Query gi|254780256|ref|YP_003064669.1| 50S ribosomal protein L22 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 131 No_of_seqs 114 out of 1450 Neff 5.6 Searched_HMMs 39220 Date Tue May 24 10:03:51 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780256.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK12279 50S ribosomal protein 100.0 2.8E-44 0 281.7 11.4 115 15-129 1-116 (311) 2 CHL00034 rpl22 ribosomal prote 100.0 1.6E-43 0 277.3 12.4 111 16-126 1-111 (112) 3 PRK00565 rplV 50S ribosomal pr 100.0 7.4E-43 0 273.4 12.4 111 15-125 1-111 (111) 4 TIGR01044 rplV_bact ribosomal 100.0 1.5E-42 0 271.5 8.5 103 19-121 1-103 (103) 5 COG0091 RplV Ribosomal protein 100.0 7.8E-41 1.4E-45 261.4 11.7 113 13-125 7-119 (120) 6 pfam00237 Ribosomal_L22 Riboso 100.0 2E-39 5.2E-44 253.1 11.4 105 19-123 1-105 (105) 7 cd00336 Ribosomal_L22 Ribosoma 100.0 7.2E-37 1.8E-41 238.1 11.1 105 17-121 1-105 (105) 8 PRK04223 rpl22p 50S ribosomal 100.0 1.3E-35 3.2E-40 230.7 11.9 119 6-125 5-154 (154) 9 TIGR01038 L22_arch ribosomal p 100.0 1.9E-31 4.9E-36 206.1 8.8 115 9-124 4-151 (151) 10 KOG1711 consensus 100.0 2.4E-31 6E-36 205.5 8.0 113 15-127 70-183 (218) 11 PTZ00178 60S ribosomal protein 99.9 5.3E-27 1.4E-31 179.8 9.2 120 7-127 5-156 (177) 12 KOG3353 consensus 99.1 8.4E-13 2.1E-17 96.1 -5.2 113 12-125 4-148 (175) 13 PRK11325 scaffold protein; Pro 67.5 11 0.00027 18.8 5.8 60 17-76 56-125 (127) 14 TIGR03419 NifU_clost FeS clust 66.7 11 0.00029 18.7 6.0 61 17-77 50-121 (121) 15 TIGR02871 spore_ylbJ sporulati 55.4 9.9 0.00025 19.0 2.4 39 37-75 174-212 (384) 16 TIGR01994 SUF_scaf_2 SUF syste 36.8 35 0.0009 15.7 3.0 35 17-51 55-89 (139) 17 pfam01024 Colicin Colicin pore 35.8 37 0.00094 15.6 3.7 45 29-73 36-83 (187) 18 pfam01592 NifU_N NifU-like N t 33.0 41 0.001 15.4 4.5 57 17-73 53-120 (126) 19 TIGR01803 CM-like chorismate m 28.0 47 0.0012 15.0 2.3 22 59-81 44-65 (82) 20 TIGR02709 branched_ptb branche 26.7 44 0.0011 15.2 2.0 25 60-84 12-45 (271) 21 TIGR02607 antidote_HigA addict 20.3 64 0.0016 14.2 1.8 42 15-56 21-62 (81) No 1 >PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional Probab=100.00 E-value=2.8e-44 Score=281.72 Aligned_cols=115 Identities=23% Similarity=0.339 Sum_probs=110.5 Q ss_pred HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-CCCCCHHHEEEEEEEECCC Q ss_conf 123112148750889999999984798699999888658202479999999999999984-0599823369999998898 Q gi|254780256|r 15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAEN-NHDLDVDRLIVSEAYVGKS 93 (131) Q Consensus 15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~-n~~ld~~~L~I~~~~v~~G 93 (131) +|++|.+||+|+||+|+|+|+|+|||++|++|+++|.|+|+++|.+|.|+|.||+|||++ |+|+|+|+|||++|+||+| T Consensus 1 MEAKAiaRyVRISPrKARlV~DlIRGK~V~EAlaILkFTPKKAA~iV~KvLkSAiANAe~NN~glD~D~LyVkea~VDEG 80 (311) T PRK12279 1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILSNTPKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQG 80 (311) T ss_pred CCCEEEECCCEECHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEEEECCC T ss_conf 96054525534167899999998879979999999840843236999999999999998610389867849999997888 Q ss_pred CEEEEEEECCCCCCCCEECCCCEEEEEEEECCCCCC Q ss_conf 114201025666637201785008999985172332 Q gi|254780256|r 94 VFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDEGK 129 (131) Q Consensus 94 ~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~~k 129 (131) |++|||+|||||||++|+||||||||||++..+|.+ T Consensus 81 PTLKRfrPRArGRA~rIrKRTSHITIVLSDDvner~ 116 (311) T PRK12279 81 PTMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNERE 116 (311) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHH T ss_conf 720143703268634301566767999788865557 No 2 >CHL00034 rpl22 ribosomal protein L22 Probab=100.00 E-value=1.6e-43 Score=277.30 Aligned_cols=111 Identities=34% Similarity=0.477 Sum_probs=109.2 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCE Q ss_conf 23112148750889999999984798699999888658202479999999999999984059982336999999889811 Q gi|254780256|r 16 EANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVF 95 (131) Q Consensus 16 e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~ 95 (131) |++|.+||+|+||+|+|+|+|+|||++|++|++||+|+|+++|.+|+|+|+||++||+||+|+|+|+|||+++|||+||+ T Consensus 1 E~~A~~r~ir~SprK~r~v~~~IRG~~v~~Al~~L~f~~kk~A~~i~K~l~SAvaNA~~n~~~d~~~L~V~~~~v~~G~~ 80 (112) T CHL00034 1 EVYALAKYIRMSPHKVRRVIDQIRGRSYEEALMILEFMPYRACYPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPT 80 (112) T ss_pred CCEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHEEEEEEEECCCCC T ss_conf 94898087623879999999998699199999997118633699999999999999984616881114999999899970 Q ss_pred EEEEEECCCCCCCCEECCCCEEEEEEEECCC Q ss_conf 4201025666637201785008999985172 Q gi|254780256|r 96 MKRFHCRGRQRIGRIVRPFSRLTVIVREVSD 126 (131) Q Consensus 96 ~KR~~prarGRa~~i~k~~sHi~VvL~e~~~ 126 (131) +|||+||||||+++|+||+|||+|+|+|.+. T Consensus 81 lKR~rprarGRa~~i~K~~sHi~Vvl~e~~k 111 (112) T CHL00034 81 LKRFRPRAQGRSYPIKKPTCHITIVLKDISK 111 (112) T ss_pred CCCCCCHHCCCCCCCCCCCCEEEEEEEECCC T ss_conf 1202841048866562553039999986547 No 3 >PRK00565 rplV 50S ribosomal protein L22; Reviewed Probab=100.00 E-value=7.4e-43 Score=273.38 Aligned_cols=111 Identities=51% Similarity=0.697 Sum_probs=108.9 Q ss_pred HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCC Q ss_conf 12311214875088999999998479869999988865820247999999999999998405998233699999988981 Q gi|254780256|r 15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSV 94 (131) Q Consensus 15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~ 94 (131) +|++|.+||+|+||+|+++|+|+|||++|+||+.||+|+|+++|.+|.|+|+||++||++|+|+|+|+|||+++|||+|| T Consensus 1 m~~~A~~k~ir~Sp~K~r~v~~~IrG~~v~eAl~~L~f~~kkaA~~i~k~L~SA~aNA~~~~~ld~~~L~I~~~~v~~G~ 80 (111) T PRK00565 1 MEAKAKARFVRISPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLKSAIANAENNHGLDIDELVVKEAFVDEGP 80 (111) T ss_pred CEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCC T ss_conf 91798718775488999999999869919999999821972047899999999999998602687010599999989998 Q ss_pred EEEEEEECCCCCCCCEECCCCEEEEEEEECC Q ss_conf 1420102566663720178500899998517 Q gi|254780256|r 95 FMKRFHCRGRQRIGRIVRPFSRLTVIVREVS 125 (131) Q Consensus 95 ~~KR~~prarGRa~~i~k~~sHi~VvL~e~~ 125 (131) ++|||+||||||+++++||+|||+|+|+|.+ T Consensus 81 ~lKR~~prarGRa~~i~k~~sHi~vvL~e~~ 111 (111) T PRK00565 81 TLKRFRPRARGRASRIRKRTSHITVVVSERK 111 (111) T ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEECCC T ss_conf 2567698536898874488656899994389 No 4 >TIGR01044 rplV_bact ribosomal protein L22; InterPro: IPR005727 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 model decribes bacterial and chloroplast ribosomal protein L22; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit. Probab=100.00 E-value=1.5e-42 Score=271.51 Aligned_cols=103 Identities=44% Similarity=0.636 Sum_probs=101.3 Q ss_pred EECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEE Q ss_conf 12148750889999999984798699999888658202479999999999999984059982336999999889811420 Q gi|254780256|r 19 AIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKR 98 (131) Q Consensus 19 A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR 98 (131) |.+|++|+||+|+|+|+|+||||+|.+||.+|+|+|+++|.+|.|+|.||+||||||+|+|+++|.|.++|||+||++|| T Consensus 1 A~~R~vR~sp~KARLV~DLirGk~v~~Al~iL~~tP~~Aa~~~~KVl~SA~ANAehN~~~D~~~L~v~~~~vD~GP~lkR 80 (103) T TIGR01044 1 AKARFVRISPRKARLVADLIRGKSVAEALDILRFTPKKAAELIKKVLASAIANAEHNNGLDADNLVVVTIFVDEGPTLKR 80 (103) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCC T ss_conf 98751021444788898873574778899987307040137899999998763205654582231587788778496000 Q ss_pred EEECCCCCCCCEECCCCEEEEEE Q ss_conf 10256666372017850089999 Q gi|254780256|r 99 FHCRGRQRIGRIVRPFSRLTVIV 121 (131) Q Consensus 99 ~~prarGRa~~i~k~~sHi~VvL 121 (131) |+|||+|||..|+|+||||||++ T Consensus 81 ~~PRA~GRA~~I~KrTSHi~V~V 103 (103) T TIGR01044 81 IRPRAKGRASRIRKRTSHITVVV 103 (103) T ss_pred CCCHHCCCHHHCCCCCCCEEEEC T ss_conf 13000240331268876446528 No 5 >COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=7.8e-41 Score=261.43 Aligned_cols=113 Identities=51% Similarity=0.648 Sum_probs=110.9 Q ss_pred HHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECC Q ss_conf 01123112148750889999999984798699999888658202479999999999999984059982336999999889 Q gi|254780256|r 13 GDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGK 92 (131) Q Consensus 13 ~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~ 92 (131) ++++++|.++++|+||+|+++|+++|||+++++|+.+|+|+|+|+|+.|.|+|.||++||++|+|||+|+|||++||||+ T Consensus 7 ~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~ 86 (120) T COG0091 7 PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFVPKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDK 86 (120) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECC T ss_conf 03667764123767868999999998399499999999867488899999999999965775149986787999998478 Q ss_pred CCEEEEEEECCCCCCCCEECCCCEEEEEEEECC Q ss_conf 811420102566663720178500899998517 Q gi|254780256|r 93 SVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS 125 (131) Q Consensus 93 G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~ 125 (131) ||++|||+|||+||++++.+|+|||||||+|.+ T Consensus 87 gp~lKR~~pRA~GRa~~i~k~tshItvvv~e~~ 119 (120) T COG0091 87 GPVLKRFMPRARGRATRINKRTSHITVVVREKE 119 (120) T ss_pred CCEEEEECCCCCCCCCCCCCCCCEEEEEEEECC T ss_conf 842220134136765632478700899996068 No 6 >pfam00237 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. Probab=100.00 E-value=2e-39 Score=253.07 Aligned_cols=105 Identities=48% Similarity=0.632 Sum_probs=103.2 Q ss_pred EECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEE Q ss_conf 12148750889999999984798699999888658202479999999999999984059982336999999889811420 Q gi|254780256|r 19 AIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKR 98 (131) Q Consensus 19 A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR 98 (131) |.++|+++||+|+++|+++||||+|++|++||+|+|+|+|.+|.|+|+||++||++++|+|+|+|||+++|||+||++|| T Consensus 1 A~~r~ir~S~kK~r~v~~~Irg~~v~~A~~~L~~~p~kaa~~i~k~L~sA~aNA~~~~~~d~~~L~I~~~~v~~g~~~KR 80 (105) T pfam00237 1 AVARYIRISPKKARLVADLIRGKSVEEALAILEFVPKKAAKIILKLLKSAVANAENNKGLDPDNLYIKEIFVDKGPTLKR 80 (105) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCCCCC T ss_conf 96153614889999999998699199999998319876899999999999998987036885684999999834870557 Q ss_pred EEECCCCCCCCEECCCCEEEEEEEE Q ss_conf 1025666637201785008999985 Q gi|254780256|r 99 FHCRGRQRIGRIVRPFSRLTVIVRE 123 (131) Q Consensus 99 ~~prarGRa~~i~k~~sHi~VvL~e 123 (131) ++||||||++++++|+|||+|+|+| T Consensus 81 ~~prarGRa~~i~k~~~Hi~vvl~e 105 (105) T pfam00237 81 FRPRARGRATPIRKRTSHITIVLSE 105 (105) T ss_pred CCCCCCCCCCCCCCCCCCEEEEEEC T ss_conf 7857788887753796018999829 No 7 >cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome. Probab=100.00 E-value=7.2e-37 Score=238.06 Aligned_cols=105 Identities=43% Similarity=0.495 Sum_probs=103.0 Q ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEE Q ss_conf 31121487508899999999847986999998886582024799999999999999840599823369999998898114 Q gi|254780256|r 17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFM 96 (131) Q Consensus 17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~ 96 (131) ++|.++|+++||+|+++|+++||||+|++|+.||+|+|+++|..|.++|+||.+||++++++|+|+|||+++|||+||++ T Consensus 1 ~ka~~~~ir~S~kK~~~v~~~IrG~~v~~A~~~L~~~~~k~a~~i~k~l~sa~~nA~~~~~~d~~~L~I~~~~v~~G~~~ 80 (105) T cd00336 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLDDPDKLYIKHIQVNKGPTL 80 (105) T ss_pred CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEEEEECCCCC T ss_conf 92202776057899999999986991999999986688518999999999999989982699857849999999048715 Q ss_pred EEEEECCCCCCCCEECCCCEEEEEE Q ss_conf 2010256666372017850089999 Q gi|254780256|r 97 KRFHCRGRQRIGRIVRPFSRLTVIV 121 (131) Q Consensus 97 KR~~prarGRa~~i~k~~sHi~VvL 121 (131) ||++||||||++++++++|||+|+| T Consensus 81 kr~~~rarGR~~~~~k~~~hi~vvl 105 (105) T cd00336 81 KRRRPRARGRANPIRKRTCHITVVL 105 (105) T ss_pred CCCCCCCCCCCCCCCCCCCCEEEEC T ss_conf 6768777888888626850389969 No 8 >PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed Probab=100.00 E-value=1.3e-35 Score=230.71 Aligned_cols=119 Identities=29% Similarity=0.291 Sum_probs=111.5 Q ss_pred HHHHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC-------------------------------C Q ss_conf 576742101123112148750889999999984798699999888658-------------------------------2 Q gi|254780256|r 6 SVSKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS-------------------------------R 54 (131) Q Consensus 6 ~~~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~-------------------------------~ 54 (131) .++-...+++.++|.++++|+||+|+++||++||||++++|+.+|++. | T Consensus 5 ~Ys~~~d~~k~akA~~~~lriS~K~~~eva~~IrGm~~~~A~~~L~~Vi~~k~~VPf~r~~~~vghr~~~~~~~~~GR~P 84 (154) T PRK04223 5 KYSVEIDPEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRPVPFKRHNKKVGHRKGIWAGWKAGRYP 84 (154) T ss_pred ECCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCC T ss_conf 03778998622467516774056999999999869909999999999875044302574158766542212478877680 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECC Q ss_conf 02479999999999999984059982336999999889811420102566663720178500899998517 Q gi|254780256|r 55 KRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS 125 (131) Q Consensus 55 kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~ 125 (131) +|+|+.|.|+|+||.+||+++ |||+|+|||.+++||+||++||++|||+||++++++++|||+|||+|.. T Consensus 85 ~Kaa~~ilklL~sA~aNA~~k-glD~d~L~I~~i~v~~G~~~kR~~pRA~GRa~~~~k~~~HIeivl~E~~ 154 (154) T PRK04223 85 VKAAKAILKLLENAENNAEYK-GLDTEKLVIVHIAAHKGRVIKRYMPRAFGRATPKNTETVHIEVIVEEVR 154 (154) T ss_pred HHHHHHHHHHHHHHHHHHHHC-CCCCHHEEEEEEEECCCCEECCCCCCCCCCCCCCCCCCCCEEEEEEECC T ss_conf 889999999999999778754-9980133999999688842015573237887875589844799998439 No 9 >TIGR01038 L22_arch ribosomal protein L22; InterPro: IPR005721 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 family describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit. Probab=99.97 E-value=1.9e-31 Score=206.07 Aligned_cols=115 Identities=26% Similarity=0.268 Sum_probs=108.1 Q ss_pred HHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC---------------------------------CC Q ss_conf 742101123112148750889999999984798699999888658---------------------------------20 Q gi|254780256|r 9 KRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS---------------------------------RK 55 (131) Q Consensus 9 ~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~---------------------------------~k 55 (131) +...+++.++|.++|+++|||-++.||+.|+||.++||.-+|+=. |. T Consensus 4 ~~~d~~k~A~A~G~~l~iS~K~a~E~craI~Gm~l~~A~KYLe~Vi~~~raVPFRR~~~kvGhr~G~ak~~Gw~~GRYP~ 83 (151) T TIGR01038 4 KPEDESKSAKARGRNLRISFKHAREICRAIRGMKLEEARKYLEDVIEMKRAVPFRRYNKKVGHRRGLAKKWGWTAGRYPV 83 (151) T ss_pred CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCH T ss_conf 88873343431026786465547899987369636888888999998608852020167613577761205777888607 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEEC Q ss_conf 247999999999999998405998233699999988981142010256666372017850089999851 Q gi|254780256|r 56 RIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREV 124 (131) Q Consensus 56 k~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~ 124 (131) |+|+.|.|+|..|.||||++ |||+|+|+|.+|.|++||+++|+.|||.||++|....+|||.|||+|. T Consensus 84 KaAk~~lk~L~NaeANAE~K-GLD~ekL~I~Hi~~~kGp~~rR~~PRAfGRaTP~~~~~~HIE~v~~E~ 151 (151) T TIGR01038 84 KAAKFILKVLQNAEANAEYK-GLDVEKLKIIHIQANKGPVIRRWMPRAFGRATPYNSSTTHIELVVEEK 151 (151) T ss_pred HHHHHHHHHHHHHHHHHHHC-CCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEC T ss_conf 89999999999999888752-899642678887414885023558742133078898971588775529 No 10 >KOG1711 consensus Probab=99.97 E-value=2.4e-31 Score=205.53 Aligned_cols=113 Identities=42% Similarity=0.564 Sum_probs=109.0 Q ss_pred HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEE-EEEEECCC Q ss_conf 12311214875088999999998479869999988865820247999999999999998405998233699-99998898 Q gi|254780256|r 15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIV-SEAYVGKS 93 (131) Q Consensus 15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I-~~~~v~~G 93 (131) .|+.|..+.|++||+||+++|++|+||+|++||.||+|+++|+|.+|+++|.||.+||.+|+|+|+++|+| +++|+++| T Consensus 70 ~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~~s~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g 149 (218) T KOG1711 70 PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLEFSDKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQG 149 (218) T ss_pred HHHHHHHHHHHHCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCC T ss_conf 66899999986288999999999839979999987522067888999999999876557751999622279875103530 Q ss_pred CEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC Q ss_conf 1142010256666372017850089999851723 Q gi|254780256|r 94 VFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE 127 (131) Q Consensus 94 ~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~ 127 (131) .++||.+++||||-++|++++|||+|+|.|.++. T Consensus 150 ~~~Krl~~hargr~~ii~~~yvhi~v~L~e~s~~ 183 (218) T KOG1711 150 NELKRLKVHARGRFGIIRRPYVHIFVKLEEGSPP 183 (218) T ss_pred HHHHHEEEECCCCCCCEECCCEEEEEEEEECCCC T ss_conf 2444302213676541001314589998306876 No 11 >PTZ00178 60S ribosomal protein L22/L17e; Provisional Probab=99.94 E-value=5.3e-27 Score=179.84 Aligned_cols=120 Identities=24% Similarity=0.232 Sum_probs=110.5 Q ss_pred HHHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC--------------------------------C Q ss_conf 76742101123112148750889999999984798699999888658--------------------------------2 Q gi|254780256|r 7 VSKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS--------------------------------R 54 (131) Q Consensus 7 ~~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~--------------------------------~ 54 (131) ......+++.++|...++++|++.++.+|+.|+||++++|..+|+-. | T Consensus 5 s~~~~~p~k~aKArg~~lrVsfK~t~Eia~aIkGm~l~kA~~yLe~Vi~~K~~VPFrRyn~gvg~~~q~k~~g~~~GRwP 84 (177) T PTZ00178 5 ARKPSVSSKSAKAKGSDLRVHFKNTYETARAIKGMTLRKAQQYLQDVLAKKRCVPFRRFNGGVGRTAQAKEFGQTQGRWP 84 (177) T ss_pred CCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCCCCCCCC T ss_conf 57989930445632678854406399999998498799999999999864350357874598877565221589877682 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC Q ss_conf 0247999999999999998405998233699999988981142010256666372017850089999851723 Q gi|254780256|r 55 KRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE 127 (131) Q Consensus 55 kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~ 127 (131) +|+|+.|.++|++|.+||+. .|||+|+|+|.++.|++||.++|+.|||+||++|+..++|||+++|.|.++. T Consensus 85 ~Ksa~~iL~lLkna~aNAe~-kGLD~d~L~I~hi~vnka~~~rrr~~RAhGRi~p~~s~p~hIeiil~E~~~~ 156 (177) T PTZ00178 85 EKSVVFVLSLLKNAEANAEV-KGLDPEKLVIKHVQVNRAPRGRRRTYRAHGRINPFMSSPCHVELIAAEKDER 156 (177) T ss_pred HHHHHHHHHHHHHHHHCCCC-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCC T ss_conf 89999999999756740140-4887665389998863464224767654776677769980289997146555 No 12 >KOG3353 consensus Probab=99.11 E-value=8.4e-13 Score=96.10 Aligned_cols=113 Identities=27% Similarity=0.237 Sum_probs=103.3 Q ss_pred HHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC--------------------------------CCHHHH Q ss_conf 101123112148750889999999984798699999888658--------------------------------202479 Q gi|254780256|r 12 MGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS--------------------------------RKRIAG 59 (131) Q Consensus 12 ~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~--------------------------------~kk~A~ 59 (131) ..++..+|...+++.+.+..+..+..|++++...|+..|.-. |+++|. T Consensus 4 ~~~k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksae 83 (175) T KOG3353 4 NPTKSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAE 83 (175) T ss_pred CCCHHHHCCCCCEEEEECCCCCCCHHCCCCCCCCCEEEECCCHHHCCCCCCEECCCCCCCCCHHHHHCCCCCCCCCHHHH T ss_conf 33222302655278873257644100047650222343212012200234145589868643223302354766423889 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECC Q ss_conf 999999999999984059982336999999889811420102566663720178500899998517 Q gi|254780256|r 60 EVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS 125 (131) Q Consensus 60 ~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~ 125 (131) .+.-.|+.|.+||+.+ |+|.|.|+|.++.|++.|.+.|-.+||.||..++-.-.|||.+||.|.+ T Consensus 84 fll~~LkN~esnaElk-gldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke 148 (175) T KOG3353 84 FLLHMLKNAESNAELK-GLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKE 148 (175) T ss_pred HHHHHHHHHHHCCCCC-CCCCCEEEEEEHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHC T ss_conf 8899987366242113-7676646743013302413666788753532565688699999997531 No 13 >PRK11325 scaffold protein; Provisional Probab=67.55 E-value=11 Score=18.79 Aligned_cols=60 Identities=18% Similarity=0.197 Sum_probs=44.4 Q ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHH--------HHHC--CCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 311214875088999999998479869999988--------8658--20247999999999999998405 Q gi|254780256|r 17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALAD--------LEFS--RKRIAGEVRKTLCSAVANAENNH 76 (131) Q Consensus 17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~--------L~f~--~kk~A~~i~k~L~SA~aNA~~n~ 76 (131) ++-.+..--+|--=.-.++.++.|++++||+.+ |.+. ..+.|.+-.++|+.|+.+.+.+. T Consensus 56 ~~F~~~GC~is~AsaS~~te~~~Gkt~~ea~~i~~~~i~e~l~lpp~r~~CA~La~~aL~~Ai~~y~~kq 125 (127) T PRK11325 56 AKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQ 125 (127) T ss_pred EEEEECCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8897128589999999999998399799998555688998617993101799999999999999999850 No 14 >TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. Probab=66.69 E-value=11 Score=18.69 Aligned_cols=61 Identities=10% Similarity=0.117 Sum_probs=45.1 Q ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH---------H--CCCHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 31121487508899999999847986999998886---------5--8202479999999999999984059 Q gi|254780256|r 17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE---------F--SRKRIAGEVRKTLCSAVANAENNHD 77 (131) Q Consensus 17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~---------f--~~kk~A~~i~k~L~SA~aNA~~n~~ 77 (131) ++-.+..--+|.==.-.++++|+|++++||+.+-. + ...+.|.+-..+|+.|+.+.+.+.| T Consensus 50 i~F~~~GCais~AsaS~~~e~i~Gk~l~ea~~i~~~~i~~~l~~lpp~r~~CA~La~~Al~~Al~~y~~k~g 121 (121) T TIGR03419 50 VKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 (121) T ss_pred EEEEEECCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999965558899999999999849949999863548999997599931166999999999999999987269 No 15 >TIGR02871 spore_ylbJ sporulation integral membrane protein YlbJ; InterPro: IPR014226 Members of this entry include YlbJ, from Bacillus subtilis. They are found exclusively in the Firmicutes (low-GC Gram-positive bacteria) and are known from studies in B. subtilis to be part of the sigma-E regulon . Mutation leads to a sporulation defect, confirming that members of this entry are involved in sporulation. The protein appears to be universal among endospore-forming bacteria, and in Symbiobacterium thermophilum IAM 14863, there are two ORFs encoding YlbJ that are distant from each other.. Probab=55.35 E-value=9.9 Score=19.00 Aligned_cols=39 Identities=26% Similarity=0.215 Sum_probs=33.8 Q ss_pred HHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 847986999998886582024799999999999999840 Q gi|254780256|r 37 MIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENN 75 (131) Q Consensus 37 ~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n 75 (131) .++--++.+|+.-+.-..-+.-..+.++|++|+.||.++ T Consensus 174 ~~~~fS~~~AL~~l~~~~~~s~~~~G~~L~~aie~av~t 212 (384) T TIGR02871 174 KKTEFSLKDALTGLHSIRLKSKKNIGKLLKEAIENAVKT 212 (384) T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 687665788988783235406788768999999999999 No 16 >TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family; InterPro: IPR011341 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This family represents SufU, NifU-like proteins that are part of the SUF system, one of the two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.; GO: 0005506 iron ion binding, 0005515 protein binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly. Probab=36.82 E-value=35 Score=15.74 Aligned_cols=35 Identities=23% Similarity=0.305 Sum_probs=25.8 Q ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 31121487508899999999847986999998886 Q gi|254780256|r 17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE 51 (131) Q Consensus 17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~ 51 (131) ++=....--||.==+-.++++|+|++|.||+..-+ T Consensus 55 ~~F~G~GCsIS~ASaSmM~e~i~Gk~~~eA~~~~~ 89 (139) T TIGR01994 55 IAFEGEGCSISQASASMMTELIKGKTVEEALKLVE 89 (139) T ss_pred EEEECCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 88735767089988999999745989889999999 No 17 >pfam01024 Colicin Colicin pore forming domain. Probab=35.77 E-value=37 Score=15.64 Aligned_cols=45 Identities=27% Similarity=0.289 Sum_probs=28.4 Q ss_pred HHHHHHHHHHCCC---CHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 9999999984798---69999988865820247999999999999998 Q gi|254780256|r 29 QKLNLVAAMIRGK---RVSDALADLEFSRKRIAGEVRKTLCSAVANAE 73 (131) Q Consensus 29 ~K~r~va~~IrG~---~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~ 73 (131) +=.+.+++.++|+ +++||+..++=...-...-+-+.=+.|+.||- T Consensus 36 ~lA~elA~~~KGKkIRn~~dAl~s~eK~~~n~nkK~~~~Dr~AI~nAl 83 (187) T pfam01024 36 KLARELADDAKGKKIRSVDEALASFEKYKANLNKKINAADRDAIANAL 83 (187) T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHCCHHHHHHHHHHH T ss_conf 999999987067713789999999999872820214561199999999 No 18 >pfam01592 NifU_N NifU-like N terminal domain. This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters. Probab=32.99 E-value=41 Score=15.37 Aligned_cols=57 Identities=16% Similarity=0.093 Sum_probs=40.3 Q ss_pred EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHH-----HH------CCCHHHHHHHHHHHHHHHHHH Q ss_conf 3112148750889999999984798699999888-----65------820247999999999999998 Q gi|254780256|r 17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADL-----EF------SRKRIAGEVRKTLCSAVANAE 73 (131) Q Consensus 17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L-----~f------~~kk~A~~i~k~L~SA~aNA~ 73 (131) ++-.+..--+|-==+-.+++++.|++++||..+- ++ ...+.+.+-..+|++|+.+-. T Consensus 53 i~F~~~GCais~AsaS~l~e~i~Gk~~~ea~~i~~~~i~~~lg~l~~~r~~Ca~La~~al~~av~~y~ 120 (126) T pfam01592 53 AKFKTFGCGSAIASSSALTELVKGKTLDEALKITNTDIAEELGGLPPVKMHCSVLGDDALKAAIADYK 120 (126) T ss_pred EEEEEECCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 89986376888999999999986993999986169999999737999740089999999999999817 No 19 >TIGR01803 CM-like chorismate mutase related enzymes; InterPro: IPR008241 Isochorismate pyruvate-lyase (IPL; PchB) catalyses the second reaction in the pyochelin biosynthetic pathway of Pseudomonas aeruginosa, conversion of isochorismate to salicylate plus pyruvate (following the initial PchA-dependent conversion of chorismate to isochorismate) . This enzyme can also carry out the chorismate mutase (CM) reaction, but with a low catalytic efficiency. It is unlikely that PchB plays a significant role in aromatic amino acid biosynthesis. This enzyme is a stand-alone version of a chorismate mutase domain of the AroQ class. The three types of CM are AroQ class, Prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, Eukaryotic type (IPR008238 from INTERPRO); and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved . The PchB-type of chorismate mutase domain, while sharing conserved residues and the predicted secondary structure with the other subgroups of the AroQ class (Prokaryotic type), has isochorismate pyruvate-lyase (IPL) as a primary catalytic activity. PchB can still use the same active site either for the IPL or for the CM reaction. It has been suggested that PchB was derived from an AroQ-class CM by a gene duplication event followed by selection for efficient IPL function in the course of the evolution of the pyochelin siderophore pathway, with only residual CM activity remaining. It can be further speculated that contemporary CMs may already possess (weak) IPL activity . For additional information please see , , .. Probab=27.96 E-value=47 Score=15.02 Aligned_cols=22 Identities=27% Similarity=0.199 Sum_probs=17.5 Q ss_pred HHHHHHHHHHHHHHHHCCCCCHH Q ss_conf 99999999999999840599823 Q gi|254780256|r 59 GEVRKTLCSAVANAENNHDLDVD 81 (131) Q Consensus 59 ~~i~k~L~SA~aNA~~n~~ld~~ 81 (131) .-|..+..+|.=||+. +||||+ T Consensus 44 ~RvA~v~~naaR~A~e-~GlDp~ 65 (82) T TIGR01803 44 ERVAEVKENAARYAAE-LGLDPD 65 (82) T ss_pred HHHHHHHHHHHHHHHH-CCCCHH T ss_conf 4689862877766786-389988 No 20 >TIGR02709 branched_ptb branched-chain phosphotransacylase; InterPro: IPR014081 This entry distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase 2.3.1.19 from EC, (IPR014079 from INTERPRO) and phosphate acetyltransferase 2.3.1.8 from EC, (IPR004614 from INTERPRO). Members of this family and of IPR014079 from INTERPRO show considerable cross reactivity, and the occurrence of a member of either family proximate to an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds.. Probab=26.69 E-value=44 Score=15.18 Aligned_cols=25 Identities=32% Similarity=0.474 Sum_probs=11.1 Q ss_pred HHHHHHHHHHHHHHH---------CCCCCHHHEE Q ss_conf 999999999999984---------0599823369 Q gi|254780256|r 60 EVRKTLCSAVANAEN---------NHDLDVDRLI 84 (131) Q Consensus 60 ~i~k~L~SA~aNA~~---------n~~ld~~~L~ 84 (131) .|..+++.|...|++ |.+||.++|| T Consensus 12 eilqlvkkalkeaeqPlqfivfdtnenldtenlW 45 (271) T TIGR02709 12 EILQLVKKALKEAEQPLQFIVFDTNENLDTENLW 45 (271) T ss_pred HHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHH T ss_conf 7999999987631287068997155554512431 No 21 >TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding. Probab=20.31 E-value=64 Score=14.23 Aligned_cols=42 Identities=24% Similarity=0.123 Sum_probs=36.6 Q ss_pred HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCH Q ss_conf 123112148750889999999984798699999888658202 Q gi|254780256|r 15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKR 56 (131) Q Consensus 15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk 56 (131) -++.+.++.+.+|+.-+..|++.=+|.+.|-|+-.-+|.-.. T Consensus 21 ~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~s 62 (81) T TIGR02607 21 LSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTS 62 (81) T ss_pred HHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCC T ss_conf 068999987099978888887448998888999999973898 Done!