Query 026785
Match_columns 233
No_of_seqs 169 out of 406
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 12:40:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026785hhsearch_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 5.8E-49 1.3E-53 313.4 -1.3 107 126-233 1-108 (108)
2 KOG1694 60s ribosomal protein 100.0 1.6E-42 3.4E-47 290.6 7.7 140 61-233 12-152 (152)
3 COG2163 RPL14A Ribosomal prote 99.8 2E-19 4.4E-24 147.1 8.4 123 85-208 1-124 (125)
4 PF03868 Ribosomal_L6e_N: Ribo 99.5 8.3E-16 1.8E-20 111.2 -1.6 41 1-41 1-41 (59)
5 PTZ00471 60S ribosomal protein 99.4 2.4E-13 5.1E-18 112.5 6.5 62 88-149 4-90 (134)
6 PRK04333 50S ribosomal protein 99.1 1.9E-10 4E-15 88.6 6.6 62 88-150 3-64 (84)
7 KOG3418 60S ribosomal protein 98.4 4.2E-07 9E-12 75.6 5.3 63 86-151 2-92 (136)
8 PTZ00065 60S ribosomal protein 97.9 2.7E-05 5.9E-10 64.6 6.3 62 88-150 7-68 (130)
9 CHL00141 rpl24 ribosomal prote 94.9 0.036 7.8E-07 42.6 3.8 65 86-153 6-76 (83)
10 PRK12281 rplX 50S ribosomal pr 94.4 0.052 1.1E-06 41.1 3.6 62 88-152 6-73 (76)
11 PTZ00194 60S ribosomal protein 94.4 0.14 3.1E-06 43.4 6.5 63 88-159 46-111 (143)
12 PRK01191 rpl24p 50S ribosomal 94.1 0.084 1.8E-06 43.5 4.6 57 88-153 45-102 (120)
13 TIGR01080 rplX_A_E ribosomal p 93.8 0.11 2.4E-06 42.3 4.7 63 88-159 41-106 (114)
14 KOG1694 60s ribosomal protein 91.8 0.022 4.8E-07 48.5 -2.0 125 8-138 1-152 (152)
15 PRK00004 rplX 50S ribosomal pr 91.5 0.22 4.8E-06 39.7 3.5 63 88-153 4-72 (105)
16 TIGR01079 rplX_bact ribosomal 90.7 0.45 9.8E-06 38.0 4.5 63 88-153 3-72 (104)
17 COG0198 RplX Ribosomal protein 90.5 0.44 9.4E-06 38.4 4.3 58 89-153 5-70 (104)
18 KOG3421 60S ribosomal protein 90.4 0.34 7.4E-06 40.8 3.7 61 86-148 4-64 (136)
19 smart00739 KOW KOW (Kyprides, 85.3 1.2 2.7E-05 26.1 3.0 24 89-112 2-25 (28)
20 PF00467 KOW: KOW motif; Inte 79.9 3 6.4E-05 26.2 3.3 26 91-116 1-26 (32)
21 PF10543 ORF6N: ORF6N domain; 52.6 1.8 3.8E-05 33.1 -2.3 28 101-138 6-33 (88)
22 COG2350 Uncharacterized protei 36.5 11 0.00023 29.7 -0.2 18 108-125 26-44 (92)
23 PF06080 DUF938: Protein of un 25.4 28 0.0006 31.1 0.4 16 114-129 133-148 (204)
24 TIGR00922 nusG transcription t 24.1 1.4E+02 0.0029 24.7 4.3 34 87-120 118-152 (172)
25 KOG0116 RasGAP SH3 binding pro 23.5 66 0.0014 31.7 2.6 31 115-145 91-121 (419)
26 COG2805 PilT Tfp pilus assembl 22.6 46 0.00099 32.2 1.3 11 114-124 124-134 (353)
27 PRK05609 nusG transcription an 21.8 1.5E+02 0.0032 24.6 4.2 27 87-113 125-151 (181)
28 KOG1999 RNA polymerase II tran 21.7 89 0.0019 34.1 3.3 48 81-128 452-499 (1024)
29 PRK08666 5'-methylthioadenosin 21.6 63 0.0014 29.0 2.0 52 91-145 30-85 (261)
30 KOG0012 DNA damage inducible p 20.6 57 0.0012 31.8 1.6 38 172-213 193-230 (380)
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=5.8e-49 Score=313.44 Aligned_cols=107 Identities=59% Similarity=0.963 Sum_probs=98.4
Q ss_pred ecCcceeeeecceEEeeeeeeecCCccc-CccChhhhhhhHhhhhcccccccccccchhcccCChhHHHhhhhccHHHHH
Q 026785 126 INGVPLRRVNQSYVIGTSTKVDISGVNV-DKFDDKYFAKEVERKKKKGENEFFESEKEEKKSLPQEKKDDQKSVDAPLIK 204 (233)
Q Consensus 126 lNgvPlrRv~q~yVIaTstkvdis~vki-~~l~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 569999999988777888999999966 57999999999999999999999
Q ss_pred HhhccchHHhhhcCcccccCCCCccccCC
Q 026785 205 AIEAVPDLKAYLGARFSLRAGMKPHELVF 233 (233)
Q Consensus 205 ~Ikk~p~L~~YL~s~FsL~~g~~PH~l~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=1.6e-42 Score=290.63 Aligned_cols=140 Identities=51% Similarity=0.824 Sum_probs=130.7
Q ss_pred CCCCCCCCCCCCccCCCCCCCccccccCcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecceEE
Q 026785 61 PPKFYPADDVKKPLVNKRKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVI 140 (233)
Q Consensus 61 ~p~~Yptedv~~~~~~~k~~~~~klR~SitpGtvlIlL~G~~~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 8889998 23345677999999999999999999 6999999999999999
Q ss_pred eeeeeeecCCcccC-ccChhhhhhhHhhhhcccccccccccchhcccCChhHHHhhhhccHHHHHHhhccchHHhhhcCc
Q 026785 141 GTSTKVDISGVNVD-KFDDKYFAKEVERKKKKGENEFFESEKEEKKSLPQEKKDDQKSVDAPLIKAIEAVPDLKAYLGAR 219 (233)
Q Consensus 141 aTstkvdis~vki~-~l~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~~~e-kekyeIteq~kiDqKaVDs~il~~iK~ip~lk~yl~~~ 138 (152)
T KOG1694|consen 61 TTSK-IDPSNVKIPEHLTDAYFKKKKLKKKKTQEGEIFAEE-KEKYEITEQRKIDQKAVDSQILPKIKAIPQLKKYLGSV 138 (152)
T ss_pred eeee-eccccccccccccHHHHhhhhccccccccchhhccc-ccccccchhhhhhHHHHHHHHHHHHhhchHhhhccchh
Confidence 9988 999999995 69999999998888999999999987 58999999999999999999999999999999999999
Q ss_pred ccccCCCCccccCC
Q 026785 220 FSLRAGMKPHELVF 233 (233)
Q Consensus 220 FsL~~g~~PH~l~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=99.79 E-value=2e-19 Score=147.06 Aligned_cols=123 Identities=30% Similarity=0.420 Sum_probs=97.9
Q ss_pred cccCcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeeeecCCccc-CccChhhhhh
Q 026785 85 LRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNV-DKFDDKYFAK 163 (233)
Q Consensus 85 lR~SitpGtvlIlL~G~~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~yVIaTstkvdis~vki-~~l~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 478899999999999999999999999999999999999999999999999999999999998876544 5577777776
Q ss_pred hHhhhhcccccccccccchhcccCChhHHHhhhhccHHHHHHhhc
Q 026785 164 EVERKKKKGENEFFESEKEEKKSLPQEKKDDQKSVDAPLIKAIEA 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 5432222222 3333332223345668899999999999988765
No 4
>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=99.51 E-value=8.3e-16 Score=111.25 Aligned_cols=41 Identities=63% Similarity=1.045 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCCCcccccCccccchhhhhhccccceeeecC
Q 026785 1 MAPKQGKPRVSRNPELIRGIGKFSRSKMYHKRGLWAIKAKN 41 (233)
Q Consensus 1 m~~k~~~p~~~~n~~l~~Gi~r~S~s~~y~rk~~~~~k~k~ 41 (233)
||+++++|||+||++|++||+|||||+||+|+++|+.|.+.
T Consensus 1 m~~kK~k~~~~RN~~L~~GI~RySrS~my~kralyk~K~k~ 41 (59)
T PF03868_consen 1 MAPKKKKPHCSRNPVLVRGIGRYSRSAMYHKRALYKRKKKA 41 (59)
T ss_dssp ------------HHHHHTTTSHHHHHHHHHHHHH-S-THHH
T ss_pred CccccccccccCChhhhCccccccHHHHHHHHHHHHHhccc
Confidence 89999999999999999999999999999999999866543
No 5
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.43 E-value=2.4e-13 Score=112.48 Aligned_cols=62 Identities=37% Similarity=0.675 Sum_probs=58.8
Q ss_pred CcCCCcEEEEecceecCceEEEeeecCC-------ceEEEec----ccee--------------cCcceeeeecceEEee
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQLPS-------GLLLVSG----PFKI--------------NGVPLRRVNQSYVIGT 142 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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 4789999999999999999999999998 5999999 9998 8888899999999999
Q ss_pred eeeeecC
Q 026785 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 6
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.10 E-value=1.9e-10 Score=88.55 Aligned_cols=62 Identities=35% Similarity=0.506 Sum_probs=58.9
Q ss_pred CcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeeeecCC
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISG 150 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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=98.40 E-value=4.2e-07 Score=75.57 Aligned_cols=63 Identities=30% Similarity=0.621 Sum_probs=56.3
Q ss_pred ccCcCCCcEEEEecceecCceEEEeeecCCc-------eEEEeccceecCcce---------------------eeeecc
Q 026785 86 RASITPGTVLIILAGRFKGKRVVFLKQLPSG-------LLLVSGPFKINGVPL---------------------RRVNQS 137 (233)
Q Consensus 86 R~SitpGtvlIlL~G~~~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 888887 458999
Q ss_pred eEEeeeeeeecCCc
Q 026785 138 YVIGTSTKVDISGV 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 99999999998643
No 8
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=97.91 E-value=2.7e-05 Score=64.65 Aligned_cols=62 Identities=24% Similarity=0.327 Sum_probs=58.0
Q ss_pred CcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeeeecCC
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISG 150 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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 67799999999999999999998853
No 9
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.86 E-value=0.036 Score=42.60 Aligned_cols=65 Identities=23% Similarity=0.231 Sum_probs=47.3
Q ss_pred ccCcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCcc-----eeeeecceEEeeeeeeecCCccc
Q 026785 86 RASITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVP-----LRRVNQSYVIGTSTKVDISGVNV 153 (233)
Q Consensus 86 R~SitpGtvlIlL~G~~~GKRvVfLKqL-~sglLLVTGP~~lNgvP-----lrRv~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 3468899999999999999999999985 578899999 55321 11122334555566778888865
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.40 E-value=0.052 Score=41.11 Aligned_cols=62 Identities=23% Similarity=0.318 Sum_probs=43.7
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCcce-----eeeecceEEeeeeeeecCCcc
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPL-----RRVNQSYVIGTSTKVDISGVN 152 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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 665311 111123344444456666663
No 11
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.37 E-value=0.14 Score=43.35 Aligned_cols=63 Identities=13% Similarity=0.206 Sum_probs=49.3
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeeeecCCccc--CccChh
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNV--DKFDDK 159 (233)
Q Consensus 88 SitpGtvlIlL~G~~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlrRv~q~yVIaTstkvdis~vki--~~l~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---ITR---EKANGEP---VQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC---eEE---EecCCCE---eecCcCchheEEEccccCch
Confidence 37889999999999999999999986 477899888 443 3444443 345789999988 458877
No 12
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=94.14 E-value=0.084 Score=43.50 Aligned_cols=57 Identities=18% Similarity=0.313 Sum_probs=44.8
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeeeecCCccc
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNV 153 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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 37899999999999999999999986 478899999 55321 122 34556789999987
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=93.78 E-value=0.11 Score=42.29 Aligned_cols=63 Identities=24% Similarity=0.325 Sum_probs=47.5
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCcceeeeecceEEeeeeeeecCCcccC--ccChh
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDISGVNVD--KFDDK 159 (233)
Q Consensus 88 SitpGtvlIlL~G~~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlrRv~q~yVIaTstkvdis~vki~--~l~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 37789999999999999999999986 477799999 55322 12 2 456667999999873 25543
No 14
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=91.83 E-value=0.022 Score=48.55 Aligned_cols=125 Identities=15% Similarity=0.107 Sum_probs=83.5
Q ss_pred CCCCCCcccccCccccchhhhhhcccc-cee-eec-----CCCcC-----CCCCC----CCcc--eeecCCCCC-----C
Q 026785 8 PRVSRNPELIRGIGKFSRSKMYHKRGL-WAI-KAK-----NGGVF-----PRHDP----KPKA--AAPAEKPPK-----F 64 (233)
Q Consensus 8 p~~~~n~~l~~Gi~r~S~s~~y~rk~~-~~~-k~k-----~gg~~-----~kng~----~~~r--~v~~~k~p~-----~ 64 (233)
|||++|+ |++| .++||.+... +.. +++ .-|.+ +.||. .+++ +.....++. +
T Consensus 1 ~~~~~~~----~~~~--~~~~yp~~k~~~~~~~~k~r~~l~~gtvliil~~~ng~~~~~v~~~~~~~ts~i~~~~vk~~e 74 (152)
T KOG1694|consen 1 PHCSKNP----GIGR--PPADYPRKKARYSAKPSKLRASLTPGTVLIILAPINGVPLKRVNERYVATTSKIDPSNVKIPE 74 (152)
T ss_pred CCcccCC----CCCC--ChhhccchhccccccchhhhhccCCCeeEEEecccCCcCcccccceEEeeeeeeccccccccc
Confidence 6899998 8888 7888887211 111 111 11110 12331 1222 223334444 5
Q ss_pred CCCCCCCCccCCCC----CCCccccccCcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecce
Q 026785 65 YPADDVKKPLVNKR----KPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSY 138 (233)
Q Consensus 65 Yptedv~~~~~~~k----~~~~~klR~SitpGtvlIlL~G~~~GKRvVfLKqL~sglLLVTGP~~lNgvPlrRv~q~y 138 (233)
|.+++...+....+ .++....+++..++|......+.+.+.++++..++-.+|..+.|+...+..++.+.++.|
T Consensus 75 ~~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 75 HLTDAYFKKKKLKKKKTQEGEIFAEEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLKKYLGSVFALTNGIYPHKLKF 152 (152)
T ss_pred cccHHHHhhhhccccccccchhhcccccccccchhhhhhHHHHHHHHHHHHhhchHhhhccchhhhccCCCCcccccC
Confidence 57777655543222 356778889999999999999999999999999988889999999999998888877765
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=91.54 E-value=0.22 Score=39.71 Aligned_cols=63 Identities=33% Similarity=0.468 Sum_probs=47.5
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCccee-e----eecceEEeeeeeeecCCccc
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLR-R----VNQSYVIGTSTKVDISGVNV 153 (233)
Q Consensus 88 SitpGtvlIlL~G~~~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 5543211 1 12344566677888999976
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=90.71 E-value=0.45 Score=38.00 Aligned_cols=63 Identities=30% Similarity=0.432 Sum_probs=48.3
Q ss_pred CcCCCcEEEEecceecCceEEEeeec-CCceEEEeccceecCccee----eee--cceEEeeeeeeecCCccc
Q 026785 88 SITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLVSGPFKINGVPLR----RVN--QSYVIGTSTKVDISGVNV 153 (233)
Q Consensus 88 SitpGtvlIlL~G~~~GKRvVfLKqL-~sglLLVTGP~~lNgvPlr----Rv~--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 37899999999999999999999996 478899999 5543221 111 455677777888999876
No 17
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=90.54 E-value=0.44 Score=38.44 Aligned_cols=58 Identities=29% Similarity=0.480 Sum_probs=46.0
Q ss_pred cCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecc--------eEEeeeeeeecCCccc
Q 026785 89 ITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQS--------YVIGTSTKVDISGVNV 153 (233)
Q Consensus 89 itpGtvlIlL~G~~~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 88777 446677776 2444446688899876
No 18
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=90.43 E-value=0.34 Score=40.78 Aligned_cols=61 Identities=25% Similarity=0.344 Sum_probs=51.4
Q ss_pred ccCcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecCcceeeeecceEEeeeeeeec
Q 026785 86 RASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSYVIGTSTKVDI 148 (233)
Q Consensus 86 R~SitpGtvlIlL~G~~~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 56788777776666666655554
No 19
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=85.33 E-value=1.2 Score=26.08 Aligned_cols=24 Identities=33% Similarity=0.499 Sum_probs=21.5
Q ss_pred cCCCcEEEEecceecCceEEEeee
Q 026785 89 ITPGTVLIILAGRFKGKRVVFLKQ 112 (233)
Q Consensus 89 itpGtvlIlL~G~~~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=79.91 E-value=3 Score=26.15 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=23.0
Q ss_pred CCcEEEEecceecCceEEEeeecCCc
Q 026785 91 PGTVLIILAGRFKGKRVVFLKQLPSG 116 (233)
Q Consensus 91 pGtvlIlL~G~~~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=52.64 E-value=1.8 Score=33.13 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=24.1
Q ss_pred eecCceEEEeeecCCceEEEeccceecCcceeeeecce
Q 026785 101 RFKGKRVVFLKQLPSGLLLVSGPFKINGVPLRRVNQSY 138 (233)
Q Consensus 101 ~~~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 8889988888865
No 22
>COG2350 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.50 E-value=11 Score=29.67 Aligned_cols=18 Identities=61% Similarity=0.798 Sum_probs=14.8
Q ss_pred EEeeecC-CceEEEeccce
Q 026785 108 VFLKQLP-SGLLLVSGPFK 125 (233)
Q Consensus 108 VfLKqL~-sglLLVTGP~~ 125 (233)
=+|+++. +|-|+++|||.
T Consensus 26 ~~L~~~~a~G~ll~sGP~~ 44 (92)
T COG2350 26 ARLKQLYAEGRLLTSGPFP 44 (92)
T ss_pred HHHHHhhhcCeEEEeCCCC
Confidence 3678874 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=25.38 E-value=28 Score=31.07 Aligned_cols=16 Identities=50% Similarity=1.065 Sum_probs=14.3
Q ss_pred CCceEEEeccceecCc
Q 026785 114 PSGLLLVSGPFKINGV 129 (233)
Q Consensus 114 ~sglLLVTGP~~lNgv 129 (233)
+.|+|++=|||..||.
T Consensus 133 ~gG~L~~YGPF~~~G~ 148 (204)
T PF06080_consen 133 PGGLLFLYGPFNRDGK 148 (204)
T ss_pred CCCEEEEeCCcccCCE
Confidence 4799999999999994
No 24
>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=24.14 E-value=1.4e+02 Score=24.75 Aligned_cols=34 Identities=15% Similarity=0.052 Sum_probs=27.4
Q ss_pred cCcCCCcEEEEecceecCceEEEeeec-CCceEEE
Q 026785 87 ASITPGTVLIILAGRFKGKRVVFLKQL-PSGLLLV 120 (233)
Q Consensus 87 ~SitpGtvlIlL~G~~~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 25
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=23.47 E-value=66 Score=31.71 Aligned_cols=31 Identities=19% Similarity=0.428 Sum_probs=27.3
Q ss_pred CceEEEeccceecCcceeeeecceEEeeeee
Q 026785 115 SGLLLVSGPFKINGVPLRRVNQSYVIGTSTK 145 (233)
Q Consensus 115 sglLLVTGP~~lNgvPlrRv~q~yVIaTstk 145 (233)
.-+++|||=+..|+-|+||.-|-|++|-.-+
T Consensus 91 GvvI~VtG~lt~~~~~rRkF~QtFfLapq~~ 121 (419)
T KOG0116|consen 91 GVVIMVTGYLTNKDGPRRKFSQTFFLAPQEK 121 (419)
T ss_pred CeEEEEEEEEEeCCCcceEEEEEEEEeecCC
Confidence 3567899999999999999999999997665
No 26
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.61 E-value=46 Score=32.17 Aligned_cols=11 Identities=64% Similarity=1.262 Sum_probs=9.2
Q ss_pred CCceEEEeccc
Q 026785 114 PSGLLLVSGPF 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 27
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=21.80 E-value=1.5e+02 Score=24.61 Aligned_cols=27 Identities=11% Similarity=0.149 Sum_probs=24.2
Q ss_pred cCcCCCcEEEEecceecCceEEEeeec
Q 026785 87 ASITPGTVLIILAGRFKGKRVVFLKQL 113 (233)
Q Consensus 87 ~SitpGtvlIlL~G~~~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 28
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=21.71 E-value=89 Score=34.12 Aligned_cols=48 Identities=21% Similarity=0.377 Sum_probs=36.9
Q ss_pred CccccccCcCCCcEEEEecceecCceEEEeeecCCceEEEeccceecC
Q 026785 81 KPTKLRASITPGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKING 128 (233)
Q Consensus 81 ~~~klR~SitpGtvlIlL~G~~~GKRvVfLKqL~sglLLVTGP~~lNg 128 (233)
..+.||+-+.||+.+=+++|+|.|..-++++.-.+-+.|++--+.=+.
T Consensus 452 ~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel 499 (1024)
T KOG1999|consen 452 PASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEEL 499 (1024)
T ss_pred chHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCcccee
Confidence 367899999999999999999999887777766655555555444343
No 29
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=21.59 E-value=63 Score=28.99 Aligned_cols=52 Identities=29% Similarity=0.435 Sum_probs=35.7
Q ss_pred CCcEEEEecceecCceEEEeeecCCceEEEeccceecC----cceeeeecceEEeeeee
Q 026785 91 PGTVLIILAGRFKGKRVVFLKQLPSGLLLVSGPFKING----VPLRRVNQSYVIGTSTK 145 (233)
Q Consensus 91 pGtvlIlL~G~~~GKRvVfLKqL~sglLLVTGP~~lNg----vPlrRv~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--PPHKINYRANIWALKELGVERILATSAV 85 (261)
T ss_pred CCCC-EEEEEEECCEEEEEEeCCCCCCcc--ChhhcchHHHHHHHHHCCCCEEEEeccc
Confidence 3443 356789999999998865544333 4778872 12677788899998764
No 30
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=20.59 E-value=57 Score=31.83 Aligned_cols=38 Identities=24% Similarity=0.308 Sum_probs=27.6
Q ss_pred cccccccccchhcccCChhHHHhhhhccHHHHHHhhccchHH
Q 026785 172 GENEFFESEKEEKKSLPQEKKDDQKSVDAPLIKAIEAVPDLK 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 466777643 23445444 489999999999999999754
Done!