Query gi|254780626|ref|YP_003065039.1| 30S ribosomal protein S20 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 90 No_of_seqs 107 out of 1206 Neff 5.5 Searched_HMMs 39220 Date Sun May 29 21:11:50 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780626.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00239 rpsT 30S ribosomal pr 100.0 6.7E-28 1.7E-32 187.4 12.7 88 1-88 1-88 (88) 2 COG0268 RpsT Ribosomal protein 99.9 3.6E-27 9.1E-32 183.0 12.1 88 1-88 1-88 (88) 3 pfam01649 Ribosomal_S20p Ribos 99.9 1.2E-26 3.2E-31 179.8 11.5 84 2-85 1-84 (84) 4 CHL00102 rps20 ribosomal prote 99.9 1.1E-25 2.8E-30 174.1 11.8 86 1-86 1-91 (93) 5 TIGR00029 S20 ribosomal protei 99.9 5.7E-26 1.4E-30 175.8 8.9 87 1-87 1-94 (94) 6 PTZ00151 translationally contr 39.5 29 0.00074 15.5 6.4 39 22-60 87-125 (173) 7 pfam10938 YfdX YfdX protein. Y 34.2 35 0.0009 15.0 4.7 32 33-64 7-38 (155) 8 smart00668 CTLH C-terminal to 34.2 35 0.0009 15.0 3.8 31 32-62 5-35 (58) 9 pfam00838 TCTP Translationally 33.7 36 0.00091 15.0 6.2 38 22-59 83-120 (166) 10 TIGR00683 nanA N-acetylneurami 30.2 41 0.001 14.6 4.3 36 33-68 215-250 (294) 11 PRK10316 hypothetical protein; 28.8 43 0.0011 14.5 3.5 30 34-63 60-89 (209) 12 COG1849 Uncharacterized protei 27.6 46 0.0012 14.3 5.8 48 22-69 35-82 (90) 13 pfam03194 LUC7 LUC7 N_terminus 26.5 48 0.0012 14.2 5.0 37 22-58 126-162 (252) 14 KOG0796 consensus 26.2 48 0.0012 14.2 4.7 34 26-59 129-162 (319) 15 PRK10564 maltose regulon perip 24.8 51 0.0013 14.0 3.5 24 34-57 263-286 (303) 16 TIGR00823 EIIA-LAC PTS system, 23.9 53 0.0014 13.9 5.0 34 28-61 17-50 (99) 17 pfam07148 MalM Maltose operon 21.7 59 0.0015 13.7 4.1 24 34-57 239-262 (279) 18 pfam10925 DUF2680 Protein of u 20.8 62 0.0016 13.5 4.4 33 55-87 21-53 (59) No 1 >PRK00239 rpsT 30S ribosomal protein S20; Reviewed Probab=99.95 E-value=6.7e-28 Score=187.42 Aligned_cols=88 Identities=44% Similarity=0.583 Sum_probs=86.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 96898999999999999999999999999999999999960898999999999999999998658861669999999999 Q gi|254780626|r 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFHGNAASRKVSRLS 80 (90) Q Consensus 1 Man~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDka~kkgiihkn~AsRkKSrL~ 80 (90) ||||+||+||+||+++++++|++++|.+||++|+|+.+|++||.+++.++|+.+++.||+++++||||+|+|+|++|||+ T Consensus 1 Man~kSA~Kr~rq~~krr~~N~~~ks~~kT~iKk~~~ai~~~d~~~a~~~~~~~~s~iDkaa~kgiihkN~AaRkKSrL~ 80 (88) T PRK00239 1 MANIKSAKKRIRQNEKRRLRNKSRKSRLRTAIKKVRAAIEAGDKEAAEEALKAAQSKLDKAASKGVIHKNKAARKKSRLA 80 (88) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 99808889999999999999999999999999999999984899999999999999999998669876315889999999 Q ss_pred HHHHHHHH Q ss_conf 99999842 Q gi|254780626|r 81 KRLKGILT 88 (90) Q Consensus 81 ~~v~~~~~ 88 (90) ++||+++. T Consensus 81 k~ln~l~~ 88 (88) T PRK00239 81 AKVNALAA 88 (88) T ss_pred HHHHHHCC T ss_conf 99977639 No 2 >COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis] Probab=99.95 E-value=3.6e-27 Score=183.05 Aligned_cols=88 Identities=43% Similarity=0.568 Sum_probs=86.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 96898999999999999999999999999999999999960898999999999999999998658861669999999999 Q gi|254780626|r 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFHGNAASRKVSRLS 80 (90) Q Consensus 1 Man~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDka~kkgiihkn~AsRkKSrL~ 80 (90) |||++||+||++|+++++++|.+++|++||+||+|+.+|+.||.+.+.++|..+++.||+++++||||+|+|+|++|||+ T Consensus 1 MAN~~SA~KR~r~~~krr~rN~~~kS~~rT~iKk~~~ai~~gd~~~A~~~l~~a~~~idkaa~KGvihkN~AaR~kSRLa 80 (88) T COG0268 1 MANIKSAKKRARQSEKRRLRNKSRKSALRTAIKKVEAAIEAGDKEAAKAALKEAQKKIDKAASKGVIHKNKAARKKSRLA 80 (88) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH T ss_conf 99707789999999999998599999999999999999984779999999999999999998728634338888999999 Q ss_pred HHHHHHHH Q ss_conf 99999842 Q gi|254780626|r 81 KRLKGILT 88 (90) Q Consensus 81 ~~v~~~~~ 88 (90) ..++++.. T Consensus 81 ~~~~~~~~ 88 (88) T COG0268 81 AKLNKLAA 88 (88) T ss_pred HHHHHHCC T ss_conf 99865349 No 3 >pfam01649 Ribosomal_S20p Ribosomal protein S20. Bacterial ribosomal protein S20 interacts with 16S rRNA. Probab=99.94 E-value=1.2e-26 Score=179.79 Aligned_cols=84 Identities=44% Similarity=0.576 Sum_probs=82.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 68989999999999999999999999999999999999608989999999999999999986588616699999999999 Q gi|254780626|r 2 ANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFHGNAASRKVSRLSK 81 (90) Q Consensus 2 an~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDka~kkgiihkn~AsRkKSrL~~ 81 (90) |||+||+||+||++++|++|++++|.|||++|+|+.+|++||.++|.++|+.+++.||+++++||||+|+|+|++|||+. T Consensus 1 AN~kSA~KR~rq~~krr~~N~~~kS~~rT~iKkv~~ai~~gd~~~A~~~l~~a~~~iDkaa~KGiiHkN~AARkkSRL~~ 80 (84) T pfam01649 1 ANIKSAKKRIRQNEKRRLRNKSYKSKMRTLIKKVREAIEAGEKDKAKEALKEVQSKIDKAAKKGVIHKNTAARKKSRLAA 80 (84) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 97188999999999999999999999999999999999858999999999999999999974586643068889999999 Q ss_pred HHHH Q ss_conf 9999 Q gi|254780626|r 82 RLKG 85 (90) Q Consensus 82 ~v~~ 85 (90) .||+ T Consensus 81 ~vnK 84 (84) T pfam01649 81 ILNK 84 (84) T ss_pred HHCC T ss_conf 8629 No 4 >CHL00102 rps20 ribosomal protein S20 Probab=99.93 E-value=1.1e-25 Score=174.10 Aligned_cols=86 Identities=35% Similarity=0.370 Sum_probs=83.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 96898999999999999999999999999999999999960-----8989999999999999999986588616699999 Q gi|254780626|r 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITF-----GKIEEATEACRKAESVIQKAKSKGIFHGNAASRK 75 (90) Q Consensus 1 Man~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~-----~d~~~a~~~~~~~~s~lDka~kkgiihkn~AsRk 75 (90) |||++||+||++++|++|++|++|+|.+||++|+|..+++. +|.+.+...++.+||.||+|+++||||+|+++|+ T Consensus 1 MAN~kSa~KRi~~~ErnRlrNkayKS~vrT~~Kk~~~a~e~~~~~~~~~~~~~~~l~~a~s~IDKAVkkGvlHkNtaArk 80 (93) T CHL00102 1 MANNKSAIKRIQISERNRLRNRAYKSVVKTLTKKYLKDLENYKNSNNNKEKLQLLLSIVYSKIDKAVKKGVFHKNTAARK 80 (93) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH T ss_conf 99708789999999999998799999999999999999998723898199999999999999999987288677608889 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999998 Q gi|254780626|r 76 VSRLSKRLKGI 86 (90) Q Consensus 76 KSrL~~~v~~~ 86 (90) ||||+..++.. T Consensus 81 KSrLa~~~k~~ 91 (93) T CHL00102 81 KSKLAKALKIS 91 (93) T ss_pred HHHHHHHHHHH T ss_conf 99999998774 No 5 >TIGR00029 S20 ribosomal protein S20; InterPro: IPR002583 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 consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=99.93 E-value=5.7e-26 Score=175.84 Aligned_cols=87 Identities=39% Similarity=0.538 Sum_probs=85.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH-------HHHHHHHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 96898999999999999999999999999999999999960898-------99999999999999999865886166999 Q gi|254780626|r 1 MANKDSAKKMIRKIARRTLINKSRRSSVRSFMRHANEAITFGKI-------EEATEACRKAESVIQKAKSKGIFHGNAAS 73 (90) Q Consensus 1 Man~kSa~Kr~r~~~krr~~N~~~ks~~kt~iKk~~~ai~~~d~-------~~a~~~~~~~~s~lDka~kkgiihkn~As 73 (90) ||||+||+||++|+++++++|.+++|.|||.||+|...|+.|+. ++|.+.|..+++.||++|.+||||+|+|+ T Consensus 1 maNiKSA~KR~~q~~kr~~~N~~~Ks~~kT~iK~~~~~v~~~~~dPnPekl~~A~~~~~~~~k~~D~~a~kgiihkN~Aa 80 (94) T TIGR00029 1 MANIKSAEKRIRQNIKRRLRNKSYKSKLKTIIKKVYASVAAGEKDPNPEKLDKAQEALKEAAKKIDKAARKGIIHKNKAA 80 (94) T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 97410367778887873104730555987899999999851267998423899999999987886189850730233476 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999984 Q gi|254780626|r 74 RKVSRLSKRLKGIL 87 (90) Q Consensus 74 RkKSrL~~~v~~~~ 87 (90) |+||||+..|+++. T Consensus 81 R~KSrL~~~l~k~~ 94 (94) T TIGR00029 81 RKKSRLAAQLNKLA 94 (94) T ss_pred HHHHHHHHHHHHCC T ss_conf 79999999986209 No 6 >PTZ00151 translationally controlled tumor protein; Provisional Probab=39.53 E-value=29 Score=15.53 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=30.1 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999608989999999999999999 Q gi|254780626|r 22 KSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQK 60 (90) Q Consensus 22 ~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDk 60 (90) .++++-||.++|++..-+++++++.+..+-..++..+-+ T Consensus 87 k~y~~yiK~YmK~v~~kLee~~perV~~Fk~~a~~~vK~ 125 (173) T PTZ00151 87 KEYSSYIKKYIQRIVAYLEEKNPDRVEPFKTKAQPFVKH 125 (173) T ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH T ss_conf 999999999999999998632988999999988999999 No 7 >pfam10938 YfdX YfdX protein. YfdX is a protein found in Proteobacteria of unknown function. The protein coding for this gene is regulated by EvgA in E. coli. Probab=34.19 E-value=35 Score=15.02 Aligned_cols=32 Identities=28% Similarity=0.420 Sum_probs=20.9 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999996089899999999999999999865 Q gi|254780626|r 33 RHANEAITFGKIEEATEACRKAESVIQKAKSK 64 (90) Q Consensus 33 Kk~~~ai~~~d~~~a~~~~~~~~s~lDka~kk 64 (90) .....+|..|+.+.|...+..+...|+.+... T Consensus 7 ~~Ar~ai~~g~~~~A~~~l~~A~~~l~~~~a~ 38 (155) T pfam10938 7 QQARAALDNGKTEQAKKALERATGLLEAALAD 38 (155) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999998799899999999999889988631 No 8 >smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function. Probab=34.15 E-value=35 Score=15.01 Aligned_cols=31 Identities=19% Similarity=0.165 Sum_probs=26.0 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999960898999999999999999998 Q gi|254780626|r 32 MRHANEAITFGKIEEATEACRKAESVIQKAK 62 (90) Q Consensus 32 iKk~~~ai~~~d~~~a~~~~~~~~s~lDka~ 62 (90) ...+..+|..||.+.|..++...+..+...- T Consensus 5 r~~i~~~i~~G~~~~Al~~~~~~~~~l~~~~ 35 (58) T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPLLERN 35 (58) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHCHHHHHCC T ss_conf 9999999995999999999998598988529 No 9 >pfam00838 TCTP Translationally controlled tumour protein. Probab=33.69 E-value=36 Score=14.97 Aligned_cols=38 Identities=11% Similarity=0.206 Sum_probs=28.2 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999960898999999999999999 Q gi|254780626|r 22 KSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQ 59 (90) Q Consensus 22 ~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lD 59 (90) .+|++-+|.++|++..-++..+++....+-..++..+- T Consensus 83 k~y~~yiK~YmK~v~~~L~e~~pe~V~~Fk~~a~~~vK 120 (166) T pfam00838 83 KSFKTYIKGYMKAVKAKLQEENPERVSLFKKNIQGWVK 120 (166) T ss_pred HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH T ss_conf 99999999999999998765196789999998899999 No 10 >TIGR00683 nanA N-acetylneuraminate lyase; InterPro: IPR005264 N-acetylneuraminate lyase catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. The enzyme plays an important role in the regulation of sialic acid metabolism in bacteria.. Probab=30.24 E-value=41 Score=14.62 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=32.1 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCH Q ss_conf 999999960898999999999999999998658861 Q gi|254780626|r 33 RHANEAITFGKIEEATEACRKAESVIQKAKSKGIFH 68 (90) Q Consensus 33 Kk~~~ai~~~d~~~a~~~~~~~~s~lDka~kkgiih 68 (90) +.+.+++.+||..+|.+.=.+++.+||-..+.|++. T Consensus 215 ~~I~~~~K~G~~~~A~~~Q~~~N~~I~~~~~~G~y~ 250 (294) T TIGR00683 215 RQIVKLLKEGDLAEALKLQTVTNDLIDLLLKTGLYL 250 (294) T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCHHH T ss_conf 889998607877899999888889999998504478 No 11 >PRK10316 hypothetical protein; Provisional Probab=28.77 E-value=43 Score=14.46 Aligned_cols=30 Identities=23% Similarity=0.294 Sum_probs=25.0 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999608989999999999999999986 Q gi|254780626|r 34 HANEAITFGKIEEATEACRKAESVIQKAKS 63 (90) Q Consensus 34 k~~~ai~~~d~~~a~~~~~~~~s~lDka~k 63 (90) -.+.+|-.|+.+.|..++..+...||++.. T Consensus 60 lAR~Aif~G~~~~Ak~Ll~~A~~~L~~a~~ 89 (209) T PRK10316 60 VARLALFHGDPEKAKELTNEASALLSDDST 89 (209) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 999998659977889999999999864223 No 12 >COG1849 Uncharacterized protein conserved in archaea [Function unknown] Probab=27.59 E-value=46 Score=14.34 Aligned_cols=48 Identities=17% Similarity=0.147 Sum_probs=39.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 999999999999999999608989999999999999999986588616 Q gi|254780626|r 22 KSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVIQKAKSKGIFHG 69 (90) Q Consensus 22 ~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDka~kkgiihk 69 (90) ..+-...+.+...-.-..+.||.-.|...++=+.-.||-.+.=|+++- T Consensus 35 e~~~~ma~~Y~~Dakyf~ekGD~vtAfa~~sYa~g~lDag~~lGv~d~ 82 (90) T COG1849 35 EDFVDMAESYFEDAKYFLEKGDYVTAFAALSYAHGWLDAGVRLGVFDV 82 (90) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998889999847689999999999999998888625777 No 13 >pfam03194 LUC7 LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP). Probab=26.45 E-value=48 Score=14.21 Aligned_cols=37 Identities=16% Similarity=0.233 Sum_probs=30.4 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 9999999999999999996089899999999999999 Q gi|254780626|r 22 KSRRSSVRSFMRHANEAITFGKIEEATEACRKAESVI 58 (90) Q Consensus 22 ~~~ks~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~l 58 (90) ...-..|...+.+++.+-+.|+.++|+.++..+..+- T Consensus 126 ~~l~~~I~~ll~e~E~LGe~G~VdeA~~~~~~~e~Lk 162 (252) T pfam03194 126 AELDEEIGKLLAEAEALGEEGKVDEAMKLMKEVEELK 162 (252) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 9999999999999999986799999999999999999 No 14 >KOG0796 consensus Probab=26.23 E-value=48 Score=14.19 Aligned_cols=34 Identities=24% Similarity=0.350 Sum_probs=29.5 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 9999999999999960898999999999999999 Q gi|254780626|r 26 SSVRSFMRHANEAITFGKIEEATEACRKAESVIQ 59 (90) Q Consensus 26 s~~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lD 59 (90) -.|...+.+++.+.++|+.++|++++..+..+-- T Consensus 129 e~I~~~l~~~E~LG~eG~Veeaq~~~~e~E~lk~ 162 (319) T KOG0796 129 EKIGKLLEKAEELGEEGNVEEAQKAMKEVEELKA 162 (319) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 9999999999997626888999999999999999 No 15 >PRK10564 maltose regulon periplasmic protein; Provisional Probab=24.77 E-value=51 Score=14.03 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=17.2 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999999608989999999999999 Q gi|254780626|r 34 HANEAITFGKIEEATEACRKAESV 57 (90) Q Consensus 34 k~~~ai~~~d~~~a~~~~~~~~s~ 57 (90) .++.||++||.+.|..++.++..+ T Consensus 263 aI~~AVk~~DI~KAL~LldEAe~L 286 (303) T PRK10564 263 AIKDAVKKGDVDKALKLLNEAERL 286 (303) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 999999759999999999999985 No 16 >TIGR00823 EIIA-LAC PTS system, lactose-specific IIa component; InterPro: IPR003188 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion . Separation into subunits is thought to occur after phosphorylation. ; GO: 0005351 sugar:hydrogen ion symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane. Probab=23.95 E-value=53 Score=13.93 Aligned_cols=34 Identities=26% Similarity=0.237 Sum_probs=27.2 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999996089899999999999999999 Q gi|254780626|r 28 VRSFMRHANEAITFGKIEEATEACRKAESVIQKA 61 (90) Q Consensus 28 ~kt~iKk~~~ai~~~d~~~a~~~~~~~~s~lDka 61 (90) -|+..=....+-+.||.++|..++..+...|..| T Consensus 17 aRS~a~eAl~AA~~Gdf~~A~~l~~~a~~~l~~A 50 (99) T TIGR00823 17 ARSKALEALKAAKAGDFAKARELVEQAGEELNEA 50 (99) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999999999882063899999999989999999 No 17 >pfam07148 MalM Maltose operon periplasmic protein precursor (MalM). This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown. Probab=21.74 E-value=59 Score=13.66 Aligned_cols=24 Identities=21% Similarity=0.302 Sum_probs=17.4 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999999608989999999999999 Q gi|254780626|r 34 HANEAITFGKIEEATEACRKAESV 57 (90) Q Consensus 34 k~~~ai~~~d~~~a~~~~~~~~s~ 57 (90) .++.||+.||.+.|..++.++... T Consensus 239 aI~~AVk~~DI~KAL~LldEAe~L 262 (279) T pfam07148 239 AIEQAVAKGDIPKALSLLDEAKAL 262 (279) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 999999759999999999999985 No 18 >pfam10925 DUF2680 Protein of unknown function (DUF2680). Members in this family of proteins are annotated as yckD however currently no function is known. Probab=20.76 E-value=62 Score=13.54 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=29.2 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999986588616699999999999999984 Q gi|254780626|r 55 ESVIQKAKSKGIFHGNAASRKVSRLSKRLKGIL 87 (90) Q Consensus 55 ~s~lDka~kkgiihkn~AsRkKSrL~~~v~~~~ 87 (90) -.+||+.+.=|+|.+-.|.-.++.+-.+++.+. T Consensus 21 Kqii~KyVe~G~iT~eQa~~i~~~id~r~~~~~ 53 (59) T pfam10925 21 KQVIDKYVEAGVITKEQADHIKKNIDKRVEYMK 53 (59) T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 999999998275649999999999999999999 Done!