Query 026764
Match_columns 233
No_of_seqs 170 out of 400
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:21:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026764.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026764hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01159 Ribosomal_L6e: Riboso 100.0 3.6E-49 7.9E-54 314.7 -2.8 107 126-233 1-108 (108)
2 KOG1694 60s ribosomal protein 100.0 8.8E-43 1.9E-47 292.2 8.1 140 61-233 12-152 (152)
3 COG2163 RPL14A Ribosomal prote 99.8 5.4E-20 1.2E-24 150.5 8.5 123 85-208 1-124 (125)
4 PTZ00471 60S ribosomal protein 99.4 1.2E-13 2.7E-18 114.2 6.3 62 88-149 4-90 (134)
5 PF03868 Ribosomal_L6e_N: Ribo 99.4 5.2E-14 1.1E-18 102.0 -1.7 44 1-44 1-44 (59)
6 PRK04333 50S ribosomal protein 99.1 1.2E-10 2.6E-15 89.7 6.7 62 88-150 3-64 (84)
7 KOG3418 60S ribosomal protein 98.4 3E-07 6.6E-12 76.4 5.3 63 86-151 2-92 (136)
8 PTZ00065 60S ribosomal protein 98.0 1.9E-05 4.1E-10 65.6 6.4 62 88-150 7-68 (130)
9 CHL00141 rpl24 ribosomal prote 95.0 0.028 6.1E-07 43.2 3.6 65 86-153 6-76 (83)
10 PRK12281 rplX 50S ribosomal pr 94.6 0.046 1E-06 41.4 3.8 62 88-152 6-73 (76)
11 PTZ00194 60S ribosomal protein 94.5 0.12 2.6E-06 43.8 6.4 63 88-159 46-111 (143)
12 PRK01191 rpl24p 50S ribosomal 94.4 0.072 1.6E-06 43.9 4.7 57 88-153 45-102 (120)
13 TIGR01080 rplX_A_E ribosomal p 94.2 0.073 1.6E-06 43.4 4.3 63 88-159 41-106 (114)
14 PRK00004 rplX 50S ribosomal pr 92.2 0.19 4.1E-06 40.1 3.8 63 88-153 4-72 (105)
15 KOG3421 60S ribosomal protein 91.4 0.24 5.3E-06 41.7 3.7 61 86-148 4-64 (136)
16 TIGR01079 rplX_bact ribosomal 91.3 0.28 6E-06 39.2 3.8 63 88-153 3-72 (104)
17 COG0198 RplX Ribosomal protein 90.9 0.39 8.5E-06 38.7 4.3 58 89-153 5-70 (104)
18 KOG1694 60s ribosomal protein 87.1 0.079 1.7E-06 45.2 -2.2 75 64-138 74-152 (152)
19 smart00739 KOW KOW (Kyprides, 86.1 1.1 2.3E-05 26.4 3.0 24 89-112 2-25 (28)
20 PF00467 KOW: KOW motif; Inte 81.0 2.7 5.8E-05 26.4 3.4 26 91-116 1-26 (32)
21 PF10543 ORF6N: ORF6N domain; 52.1 1.9 4.2E-05 32.9 -2.2 28 101-138 6-33 (88)
22 COG2350 Uncharacterized protei 39.1 8.8 0.00019 30.1 -0.3 17 109-125 27-44 (92)
23 PF06080 DUF938: Protein of un 28.3 23 0.0005 31.6 0.5 17 114-130 133-149 (204)
24 KOG0116 RasGAP SH3 binding pro 26.0 56 0.0012 32.2 2.7 46 115-161 91-137 (419)
25 TIGR00922 nusG transcription t 24.8 1.3E+02 0.0028 24.9 4.3 34 87-120 118-152 (172)
26 PF00122 E1-E2_ATPase: E1-E2 A 24.2 1.6E+02 0.0036 24.8 5.0 52 86-147 49-113 (230)
27 COG2805 PilT Tfp pilus assembl 23.7 42 0.00092 32.4 1.4 11 114-124 124-134 (353)
28 PRK08666 5'-methylthioadenosin 22.9 58 0.0013 29.2 2.0 51 91-145 30-85 (261)
29 PRK05609 nusG transcription an 22.5 1.4E+02 0.0031 24.7 4.2 27 87-113 125-151 (181)
30 KOG0012 DNA damage inducible p 21.9 55 0.0012 32.0 1.7 38 172-213 193-230 (380)
31 KOG1999 RNA polymerase II tran 20.4 98 0.0021 33.8 3.4 45 81-125 452-496 (1024)
32 TIGR00405 L26e_arch ribosomal 20.2 1.1E+02 0.0023 24.9 2.9 35 87-121 85-120 (145)
No 1
>PF01159 Ribosomal_L6e: Ribosomal protein L6e ; InterPro: IPR000915 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 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_E 4A1D_E 4A19_E 4A1B_E 3IZR_G 3O58_F 3O5H_F 3IZS_G.
Probab=100.00 E-value=3.6e-49 Score=314.67 Aligned_cols=107 Identities=59% Similarity=0.945 Sum_probs=98.2
Q ss_pred ecCcceeeeecceEEeeeeeEecCCccc-CCCChhhhhHHHhhhhcccccccccccccccccCChhhHHhHHHHHHHHHH
Q 026764 126 VNGVPLRRVNQSYVIATSTKVDISGVDL-GKFDDQYFEKEAEKKKKKGEGEFFEAEKEEKKVLPDDKKDDQKTVDAQLIK 204 (233)
Q Consensus 126 lNgvPlrRv~q~yVIaTSTkvdis~vki-~~~~D~YF~k~~~~k~k~~e~eiF~~~k~~k~~vseqrk~dQK~VD~~il~ 204 (233)
|||||||||||+|||||||+||||+|++ ++|||+||++.+.++++++|++||+.+ +++|++||||++|||+||++||+
T Consensus 1 iNGVPLRRVnQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~~~k~k~~e~~~f~~~-~~k~~~se~rk~dQK~VD~~ll~ 79 (108)
T PF01159_consen 1 INGVPLRRVNQAYVIATSTKVDISGVKIPEKIDDAYFKRKKKKKKKKGEGDFFAEK-KEKYKVSEQRKADQKAVDAQLLA 79 (108)
T ss_dssp SSS--SEEESSCCCEECSCESCHCCHHH-CCTTGSSSCHCCCCHHHHHHCHCCHHH-HHCCCCHHHHHHHHHCSHHCSHC
T ss_pred CCCCcceecccceEEEEeeEEeccccchhhccchHHHHhhhhccccccHHHHHhcc-cccccCCHHHHHHHHHHHHHHHH
Confidence 7999999999999999999999999999 559999999988777788999999966 47999999999999999999999
Q ss_pred HHHhhhhHHhhhcCcccccCCCCccccCC
Q 026764 205 SIEAVLDLKTYLSARFSLKSGMKPHELVF 233 (233)
Q Consensus 205 ~Ikk~p~L~~YL~s~FsL~~g~~PH~m~F 233 (233)
+|+++|+|++||+|+|+|++|||||+|+|
T Consensus 80 aIkk~p~L~~YL~s~FsL~~g~~PH~m~F 108 (108)
T PF01159_consen 80 AIKKHPELKGYLKSRFSLRKGDYPHKMKF 108 (108)
T ss_dssp CCCTCCCTHHHHHCCCCHCTTTSSSSS--
T ss_pred HHhcCHHHHHhhhhheeCCCCCcCccCCC
Confidence 99999999999999999999999999998
No 2
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.8e-43 Score=292.17 Aligned_cols=140 Identities=50% Similarity=0.810 Sum_probs=131.2
Q ss_pred CCCCCCCCCCCCccccCCCCCcccccccccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecceEE
Q 026764 61 PPKFYPADDVKKPLVNKRKHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVI 140 (233)
Q Consensus 61 ~p~~Yptedv~~~~~~~k~~~~~klR~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVI 140 (233)
+|.|||+ ...+.+.++++||+||+||||||||+ .+||+|++|++|+|+|
T Consensus 12 ~~~~yp~------~k~~~~~~~~k~r~~l~~gtvliil~-------------------------~~ng~~~~~v~~~~~~ 60 (152)
T KOG1694|consen 12 PPADYPR------KKARYSAKPSKLRASLTPGTVLIILA-------------------------PINGVPLKRVNERYVA 60 (152)
T ss_pred Chhhccc------hhccccccchhhhhccCCCeeEEEec-------------------------ccCCcCcccccceEEe
Confidence 8999998 23345678999999999999999999 6999999999999999
Q ss_pred eeeeeEecCCcccCC-CChhhhhHHHhhhhcccccccccccccccccCChhhHHhHHHHHHHHHHHHHhhhhHHhhhcCc
Q 026764 141 ATSTKVDISGVDLGK-FDDQYFEKEAEKKKKKGEGEFFEAEKEEKKVLPDDKKDDQKTVDAQLIKSIEAVLDLKTYLSAR 219 (233)
Q Consensus 141 aTSTkvdis~vki~~-~~D~YF~k~~~~k~k~~e~eiF~~~k~~k~~vseqrk~dQK~VD~~il~~Ikk~p~L~~YL~s~ 219 (233)
+||+ ||+++|+++. +||+||.+.+.++.+++|++||++++ |+|+++||++.|||+||++||++|+.+|+|+.||.++
T Consensus 61 ~ts~-i~~~~vk~~e~~td~yf~K~k~~~~k~~e~~i~~~ek-ekyeIteq~kiDqKaVDs~il~~iK~ip~lk~yl~~~ 138 (152)
T KOG1694|consen 61 TTSK-IDPSNVKIPEHLTDAYFKKKKLKKKKTQEGEIFAEEK-EKYEITEQRKIDQKAVDSQILPKIKAIPQLKKYLGSV 138 (152)
T ss_pred eeee-eccccccccccccHHHHhhhhccccccccchhhcccc-cccccchhhhhhHHHHHHHHHHHHhhchHhhhccchh
Confidence 9988 9999999965 99999999988889999999999874 8999999999999999999999999999999999999
Q ss_pred ccccCCCCccccCC
Q 026764 220 FSLKSGMKPHELVF 233 (233)
Q Consensus 220 FsL~~g~~PH~m~F 233 (233)
|+|++|+|||+|+|
T Consensus 139 f~l~~g~~Ph~l~f 152 (152)
T KOG1694|consen 139 FALTNGIYPHKLKF 152 (152)
T ss_pred hhccCCCCcccccC
Confidence 99999999999998
No 3
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=5.4e-20 Score=150.49 Aligned_cols=123 Identities=29% Similarity=0.406 Sum_probs=98.8
Q ss_pred ccccccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecceEEeeeeeEecCCccc-CCCChhhhhH
Q 026764 85 LRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISGVDL-GKFDDQYFEK 163 (233)
Q Consensus 85 lR~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~vki-~~~~D~YF~k 163 (233)
++.+|.||+|+++++||++||+||+|++++.+.+|++||..+||||.+|+|.+|+++|++.+|+..... +.+.-+|+..
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a~ 80 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEAA 80 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHhh
Confidence 478899999999999999999999999999999999999999999999999999999999999877544 5577777776
Q ss_pred HHhhhhcccccccccccccccccCChhhHHhHHHHHHHHHHHHHh
Q 026764 164 EAEKKKKKGEGEFFEAEKEEKKVLPDDKKDDQKTVDAQLIKSIEA 208 (233)
Q Consensus 164 ~~~~k~k~~e~eiF~~~k~~k~~vseqrk~dQK~VD~~il~~Ikk 208 (233)
...-+.-..+ +-|..++-.+.....++.++||.++++.+..+++
T Consensus 81 ~~~~~~~~~~-~~~~~k~~~~~~~~~~r~~~~k~~~~~~~~~~k~ 124 (125)
T COG2163 81 GVLAKLDKSA-KNLETKKVREPLTDAERFKVMKLVKEERLQVGKA 124 (125)
T ss_pred hhhccccccc-hhhhhhhhhcccchHHHHHHHHHHHHHHhhhhcc
Confidence 5433222222 3333332233445678999999999999988765
No 4
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.45 E-value=1.2e-13 Score=114.20 Aligned_cols=62 Identities=39% Similarity=0.670 Sum_probs=59.0
Q ss_pred cccCCcEEEEecceecCceEEEEeeccC-------ceEEEec----ccee--------------cCcceeeeecceEEee
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQLTS-------GLLLVTG----PFKV--------------NGVPLRRVNQSYVIAT 142 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL~s-------glLLVTG----P~~l--------------NgvPlrRv~q~yVIaT 142 (233)
-+.||.|+|+|+|||+|+++|+||++++ |.+||+| |.++ ....+..+|.+|+++|
T Consensus 4 ~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHlmPT 83 (134)
T PTZ00471 4 FLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHFLPT 83 (134)
T ss_pred cccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeeceeccc
Confidence 4789999999999999999999999999 5999999 9999 8889999999999999
Q ss_pred eeeEecC
Q 026764 143 STKVDIS 149 (233)
Q Consensus 143 STkvdis 149 (233)
++.+||+
T Consensus 84 RY~vdi~ 90 (134)
T PTZ00471 84 RYNMDMS 90 (134)
T ss_pred ceeeecc
Confidence 9999998
No 5
>PF03868 Ribosomal_L6e_N: Ribosomal protein L6, N-terminal domain; InterPro: IPR005568 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 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 [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_G.
Probab=99.35 E-value=5.2e-14 Score=101.95 Aligned_cols=44 Identities=52% Similarity=0.837 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCCCcccccCccccchhhhhhccccceeeecCCCc
Q 026764 1 MAPKAATGRTSRNPDLIRGVGKFSRSKMYHKRGLWAIKAKNGGV 44 (233)
Q Consensus 1 ma~~~~~~~~~rn~~l~~Gi~r~Srs~~y~rk~~~~~k~k~gg~ 44 (233)
||++-...||+||++|++||+|||||+||+|+|+|+.|.+.++.
T Consensus 1 m~~kK~k~~~~RN~~L~~GI~RySrS~my~kralyk~K~k~~~~ 44 (59)
T PF03868_consen 1 MAPKKKKPHCSRNPVLVRGIGRYSRSAMYHKRALYKRKKKAAKK 44 (59)
T ss_dssp ------------HHHHHTTTSHHHHHHHHHHHHH-S-THHHHHH
T ss_pred CccccccccccCChhhhCccccccHHHHHHHHHHHHHhcccCCc
Confidence 77777777799999999999999999999999999877544333
No 6
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.13 E-value=1.2e-10 Score=89.67 Aligned_cols=62 Identities=37% Similarity=0.527 Sum_probs=58.9
Q ss_pred cccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecceEEeeeeeEecCC
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISG 150 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~ 150 (233)
.+.+|.|+++++|+++|+.+|+++.++++.+||.||+. +++|-++.|.+++..|+++++++.
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~~~-~~~~rk~kn~khl~lt~~ki~~~~ 64 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSL-TGVKRRRCNIKHLEPTDKKVDIEK 64 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCCEEEEECCCc-CCCCCeeechHHEEEeeEEEECCC
Confidence 57899999999999999999999999999999999998 999999999999999999998754
No 7
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=98.44 E-value=3e-07 Score=76.44 Aligned_cols=63 Identities=32% Similarity=0.616 Sum_probs=56.2
Q ss_pred cccccCCcEEEEecceecCceEEEEeeccCc-------eEEEeccceecCcce---------------------eeeecc
Q 026764 86 RASITPGTVFILLAGRFMGKRVVFLKQLTSG-------LLLVTGPFKVNGVPL---------------------RRVNQS 137 (233)
Q Consensus 86 R~SitpGtvlIlL~Gr~~GKRvVfLKqL~sg-------lLLVTGP~~lNgvPl---------------------rRv~q~ 137 (233)
.+-+.||.||++++|+++|+++|++|+.+.| .+||.| |...|+ .-+|-.
T Consensus 2 ~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAg---i~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~ 78 (136)
T KOG3418|consen 2 AKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAG---VDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYN 78 (136)
T ss_pred cccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeee---hhhccccccccccchhhhhcccceeEEEEeecc
Confidence 3568899999999999999999999999987 999999 778887 458999
Q ss_pred eEEeeeeeEecCCc
Q 026764 138 YVIATSTKVDISGV 151 (233)
Q Consensus 138 yVIaTSTkvdis~v 151 (233)
++++|...+|+-..
T Consensus 79 hlMptRy~vdv~~~ 92 (136)
T KOG3418|consen 79 HLMPTRYTVDVLAL 92 (136)
T ss_pred cccCcceEEeehhh
Confidence 99999999998644
No 8
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=97.97 E-value=1.9e-05 Score=65.59 Aligned_cols=62 Identities=23% Similarity=0.345 Sum_probs=58.2
Q ss_pred cccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecceEEeeeeeEecCC
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISG 150 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~ 150 (233)
-+.+|.|+.|..|.+.||-||++--++..-+||.|| ...|||-+.+|-+.+.-|.-+|+|.-
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP-~~tgV~Rq~i~~k~l~LT~~~v~i~r 68 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGA-FITGVKRQSIPLKRLKLTDEKIKINR 68 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCC-CcCCcceeEEeccceEEccEEEecCC
Confidence 467999999999999999999999999999999999 67799999999999999999998854
No 9
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.04 E-value=0.028 Score=43.22 Aligned_cols=65 Identities=20% Similarity=0.208 Sum_probs=47.6
Q ss_pred cccccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCcce-----eeeecceEEeeeeeEecCCccc
Q 026764 86 RASITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPL-----RRVNQSYVIATSTKVDISGVDL 153 (233)
Q Consensus 86 R~SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPl-----rRv~q~yVIaTSTkvdis~vki 153 (233)
.-.|.+|+.+++++|+++||.-..++-+ +++.++|.| +|-+-- ..-.+.-++.-..-|++|||.+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~l 76 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG---INIKFKHIKPNKENEVGEIKQFEAPIHSSNVML 76 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCccCCCCCCEEEEECCCCHHHEEE
Confidence 3368899999999999999999999986 578999999 553211 1122344555566778888865
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.61 E-value=0.046 Score=41.44 Aligned_cols=62 Identities=23% Similarity=0.284 Sum_probs=44.1
Q ss_pred cccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCcce-----eeeecceEEeeeeeEecCCcc
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPL-----RRVNQSYVIATSTKVDISGVD 152 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPl-----rRv~q~yVIaTSTkvdis~vk 152 (233)
.|..|+-+++++|+++||.-..++-+ .++-++|.| +|-+-- ..-.+-=++....-|++|||.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~ 73 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG---VKIAKKAIKPSQKNPNGGFIEKEMPIHISNVK 73 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCCccCCCCCEEEEEcCcCHHHce
Confidence 58899999999999999999999985 588899999 665421 111123344445566667664
No 11
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.52 E-value=0.12 Score=43.79 Aligned_cols=63 Identities=10% Similarity=0.150 Sum_probs=49.2
Q ss_pred cccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCcceeeeecceEEeeeeeEecCCccc--CCCChh
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISGVDL--GKFDDQ 159 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~vki--~~~~D~ 159 (233)
.|.-|+.|+|++|.|+|++--.++-+ .++-++|.| || +..-|.+= ...-|++|||-| +.++|.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEg---vn---~~Kk~gk~---~e~PIh~SNV~iv~l~l~~~ 111 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEK---IT---REKANGEP---VQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC---eE---EEecCCCE---eecCcCchheEEEccccCch
Confidence 37889999999999999999999986 477899888 44 33444433 355889999998 458877
No 12
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=94.39 E-value=0.072 Score=43.92 Aligned_cols=57 Identities=18% Similarity=0.271 Sum_probs=45.0
Q ss_pred cccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCcceeeeecceEEeeeeeEecCCccc
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISGVDL 153 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~vki 153 (233)
-|..|+.|+|++|.|+|+.--.++-+ +.+-++|.| +|-+- .+- +....-|++|||.+
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG---vn~~k----~~G--~~~e~pIh~SNV~l 102 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG---VTVKK----ADG--TEVPRPIHPSNVMI 102 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC---cEEEC----CCC--eEEEcccchhHeEE
Confidence 37799999999999999999999986 478899999 55322 122 44556789999987
No 13
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=94.20 E-value=0.073 Score=43.40 Aligned_cols=63 Identities=24% Similarity=0.297 Sum_probs=47.6
Q ss_pred cccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCcceeeeecceEEeeeeeEecCCcccCC--CChh
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDISGVDLGK--FDDQ 159 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdis~vki~~--~~D~ 159 (233)
.|.-|+.|+|++|.|+|+.-.+++-+ ..+.++|.| ||-+- -+ - +....-|++|||.+-. +||+
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg---vn~~k---~~-G--~~~e~pIh~SnV~l~~l~l~~~ 106 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG---VTKEK---VN-G--TEVPVPIHPSNVMITKLNLDDE 106 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC---eEEEC---CC-C--eEEEeeechHHeEEEeccCChH
Confidence 47789999999999999999999986 477899999 55332 12 2 4566679999998733 5543
No 14
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=92.17 E-value=0.19 Score=40.10 Aligned_cols=63 Identities=35% Similarity=0.447 Sum_probs=47.9
Q ss_pred cccCCcEEEEecceecCceEEEEeec-cCceEEEeccceecCccee-e----eecceEEeeeeeEecCCccc
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLVTGPFKVNGVPLR-R----VNQSYVIATSTKVDISGVDL 153 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlr-R----v~q~yVIaTSTkvdis~vki 153 (233)
.|.+|+-+.+++|+++||.-..++-+ .++-++|.| +|-+... + -++-=++....-|.+|||.+
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg---vn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~l 72 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEG---VNIVKKHQKPNQENPQGGIIEKEAPIHISNVAL 72 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEecCCCCCCCCCceEEEECCcCHHHEEE
Confidence 47899999999999999999999986 478899988 5543221 1 12344566677889999976
No 15
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=91.41 E-value=0.24 Score=41.67 Aligned_cols=61 Identities=25% Similarity=0.354 Sum_probs=52.5
Q ss_pred cccccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecceEEeeeeeEec
Q 026764 86 RASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSYVIATSTKVDI 148 (233)
Q Consensus 86 R~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVIaTSTkvdi 148 (233)
..+...|.|.++..|.+.||=|+++-+.++...||-|| ..+||..-+|-.-+.-|--.+|+
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp--~t~v~rq~~~~~~~~LT~~~~kf 64 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGP--CTGVPRQAMNLKCLQLTDFVLKF 64 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCc--ccccchhhcchhheeeeeeeEec
Confidence 45678999999999999999999999999999999999 56888877777777777666665
No 16
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=91.28 E-value=0.28 Score=39.24 Aligned_cols=63 Identities=32% Similarity=0.402 Sum_probs=48.7
Q ss_pred cccCCcEEEEecceecCceEEEEeecc-CceEEEeccceecCcceee----ee--cceEEeeeeeEecCCccc
Q 026764 88 SITPGTVFILLAGRFMGKRVVFLKQLT-SGLLLVTGPFKVNGVPLRR----VN--QSYVIATSTKVDISGVDL 153 (233)
Q Consensus 88 SitpGtvlIlL~Gr~~GKRvVfLKqL~-sglLLVTGP~~lNgvPlrR----v~--q~yVIaTSTkvdis~vki 153 (233)
.|..|+-+.+++|+++||.-..++-+. ++-++|.| +|-+.-+- .+ +--++....-|.+|||.+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~l 72 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG---VNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVML 72 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC---cEEEEEecCcccCCCCCCceEEEEccCCHHHeEE
Confidence 377999999999999999999999974 78899999 65432211 12 456677777889999976
No 17
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=90.91 E-value=0.39 Score=38.72 Aligned_cols=58 Identities=26% Similarity=0.386 Sum_probs=46.4
Q ss_pred ccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecc--------eEEeeeeeEecCCccc
Q 026764 89 ITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQS--------YVIATSTKVDISGVDL 153 (233)
Q Consensus 89 itpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~--------yVIaTSTkvdis~vki 153 (233)
|.-|+.+++++|.++|+.-..|+-+... ++|-| |-+...|++ =+|-.-.-|++|||.|
T Consensus 5 IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEG------vnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i 70 (104)
T COG0198 5 VKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEG------VNVVKKHIKPSQENPEGGIINKEAPIHISNVAI 70 (104)
T ss_pred eecCCEEEEEecCCCCcceEEEEEecCe-EEEEC------cEEEEecCCCCCcCCCCceeeeeecccHHHeEE
Confidence 5679999999999999999999999877 77776 556677776 2444446788999977
No 18
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=87.10 E-value=0.079 Score=45.23 Aligned_cols=75 Identities=8% Similarity=-0.136 Sum_probs=60.4
Q ss_pred CCCCCCCCCccccCC----CCCcccccccccCCcEEEEecceecCceEEEEeeccCceEEEeccceecCcceeeeecce
Q 026764 64 FYPADDVKKPLVNKR----KHKPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSY 138 (233)
Q Consensus 64 ~Yptedv~~~~~~~k----~~~~~klR~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~y 138 (233)
+|.+|+...+....+ .++....+++..++|.....-+.+.+.++++..++-.+|..+.|+...+..++.+-++.|
T Consensus 74 e~~td~yf~K~k~~~~k~~e~~i~~~ekekyeIteq~kiDqKaVDs~il~~iK~ip~lk~yl~~~f~l~~g~~Ph~l~f 152 (152)
T KOG1694|consen 74 EHLTDAYFKKKKLKKKKTQEGEIFAEEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLKKYLGSVFALTNGIYPHKLKF 152 (152)
T ss_pred ccccHHHHhhhhccccccccchhhcccccccccchhhhhhHHHHHHHHHHHHhhchHhhhccchhhhccCCCCcccccC
Confidence 557777655543222 345678888999999999999999999999999988899999999999999888877765
No 19
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=86.14 E-value=1.1 Score=26.38 Aligned_cols=24 Identities=29% Similarity=0.394 Sum_probs=21.5
Q ss_pred ccCCcEEEEecceecCceEEEEee
Q 026764 89 ITPGTVFILLAGRFMGKRVVFLKQ 112 (233)
Q Consensus 89 itpGtvlIlL~Gr~~GKRvVfLKq 112 (233)
+.+|+.+.|+.|.|+|.-.++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 579999999999999998888764
No 20
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=81.01 E-value=2.7 Score=26.38 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=23.0
Q ss_pred CCcEEEEecceecCceEEEEeeccCc
Q 026764 91 PGTVFILLAGRFMGKRVVFLKQLTSG 116 (233)
Q Consensus 91 pGtvlIlL~Gr~~GKRvVfLKqL~sg 116 (233)
+|+.+.|+.|+|+|.-...++-..+.
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 68999999999999999999887654
No 21
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=52.10 E-value=1.9 Score=32.92 Aligned_cols=28 Identities=25% Similarity=0.570 Sum_probs=24.0
Q ss_pred eecCceEEEEeeccCceEEEeccceecCcceeeeecce
Q 026764 101 RFMGKRVVFLKQLTSGLLLVTGPFKVNGVPLRRVNQSY 138 (233)
Q Consensus 101 r~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~y 138 (233)
.|+|.|||-.++|+. +.|+|.+++++.|
T Consensus 6 e~rg~rV~t~~~lA~----------~yg~~~~~i~~~~ 33 (88)
T PF10543_consen 6 EYRGQRVMTDEDLAE----------LYGVETKTINRNF 33 (88)
T ss_pred EEcCEEEEEHHHHHH----------HhCcCHHHHHHHH
Confidence 589999999999985 7889998888864
No 22
>COG2350 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.14 E-value=8.8 Score=30.13 Aligned_cols=17 Identities=59% Similarity=0.852 Sum_probs=14.3
Q ss_pred EEeecc-CceEEEeccce
Q 026764 109 FLKQLT-SGLLLVTGPFK 125 (233)
Q Consensus 109 fLKqL~-sglLLVTGP~~ 125 (233)
+|+++. +|-||++|||.
T Consensus 27 ~L~~~~a~G~ll~sGP~~ 44 (92)
T COG2350 27 RLKQLYAEGRLLTSGPFP 44 (92)
T ss_pred HHHHhhhcCeEEEeCCCC
Confidence 677774 79999999985
No 23
>PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
Probab=28.32 E-value=23 Score=31.60 Aligned_cols=17 Identities=41% Similarity=0.790 Sum_probs=14.9
Q ss_pred cCceEEEeccceecCcc
Q 026764 114 TSGLLLVTGPFKVNGVP 130 (233)
Q Consensus 114 ~sglLLVTGP~~lNgvP 130 (233)
+.|+|++=|||..||..
T Consensus 133 ~gG~L~~YGPF~~~G~~ 149 (204)
T PF06080_consen 133 PGGLLFLYGPFNRDGKF 149 (204)
T ss_pred CCCEEEEeCCcccCCEe
Confidence 47999999999999864
No 24
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=25.99 E-value=56 Score=32.18 Aligned_cols=46 Identities=26% Similarity=0.427 Sum_probs=33.7
Q ss_pred CceEEEeccceecCcceeeeecceEEeeeee-EecCCcccCCCChhhh
Q 026764 115 SGLLLVTGPFKVNGVPLRRVNQSYVIATSTK-VDISGVDLGKFDDQYF 161 (233)
Q Consensus 115 sglLLVTGP~~lNgvPlrRv~q~yVIaTSTk-vdis~vki~~~~D~YF 161 (233)
.-+++|||=+..|+-|+||..|-|++|-.-+ ..|.| ||=.+-|++|
T Consensus 91 GvvI~VtG~lt~~~~~rRkF~QtFfLapq~~~yfVlN-DiFRfvde~~ 137 (419)
T KOG0116|consen 91 GVVIMVTGYLTNKDGPRRKFSQTFFLAPQEKGYFVLN-DIFRFVDEEF 137 (419)
T ss_pred CeEEEEEEEEEeCCCcceEEEEEEEEeecCCceEEEe-chhhhccccc
Confidence 3467899999999999999999999998765 44444 2322445555
No 25
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=24.83 E-value=1.3e+02 Score=24.88 Aligned_cols=34 Identities=15% Similarity=0.024 Sum_probs=27.4
Q ss_pred ccccCCcEEEEecceecCceEEEEeec-cCceEEE
Q 026764 87 ASITPGTVFILLAGRFMGKRVVFLKQL-TSGLLLV 120 (233)
Q Consensus 87 ~SitpGtvlIlL~Gr~~GKRvVfLKqL-~sglLLV 120 (233)
..+.+|+.+.|..|.|+|-..++.+.- ..+-+.|
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V 152 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKV 152 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEE
Confidence 447899999999999999999999875 3445544
No 26
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=24.20 E-value=1.6e+02 Score=24.77 Aligned_cols=52 Identities=25% Similarity=0.475 Sum_probs=34.1
Q ss_pred cccccCCcEEEEecceecCceEEEEeeccCceEEEe-ccceec-------Ccceeee-----ecceEEeeeeeEe
Q 026764 86 RASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVT-GPFKVN-------GVPLRRV-----NQSYVIATSTKVD 147 (233)
Q Consensus 86 R~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVT-GP~~lN-------gvPlrRv-----~q~yVIaTSTkvd 147 (233)
-++|.||++++|-.|.. .+...+++. |...+| ..|..+. ...++.+-|.-++
T Consensus 49 ~~~L~~GDiI~l~~g~~----------vPaD~~ll~~g~~~vd~s~ltGes~pv~k~~~~~~~~~~i~~Gs~v~~ 113 (230)
T PF00122_consen 49 SSELVPGDIIILKAGDI----------VPADGILLESGSAYVDESALTGESEPVKKTPLPLNPGNIIFAGSIVVS 113 (230)
T ss_dssp GGGT-TTSEEEEETTEB----------ESSEEEEEESSEEEEECHHHHSBSSEEEESSSCCCTTTEE-TTEEEEE
T ss_pred Hhhccceeeeecccccc----------cccCccceeccccccccccccccccccccccccccccchhhccccccc
Confidence 46789999999988763 253333344 766666 3788888 7777777666553
No 27
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=23.73 E-value=42 Score=32.41 Aligned_cols=11 Identities=64% Similarity=1.065 Sum_probs=9.2
Q ss_pred cCceEEEeccc
Q 026764 114 TSGLLLVTGPF 124 (233)
Q Consensus 114 ~sglLLVTGP~ 124 (233)
+.||+|||||=
T Consensus 124 ~~GLILVTGpT 134 (353)
T COG2805 124 PRGLILVTGPT 134 (353)
T ss_pred CCceEEEeCCC
Confidence 35999999984
No 28
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=22.88 E-value=58 Score=29.21 Aligned_cols=51 Identities=29% Similarity=0.458 Sum_probs=36.0
Q ss_pred CCcEEEEecceecCceEEEEeeccCceEEEeccceec-----CcceeeeecceEEeeeee
Q 026764 91 PGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFKVN-----GVPLRRVNQSYVIATSTK 145 (233)
Q Consensus 91 pGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~lN-----gvPlrRv~q~yVIaTSTk 145 (233)
-|.+ =+..|.+.|++||||-+-.-|..+ -|.++| .+ |....-++||.|.+-
T Consensus 30 ~g~~-~~~~G~~~g~~Vv~l~~~G~gh~~--~~~kVn~~a~~~~-l~~~Gv~~II~tgsa 85 (261)
T PRK08666 30 YGEV-KVKIGTYAGEEVAFLARHGEGHSV--PPHKINYRANIWA-LKELGVERILATSAV 85 (261)
T ss_pred CCCC-EEEEEEECCEEEEEEeCCCCCCcc--ChhhcchHHHHHH-HHHCCCCEEEEeccc
Confidence 3443 366799999999998865544333 477887 23 677788999999863
No 29
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=22.51 E-value=1.4e+02 Score=24.73 Aligned_cols=27 Identities=11% Similarity=0.108 Sum_probs=24.2
Q ss_pred ccccCCcEEEEecceecCceEEEEeec
Q 026764 87 ASITPGTVFILLAGRFMGKRVVFLKQL 113 (233)
Q Consensus 87 ~SitpGtvlIlL~Gr~~GKRvVfLKqL 113 (233)
..+.+|+.+-|..|.|+|-..++++.-
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~ 151 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVD 151 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEe
Confidence 447899999999999999999999875
No 30
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=21.88 E-value=55 Score=31.99 Aligned_cols=38 Identities=21% Similarity=0.233 Sum_probs=27.7
Q ss_pred cccccccccccccccCChhhHHhHHHHHHHHHHHHHhhhhHH
Q 026764 172 GEGEFFEAEKEEKKVLPDDKKDDQKTVDAQLIKSIEAVLDLK 213 (233)
Q Consensus 172 ~e~eiF~~~k~~k~~vseqrk~dQK~VD~~il~~Ikk~p~L~ 213 (233)
-|++-|+-| .+..|-|+ .+|.+||.|...+|..+|+..
T Consensus 193 ~eanPfd~E--~q~rIee~--irq~~i~eq~~~ai~~~pe~f 230 (380)
T KOG0012|consen 193 LEANPFDLE--AQRRIEEK--IRQNAIDEQMSHAIEYHPEDF 230 (380)
T ss_pred HhcCCcchh--hhhhhhHH--HHHHHHHHHHHHhhhcCcccc
Confidence 466666643 23445554 589999999999999999854
No 31
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.42 E-value=98 Score=33.83 Aligned_cols=45 Identities=20% Similarity=0.398 Sum_probs=34.9
Q ss_pred CcccccccccCCcEEEEecceecCceEEEEeeccCceEEEeccce
Q 026764 81 KPTKLRASITPGTVFILLAGRFMGKRVVFLKQLTSGLLLVTGPFK 125 (233)
Q Consensus 81 ~~~klR~SitpGtvlIlL~Gr~~GKRvVfLKqL~sglLLVTGP~~ 125 (233)
..+.||+-+.||+.+=+++|+|.|.--++++--.+-+.|++--+.
T Consensus 452 ~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~ 496 (1024)
T KOG1999|consen 452 PASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTM 496 (1024)
T ss_pred chHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCcc
Confidence 357899999999999999999999877777765555555554433
No 32
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=20.23 E-value=1.1e+02 Score=24.87 Aligned_cols=35 Identities=20% Similarity=0.386 Sum_probs=27.6
Q ss_pred ccccCCcEEEEecceecCceEEEEeecc-CceEEEe
Q 026764 87 ASITPGTVFILLAGRFMGKRVVFLKQLT-SGLLLVT 121 (233)
Q Consensus 87 ~SitpGtvlIlL~Gr~~GKRvVfLKqL~-sglLLVT 121 (233)
..+.+|+.+.|..|.|+|-..++.+.=. ...++|.
T Consensus 85 ~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~ 120 (145)
T TIGR00405 85 ESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLE 120 (145)
T ss_pred cccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEE
Confidence 3488999999999999999999998742 3455543
Done!