v~~im~~~GL~ 749 (877) T TIGR01418 685 PMLGWRGASRYYSESYEEAFRLECKAIKRVREEMGLTNVEVMIPFVRTPEEGKR-VLEIMAEEGLK 749 (877) T ss_pred CCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHH-HHHHHHHCCCC T ss_conf 783324404026766047999999999988765085133113575488899999-99999972888 No 23 >PTZ00079 NADP-specific glutamate dehydrogenase; Provisional Probab=82.84 E-value=4.3 Score=21.45 Aligned_cols=77 Identities=14% Similarity=0.199 Sum_probs=56.2 Q ss_pred CCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCC Q ss_conf 89988997404443557754335203789999999999986981999999779986788877876369369999963889 Q gi|254780238|r 37 PHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMI 116 (129) Q Consensus 37 ~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~i 116 (129) +.|+.+.| +|+ .++..+|-|-....++.+++. ....++.-.|.+.|||+=-..+.+-|...|-+|+.+.|.... T Consensus 214 vTGKp~~~--GGs---~gR~eATG~G~vy~~~e~l~~-~~~~l~gk~vaIqGfGNVg~~aA~kl~e~GakVVavSDs~G~ 287 (469) T PTZ00079 214 LTGKNVKW--GGS---NIRPEATGYGAVYFVEEVLKS-LNIVVEKKTAVVSGSGNVAQYCVEKLLQLGAKVLTLSDSNGY 287 (469) T ss_pred EECCCCCC--CCC---CCCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCE T ss_conf 71887100--686---786762428899999999986-799857888999766738999999999769989999838943 Q ss_pred CCC Q ss_conf 888 Q gi|254780238|r 117 AHN 119 (129) Q Consensus 117 p~n 119 (129) -|| T Consensus 288 Iy~ 290 (469) T PTZ00079 288 IVE 290 (469) T ss_pred EEC T ss_conf 988 No 24 >PRK09414 glutamate dehydrogenase; Provisional Probab=81.65 E-value=4.8 Score=21.18 Aligned_cols=76 Identities=13% Similarity=0.166 Sum_probs=55.1 Q ss_pred CCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCC Q ss_conf 99889974044435577543352037899999999999869819999997799867888778763693699999638898 Q gi|254780238|r 38 HGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIA 117 (129) Q Consensus 38 ~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip 117 (129) .|+.+.| +|++ ++...|-|-....++.+++. ....++.-.|.+.|||.=-..+.+-|...|-+|+.+.|.+..- T Consensus 192 TGKp~~~--GGs~---gR~eATG~Gv~y~~~e~l~~-~g~~l~gk~v~IqGfGNVg~~aA~~l~e~GakvVavSDs~G~I 265 (446) T PRK09414 192 TGKGLSF--GGSL---IRPEATGYGLVYFAEEMLKA-RGDSFEGKTVVVSGSGNVAIYAIEKAMELGAKVVTCSDSSGYV 265 (446) T ss_pred CCCCCCC--CCCC---CCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEE T ss_conf 8997210--6886---87653228999999999997-4999578879997777799999999997699799998378607 Q ss_pred CC Q ss_conf 88 Q gi|254780238|r 118 HN 119 (129) Q Consensus 118 ~n 119 (129) || T Consensus 266 y~ 267 (446) T PRK09414 266 YD 267 (446) T ss_pred EC T ss_conf 88 No 25 >cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral Probab=69.60 E-value=10 Score=19.19 Aligned_cols=56 Identities=20% Similarity=0.203 Sum_probs=39.0 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 789999999999986981999999779986788877876369369999963889888 Q gi|254780238|r 63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 63 a~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) ...+.+.+++. ....++...|.+.|||.=-..+.+-|...|.+|+.|.|.+.--|| T Consensus 6 v~~~~~~a~~~-~~~~l~g~~vaVqGfGnVG~~~a~~l~~~GakvvavsD~~G~i~~ 61 (217) T cd05211 6 VVVAMKAAMKH-LGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYD 61 (217) T ss_pred HHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC T ss_conf 99999999997-696857999999898899999999999859989999857871778 No 26 >pfam00044 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold. Probab=57.05 E-value=13 Score=18.45 Aligned_cols=16 Identities=13% Similarity=0.154 Sum_probs=7.2 Q ss_pred HHCCCCEEEEEEECCCCC Q ss_conf 986981999999779986 Q gi|254780238|r 75 QNHGMSSLEVKVSGLGAG 92 (129) Q Consensus 75 ~~~gi~~v~v~ikG~G~G 92 (129) .+.|.+.|.| .+|.+. T Consensus 108 l~~GaKkVii--SaP~~d 123 (150) T pfam00044 108 LKAGAKKVII--SAPAKD 123 (150) T ss_pred HHCCCCEEEE--ECCCCC T ss_conf 7579877999--579988 No 27 >smart00846 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold. Probab=56.38 E-value=12 Score=18.64 Aligned_cols=16 Identities=13% Similarity=0.167 Sum_probs=8.4 Q ss_pred HHCCCCEEEEEEECCCCC Q ss_conf 986981999999779986 Q gi|254780238|r 75 QNHGMSSLEVKVSGLGAG 92 (129) Q Consensus 75 ~~~gi~~v~v~ikG~G~G 92 (129) .+.|.+.| ++.+|.+. T Consensus 108 l~~gakkV--iisaP~~d 123 (149) T smart00846 108 LKAGAKKV--IISAPAKD 123 (149) T ss_pred HHCCCCEE--EECCCCCC T ss_conf 64796769--98279889 No 28 >PTZ00032 60S ribosomal protein L18; Provisional Probab=55.86 E-value=18 Score=17.64 Aligned_cols=87 Identities=21% Similarity=0.198 Sum_probs=55.5 Q ss_pred EEEEEECCCCEEEEEECC-CCCEEEEECC---------CCCCCCCC-----CCCCCCHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 899991798779999708-9988997404---------44355775-----43352037899999999999869819999 Q gi|254780238|r 20 RAHVVSTFNNTRITITDP-HGNTIAWSSP---------KVVGFSGS-----RKNSPFAAQVATDDCSAKAQNHGMSSLEV 84 (129) Q Consensus 20 iihI~~t~NNTiitlTd~-~Gn~i~~~S~---------G~~gfkg~-----kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v 84 (129) .+-|+-|.|-...|+.|- .-.+++..++ |..--|.. .-++-.||+.+++.++++|.+.||+.|.. T Consensus 107 Rl~iK~Tnn~iyAtIvDDy~r~vlCf~cs~~~~lS~I~Gty~~k~tnr~~nnGg~i~aA~eVGk~IakkA~~kGI~~VvF 186 (211) T PTZ00032 107 RLTLKNTNNQMYATIVDDYTRYVLCFTCTNFKYLSHIFGTYPTKATNRVRNNGGTIKAAYELGKLIGRKALSKGISKVRF 186 (211) T ss_pred CEEEECCCCEEEEEEECCCCCEEEEEECCCCCHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 06875267736787730200057999625882176663466666767375589765999999999999999879988998 Q ss_pred EEECCCC-CHHHHHH-HHHHCCCE Q ss_conf 9977998-6788877-87636936 Q gi|254780238|r 85 KVSGLGA-GRDSALR-ALRAIGFT 106 (129) Q Consensus 85 ~ikG~G~-GR~~~ik-~l~~~glk 106 (129) -=.|+=. ||-.++- +-...||+ T Consensus 187 DRggy~YHGRVkALAe~ARe~GL~ 210 (211) T PTZ00032 187 DRAHYKYAGKVEALAEGARAVGLQ 210 (211) T ss_pred CCCCCCCCHHHHHHHHHHHHHCCC T ss_conf 799973202899999999971889 No 29 >pfam07733 DNA_pol3_alpha Bacterial DNA polymerase III alpha subunit. Probab=49.97 E-value=13 Score=18.41 Aligned_cols=46 Identities=28% Similarity=0.409 Sum_probs=31.5 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 789999999999986981999999779986788877876369369999963889888 Q gi|254780238|r 63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 63 a~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) .+++...+.+.|++.||- .||||-++--+|..- ..-|+|+-|++|| T Consensus 40 YFLiv~d~v~~a~~~gi~--------vgpgRGSaagSlV~y---~LgIT~vDPi~~~ 85 (381) T pfam07733 40 YFLIVWDLVKWAKDNGIP--------VGPGRGSAAGSLVAY---LLGITEVDPLKHD 85 (381) T ss_pred CHHHHHHHHHHHHHCCCE--------ECCCCCCHHHHHHHH---HHCCCCCCCCCCC T ss_conf 479999999999987961--------379987379999999---8568240863147 No 30 >PRK08356 hypothetical protein; Provisional Probab=48.83 E-value=23 Score=16.95 Aligned_cols=27 Identities=11% Similarity=0.409 Sum_probs=13.6 Q ss_pred EEEEECCCCCHHHHHHHHHHCCCEEEEEE Q ss_conf 99997799867888778763693699999 Q gi|254780238|r 83 EVKVSGLGAGRDSALRALRAIGFTIVSIC 111 (129) Q Consensus 83 ~v~ikG~G~GR~~~ik~l~~~glkI~~I~ 111 (129) .+++.|.-.- .=+..|.+.+..++.|. T Consensus 96 ~vVIdgiR~~--~Eve~lk~~~~~lI~V~ 122 (195) T PRK08356 96 NIAIDGVRSR--GEVEAIKRMGGKVIYVE 122 (195) T ss_pred CEEEECCCCH--HHHHHHHHCCCEEEEEE T ss_conf 7899489988--99999996599799996 No 31 >TIGR00423 TIGR00423 conserved hypothetical protein TIGR00423; InterPro: IPR005244 This entry describes a family of conserved hypothetical proteins with no known function. . Probab=48.69 E-value=13 Score=18.54 Aligned_cols=58 Identities=21% Similarity=0.302 Sum_probs=40.5 Q ss_pred CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH---CCCCEEEEEEECCCCC Q ss_conf 8779999708998899740444355775433520378999999999998---6981999999779986 Q gi|254780238|r 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQN---HGMSSLEVKVSGLGAG 92 (129) Q Consensus 28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~---~gi~~v~v~ikG~G~G 92 (129) +|..|-.|| |+..-|.-|-|+..++. ..|..+-.+.+.+|+.+ .|.++|.+. -|..|. T Consensus 5 VNRNINfTN-----IC~~~C~FCAF~~~~k~-~~~Y~Ls~eEI~~Kv~ea~~~G~tE~~iQ-GGlnP~ 65 (331) T TIGR00423 5 VNRNINFTN-----ICVGKCKFCAFRRREKD-KDAYVLSLEEILRKVKEAVAKGATEICIQ-GGLNPQ 65 (331) T ss_pred CCCCCCCCH-----HHHHCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHCCCEEEEEE-CCCCCC T ss_conf 166567530-----02324796331134689-88814077999999999997198278852-342788 No 32 >PRK07012 consensus Probab=45.46 E-value=15 Score=18.07 Aligned_cols=23 Identities=13% Similarity=0.143 Sum_probs=13.7 Q ss_pred EEECCCC--EEEEEECCCC--CEEEEE Q ss_conf 9917987--7999970899--889974 Q gi|254780238|r 23 VVSTFNN--TRITITDPHG--NTIAWS 45 (129) Q Consensus 23 I~~t~NN--TiitlTd~~G--n~i~~~ 45 (129) ...|++. .|+||-|..| +++.|. T Consensus 997 ~~~tk~G~maf~tleD~tg~~ev~vfp 1023 (1173) T PRK07012 997 TQMTQRGKMVIALLDDGTGQCEITVFN 1023 (1173) T ss_pred ECCCCCCCEEEEEEEECCCCEEEEECH T ss_conf 788887778999999799878999978 No 33 >COG0334 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism] Probab=43.71 E-value=28 Score=16.47 Aligned_cols=65 Identities=20% Similarity=0.258 Sum_probs=46.4 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 754335203789999999999986981999999779986788877876369369999963889888 Q gi|254780238|r 54 GSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 54 g~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) ++...|.|-.....+ .+.+....++....|-+.|+|.=-..+.+-|...|-+|+.+.|....-|| T Consensus 181 ~r~~aTg~Gv~~~~~-~a~~~~g~~l~G~rVaVQG~GNVg~~aa~~l~~~GAkvv~~sds~g~i~~ 245 (411) T COG0334 181 GRSEATGYGVFYAIR-EALKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVSDSKGGIYD 245 (411) T ss_pred CCCCCCCEEEHHHHH-HHHHHCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCEEC T ss_conf 998651033079999-99998177768878999776289999999999749979999767884416 No 34 >PRK08744 consensus Probab=43.62 E-value=18 Score=17.63 Aligned_cols=11 Identities=18% Similarity=0.401 Sum_probs=8.0 Q ss_pred EEEEEECCCCC Q ss_conf 79999708998 Q gi|254780238|r 30 TRITITDPHGN 40 (129) Q Consensus 30 TiitlTd~~Gn 40 (129) .|+||-|..|. T Consensus 1044 af~tleD~tg~ 1054 (1195) T PRK08744 1044 VFVQLEDGRGR 1054 (1195) T ss_pred EEEEEEECCCC T ss_conf 99999968973 No 35 >PRK08957 consensus Probab=42.82 E-value=16 Score=17.96 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=12.3 Q ss_pred EECCCC---EEEEEECCCCC Q ss_conf 917987---79999708998 Q gi|254780238|r 24 VSTFNN---TRITITDPHGN 40 (129) Q Consensus 24 ~~t~NN---TiitlTd~~Gn 40 (129) ..|+++ .|+|+-|..|. T Consensus 1005 ~~tkkg~~maf~~leD~tg~ 1024 (1159) T PRK08957 1005 MVTKRGNRIGICTLDDRSGR 1024 (1159) T ss_pred CCCCCCCEEEEEEEEECCCC T ss_conf 57899898899999989986 No 36 >PRK09532 DNA polymerase III subunit alpha; Reviewed Probab=42.56 E-value=17 Score=17.77 Aligned_cols=12 Identities=42% Similarity=0.722 Sum_probs=4.9 Q ss_pred HHCCCEEEEEEE Q ss_conf 636936999996 Q gi|254780238|r 101 RAIGFTIVSICD 112 (129) Q Consensus 101 ~~~glkI~~I~D 112 (129) ...++.++...| T Consensus 195 ~~~~iplVATnd 206 (874) T PRK09532 195 RELGIKIVATND 206 (874) T ss_pred HHHCCCEEECCC T ss_conf 981999886186 No 37 >PRK07279 dnaE DNA polymerase III DnaE; Reviewed Probab=41.16 E-value=14 Score=18.36 Aligned_cols=10 Identities=10% Similarity=0.321 Sum_probs=5.1 Q ss_pred EEEEEECCCC Q ss_conf 7999970899 Q gi|254780238|r 30 TRITITDPHG 39 (129) Q Consensus 30 TiitlTd~~G 39 (129) .|+||.|..| T Consensus 908 af~tleD~tg 917 (1033) T PRK07279 908 AFLSVNDTKK 917 (1033) T ss_pred EEEEEEECCC T ss_conf 9999998998 No 38 >PRK08444 hypothetical protein; Provisional Probab=41.15 E-value=19 Score=17.54 Aligned_cols=68 Identities=15% Similarity=0.228 Sum_probs=39.4 Q ss_pred CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH---HHCCCCEEEEEEECCCCCH-----HHHHHH Q ss_conf 87799997089988997404443557754335203789999999999---9869819999997799867-----888778 Q gi|254780238|r 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA---QNHGMSSLEVKVSGLGAGR-----DSALRA 99 (129) Q Consensus 28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~---~~~gi~~v~v~ikG~G~GR-----~~~ik~ 99 (129) .|.+|.+|+ ++..+|+-|+|... ...+.|.....+.+.+++ .+.|.++|.+. -|..|-- +-.++. T Consensus 49 ~n~~IN~TN-----iC~~~C~FCaF~r~-~~~~~aY~ls~eei~~~~~ea~~~G~tev~i~-GG~~P~~~~eyY~~l~r~ 121 (353) T PRK08444 49 INRHINPTN-----ICADVCKFCAFSAH-RKNPNPYTMSHEEILEIVKESVKRGIKEVHIV-SAHNPNYGYQWYLEIFKM 121 (353) T ss_pred ECCCCCCCC-----CCCCCCCCCCCCCC-CCCCCCEECCHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHHHHHHHH T ss_conf 205745664-----45688856756168-99998766699999999999997598789981-475989975889999999 Q ss_pred HHH Q ss_conf 763 Q gi|254780238|r 100 LRA 102 (129) Q Consensus 100 l~~ 102 (129) +.. T Consensus 122 ik~ 124 (353) T PRK08444 122 IKE 124 (353) T ss_pred HHH T ss_conf 998 No 39 >pfam08901 DUF1847 Protein of unknown function (DUF1847). This family of proteins are functionally uncharacterized. THey contain 4 N-terminal cysteines that may form a zinc binding domain. Probab=39.59 E-value=32 Score=16.07 Aligned_cols=54 Identities=19% Similarity=0.340 Sum_probs=41.7 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCEEEEEE-ECCCCCHHHHHHHHHHCCCEEEEEE Q ss_conf 35203789999999999986981999999-7799867888778763693699999 Q gi|254780238|r 58 NSPFAAQVATDDCSAKAQNHGMSSLEVKV-SGLGAGRDSALRALRAIGFTIVSIC 111 (129) Q Consensus 58 ~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i-kG~G~GR~~~ik~l~~~glkI~~I~ 111 (129) +..|.-..=.|.+.+.|+.+|++.+=|-+ -|+-.-.+.+.+.|...||.+.++. T Consensus 34 ~~~Y~~~tRvEEii~FAk~mgykkiGiAfCiGL~~Ea~~~~~il~~~gFev~sV~ 88 (157) T pfam08901 34 GEGYGKLTRVEEIIEFAKRMGYKKIGIAFCIGLLNEARILAKILKAKGFEVYSVC 88 (157) T ss_pred HHHCCCHHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 8641205659999999998599755302237389999999999997898898888 No 40 >PRK06658 consensus Probab=39.22 E-value=19 Score=17.50 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=13.7 Q ss_pred EEECCCC---EEEEEECCCCC--EEEE Q ss_conf 9917987---79999708998--8997 Q gi|254780238|r 23 VVSTFNN---TRITITDPHGN--TIAW 44 (129) Q Consensus 23 I~~t~NN---TiitlTd~~Gn--~i~~ 44 (129) ...|+++ .|+|+-|..|. ++.| T Consensus 992 ~~~tk~g~~maf~~leD~tg~~e~~~f 1018 (1145) T PRK06658 992 VIQTKRGAKMAFGVFEDLKGAIDIVVF 1018 (1145) T ss_pred ECCCCCCCEEEEEEEEECCCCEEEEEC T ss_conf 435799997899999968986899997 No 41 >TIGR01534 GAPDH-I glyceraldehyde-3-phosphate dehydrogenase, type I; InterPro: IPR006424 This group of sequences represent glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilise NAD (1.2.1.12 from EC), NADP (1.2.1.13 from EC) or either (1.2.1.59 from EC). In some species, NAD- and NADP- utilising forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively . An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine . This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria . This enzyme is described by IPR006422 from INTERPRO. These two groups of sequences exhibit a close evolutionary relationship. There exists the possibility that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to possess a limited E4PD activity as well as a robust GAPDH activity ).; GO: 0008943 glyceraldehyde-3-phosphate dehydrogenase activity, 0051287 NAD binding, 0006006 glucose metabolic process. Probab=38.25 E-value=33 Score=16.05 Aligned_cols=32 Identities=41% Similarity=0.631 Sum_probs=22.1 Q ss_pred EEEEECCCC-CHHHHHHH-HHHC----CCEE-EEEEEC-CC Q ss_conf 999977998-67888778-7636----9369-999963-88 Q gi|254780238|r 83 EVKVSGLGA-GRDSALRA-LRAI----GFTI-VSICDV-TM 115 (129) Q Consensus 83 ~v~ikG~G~-GR~~~ik~-l~~~----glkI-~~I~D~-T~ 115 (129) .|-|.|||. ||. ++|. +... .|+| .-|-|. +- T Consensus 1 kvgINGFGRIGRl-vlR~~~~~~~~g~~~~viv~inD~~~~ 40 (366) T TIGR01534 1 KVGINGFGRIGRL-VLRAILEKQGSGLDLEVIVAINDLSTD 40 (366) T ss_pred CEEEECCCHHHHH-HHHHHHCCCCCCCEEEEEEEECCCCCC T ss_conf 9365147858999-999985057889705899831488768 No 42 >PRK06115 dihydrolipoamide dehydrogenase; Reviewed Probab=37.01 E-value=32 Score=16.13 Aligned_cols=45 Identities=16% Similarity=0.023 Sum_probs=26.2 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEEECC--CC-----CHHHHHHHHHHCCCEEE Q ss_conf 789999999999986981999999779--98-----67888778763693699 Q gi|254780238|r 63 AQVATDDCSAKAQNHGMSSLEVKVSGL--GA-----GRDSALRALRAIGFTIV 108 (129) Q Consensus 63 a~~~a~~~~~~~~~~gi~~v~v~ikG~--G~-----GR~~~ik~l~~~glkI~ 108 (129) +-.++-.+++....+|. .|.+.-++. -+ -.+.+.+.|...|++|. T Consensus 182 gG~ig~E~A~~~~~lG~-~Vtlv~~~~~lL~~~D~~~~~~l~~~l~~~gi~i~ 233 (466) T PRK06115 182 AGVIGLELGSVWRRLGA-QVTVVEYLDRICPGTDGETAKTLQKALAKQGMRFK 233 (466) T ss_pred CCHHHHHHHHHHHHCCC-EEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCEEE T ss_conf 85899999999986198-47899833421434341236888889987694999 No 43 >PRK09074 consensus Probab=36.71 E-value=18 Score=17.57 Aligned_cols=18 Identities=22% Similarity=0.362 Sum_probs=11.5 Q ss_pred EEECCCC---EEEEEECCCCC Q ss_conf 9917987---79999708998 Q gi|254780238|r 23 VVSTFNN---TRITITDPHGN 40 (129) Q Consensus 23 I~~t~NN---TiitlTd~~Gn 40 (129) ...|++. .|+||.|..|. T Consensus 1001 ~~~tk~G~~maf~tleD~tg~ 1021 (1149) T PRK09074 1001 ERKTKTGNKMGIVQLSDPTGQ 1021 (1149) T ss_pred ECCCCCCCEEEEEEEEECCCC T ss_conf 535899997899999979985 No 44 >PRK07374 dnaE DNA polymerase III subunit alpha; Validated Probab=36.60 E-value=26 Score=16.64 Aligned_cols=11 Identities=18% Similarity=0.601 Sum_probs=4.4 Q ss_pred HCCCEEEEEEE Q ss_conf 36936999996 Q gi|254780238|r 102 AIGFTIVSICD 112 (129) Q Consensus 102 ~~glkI~~I~D 112 (129) ..|+.++.--| T Consensus 198 ~~~iplVATnd 208 (1171) T PRK07374 198 ELGIKLIATND 208 (1171) T ss_pred HHCCCEEEECC T ss_conf 80979899688 No 45 >PRK05673 dnaE DNA polymerase III subunit alpha; Validated Probab=36.31 E-value=30 Score=16.31 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=13.0 Q ss_pred EEECCCC---EEEEEECCCCC--EEEE Q ss_conf 9917987---79999708998--8997 Q gi|254780238|r 23 VVSTFNN---TRITITDPHGN--TIAW 44 (129) Q Consensus 23 I~~t~NN---TiitlTd~~Gn--~i~~ 44 (129) ...|+++ .|+|+.|..|. ++.| T Consensus 993 ~~~TkkG~~maf~tleD~tg~~e~vvf 1019 (1143) T PRK05673 993 VRVTKRGNKMAIVTLEDRSGRIEVMLF 1019 (1143) T ss_pred ECCCCCCCEEEEEEEEECCCCEEEEEC T ss_conf 511799898999999989984899997 No 46 >PTZ00069 60S ribosomal protein L5; Provisional Probab=35.39 E-value=38 Score=15.67 Aligned_cols=105 Identities=18% Similarity=0.108 Sum_probs=68.2 Q ss_pred CEEEECCCEEEEEEECCCCEEEEEEC--CCCCEE-EEECC---CCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-CC---- Q ss_conf 30012252189999179877999970--899889-97404---443557754335203789999999999986-98---- Q gi|254780238|r 11 RERKNIVSGRAHVVSTFNNTRITITD--PHGNTI-AWSSP---KVVGFSGSRKNSPFAAQVATDDCSAKAQNH-GM---- 79 (129) Q Consensus 11 k~~~~i~~GiihI~~t~NNTiitlTd--~~Gn~i-~~~S~---G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~-gi---- 79 (129) |.+-.-|+..+-|..|..++++.+.. ..|+.+ +.+.+ -..|++..-.+.+ ||+.++-.++..+... |+ T Consensus 41 knKyntpKyRlVVR~TN~~iicQiv~a~~~GD~v~~aA~s~EL~kyG~k~gltNya-AAY~TGlLlarR~L~kl~ld~~y 119 (300) T PTZ00069 41 KNKYNSPKYRLVVRITNKDIICQIVYAKIVGDKVVAAAYSHELPRFGIPVGLTNYA-AAYATGLLLARRTLKKLKLADKF 119 (300) T ss_pred CCCCCCCCCEEEEEEECCEEEEEEEEECCCCCEEEEEEECCHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHCCCHHHH T ss_conf 02358987449999877828999998506898999985112042358878877408-99998999999999860622331 Q ss_pred ---CE------------------EEEEEE-C-----CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCC Q ss_conf ---19------------------999997-7-----9986788877876369369999963889888868888 Q gi|254780238|r 80 ---SS------------------LEVKVS-G-----LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK 125 (129) Q Consensus 80 ---~~------------------v~v~ik-G-----~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K 125 (129) .+ +..++. | .|.---+++++....||. |||+-.|-|. T Consensus 120 ~G~~e~~g~~~~v~e~~~~~~rpFka~LDvGL~rtTtG~RVFaaLKGAvDgGl~---------IPHs~krFpG 183 (300) T PTZ00069 120 EGVKEADGSYYAVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLA---------IPHRPNRFPG 183 (300) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHCCCCCCCC---------CCCCCCCCCC T ss_conf 575214575101222355787764799732544477653244532123357735---------7888875888 No 47 >pfam00728 Glyco_hydro_20 Glycosyl hydrolase family 20, catalytic domain. This domain has a TIM barrel fold. Probab=35.28 E-value=38 Score=15.66 Aligned_cols=73 Identities=22% Similarity=0.251 Sum_probs=47.0 Q ss_pred CCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHH Q ss_conf 798779999708998899740444355775433520378999999999998698199999977998678887787 Q gi|254780238|r 26 TFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRAL 100 (129) Q Consensus 26 t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l 100 (129) -+|--|++|||-.|=.+...+=..+--+|+.+...|=.+.-...+.+.|.++|| .|.--|.-||-.+ +++++. T Consensus 31 K~N~lhlHltD~~~~r~~~~~~p~l~~~ga~~~~~~yT~~ei~~lv~yA~~rgI-~viPEiD~PgH~~-a~~~~~ 103 (335) T pfam00728 31 KLNVLHWHLTDDQGWRLEIKAYPELTEVGAYRGSDFYTQEDIREIVAYAAARGI-EVIPEIDMPGHAR-AALKAY 103 (335) T ss_pred CCCEEEEEEECCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHCCC-EEEECCCCHHHHH-HHHHHC T ss_conf 896799998537876201566644212367788876299999999999998599-8986256426789-999748 No 48 >PRK06292 dihydrolipoamide dehydrogenase; Validated Probab=34.51 E-value=39 Score=15.58 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=16.6 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEEECC Q ss_conf 789999999999986981999999779 Q gi|254780238|r 63 AQVATDDCSAKAQNHGMSSLEVKVSGL 89 (129) Q Consensus 63 a~~~a~~~~~~~~~~gi~~v~v~ikG~ 89 (129) +-.++-.++..+..+|. .|.|+-++. T Consensus 177 gG~ig~E~A~~l~~~G~-~Vtvv~~~~ 202 (460) T PRK06292 177 GGVIGLELGQALSRLGV-KVTVFERGD 202 (460) T ss_pred CCHHHHHHHHHHHHCCC-EEEEEEECC T ss_conf 86788799999984698-699996247 No 49 >PRK06245 cofG FO synthase subunit 1; Reviewed Probab=34.50 E-value=39 Score=15.58 Aligned_cols=55 Identities=13% Similarity=0.110 Sum_probs=30.9 Q ss_pred CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC Q ss_conf 8779999708998899740444355775433520378999999999998698199999977 Q gi|254780238|r 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG 88 (129) Q Consensus 28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG 88 (129) .|.+|.+|+ ++...|+-|.|+......++=...-....++.+.+.|.+++.+. -| T Consensus 12 ~n~~In~TN-----iC~~~C~fCaF~~~~~~a~~ls~eev~~~~~ea~~~G~tEvl~~-gG 66 (336) T PRK06245 12 RNVFIPLTY-----ECRNRCGYCTFRPDPGEASLLSPEEVREILERGQDAGCTEALFT-FG 66 (336) T ss_pred CCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEE-CC T ss_conf 862616775-----40268825867468875687799999999999997698399980-57 No 50 >PRK06826 dnaE DNA polymerase III DnaE; Reviewed Probab=33.93 E-value=29 Score=16.42 Aligned_cols=10 Identities=40% Similarity=0.444 Sum_probs=7.8 Q ss_pred EEEEECCCCC Q ss_conf 9999708998 Q gi|254780238|r 31 RITITDPHGN 40 (129) Q Consensus 31 iitlTd~~Gn 40 (129) |+|+.|..|. T Consensus 1021 f~tleD~tG~ 1030 (1157) T PRK06826 1021 FITLEDLYGT 1030 (1157) T ss_pred EEEEEECCCC T ss_conf 9999968986 No 51 >PRK06920 dnaE DNA polymerase III DnaE; Reviewed Probab=32.95 E-value=21 Score=17.23 Aligned_cols=16 Identities=25% Similarity=0.237 Sum_probs=10.3 Q ss_pred ECCCC---EEEEEECCCCC Q ss_conf 17987---79999708998 Q gi|254780238|r 25 STFNN---TRITITDPHGN 40 (129) Q Consensus 25 ~t~NN---TiitlTd~~Gn 40 (129) .|+++ .|+|+-|..|. T Consensus 959 ~tk~g~~maf~~leD~tg~ 977 (1107) T PRK06920 959 RTKKGQKMAFITFCDQNDE 977 (1107) T ss_pred ECCCCCEEEEEEEEECCCC T ss_conf 3688996999999979986 No 52 >PRK07135 dnaE DNA polymerase III DnaE; Validated Probab=32.31 E-value=22 Score=17.05 Aligned_cols=27 Identities=30% Similarity=0.445 Sum_probs=15.7 Q ss_pred CCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 986788877876369369999963889888 Q gi|254780238|r 90 GAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) ||||.++--+|..- ..-|+|+-|+.|| T Consensus 289 GPGRGSaAGSLVaY---~LgIT~VDPi~y~ 315 (987) T PRK07135 289 GPGRGSASGSLVSY---LLEITSVNPLKYD 315 (987) T ss_pred CCCCCCHHHHHHHH---HHCCCCCCHHHCC T ss_conf 68877378899999---9668763876548 No 53 >PRK05802 hypothetical protein; Provisional Probab=31.65 E-value=44 Score=15.29 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=32.6 Q ss_pred CEEEEEEECCCCC-HHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 1999999779986-788877876369369999963889888 Q gi|254780238|r 80 SSLEVKVSGLGAG-RDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 80 ~~v~v~ikG~G~G-R~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) ...-|..+|+|.. --.++|-|...|=+|..|.|.+|..+| T Consensus 174 ~k~LvIaRGIgqAP~vpVikkL~~n~NkV~vIid~~~~~~~ 214 (328) T PRK05802 174 GKSLVIARGIGQAPAVPVIKKLYSNGNKVIVILDKGPFENN 214 (328) T ss_pred CEEEEEECCCCCCCCHHHHHHHHHCCCEEEEEECCCCCCCH T ss_conf 73999935623255559999998689979999858855316 No 54 >PRK08010 pyridine nucleotide-disulfide oxidoreductase; Provisional Probab=31.25 E-value=44 Score=15.25 Aligned_cols=44 Identities=16% Similarity=0.126 Sum_probs=27.3 Q ss_pred HHHHHHHHHHHHHCCCCEEEEEEECCC--C-----CHHHHHHHHHHCCCEEE Q ss_conf 899999999999869819999997799--8-----67888778763693699 Q gi|254780238|r 64 QVATDDCSAKAQNHGMSSLEVKVSGLG--A-----GRDSALRALRAIGFTIV 108 (129) Q Consensus 64 ~~~a~~~~~~~~~~gi~~v~v~ikG~G--~-----GR~~~ik~l~~~glkI~ 108 (129) -..+-.+++....+|. .|.|.-++.- + -.+.+.+.|...|+++. T Consensus 167 G~ig~E~A~~~~~lG~-~Vtiie~~~~il~~~D~~~~~~l~~~l~~~Gi~i~ 217 (441) T PRK08010 167 GYIGVEFASMFANFGS-KVTILEAASLFLPREDRDIADNIATILRDQGVDII 217 (441) T ss_pred CHHHHHHHHHHHHCCC-EEEEEECCCCCCCCCHHHHHHHHHHHHHHCCEEEE T ss_conf 5899999999997598-78897046732663114689999999987885997 No 55 >PRK05898 dnaE DNA polymerase III DnaE; Validated Probab=31.11 E-value=31 Score=16.17 Aligned_cols=27 Identities=41% Similarity=0.539 Sum_probs=14.4 Q ss_pred CCCHHHHHHHHHHCCCEEEEEEECCCCCCC Q ss_conf 986788877876369369999963889888 Q gi|254780238|r 90 GAGRDSALRALRAIGFTIVSICDVTMIAHN 119 (129) Q Consensus 90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~n 119 (129) ||||.++--+|..- ...|+|+-|+.|| T Consensus 292 GPGRGSaAGSLVaY---~LgIT~iDPi~~~ 318 (971) T PRK05898 292 GPGRGSAAGSLIAY---LLHITDIDPIKYN 318 (971) T ss_pred CCCCCCHHHHHHHH---HHCCCCCCHHHCC T ss_conf 78876269899999---9748775822158 No 56 >COG4782 Uncharacterized protein conserved in bacteria [Function unknown] Probab=29.89 E-value=47 Score=15.11 Aligned_cols=74 Identities=22% Similarity=0.331 Sum_probs=44.6 Q ss_pred CCCCEEEE-------EECCCCC-----EEEEECCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC Q ss_conf 79877999-------9708998-----8997404443-557754335203789999999999986981999999779986 Q gi|254780238|r 26 TFNNTRIT-------ITDPHGN-----TIAWSSPKVV-GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAG 92 (129) Q Consensus 26 t~NNTiit-------lTd~~Gn-----~i~~~S~G~~-gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~G 92 (129) -|||+|.- +....|+ +.+|-|.|.+ ||---|.++.|+.-....-+-..+.+.+.+.|+|.-.-.|. T Consensus 124 GfNntf~dav~R~aqI~~d~g~~~~pVvFSWPS~g~l~~Yn~DreS~~~Sr~aLe~~lr~La~~~~~~~I~ilAHSMGt- 202 (377) T COG4782 124 GFNNTFEDAVYRTAQIVHDSGNDGVPVVFSWPSRGSLLGYNYDRESTNYSRPALERLLRYLATDKPVKRIYLLAHSMGT- 202 (377) T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCHH- T ss_conf 2587355778999988763189820699974788732000145556553389999999999747888628999854427- Q ss_pred HHHHHHHHH Q ss_conf 788877876 Q gi|254780238|r 93 RDSALRALR 101 (129) Q Consensus 93 R~~~ik~l~ 101 (129) -.+..+|+ T Consensus 203 -wl~~e~Lr 210 (377) T COG4782 203 -WLLMEALR 210 (377) T ss_pred -HHHHHHHH T ss_conf -99999999 No 57 >TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria. Probab=29.54 E-value=37 Score=15.72 Aligned_cols=57 Identities=14% Similarity=0.098 Sum_probs=31.5 Q ss_pred CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH---HHHCCCCEEEEEEECCCC Q ss_conf 8779999708998899740444355775433520378999999999---998698199999977998 Q gi|254780238|r 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAK---AQNHGMSSLEVKVSGLGA 91 (129) Q Consensus 28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~---~~~~gi~~v~v~ikG~G~ 91 (129) +|.+|.+|+ ++...|+-|.|... .+.+.|.....+.+.++ +.+.|.++|.+. -|..| T Consensus 4 ~N~~In~TN-----iC~~~C~FCaF~r~-~~~~~ay~ls~eei~~~~~ea~~~G~tEv~i~-gG~~P 63 (322) T TIGR03550 4 RNVFIPLTR-----LCRNRCGYCTFRRP-PGELEAALLSPEEVLEILRKGAAAGCTEALFT-FGEKP 63 (322) T ss_pred CCCCCCCCC-----CHHCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEC-CCCCH T ss_conf 721568872-----03176967885168-99988774799999999999997798799964-88680 No 58 >PRK05249 soluble pyridine nucleotide transhydrogenase; Provisional Probab=29.11 E-value=48 Score=15.03 Aligned_cols=42 Identities=12% Similarity=0.066 Sum_probs=20.8 Q ss_pred HHHHHHHHHHHCCCCEEEEEEECCCC-------CHHHHHHHHHHCCCEEE Q ss_conf 99999999998698199999977998-------67888778763693699 Q gi|254780238|r 66 ATDDCSAKAQNHGMSSLEVKVSGLGA-------GRDSALRALRAIGFTIV 108 (129) Q Consensus 66 ~a~~~~~~~~~~gi~~v~v~ikG~G~-------GR~~~ik~l~~~glkI~ 108 (129) .+-.++.....+|. .|.|.-+.... -.+.+.+.|...|++|. T Consensus 187 ig~E~A~~~~~lG~-~Vtiv~~~~~ll~~~d~~~~~~l~~~l~~~gI~i~ 235 (465) T PRK05249 187 IGCEYASIFRGLGV-KVDLINTRDRLLSFLDDEISDALSYHFRNSGVVIR 235 (465) T ss_pred CHHHHHHHHHHHCC-EEEEEECCCCCHHHCCHHHHHHHHHHHHHCCCEEE T ss_conf 17999999996098-77897216600022189999999999998792999 No 59 >TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases. Probab=25.00 E-value=45 Score=15.22 Aligned_cols=58 Identities=17% Similarity=0.294 Sum_probs=36.5 Q ss_pred CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHH---HHHHHCCCCEEEEEEECCCCC Q ss_conf 87799997089988997404443557754335203789999999---999986981999999779986 Q gi|254780238|r 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCS---AKAQNHGMSSLEVKVSGLGAG 92 (129) Q Consensus 28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~---~~~~~~gi~~v~v~ikG~G~G 92 (129) .|.+|.+|+ ++..+|+-|+|... .+.+.|....-+.+. +.+.+.|.+++.+. -|..|- T Consensus 39 ~n~~In~TN-----iC~~~C~fCaF~r~-p~~~~ay~lt~eei~~~~~~a~~~G~~Ei~~~-gG~~Pe 99 (343) T TIGR03551 39 VNRNINFTN-----VCYGGCGFCAFRKR-KGDADAYLLSLEEIAERAAEAWKAGATEVCIQ-GGIHPD 99 (343) T ss_pred CCCCCCHHH-----HHHCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEE-CCCCCC T ss_conf 500625526-----87478976778668-99986600799999999999997699689982-586878 No 60 >TIGR01438 TGR thioredoxin and glutathione reductase; InterPro: IPR006338 This homodimeric, FAD-containing member of the pyridine nucleotide disulphide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-terminal arm of the protein is proposed to allow broad substrate specificity , .; GO: 0016654 oxidoreductase activity acting on NADH or NADPH disulfide as acceptor, 0050660 FAD binding, 0050661 NADP binding, 0006118 electron transport. Probab=24.57 E-value=58 Score=14.52 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=9.6 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEE Q ss_conf 789999999999986981999999 Q gi|254780238|r 63 AQVATDDCSAKAQNHGMSSLEVKV 86 (129) Q Consensus 63 a~~~a~~~~~~~~~~gi~~v~v~i 86 (129) |.=+|-.++=.+-.+|+ .|+|.+ T Consensus 196 asYVALECaGFL~~~g~-dV~V~V 218 (513) T TIGR01438 196 ASYVALECAGFLAALGL-DVTVLV 218 (513) T ss_pred CCHHHHHHHHHHHHCCC-CEEEEE T ss_conf 61423577889863399-649999 No 61 >TIGR02183 GRXA Glutaredoxin, GrxA family; InterPro: IPR011902 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry includes the Escherichia coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase .; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis. Probab=23.55 E-value=61 Score=14.40 Aligned_cols=34 Identities=9% Similarity=0.372 Sum_probs=28.8 Q ss_pred CCCCH--HHHHHHHHHHHHHHCCCCEEEEEEECCCC Q ss_conf 35203--78999999999998698199999977998 Q gi|254780238|r 58 NSPFA--AQVATDDCSAKAQNHGMSSLEVKVSGLGA 91 (129) Q Consensus 58 ~t~~A--a~~~a~~~~~~~~~~gi~~v~v~ikG~G~ 91 (129) +=||. |.++||++....-+..+++|++.--|+.+ T Consensus 9 gC~YCVRA~~LaEkl~~~~~DF~fry~Di~AEGI~K 44 (86) T TIGR02183 9 GCPYCVRAKQLAEKLAEELADFEFRYIDIHAEGISK 44 (86) T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCH T ss_conf 984023368889998864035562058887458871 No 62 >COG4911 Uncharacterized conserved protein [Function unknown] Probab=23.17 E-value=62 Score=14.36 Aligned_cols=51 Identities=18% Similarity=0.203 Sum_probs=34.0 Q ss_pred EECCCEEEEEEECCCCEEEEEECC-CCCEEEEECCCCCCCCCCCCCCCCHHH Q ss_conf 122521899991798779999708-998899740444355775433520378 Q gi|254780238|r 14 KNIVSGRAHVVSTFNNTRITITDP-HGNTIAWSSPKVVGFSGSRKNSPFAAQ 64 (129) Q Consensus 14 ~~i~~GiihI~~t~NNTiitlTd~-~Gn~i~~~S~G~~gfkg~kk~t~~Aa~ 64 (129) +.+..|++---+-.||-.+-+.=. ..|.+.++-.-..||+|+++-++|--+ T Consensus 68 rd~d~glVDFpa~~Ng~~~~lCWK~DE~~imywH~~~EGFrGRrr~~~~e~~ 119 (123) T COG4911 68 RDIDIGLVDFPAIINGKPAFLCWKIDENDIMYWHYMDEGFRGRRRLTGYEDI 119 (123) T ss_pred ECCCCCCCCCHHHHCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHHH T ss_conf 3254201215354379068999831786244332466212366668627656 No 63 >PRK08013 hypothetical protein; Provisional Probab=23.06 E-value=62 Score=14.34 Aligned_cols=10 Identities=40% Similarity=0.418 Sum_probs=5.1 Q ss_pred CHHHHHHHHH Q ss_conf 6788877876 Q gi|254780238|r 92 GRDSALRALR 101 (129) Q Consensus 92 GR~~~ik~l~ 101 (129) |+.+.+|... T Consensus 165 G~~S~vR~~~ 174 (400) T PRK08013 165 GANSWLRNKA 174 (400) T ss_pred CCCCHHHHHC T ss_conf 8761323313 No 64 >PRK01259 ribose-phosphate pyrophosphokinase; Provisional Probab=22.93 E-value=63 Score=14.33 Aligned_cols=59 Identities=8% Similarity=-0.007 Sum_probs=45.0 Q ss_pred HHHHHHHHHHHCCCCEEEEEE-ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCC Q ss_conf 999999999986981999999-7799867888778763693699999638898888688886 Q gi|254780238|r 66 ATDDCSAKAQNHGMSSLEVKV-SGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126 (129) Q Consensus 66 ~a~~~~~~~~~~gi~~v~v~i-kG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~ 126 (129) +...+++.+++.|-+.|.+.. .|.- -..++.-|..+++.=+-++|..|.|-+...++|- T Consensus 223 Tl~~aa~~Lk~~GA~~V~~~~THglf--s~~A~~rl~~s~i~~iv~TnTip~~~~~~~~~kl 282 (309) T PRK01259 223 TLCKAAEALKERGAKSVFAYATHPVL--SGGAAERIANSVLDELVVTDSIPLSEEIKKCPKI 282 (309) T ss_pred HHHHHHHHHHHCCCCEEEEEEECHHC--CHHHHHHHHHCCCCEEEEECCCCCCHHHCCCCCC T ss_conf 59999999975699669999876313--9459999870899889981896686222458981 No 65 >TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.. Probab=22.25 E-value=41 Score=15.44 Aligned_cols=38 Identities=26% Similarity=0.369 Sum_probs=26.5 Q ss_pred HHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCC Q ss_conf 89999999999986981999999779986788877876369 Q gi|254780238|r 64 QVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIG 104 (129) Q Consensus 64 ~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~g 104 (129) -.+...++.-|+.+||+.|= +-.|-+||+..|+|...| T Consensus 33 ~~~~~ALG~iArArGMtqlA---~~tGlsREsLYkALs~~G 70 (91) T TIGR02684 33 ALIAAALGVIARARGMTQLA---KKTGLSRESLYKALSGGG 70 (91) T ss_pred HHHHHHHHHHHHHCCHHHHH---HHHCCCHHHHHHHHCCCC T ss_conf 89999988998651657899---982876788788735688 No 66 >TIGR02530 flg_new flagellar operon protein; InterPro: IPR013367 Proteins in this entry are encoded in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function of this protein is unknown.. Probab=21.93 E-value=64 Score=14.26 Aligned_cols=21 Identities=43% Similarity=0.305 Sum_probs=17.0 Q ss_pred EEEEEEECCCCEEEEEECCCC Q ss_conf 189999179877999970899 Q gi|254780238|r 19 GRAHVVSTFNNTRITITDPHG 39 (129) Q Consensus 19 GiihI~~t~NNTiitlTd~~G 39 (129) -.+-|-+.+|||-||+-|..- T Consensus 78 d~ALVVs~KN~TVITamD~~~ 98 (113) T TIGR02530 78 DAALVVSVKNRTVITAMDKDE 98 (113) T ss_pred CCEEEEECCCCEEEEEECHHH T ss_conf 851477235780542222331 No 67 >KOG4120 consensus Probab=21.62 E-value=25 Score=16.75 Aligned_cols=69 Identities=14% Similarity=0.246 Sum_probs=47.4 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHH-------------HHHCCC---EEEEEEECC Q ss_conf 5577543352037899999999999869819999997799867888778-------------763693---699999638 Q gi|254780238|r 51 GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRA-------------LRAIGF---TIVSICDVT 114 (129) Q Consensus 51 gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~-------------l~~~gl---kI~~I~D~T 114 (129) -||-.+|.+.|......+.+.+-+-+.=...++++|=|++||-.++.++ |..+|| ......|-+ T Consensus 118 ~~k~~kK~drfng~se~e~l~~tvPD~lc~NldiVIVGiNPGl~aayKGHhyagPgNhFWKcL~~sgL~e~q~t~~~Dh~ 197 (426) T KOG4120 118 LKKSVKKSDRFNGNSEDEALLQTVPDYLCENLDIVIVGINPGLTAAYKGHHYAGPGNHFWKCLNKSGLLEAQFTYLNDHD 197 (426) T ss_pred HHHHHHHHHHHCCCCHHHHHHHCCCHHHHCCCCEEEEECCCHHHHHHCCCCCCCCCCHHHHHHHHHCCCHHHHHCCCCCC T ss_conf 16666555430475265788734745663576679994370155552367678984259999877101287750235555 Q ss_pred CCCCC Q ss_conf 89888 Q gi|254780238|r 115 MIAHN 119 (129) Q Consensus 115 ~ip~n 119 (129) -..|+ T Consensus 198 Lpk~G 202 (426) T KOG4120 198 LPKHG 202 (426) T ss_pred CCCCC T ss_conf 50015 No 68 >pfam05990 DUF900 Alpha/beta hydrolase of unknown function (DUF900). This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold. Probab=21.53 E-value=67 Score=14.15 Aligned_cols=78 Identities=17% Similarity=0.227 Sum_probs=44.4 Q ss_pred EEEEECCCCEEEE----------EECCCCCE--EEEECCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE Q ss_conf 9999179877999----------97089988--997404443-5577543352037899999999999869819999997 Q gi|254780238|r 21 AHVVSTFNNTRIT----------ITDPHGNT--IAWSSPKVV-GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS 87 (129) Q Consensus 21 ihI~~t~NNTiit----------lTd~~Gn~--i~~~S~G~~-gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik 87 (129) ++|+ -|||++-. ..+..|.+ ..|-|+|.. +|..-+.+..++....++-+...+.+.+.+.|+|.-. T Consensus 23 vFVH-GyN~~f~~a~~r~aQl~~d~~~~g~~v~FSWPS~g~~~~Y~~D~~sa~~s~~~l~~~L~~l~~~~~~~~I~ilAH 101 (230) T pfam05990 23 VFVH-GYNNSFEDAVYRFAQIAHDLGFPGVPVVFTWPSGASLFGYNYDRESANYSRDALERLLRYLATTPPVKRIHLIAH 101 (230) T ss_pred EEEC-CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEE T ss_conf 9975-899998999999999998469997469996889996134487999999999999999999986669874899985 Q ss_pred CCCCCHHHHHHHHH Q ss_conf 79986788877876 Q gi|254780238|r 88 GLGAGRDSALRALR 101 (129) Q Consensus 88 G~G~GR~~~ik~l~ 101 (129) ..| -..+..+|. T Consensus 102 SMG--~rl~~~aL~ 113 (230) T pfam05990 102 SMG--TWLVMEALR 113 (230) T ss_pred CCH--HHHHHHHHH T ss_conf 817--899999999 No 69 >pfam01019 G_glu_transpept Gamma-glutamyltranspeptidase. Probab=21.50 E-value=67 Score=14.15 Aligned_cols=22 Identities=23% Similarity=0.370 Sum_probs=17.6 Q ss_pred CCCCEEEEEECCCCCEEEEECC Q ss_conf 7987799997089988997404 Q gi|254780238|r 26 TFNNTRITITDPHGNTIAWSSP 47 (129) Q Consensus 26 t~NNTiitlTd~~Gn~i~~~S~ 47 (129) ...-|++++.|..||.++..++ T Consensus 320 ~~~Tth~svvD~~GnaVS~t~S 341 (506) T pfam01019 320 DGGTTHFSVVDRDGNAVSATSS 341 (506) T ss_pred CCCCEEEEEEECCCCEEEEECC T ss_conf 9997899999089899988414 No 70 >smart00300 ChSh Chromo Shadow Domain. Probab=21.40 E-value=67 Score=14.14 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=29.6 Q ss_pred EEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 79999708998899740444355775433520378999999999998 Q gi|254780238|r 30 TRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQN 76 (129) Q Consensus 30 TiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~ 76 (129) -|+-.||.+|...+. +.+|+ ....-..|..+-.++-+.+++ T Consensus 11 ~Iigatd~~G~l~fl-----~kWk~-de~~lvpa~~an~k~Pq~VI~ 51 (61) T smart00300 11 DIVGITKDDGELTFL-----IKWKD-DAASLVPNKEANVKCPQKVIR 51 (61) T ss_pred HHEEEECCCCEEEEE-----EEECC-CCCCEEEHHHHHHHCCHHHHH T ss_conf 903567779979999-----99849-974321389987468699999 Done!