Query gi|254780194|ref|YP_003064607.1| 50S ribosomal protein L31 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 74 No_of_seqs 107 out of 844 Neff 5.1 Searched_HMMs 39220 Date Mon May 23 10:39:34 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780194.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00528 rpmE 50S ribosomal pr 100.0 2.2E-31 5.7E-36 207.1 9.4 71 1-71 1-71 (71) 2 PRK01678 rpmE2 50S ribosomal p 100.0 1.3E-30 3.2E-35 202.7 7.9 73 1-74 1-83 (86) 3 PRK00019 rpmE 50S ribosomal pr 100.0 2.7E-29 7E-34 194.8 8.5 70 1-74 1-70 (71) 4 COG0254 RpmE Ribosomal protein 99.9 7.1E-28 1.8E-32 186.4 8.5 70 1-73 1-72 (75) 5 pfam01197 Ribosomal_L31 Riboso 99.9 1.2E-27 2.9E-32 185.2 8.7 67 1-70 1-68 (69) 6 TIGR00105 L31 ribosomal protei 99.9 5E-27 1.3E-31 181.4 5.9 67 1-70 2-69 (77) 7 PRK01397 50S ribosomal protein 99.9 2.8E-26 7E-31 177.0 8.1 71 1-74 1-72 (78) 8 CHL00136 rpl31 ribosomal prote 99.9 3.3E-26 8.5E-31 176.5 7.3 67 1-72 2-69 (72) 9 PRK03564 formate dehydrogenase 67.1 3.2 8.2E-05 22.9 1.6 52 8-62 221-274 (307) 10 pfam04216 FdhE Protein involve 59.1 5.4 0.00014 21.5 1.6 38 8-45 200-239 (283) 11 TIGR03442 conserved hypothetic 58.8 5 0.00013 21.8 1.4 25 40-66 100-124 (251) 12 TIGR01393 lepA GTP-binding pro 54.6 4.5 0.00011 22.0 0.6 47 1-55 518-568 (598) 13 TIGR01562 FdhE formate dehydro 51.0 13 0.00033 19.3 2.5 47 8-55 223-280 (312) 14 cd01908 YafJ Glutamine amidotr 33.9 23 0.00058 17.9 1.5 25 40-66 97-121 (257) 15 COG0121 Predicted glutamine am 31.5 17 0.00043 18.6 0.5 25 41-66 88-115 (252) 16 KOG4584 consensus 27.0 25 0.00063 17.7 0.7 37 35-71 29-69 (348) 17 COG2139 RPL21A Ribosomal prote 25.5 64 0.0016 15.2 3.4 31 30-61 34-70 (98) 18 TIGR01246 dapE_proteo succinyl 24.4 28 0.00071 17.3 0.6 43 30-73 284-330 (383) 19 pfam00845 Gemini_BL1 Geminivir 22.8 23 0.00058 17.9 -0.1 35 17-53 192-226 (276) No 1 >PRK00528 rpmE 50S ribosomal protein L31; Reviewed Probab=99.97 E-value=2.2e-31 Score=207.14 Aligned_cols=71 Identities=63% Similarity=1.091 Sum_probs=68.0 Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCC Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026 Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGL 71 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~ 71 (74) |||||||+|++++++|+||++|+|+||+|+++|+|+|||||+|||||++|+|+++|++|||||||+|||+| T Consensus 1 MKk~IHP~y~~~~v~~~~G~~~~t~st~G~~~~~i~vdi~s~~HPfyTgG~q~~~dt~GRV~kF~kryg~l 71 (71) T PRK00528 1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKEGPELRLDIDSGNHPAWTGGTQKILDTGGRVAKFKKKFGGL 71 (71) T ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCCCCEECCCEEEECCCCCHHHHHHHHCCC T ss_conf 98987999887899994999999867678778859998679888768589248971665699998770699 No 2 >PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed Probab=99.97 E-value=1.3e-30 Score=202.70 Aligned_cols=73 Identities=33% Similarity=0.549 Sum_probs=68.9 Q ss_pred CCCCCCCCCEEEEEE-ECCCCEEEEEEEE---------CCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC Q ss_conf 988788984079999-8799979988765---------476886999854877897116817897213648999977602 Q gi|254780194|r 1 MKKNIHPETHLITVV-MTDGTQYQTRSTW---------KEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74) Q Consensus 1 MKk~IHP~y~~v~v~-~t~g~~~~t~sT~---------g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74) ||+||||+|++|+|. |+||++|.++||+ |++||++.|||||+||| ||||+|+++|++|||||||+|||+ T Consensus 1 MKk~IHP~Y~~v~f~d~s~g~~f~~~ST~~~~~t~~~eG~~yP~~~vdi~S~~HP-FyTG~qk~vdt~GRVekF~kRy~~ 79 (86) T PRK01678 1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEGKTYPLVKVEVSSASHP-FYTGKQKFVDTEGRVEKFNKRFGR 79 (86) T ss_pred CCCCCCCCCEEEEEEECCCCCEEEECCCCCCCCEEEECCEECCEEEEEECCCCCC-CEECCEEEEECCHHHHHHHHHHHH T ss_conf 9898799980688898879999982754367840667786777698610688885-481876786143129999988731 Q ss_pred CCCC Q ss_conf 6789 Q gi|254780194|r 71 LSIE 74 (74) Q Consensus 71 ~~~k 74 (74) +..+ T Consensus 80 ~~~~ 83 (86) T PRK01678 80 FASK 83 (86) T ss_pred HCCC T ss_conf 0223 No 3 >PRK00019 rpmE 50S ribosomal protein L31; Reviewed Probab=99.96 E-value=2.7e-29 Score=194.78 Aligned_cols=70 Identities=40% Similarity=0.656 Sum_probs=66.1 Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026789 Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74) ||++|||+|++++|.|+||++|.++||++.+ +.|||||+||| ||||+|+++|++|||||||+|||.++.+ T Consensus 1 MKk~IHP~y~~v~~~cscg~~f~~~ST~~~~---~~vdi~s~~HP-FyTG~q~~~dt~GRVekF~kry~~~~~~ 70 (71) T PRK00019 1 MKKDIHPKYEEVTVTCSCGNVFKTRSTKGKD---INIDVCSKCHP-FYTGKQKIVDTGGRVERFNKRFGKPGAK 70 (71) T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCCCCC---EEEEECCCCCC-CEECCEEEEECCCCHHHHHHHHCCCCCC T ss_conf 9887799988899998889989851324753---88887689876-1848777871467699999877023468 No 4 >COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis] Probab=99.95 E-value=7.1e-28 Score=186.41 Aligned_cols=70 Identities=40% Similarity=0.645 Sum_probs=65.3 Q ss_pred CCCCCCCCC-EEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCC Q ss_conf 988788984-07999987-99979988765476886999854877897116817897213648999977602678 Q gi|254780194|r 1 MKKNIHPET-HLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSI 73 (74) Q Consensus 1 MKk~IHP~y-~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~ 73 (74) ||+||||+| ++++|.|+ ||+.|.|+||++.+ +|.|||||+||| ||||+|+++|++|||||||+|||.+.. T Consensus 1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~--~i~vdV~s~~HP-FyTG~qk~~d~~GRv~kF~kRf~~~~~ 72 (75) T COG0254 1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTD--EINLDVCSKCHP-FYTGKQKIVDTEGRVEKFNKRFGGFKG 72 (75) T ss_pred CCCCCCCCCCCEEEEEECCCCCEEEEEECCCCC--EEEEEECCCCCC-CCCCCEEEECCCCCHHHHHHHHCCCCC T ss_conf 988769876324899967899789977516886--089986799877-693854576065539999877634344 No 5 >pfam01197 Ribosomal_L31 Ribosomal protein L31. Probab=99.95 E-value=1.2e-27 Score=185.18 Aligned_cols=67 Identities=40% Similarity=0.625 Sum_probs=63.3 Q ss_pred CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC Q ss_conf 98878898407999987-99979988765476886999854877897116817897213648999977602 Q gi|254780194|r 1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74) ||+||||+|++++|.|+ ||++|.|+||. ++|++.|||||+||| ||||+|+++|++|||||||+||+. T Consensus 1 MKk~IHP~y~~v~~~c~~cg~~f~t~ST~--~~~~i~vdi~s~cHP-fyTG~~~~~dt~GRVeKF~kkf~~ 68 (69) T pfam01197 1 MKKGIHPEYREVVFTCSSCGNVFVTRSTK--EYPVIKIDVCSACHP-FYTGKQKLVDTAGRVEKFNKRFGK 68 (69) T ss_pred CCCCCCCCCEEEEEEECCCCCEEEEEECC--CCCCEEEEECCCCCC-EECCCEEEECCCHHHHHHHHHHCC T ss_conf 98877998735689999999799973703--586099986489888-481987885142359999888746 No 6 >TIGR00105 L31 ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=99.94 E-value=5e-27 Score=181.42 Aligned_cols=67 Identities=37% Similarity=0.561 Sum_probs=63.2 Q ss_pred CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC Q ss_conf 98878898407999987-99979988765476886999854877897116817897213648999977602 Q gi|254780194|r 1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74) ||+||||+|.++...|+ |++.+.++||.++ ++|.|||||.||| ||||+|+++|++||||||++||+- T Consensus 2 MK~~IHP~y~~~~~~~~~C~~~~~~~s~~~k--~e~~~dics~CHP-FYtG~~~~~~t~GRVerf~~kf~~ 69 (77) T TIGR00105 2 MKKGIHPEYQEIPAACVSCNNGFEIESTSTK--KEINIDICSKCHP-FYTGKQKIVDTGGRVERFNKKFNL 69 (77) T ss_pred CCCCCCCCCCCEECEEEEECCCEEEEECCCC--CEEEEEECCCCCC-CEECCEEEEECCCCHHHHHHHCCC T ss_conf 8887898953010106662597787552777--3146886489889-420440367426641311213288 No 7 >PRK01397 50S ribosomal protein L31; Provisional Probab=99.93 E-value=2.8e-26 Score=177.01 Aligned_cols=71 Identities=32% Similarity=0.519 Sum_probs=67.0 Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCH-HHHHHHHHHCCCCC Q ss_conf 988788984079999879997998876547688699985487789711681789721364-89999776026789 Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ-VSRFKKRFAGLSIE 74 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Gr-veKF~kkfg~~~~k 74 (74) ||++|||+|+.|+|.|+ |++|+|+||+ +++++.||||+.|||||++|.++++|+.|| |+||||||+||++. T Consensus 1 MKkdIHPdYh~I~V~~~-G~~f~trST~--~gd~l~LDIDp~~HPAWTGg~~~lld~ggrqVskFnKrf~gL~f~ 72 (78) T PRK01397 1 MKSGIHPEYKKFLIKVG-SDVFETMSTH--PTGEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLSFG 72 (78) T ss_pred CCCCCCCCCEEEEEEEC-CCEEEEEECC--CCCEEEEECCCCCCCCEECCCCEEEECCCCCHHHHHHHCCCCCCC T ss_conf 98776888748999968-9778876024--797689823898887446786267806896547754013566657 No 8 >CHL00136 rpl31 ribosomal protein L31; Validated Probab=99.93 E-value=3.3e-26 Score=176.54 Aligned_cols=67 Identities=33% Similarity=0.356 Sum_probs=57.7 Q ss_pred CCCCCCCCCEE-EEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCC Q ss_conf 98878898407-9999879997998876547688699985487789711681789721364899997760267 Q gi|254780194|r 1 MKKNIHPETHL-ITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLS 72 (74) Q Consensus 1 MKk~IHP~y~~-v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~ 72 (74) ||+||||+|++ +.+.|+||+.+.+.|| +++++|||||+||| ||||+|+++|++||||||++|||--+ T Consensus 2 ~Kk~IHP~y~~~~~v~c~g~~~~~~~st----~~~~~vdIcS~cHP-FyTG~Qr~vdt~GRVekF~kryg~~~ 69 (72) T CHL00136 2 PKKNIHPTWYPDAKVYCDGQLVMTIGST----KPELHVDIWSGNHP-FYTGSQKIIDTEGRVERFMRKYGLNS 69 (72) T ss_pred CCCCCCCCCEEEEEEECCCCCEEEECCC----CCCEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCC T ss_conf 8887898763148999389858986655----77589888689988-58487678714756999977547876 No 9 >PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Probab=67.07 E-value=3.2 Score=22.87 Aligned_cols=52 Identities=13% Similarity=0.056 Sum_probs=29.5 Q ss_pred CCEEEEEEEC-CCCEEEEE-EEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHH Q ss_conf 8407999987-99979988-7654768869998548778971168178972136489 Q gi|254780194|r 8 ETHLITVVMT-DGTQYQTR-STWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVS 62 (74) Q Consensus 8 ~y~~v~v~~t-~g~~~~t~-sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Grve 62 (74) +|+-+-+.|+ ||++-.+. .++..+.+-+++|+|..||- | . |.-....++.++ T Consensus 221 eW~~~R~~C~~C~~~~~l~y~~~~~~~~~vrae~C~~C~~-Y-l-K~l~~~kd~~~~ 274 (307) T PRK03564 221 EWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGT-Y-L-KILYQEKDPKVE 274 (307) T ss_pred CCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEECCCHHH-H-H-HHHHHHCCCCCC T ss_conf 4021353468888988820366637876467764640665-7-8-787450088888 No 10 >pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase. Probab=59.11 E-value=5.4 Score=21.55 Aligned_cols=38 Identities=18% Similarity=0.135 Sum_probs=23.3 Q ss_pred CCEEEEEEEC-CCCEEEEE-EEECCCCCEEEEEECCCCCC Q ss_conf 8407999987-99979988-76547688699985487789 Q gi|254780194|r 8 ETHLITVVMT-DGTQYQTR-STWKEEGAVMKLDIDPLSHF 45 (74) Q Consensus 8 ~y~~v~v~~t-~g~~~~t~-sT~g~~~~~~~vdi~s~~HP 45 (74) +|+-+-+.|+ ||++=... ...-.+.+-+++|+|..||- T Consensus 200 eW~~~R~~C~~Cg~~~~~~~~~~~~~~~~~r~e~C~~C~~ 239 (283) T pfam04216 200 EWHFVRVKCTNCGSTKGLAYWSLEEGEPGVRAETCDTCHS 239 (283) T ss_pred CCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEECCCCCC T ss_conf 3242265479999999643033316887666640563110 No 11 >TIGR03442 conserved hypothetical protein TIGR03442. Members of this strictly bacterial protein family show similarity to class II glutamine amidotransferases (see pfam00310). They are distinguished by appearing in a genome context with, and usually adjacent to or between, members of families TIGR03438 (an uncharacterized methyltransferase) and TIGR03440 (an uncharacterized protein). Probab=58.79 E-value=5 Score=21.75 Aligned_cols=25 Identities=20% Similarity=0.380 Sum_probs=18.0 Q ss_pred CCCCCCCEECCCEEEEECCCHHHHHHH Q ss_conf 487789711681789721364899997 Q gi|254780194|r 40 DPLSHFAWIGGRQKITDRGGQVSRFKK 66 (74) Q Consensus 40 ~s~~HP~fytgkq~~~dt~GrveKF~k 66 (74) -++||| |.-|+--++-. |.|+.|.+ T Consensus 100 ~~NcHP-F~~g~~lF~HN-G~I~~f~~ 124 (251) T TIGR03442 100 ESACAP-FSDGRWLFSHN-GFVDNFRQ 124 (251) T ss_pred CCCCCC-CEECCEEEEEC-CCCCCHHH T ss_conf 234788-33577899947-72377458 No 12 >TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297 LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding. Probab=54.58 E-value=4.5 Score=22.04 Aligned_cols=47 Identities=23% Similarity=0.367 Sum_probs=40.2 Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECC----CEEEE Q ss_conf 98878898407999987999799887654768869998548778971168----17897 Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGG----RQKIT 55 (74) Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytg----kq~~~ 55 (74) ||.=|+++..+|.+.-+=|+...-|+|+.. ++=||.++| ||| |++++ T Consensus 518 LKE~IPRQqF~ipIQA~IG~KIIARETiKa----~RKdVtAKC----YGGDiTRKrKLL 568 (598) T TIGR01393 518 LKELIPRQQFEIPIQAAIGGKIIARETIKA----LRKDVTAKC----YGGDITRKRKLL 568 (598) T ss_pred HHHCCCCCCCCCCHHEECCCEEEEECCCCC----CCCCEEEEE----CCCCCCHHHHHH T ss_conf 662286346664110221880687503541----225502352----087704324545 No 13 >TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. . Probab=50.96 E-value=13 Score=19.27 Aligned_cols=47 Identities=17% Similarity=0.136 Sum_probs=31.4 Q ss_pred CCEEEEEEEC-CCCE----EEEEEEEC--CCCCEEEEEECCCCCCCE----ECCCEEEE Q ss_conf 8407999987-9997----99887654--768869998548778971----16817897 Q gi|254780194|r 8 ETHLITVVMT-DGTQ----YQTRSTWK--EEGAVMKLDIDPLSHFAW----IGGRQKIT 55 (74) Q Consensus 8 ~y~~v~v~~t-~g~~----~~t~sT~g--~~~~~~~vdi~s~~HP~f----ytgkq~~~ 55 (74) ++|.|-|.|+ ||++ |....+.+ .|...|+-|+|..|.- | |-.+.+.+ T Consensus 223 ~Wh~VRvKCs~Ce~sk~l~Y~sle~~~qPaE~A~~kAE~Cd~C~~-ylKilY~ekdp~~ 280 (312) T TIGR01562 223 EWHVVRVKCSACEESKKLAYLSLEDDDQPAEKAVVKAEVCDDCDS-YLKILYQEKDPKL 280 (312) T ss_pred CCCEEEEEECCCCCCCCEEEEEECCCCCCHHHHEEECCCCCCCCH-HHHHHHHCCCCCC T ss_conf 767066665277876760256632787743462330256887115-8888744148852 No 14 >cd01908 YafJ Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II glutamine amidotransferases including lucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The YafJ fold is also somwhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits. Probab=33.90 E-value=23 Score=17.85 Aligned_cols=25 Identities=24% Similarity=0.333 Sum_probs=16.9 Q ss_pred CCCCCCCEECCCEEEEECCCHHHHHHH Q ss_conf 487789711681789721364899997 Q gi|254780194|r 40 DPLSHFAWIGGRQKITDRGGQVSRFKK 66 (74) Q Consensus 40 ~s~~HP~fytgkq~~~dt~GrveKF~k 66 (74) -.+||| |.-|.= +.--.|.|++|.. T Consensus 97 ~~N~HP-F~~~~~-~F~HNG~i~~~~~ 121 (257) T cd01908 97 LENCHP-FTRGRW-LFAHNGQLDGFRL 121 (257) T ss_pred CCCCCC-EEECCE-EEEECCCCCCHHH T ss_conf 356787-266579-9996773478788 No 15 >COG0121 Predicted glutamine amidotransferase [General function prediction only] Probab=31.53 E-value=17 Score=18.61 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=16.2 Q ss_pred CCCCCCEECCCE---EEEECCCHHHHHHH Q ss_conf 877897116817---89721364899997 Q gi|254780194|r 41 PLSHFAWIGGRQ---KITDRGGQVSRFKK 66 (74) Q Consensus 41 s~~HP~fytgkq---~~~dt~GrveKF~k 66 (74) ++||| |+-+.- -+.--.|.|++|.. T Consensus 88 ~ntHP-F~~~~~~~~~~FaHNG~l~~~~~ 115 (252) T COG0121 88 SNTHP-FTRELWGYIWLFAHNGQLDKFKL 115 (252) T ss_pred CCCCC-CCCCCCCCCEEEEECCCCCCCCC T ss_conf 57898-04157774079985680266541 No 16 >KOG4584 consensus Probab=26.99 E-value=25 Score=17.65 Aligned_cols=37 Identities=19% Similarity=0.358 Sum_probs=20.9 Q ss_pred EEEEECCCCCCCEEC---CCEE-EEECCCHHHHHHHHHHCC Q ss_conf 999854877897116---8178-972136489999776026 Q gi|254780194|r 35 MKLDIDPLSHFAWIG---GRQK-ITDRGGQVSRFKKRFAGL 71 (74) Q Consensus 35 ~~vdi~s~~HP~fyt---gkq~-~~dt~GrveKF~kkfg~~ 71 (74) +-+++-+++-|-|.- ..|. ..|+.-|.|+|.+||.++ T Consensus 29 ~Wi~~f~~~ip~f~krA~asq~~~~DA~~RAe~F~~~y~~~ 69 (348) T KOG4584 29 YWINVFSNSIPSFKKRAEASQENVPDAPARAEKFAQRYAGI 69 (348) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH T ss_conf 79999987767888888615788985567899999999999 No 17 >COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis] Probab=25.47 E-value=64 Score=15.21 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=20.9 Q ss_pred CCCCEEEEEECCCC-----CCCEECCC-EEEEECCCHH Q ss_conf 76886999854877-----89711681-7897213648 Q gi|254780194|r 30 EEGAVMKLDIDPLS-----HFAWIGGR-QKITDRGGQV 61 (74) Q Consensus 30 ~~~~~~~vdi~s~~-----HP~fytgk-q~~~dt~Grv 61 (74) ++++.+.|+|++.- ||. |-|+ -.++...||. T Consensus 34 ~~Gd~V~I~IdpSv~kGmPh~r-f~G~TG~Vvg~~g~a 70 (98) T COG2139 34 KVGDKVHIDIDPSVHKGMPHPR-FQGKTGTVVGVRGRA 70 (98) T ss_pred CCCCEEEEEECCCCCCCCCCCC-CCCCCEEEEECCCCE T ss_conf 7998799984762026987753-047630798414877 No 18 >TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase; InterPro: IPR005941 The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants . Succinyl-diaminopimelate desuccinylase (3.5.1.18 from EC) hydrolyses N-succinyl-L,L-diaminopimelic acid which is required for the bacterial synthesis of lysine and meso-diaminopimelic acid. This group of bacterial sequences belong to the MEROPS peptidase family M20 (clan MH), subfamily M20A (non-peptidase homologs). ; GO: 0009014 succinyl-diaminopimelate desuccinylase activity, 0009089 lysine biosynthetic process via diaminopimelate. Probab=24.45 E-value=28 Score=17.32 Aligned_cols=43 Identities=14% Similarity=0.131 Sum_probs=32.5 Q ss_pred CCCCE-EEEEECCCCCCCEECC--CEEEEECCCH-HHHHHHHHHCCCC Q ss_conf 76886-9998548778971168--1789721364-8999977602678 Q gi|254780194|r 30 EEGAV-MKLDIDPLSHFAWIGG--RQKITDRGGQ-VSRFKKRFAGLSI 73 (74) Q Consensus 30 ~~~~~-~~vdi~s~~HP~fytg--kq~~~dt~Gr-veKF~kkfg~~~~ 73 (74) +||.+ |.|+.....-| |+|. .-+++++.-. |++|.+.=..++. T Consensus 284 keY~l~Y~lew~~Sg~p-FlT~P~~g~l~~~~~~~i~~~~~~~P~lsT 330 (383) T TIGR01246 284 KEYGLDYDLEWSLSGEP-FLTNPIDGKLIDKVREAIEETNGIKPELST 330 (383) T ss_pred CCCCCCEEEEECCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCCC T ss_conf 00388416987215855-278888763899999999997086755347 No 19 >pfam00845 Gemini_BL1 Geminivirus BL1 movement protein. Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation. Probab=22.79 E-value=23 Score=17.87 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=25.5 Q ss_pred CCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEE Q ss_conf 7999799887654768869998548778971168178 Q gi|254780194|r 17 TDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQK 53 (74) Q Consensus 17 t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~ 53 (74) .-|.++.++||+|.....-.-++....|| |-+-.+ T Consensus 192 ~PGEsWAsrS~IG~~~s~~~~~~~~~~~P--Yr~L~r 226 (276) T pfam00845 192 QPGETWATRSTIGPSQSETDSEVENAEHP--YRHLHR 226 (276) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCC--HHHHCC T ss_conf 89974302212377766566543212363--567535 Done!