Query gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 155 No_of_seqs 111 out of 1699 Neff 4.9 Searched_HMMs 39220 Date Tue May 24 16:17:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780292.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01066 rplM_bact ribosomal 100.0 0 0 458.8 6.9 141 4-144 1-145 (145) 2 CHL00159 rpl13 ribosomal prote 100.0 0 0 420.6 10.1 143 1-144 1-143 (143) 3 PRK09216 rplM 50S ribosomal pr 100.0 0 0 419.6 10.3 144 2-146 1-144 (144) 4 COG0102 RplM Ribosomal protein 100.0 0 0 384.0 10.1 147 2-148 1-147 (148) 5 pfam00572 Ribosomal_L13 Riboso 100.0 0 0 354.5 9.8 128 16-144 1-128 (128) 6 KOG3203 consensus 100.0 0 0 342.2 8.4 132 10-142 17-154 (165) 7 cd00392 Ribosomal_L13 Ribosoma 100.0 0 0 313.2 9.1 114 16-130 1-114 (114) 8 PRK06394 rpl13p 50S ribosomal 100.0 1.4E-41 0 264.8 10.1 125 17-154 2-128 (143) 9 TIGR01077 L13_A_E ribosomal pr 100.0 2.2E-29 5.6E-34 193.3 8.0 122 17-151 1-125 (144) 10 PTZ00068 60S ribosomal protein 99.9 3.2E-25 8E-30 168.9 8.1 119 15-149 4-130 (201) 11 KOG3204 consensus 99.6 3.2E-15 8.1E-20 110.3 5.6 107 13-139 4-111 (197) 12 TIGR02845 spore_V_AD stage V s 45.8 20 0.00051 17.8 2.7 43 25-69 231-276 (331) 13 TIGR01704 MTA/SAH-Nsdase MTA/S 41.7 26 0.00066 17.2 2.8 38 26-63 49-97 (229) 14 TIGR02743 TraW type-F conjugat 28.8 35 0.00089 16.4 1.7 57 11-81 132-189 (217) 15 TIGR01135 glmS glucosamine--fr 28.3 32 0.00082 16.6 1.5 13 46-58 88-100 (628) 16 PRK10793 D-alanyl-D-alanine ca 24.9 50 0.0013 15.5 2.0 26 2-27 34-61 (403) 17 PRK05461 apaG ApaG; Reviewed 23.7 44 0.0011 15.8 1.5 14 12-25 45-58 (124) 18 KOG3834 consensus 22.0 71 0.0018 14.6 2.4 53 12-82 107-159 (462) 19 pfam06303 MatP Organiser of ma 21.5 61 0.0016 15.0 1.9 51 96-146 48-100 (148) 20 pfam06088 TLP-20 Nucleopolyhed 21.0 51 0.0013 15.4 1.4 26 36-62 53-78 (162) 21 PRK05097 hypothetical protein; 20.6 65 0.0017 14.8 1.9 51 96-146 48-100 (150) No 1 >TIGR01066 rplM_bact ribosomal protein L13; InterPro: IPR005823 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 L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This entry represents ribosomal protein L13 from bacteria, mitochondria and chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=100.00 E-value=0 Score=458.75 Aligned_cols=141 Identities=55% Similarity=0.930 Sum_probs=137.3 Q ss_pred EEECC-HHHCCEEEEEEECC--CCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCC Q ss_conf 13268-43602006999789--8745767999999984656521034556688899975101001560121133331157 Q gi|254780292|r 4 TFFQK-SSEVEKKWILVDAK--GLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTG 80 (155) Q Consensus 4 T~~~k-~~~~~r~W~iiDA~--~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htg 80 (155) |++++ .++++|+||||||+ |++||||||+||.+|||||||+||||+||||||||||||+|.|||+|.++|+||+||| T Consensus 1 T~~~k~~~~~~r~WyvvDA~rdg~~LGRLA~~vA~~LRGKHKp~YTP~~D~GD~VIvINA~Kv~lTG~K~~~K~Yy~HSg 80 (145) T TIGR01066 1 TTLAKAEDEVERKWYVVDAARDGKTLGRLASEVAKLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKLYYRHSG 80 (145) T ss_pred CCCCCCHHHCCCCCEEEEEEECCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCEEECCCCCCCCEEEEECC T ss_conf 94447632444530688643188361078898999843788884347861487269970475786387656837888668 Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC-HHHCCCEEEEH Q ss_conf 55763363020000124879999999973089985478999627010789997-13208547616 Q gi|254780292|r 81 YPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHP-HEAQKPVFMDI 144 (155) Q Consensus 81 ypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hp-h~aq~P~~l~~ 144 (155) ||||+|+.|+.+|+++|.|+++|+.||+||||||+|||++|++|+||.|++|| |+||||+.+|+ T Consensus 81 ypGG~k~~t~~~m~~~r~P~~~~~~AVkGMLPkn~Lgr~~~~kLkVY~G~~Hp~h~AQ~P~~l~~ 145 (145) T TIGR01066 81 YPGGLKSRTFEEMIADRKPEKVLELAVKGMLPKNRLGRKLFKKLKVYAGSEHPYHEAQKPIVLDI 145 (145) T ss_pred CCCCCCHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHCCCEECCCCCCCCCCCCCEECCC T ss_conf 34887003489997427810247865016899883212121104224489874001478450479 No 2 >CHL00159 rpl13 ribosomal protein L13; Validated Probab=100.00 E-value=0 Score=420.57 Aligned_cols=143 Identities=50% Similarity=0.863 Sum_probs=140.7 Q ss_pred CCEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCC Q ss_conf 95113268436020069997898745767999999984656521034556688899975101001560121133331157 Q gi|254780292|r 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTG 80 (155) Q Consensus 1 ~~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htg 80 (155) |+|||++++++++|+||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.+|.||+||| T Consensus 1 m~kT~~~~~~~~~r~W~viDA~~~~lGRLAs~iA~~L~GK~Kp~ytP~~d~GD~VVViNa~ki~~TG~K~~~K~y~~htg 80 (143) T CHL00159 1 MNKTFIPSKNYKKRKWYIIDAKDQKLGRLATEISSLLRGKNKPSYTPSVDTGDYVIVINADKIIVTGNKNTQKFYVRHSG 80 (143) T ss_pred CCCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECHHEEEECCCCCCEEEEEEEE T ss_conf 97433188202466689996999944889999999975478773567887799999983714187177300108899876 Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH Q ss_conf 5576336302000012487999999997308998547899962701078999713208547616 Q gi|254780292|r 81 YPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI 144 (155) Q Consensus 81 ypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~ 144 (155) ||||+++.++++++ +++|++||++||+||||+|+||+.+|+||+||+|++|||+||||+.|++ T Consensus 81 ypGg~k~~~~~~~~-~r~P~~il~~AVkgMLPkn~lgr~~lkrLkVy~G~~Hph~aQ~P~~l~i 143 (143) T CHL00159 81 RPGGLKVETFKELQ-NRLPNRIIEKAVKGMLPKGPLGRKLFKKLKVYAGSSHPHEAQKPIIINI 143 (143) T ss_pred CCCCCCCCCHHHHH-HCCCHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC T ss_conf 25887565678964-2280579999998618998129999858888698999855689877279 No 3 >PRK09216 rplM 50S ribosomal protein L13; Reviewed Probab=100.00 E-value=0 Score=419.56 Aligned_cols=144 Identities=51% Similarity=0.931 Sum_probs=141.1 Q ss_pred CEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC Q ss_conf 51132684360200699978987457679999999846565210345566888999751010015601211333311575 Q gi|254780292|r 2 IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY 81 (155) Q Consensus 2 ~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy 81 (155) |+||++++++++|+||||||+|++||||||.||++|+|||||+|||++||||+||||||++|.+||+||.+|.||+|||| T Consensus 1 ~kT~~~k~~~~~~~W~vIDA~~~~lGRLAs~iA~~L~GKhKp~ytP~~d~GD~VVVINa~ki~itG~K~~~K~y~~htgy 80 (144) T PRK09216 1 MKTFSAKPAEVERKWYVVDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRHSGY 80 (144) T ss_pred CCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECHHEEEECCCCCCEEEEEECCC T ss_conf 96423882015676599969998118999999999747887843688758988999700582773672011368860456 Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH Q ss_conf 57633630200001248799999999730899854789996270107899971320854761665 Q gi|254780292|r 82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK 146 (155) Q Consensus 82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~ 146 (155) |||++++++++++ .++|++||++||+||||+|+||+.+|+||+||+|++|||+||+|+.+++++ T Consensus 81 pGg~k~~~~~~~~-~r~P~~il~~AVkgMLPkn~lgr~~~krLkvy~g~~Hph~aQ~P~~~~~~~ 144 (144) T PRK09216 81 PGGLKERTFGELL-AKKPERVIEKAVKGMLPKNPLGRAMLKKLKVYAGAEHPHAAQQPEVLDIKS 144 (144) T ss_pred CCCCEECCHHHHH-CCCCHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECCCC T ss_conf 8884011689974-038268999999712899736999984867848999985557985750459 No 4 >COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=384.01 Aligned_cols=147 Identities=52% Similarity=0.909 Sum_probs=143.5 Q ss_pred CEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC Q ss_conf 51132684360200699978987457679999999846565210345566888999751010015601211333311575 Q gi|254780292|r 2 IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY 81 (155) Q Consensus 2 ~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy 81 (155) |+|++++++++.++||||||+|++||||||.||++|+|||||+||||+||||+|||||||++++||+|..+|.||+|||| T Consensus 1 ~~t~~~k~~~~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~ 80 (148) T COG0102 1 MKTFTAKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRHSGY 80 (148) T ss_pred CCEECCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECEEEEEECCCHHCEEEEEEECC T ss_conf 95222575100351899958997668889999999965898876867677878999856026886261000357776316 Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCC Q ss_conf 5763363020000124879999999973089985478999627010789997132085476166528 Q gi|254780292|r 82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMN 148 (155) Q Consensus 82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~ 148 (155) |||++..++.++++++.|++|+++||+||||+|+|||++|+||+||.|++|||++|+|+.+++..++ T Consensus 81 ~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~~~~~~ 147 (148) T COG0102 81 PGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALELKLLK 147 (148) T ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCHHHHHHCCC T ss_conf 7764456401145667889999999702188986599997471586489986022466334330257 No 5 >pfam00572 Ribosomal_L13 Ribosomal protein L13. Probab=100.00 E-value=0 Score=354.51 Aligned_cols=128 Identities=56% Similarity=0.960 Sum_probs=125.6 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCC Q ss_conf 69997898745767999999984656521034556688899975101001560121133331157557633630200001 Q gi|254780292|r 16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILA 95 (155) Q Consensus 16 W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~ 95 (155) ||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.++.|++|||||||+++.+++++++ T Consensus 1 w~viDA~~~~lGRlAs~iAk~L~GK~kp~y~p~~d~Gd~VvViNa~~i~itG~k~~~k~y~~htg~pgg~~~~~~~~~~~ 80 (128) T pfam00572 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVVNAEKIVLTGKKRDQKKYYRHTGYPGGLKNPTAKGPLE 80 (128) T ss_pred CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEHHHEEEECCHHHHHEEEEEECCCCCCCCCCHHHHHH T ss_conf 98995899943889999999983467886478987787899983168176065565200003440568640167799874 Q ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH Q ss_conf 2487999999997308998547899962701078999713208547616 Q gi|254780292|r 96 GASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI 144 (155) Q Consensus 96 ~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~ 144 (155) ++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++ T Consensus 81 -r~P~~il~~aVrgMLP~n~~g~~~~krLkiy~g~~hp~~~q~p~~~~~ 128 (128) T pfam00572 81 -RKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAAQKPEVLEI 128 (128) T ss_pred -HCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCC T ss_conf -077899999998628997449999858789699998856679876179 No 6 >KOG3203 consensus Probab=100.00 E-value=0 Score=342.21 Aligned_cols=132 Identities=49% Similarity=0.847 Sum_probs=125.0 Q ss_pred HHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEE Q ss_conf 36020069997898745767999999984656521034556688899975101001560121133331157557633630 Q gi|254780292|r 10 SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTT 89 (155) Q Consensus 10 ~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~ 89 (155) ..+.|.||+|||++|+||||||.||..|+|||||+|||+.||||+|||+||++|.+||+||++|+|++|||||||++.++ T Consensus 17 ~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~~~ 96 (165) T KOG3203 17 LAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQTT 96 (165) T ss_pred HHHHHHHEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHEECCCHHHHHHHHHCCCCCCCHHHHH T ss_conf 87766512533456756899999999986046776487667788799954556441220042340110178987302308 Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCC------HHHCCCEEE Q ss_conf 20000124879999999973089985478999627010789997------132085476 Q gi|254780292|r 90 AKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHP------HEAQKPVFM 142 (155) Q Consensus 90 ~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hp------h~aq~P~~l 142 (155) +++ +++++|++|+++||+||||+|+||+.+|.|||+|.|++|| +++++|..+ T Consensus 97 ~~q-~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~Ni~~~~~q~~~v 154 (165) T KOG3203 97 ADQ-LADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKVNIGSELHQPQGV 154 (165) T ss_pred HHH-HHHHCHHHHHHHHHHHHCCCCHHHHHHHHEEECCCCCCCCHHHHHHHHHCCCCCC T ss_conf 999-8541779999999970276233788776503435886570132067774366687 No 7 >cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies. Probab=100.00 E-value=0 Score=313.23 Aligned_cols=114 Identities=52% Similarity=0.913 Sum_probs=111.8 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCC Q ss_conf 69997898745767999999984656521034556688899975101001560121133331157557633630200001 Q gi|254780292|r 16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILA 95 (155) Q Consensus 16 W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~~~~ 95 (155) ||||||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.++.||+|||||||+++.++++++ T Consensus 1 w~viDA~~~~lGRLAs~iA~~L~GK~kp~y~p~~d~Gd~ViViNa~~i~~tG~k~~~k~y~~~~~~~gg~~~~~~~~~~- 79 (114) T cd00392 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLH- 79 (114) T ss_pred CEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEHHHEEEECCHHHCEEEEEEECCCCCCCCCCCHHHH- T ss_conf 9899589993588999999999637578867787689889998326836605312101246750478987347704544- Q ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCC Q ss_conf 24879999999973089985478999627010789 Q gi|254780292|r 96 GASPTNILKKAIARMLPRGPLARKQMKNLHIYAED 130 (155) Q Consensus 96 ~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~ 130 (155) +++|++||++||+||||+|++|+.+|+||+||+|+ T Consensus 80 ~~~P~~il~~aV~gMLPkn~~gr~~lkrL~vy~G~ 114 (114) T cd00392 80 PRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114 (114) T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCC T ss_conf 13989999999986189972399998598882799 No 8 >PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed Probab=100.00 E-value=1.4e-41 Score=264.75 Aligned_cols=125 Identities=28% Similarity=0.381 Sum_probs=113.1 Q ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH-HHHHHCCCCCCCCEEEECCCCCC Q ss_conf 99978987457679999999846565210345566888999751010015601211-33331157557633630200001 Q gi|254780292|r 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ-KTYYRHTGYPGGIKKTTAKEILA 95 (155) Q Consensus 17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~-k~y~~htgypGG~k~~~~~~~~~ 95 (155) .||||+|++||||||.||++|+| ||+|||||||+|.+||+|... +.|++|++++|+.....+... + T Consensus 2 ivIDA~~~vlGRLAs~vAk~L~g------------Gd~ViVINAeKi~iTG~K~~~~~~Y~~~~~~~~~~~~~~~~~~-~ 68 (143) T PRK06394 2 VVIDAEGAILGRLASYVAKLLLS------------GEEVVIVNAEKAVITGNREFIFEKYKQRRERKTISNPRRFGPY-Y 68 (143) T ss_pred EEEECCCCEEHHHHHHHHHHHHC------------CCEEEEEECCCEEEECCHHHHHHHEEEECCCCCCCCCCCCCCC-C T ss_conf 89978998808899999999858------------9979999761348846537744340453578989886212100-0 Q ss_pred CCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCCCC Q ss_conf 24879999999973089-985478999627010789997132085476166528131236 Q gi|254780292|r 96 GASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRR 154 (155) Q Consensus 96 ~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~~~ 154 (155) .+.|++|+++||+|||| ||++|+++|+||+||+|.+|||++|+|+.++++.++++|..+ T Consensus 69 ~r~P~~il~~aVrGMLP~K~~lGr~~~k~LkvY~G~ph~~~aqkp~~~~~a~~~~~~~~k 128 (143) T PRK06394 69 PKRPDNIVKRTIRGMLPYKKDRGREAFKRLKVYVGVPKELEGKEFETIDDADVSRLSGIK 128 (143) T ss_pred CCCHHHHHHHHHHCCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCHHHHHCCCCCC T ss_conf 029599999988334899985799998498897689986356787505778850648984 No 9 >TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755 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 L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit. Probab=99.96 E-value=2.2e-29 Score=193.31 Aligned_cols=122 Identities=28% Similarity=0.436 Sum_probs=97.7 Q ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECC-CCCC Q ss_conf 999789874576799999998465652103455668889997510100156012113333115755763363020-0001 Q gi|254780292|r 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAK-EILA 95 (155) Q Consensus 17 ~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~-~~~~ 95 (155) .||||+|.+||||||.||+.|+ .|..|||||||+|++||++...+.-|..+ +-+....-+-. ..++ T Consensus 1 ~ViDa~G~ilGRLAS~VAK~lL------------~G~~vVvVnAE~~vItG~~~~~~~~Y~~~-~~~~~~~n~~r~GP~~ 67 (144) T TIGR01077 1 TVIDASGHILGRLASVVAKRLL------------NGERVVVVNAEKIVITGNKYMVFEKYKEF-LRKRTKTNPRRFGPYF 67 (144) T ss_pred CEECCCCCHHHHHHHHHHHHHH------------CCCEEEEEECCEEEECCCCHHHHHHHHHH-HHHHHHCCCCCCCCCC T ss_conf 9567874313768999999875------------79867897226025227830456877887-6313213773679989 Q ss_pred CCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH-CCCCC Q ss_conf 24879999999973089-9854789996270107899971320854761665-28131 Q gi|254780292|r 96 GASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK-MNPKN 151 (155) Q Consensus 96 ~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~-~~~kn 151 (155) +|.|++|+++||+|||| |+..|+++|+||+||.|-+-|++.++-+.++-+. ..+-+ T Consensus 68 PR~P~rIf~rtvRGMLP~K~~RGr~Al~RLkVy~G~P~el~~k~~~~v~~A~~~~rL~ 125 (144) T TIGR01077 68 PRRPDRIFKRTVRGMLPWKTARGRAALRRLKVYVGIPKELQGKEFVTVPEALKVSRLS 125 (144) T ss_pred CCCCHHHHHHHHCCCCCCCCHHHHHHHHHCEECCCCCCCCCCCEEEEHHHHHHHHCCC T ss_conf 9870789998640358877743588885150015875851576056610122111268 No 10 >PTZ00068 60S ribosomal protein L13a; Provisional Probab=99.92 E-value=3.2e-25 Score=168.94 Aligned_cols=119 Identities=25% Similarity=0.445 Sum_probs=92.9 Q ss_pred EEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHH-C--CCCCCCCEEEECC Q ss_conf 069997898745767999999984656521034556688899975101001560121133331-1--5755763363020 Q gi|254780292|r 15 KWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR-H--TGYPGGIKKTTAK 91 (155) Q Consensus 15 ~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~-h--tgypGG~k~~~~~ 91 (155) +=.||||+|++||||||.||+.|+ .|..|||||||+|.+||+...++.-|. . ..--+. +.. T Consensus 4 k~iVIDa~ghllGRLAS~VAK~lL------------~G~kVvVVncE~i~ISG~~~r~k~ky~~~lrkr~~~n----p~~ 67 (201) T PTZ00068 4 KIIVIDGKGHLLGRLASVVAKELL------------LGQKIVVVRCELINISGSLFRNKLKYLEFLRKRTNTN----PRR 67 (201) T ss_pred CCEEEECCCCHHHHHHHHHHHHHH------------CCCEEEEEECHHHEECCCHHHHHHHHHHHHHHHHCCC----CCC T ss_conf 618996887389889999999995------------6995999962041222628999999999999987279----999 Q ss_pred CCCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCC----CEEEEHHHCCC Q ss_conf 000124879999999973089-98547899962701078999713208----54761665281 Q gi|254780292|r 92 EILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQK----PVFMDIAKMNP 149 (155) Q Consensus 92 ~~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~----P~~l~~~~~~~ 149 (155) ..++.+.|++|++++|+|||| |+..|+.+|+||+||+|.+.|++-++ |..+-+-.+++ T Consensus 68 GPf~~R~Ps~I~~RtVRGMLP~Kt~RG~~Al~rLkvyeGvP~pyd~~kr~vvP~Alrv~rlkp 130 (201) T PTZ00068 68 GPFHHRAPSKIFWRVVRGMLPHKTKRGAAALKRLKVYEGVPPPYDTGKRVVVPSALRHLRLKP 130 (201) T ss_pred CCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECHHHHHHHCCC T ss_conf 999888988999998637577687679999970744258996502588678025789875289 No 11 >KOG3204 consensus Probab=99.57 E-value=3.2e-15 Score=110.34 Aligned_cols=107 Identities=28% Similarity=0.477 Sum_probs=89.7 Q ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCC Q ss_conf 20069997898745767999999984656521034556688899975101001560121133331157557633630200 Q gi|254780292|r 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKE 92 (155) Q Consensus 13 ~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgypGG~k~~~~~~ 92 (155) ...-.++|+.++.+||||+.+|+.|+ .|+.|||+-||.|.++|+-|.+|-|-++ +=+.. . T Consensus 4 ~~~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk---~~~~n-----g 63 (197) T KOG3204 4 EVKLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRK---RLNRN-----G 63 (197) T ss_pred EEEEEECCCHHHHHHHHHHHHHHHHH------------CCCEEEEEEEEEEEEEEEEECCHHHHHH---HHCCC-----C T ss_conf 37875313403566358999999996------------1882899997668886001001577764---53046-----7 Q ss_pred CCCCCCHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCCHHHCCC Q ss_conf 00124879999999973089-985478999627010789997132085 Q gi|254780292|r 93 ILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEAQKP 139 (155) Q Consensus 93 ~~~~~~P~~il~~aV~gMLP-kn~lgr~~lkrL~vy~g~~Hph~aq~P 139 (155) .++.+-|.+|++++|+||+| +...|+..+.+|.+|+|-.+|++-|++ T Consensus 64 ~~hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r 111 (197) T KOG3204 64 PFHFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKR 111 (197) T ss_pred CCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHCCC T ss_conf 401112789998855051136788607799988873778982550687 No 12 >TIGR02845 spore_V_AD stage V sporulation protein AD; InterPro: IPR010894 This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation .. Probab=45.84 E-value=20 Score=17.83 Aligned_cols=43 Identities=26% Similarity=0.337 Sum_probs=36.0 Q ss_pred CHHHHHHHHHHHHHCCC-CCCCCCC-CCCCCEEEEECCCCC-CCCCCH Q ss_conf 45767999999984656-5210345-566888999751010-015601 Q gi|254780292|r 25 IVGRLASQIALRLRGKN-KPTYTPS-ADDGDHVVIINASKV-AFSGKK 69 (155) Q Consensus 25 ~lGRlAs~iA~~L~GKh-Kp~y~P~-~d~GD~VvViNa~ki-~~tG~K 69 (155) .|||+-+.|+.-|+-|+ .-.++-. .||| |-|=++++= +++|-- T Consensus 231 DL~rvG~~I~~~LL~e~yg~~~~~~Y~DCG--~~IY~~dqqdV~AGGS 276 (331) T TIGR02845 231 DLARVGSEILRKLLKEEYGYDVTEKYDDCG--VMIYRPDQQDVFAGGS 276 (331) T ss_pred CHHHHHHHHHHHHHHHHHCCCCCCEECCCC--EEEECCCCCCCCCCCC T ss_conf 300214899999988860875000104564--6753388781057785 No 13 >TIGR01704 MTA/SAH-Nsdase MTA/SAH nucleosidase; InterPro: IPR010049 This entry represents the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulphur ligands to an acceptor. In the case of 5'-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria , ,]. This enzyme is widely distributed in bacteria. ; GO: 0008782 adenosylhomocysteine nucleosidase activity, 0008930 methylthioadenosine nucleosidase activity, 0009164 nucleoside catabolic process, 0019509 methionine salvage. Probab=41.74 E-value=26 Score=17.15 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=29.1 Q ss_pred HHHHHHHHH-HHHHCCCCCCC----------CCCCCCCCEEEEECCCCC Q ss_conf 576799999-99846565210----------345566888999751010 Q gi|254780292|r 26 VGRLASQIA-LRLRGKNKPTY----------TPSADDGDHVVIINASKV 63 (155) Q Consensus 26 lGRlAs~iA-~~L~GKhKp~y----------~P~~d~GD~VvViNa~ki 63 (155) .|+++.-+. .+|+-..||+| +|....||-||=..+.+= T Consensus 49 IGKV~AA~~~TLLL~~~KPD~~INTGSAGGl~~TL~VGD~V~S~~~R~H 97 (229) T TIGR01704 49 IGKVAAALSATLLLDRYKPDVVINTGSAGGLAHTLKVGDVVVSDDVRYH 97 (229) T ss_pred CHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEEEECCCEEC T ss_conf 2378999888888750799769858875442331320567871674021 No 14 >TIGR02743 TraW type-F conjugative transfer system protein TraW; InterPro: IPR014114 This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm , .. Probab=28.75 E-value=35 Score=16.39 Aligned_cols=57 Identities=18% Similarity=0.311 Sum_probs=37.8 Q ss_pred HCCEEEEEEECCC-CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC Q ss_conf 6020069997898-7457679999999846565210345566888999751010015601211333311575 Q gi|254780292|r 11 EVEKKWILVDAKG-LIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY 81 (155) Q Consensus 11 ~~~r~W~iiDA~~-~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy 81 (155) .+++.|+.|||+| +.|......-+... |+- .+|.++-+--.+. +.|+.++||-.-|. T Consensus 132 ~ls~~LlFfDAdD~~Q~~wA~~~~~~~~-G~~------------K~ILt~Gs~~el~-~~L~~~IYFDQ~G~ 189 (217) T TIGR02743 132 SLSKTLLFFDADDPKQLAWAQQLLAQLP-GEV------------KWILTGGSVKELE-KRLDSRIYFDQNGK 189 (217) T ss_pred CCCCCEEEEECCCHHHHHHHHHHHHCCC-CCC------------EEEECCCCHHHHH-HHCCCCCEECCCCH T ss_conf 3276178881888899999998732038-983------------0887178979999-85289604636763 No 15 >TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855 Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars. This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm. Probab=28.33 E-value=32 Score=16.61 Aligned_cols=13 Identities=23% Similarity=0.815 Sum_probs=9.5 Q ss_pred CCCCCCCCEEEEE Q ss_conf 3455668889997 Q gi|254780292|r 46 TPSADDGDHVVII 58 (155) Q Consensus 46 ~P~~d~GD~VvVi 58 (155) |||+||+..|+|| T Consensus 88 HPH~d~~g~iaVV 100 (628) T TIGR01135 88 HPHTDEGGRIAVV 100 (628) T ss_pred CCCCCCCCCEEEE T ss_conf 8722699527999 No 16 >PRK10793 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional Probab=24.89 E-value=50 Score=15.46 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=19.1 Q ss_pred CEEEECCHHHCC-EEEEEEEC-CCCCHH Q ss_conf 511326843602-00699978-987457 Q gi|254780292|r 2 IPTFFQKSSEVE-KKWILVDA-KGLIVG 27 (155) Q Consensus 2 ~kT~~~k~~~~~-r~W~iiDA-~~~~lG 27 (155) .+|+.|.+-+++ +.|+++|| +|++|. T Consensus 34 ~~~~~p~~P~i~A~sailiD~~TG~VLy 61 (403) T PRK10793 34 IKTMIPGVPQIDAESYILIDYNSGKVLA 61 (403) T ss_pred CCCCCCCCCCCCCEEEEEEECCCCCCHH T ss_conf 4563799897554199999999994913 No 17 >PRK05461 apaG ApaG; Reviewed Probab=23.75 E-value=44 Score=15.80 Aligned_cols=14 Identities=36% Similarity=0.992 Sum_probs=12.0 Q ss_pred CCEEEEEEECCCCC Q ss_conf 02006999789874 Q gi|254780292|r 12 VEKKWILVDAKGLI 25 (155) Q Consensus 12 ~~r~W~iiDA~~~~ 25 (155) +.|.|.|.|+.|++ T Consensus 45 ~~R~W~I~d~~g~~ 58 (124) T PRK05461 45 LSRHWIITDANGRV 58 (124) T ss_pred EEEEEEEECCCCCE T ss_conf 96589999699988 No 18 >KOG3834 consensus Probab=22.03 E-value=71 Score=14.58 Aligned_cols=53 Identities=19% Similarity=0.172 Sum_probs=32.4 Q ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCC Q ss_conf 02006999789874576799999998465652103455668889997510100156012113333115755 Q gi|254780292|r 12 VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYP 82 (155) Q Consensus 12 ~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgyp 82 (155) ..-.||+++-..-..--+|..++ -+|| ||++..+++.+.+-.-...-.|.+.| T Consensus 107 ~~~vwHvl~V~p~SPaalAgl~~----------------~~DY--ivG~~~~~~~~~eDl~~lIeshe~kp 159 (462) T KOG3834 107 VESVWHVLSVEPNSPAALAGLRP----------------YTDY--IVGIWDAVMHEEEDLFTLIESHEGKP 159 (462) T ss_pred HHHEEEEEECCCCCHHHHCCCCC----------------CCCE--EECCHHHHCCCHHHHHHHHHHCCCCC T ss_conf 11123446438998788505533----------------6535--74354552341578999998602787 No 19 >pfam06303 MatP Organiser of macrodomain of Terminus of chromosome. This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localizes with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial c Probab=21.55 E-value=61 Score=14.96 Aligned_cols=51 Identities=14% Similarity=0.167 Sum_probs=40.9 Q ss_pred CCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH Q ss_conf 24879999999973089--9854789996270107899971320854761665 Q gi|254780292|r 96 GASPTNILKKAIARMLP--RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK 146 (155) Q Consensus 96 ~~~P~~il~~aV~gMLP--kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~ 146 (155) ...|..|++.--.-|-| .|++....-.|=+-|-.++|.|.-++.+.|++.- T Consensus 48 e~~P~~V~~WI~~hm~p~l~nkmkQaIRArRKRhFNAE~qhTrKKSIDLey~v 100 (148) T pfam06303 48 EHEPVKVLEWIKAHMNPELENKMKQAIRARRKRHFNAEKQHTRKKSIDLEYRV 100 (148) T ss_pred CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCHHHH T ss_conf 56819999999986699999999999999988106333122201342333999 No 20 >pfam06088 TLP-20 Nucleopolyhedrovirus telokin-like protein-20 (TLP20). This family consists of several Nucleopolyhedrovirus telokin-like protein-20 (TLP20) sequences. The function of this family is unknown but TLP20 is known to shares some antigenic similarities to the smooth muscle protein telokin although the amino acid sequence shows no homologies to telokin. Probab=21.00 E-value=51 Score=15.45 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=17.1 Q ss_pred HHHCCCCCCCCCCCCCCCEEEEECCCC Q ss_conf 984656521034556688899975101 Q gi|254780292|r 36 RLRGKNKPTYTPSADDGDHVVIINASK 62 (155) Q Consensus 36 ~L~GKhKp~y~P~~d~GD~VvViNa~k 62 (155) .|..-|.-.| -.+.||||+|+-|+-. T Consensus 53 ~L~~L~~~~~-~ti~~GdY~v~yN~~~ 78 (162) T pfam06088 53 LLDALHNNAH-STITCGDYTVVYNLVS 78 (162) T ss_pred HHHHHHHCCC-EEEEECCEEEEEEEEE T ss_conf 8788860883-3898368799987130 No 21 >PRK05097 hypothetical protein; Provisional Probab=20.65 E-value=65 Score=14.81 Aligned_cols=51 Identities=16% Similarity=0.181 Sum_probs=40.6 Q ss_pred CCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHH Q ss_conf 24879999999973089--9854789996270107899971320854761665 Q gi|254780292|r 96 GASPTNILKKAIARMLP--RGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAK 146 (155) Q Consensus 96 ~~~P~~il~~aV~gMLP--kn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~ 146 (155) ...|..|+..--.-|-| .|++....-.|=+-|-.++|.|.-++.+.|++.- T Consensus 48 e~~P~~v~~WI~~hm~p~L~nkmkQ~IRArRKRhFNAE~~hTrKKSIDLey~V 100 (150) T PRK05097 48 ENEPVKVLEWIDKHMNPELVNRMKQTIRARRKRHFNAEHQHTRKKSIDLEYAV 100 (150) T ss_pred CCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCHHH T ss_conf 35828999999985698889899999999988325422100001332442899 Done!