Query gi|254780148|ref|YP_003064561.1| transcription antitermination protein NusG [Candidatus Liberibacter asiaticus str. psy62] Match_columns 177 No_of_seqs 123 out of 1849 Neff 8.0 Searched_HMMs 39220 Date Sun May 22 16:43:09 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780148.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00922 nusG transcription t 100.0 0 0 330.6 16.5 172 5-176 1-193 (193) 2 PRK05609 nusG transcription an 100.0 0 0 323.6 20.3 176 1-176 4-182 (183) 3 PRK09014 rfaH transcriptional 100.0 5.6E-45 0 289.1 17.2 161 3-176 2-162 (162) 4 COG0250 NusG Transcription ant 100.0 9.8E-45 0 287.8 17.5 177 1-177 1-178 (178) 5 TIGR01955 RfaH transcriptional 100.0 9.7E-40 2.5E-44 257.9 5.2 160 5-174 1-162 (162) 6 TIGR01956 NusG_myco NusG famil 100.0 6.7E-29 1.7E-33 193.0 14.9 172 4-175 1-335 (335) 7 smart00738 NGN In Spt5p, this 100.0 7E-29 1.8E-33 192.9 10.0 105 4-108 1-105 (106) 8 PRK08559 nusG transcription an 99.9 1.3E-24 3.2E-29 167.4 14.3 143 3-176 6-148 (153) 9 pfam02357 NusG Transcription t 99.8 4.6E-21 1.2E-25 146.1 8.5 89 3-101 1-90 (90) 10 TIGR00405 L26e_arch ribosomal 99.6 1.4E-14 3.6E-19 107.3 10.5 143 6-174 1-144 (151) 11 KOG1999 consensus 98.1 9.3E-05 2.4E-09 48.5 12.3 52 123-176 408-459 (1024) 12 pfam03439 Spt5-NGN Early trans 97.9 2.5E-05 6.3E-10 51.9 4.9 79 6-106 2-81 (82) 13 TIGR01080 rplX_A_E ribosomal p 96.7 0.0018 4.6E-08 40.8 3.4 53 119-171 38-94 (116) 14 pfam00467 KOW KOW motif. This 96.6 0.0022 5.5E-08 40.3 3.6 30 125-154 1-30 (32) 15 smart00739 KOW KOW (Kyprides, 96.6 0.0021 5.4E-08 40.4 3.3 27 122-148 1-27 (28) 16 PRK01191 rpl24p 50S ribosomal 96.6 0.0065 1.7E-07 37.5 5.7 53 119-171 43-99 (119) 17 KOG1999 consensus 96.1 0.016 4.1E-07 35.1 5.7 133 2-162 164-296 (1024) 18 PTZ00194 60S ribosomal protein 95.7 0.016 4.1E-07 35.1 4.2 37 120-156 44-80 (143) 19 PRK00004 rplX 50S ribosomal pr 95.6 0.026 6.8E-07 33.8 5.1 38 122-159 3-41 (102) 20 PRK12281 rplX 50S ribosomal pr 95.5 0.028 7.2E-07 33.6 4.9 41 120-160 4-45 (77) 21 CHL00141 rpl24 ribosomal prote 95.3 0.037 9.5E-07 32.9 5.0 41 120-160 9-50 (90) 22 COG0198 RplX Ribosomal protein 94.5 0.067 1.7E-06 31.4 4.6 33 122-156 4-36 (104) 23 COG5164 SPT5 Transcription elo 93.9 0.4 1E-05 26.7 7.6 42 123-166 352-393 (607) 24 TIGR01079 rplX_bact ribosomal 91.6 0.38 9.6E-06 26.9 4.8 38 122-159 3-41 (109) 25 PRK06531 yajC preprotein trans 91.3 0.76 1.9E-05 25.1 6.0 49 121-177 35-83 (120) 26 pfam11623 DUF3252 Protein of u 90.2 1.2 3E-05 24.0 6.1 50 123-174 2-53 (53) 27 PRK00409 recombination and DNA 82.9 3.8 9.6E-05 20.9 7.7 48 121-176 633-680 (780) 28 pfam02211 NHase_beta Nitrile h 79.3 3.9 9.8E-05 20.9 4.5 51 97-147 107-167 (220) 29 KOG1708 consensus 77.9 3.1 8E-05 21.4 3.7 34 122-155 72-105 (236) 30 TIGR00739 yajC preprotein tran 75.2 6.6 0.00017 19.5 5.5 49 121-176 36-84 (86) 31 PRK11865 pyruvate ferredoxin o 75.1 3.3 8.5E-05 21.2 3.2 108 5-114 175-291 (298) 32 PRK11864 2-ketoisovalerate fer 75.0 4.7 0.00012 20.3 3.9 108 5-114 173-289 (300) 33 COG1862 YajC Preprotein transl 74.2 7 0.00018 19.3 5.3 45 121-174 42-86 (97) 34 PTZ00065 60S ribosomal protein 73.6 6.1 0.00016 19.7 4.2 36 122-158 7-42 (130) 35 pfam06003 SMN Survival motor n 67.3 10 0.00025 18.4 4.3 33 123-157 69-104 (264) 36 TIGR01069 mutS2 MutS2 family p 66.0 11 0.00027 18.2 4.9 49 121-176 670-718 (834) 37 cd01734 YlxS_C YxlS is a Bacil 66.0 11 0.00027 18.2 6.9 50 125-176 24-77 (83) 38 PRK05585 yajC preprotein trans 64.3 11 0.00029 18.0 6.0 47 121-176 52-98 (107) 39 COG2139 RPL21A Ribosomal prote 61.5 13 0.00033 17.7 6.7 52 122-175 32-93 (98) 40 PRK11760 putative RNA 2'-O-rib 61.3 13 0.00033 17.7 6.3 27 6-32 4-30 (356) 41 TIGR02361 dak_ATP dihydroxyace 60.5 11 0.00027 18.2 3.3 49 78-132 236-286 (627) 42 COG2933 Predicted SAM-dependen 57.2 15 0.00039 17.3 5.7 26 6-31 4-29 (358) 43 pfam02699 YajC Preprotein tran 55.5 16 0.00042 17.1 5.2 48 121-177 36-83 (83) 44 PRK04333 50S ribosomal protein 55.5 16 0.00042 17.1 4.5 34 122-156 3-36 (83) 45 TIGR02249 integrase_gron integ 53.6 7.9 0.0002 19.0 1.7 72 85-156 89-169 (320) 46 cd01737 LSm16_N LSm16 belongs 51.7 19 0.00048 16.7 5.5 51 125-176 5-61 (62) 47 TIGR01941 nqrF NADH:ubiquinone 50.5 10 0.00026 18.3 1.9 19 122-141 261-279 (425) 48 COG1509 KamA Lysine 2,3-aminom 47.6 14 0.00036 17.5 2.2 70 58-131 121-201 (369) 49 pfam02941 FeThRed_A Ferredoxin 42.0 27 0.00068 15.8 3.1 22 125-146 1-36 (67) 50 PRK04306 50S ribosomal protein 41.3 27 0.0007 15.8 6.9 52 122-175 33-94 (97) 51 COG2163 RPL14A Ribosomal prote 39.6 29 0.00074 15.6 4.6 32 122-154 4-35 (125) 52 COG4873 Uncharacterized protei 36.2 33 0.00084 15.3 3.5 42 123-170 24-65 (81) 53 pfam04943 Pox_F11 Poxvirus F11 35.1 34 0.00088 15.2 5.1 107 57-168 26-145 (366) 54 CHL00084 rpl19 ribosomal prote 34.9 35 0.00088 15.1 5.5 45 103-148 4-55 (117) 55 pfam10574 UPF0552 Uncharacteri 34.5 35 0.0009 15.1 6.8 37 120-162 149-188 (224) 56 PRK10724 hypothetical protein; 33.7 36 0.00092 15.0 4.0 35 123-157 81-119 (158) 57 TIGR01200 TIGR01200 Porphyromo 32.9 30 0.00077 15.5 2.0 38 126-163 194-234 (300) 58 pfam08345 YscJ_FliF_C Flagella 32.6 38 0.00096 14.9 3.9 38 94-136 125-162 (162) 59 TIGR02888 spore_YlmC_YmxH spor 32.4 38 0.00097 14.9 3.5 32 145-176 28-67 (76) 60 KOG0107 consensus 31.6 25 0.00063 16.0 1.4 26 60-85 45-70 (195) 61 TIGR01108 oadA oxaloacetate de 31.2 30 0.00076 15.5 1.7 76 19-110 299-390 (616) 62 PRK00092 hypothetical protein; 30.2 42 0.0011 14.7 6.3 49 124-176 93-145 (153) 63 COG4464 CapC Capsular polysacc 29.0 44 0.0011 14.5 3.0 11 63-73 103-113 (254) 64 PRK08384 thiamine biosynthesis 28.4 45 0.0011 14.5 4.7 57 11-89 19-75 (310) 65 PRK09206 pyruvate kinase; Prov 28.3 31 0.00079 15.4 1.4 74 52-138 385-458 (470) 66 pfam01245 Ribosomal_L19 Riboso 28.1 45 0.0012 14.4 4.2 29 120-148 16-51 (113) 67 pfam08223 PaaX_C PaaX-like pro 27.8 46 0.0012 14.4 4.5 38 3-40 6-43 (170) 68 pfam09953 DUF2187 Uncharacteri 27.8 46 0.0012 14.4 3.2 40 124-169 5-44 (57) 69 COG0779 Uncharacterized protei 26.7 48 0.0012 14.3 4.5 45 125-175 98-146 (153) 70 KOG4315 consensus 26.7 29 0.00074 15.6 1.0 50 122-173 393-442 (455) 71 pfam02576 DUF150 Uncharacteriz 25.6 50 0.0013 14.2 4.9 50 125-176 86-139 (141) 72 PRK12289 ribosome-associated G 25.5 51 0.0013 14.2 4.1 11 3-13 18-28 (351) 73 PRK04313 30S ribosomal protein 24.9 52 0.0013 14.1 3.6 39 119-157 168-208 (237) 74 pfam01157 Ribosomal_L21e Ribos 24.6 52 0.0013 14.1 6.7 54 122-175 32-97 (99) 75 pfam11572 DUF3234 Protein of u 23.6 55 0.0014 13.9 2.1 25 3-28 6-30 (102) 76 PRK06488 sulfur carrier protei 23.4 55 0.0014 13.9 3.6 41 93-133 7-60 (65) 77 COG1532 Predicted RNA-binding 23.0 56 0.0014 13.9 3.4 31 125-155 23-55 (57) 78 PRK05464 Na(+)-translocating N 22.2 59 0.0015 13.8 2.1 19 122-141 251-269 (408) 79 pfam03792 PBC PBC domain. The 22.0 20 0.00051 16.6 -0.5 35 81-115 135-169 (192) 80 PTZ00300 pyruvate kinase; Prov 22.0 55 0.0014 14.0 1.7 81 52-141 363-443 (454) 81 pfam04452 Methyltrans_RNA RNA 22.0 59 0.0015 13.8 4.4 13 127-139 175-187 (225) 82 PRK05338 rplS 50S ribosomal pr 21.5 60 0.0015 13.7 5.0 30 119-148 15-51 (112) 83 cd05697 S1_Rrp5_repeat_hs5 S1_ 21.5 61 0.0015 13.7 3.5 26 120-155 42-67 (69) 84 KOG3421 consensus 21.5 61 0.0015 13.7 2.7 33 123-156 7-39 (136) 85 pfam12073 DUF3553 Protein of u 20.9 62 0.0016 13.6 3.9 50 123-176 1-50 (52) 86 pfam09087 Cyc-maltodext_N Cycl 20.9 62 0.0016 13.6 1.9 20 54-73 40-59 (88) 87 KOG3401 consensus 20.7 63 0.0016 13.6 3.6 42 119-162 45-87 (145) No 1 >TIGR00922 nusG transcription termination/antitermination factor NusG; InterPro: IPR001062 Bacterial transcription antitermination protein, nusG, is a component of the transcription complex and interacts with the termination factor Rho and RNA polymerase , . NusG is a bacterial transcriptional elongation factor involved in transcription termination and anti-termination .; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=330.55 Aligned_cols=172 Identities=47% Similarity=0.861 Sum_probs=167.6 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEE-CCEEE---EEECCEECEEEEEEEECCCCCHHHHH Q ss_conf 189995288538999999999997798111432663131012772-02035---66412033099999961865224442 Q gi|254780148|r 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVR-KGRKV---NSERRFFPGYVLIKAVMTDKVYHTIK 80 (177) Q Consensus 5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~-~g~~~---~~~~plfpgYiFv~~~~~~~~~~~i~ 80 (177) ||||||.||+|+||+++|+++++.++++|++.+|.+|.+++...+ +|+++ .+++.+|||||||+++|++++|+.|+ T Consensus 1 WYvvq~~SG~E~~Vk~~l~~~~~~~~~~D~i~~v~vP~E~v~Ei~~~Gk~~~KI~~erK~fPGYvLv~m~l~D~~W~~v~ 80 (193) T TIGR00922 1 WYVVQTYSGYEKKVKKNLEELIELLGMTDVIFEVIVPTEEVVEIKKKGKKKTKIVVERKIFPGYVLVKMDLTDESWHLVK 80 (193) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEECCEEEEEEEEEEEECCCEEEEEEECCHHHHHHHH T ss_conf 94886024783789999999998538886035788212233888547903201466211548648999973868898887 Q ss_pred C----CCEEEEEECCCCCCCCCCH-----------HHHHHHHHHHHHHH--HHHCCCCCCCCCCEEEEECCCCCCCEEEE Q ss_conf 0----3303664327886100258-----------89999997653222--10000123478977999518778971999 Q gi|254780148|r 81 D----TPKVIGFLGTGENPSPVTD-----------SEIEHIMNQVEAAV--QRPVSSVFFEVGERVCVSDGPFASFNGIV 143 (177) Q Consensus 81 ~----t~gV~~~l~~~~~P~~i~~-----------~ei~~l~~~~~~~~--~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v 143 (177) + ||||+||||+++.|.++++ +|++.+++.+.... ..+.....|+.|+.|+|++|||++|.|.| T Consensus 81 n~i~k~PgV~gFvG~~~~~~~~~~~~~lLP~~~~~~Ev~~il~~~~~~~~~~~p~~~~~fE~Ge~Vrv~dGPF~~F~G~V 160 (193) T TIGR00922 81 NEIRKTPGVTGFVGSGGKPKALSEDDFLLPRKLSKEEVKNILNKLEEGKADKKPKVKIDFEVGEQVRVNDGPFANFTGTV 160 (193) T ss_pred HCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCEEE T ss_conf 41764884400066788888777676257806328999999999874303454533432357988898038888851479 Q ss_pred EEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 998288988999998168704788567871233 Q gi|254780148|r 144 KNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 144 ~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) .++|.+++|++|.++||||+|||||++.||||+ T Consensus 161 eev~~Ek~kLkV~VSIFGR~TPVEL~F~QVEK~ 193 (193) T TIGR00922 161 EEVDYEKSKLKVSVSIFGRETPVELEFTQVEKI 193 (193) T ss_pred EEEEHHCCEEEEEEECCCCCCCEEECCCEEECC T ss_conf 888021376999997168787146051112039 No 2 >PRK05609 nusG transcription antitermination protein NusG; Validated Probab=100.00 E-value=0 Score=323.61 Aligned_cols=176 Identities=51% Similarity=0.914 Sum_probs=166.5 Q ss_pred CCCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHH Q ss_conf 98861899952885389999999999977981114326631310127720203566412033099999961865224442 Q gi|254780148|r 1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIK 80 (177) Q Consensus 1 M~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~ 80 (177) |.++|||++|+||+|++|+++|++++...|++++++++|+|.++..++++|+++.+.+|||||||||+++++++.|+.|+ T Consensus 4 m~k~WYvv~tk~~~E~~v~~~L~~~~~~~~l~~~~~~v~~P~~~~~~~~~gk~~~v~~pLFPGYiFv~~~~~~~~~~~Ir 83 (183) T PRK05609 4 MKKRWYVVQTYSGYEKKVKENLEERIKTLGMEDLIGEVLVPTEEVVEVKNGKKKVVERKFFPGYVLVKMVMTDESWHLVR 83 (183) T ss_pred CCCCEEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCEEECCCEEEEEEECCEEEEEEEEEECCEEEEEEECCCHHHHHHH T ss_conf 57868999977892899999999999865841022389767889999958908999998507279999644751277886 Q ss_pred CCCEEEEEECCC---CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE Q ss_conf 033036643278---86100258899999976532221000012347897799951877897199999828898899999 Q gi|254780148|r 81 DTPKVIGFLGTG---ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEV 157 (177) Q Consensus 81 ~t~gV~~~l~~~---~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v 157 (177) +|+||++||+++ .+|.|++++|++.++....++.....+...|++||+|+|++|||+|++|.|.++|.+++|+.|++ T Consensus 84 ~t~GV~~~vg~~~~~~~P~pv~~~ei~~i~~~~~~~~~~~~~~~~~~~Gd~V~I~~GPf~g~~g~v~~~d~~k~Rv~V~l 163 (183) T PRK05609 84 NTPGVTGFVGSHGTRSKPTPLSEKEVERILNRKQEGVEKPKPKVDFEVGEVVRVTDGPFADFNGTVEEVDYEKSKLKVLV 163 (183) T ss_pred CCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE T ss_conf 58981499604887787898887999999876651444565343322798999936789996899999838789999999 Q ss_pred EECCCEEEEEECHHHHEEC Q ss_conf 8168704788567871233 Q gi|254780148|r 158 VIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 158 ~i~Gr~~~v~l~~~~ieki 176 (177) +||||.|+|+++++||||| T Consensus 164 ~i~Gr~~~vel~~~~veki 182 (183) T PRK05609 164 SIFGRETPVELEFSQVEKI 182 (183) T ss_pred EECCCCEEEEECHHHEEEC T ss_conf 8369961798678997966 No 3 >PRK09014 rfaH transcriptional activator RfaH; Provisional Probab=100.00 E-value=5.6e-45 Score=289.07 Aligned_cols=161 Identities=17% Similarity=0.295 Sum_probs=146.3 Q ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCC Q ss_conf 86189995288538999999999997798111432663131012772020356641203309999996186522444203 Q gi|254780148|r 3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDT 82 (177) Q Consensus 3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t 82 (177) ++|||++|+||+|++|+++|++ +++++|+|+.++.+.++|+++.+.+|||||||||++++++..|+.|++| T Consensus 2 k~Wyvv~tk~~~E~ka~~~L~~---------qg~~~~~P~~~~~~~~~~k~~~~~~pLFPgYlFv~~~~~~~~~~~I~~t 72 (162) T PRK09014 2 KSWYLLYCKRGQLQRAQEHLER---------QGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRAT 72 (162) T ss_pred CCEEEEEEECCHHHHHHHHHHH---------CCCEEEEEEEEEEEEECCEEEEEEEECCCCEEEEEECCCCCCEEEEECC T ss_conf 8599999629889999999997---------7997997779999997991899989646717999963576770104068 Q ss_pred CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC Q ss_conf 30366432788610025889999997653222100001234789779995187789719999982889889999981687 Q gi|254780148|r 83 PKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR 162 (177) Q Consensus 83 ~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177) +||++||++|++|++||+++|+.|+...++... ....+++||+|+|++|||+|++|++.++|++ .|+.|++++||| T Consensus 73 ~GV~~~v~~g~~p~~v~~~~I~~l~~~~~~~~~---~~~~~~~Gd~V~I~~GPf~g~~g~v~~~~~~-~R~~vll~~lgr 148 (162) T PRK09014 73 RGVSHFVRFGAQPAIVPSDVIYQLKAYKPDEIV---DPETPKPGDKVIITEGAFEGIQAIYTEPDGE-ARSILLLNLLNK 148 (162) T ss_pred CCCCEEECCCCEECCCCHHHHHHHHHHHHCCCC---CCCCCCCCCEEEEEECCCCCCEEEEEEECCC-CCEEEEEEECCC T ss_conf 990589778999341899999998713003554---3456999999999437999808999988687-878999620399 Q ss_pred EEEEEECHHHHEEC Q ss_conf 04788567871233 Q gi|254780148|r 163 VTPVELAYNQVEKI 176 (177) Q Consensus 163 ~~~v~l~~~~ieki 176 (177) .|+|+++.+||||| T Consensus 149 ~~~v~v~~~~leKi 162 (162) T PRK09014 149 EVKHSVDNTDFRKL 162 (162) T ss_pred CEEEEECHHHEEEC T ss_conf 44899858994859 No 4 >COG0250 NusG Transcription antiterminator [Transcription] Probab=100.00 E-value=9.8e-45 Score=287.77 Aligned_cols=177 Identities=47% Similarity=0.826 Sum_probs=167.2 Q ss_pred CCCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHH Q ss_conf 98861899952885389999999999977981114326631310127720203566412033099999961865224442 Q gi|254780148|r 1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIK 80 (177) Q Consensus 1 M~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~ 80 (177) |.++||+++|++|+|++|+++|+++....++++++.++.+|.+++...++|++..+++++|||||||++++++++|+.|+ T Consensus 1 ~~~~Wyvv~~~sg~E~~V~~~l~~~~~~~~~~~~~~~v~vp~E~v~e~~~~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr 80 (178) T COG0250 1 LMKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKLFPGYVLVEMDMTDEAWHLVR 80 (178) T ss_pred CCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEECEEEEEEECCCEEEEEECCCCCCEEEEEEECCCCEEEEEE T ss_conf 98528999943547999999999999866996302467723278998317558997126788579999982774589986 Q ss_pred CCCEEEEEECCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEE Q ss_conf 033036643278-8610025889999997653222100001234789779995187789719999982889889999981 Q gi|254780148|r 81 DTPKVIGFLGTG-ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVI 159 (177) Q Consensus 81 ~t~gV~~~l~~~-~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i 159 (177) +||||+||+|++ .+|.|++++|+++++...+.....+.....|++||.|+|++|||+|+.|.|.++|.++++++|++++ T Consensus 81 ~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~i 160 (178) T COG0250 81 NTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSI 160 (178) T ss_pred CCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEECCCCCEEEEEEEE T ss_conf 48971798636899870268999998876401224588632467899889991667899517899984767689999997 Q ss_pred CCCEEEEEECHHHHEECC Q ss_conf 687047885678712339 Q gi|254780148|r 160 FGRVTPVELAYNQVEKIV 177 (177) Q Consensus 160 ~Gr~~~v~l~~~~ieki~ 177 (177) |||.|||+++++||+|+- T Consensus 161 fgr~tPVel~~~qVek~~ 178 (178) T COG0250 161 FGRPTPVELEFDQVEKLK 178 (178) T ss_pred ECCCEEEEEECCCEEEEC T ss_conf 177407998601089709 No 5 >TIGR01955 RfaH transcriptional activator RfaH; InterPro: IPR010215 This entry represents the transcriptional activator protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (IPR001062 from INTERPRO) and contains the KOW motif (IPR005824 from INTERPRO) . This protein appears to be limited to the proteobacteria. In Escherichia coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=9.7e-40 Score=257.94 Aligned_cols=160 Identities=25% Similarity=0.441 Sum_probs=143.5 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCC-CCHHHHHCCC Q ss_conf 189995288538999999999997798111432663131012772020356641203309999996186-5224442033 Q gi|254780148|r 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTD-KVYHTIKDTP 83 (177) Q Consensus 5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~-~~~~~i~~t~ 83 (177) ||+||||||+|.+|.++|+. |.++||.|.....+.++|++..+.+||||+|+||.+|... ++|..||+|+ T Consensus 1 WYLlYcKpr~e~RA~~hL~r---------Q~~e~~~P~~~~ek~~rG~~~~v~ePLFP~YLFi~fD~~~G~~~~~irSTR 71 (162) T TIGR01955 1 WYLLYCKPRQEQRAEEHLER---------QDVECYLPMVSVEKIKRGKKQLVEEPLFPNYLFIEFDPEKGDSWTPIRSTR 71 (162) T ss_pred CCCCCCCCHHHHHHHHHHHH---------CCCCCCCHHHHHHHHHHCCHHEECCCCCCCEEEEEECCCCCCCCCEEEEEE T ss_conf 96310081457999998861---------681001005678887620201121578987326770456788121254110 Q ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC Q ss_conf 036643278861002588999999765322210000-1234789779995187789719999982889889999981687 Q gi|254780148|r 84 KVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVS-SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR 162 (177) Q Consensus 84 gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~-~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177) ||+.||++|++|++|+++.|+.|+.........+.. ...|+.||+|+|++|+|+|+||++.+-|++ .|+.++++|+|| T Consensus 72 GVS~~VrfG~~P~~v~~~~I~~l~~~~~~~~~~~~~~P~~~~~G~~V~i~~G~fag~EAIF~~~dG~-~R~~~Llnm~~~ 150 (162) T TIGR01955 72 GVSRIVRFGGHPAPVPDDLIHQLRQKELEASVPAKKTPLLFKKGDKVRITDGSFAGLEAIFLEPDGE-KRSVLLLNMIGK 150 (162) T ss_pred CCEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCEEEECCCCC-HHHHHHHHHHCC T ss_conf 5144460489772236689898640343225583135657789887998628713600354078842-477665466365 Q ss_pred EEEEEECHHHHE Q ss_conf 047885678712 Q gi|254780148|r 163 VTPVELAYNQVE 174 (177) Q Consensus 163 ~~~v~l~~~~ie 174 (177) .++++|+.++++ T Consensus 151 ~~~~~vp~~s~~ 162 (162) T TIGR01955 151 QVKVSVPNTSVE 162 (162) T ss_pred EEEEEEECCCCC T ss_conf 046886145459 No 6 >TIGR01956 NusG_myco NusG family protein; InterPro: IPR010216 This entry represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged from those in bacterial species, and although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system, which includes this family as a member.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=99.96 E-value=6.7e-29 Score=193.05 Aligned_cols=172 Identities=28% Similarity=0.582 Sum_probs=140.6 Q ss_pred CEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEE---------------------------E---CCEE Q ss_conf 618999528853899999999999779811143266313101277---------------------------2---0203 Q gi|254780148|r 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSV---------------------------R---KGRK 53 (177) Q Consensus 4 ~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~---------------------------~---~g~~ 53 (177) |||++.|-+|.|++|.++|++.+...+|++++.++-+-+++.+.. . .||. T Consensus 1 qWYi~t~~~gnE~~Vi~niK~KV~a~~~~~~~~D~k~~K~r~~~~~~f~~~NP~~~~P~s~kN~~~~kW~t~~vdG~~~Y 80 (335) T TIGR01956 1 QWYIVTVINGNEDEVIKNIKDKVRALGFEDKILDLKVLKEREVEEKVFDPKNPSNKAPRSMKNTASIKWETLDVDGEGKY 80 (335) T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECCCCEE T ss_conf 94889840787178999998887542767635525888767899998047888877776533652036999982399715 Q ss_pred ---EEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCC---CCCCCCHHHHHHHHHH------------------ Q ss_conf ---5664120330999999618652244420330366432788---6100258899999976------------------ Q gi|254780148|r 54 ---VNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGE---NPSPVTDSEIEHIMNQ------------------ 109 (177) Q Consensus 54 ---~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~---~P~~i~~~ei~~l~~~------------------ 109 (177) +..+..+||||||++|.+++++|+.||+|+|||||||+.| +|+|||+.+.+.|... T Consensus 81 ~K~kI~e~N~~~GYIyIKM~m~~~aWf~iRNT~~vTG~VGSSGkGAkPiP~s~~~~~NLf~~~~~k~I~~n~~krvlv~~ 160 (335) T TIGR01956 81 KKTKIKEKNKYNGYIYIKMIMTDDAWFLIRNTEGVTGLVGSSGKGAKPIPISDAEAENLFELKMLKGISVNKKKRVLVTQ 160 (335) T ss_pred EEEEEEECCCCCCEEEEEEEEECCEEEEEECCCCCCEEECCCCCCCCCCCCCHHHHHHCCHHHHHCCCCCCCCCCEEEEC T ss_conf 57754422658970799999724714798547894367721588852664771124311106661321136666678705 Q ss_pred --------------HHHH---------------------------HH--------------------------------- Q ss_conf --------------5322---------------------------21--------------------------------- Q gi|254780148|r 110 --------------VEAA---------------------------VQ--------------------------------- 115 (177) Q Consensus 110 --------------~~~~---------------------------~~--------------------------------- 115 (177) ++++ .. T Consensus 161 ~~~~~~e~~~riefldsGnnf~ek~~~il~~~~~k~~~~~~~seS~e~~~~~~~~~~~~~~~~~nvE~D~~~E~~~~~~~ 240 (335) T TIGR01956 161 TAIVEMEENKRIEFLDSGNNFDEKDEYILKEKAAKTKAEKKKSESAEKVDSSNVEEVLVEANKANVEVDENVEDVALVKS 240 (335) T ss_pred CCCCCCHHCCEEEEECCCCCHHHHHHHHHHHHHHCHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECC T ss_conf 74236111040424106786112335555443202134542022101245122666765332012112443114445515 Q ss_pred --------------------------------HHCCCCCCCCCCEEEEECCCCCC--CEEEEEEECCC-CCEEEEEEEEC Q ss_conf --------------------------------00001234789779995187789--71999998288-98899999816 Q gi|254780148|r 116 --------------------------------RPVSSVFFEVGERVCVSDGPFAS--FNGIVKNVDEE-KSRVHVEVVIF 160 (177) Q Consensus 116 --------------------------------~~~~~~~~~~G~~V~I~~Gpf~g--~~g~v~~i~~~-~~r~~V~v~i~ 160 (177) .......|++|..|.|..|+|.| ..|.|.+++.+ +..++|++++| T Consensus 241 ~Geveevti~~~VD~~~~~~~~~~~e~~~e~~~~~~~~~F~VG~~V~I~~~~~~gde~~g~I~~i~~~tk~~a~Veve~l 320 (335) T TIGR01956 241 DGEVEEVTIAEDVDNKVLIEYLEKVELVEEKEKDDNLSKFKVGNLVEILAGSFKGDEIEGKIKKIDQETKDKAIVEVEIL 320 (335) T ss_pred CCCEEEEEECCCCCCCHHHCCCCCEEEEECCCCHHHHCCCCCCCEEEEEECCCCCCCEEEEEEEHHCCCCCEEEEEEEEE T ss_conf 88346776213477101101245154531433011200133587889974675586011332120046775689999972 Q ss_pred CCEEEEEECHHHHEE Q ss_conf 870478856787123 Q gi|254780148|r 161 GRVTPVELAYNQVEK 175 (177) Q Consensus 161 Gr~~~v~l~~~~iek 175 (177) ||.+.|+|++.+|+. T Consensus 321 GK~~~~~l~~~~l~l 335 (335) T TIGR01956 321 GKLVLVDLNFKELKL 335 (335) T ss_pred CEEEEEECCHHHHCC T ss_conf 707896547678079 No 7 >smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p Probab=99.96 E-value=7e-29 Score=192.93 Aligned_cols=105 Identities=39% Similarity=0.779 Sum_probs=102.1 Q ss_pred CEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCC Q ss_conf 61899952885389999999999977981114326631310127720203566412033099999961865224442033 Q gi|254780148|r 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTP 83 (177) Q Consensus 4 ~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~ 83 (177) +||+++|+||+|++|+++|+++....+++++++++|+|+++..+.++|+++.+.+|||||||||+++++++.|+.|++|+ T Consensus 1 nWYvv~t~~g~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~r~gk~~~~~~~lFPGYiFv~~~~~~~~~~~i~~t~ 80 (106) T smart00738 1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIRGTP 80 (106) T ss_pred CEEEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEECCCEEEEEEECCCEEEEEEEECCCEEEEEEECCCCCEEEEECCC T ss_conf 98999998980999999999987665675241799897199999847826999886218589999883877031021699 Q ss_pred EEEEEECCCCCCCCCCHHHHHHHHH Q ss_conf 0366432788610025889999997 Q gi|254780148|r 84 KVIGFLGTGENPSPVTDSEIEHIMN 108 (177) Q Consensus 84 gV~~~l~~~~~P~~i~~~ei~~l~~ 108 (177) ||++||+++++|.|||++||+.|++ T Consensus 81 gV~~fv~~~~~P~~v~~~ei~~il~ 105 (106) T smart00738 81 GVRGFVGGGGKPTPVPDDEIEKILK 105 (106) T ss_pred CCEEECCCCCEEEECCHHHHHHHHC T ss_conf 9629738999853679999999738 No 8 >PRK08559 nusG transcription antitermination protein NusG; Validated Probab=99.93 E-value=1.3e-24 Score=167.44 Aligned_cols=143 Identities=27% Similarity=0.413 Sum_probs=127.3 Q ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCC Q ss_conf 86189995288538999999999997798111432663131012772020356641203309999996186522444203 Q gi|254780148|r 3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDT 82 (177) Q Consensus 3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t 82 (177) .+-|+++|.+|+|+.++..|.++....+++ ++.+++|.. ++|||||+++...+.|+.++++ T Consensus 6 ~~~y~Vkt~~G~E~~Va~~L~~r~~~~~l~--I~SI~~P~~-----------------lkGYV~VEa~~~~~v~~~i~gi 66 (153) T PRK08559 6 SMIYAVRTTAGQERNVALLLASRAEKENLD--IYSILVPPE-----------------LKGYVFVEAESKGAVEEAIRGI 66 (153) T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHCCCC--EEEEECCCC-----------------CCCEEEEEECCHHHHHHHHHCC T ss_conf 818999941773999999999998626996--589985588-----------------8617999956788999998477 Q ss_pred CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC Q ss_conf 30366432788610025889999997653222100001234789779995187789719999982889889999981687 Q gi|254780148|r 83 PKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR 162 (177) Q Consensus 83 ~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177) ++++|++ |.++|.+||++++.. ......+++||.|+|.+|||+|+.|.|.++|.++++++|.+-.+++ T Consensus 67 ~~v~g~~-----p~~v~~~Ei~~~L~~-------~~~~~~i~~G~~V~v~~Gpfkg~~a~V~~Vd~~k~~vtV~l~~~~~ 134 (153) T PRK08559 67 PHVRGVV-----PGEISFEEVEHFLKP-------KPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAV 134 (153) T ss_pred CCEEEEC-----CCCCCHHHHHHHCCC-------CCCCCCCCCCCEEEEECCCCCCCCEEEEEECCCCCEEEEEEEEECC T ss_conf 6468564-----776798999876375-------7652346899999991357699617999981668899999996354 Q ss_pred EEEEEECHHHHEEC Q ss_conf 04788567871233 Q gi|254780148|r 163 VTPVELAYNQVEKI 176 (177) Q Consensus 163 ~~~v~l~~~~ieki 176 (177) .+||++..+||+.+ T Consensus 135 p~pvtv~~d~Vr~i 148 (153) T PRK08559 135 PIPVTVRGDQVRLV 148 (153) T ss_pred EEEEEEECCEEEEE T ss_conf 04689766769987 No 9 >pfam02357 NusG Transcription termination factor nusG. Probab=99.85 E-value=4.6e-21 Score=146.14 Aligned_cols=89 Identities=39% Similarity=0.750 Sum_probs=76.0 Q ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEE-ECCEEEEEECCEECEEEEEEEECCCCCHHHHHC Q ss_conf 8618999528853899999999999779811143266313101277-202035664120330999999618652244420 Q gi|254780148|r 3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSV-RKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKD 81 (177) Q Consensus 3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~-~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~ 81 (177) ++|||++|+||+|++|+++|++ +++++|+|..+..+. ++|+++.+.+|||||||||+++++++ |..|++ T Consensus 1 ~~Wyvl~t~~~~E~~v~~~L~~---------~~~~~~~p~~~~~~~~~~g~~~~~~~plfPGYvFV~~~~~~~-~~~i~~ 70 (90) T pfam02357 1 KKWYVLRTKSGQEKKVAENLER---------QGIESFLPTEEVVEVRKNGKKKKVERPLFPGYVFVRMDLNDE-TWKIRS 70 (90) T ss_pred CEEEEEEEECCHHHHHHHHHHH---------CCCEEEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEECCCC-HHHHHC T ss_conf 9599999969859999999997---------199599667999999729989999997578379999874668-435336 Q ss_pred CCEEEEEECCCCCCCCCCHH Q ss_conf 33036643278861002588 Q gi|254780148|r 82 TPKVIGFLGTGENPSPVTDS 101 (177) Q Consensus 82 t~gV~~~l~~~~~P~~i~~~ 101 (177) |+||++||++|++|.+|||+ T Consensus 71 ~~gv~~~v~~g~~p~~i~d~ 90 (90) T pfam02357 71 TPGVSGFVGFGGKPAPVPDE 90 (90) T ss_pred CCCCCEECCCCCEEEECCCC T ss_conf 98902992889991128999 No 10 >TIGR00405 L26e_arch ribosomal protein L24; InterPro: IPR011590 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 protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.. Probab=99.59 E-value=1.4e-14 Score=107.28 Aligned_cols=143 Identities=26% Similarity=0.389 Sum_probs=113.7 Q ss_pred EEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCEE Q ss_conf 89995288538999999999997798111432663131012772020356641203309999996186522444203303 Q gi|254780148|r 6 YIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKV 85 (177) Q Consensus 6 yvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV 85 (177) |+++|..|||+.++..|..+....+++ ++.++.|. =+.|||+|++.-..|....++..|+| T Consensus 1 fAvkT~vgQEknvA~lma~~ark~~l~--vysILape-----------------sLkGYilVEaetk~D~~~~i~g~Phv 61 (151) T TIGR00405 1 FAVKTSVGQEKNVARLMARKARKENLE--VYSILAPE-----------------SLKGYILVEAETKDDLREAIKGLPHV 61 (151) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHCCCE--EEEEECCC-----------------CCCCCEEEECCCHHHHHHHHHCCCCC T ss_conf 930035604688999998888764880--89997475-----------------34701899706947989897528820 Q ss_pred EEEECCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEE Q ss_conf 6643278-861002588999999765322210000123478977999518778971999998288988999998168704 Q gi|254780148|r 86 IGFLGTG-ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVT 164 (177) Q Consensus 86 ~~~l~~~-~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~ 164 (177) .|++.+. ..-..|+=+|++.|+.- .. .-...+.||.|.|++|||+|=.+.|.++|.++.-+++.+.=--=.. T Consensus 62 rGvV~skteGegeI~feEie~fL~P------kk-iie~I~kGd~VEiisGPFKGErAkViRvDe~keEvtlEL~eAaVPI 134 (151) T TIGR00405 62 RGVVESKTEGEGEIDFEEIERFLTP------KK-IIESIKKGDVVEIISGPFKGERAKVIRVDESKEEVTLELLEAAVPI 134 (151) T ss_pred CEEECCCCCCCEEEEHHHHHHHCCC------CH-HHHCCCCCCEEEEEECCCCCCEEEEEEEECCCCEEEEEEECCCCCC T ss_conf 1155476787313647560200584------21-4531347888899538997644689863078762667632163566 Q ss_pred EEEECHHHHE Q ss_conf 7885678712 Q gi|254780148|r 165 PVELAYNQVE 174 (177) Q Consensus 165 ~v~l~~~~ie 174 (177) ||++.-++|+ T Consensus 135 PvTvk~d~vr 144 (151) T TIGR00405 135 PVTVKADQVR 144 (151) T ss_pred CEEECCCEEE T ss_conf 4452487158 No 11 >KOG1999 consensus Probab=98.15 E-value=9.3e-05 Score=48.49 Aligned_cols=52 Identities=25% Similarity=0.330 Sum_probs=31.9 Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) |.+||.|.|+.|-+.|+.|.|..+|+ ..+++.-+.=+...+++++...|.|. T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg--~~vti~~~~e~l~~pl~~~~~eLrKy 459 (1024) T KOG1999 408 FSPGDAVEVIVGELKGLKGKVESVDG--TIVTIMSKHEDLKGPLEVPASELRKY 459 (1024) T ss_pred CCCCCEEEEEEEEECCCEEEEEECCC--CEEEEEECCCCCCCCCCCCHHHHHHH T ss_conf 37888389962124052568996168--65998523456898611352766542 No 12 >pfam03439 Spt5-NGN Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit. Probab=97.86 E-value=2.5e-05 Score=51.94 Aligned_cols=79 Identities=20% Similarity=0.284 Sum_probs=54.3 Q ss_pred EEEEECCCCHHHHHHHHHHHHHHC-CCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCE Q ss_conf 899952885389999999999977-9811143266313101277202035664120330999999618652244420330 Q gi|254780148|r 6 YIVQVYSNCEKKAVESIGGRLSRS-GLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPK 84 (177) Q Consensus 6 yvv~t~~~~E~~v~~~L~~~~~~~-~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~g 84 (177) |+++|++|+|+.++..|.++.... .-+-.++.+++| +=++|||||++.........++..++ T Consensus 2 ~~Vk~~~G~E~~va~~l~~k~~~~~~~~l~I~Si~~p-----------------~~lkGyIyVEA~~~~~v~~ai~gi~~ 64 (82) T pfam03439 2 WAVKCTAGQEREVAISLMNKAEALKKENLEIYSIFVP-----------------DGLKGYIYVEADRQADVERALEGLPH 64 (82) T ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC-----------------CCCCEEEEEEECCHHHHHHHHHHHHH T ss_conf 7587389819999999999998704688745999954-----------------89846999987988999999960377 Q ss_pred EEEEECCCCCCCCCCHHHHHHH Q ss_conf 3664327886100258899999 Q gi|254780148|r 85 VIGFLGTGENPSPVTDSEIEHI 106 (177) Q Consensus 85 V~~~l~~~~~P~~i~~~ei~~l 106 (177) +.+. .+..+|-+||.++ T Consensus 65 v~~~-----~~~~Vp~~E~~~~ 81 (82) T pfam03439 65 VRGV-----VMGLVPIKEMEHL 81 (82) T ss_pred HHCC-----CCCCCCHHHHHCC T ss_conf 7465-----7752888997510 No 13 >TIGR01080 rplX_A_E ribosomal protein L24; InterPro: IPR005756 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 L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This entry represents the archaeal and eukaryotic branch of these proteins, known as the L26 family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit. Probab=96.65 E-value=0.0018 Score=40.78 Aligned_cols=53 Identities=26% Similarity=0.396 Sum_probs=36.8 Q ss_pred CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE----EECCCEEEEEECHH Q ss_conf 012347897799951877897199999828898899999----81687047885678 Q gi|254780148|r 119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEV----VIFGRVTPVELAYN 171 (177) Q Consensus 119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v----~i~Gr~~~v~l~~~ 171 (177) .+.+...||.|+|+-|.|+|.||.|.++|..+.++.|.= ..=|..+.+.+..+ T Consensus 38 r~lP~RkgD~V~i~RG~fkG~EGkv~~Vd~kr~~i~ve~~t~~k~~G~~V~~~~hpS 94 (116) T TIGR01080 38 RALPVRKGDKVRIVRGDFKGHEGKVLEVDLKRYRIYVEGVTKEKVNGTEVPVPIHPS 94 (116) T ss_pred CCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCEEEECCCCC T ss_conf 537612398789974662587551688730388898813101023885664246766 No 14 >pfam00467 KOW KOW motif. This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. Probab=96.62 E-value=0.0022 Score=40.32 Aligned_cols=30 Identities=47% Similarity=0.712 Sum_probs=25.8 Q ss_pred CCCEEEEECCCCCCCEEEEEEECCCCCEEE Q ss_conf 897799951877897199999828898899 Q gi|254780148|r 125 VGERVCVSDGPFASFNGIVKNVDEEKSRVH 154 (177) Q Consensus 125 ~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~ 154 (177) +||.|+|++|||+|..|.|.+++.++.++. T Consensus 1 ~G~~V~V~~G~~~G~~g~I~~i~~~~~~v~ 30 (32) T pfam00467 1 KGDVVRVISGPFKGKKGKVVEVDDSKARVH 30 (32) T ss_pred CCCEEEEECCCCCCCCCCEEEECCCCEEEE T ss_conf 987899934675687554899607520685 No 15 >smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54. Probab=96.56 E-value=0.0021 Score=40.36 Aligned_cols=27 Identities=48% Similarity=0.642 Sum_probs=24.6 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECC Q ss_conf 347897799951877897199999828 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDE 148 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~ 148 (177) .|++|+.|+|++|||+|..|.|.+++. T Consensus 1 ~~~~G~~V~V~~G~~~g~~g~V~~i~~ 27 (28) T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28) T ss_pred CCCCCCEEEEEECCCCCCCCEEEEECC T ss_conf 940276889972255774113898238 No 16 >PRK01191 rpl24p 50S ribosomal protein L24P; Validated Probab=96.55 E-value=0.0065 Score=37.46 Aligned_cols=53 Identities=28% Similarity=0.308 Sum_probs=39.5 Q ss_pred CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE----EEECCCEEEEEECHH Q ss_conf 01234789779995187789719999982889889999----981687047885678 Q gi|254780148|r 119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE----VVIFGRVTPVELAYN 171 (177) Q Consensus 119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~----v~i~Gr~~~v~l~~~ 171 (177) -......||.|.|+.|.|+|.+|.|.+++..++++.|+ ...=|..+++-++.+ T Consensus 43 Rs~~IrkgD~V~V~rG~~kG~~GkV~~V~~k~~~V~VEgv~~~K~~G~~v~~pIhpS 99 (119) T PRK01191 43 RSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRYRIYVEGVTIKKADGTEVPYPIHPS 99 (119) T ss_pred CCCCEECCCEEEEEECCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCEEEEEECCC T ss_conf 744354699999955277896231899973688999943699847998786422563 No 17 >KOG1999 consensus Probab=96.12 E-value=0.016 Score=35.08 Aligned_cols=133 Identities=20% Similarity=0.267 Sum_probs=83.1 Q ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHC Q ss_conf 88618999528853899999999999779811143266313101277202035664120330999999618652244420 Q gi|254780148|r 2 TPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKD 81 (177) Q Consensus 2 ~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~ 81 (177) .|+=|.|+|+.|.|+.++-.|-++.......+- |.+ -+....+-=+.|||||++.--. +...- T Consensus 164 DP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~------plq--------I~Sv~a~D~lkGyIYIEA~Kqs---hV~~A 226 (1024) T KOG1999 164 DPNLWIVKCKIGREREVAFCLMRKFIELDKTDT------PLQ--------IKSVFAKDHLKGYIYIEADKQS---HVKEA 226 (1024) T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCC------CCE--------EEEEEECCCCCEEEEEEECHHH---HHHHH T ss_conf 987158983366078899999999986024699------722--------7899821555216999821567---89999 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECC Q ss_conf 33036643278861002588999999765322210000123478977999518778971999998288988999998168 Q gi|254780148|r 82 TPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFG 161 (177) Q Consensus 82 t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~G 161 (177) +.||.++-.+ +-..||-.||-.++...++ ...+++|.=|||..|-++|-.|.|..++..+.+ |.|.+.= T Consensus 227 i~gv~niy~~--~~~lVPikEM~dvLkV~K~-------~v~L~~gswVRiKrG~YKgDLAqVd~Vd~~~n~--v~lKlIP 295 (1024) T KOG1999 227 IEGVRNIYAN--RILLVPIKEMPDVLKVVKK-------VVQLSEGSWVRIKRGKYKGDLAQVDDVDENRNR--VRLKLIP 295 (1024) T ss_pred HHHHHHHEEC--CEEEEEHHHHHHHHHHHHH-------HHCCCCCCEEEEECCCCCCCEEEEEEECCCCCE--EEEEEEC T ss_conf 8520332014--1798754574445413344-------321376625887545015630125664256777--8999832 Q ss_pred C Q ss_conf 7 Q gi|254780148|r 162 R 162 (177) Q Consensus 162 r 162 (177) | T Consensus 296 R 296 (1024) T KOG1999 296 R 296 (1024) T ss_pred C T ss_conf 1 No 18 >PTZ00194 60S ribosomal protein L26; Provisional Probab=95.67 E-value=0.016 Score=35.11 Aligned_cols=37 Identities=22% Similarity=0.302 Sum_probs=31.2 Q ss_pred CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE Q ss_conf 1234789779995187789719999982889889999 Q gi|254780148|r 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156 (177) Q Consensus 120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~ 156 (177) ..++..||.|.|..|.|+|.+|.|.+++..+.++.|. T Consensus 44 s~pIRkgDeV~V~RG~fkG~eGKV~~V~~kk~~I~VE 80 (143) T PTZ00194 44 AMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHID 80 (143) T ss_pred CCCCCCCCEEEEEECCCCCCCCEEEEEEEEEEEEEEE T ss_conf 1001159999998555368776599999500099995 No 19 >PRK00004 rplX 50S ribosomal protein L24; Reviewed Probab=95.62 E-value=0.026 Score=33.80 Aligned_cols=38 Identities=34% Similarity=0.311 Sum_probs=33.4 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEE Q ss_conf 34789779995187789719999982889889999-981 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVI 159 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i 159 (177) .+..||.|.|++|..+|-.|.|.+++.+++++.|. +++ T Consensus 3 kikkGD~V~VisGkdKGk~G~V~~v~~~~~~viVeGvN~ 41 (102) T PRK00004 3 KIKKGDTVIVIAGKDKGKQGKVLKVLPKKDKVIVEGVNI 41 (102) T ss_pred CEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEE T ss_conf 206799999927799997368999998799999977478 No 20 >PRK12281 rplX 50S ribosomal protein L24; Reviewed Probab=95.52 E-value=0.028 Score=33.65 Aligned_cols=41 Identities=34% Similarity=0.279 Sum_probs=34.6 Q ss_pred CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEEC Q ss_conf 1234789779995187789719999982889889999-9816 Q gi|254780148|r 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVIF 160 (177) Q Consensus 120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i~ 160 (177) ...++.||.|.|++|.-+|-.|.|.+++++++++.|. +++- T Consensus 4 K~kIkkGD~V~VisGkdKGk~G~Vl~v~~~~~rviVeGvN~~ 45 (77) T PRK12281 4 KLHVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVNIR 45 (77) T ss_pred EEEEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEEE T ss_conf 048758999999466789972789999877999999486379 No 21 >CHL00141 rpl24 ribosomal protein L24; Validated Probab=95.29 E-value=0.037 Score=32.91 Aligned_cols=41 Identities=22% Similarity=0.220 Sum_probs=34.7 Q ss_pred CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEEC Q ss_conf 1234789779995187789719999982889889999-9816 Q gi|254780148|r 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVIF 160 (177) Q Consensus 120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i~ 160 (177) ...+..||.|.|++|.-+|-.|.|.+++..++++.|. +++- T Consensus 9 K~kIkkGD~V~VisGkdKGk~G~Vl~v~~~~~~viVeGvN~~ 50 (90) T CHL00141 9 KMHVKKGDTVQVISGKDKGKIGEVLKIIRKSNKVIVKGINIK 50 (90) T ss_pred CEEEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEEE T ss_conf 406708999999166789973579999867999999795888 No 22 >COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis] Probab=94.53 E-value=0.067 Score=31.38 Aligned_cols=33 Identities=33% Similarity=0.251 Sum_probs=27.8 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE Q ss_conf 34789779995187789719999982889889999 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~ 156 (177) .+..||.|.|++|.++|-+|.|.++++.. +.|. T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104) T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104) T ss_pred CEECCCEEEEEECCCCCCCEEEEEEECCE--EEEE T ss_conf 24369999998668899614899991573--8997 No 23 >COG5164 SPT5 Transcription elongation factor [Transcription] Probab=93.94 E-value=0.4 Score=26.74 Aligned_cols=42 Identities=24% Similarity=0.401 Sum_probs=32.5 Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEE Q ss_conf 47897799951877897199999828898899999816870478 Q gi|254780148|r 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPV 166 (177) Q Consensus 123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v 166 (177) -..|..|+|.+||++|+-|+|+.++++ .++|.++-=.+.+.+ T Consensus 352 ~aigktVrIr~g~yKG~lGVVKdv~~~--~arVeLhs~nK~VTI 393 (607) T COG5164 352 PAIGKTVRIRCGEYKGHLGVVKDVDRN--IARVELHSNNKFVTI 393 (607) T ss_pred CCCCCEEEEEECCCCCCCCEEEECCCC--EEEEEEECCCCEEEE T ss_conf 345846899623645544246643686--489997058816986 No 24 >TIGR01079 rplX_bact ribosomal protein L24; InterPro: IPR003256 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 L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This domain is found in L24 and L26 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=91.63 E-value=0.38 Score=26.91 Aligned_cols=38 Identities=32% Similarity=0.315 Sum_probs=32.8 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEE Q ss_conf 34789779995187789719999982889889999-981 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVI 159 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i 159 (177) .++.||+|.|++|-=+|-.|.|.++.+++++|.|. +++ T Consensus 3 kiKKGD~V~VIsGKdKGK~GkVl~v~~~~~kViVEGvN~ 41 (109) T TIGR01079 3 KIKKGDTVVVISGKDKGKRGKVLKVLPKKNKVIVEGVNM 41 (109) T ss_pred EEEECCEEEEEECCCCCCEEEEEEEECCCCEEEEECCCE T ss_conf 133098888886889887238999525788388831533 No 25 >PRK06531 yajC preprotein translocase subunit YajC; Validated Probab=91.27 E-value=0.76 Score=25.09 Aligned_cols=49 Identities=22% Similarity=0.447 Sum_probs=32.5 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEECC Q ss_conf 234789779995187789719999982889889999981687047885678712339 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki~ 177 (177) ..+++||.|. +.| |+.|.|.++|.++.++.+.++ | +-+.++..-|.+|+ T Consensus 35 ~~L~kGdeVv-TiG---Gl~G~V~~Vd~e~~tV~Ld~~--G--v~l~f~r~AI~~Vv 83 (120) T PRK06531 35 NAIQKGDEVV-TIG---GLFGTVDEVDTEAKKIVLDVD--G--VYLTFELSAIKRVV 83 (120) T ss_pred HHCCCCCEEE-ECC---CCEEEEEEEECCCCEEEEEEC--C--EEEEEEHHHHHHHC T ss_conf 7257999899-789---828999999278988999828--9--79999867765225 No 26 >pfam11623 DUF3252 Protein of unknown function (DUF3252). This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. Probab=90.18 E-value=1.2 Score=23.98 Aligned_cols=50 Identities=18% Similarity=0.191 Sum_probs=38.5 Q ss_pred CCCCCEEEEEC--CCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHE Q ss_conf 47897799951--87789719999982889889999981687047885678712 Q gi|254780148|r 123 FEVGERVCVSD--GPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVE 174 (177) Q Consensus 123 ~~~G~~V~I~~--Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ie 174 (177) +-||..|+|.+ -++-|++|.|.++.+ ++|-|+++=-.=.-.|++.++++| T Consensus 2 ilPG~~V~V~n~~~~Y~gy~G~VQRvsd--~kaaVLFeggnWdKlvTf~l~~Le 53 (53) T pfam11623 2 ILPGMTVKVKNPNDIYYGYEGQVQRVSD--GKAAVLFEGGNWDKLVTFRLSELE 53 (53) T ss_pred CCCCCEEEEECCCCCCHHCEEEEEEECC--CEEEEEECCCCCEEEEEEEHHHCC T ss_conf 2599789986887760020489999419--908999569972178998755678 No 27 >PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed Probab=82.92 E-value=3.8 Score=20.92 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=34.8 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 23478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) ..+++||.|+|.+- |..|.|.++.+ ++.+.|.+.. ..+.++.++|+++ T Consensus 633 ~~~~~Gd~V~v~~~---~~~G~V~~i~~-~~~~~V~~g~----~k~~v~~~~l~~~ 680 (780) T PRK00409 633 EELKVGDEVKYLSL---GQKGEVLSIPD-NKEAIVQAGI----MKMKVPLSDLEKI 680 (780) T ss_pred CCCCCCCEEEECCC---CCEEEEEEECC-CCEEEEEECC----EEEEEEHHHCEEC T ss_conf 79999998998579---96799999869-9819999797----6999779993137 No 28 >pfam02211 NHase_beta Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit. Probab=79.35 E-value=3.9 Score=20.86 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=33.9 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECC----------CCCCCEEEEEEEC Q ss_conf 02588999999765322210000123478977999518----------7789719999982 Q gi|254780148|r 97 PVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDG----------PFASFNGIVKNVD 147 (177) Q Consensus 97 ~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~G----------pf~g~~g~v~~i~ 147 (177) .++.+.+...+..-............|++||+|++.+- ...|..|+|..+. T Consensus 107 ~~~a~~v~~~l~~G~p~~R~~~~~p~F~vGd~Vrv~~~~~~gHtRlP~Y~rgk~G~I~~~~ 167 (220) T pfam02211 107 VLPADQVAAVLARGGPADRPADAPPRFAVGDRVRTRNINPNGHTRLPRYVRGKTGTIVRVH 167 (220) T ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCEEEEEEEE T ss_conf 5788899999746898778899999779999899822799975235367678745899884 No 29 >KOG1708 consensus Probab=77.92 E-value=3.1 Score=21.39 Aligned_cols=34 Identities=32% Similarity=0.261 Sum_probs=24.4 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE Q ss_conf 3478977999518778971999998288988999 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV 155 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V 155 (177) .|..||+|.|+.|-=+|-.|.|..+-.+++-+.| T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV 105 (236) T KOG1708 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVV 105 (236) T ss_pred EEECCCEEEEEECCCCCCCCEEEEEEECCCEEEE T ss_conf 6834987999751567743138998604764897 No 30 >TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849 This entry describes proteins of unknown function.. Probab=75.23 E-value=6.6 Score=19.46 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=32.8 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 23478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) ..+++||+|...+ |..|.|.++..+.+.+.+.++ -.|.+++.-+-|..+ T Consensus 36 ~~L~KGd~V~T~g----Gi~G~V~~i~e~~~~i~i~~~---~~t~~~~~K~aI~~~ 84 (86) T TIGR00739 36 ESLKKGDKVLTIG----GIIGTVTKIAENTNNIVIELN---DNTEITFSKNAIVEV 84 (86) T ss_pred HCCCCCCEEEECC----CEEEEEEEEECCCCEEEEEEC---CCCEEEEEHHHHHHH T ss_conf 5279977899838----838999885238867899987---994899860342422 No 31 >PRK11865 pyruvate ferredoxin oxidoreductase subunit beta; Provisional Probab=75.10 E-value=3.3 Score=21.23 Aligned_cols=108 Identities=10% Similarity=0.153 Sum_probs=65.8 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEE-----EEEECCEECEEEEEEEE--CCCC--C Q ss_conf 1899952885389999999999977981114326631310127720203-----56641203309999996--1865--2 Q gi|254780148|r 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRK-----VNSERRFFPGYVLIKAV--MTDK--V 75 (177) Q Consensus 5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~-----~~~~~plfpgYiFv~~~--~~~~--~ 75 (177) =||.++.++.-....+.+++.++..|+. ..++|.||..-|.....+. .-++.-+||=|=+-.-. .+.. . T Consensus 175 ~YVA~~s~~~~~~l~~~i~kA~~~~G~s--~i~v~sPCp~gw~~~~~~t~~~~klAVetg~wpLye~~~g~~~~~~~p~~ 252 (298) T PRK11865 175 PYVATASIGYPEDFMKKVKKAAEVDGPA--YIQVLQPCPTGWGFPPEKTIEIGRLAVETGYWPLFEIENGKFNISYEPLH 252 (298) T ss_pred CEEEEEECCCHHHHHHHHHHHHHCCCCE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCC T ss_conf 8899982579999999999998089987--99997889566887835799999999980980489950882355678866 Q ss_pred HHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 244420330366432788610025889999997653222 Q gi|254780148|r 76 YHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAV 114 (177) Q Consensus 76 ~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~ 114 (177) ....+...-|..||...++..-+.+++++.|...++..- T Consensus 253 ~~~~~~k~pv~eyL~~q~Rf~~L~~e~~~~lq~~vD~~w 291 (298) T PRK11865 253 CLDIETRKPIEEYLKVQGRFKHLTPEDIEELQKYIDAMW 291 (298) T ss_pred CCCCCCCCCHHHHHHHCCCHHCCCHHHHHHHHHHHHHHH T ss_conf 444678879999987360420189989999999999999 No 32 >PRK11864 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional Probab=75.04 E-value=4.7 Score=20.35 Aligned_cols=108 Identities=10% Similarity=0.125 Sum_probs=66.9 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEE-----EEEECCEECEEEEEE--EECCCCCH- Q ss_conf 1899952885389999999999977981114326631310127720203-----566412033099999--96186522- Q gi|254780148|r 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRK-----VNSERRFFPGYVLIK--AVMTDKVY- 76 (177) Q Consensus 5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~-----~~~~~plfpgYiFv~--~~~~~~~~- 76 (177) =||.++.+++-....+.+++..+..|.. ..++|.||-.-|+.....- .-++.-+||=|=+.. +..+.... T Consensus 173 ~YVA~~~~a~~~~l~~~i~kA~~~~G~s--~i~v~spCp~gw~~~~~~t~~~~klAVesg~wpLye~~~g~~~~~~~~~~ 250 (300) T PRK11864 173 PYVATASIAYPEDFIRKLKKAAEIPGFK--FIHLLAPCPPGWRFDPAKTIEIARLAVETGAWPLFEYENGKFKLNPPSTT 250 (300) T ss_pred CEEEEEECCCHHHHHHHHHHHHCCCCCE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCCC T ss_conf 8799985569999999999997189987--99997889565886813689999999980995379977897650588755 Q ss_pred -HHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf -44420330366432788610025889999997653222 Q gi|254780148|r 77 -HTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAV 114 (177) Q Consensus 77 -~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~ 114 (177) ...+.-.-|..+|...++...+.+++++.+....+..- T Consensus 251 ~~~~~~~~pv~eyl~~q~Rf~hL~~e~~~~~q~~vd~~w 289 (300) T PRK11864 251 LADKKKRKPVEEYLKLQGRFKHLTEEDIKALQEEIEEEW 289 (300) T ss_pred CCCCCCCCCHHHHHHHCCCCHHCCHHHHHHHHHHHHHHH T ss_conf 457778879999976274621049999999999999999 No 33 >COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion] Probab=74.18 E-value=7 Score=19.30 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=30.0 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHE Q ss_conf 234789779995187789719999982889889999981687047885678712 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVE 174 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ie 174 (177) ..+++||+|. +.| |+.|.|.+++.+. +.|.++ ..|.+.+..+.|- T Consensus 42 ~sL~kGD~Vv-T~g---Gi~G~V~~v~d~~--v~I~l~---~~~~i~~~k~aI~ 86 (97) T COG1862 42 NSLKKGDEVV-TIG---GIVGTVTKVGDDT--VEIELG---DGTKIKFEKEAIA 86 (97) T ss_pred HHCCCCCEEE-ECC---CEEEEEEEEECCC--EEEEEC---CCEEEEEEHHHHH T ss_conf 7456899899-758---7399999970681--899978---9869999879988 No 34 >PTZ00065 60S ribosomal protein L14; Provisional Probab=73.61 E-value=6.1 Score=19.66 Aligned_cols=36 Identities=25% Similarity=0.306 Sum_probs=28.7 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEE Q ss_conf 3478977999518778971999998288988999998 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVV 158 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~ 158 (177) ..++|--|.|..||.+|-.+.|..|- |..|+.|.=. T Consensus 7 fVEvGRVv~i~~Gp~~GKL~~IVDII-D~nRvLVDGP 42 (130) T PTZ00065 7 FVEPGRLCLITYGPDAGKLCFIVDIV-TPTRVLVDGA 42 (130) T ss_pred CEECCEEEEEEECCCCCCEEEEEEEE-CCCEEEECCC T ss_conf 03426599994078889789999986-1764674087 No 35 >pfam06003 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs. Probab=67.31 E-value=10 Score=18.38 Aligned_cols=33 Identities=18% Similarity=0.441 Sum_probs=13.3 Q ss_pred CCCCCEEEEE---CCCCCCCEEEEEEECCCCCEEEEEE Q ss_conf 4789779995---1877897199999828898899999 Q gi|254780148|r 123 FEVGERVCVS---DGPFASFNGIVKNVDEEKSRVHVEV 157 (177) Q Consensus 123 ~~~G~~V~I~---~Gpf~g~~g~v~~i~~~~~r~~V~v 157 (177) +++||..+-+ || ..++|.|..||..++.++|.. T Consensus 69 wkVGD~C~A~yseDG--~~YeAtI~SId~k~gtCvV~Y 104 (264) T pfam06003 69 WQVGDSCNAVWSEDG--NLYTATITSIDQKRGTCVVFY 104 (264) T ss_pred EECCCEEEEEECCCC--CCCEEEEEEECCCCCCEEEEE T ss_conf 111885676652578--520136777526787068998 No 36 >TIGR01069 mutS2 MutS2 family protein; InterPro: IPR005747 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure , and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts . This entry represents a family of MutS proteins.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0045005 maintenance of fidelity during DNA-dependent DNA replication. Probab=66.04 E-value=11 Score=18.23 Aligned_cols=49 Identities=22% Similarity=0.360 Sum_probs=35.3 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 23478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) ..|++||+++|. +.|..|.|.++......+.|.+.+|- +.++..+|+++ T Consensus 670 ~~Fk~Gd~~~~~---~~g~kg~~~~~~~~g~~~~V~~g~~~----m~v~~~~l~~~ 718 (834) T TIGR01069 670 ADFKVGDKVKVE---SFGQKGKIVEIKGKGNKWNVTVGLLR----MKVKESELEKI 718 (834) T ss_pred CCCCCCCCCEEE---ECCCEEEEEEEECCCCEEEEEEEEEE----EEECHHHHHHH T ss_conf 787357401112---15864799998056557776652104----43137888874 No 37 >cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3. Probab=66.00 E-value=11 Score=18.22 Aligned_cols=50 Identities=34% Similarity=0.498 Sum_probs=36.7 Q ss_pred CCCEEEEE-CCCCCC---CEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 89779995-187789---71999998288988999998168704788567871233 Q gi|254780148|r 125 VGERVCVS-DGPFAS---FNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 125 ~G~~V~I~-~Gpf~g---~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) .|..|.|. ..|..| +.|.+.+++. +.+.+.++.-++...+++++++|+|. T Consensus 24 ~G~~v~v~l~~~~~g~k~f~G~L~~v~~--~~i~l~~~~~~~~~~~~i~~~~I~kA 77 (83) T cd01734 24 VGKYVHVKLYQPIDGQKEFEGTLLGVDD--DTVTLEVDIKTRGKTVEIPLDKIAKA 77 (83) T ss_pred CCCEEEEEEECCCCCCEEEEEEEEEEEC--CEEEEEEECCCCCEEEEEEHHHHCEE T ss_conf 7987999991501891899999998839--99999995277878999746982147 No 38 >PRK05585 yajC preprotein translocase subunit YajC; Validated Probab=64.32 E-value=11 Score=18.03 Aligned_cols=47 Identities=19% Similarity=0.331 Sum_probs=30.1 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 23478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) ..+++||+|. +.| |+.|.|.+++++ .+.+ ++- ..+.+.+.-.-|-.| T Consensus 52 ~~L~~Gd~Vv-T~g---Gi~G~I~~v~d~--~v~l--eia-~gv~i~~~r~aI~~V 98 (107) T PRK05585 52 SSLAKGDEVV-TNG---GIIGKVTKVSED--FVII--ELN-DDTEIKIQKSAIAAV 98 (107) T ss_pred HHCCCCCEEE-ECC---CCEEEEEEEECC--EEEE--EEC-CCCEEEEEHHHHHHH T ss_conf 8458999999-899---858999999799--8999--988-995899995896643 No 39 >COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis] Probab=61.45 E-value=13 Score=17.71 Aligned_cols=52 Identities=21% Similarity=0.286 Sum_probs=36.6 Q ss_pred CCCCCCEEEEECCC----------CCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE Q ss_conf 34789779995187----------7897199999828898899999816870478856787123 Q gi|254780148|r 122 FFEVGERVCVSDGP----------FASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175 (177) Q Consensus 122 ~~~~G~~V~I~~Gp----------f~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek 175 (177) .|++||.|.|.--| |.|..|+|....+ .-..|.+..-++.-.+-+..+.|++ T Consensus 32 ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g--~ay~V~v~~G~k~K~liv~peHLk~ 93 (98) T COG2139 32 EYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRG--RAYKVEVYDGNKEKTLIVRPEHLKP 93 (98) T ss_pred HCCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEECCC--CEEEEEEECCCCEEEEEECHHHCCC T ss_conf 6079987999847620269877530476307984148--7799999618945899867788544 No 40 >PRK11760 putative RNA 2'-O-ribose methyltransferase; Provisional Probab=61.32 E-value=13 Score=17.70 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=22.7 Q ss_pred EEEEECCCCHHHHHHHHHHHHHHCCCH Q ss_conf 899952885389999999999977981 Q gi|254780148|r 6 YIVQVYSNCEKKAVESIGGRLSRSGLD 32 (177) Q Consensus 6 yvv~t~~~~E~~v~~~L~~~~~~~~~~ 32 (177) .+++|+||.|+.++.-|..+.+..++. T Consensus 4 lllyCRpGFE~e~AaEi~~~aa~~gv~ 30 (356) T PRK11760 4 LLLYCRPGFEKECAAEITDKAAELGVF 30 (356) T ss_pred EEEEECCCCCHHHHHHHHHHHHHCCCC T ss_conf 534417986389999999999963887 No 41 >TIGR02361 dak_ATP dihydroxyacetone kinase; InterPro: IPR012734 This family consists of examples of the single chain form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (2.7.1.29 from EC) as the phosphate donor, rather than a phosphoprotein as in Escherichia coli. This form has separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii. The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses . ; GO: 0004371 glycerone kinase activity, 0005524 ATP binding. Probab=60.45 E-value=11 Score=18.23 Aligned_cols=49 Identities=22% Similarity=0.401 Sum_probs=33.9 Q ss_pred HHHCCCEEEEEECCCCCCCC-CCHHHHHH-HHHHHHHHHHHHCCCCCCCCCCEEEEE Q ss_conf 44203303664327886100-25889999-997653222100001234789779995 Q gi|254780148|r 78 TIKDTPKVIGFLGTGENPSP-VTDSEIEH-IMNQVEAAVQRPVSSVFFEVGERVCVS 132 (177) Q Consensus 78 ~i~~t~gV~~~l~~~~~P~~-i~~~ei~~-l~~~~~~~~~~~~~~~~~~~G~~V~I~ 132 (177) -|++=||+.++ .|+| + ++.|.+ |+..+-+......+.+.|.+||+|.+. T Consensus 236 GIHnEpG~~r~-----~~~pS~-~~lv~~~mLk~lLd~~D~dR~yV~~~~~~~vVLl 286 (627) T TIGR02361 236 GIHNEPGVKRI-----SPIPSI-EDLVVKLMLKKLLDESDEDRSYVKFEEGDEVVLL 286 (627) T ss_pred CCCCCCCCEEE-----CCCCCH-HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEE T ss_conf 86476664532-----466887-8999997557655787865531021799817998 No 42 >COG2933 Predicted SAM-dependent methyltransferase [General function prediction only] Probab=57.20 E-value=15 Score=17.27 Aligned_cols=26 Identities=12% Similarity=0.172 Sum_probs=21.1 Q ss_pred EEEEECCCCHHHHHHHHHHHHHHCCC Q ss_conf 89995288538999999999997798 Q gi|254780148|r 6 YIVQVYSNCEKKAVESIGGRLSRSGL 31 (177) Q Consensus 6 yvv~t~~~~E~~v~~~L~~~~~~~~~ 31 (177) .+++|+||.|+.++..|.++.+..++ T Consensus 4 l~lyCRpGFEkE~aAEi~d~Aa~l~I 29 (358) T COG2933 4 LALYCRPGFEKECAAEITDKAAQLEI 29 (358) T ss_pred EEEEECCCCCHHHHHHHHHHHHHHCC T ss_conf 12331588747888999876665246 No 43 >pfam02699 YajC Preprotein translocase subunit. See. Probab=55.51 E-value=16 Score=17.10 Aligned_cols=48 Identities=21% Similarity=0.404 Sum_probs=31.5 Q ss_pred CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEECC Q ss_conf 234789779995187789719999982889889999981687047885678712339 Q gi|254780148|r 121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177 (177) Q Consensus 121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki~ 177 (177) ..+++||+|. +.| |+.|.|.++++ +.+.+. + +..+.++++-.-|-+++ T Consensus 36 ~~L~~Gd~Vv-T~g---Gi~G~V~~i~~--~~v~le--i-~~gv~i~v~r~aI~~v~ 83 (83) T pfam02699 36 SSLKKGDEVV-TIG---GIHGKIVKVDD--DTVVLE--I-ADGVKVKVDKSAIARVL 83 (83) T ss_pred HHCCCCCEEE-ECC---CEEEEEEEEEC--CEEEEE--E-CCCCEEEEEHHHHHHHC T ss_conf 8578999999-899---71999999979--999999--8-89939999969867449 No 44 >PRK04333 50S ribosomal protein L14e; Validated Probab=55.47 E-value=16 Score=17.10 Aligned_cols=34 Identities=24% Similarity=0.245 Sum_probs=27.1 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE Q ss_conf 34789779995187789719999982889889999 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~ 156 (177) ..++|--+.+..||.+|-.+.|..+- |++|+.|. T Consensus 3 ~VEvGRV~~i~~G~~aGkl~vIVDiI-D~nrvLVd 36 (83) T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDII-DKNFVLVT 36 (83) T ss_pred CEEECEEEEEECCCCCCCEEEEEEEE-CCCEEEEE T ss_conf 56703499993177679789999997-38879988 No 45 >TIGR02249 integrase_gron integron integrase; InterPro: IPR011946 Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration. Probab=53.59 E-value=7.9 Score=18.97 Aligned_cols=72 Identities=18% Similarity=0.168 Sum_probs=53.2 Q ss_pred EEEEECCC---CCCCCCCHHHHHHHHHHHH-HHHHHHC-----CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE Q ss_conf 36643278---8610025889999997653-2221000-----0123478977999518778971999998288988999 Q gi|254780148|r 85 VIGFLGTG---ENPSPVTDSEIEHIMNQVE-AAVQRPV-----SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV 155 (177) Q Consensus 85 V~~~l~~~---~~P~~i~~~ei~~l~~~~~-~~~~~~~-----~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V 155 (177) ..+|+++. .-|..++.+|+.+++..++ ....... +..++-++-+.||.|=.|.-.+-.|-.-++.|+|++. T Consensus 89 ~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~y~L~a~LLYGsGMRlmE~LRLRikDiDF~~~~I~vr~GKG~KdR~v~ 168 (320) T TIGR02249 89 MENFVRAKRPRKLPVVLTREEVARLLEHLEEGKYRLIAKLLYGSGMRLMECLRLRIKDIDFDYGEIRVRDGKGGKDRVVT 168 (320) T ss_pred HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCEEEECCCEEEEEECCCCCCCCCC T ss_conf 22220678887377335988999998425786131122231255158988875101103433766899736689886126 Q ss_pred E Q ss_conf 9 Q gi|254780148|r 156 E 156 (177) Q Consensus 156 ~ 156 (177) + T Consensus 169 L 169 (320) T TIGR02249 169 L 169 (320) T ss_pred C T ss_conf 8 No 46 >cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function. Probab=51.72 E-value=19 Score=16.73 Aligned_cols=51 Identities=22% Similarity=0.377 Sum_probs=37.2 Q ss_pred CCCEEEEECCCCCC-CEEEEEEECCCCCEEEEEEEECCC-----EEEEEECHHHHEEC Q ss_conf 89779995187789-719999982889889999981687-----04788567871233 Q gi|254780148|r 125 VGERVCVSDGPFAS-FNGIVKNVDEEKSRVHVEVVIFGR-----VTPVELAYNQVEKI 176 (177) Q Consensus 125 ~G~~V~I~~Gpf~g-~~g~v~~i~~~~~r~~V~v~i~Gr-----~~~v~l~~~~ieki 176 (177) .|..|-|..||=.| |.|.|+.++.... ...+-.-|+- ...|++...+|+.+ T Consensus 5 iG~~VSI~C~~~lGv~QG~I~~v~~~~q-tItl~~~f~ngi~~~~~EVtl~a~dI~~L 61 (62) T cd01737 5 LGSIVSINCGETLGVYQGLVSAVDQESQ-TISLAFPFHNGVKCLVPEVTFRAGDIREL 61 (62) T ss_pred EEEEEEEEECCCCCEEEEEEEEECCCCC-EEEEEECCCCCCCCCCCEEEEEHHHHHHC T ss_conf 4068999867985288889998576663-89984056688658883599983564333 No 47 >TIGR01941 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit; InterPro: IPR010205 This entry represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0051537 2 iron 2 sulfur cluster binding, 0006814 sodium ion transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=50.55 E-value=10 Score=18.28 Aligned_cols=19 Identities=32% Similarity=0.698 Sum_probs=15.7 Q ss_pred CCCCCCEEEEECCCCCCCEE Q ss_conf 34789779995187789719 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNG 141 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g 141 (177) .+++||+| .++|||-.+-. T Consensus 261 sLKpGDKv-~~sGPfGefF~ 279 (425) T TIGR01941 261 SLKPGDKV-TVSGPFGEFFA 279 (425) T ss_pred ECCCCCEE-EEECCCCCCEE T ss_conf 44798777-99778885302 No 48 >COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism] Probab=47.61 E-value=14 Score=17.48 Aligned_cols=70 Identities=17% Similarity=0.379 Sum_probs=47.3 Q ss_pred CCEECEEEEEEEE-------CCCC----CHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 1203309999996-------1865----2244420330366432788610025889999997653222100001234789 Q gi|254780148|r 58 RRFFPGYVLIKAV-------MTDK----VYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVG 126 (177) Q Consensus 58 ~plfpgYiFv~~~-------~~~~----~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G 126 (177) .+++..|.|=+-- ++.+ ...-|+.+|-+..+|-+||.|..+++.+++.|+..+.+..... .+..| T Consensus 121 C~vyCRyCfRr~~~~~~~~~~~~~~~~~al~YIa~hPeI~eVllSGGDPL~ls~~~L~~ll~~L~~IpHv~----iiRi~ 196 (369) T COG1509 121 CAVYCRYCFRRRFVGQDNQGFNKEEWDKALDYIAAHPEIREVLLSGGDPLSLSDKKLEWLLKRLRAIPHVK----IIRIG 196 (369) T ss_pred CCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHEEEECCCCCCCCCHHHHHHHHHHHHCCCCEE----EEEEE T ss_conf 64521000134555666566788999999999973951651774078756368899999999875489646----99862 Q ss_pred CEEEE Q ss_conf 77999 Q gi|254780148|r 127 ERVCV 131 (177) Q Consensus 127 ~~V~I 131 (177) .++-| T Consensus 197 TR~pv 201 (369) T COG1509 197 TRLPV 201 (369) T ss_pred CCCCE T ss_conf 46743 No 49 >pfam02941 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain. Probab=41.95 E-value=27 Score=15.81 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=14.6 Q ss_pred CCCEEEEECC--------------CCCCCEEEEEEE Q ss_conf 8977999518--------------778971999998 Q gi|254780148|r 125 VGERVCVSDG--------------PFASFNGIVKNV 146 (177) Q Consensus 125 ~G~~V~I~~G--------------pf~g~~g~v~~i 146 (177) +||+|+|.+- .++|++|+|..+ T Consensus 1 vGdrVrV~~sv~VyhhP~hr~~~fDl~G~eGeV~~~ 36 (67) T pfam02941 1 VGDRVRVKTSVVVYHHPEHRGPAFDLKGMEGEIKQY 36 (67) T ss_pred CCCEEEECCCEEEEECCCCCCCCCCCCCCEEEEEEE T ss_conf 997489810189985865358874446777777567 No 50 >PRK04306 50S ribosomal protein L21e; Reviewed Probab=41.30 E-value=27 Score=15.75 Aligned_cols=52 Identities=21% Similarity=0.162 Sum_probs=35.5 Q ss_pred CCCCCCEEEEEC-C---------CCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE Q ss_conf 347897799951-8---------77897199999828898899999816870478856787123 Q gi|254780148|r 122 FFEVGERVCVSD-G---------PFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175 (177) Q Consensus 122 ~~~~G~~V~I~~-G---------pf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek 175 (177) .|++||.|.|.- + -|.|..|.|....+ .-..|.+..-++.-.+-+-.+.|.+ T Consensus 33 ~f~~GD~V~I~idpsv~kGmPh~ryhGkTG~V~~~~g--~a~~V~v~~g~k~K~i~vr~eHlr~ 94 (97) T PRK04306 33 EFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRG--RAYIVEVKDGGKEKTLIARPEHLRP 94 (97) T ss_pred HCCCCCEEEEEECCCCCCCCCCCEECCCCEEEEEECC--EEEEEEEEECCEEEEEEECHHHCCC T ss_conf 4779988999868862069985404687559993145--3999999979905899958768166 No 51 >COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis] Probab=39.55 E-value=29 Score=15.59 Aligned_cols=32 Identities=28% Similarity=0.397 Sum_probs=22.1 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEE Q ss_conf 347897799951877897199999828898899 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVH 154 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~ 154 (177) .+.+|.-|.++.|-|+|-.++|.++-+++ .+. T Consensus 4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~ 35 (125) T COG2163 4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVL 35 (125) T ss_pred CCCCCEEEEEECCEECCCEEEEEEECCCC-EEE T ss_conf 56387699996250279549999982278-799 No 52 >COG4873 Uncharacterized protein conserved in bacteria [Function unknown] Probab=36.21 E-value=33 Score=15.27 Aligned_cols=42 Identities=33% Similarity=0.545 Sum_probs=31.2 Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECH Q ss_conf 478977999518778971999998288988999998168704788567 Q gi|254780148|r 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAY 170 (177) Q Consensus 123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~ 170 (177) -++|+.+...+| +.|.|++++. ++ +.|.+.++..-..++++. T Consensus 24 a~vgniief~dg----l~g~vek~ne-ns-vivdlt~menf~dl~l~e 65 (81) T COG4873 24 AKVGNIIEFKDG----LTGVVEKVNE-NS-VIVDLTIMENFRDLELDE 65 (81) T ss_pred ECCCCEEEECCC----CEEEEEEECC-CC-EEEEEEEECCCCCCCCCH T ss_conf 100646887045----4011124058-84-899875101130059961 No 53 >pfam04943 Pox_F11 Poxvirus F11 protein. The protein F11 is an early virus protein. Probab=35.10 E-value=34 Score=15.16 Aligned_cols=107 Identities=11% Similarity=0.099 Sum_probs=56.2 Q ss_pred ECCEECEEEEEEEECCCCCHHHHHC----CCEEE--EEECCCCCCCCCCHHHHHHHHHHHHHHHHHH------CCCCCCC Q ss_conf 4120330999999618652244420----33036--6432788610025889999997653222100------0012347 Q gi|254780148|r 57 ERRFFPGYVLIKAVMTDKVYHTIKD----TPKVI--GFLGTGENPSPVTDSEIEHIMNQVEAAVQRP------VSSVFFE 124 (177) Q Consensus 57 ~~plfpgYiFv~~~~~~~~~~~i~~----t~gV~--~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~------~~~~~~~ 124 (177) ..|..-+++||.....+.....+.+ +.-.+ ..+.++-+|.+|++.-++.++....--.... .+...|. T Consensus 26 ~~~vL~dsvfi~~~di~~~~~~vs~l~~~~~~~~~~~~~~y~~kkV~i~~~~l~~l~D~eg~Fev~d~~lvkL~HGn~f~ 105 (366) T pfam04943 26 DNPVLVDSVFISIMDIENLLNDVSSLTDSTGSKTKSTLFTYSWKKVPVDSIKLRFLLDAEGYFEVSDCFLVKLEHGNGFM 105 (366) T ss_pred CCCEEEEEEEEEECCHHHHCCCHHHHCCCCCCCCCCCCCCCCEEEECCCHHHHHHHHCCCCCEEHHHEEEEEEECCCCCC T ss_conf 98367544678504376520405540178755321244323136612566777665122475211246899961367512 Q ss_pred CCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECC-CEEEEEE Q ss_conf 8977999518778971999998288988999998168-7047885 Q gi|254780148|r 125 VGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFG-RVTPVEL 168 (177) Q Consensus 125 ~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~G-r~~~v~l 168 (177) .|.. -.|-..||.++|. +. ..|++-+.++-.- ..+.++. T Consensus 106 ~~~~---~~~~s~gF~A~IC-Ik-NeG~Sgi~V~~t~~l~~~m~~ 145 (366) T pfam04943 106 KGAL---YVDNSAGFTAVIC-IK-NEGRSGIMVNHTNVLQTNMQE 145 (366) T ss_pred CCCC---CCCCCCCEEEEEE-EC-CCCEEEEEECCCCCEEEEEEE T ss_conf 4751---1587455079999-73-787058873797513555430 No 54 >CHL00084 rpl19 ribosomal protein L19 Probab=34.93 E-value=35 Score=15.15 Aligned_cols=45 Identities=18% Similarity=0.381 Sum_probs=24.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCEEEE----ECCC---CCCCEEEEEEECC Q ss_conf 99999765322210000123478977999----5187---7897199999828 Q gi|254780148|r 103 IEHIMNQVEAAVQRPVSSVFFEVGERVCV----SDGP---FASFNGIVKNVDE 148 (177) Q Consensus 103 i~~l~~~~~~~~~~~~~~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~ 148 (177) |+.+....+.... ...-+.|.+||+|+| .+|. ..-|+|.|..... T Consensus 4 m~~li~~ie~~~~-k~~~p~f~~GDtV~V~~~i~EG~keRiQ~FeGvVIa~~~ 55 (117) T CHL00084 4 LQQLVKEIESEFL-KTDLPEIRVGDTVKVGVLIQEGNKERVQAYEGTVIAKKN 55 (117) T ss_pred HHHHHHHHHHHHC-CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEEC T ss_conf 8999999999871-135998399999999999984890698788899999708 No 55 >pfam10574 UPF0552 Uncharacterized protein family UPF0552. This family of proteins has no known function. Probab=34.55 E-value=35 Score=15.11 Aligned_cols=37 Identities=27% Similarity=0.398 Sum_probs=23.6 Q ss_pred CCCCCCCCEEEEE---CCCCCCCEEEEEEECCCCCEEEEEEEECCC Q ss_conf 1234789779995---187789719999982889889999981687 Q gi|254780148|r 120 SVFFEVGERVCVS---DGPFASFNGIVKNVDEEKSRVHVEVVIFGR 162 (177) Q Consensus 120 ~~~~~~G~~V~I~---~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177) ...|+.|+.||+. +|||..-.+ ++|. +.+.. .++-|- T Consensus 149 ~~ele~G~evRlKT~GDgpFi~Sla---KlD~--~tvtk-cNFAGD 188 (224) T pfam10574 149 KTELELGQEVRLKTRGDGPFIFSLA---KMDS--GTVTK-CNFAGD 188 (224) T ss_pred CCCCCCCCEEEEEECCCCCCEEEEE---EECC--CCEEE-EECCCC T ss_conf 0141368758998517874144443---2025--71577-631577 No 56 >PRK10724 hypothetical protein; Provisional Probab=33.69 E-value=36 Score=15.02 Aligned_cols=35 Identities=20% Similarity=0.461 Sum_probs=21.2 Q ss_pred CCCCCEE--EEECCCCCCCEEE--EEEECCCCCEEEEEE Q ss_conf 4789779--9951877897199--999828898899999 Q gi|254780148|r 123 FEVGERV--CVSDGPFASFNGI--VKNVDEEKSRVHVEV 157 (177) Q Consensus 123 ~~~G~~V--~I~~Gpf~g~~g~--v~~i~~~~~r~~V~v 157 (177) +.++..+ ..++|||+.++|. +..++.+..++...+ T Consensus 81 ~~~~~~I~~~lv~GPFk~L~~~W~F~~~~~~~c~V~f~l 119 (158) T PRK10724 81 LTSNQSILMQLVDGPFKKLIGGWKFTPLSQEACRIEFHL 119 (158) T ss_pred ECCCCEEEEEECCCCHHHEEEEEEEEECCCCCEEEEEEE T ss_conf 438762545554797022057789997799958999999 No 57 >TIGR01200 TIGR01200 Porphyromonas gingivalis paralogous family TIGR01200; InterPro: IPR005901 This family of proteins of unknown function is found in Porphyromonas gingivalis (Bacteroides gingivalis).. Probab=32.94 E-value=30 Score=15.50 Aligned_cols=38 Identities=24% Similarity=0.481 Sum_probs=26.5 Q ss_pred CCEEEEECCC--CCCCEEEEEEECC-CCCEEEEEEEECCCE Q ss_conf 9779995187--7897199999828-898899999816870 Q gi|254780148|r 126 GERVCVSDGP--FASFNGIVKNVDE-EKSRVHVEVVIFGRV 163 (177) Q Consensus 126 G~~V~I~~Gp--f~g~~g~v~~i~~-~~~r~~V~v~i~Gr~ 163 (177) -+.+.+-+|| |.|+-|.|..|.+ ++..+-++.-+.|.. T Consensus 194 ~EDIal~~GPYiF~GLPGLI~~I~~~~~EYvF~~~~~~g~I 234 (300) T TIGR01200 194 SEDIALSDGPYIFRGLPGLIVAIRSDDGEYVFELNGMQGEI 234 (300) T ss_pred CCCCCCCCCCEEECCCCEEEEEEECCCCCEEEEEHHHHHCC T ss_conf 12656898587415887048997248983201001243102 No 58 >pfam08345 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514). Probab=32.65 E-value=38 Score=14.92 Aligned_cols=38 Identities=29% Similarity=0.303 Sum_probs=27.8 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCC Q ss_conf 6100258899999976532221000012347897799951877 Q gi|254780148|r 94 NPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPF 136 (177) Q Consensus 94 ~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf 136 (177) .+.|+++++++.|...+...... .-..||.|.|..-|| T Consensus 125 ~~~~~s~ee~~~i~~lV~~AiG~-----d~~RGD~v~V~~~~F 162 (162) T pfam08345 125 AYVPRSPEELAQIEALVKSAVGF-----DAARGDSVTVVSMPF 162 (162) T ss_pred CCCCCCHHHHHHHHHHHHHHCCC-----CCCCCCEEEEEECCC T ss_conf 34667999999999999996088-----877899899994689 No 59 >TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238 Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor .. Probab=32.41 E-value=38 Score=14.90 Aligned_cols=32 Identities=22% Similarity=0.532 Sum_probs=25.7 Q ss_pred EECCCCCEEEEE--------EEECCCEEEEEECHHHHEEC Q ss_conf 982889889999--------98168704788567871233 Q gi|254780148|r 145 NVDEEKSRVHVE--------VVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 145 ~i~~~~~r~~V~--------v~i~Gr~~~v~l~~~~ieki 176 (177) .+|.+++|..-+ +.+|++...++++.++|.|| T Consensus 28 ~ID~~~G~I~~lIip~~g~~~glf~~~~~~~IpW~~IkKI 67 (76) T TIGR02888 28 EIDEEDGKIESLIIPGKGKKFGLFSKGEEIEIPWKAIKKI 67 (76) T ss_pred EEECCCCEEEEEEECCCCEEEECEECCCCEEECCHHCEEE T ss_conf 9808999598988718970522100687548663002780 No 60 >KOG0107 consensus Probab=31.58 E-value=25 Score=16.04 Aligned_cols=26 Identities=8% Similarity=0.111 Sum_probs=21.3 Q ss_pred EECEEEEEEEECCCCCHHHHHCCCEE Q ss_conf 03309999996186522444203303 Q gi|254780148|r 60 FFPGYVLIKAVMTDKVYHTIKDTPKV 85 (177) Q Consensus 60 lfpgYiFv~~~~~~~~~~~i~~t~gV 85 (177) .=|||-||+++...+....++.+.|- T Consensus 45 nPPGfAFVEFed~RDA~DAvr~LDG~ 70 (195) T KOG0107 45 NPPGFAFVEFEDPRDAEDAVRYLDGK 70 (195) T ss_pred CCCCCEEEECCCCCCHHHHHHHCCCC T ss_conf 48984677616852388888641785 No 61 >TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776 This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport. Probab=31.16 E-value=30 Score=15.54 Aligned_cols=76 Identities=24% Similarity=0.488 Sum_probs=44.3 Q ss_pred HHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEE--------------EEEEECCCCCHHHH-HCCC Q ss_conf 99999999977981114326631310127720203566412033099--------------99996186522444-2033 Q gi|254780148|r 19 VESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYV--------------LIKAVMTDKVYHTI-KDTP 83 (177) Q Consensus 19 ~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYi--------------Fv~~~~~~~~~~~i-~~t~ 83 (177) ..||.+++..||..|..-+|. +++.+.|.+- ||+ |++. +.-|.|..| +.|. T Consensus 299 ~SNL~~QLkEQna~DkLd~VL---~EiPrVreDL----------GYpPLVTPTSQIVGtQAvlNV-L~GERYk~iT~ET~ 364 (616) T TIGR01108 299 LSNLESQLKEQNALDKLDEVL---EEIPRVREDL----------GYPPLVTPTSQIVGTQAVLNV-LTGERYKTITKETK 364 (616) T ss_pred HHHHHHHHHHHHHHHHHHHHH---HHCCCCHHHC----------CCCCCCCCCCCEEEEEEEEEE-EECCCHHHHHHHHH T ss_conf 889999998623755788887---4157412326----------765697787521345667742-31451148899999 Q ss_pred EEEEEEC-CCCCCCCCCHHHHHHHHHHH Q ss_conf 0366432-78861002588999999765 Q gi|254780148|r 84 KVIGFLG-TGENPSPVTDSEIEHIMNQV 110 (177) Q Consensus 84 gV~~~l~-~~~~P~~i~~~ei~~l~~~~ 110 (177) ++.. | +|..|+||..+-+++++... T Consensus 365 ~~~k--G~YGrtPApi~~~L~~k~L~~e 390 (616) T TIGR01108 365 DYVK--GEYGRTPAPIDAELVKKILGDE 390 (616) T ss_pred HHHC--CCCCCCCCCCCHHHHHHHHCCC T ss_conf 9848--8988879777989999861444 No 62 >PRK00092 hypothetical protein; Reviewed Probab=30.19 E-value=42 Score=14.67 Aligned_cols=49 Identities=31% Similarity=0.461 Sum_probs=34.7 Q ss_pred CCCCEEEEE-CCCCCC---CEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 789779995-187789---71999998288988999998168704788567871233 Q gi|254780148|r 124 EVGERVCVS-DGPFAS---FNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 124 ~~G~~V~I~-~Gpf~g---~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) ..|..|+|. .-|..| +.|.+.+++.+. +.++.=|+...+++++++|+|. T Consensus 93 ~~G~~v~v~l~~~~~~~k~~~G~L~~~~~~~----i~l~~~~~~~~~~i~~~~I~ka 145 (153) T PRK00092 93 FVGREVKVKLREPIDGRKKFQGRLLAVDGET----VTLEVEGKPKVVEIPLDNIAKA 145 (153) T ss_pred HCCCEEEEEEECCCCCCEEEEEEEEEEECCE----EEEEECCCCEEEEEEHHHHEEE T ss_conf 6693899999446689649999999884998----9999889706999736981089 No 63 >COG4464 CapC Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane] Probab=29.03 E-value=44 Score=14.55 Aligned_cols=11 Identities=36% Similarity=0.570 Sum_probs=7.5 Q ss_pred EEEEEEEECCC Q ss_conf 09999996186 Q gi|254780148|r 63 GYVLIKAVMTD 73 (177) Q Consensus 63 gYiFv~~~~~~ 73 (177) .|++|++.++. T Consensus 103 kYlLIEF~~~~ 113 (254) T COG4464 103 KYLLIEFPMNH 113 (254) T ss_pred CEEEEECCCCC T ss_conf 34999746886 No 64 >PRK08384 thiamine biosynthesis protein ThiI; Provisional Probab=28.42 E-value=45 Score=14.49 Aligned_cols=57 Identities=12% Similarity=0.187 Sum_probs=32.1 Q ss_pred CCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEE Q ss_conf 2885389999999999977981114326631310127720203566412033099999961865224442033036643 Q gi|254780148|r 11 YSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFL 89 (177) Q Consensus 11 ~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l 89 (177) +...|+...+|+++.+...+++.. ..... .|.+++..+..++.-..+..++|+.++- T Consensus 19 R~~fe~~L~~NIk~~L~~~~~~~~----------~v~~~------------~gri~v~~~~~~~~~~~l~~vfGI~s~s 75 (310) T PRK08384 19 RRWFERILMNNIREALVSEGIEYK----------EVFAK------------HGRVIVRTNRAEEAKEVLVRVFGIVSLS 75 (310) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCE----------EEEEE------------CCEEEEECCCHHHHHHHHHHCCCCCEEE T ss_conf 899999999999999986699824----------89997------------4799997598799999998659977170 No 65 >PRK09206 pyruvate kinase; Provisional Probab=28.32 E-value=31 Score=15.43 Aligned_cols=74 Identities=15% Similarity=0.105 Sum_probs=37.8 Q ss_pred EEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEE Q ss_conf 03566412033099999961865224442033036643278861002588999999765322210000123478977999 Q gi|254780148|r 52 RKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCV 131 (177) Q Consensus 52 ~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I 131 (177) ++....+|--|=|.|. .++.....+.-..||.-++-.... +. +.+.....+. ......++.||.|.+ T Consensus 385 ~~is~~RP~~pI~a~t---~~~~~~r~l~l~~Gv~p~~~~~~~----~~---~~~~~~~~~~---~~~~g~~~~GD~vVv 451 (470) T PRK09206 385 RSVRKYFPDATILALT---TNEKTAHQLVLSKGVVPQLVKEIA----ST---DDFYRLGKEL---ALQSGLAQKGDVVVM 451 (470) T ss_pred HHHHHCCCCCCEEEEC---CCHHHHHHHHECCCEEEEEECCCC----CH---HHHHHHHHHH---HHHCCCCCCCCEEEE T ss_conf 9997039999889988---988999975652583899927889----99---9999999999---998699899898999 Q ss_pred ECCCCCC Q ss_conf 5187789 Q gi|254780148|r 132 SDGPFAS 138 (177) Q Consensus 132 ~~Gpf~g 138 (177) ++|++.+ T Consensus 452 ~~G~~~~ 458 (470) T PRK09206 452 VSGALVP 458 (470) T ss_pred ECCCCCC T ss_conf 7777789 No 66 >pfam01245 Ribosomal_L19 Ribosomal protein L19. Probab=28.09 E-value=45 Score=14.45 Aligned_cols=29 Identities=31% Similarity=0.466 Sum_probs=18.6 Q ss_pred CCCCCCCCEEEE----ECCC---CCCCEEEEEEECC Q ss_conf 123478977999----5187---7897199999828 Q gi|254780148|r 120 SVFFEVGERVCV----SDGP---FASFNGIVKNVDE 148 (177) Q Consensus 120 ~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~ 148 (177) -+.|.+||.|+| .+|. ..-|+|++..... T Consensus 16 ip~f~~GDtv~V~~~i~Eg~k~RiQ~FeGvvI~~~~ 51 (113) T pfam01245 16 LPEFRVGDTVRVHVKIKEGNKERIQVFEGVVIARRG 51 (113) T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEEC T ss_conf 998499999999999984881688899999999957 No 67 >pfam08223 PaaX_C PaaX-like protein C-terminal domain. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. Probab=27.84 E-value=46 Score=14.42 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=32.4 Q ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEE Q ss_conf 86189995288538999999999997798111432663 Q gi|254780148|r 3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITI 40 (177) Q Consensus 3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~ 40 (177) -+|.++.+.|..+....+.|++++...|++....-+|+ T Consensus 6 G~W~lv~~spe~~r~~R~~lr~~L~~lGFg~l~~glwi 43 (170) T pfam08223 6 GSWHLVVLSPESDRAARDALRRELEWLGFGELAPGLWI 43 (170) T ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEE T ss_conf 62689885886589999999999998789718899678 No 68 >pfam09953 DUF2187 Uncharacterized protein conserved in bacteria (DUF2187). This domain, found in various hypothetical bacterial proteins, has no known function. Probab=27.82 E-value=46 Score=14.42 Aligned_cols=40 Identities=30% Similarity=0.558 Sum_probs=29.1 Q ss_pred CCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEEC Q ss_conf 7897799951877897199999828898899999816870478856 Q gi|254780148|r 124 EVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELA 169 (177) Q Consensus 124 ~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~ 169 (177) ++|+.+...+| +.|+|++++. + -+.|.+.++..-..++++ T Consensus 5 ~vG~iiEFk~G----l~GiVeKvNe-N-SVIVdlT~Men~~~L~le 44 (57) T pfam09953 5 EVGNIIEFKNG----LQGIVEKVNE-N-SVIVDLTYMENFRDLDLE 44 (57) T ss_pred CCCCEEEECCC----CEEEEEEECC-C-CEEEEEEEECCCHHCCCC T ss_conf 00667997264----2010013047-8-389998853360014877 No 69 >COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Probab=26.71 E-value=48 Score=14.30 Aligned_cols=45 Identities=31% Similarity=0.499 Sum_probs=31.2 Q ss_pred CCCEEEEEC----CCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE Q ss_conf 897799951----877897199999828898899999816870478856787123 Q gi|254780148|r 125 VGERVCVSD----GPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175 (177) Q Consensus 125 ~G~~V~I~~----Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek 175 (177) .|..|.|.- .-=+-++|.+..++.+. +-+++-|+. ++++++.|.| T Consensus 98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~----v~~~~~~k~--v~Ip~~~i~k 146 (153) T COG0779 98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGET----VTLEVDGKE--VEIPFSDIAK 146 (153) T ss_pred CCCEEEEEEECCCCCCEEEEEEEEEECCCE----EEEEECCEE--EEEECCCCHH T ss_conf 695899999654488407889999972986----999977848--9987563112 No 70 >KOG4315 consensus Probab=26.69 E-value=29 Score=15.60 Aligned_cols=50 Identities=24% Similarity=0.218 Sum_probs=34.1 Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHH Q ss_conf 3478977999518778971999998288988999998168704788567871 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQV 173 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~i 173 (177) +-..|++|.|+.|+-+|..|...+-|.++.+..+.+ .--.-.|++.+++| T Consensus 393 pr~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~--~a~ndvv~~~~D~v 442 (455) T KOG4315 393 PRRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRL--VATNDVVTVYLDQV 442 (455) T ss_pred CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCEEC--CCCCCHHHHHHHHH T ss_conf 313596468985365661232220122222030211--45563245658779 No 71 >pfam02576 DUF150 Uncharacterized BCR, YhbC family COG0779. Probab=25.58 E-value=50 Score=14.18 Aligned_cols=50 Identities=32% Similarity=0.493 Sum_probs=33.1 Q ss_pred CCCEEEEE-CCCCC---CCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 89779995-18778---971999998288988999998168704788567871233 Q gi|254780148|r 125 VGERVCVS-DGPFA---SFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 125 ~G~~V~I~-~Gpf~---g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) .|..|.|. ..+.. -+.|.+.+++.+ .+.+.++--.+...+++++++|+|. T Consensus 86 ~G~~v~v~l~~~~~~~k~~~G~L~~~~~~--~i~l~~~~~~~~~~~~i~~~~I~kA 139 (141) T pfam02576 86 IGKLVKVSLKEPIEGRKNFTGKLLEVDGD--TVTIEVDDKRRKKEVEIPFADIKKA 139 (141) T ss_pred CCCEEEEEEECCCCCEEEEEEEEEEEECC--EEEEEECCCCCCEEEEEEHHHHHHC T ss_conf 59489999924669938999999988699--9999985871226899737995233 No 72 >PRK12289 ribosome-associated GTPase; Reviewed Probab=25.47 E-value=51 Score=14.16 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=7.9 Q ss_pred CCEEEEEECCC Q ss_conf 86189995288 Q gi|254780148|r 3 PRWYIVQVYSN 13 (177) Q Consensus 3 ~~Wyvv~t~~~ 13 (177) .+||-|++-.+ T Consensus 18 ~~fY~V~~d~~ 28 (351) T PRK12289 18 ANFYQVRLDQP 28 (351) T ss_pred CCEEEEEECCC T ss_conf 86799995467 No 73 >PRK04313 30S ribosomal protein S4e; Validated Probab=24.88 E-value=52 Score=14.10 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=29.9 Q ss_pred CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEE--EEEE Q ss_conf 01234789779995187789719999982889889--9999 Q gi|254780148|r 119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRV--HVEV 157 (177) Q Consensus 119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~--~V~v 157 (177) ....|++|..+-|+.|-=.|..|.|.++....+.. .|.+ T Consensus 168 ~~i~fe~G~~~~itgG~n~G~vG~I~~I~~~~~s~~~~V~~ 208 (237) T PRK04313 168 DHIPFEEGNLAMITGGKHVGEIGKIVEIQVTPSSKPNIVTL 208 (237) T ss_pred EEEECCCCCEEEEECCEEEEEEEEEEEEEECCCCCCCEEEE T ss_conf 67852799899997880525899998899605777518999 No 74 >pfam01157 Ribosomal_L21e Ribosomal protein L21e. Probab=24.64 E-value=52 Score=14.07 Aligned_cols=54 Identities=20% Similarity=0.269 Sum_probs=32.5 Q ss_pred CCCCCCEEEEEC-C---------CCCCCEEEEEEECCCCCEEEEEEEECCCE--EEEEECHHHHEE Q ss_conf 347897799951-8---------77897199999828898899999816870--478856787123 Q gi|254780148|r 122 FFEVGERVCVSD-G---------PFASFNGIVKNVDEEKSRVHVEVVIFGRV--TPVELAYNQVEK 175 (177) Q Consensus 122 ~~~~G~~V~I~~-G---------pf~g~~g~v~~i~~~~~r~~V~v~i~Gr~--~~v~l~~~~iek 175 (177) .|++||.|.|.- + -|.|..|.|.++.....=..+.+.+-++. -.+-+-.++|.+ T Consensus 32 ~f~~GD~V~I~idpsv~kGMPh~~yhGkTG~V~nv~~~~~G~~~~~~V~~~~~~K~i~vr~eHlk~ 97 (99) T pfam01157 32 EYKVGDYVDIKINGSVQKGMPHKRFHGKTGRVYNVTPGAVGVAVNKKVRDGILEKRINVRPEHIRP 97 (99) T ss_pred HCCCCCEEEEEECCCEECCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEECHHHCCC T ss_conf 436998899963486006997422158864799845860799999997588320899971677146 No 75 >pfam11572 DUF3234 Protein of unknown function (DUF3234). This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed. Probab=23.62 E-value=55 Score=13.95 Aligned_cols=25 Identities=36% Similarity=0.671 Sum_probs=20.2 Q ss_pred CCEEEEEECCCCHHHHHHHHHHHHHH Q ss_conf 86189995288538999999999997 Q gi|254780148|r 3 PRWYIVQVYSNCEKKAVESIGGRLSR 28 (177) Q Consensus 3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~ 28 (177) ..|||+---|| |.-|.+.|.++++. T Consensus 6 ~TWYVLEgdPG-EHLVvEaLG~RLS~ 30 (102) T pfam11572 6 GTWYVLEGDPG-EHLVVEALGERLSG 30 (102) T ss_pred CEEEEECCCCC-CEEHHHHHHHHHHH T ss_conf 14898628996-10089998516656 No 76 >PRK06488 sulfur carrier protein ThiS; Validated Probab=23.42 E-value=55 Score=13.93 Aligned_cols=41 Identities=5% Similarity=0.123 Sum_probs=24.5 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHH-------------CCCCCCCCCCEEEEEC Q ss_conf 8610025889999997653222100-------------0012347897799951 Q gi|254780148|r 93 ENPSPVTDSEIEHIMNQVEAAVQRP-------------VSSVFFEVGERVCVSD 133 (177) Q Consensus 93 ~~P~~i~~~ei~~l~~~~~~~~~~~-------------~~~~~~~~G~~V~I~~ 133 (177) +++..++..-+..++..++...... .....+..||+|.|+. T Consensus 7 Ge~~e~~a~tl~~Ll~elg~~~~~vAvAvN~~~Vpr~~~~~~~L~eGDriEIv~ 60 (65) T PRK06488 7 GEEIETAATTLALLLAELGYEGNWLATAVNGELVHSEARAQFVLHEGDRIEILS 60 (65) T ss_pred CEEEEECHHHHHHHHHHCCCCCCCEEEEECCEEECHHHHCCCCCCCCCEEEEEC T ss_conf 977770086899999972988880899989998742450545179999999964 No 77 >COG1532 Predicted RNA-binding protein [General function prediction only] Probab=22.97 E-value=56 Score=13.87 Aligned_cols=31 Identities=29% Similarity=0.515 Sum_probs=21.3 Q ss_pred CCCEEEEEC--CCCCCCEEEEEEECCCCCEEEE Q ss_conf 897799951--8778971999998288988999 Q gi|254780148|r 125 VGERVCVSD--GPFASFNGIVKNVDEEKSRVHV 155 (177) Q Consensus 125 ~G~~V~I~~--Gpf~g~~g~v~~i~~~~~r~~V 155 (177) .|+.|+..+ |.-+-++|.++++|-+..++.+ T Consensus 23 ~~e~V~a~Dilgd~ke~~G~vkriDldehkI~l 55 (57) T COG1532 23 TEEGVVARDILGDEKEFEGQVKRIDLDEHKIEL 55 (57) T ss_pred ECCCEEEEECCCCCEEECCEEEEEECCCCEEEE T ss_conf 258399986038721742248999746638996 No 78 >PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional Probab=22.20 E-value=59 Score=13.78 Aligned_cols=19 Identities=37% Similarity=0.791 Sum_probs=15.3 Q ss_pred CCCCCCEEEEECCCCCCCEE Q ss_conf 34789779995187789719 Q gi|254780148|r 122 FFEVGERVCVSDGPFASFNG 141 (177) Q Consensus 122 ~~~~G~~V~I~~Gpf~g~~g 141 (177) .+++||+|.+. |||-.|-- T Consensus 251 ~LK~GD~V~is-GP~G~Ffl 269 (408) T PRK05464 251 SLKPGDKVTIS-GPFGEFFA 269 (408) T ss_pred CCCCCCEEEEE-CCCCCEEE T ss_conf 38999889997-78644275 No 79 >pfam03792 PBC PBC domain. The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. Probab=22.03 E-value=20 Score=16.59 Aligned_cols=35 Identities=23% Similarity=0.409 Sum_probs=25.8 Q ss_pred CCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 03303664327886100258899999976532221 Q gi|254780148|r 81 DTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQ 115 (177) Q Consensus 81 ~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~ 115 (177) -|.+|..+|+..++..||+..||++|.+.+..... T Consensus 135 Ft~hV~nLLreQsrtRPIs~kEiErmv~iI~~KF~ 169 (192) T pfam03792 135 FTQHVMNLLREQSRTRPISQREIERMVNIISRKFN 169 (192) T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 99999999998535689988999999999999999 No 80 >PTZ00300 pyruvate kinase; Provisional Probab=22.03 E-value=55 Score=13.95 Aligned_cols=81 Identities=16% Similarity=0.096 Sum_probs=43.2 Q ss_pred EEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEE Q ss_conf 03566412033099999961865224442033036643278861002588999999765322210000123478977999 Q gi|254780148|r 52 RKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCV 131 (177) Q Consensus 52 ~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I 131 (177) ++....+|-.|=|.|- .+......+.-..||.-++-....... ++.++.+....-+. .......+.||.|.+ T Consensus 363 ~~vs~~RP~~pI~a~t---~~~~~~r~l~l~~GV~p~~~~~~~~~~--~~~~~~~i~~a~~~---~~~~g~~~~GD~vVv 434 (454) T PTZ00300 363 RLVAKYRPNCPIVCVT---TRLQTCRQLNITQGVESVFFDAERLGH--DEGKEQRVAMGVGF---AKSKGYVQSGDLMVV 434 (454) T ss_pred HHHHHHCCCCCEEEEC---CCHHHHHHHHEECCEEEEEECCCCCCC--CCCHHHHHHHHHHH---HHHCCCCCCCCEEEE T ss_conf 9999659799999989---879999865660585999866634676--56999999999999---997799889998999 Q ss_pred ECCCCCCCEE Q ss_conf 5187789719 Q gi|254780148|r 132 SDGPFASFNG 141 (177) Q Consensus 132 ~~Gpf~g~~g 141 (177) ++|+.. -.| T Consensus 435 v~g~~~-~~G 443 (454) T PTZ00300 435 VHADHK-VKG 443 (454) T ss_pred EECCCC-CCC T ss_conf 934899-997 No 81 >pfam04452 Methyltrans_RNA RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. Probab=22.02 E-value=59 Score=13.76 Aligned_cols=13 Identities=31% Similarity=0.468 Sum_probs=5.5 Q ss_pred CEEEEECCCCCCC Q ss_conf 7799951877897 Q gi|254780148|r 127 ERVCVSDGPFASF 139 (177) Q Consensus 127 ~~V~I~~Gpf~g~ 139 (177) ..+.+.=||=-|| T Consensus 175 ~~i~i~IGPEGGf 187 (225) T pfam04452 175 GKVLLIIGPEGGF 187 (225) T ss_pred CCEEEEECCCCCC T ss_conf 8458998898899 No 82 >PRK05338 rplS 50S ribosomal protein L19; Provisional Probab=21.55 E-value=60 Score=13.70 Aligned_cols=30 Identities=27% Similarity=0.413 Sum_probs=19.6 Q ss_pred CCCCCCCCCEEEE----ECCC---CCCCEEEEEEECC Q ss_conf 0123478977999----5187---7897199999828 Q gi|254780148|r 119 SSVFFEVGERVCV----SDGP---FASFNGIVKNVDE 148 (177) Q Consensus 119 ~~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~ 148 (177) .-+.|.+||.|+| .+|. ..-|+|++..... T Consensus 15 ~iP~f~~GDtV~V~~~i~EG~KeRiQ~feGvvI~~~~ 51 (112) T PRK05338 15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRG 51 (112) T ss_pred CCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEEEC T ss_conf 6998599999999999996896388756899999737 No 83 >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=21.49 E-value=61 Score=13.69 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=20.2 Q ss_pred CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE Q ss_conf 123478977999518778971999998288988999 Q gi|254780148|r 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV 155 (177) Q Consensus 120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V 155 (177) ...|++||.|+ +.|.++|.+++|+.+ T Consensus 42 ~~~fk~G~~Vk----------~rVl~vD~~~~ri~L 67 (69) T cd05697 42 EKKFKPGLKVK----------CRVLSVEPERKRLVL 67 (69) T ss_pred HHCCCCCCEEE----------EEEEEEECCCCEEEE T ss_conf 89089999999----------999999488799886 No 84 >KOG3421 consensus Probab=21.48 E-value=61 Score=13.69 Aligned_cols=33 Identities=33% Similarity=0.319 Sum_probs=22.9 Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE Q ss_conf 4789779995187789719999982889889999 Q gi|254780148|r 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156 (177) Q Consensus 123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~ 156 (177) .++|.-+-+..||..|--..|..++++ +|+.+. T Consensus 7 veVGrva~v~~G~~~GkL~AIVdviDq-nr~lvD 39 (136) T KOG3421 7 VEVGRVALVSFGPDAGKLVAIVDVIDQ-NRALVD 39 (136) T ss_pred EEECEEEEEEECCCCCEEEEEEEEECC-HHHHCC T ss_conf 000349999706777608999986253-235304 No 85 >pfam12073 DUF3553 Protein of unknown function (DUF3553). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF. Probab=20.89 E-value=62 Score=13.62 Aligned_cols=50 Identities=24% Similarity=0.230 Sum_probs=33.1 Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC Q ss_conf 478977999518778971999998288988999998168704788567871233 Q gi|254780148|r 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176 (177) Q Consensus 123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki 176 (177) |+||+.|+--+-|==| .|.|.++-. +|++|.++=.|+.+ ++.+.-.+++| T Consensus 1 lePG~~V~~P~~pdWG-iGQVQS~I~--~kvTVNFe~~GK~v-I~~~~i~L~~v 50 (52) T pfam12073 1 LEPGMLVRHPDQPDWG-VGQVQSNIG--GRITVNFEHAGKVV-IDGSRVALELV 50 (52) T ss_pred CCCCCEEECCCCCCCC-CCEEEEECC--CEEEEECCCCCCEE-EECCEEEEEEE T ss_conf 9897787689998777-002554308--87899323677589-81566889990 No 86 >pfam09087 Cyc-maltodext_N Cyclomaltodextrinase, N-terminal. Members of this family assume a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate. Probab=20.87 E-value=62 Score=13.61 Aligned_cols=20 Identities=10% Similarity=0.290 Sum_probs=14.2 Q ss_pred EEEECCEECEEEEEEEECCC Q ss_conf 56641203309999996186 Q gi|254780148|r 54 VNSERRFFPGYVLIKAVMTD 73 (177) Q Consensus 54 ~~~~~plfpgYiFv~~~~~~ 73 (177) ..+.+.==|+|+||..+..+ T Consensus 40 ~~v~~~enpNYLFv~L~i~~ 59 (88) T pfam09087 40 KSVVKTDNPNYLFVNLDISE 59 (88) T ss_pred EEEEECCCCCEEEEEEEECC T ss_conf 99896589988999989557 No 87 >KOG3401 consensus Probab=20.69 E-value=63 Score=13.59 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=30.2 Q ss_pred CCCCCCCCCEEEEECCCCCC-CEEEEEEECCCCCEEEEEEEECCC Q ss_conf 01234789779995187789-719999982889889999981687 Q gi|254780148|r 119 SSVFFEVGERVCVSDGPFAS-FNGIVKNVDEEKSRVHVEVVIFGR 162 (177) Q Consensus 119 ~~~~~~~G~~V~I~~Gpf~g-~~g~v~~i~~~~~r~~V~v~i~Gr 162 (177) ....+..+|.|.|..|-+.| .+|.+.++... +..+-++...+ T Consensus 45 rs~pir~ddev~v~rg~~kG~q~G~v~~vyrK--k~~iyie~v~~ 87 (145) T KOG3401 45 RSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRK--KYVIYIERVQR 87 (145) T ss_pred CCCCEEECCEEEEEECCCCCCCCCEEHHHHHH--HHEEEEEEEEE T ss_conf 40314643379997413344110300243453--20022366778 Done!