Query gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 135 No_of_seqs 117 out of 1182 Neff 6.9 Searched_HMMs 39220 Date Sun May 29 15:38:36 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780329.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG0360 RpsF Ribosomal protein 100.0 4.5E-31 1.1E-35 202.7 11.7 108 2-109 1-108 (112) 2 CHL00123 rps6 ribosomal protei 100.0 5.8E-31 1.5E-35 202.1 11.7 93 1-93 5-97 (97) 3 PRK00453 rpsF 30S ribosomal pr 100.0 8.1E-30 2.1E-34 195.4 12.4 95 1-95 1-95 (95) 4 pfam01250 Ribosomal_S6 Ribosom 100.0 1.9E-28 4.8E-33 187.3 11.9 92 2-93 1-92 (92) 5 TIGR00166 S6 ribosomal protein 99.6 1.4E-15 3.4E-20 111.9 5.4 94 1-94 1-101 (102) 6 KOG4708 consensus 99.5 2.6E-15 6.7E-20 110.3 3.7 95 1-96 3-101 (141) 7 pfam03059 NAS Nicotianamine sy 44.8 26 0.00067 16.4 3.2 70 3-73 193-265 (277) 8 TIGR02079 THD1 threonine dehyd 36.1 36 0.00092 15.6 3.0 44 59-102 332-376 (415) 9 PRK11230 glycolate oxidase sub 34.3 39 0.00098 15.5 3.6 72 6-77 289-368 (499) 10 cd04904 ACT_AAAH ACT domain of 32.4 41 0.0011 15.3 6.4 62 20-88 11-72 (74) 11 PRK00499 rnpA ribonuclease P; 31.9 42 0.0011 15.2 3.4 30 4-33 77-106 (116) 12 PRK05783 hypothetical protein; 31.0 44 0.0011 15.1 8.7 77 1-95 1-83 (84) 13 PHA01632 hypothetical protein 28.8 48 0.0012 14.9 3.0 35 11-45 25-63 (64) 14 COG1164 Oligoendopeptidase F [ 26.3 53 0.0014 14.6 3.8 51 34-84 342-393 (598) 15 cd04893 ACT_GcvR_1 ACT domains 25.9 54 0.0014 14.6 4.8 51 19-80 11-62 (77) 16 cd04929 ACT_TPH ACT domain of 22.4 63 0.0016 14.2 6.0 59 21-86 12-70 (74) 17 pfam05211 NLBH Neuraminyllacto 21.3 67 0.0017 14.1 4.0 73 2-79 31-113 (228) 18 PRK00464 nrdR transcriptional 20.7 50 0.0013 14.8 1.3 66 13-78 78-147 (149) 19 pfam09569 RE_ScaI ScaI restric 20.0 67 0.0017 14.0 1.8 30 42-71 114-146 (191) No 1 >COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis] Probab=99.97 E-value=4.5e-31 Score=202.71 Aligned_cols=108 Identities=37% Similarity=0.704 Sum_probs=103.3 Q ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCC Q ss_conf 87059999878999999999999999999856978999703686535303222418999999980897799999998089 Q gi|254780329|r 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRI 81 (135) Q Consensus 2 ~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~ 81 (135) ++||+|||++|+++++++...++++.++|+++||+|.++++||+|+|||||+|+++|||++++|+++|.+++||++.|++ T Consensus 1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~l~~f~~~~~~i~Eler~~ri 80 (112) T COG0360 1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRI 80 (112) T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHCEECCCCCEEEEEEEEECCHHHHHHHHHHHCC T ss_conf 93379999778889899999999999999878977998302223433022055550899999997187789999998516 Q ss_pred CCHHEEEEEEEECCCCCCCCHHHHHHHH Q ss_conf 8021001124411345564357653212 Q gi|254780329|r 82 DENVLRSLTLLVDSHEQSPTLTIQRHDR 109 (135) Q Consensus 82 ~~~VLR~l~vk~~~~~~~~~~~~~~~~~ 109 (135) |++||||||||++.....+++++...+. T Consensus 81 n~~VlR~liik~~~~~~~~~~~~~~~~~ 108 (112) T COG0360 81 NEDVLRHLIIKVEKAKEELSPMLKKKDQ 108 (112) T ss_pred CHHHHEEEEEEECHHHCCHHHHHHHHHH T ss_conf 5754400468720100211134356565 No 2 >CHL00123 rps6 ribosomal protein S6; Validated Probab=99.97 E-value=5.8e-31 Score=202.05 Aligned_cols=93 Identities=28% Similarity=0.578 Sum_probs=91.7 Q ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC Q ss_conf 98705999987899999999999999999985697899970368653530322241899999998089779999999808 Q gi|254780329|r 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR 80 (135) Q Consensus 1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk 80 (135) ||+||++||++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+ T Consensus 5 Mr~YE~~~I~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~~~~f~~~~~~i~eler~lr 84 (97) T CHL00123 5 LIKYETMYILKPDLNEEELLKWIENYKKLLTKRGAKNIIVQNRGRRKLAYKIKKYEDGIYIQMNYEGNGKLVNSLEKSLK 84 (97) T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHC T ss_conf 15211999989999989999999999999986897799998056300035156677899999999858889999999866 Q ss_pred CCCHHEEEEEEEE Q ss_conf 9802100112441 Q gi|254780329|r 81 IDENVLRSLTLLV 93 (135) Q Consensus 81 ~~~~VLR~l~vk~ 93 (135) +|++|||||+||. T Consensus 85 i~e~VlR~l~vKk 97 (97) T CHL00123 85 LDENILRYLTLKK 97 (97) T ss_pred CCCCEEEEEEEEC T ss_conf 7757037999729 No 3 >PRK00453 rpsF 30S ribosomal protein S6; Reviewed Probab=99.97 E-value=8.1e-30 Score=195.35 Aligned_cols=95 Identities=45% Similarity=0.773 Sum_probs=93.9 Q ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC Q ss_conf 98705999987899999999999999999985697899970368653530322241899999998089779999999808 Q gi|254780329|r 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR 80 (135) Q Consensus 1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk 80 (135) ||+||++||++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+ T Consensus 1 M~~YE~~~il~p~l~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk 80 (95) T PRK00453 1 MRKYEIVFILRPDLSEEQVKALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELERLFR 80 (95) T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHHHHHC T ss_conf 98625999988999989999999999999997998899985021200442306675899999999989889999999864 Q ss_pred CCCHHEEEEEEEECC Q ss_conf 980210011244113 Q gi|254780329|r 81 IDENVLRSLTLLVDS 95 (135) Q Consensus 81 ~~~~VLR~l~vk~~~ 95 (135) +|++|||||+||+++ T Consensus 81 l~~~VlR~livk~~~ 95 (95) T PRK00453 81 INEDVLRFLIVKLDK 95 (95) T ss_pred CCCCEEEEEEEEECC T ss_conf 776836899999649 No 4 >pfam01250 Ribosomal_S6 Ribosomal protein S6. Probab=99.96 E-value=1.9e-28 Score=187.33 Aligned_cols=92 Identities=47% Similarity=0.856 Sum_probs=90.7 Q ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCC Q ss_conf 87059999878999999999999999999856978999703686535303222418999999980897799999998089 Q gi|254780329|r 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRI 81 (135) Q Consensus 2 ~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~ 81 (135) |+||+++|++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|++ T Consensus 1 r~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~ 80 (92) T pfam01250 1 RKYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAELERRLRI 80 (92) T ss_pred CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHCC T ss_conf 96059999889999899999999999999878988999851310003304377889999999999998899999998647 Q ss_pred CCHHEEEEEEEE Q ss_conf 802100112441 Q gi|254780329|r 82 DENVLRSLTLLV 93 (135) Q Consensus 82 ~~~VLR~l~vk~ 93 (135) |++|||||+||+ T Consensus 81 ~~~VlR~livk~ 92 (92) T pfam01250 81 NEDVLRFLTVKL 92 (92) T ss_pred CCCEEEEEEEEC T ss_conf 878388999969 No 5 >TIGR00166 S6 ribosomal protein S6; InterPro: IPR000529 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 S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=99.59 E-value=1.4e-15 Score=111.95 Aligned_cols=94 Identities=33% Similarity=0.666 Sum_probs=91.0 Q ss_pred CCCCEEEEEECCCCCHHH---HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECC----CCCEEEEEEEEEECCHHHHH Q ss_conf 987059999878999999---99999999999985697899970368653530322----24189999999808977999 Q gi|254780329|r 1 MKLYEHVFLLRQDISSQQ---IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIR----KNRKAYYVFMNIASPPAAIH 73 (135) Q Consensus 1 M~~YE~~~i~~p~~~~~~---~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~----k~~~G~Y~~~~f~~~~~~i~ 73 (135) |+.||++++++|++++.. ....++.+...++.++|.+.....||.|.|||+|+ ++..|+|+++.|.+++..+. T Consensus 1 ~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~~~~ 80 (102) T TIGR00166 1 LRHYELIFLVRPTLSEEPKLEVKGLIERYKKLLTLNGGEIVGSEDWGLRRLAYPIKKDQEKHLRGHYYLWNFSGEGAVIK 80 (102) T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHHHHHHHHHHCCCHHHHCCCEEEEEEECCCHHHHH T ss_conf 95411577751552101333335567777655531132000012220233321210002332032157886336335789 Q ss_pred HHHHHHCCCCHHEEEEEEEEC Q ss_conf 999980898021001124411 Q gi|254780329|r 74 EMKRKMRIDENVLRSLTLLVD 94 (135) Q Consensus 74 el~~~lk~~~~VLR~l~vk~~ 94 (135) ++++.++++++|+|+++++.+ T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~ 101 (102) T TIGR00166 81 EFERTLKLNDDVLRSLVIKLE 101 (102) T ss_pred HHHHHHCCCHHHHHHHHHHCC T ss_conf 888874103667777764236 No 6 >KOG4708 consensus Probab=99.55 E-value=2.6e-15 Score=110.26 Aligned_cols=95 Identities=31% Similarity=0.477 Sum_probs=84.5 Q ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCC----CCEEEEEEEEEECCHHHHHHHH Q ss_conf 987059999878999999999999999999856978999703686535303222----4189999999808977999999 Q gi|254780329|r 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK----NRKAYYVFMNIASPPAAIHEMK 76 (135) Q Consensus 1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k----~~~G~Y~~~~f~~~~~~i~el~ 76 (135) |..||++.|+++- +..++...+.+..+.+-..||.|..++++|.|.|+|+|+| |.+|+++++.|.+++++..++. T Consensus 3 mp~yelali~~~~-~rpela~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~ 81 (141) T KOG4708 3 MPLYELALITRSL-SRPELAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIK 81 (141) T ss_pred CHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCEEEECHHCCHHHHCCHHHHHCCCCCCCEEEEEEECCCHHHHHHHH T ss_conf 3177899986246-988999999998657734487686503044043053377706752222578986508989999999 Q ss_pred HHHCCCCHHEEEEEEEECCC Q ss_conf 98089802100112441134 Q gi|254780329|r 77 RKMRIDENVLRSLTLLVDSH 96 (135) Q Consensus 77 ~~lk~~~~VLR~l~vk~~~~ 96 (135) +.|+.|.+|||+++||++.. T Consensus 82 ~~l~~D~dviR~~IVKv~~~ 101 (141) T KOG4708 82 RILKRDPDVIRWLIVKVDDI 101 (141) T ss_pred HHHHCCHHHHHHHHEECCCC T ss_conf 99702806677521132354 No 7 >pfam03059 NAS Nicotianamine synthase protein. Nicotianamine synthase EC:2.5.1.43 catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is great Probab=44.85 E-value=26 Score=16.45 Aligned_cols=70 Identities=17% Similarity=0.270 Sum_probs=44.3 Q ss_pred CCEEEEEECCC-CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCC--CEEEEEEEEEECCHHHHH Q ss_conf 70599998789-999999999999999998569789997036865353032224--189999999808977999 Q gi|254780329|r 3 LYEHVFLLRQD-ISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKN--RKAYYVFMNIASPPAAIH 73 (135) Q Consensus 3 ~YE~~~i~~p~-~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~--~~G~Y~~~~f~~~~~~i~ 73 (135) -|+++|+.-.. ...++.+.+++.+.+... -|+.+.--..||.|.|=||+=.. ..|+=++-.+.-.++.++ T Consensus 193 ~~DvV~lAALVGm~~e~K~~I~~hL~k~m~-~Ga~l~~Rsa~GlR~~LYp~vd~~~~~GFe~l~~~hP~~~ViN 265 (277) T pfam03059 193 AYDVVFLAALVGMDKEEKAKVIDHLGKHMA-PGALLVLRSAHGARAFLYPVVDPCDLRGFEVLSVYHPTDEVIN 265 (277) T ss_pred CCCEEEEHHHCCCCHHHHHHHHHHHHHHCC-CCCEEEEECCHHHHHHCCCCCCHHHCCCCEEEEEECCCCCCEE T ss_conf 476898721135433359999999997458-9967999611217876288789667387079999889998411 No 8 >TIGR02079 THD1 threonine dehydratase; InterPro: IPR011820 This entry represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases are described by IPR005787 from INTERPRO and IPR005789 from INTERPRO. The sequences described by this entry are exclusively found in species containing the rest of the isoleucine pathway and which are generally lacking in members of the other two clades of threonine dehydratases. The sequences associated with this entry are often cluster with other elements of the isoleucine pathway.; GO: 0004794 L-threonine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0009097 isoleucine biosynthetic process. Probab=36.15 E-value=36 Score=15.64 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=40.0 Q ss_pred EEEEEEEECCHHHHHHHHH-HHCCCCHHEEEEEEEECCCCCCCCH Q ss_conf 9999998089779999999-8089802100112441134556435 Q gi|254780329|r 59 YYVFMNIASPPAAIHEMKR-KMRIDENVLRSLTLLVDSHEQSPTL 102 (135) Q Consensus 59 ~Y~~~~f~~~~~~i~el~~-~lk~~~~VLR~l~vk~~~~~~~~~~ 102 (135) |||++.|.=-|-++.+|=. -|.=||+|-+|--+|..+...+|.. T Consensus 332 hYFiv~FPQRpGALreFln~vLGP~DDIT~FEY~KK~nRe~Gpal 376 (415) T TIGR02079 332 HYFIVRFPQRPGALREFLNDVLGPNDDITKFEYTKKSNRETGPAL 376 (415) T ss_pred EEEEECCCCCCCHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCEE T ss_conf 368752789886368876540678875233100020147878779 No 9 >PRK11230 glycolate oxidase subunit GlcD; Provisional Probab=34.28 E-value=39 Score=15.46 Aligned_cols=72 Identities=11% Similarity=0.111 Sum_probs=41.9 Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE--------CCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHH Q ss_conf 999987899999999999999999985697899970--------368653530322241899999998089779999999 Q gi|254780329|r 6 HVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVN--------ELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKR 77 (135) Q Consensus 6 ~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e--------~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~ 77 (135) .++++--+.++.++....+.+.+++.+.|+.-...- -|-.|+-+++.-....+.++.+.+..+.+.+.++-+ T Consensus 289 a~llve~~g~~~~~~~~~~~~~~~l~~~g~~~~~~a~~~~e~~~lW~~R~~~~~~~~~~~~~~~~~Dv~VP~~~l~~~~~ 368 (499) T PRK11230 289 AILLCELDGVESDVQEDCERVNDVLLAAGATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLE 368 (499) T ss_pred CEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHH T ss_conf 10233225887889999999999998769835899489999999999999999999965798257654312210899999 No 10 >cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy Probab=32.43 E-value=41 Score=15.28 Aligned_cols=62 Identities=13% Similarity=0.197 Sum_probs=44.4 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHHEEE Q ss_conf 999999999998569789997036865353032224189999999808977999999980898021001 Q gi|254780329|r 20 KDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRS 88 (135) Q Consensus 20 ~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~VLR~ 88 (135) ...+-++-+.+..+|..+.+.|.. |.++....|.+++.|++....+.++-..|+-.-.-+|. T Consensus 11 ~GaL~~~L~~F~~~~iNlt~IESR-------Ps~~~~~~y~FfvD~eg~~~~i~~al~~Lk~~~~~vki 72 (74) T cd04904 11 VGALARALKLFEEFGVNLTHIESR-------PSRRNGSEYEFFVDCEVDRGDLDQLISSLRRVVADVNI 72 (74) T ss_pred CCHHHHHHHHHHHCCCCEEEEECC-------CCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCCEEEE T ss_conf 648999999999879867899833-------38999975999999608989999999999974782885 No 11 >PRK00499 rnpA ribonuclease P; Reviewed Probab=31.93 E-value=42 Score=15.23 Aligned_cols=30 Identities=10% Similarity=0.276 Sum_probs=13.8 Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHC Q ss_conf 059999878999999999999999999856 Q gi|254780329|r 4 YEHVFLLRQDISSQQIKDTIGQYQSLIQEN 33 (135) Q Consensus 4 YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~ 33 (135) |.+++|.++.+.......+...+..++.+. T Consensus 77 ~DiViiar~~~~~~~~~~l~~~l~~ll~Ka 106 (116) T PRK00499 77 YDFVVIARKPAEDLDYEEIKKSLIHVLKKA 106 (116) T ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHHC T ss_conf 759999686545499999999999999982 No 12 >PRK05783 hypothetical protein; Provisional Probab=30.98 E-value=44 Score=15.13 Aligned_cols=77 Identities=12% Similarity=0.228 Sum_probs=52.8 Q ss_pred CCC-CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCH-----HHHHH Q ss_conf 987-059999878999999999999999999856978999703686535303222418999999980897-----79999 Q gi|254780329|r 1 MKL-YEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPP-----AAIHE 74 (135) Q Consensus 1 M~~-YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~-----~~i~e 74 (135) |++ .++.+.++|.+.+.+-..+... +.....|.+. +-+.|-|+.|.++++. +.+.+ T Consensus 1 M~y~v~v~I~~K~gi~DPeG~TI~~~---L~~~g~~~v~---------------~vR~GK~l~~~iea~s~eeA~~~v~~ 62 (84) T PRK05783 1 MRYAVELIITYKDGIRDPEGETIQRY---VLERMLGYSI---------------EVRAGKCLVFRIEASSPEEAQELALK 62 (84) T ss_pred CEEEEEEEEEECCCCCCCCHHHHHHH---HHHHCCCCEE---------------EEEEEEEEEEEEECCCHHHHHHHHHH T ss_conf 95999999985897759633799999---9985589648---------------98710499999947998999999999 Q ss_pred HHHHHCCCCHHEEEEEEEECC Q ss_conf 999808980210011244113 Q gi|254780329|r 75 MKRKMRIDENVLRSLTLLVDS 95 (135) Q Consensus 75 l~~~lk~~~~VLR~l~vk~~~ 95 (135) +-..|++-..|+--.+|+++. T Consensus 63 ic~~lrL~NPvI~~~~i~v~~ 83 (84) T PRK05783 63 LAKEMRLGNPIVHKIVVRVER 83 (84) T ss_pred HHHHHHCCCCCEEEEEEEEEC T ss_conf 998620349852899999962 No 13 >PHA01632 hypothetical protein Probab=28.76 E-value=48 Score=14.90 Aligned_cols=35 Identities=14% Similarity=0.339 Sum_probs=26.3 Q ss_pred CCCCCHHHHHH----HHHHHHHHHHHCCCEEEEEECCCC Q ss_conf 78999999999----999999999856978999703686 Q gi|254780329|r 11 RQDISSQQIKD----TIGQYQSLIQENGGEVRLVNELGM 45 (135) Q Consensus 11 ~p~~~~~~~~~----~~~~~~~~i~~~gg~i~~~e~wG~ 45 (135) ...-+++++.+ ++..+...|++..-+|.....||. T Consensus 25 p~kpteeelrkvlpkilkdyanmie~gk~ki~ds~ewgi 63 (64) T PHA01632 25 PQKPTEEELRKVLPKILKDYANMIENGKIKILDSKEWGI 63 (64) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCC T ss_conf 799779999999999999999998618658763510255 No 14 >COG1164 Oligoendopeptidase F [Amino acid transport and metabolism] Probab=26.33 E-value=53 Score=14.65 Aligned_cols=51 Identities=14% Similarity=0.201 Sum_probs=43.8 Q ss_pred CCEEEEEECCCCCCCCEECCCCC-EEEEEEEEEECCHHHHHHHHHHHCCCCH Q ss_conf 97899970368653530322241-8999999980897799999998089802 Q gi|254780329|r 34 GGEVRLVNELGMRTIAYRIRKNR-KAYYVFMNIASPPAAIHEMKRKMRIDEN 84 (135) Q Consensus 34 gg~i~~~e~wG~r~LAY~I~k~~-~G~Y~~~~f~~~~~~i~el~~~lk~~~~ 84 (135) ++=|.-..+-|+|.-||-+.-.. .--|++|++.+....+.-|-..|.+.-. T Consensus 342 ~~WiD~~~~~gKrsGaYs~~~~~~~~p~IlmN~~gt~~dV~TLaHElGHs~H 393 (598) T COG1164 342 ERWIDVYPRKGKRSGAYSIGFYKGDHPFILMNYDGTLRDVFTLAHELGHSVH 393 (598) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHH T ss_conf 3886235687999885268998888855876378965446687465018999 No 15 >cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int Probab=25.95 E-value=54 Score=14.60 Aligned_cols=51 Identities=12% Similarity=0.149 Sum_probs=38.4 Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEE-EEEEEECCHHHHHHHHHHHC Q ss_conf 999999999999856978999703686535303222418999-99998089779999999808 Q gi|254780329|r 19 IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY-VFMNIASPPAAIHEMKRKMR 80 (135) Q Consensus 19 ~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y-~~~~f~~~~~~i~el~~~lk 80 (135) ...++..+...+.++||.|.... ++ .--|.| ..+.++++.+.++.|+..|- T Consensus 11 rpGiv~~vs~~v~~~gcNi~dSr------mt-----~lg~~Fa~imlvsG~w~~ia~lE~~L~ 62 (77) T cd04893 11 RPGILNELTRAVSESGCNILDSR------MA-----ILGTEFALTMLVEGSWDAIAKLEAALP 62 (77) T ss_pred CCHHHHHHHHHHHHCCCCEEHHH------HH-----HHHCCEEEEEEEECCHHHHHHHHHHHH T ss_conf 86599999999998699872437------88-----873603899999528889999998627 No 16 >cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains. Probab=22.43 E-value=63 Score=14.20 Aligned_cols=59 Identities=12% Similarity=0.252 Sum_probs=45.0 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHHE Q ss_conf 999999999985697899970368653530322241899999998089779999999808980210 Q gi|254780329|r 21 DTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVL 86 (135) Q Consensus 21 ~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~VL 86 (135) ..+.++-+++.++|..+.+.|.. |-++....|.+++.++++...+.++-..|+-.-..+ T Consensus 12 GaL~~~L~~F~~~~iNlthIESR-------pSk~~~~~Y~ffvD~e~~~~~l~~~l~~Lk~~~~~v 70 (74) T cd04929 12 GGLAKALKLFQELGINVVHIESR-------KSKRRSSEFEIFVDCECDQRRLDELVQLLKREVASV 70 (74) T ss_pred CHHHHHHHHHHHCCCCEEEEECC-------CCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHCEEE T ss_conf 67999999999869777998558-------787889718999990399799999999999852099 No 17 >pfam05211 NLBH Neuraminyllactose-binding hemagglutinin precursor (NLBH). This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding hemagglutinin precursor (NLBH) or N-acetylneuraminyllactose-binding fibrillar hemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium. Probab=21.31 E-value=67 Score=14.06 Aligned_cols=73 Identities=18% Similarity=0.276 Sum_probs=42.3 Q ss_pred CCCEEEEEECCCCCHHH----------HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHH Q ss_conf 87059999878999999----------99999999999985697899970368653530322241899999998089779 Q gi|254780329|r 2 KLYEHVFLLRQDISSQQ----------IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAA 71 (135) Q Consensus 2 ~~YE~~~i~~p~~~~~~----------~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~ 71 (135) .+++++.|++|.+.-.+ -+.++.++++++++.|=++..+.+- ..|...+++ + -|.++...+.-.. T Consensus 31 ~n~h~v~ll~P~iq~sdni~k~Y~~kF~n~l~~qi~~ilek~GY~v~~fkD~--~~l~~~~Kk--k-~~lvL~m~G~v~i 105 (228) T pfam05211 31 ANDHKVLLLRPAIQYSDNIAKEYENKFKNQLTLQVEEILENQGYKVINFSDK--DDFSFAQKK--K-GYLVLAMNGEVVI 105 (228) T ss_pred CCCCEEEEECCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCH--HHCCHHHHH--H-HEEEEECCCCEEE T ss_conf 6672599963533011233678999999999999999998569357762452--223667653--1-0689962574887 Q ss_pred HHHHHHHH Q ss_conf 99999980 Q gi|254780329|r 72 IHEMKRKM 79 (135) Q Consensus 72 i~el~~~l 79 (135) +.++++.+ T Consensus 106 leD~k~~~ 113 (228) T pfam05211 106 LEDPKRTI 113 (228) T ss_pred ECCHHHHC T ss_conf 12636433 No 18 >PRK00464 nrdR transcriptional regulator NrdR; Validated Probab=20.65 E-value=50 Score=14.81 Aligned_cols=66 Identities=17% Similarity=0.274 Sum_probs=46.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEE--E--EEEEEECCHHHHHHHHHH Q ss_conf 99999999999999999985697899970368653530322241899--9--999980897799999998 Q gi|254780329|r 13 DISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAY--Y--VFMNIASPPAAIHEMKRK 78 (135) Q Consensus 13 ~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~--Y--~~~~f~~~~~~i~el~~~ 78 (135) .++.+++..+++.+..-|.+.|...+.....|..=|.+--.=..-|| | ++-.|....+...+|+.. T Consensus 78 pv~~~~ie~~v~~Ie~~l~~~~~~EI~S~~IGe~Vm~~Lk~lD~VAYvRFASVYr~F~d~~~F~~ei~~L 147 (149) T PRK00464 78 PVSSEQIEAAVSRIERQLRASGEREVPSKEIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEEL 147 (149) T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 9899999999999999999838887559999999999886209310000245606779999999999997 No 19 >pfam09569 RE_ScaI ScaI restriction endonuclease. This family includes the ScaI (recognizes and cleaves AGT^ACT) restriction endonuclease. Probab=20.03 E-value=67 Score=14.04 Aligned_cols=30 Identities=27% Similarity=0.478 Sum_probs=20.8 Q ss_pred CCCCCCCCEECC---CCCEEEEEEEEEECCHHH Q ss_conf 368653530322---241899999998089779 Q gi|254780329|r 42 ELGMRTIAYRIR---KNRKAYYVFMNIASPPAA 71 (135) Q Consensus 42 ~wG~r~LAY~I~---k~~~G~Y~~~~f~~~~~~ 71 (135) -.|.|-.+|.-+ |-+.|||+.++|+-..+. T Consensus 114 IfGNRSyg~~~~~~~Ksk~GYYLaINfekf~e~ 146 (191) T pfam09569 114 IYGNRSYGYRPDDGKKSKDGYYLAINFEKFKED 146 (191) T ss_pred EECCCCCCCCCCCCCCCCCCEEEEEEEECCCCC T ss_conf 233422144678874455755999971036777 Done!