Query 030970
Match_columns 168
No_of_seqs 117 out of 753
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:18:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030970.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030970hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0093 RplN Ribosomal protein 100.0 2E-53 4.4E-58 326.6 12.8 120 49-168 1-122 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 4.8E-52 1E-56 321.0 13.4 120 49-168 1-122 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 6.7E-52 1.5E-56 320.2 13.5 120 49-168 1-122 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 1E-51 2.2E-56 319.1 13.5 120 49-168 1-122 (122)
5 PTZ00054 60S ribosomal protein 100.0 1.3E-49 2.7E-54 313.5 13.1 117 48-168 17-139 (139)
6 PF00238 Ribosomal_L14: Riboso 100.0 5.3E-50 1.1E-54 309.0 10.5 120 49-168 1-122 (122)
7 TIGR03673 rpl14p_arch 50S ribo 100.0 1.6E-49 3.6E-54 310.2 13.2 117 48-168 9-131 (131)
8 PRK08571 rpl14p 50S ribosomal 100.0 2.2E-49 4.7E-54 309.9 13.3 117 48-168 10-132 (132)
9 PTZ00320 ribosomal protein L14 100.0 4.6E-48 9.9E-53 315.0 13.1 118 51-168 61-188 (188)
10 KOG0901 60S ribosomal protein 100.0 3.8E-36 8.2E-41 237.9 10.9 133 35-168 3-145 (145)
11 KOG3441 Mitochondrial ribosoma 99.9 3.3E-23 7.2E-28 161.7 7.5 107 49-168 31-149 (149)
12 cd03696 selB_II selB_II: this 48.5 49 0.0011 22.8 4.7 54 49-103 26-80 (83)
13 cd03695 CysN_NodQ_II CysN_NodQ 46.7 84 0.0018 21.9 5.8 53 49-104 26-79 (81)
14 PF10382 DUF2439: Protein of u 44.7 32 0.0007 24.7 3.4 28 118-146 20-49 (83)
15 PF08447 PAS_3: PAS fold; Int 42.8 50 0.0011 21.8 3.9 32 110-141 55-86 (91)
16 PF14996 RMP: Retinal Maintena 41.6 14 0.0003 29.9 1.2 34 6-46 40-73 (146)
17 cd03698 eRF3_II_like eRF3_II_l 39.4 83 0.0018 21.7 4.8 55 49-104 26-81 (83)
18 cd03693 EF1_alpha_II EF1_alpha 37.8 76 0.0016 22.4 4.4 54 49-103 30-84 (91)
19 cd04089 eRF3_II eRF3_II: domai 32.9 1.1E+02 0.0023 21.2 4.5 54 50-104 26-80 (82)
20 PF00575 S1: S1 RNA binding do 32.1 1E+02 0.0022 20.2 4.1 31 98-133 2-32 (74)
21 PF14578 GTP_EFTU_D4: Elongati 31.6 1.3E+02 0.0029 21.8 4.8 50 49-105 29-80 (81)
22 cd03694 GTPBP_II Domain II of 27.7 1.5E+02 0.0031 20.8 4.5 54 49-103 26-84 (87)
23 TIGR01024 rplS_bact ribosomal 27.0 1.3E+02 0.0028 23.3 4.3 34 78-113 18-51 (113)
24 PF01245 Ribosomal_L19: Riboso 26.2 1.6E+02 0.0035 22.5 4.8 35 78-114 18-52 (113)
25 CHL00084 rpl19 ribosomal prote 24.3 1.6E+02 0.0034 22.9 4.4 34 78-113 22-55 (117)
26 KOG0171 Mitochondrial inner me 22.7 1.3E+02 0.0029 25.1 3.9 34 121-154 114-148 (176)
27 PRK06299 rpsA 30S ribosomal pr 22.6 3E+02 0.0064 25.8 6.7 51 79-134 419-489 (565)
28 COG4959 TraF Type IV secretory 22.5 93 0.002 25.9 2.9 38 114-151 122-159 (173)
29 PRK05338 rplS 50S ribosomal pr 22.2 1.8E+02 0.0038 22.6 4.3 33 79-113 19-51 (116)
30 cd04454 S1_Rrp4_like S1_Rrp4_l 21.8 2.2E+02 0.0047 19.3 4.4 15 80-94 5-19 (82)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-53 Score=326.60 Aligned_cols=120 Identities=56% Similarity=0.863 Sum_probs=117.4
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC--ccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCceEeec
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 126 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFd 126 (168)
|||.+|+|+|+||||||+++||+++++ +++|.+||+|++|||++.|...+||||+++|||||||++++|+||++++||
T Consensus 1 miq~~t~l~vADNSGAk~v~~I~V~gg~~r~~A~vGD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~DGs~i~Fd 80 (122)
T COG0093 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRRRYAGVGDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSYIKFD 80 (122)
T ss_pred CcccccEEEEccCCCCcEEEEEEEeccccccccCCCCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcCCCCEEEeC
Confidence 899999999999999999999999986 569999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 127 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 127 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
|||+||+|++++|+||||||||++|||+++|+||+|||++++
T Consensus 81 dNA~Viin~~g~P~GtrI~GPVaRElr~~~~~kI~SlA~eVv 122 (122)
T COG0093 81 DNAAVIINPDGEPRGTRIFGPVARELRERGFMKIASLAPEVV 122 (122)
T ss_pred CceEEEECCCCCcccceEecchhHHHHhcCCceeeecceecC
Confidence 999999999999999999999999999999999999999985
No 2
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=4.8e-52 Score=321.05 Aligned_cols=120 Identities=48% Similarity=0.787 Sum_probs=117.0
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC--ccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCceEeec
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 126 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFd 126 (168)
|||.+|+|+|+|||||++++||++|++ +++|++||+|+||||++.|++++||||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~dG~~i~F~ 80 (122)
T CHL00057 1 MIQPQTYLNVADNSGARKLMCIRVLGASNRKYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMIIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCccccCCCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcCCCcEEEcC
Confidence 999999999999999999999999975 578999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 127 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 127 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 ~Na~VLin~~~~p~GTrI~Gpv~~elr~k~~~Ki~sla~~vi 122 (122)
T CHL00057 81 DNAAVVIDQEGNPKGTRVFGPIARELREKNFTKIVSLAPEVL 122 (122)
T ss_pred CceEEEECCCCCEeEeEEEccchHHHhhcCCeEEEecccccC
Confidence 999999999999999999999999999999999999999875
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=6.7e-52 Score=320.17 Aligned_cols=120 Identities=61% Similarity=0.897 Sum_probs=116.8
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC--ccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCceEeec
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 126 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFd 126 (168)
|||.+|+|+|+|||||++++||++|++ +++|++||+|+||||++.|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~g~~~~~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T PRK05483 1 MIQQETRLNVADNSGAKEVMCIKVLGGSKRRYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSYIRFD 80 (122)
T ss_pred CCCCCCEEEEeECCCCCEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecCCCCEEEcC
Confidence 999999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 127 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 127 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 dNavVLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~v~ 122 (122)
T PRK05483 81 DNAAVLLNNDGEPRGTRIFGPVARELRDKKFMKIVSLAPEVL 122 (122)
T ss_pred CCEEEEECCCCCEeEeEEeccchHHHhhcCCcEEEecccccC
Confidence 999999999999999999999999999999999999999875
No 4
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=100.00 E-value=1e-51 Score=319.07 Aligned_cols=120 Identities=56% Similarity=0.849 Sum_probs=116.9
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC--ccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCceEeec
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 126 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFd 126 (168)
|||.+|+|+|+|||||++++||++|++ +++|++||+|+||||++.|+.+++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T TIGR01067 1 MIQQQSRLNVADNSGAKKVQCIKVLGGSRRRYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSYIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeCCCCEEECC
Confidence 999999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 127 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 127 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 ~Na~VLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~i~ 122 (122)
T TIGR01067 81 DNACVLINKNKEPRGTRIFGPVARELRDKGFMKIVSLAPEVI 122 (122)
T ss_pred CceEEEECCCCCEeeeEEEccchHHHhhcCCceeeeccchhC
Confidence 999999999999999999999999999999999999999885
No 5
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=1.3e-49 Score=313.46 Aligned_cols=117 Identities=33% Similarity=0.455 Sum_probs=110.9
Q ss_pred cceeccceEEEeeCcccceEEEEEeeC---C-c--cccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCc
Q 030970 48 TFIQMRTVLKVVDNSGAKTVMCIQPLK---G-R--KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGS 121 (168)
Q Consensus 48 ~MIq~~T~L~VaDNSGak~v~cI~vl~---~-~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~ 121 (168)
.|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||+
T Consensus 17 ~mIq~~t~L~vaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p---~~kg~V~kAVIVRtKk~~rR~dGs 93 (139)
T PTZ00054 17 LGLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKP---ELRKKVLNAVIIRQRKAWRRKDGV 93 (139)
T ss_pred eeecCCCEEEEeeCCCccEEEEEEEeccCcCCccCcccccCCEEEEEEEECCC---cccCCEeeEEEEEECcceEcCCCc
Confidence 499999999999999999999999996 3 3 479999999999999999 678999999999999999999999
Q ss_pred eEeecCceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 122 EVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 122 ~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
+++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 94 ~i~F~dNA~VLin~~~~p~GTRI~GpV~rEl-~~~~~KI~SLA~~vi 139 (139)
T PTZ00054 94 FIYFEDNAGVIVNPKGEMKGSAITGPVAKEC-ADLWPKISSAAPAIV 139 (139)
T ss_pred EEEeCCcEEEEECCCCCEeeeEEeCchhHHH-HhCccHhhccccccC
Confidence 9999999999999999999999999999999 667999999999985
No 6
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=100.00 E-value=5.3e-50 Score=308.96 Aligned_cols=120 Identities=60% Similarity=0.879 Sum_probs=114.1
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC--ccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCceEeec
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 126 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFd 126 (168)
|||.+|+|+|+|||||++++||+++++ +++|++||+|++|||+.+|+.++||||+++|||||||++++|.||++++||
T Consensus 1 MIq~~t~L~v~DNSGak~v~cI~v~~~~~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~dg~~i~F~ 80 (122)
T PF00238_consen 1 MIQKGTILKVADNSGAKKVKCIKVLGGKRRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRKDGSFIKFD 80 (122)
T ss_dssp -BETTEEEEESBSSSEEEEEEEEETSSTTTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETTTSEEEEES
T ss_pred CCCCCCEEEEeeCCCCcEEEEEEEeCCcCccccccceEEEEEEeecccCccccccceEEEEEEEEeEEEEEeCCcEEEeC
Confidence 999999999999999999999999975 678999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 127 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 127 dNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
|||+||+|++++|+||||+||||+|+|+++|+||+|||++||
T Consensus 81 ~Na~VLln~~~~p~GtrI~Gpv~~elr~~~~~ki~sla~~iv 122 (122)
T PF00238_consen 81 DNAVVLLNKKGNPLGTRIFGPVPRELRKKKFPKILSLASRIV 122 (122)
T ss_dssp SEEEEEEETTSSBSSSSBCSEEEHHHHHTTSHHHHHHSSCEE
T ss_pred CccEEEEcCCCCEeeeEEEeeehHHhhHcCCchHHhhccccC
Confidence 999999999999999999999999999999999999999875
No 7
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=100.00 E-value=1.6e-49 Score=310.23 Aligned_cols=117 Identities=39% Similarity=0.568 Sum_probs=110.4
Q ss_pred cceeccceEEEeeCcccceEEEEEeeC---C--c-cccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCc
Q 030970 48 TFIQMRTVLKVVDNSGAKTVMCIQPLK---G--R-KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGS 121 (168)
Q Consensus 48 ~MIq~~T~L~VaDNSGak~v~cI~vl~---~--~-k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~ 121 (168)
.|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||+
T Consensus 9 ~mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs 85 (131)
T TIGR03673 9 RALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP---EMRKQVFKAVVVRQRKEYRRPDGT 85 (131)
T ss_pred eeeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCc---cccCCEeEEEEEEeCcceecCCCc
Confidence 499999999999999999999999983 2 3 569999999999999999 578999999999999999999999
Q ss_pred eEeecCceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 122 EVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 122 ~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
+++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 86 ~i~FddNa~VLin~~~~P~GTRI~GpV~rEl-~~~~~Ki~SlA~~vi 131 (131)
T TIGR03673 86 RVKFEDNAVVIVTPDGEPKGTEIKGPVAREA-AERWPKIASIASIIV 131 (131)
T ss_pred EEEeCCcEEEEECCCCCEeeeEEEccchHHH-HhCccHheeccchhC
Confidence 9999999999999999999999999999999 568999999999985
No 8
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=2.2e-49 Score=309.90 Aligned_cols=117 Identities=38% Similarity=0.525 Sum_probs=110.3
Q ss_pred cceeccceEEEeeCcccceEEEEEeeC---C-c--cccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCCc
Q 030970 48 TFIQMRTVLKVVDNSGAKTVMCIQPLK---G-R--KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGS 121 (168)
Q Consensus 48 ~MIq~~T~L~VaDNSGak~v~cI~vl~---~-~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG~ 121 (168)
.|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+|+||++.| ++|||+++|||||||++++|+||+
T Consensus 10 ~mIq~~T~L~VaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs 86 (132)
T PRK08571 10 RGLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP---EMRKQVLRAVVVRQRKEYRRPDGT 86 (132)
T ss_pred ceecCCCEEEEeeCCCCCeEEEEEEeccCCCCccCCccccCCEEEEEEEECCC---cccCCEeEEEEEEeccceEcCCCc
Confidence 399999999999999999999999986 2 2 469999999999999999 578999999999999999999999
Q ss_pred eEeecCceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 122 EVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 122 ~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
+++|||||+||+|++++|+||||+||||+|| +++|+||+|||++++
T Consensus 87 ~i~F~dNa~VLin~~~~p~GTRI~GpV~~El-~~~~~Ki~sLA~~vi 132 (132)
T PRK08571 87 RVKFEDNAAVIVTPEGTPKGTEIKGPVAREA-AERWPKIASIASIIV 132 (132)
T ss_pred EEEeCCcEEEEECCCCCEeeeEEeccchHHH-hhCCchheeccchhC
Confidence 9999999999999999999999999999999 567999999999885
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=4.6e-48 Score=315.03 Aligned_cols=118 Identities=25% Similarity=0.330 Sum_probs=114.4
Q ss_pred eccceEEEeeCcccceEEEEEeeCCccccccCcE----EEEEEeeecC------CCcccccceEEEEEEEeeeeeecCCC
Q 030970 51 QMRTVLKVVDNSGAKTVMCIQPLKGRKVARLGDT----IVASVKEAMP------TGKVKKGQVVHAVVVRAAMQHGRFDG 120 (168)
Q Consensus 51 q~~T~L~VaDNSGak~v~cI~vl~~~k~a~vGD~----I~vsVKk~~p------~~kvKKg~V~~AvIVRtkk~~~R~dG 120 (168)
.-+|+|+|+||||||+++||+++.++++|++||+ |+||||++.| ++++|||||++|||||||++++|+||
T Consensus 61 ~~qT~L~VaDNSGAK~V~CIkVl~~rr~A~IGDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTKK~irR~DG 140 (188)
T PTZ00320 61 SDQVKLHCVDNTNCKHVRLISKATAERFAHCRVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSG 140 (188)
T ss_pred CCCcEEEEEeCCCCcEEEEEEEecCCCceeeccccCceEEEEEeecccCccccccCceecCCEEEEEEEEECcccCCCCC
Confidence 4689999999999999999999977899999999 9999999999 78999999999999999999999999
Q ss_pred ceEeecCceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 121 SEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 121 ~~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
++++||||||||+|++++|+||||||||++|||+++|+||+|||+.++
T Consensus 141 s~IrFDdNAaVLIN~qgePlGTRIfGPVaRELR~k~f~KIvSLAp~~~ 188 (188)
T PTZ00320 141 LQTNFDRNTCILMNDQRVPLGTRVMYCAGRHVNHKYHLKAVVLANFFV 188 (188)
T ss_pred CEEEeCCcEEEEECCCCCEeeeEEecchhHHHhhcCCceeeecccccC
Confidence 999999999999999999999999999999999999999999999875
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-36 Score=237.89 Aligned_cols=133 Identities=38% Similarity=0.500 Sum_probs=121.9
Q ss_pred cccccccccccc--ccceeccceEEEeeCcccceEEEEEeeC--C----ccccccCcEEEEEEee--ecCCCcccccceE
Q 030970 35 HEMASGNFLSQQ--RTFIQMRTVLKVVDNSGAKTVMCIQPLK--G----RKVARLGDTIVASVKE--AMPTGKVKKGQVV 104 (168)
Q Consensus 35 ~~~~~~~~~~~~--~~MIq~~T~L~VaDNSGak~v~cI~vl~--~----~k~a~vGD~I~vsVKk--~~p~~kvKKg~V~ 104 (168)
.+++.++...+| ..|||++|.++|+||||||.++||++.+ | .+.|.+||+++++||+ ..|+.++|.|+++
T Consensus 3 ~~~~~gs~~~k~r~s~~~~~g~~incaDNSgAknL~~isv~g~~Grlnrl~~A~~GD~vva~vKka~~~Pe~r~k~g~~~ 82 (145)
T KOG0901|consen 3 SRGRGGSSGVKFRISLGLPVGAVINCADNSGAKNLYCISVKGIKGRLNRLPAAGVGDMVVATVKKAHGKPELRKKVGEVL 82 (145)
T ss_pred ccccCcccchhhhhhhccccceEEEecCCCCcceEEEEEEeccccccccccCCCcCCEEEEEEecccCCCccCcEecccc
Confidence 445555555555 5799999999999999999999999987 4 3589999999999999 7999999999999
Q ss_pred EEEEEEeeeeeecCCCceEeecCceEEEEcCCCCcceeEEecchhHhhhcCCcchheccccccC
Q 030970 105 HAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 168 (168)
Q Consensus 105 ~AvIVRtkk~~~R~dG~~ikFddNavVLln~k~~plGTRI~GpV~~Elr~kk~~KI~SLA~~i~ 168 (168)
+|+|||++++..|.||++++|+|||+|++|++++|.||+|+||||+|++. .|++|+|+|+.++
T Consensus 83 ~avvVr~~k~~~r~dgs~~~f~dnA~v~~~~~~e~~gs~i~G~v~~e~~~-~~~kias~A~~i~ 145 (145)
T KOG0901|consen 83 PAVVVRQKKSKRRKDGSIAYFEDNAGVIVNNKGEPKGSAITGPVGKELAD-LWPKIASLAGLVV 145 (145)
T ss_pred eeeEEeeccccccCCCcEEEEcCceEEEEcccCccccceeccccChhHhh-hhHHHHhhccccC
Confidence 99999999999999999999999999999999999999999999999999 7999999999874
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=3.3e-23 Score=161.73 Aligned_cols=107 Identities=38% Similarity=0.613 Sum_probs=95.9
Q ss_pred ceeccceEEEeeCccc--------ceEEEEEeeCCccccccCcEEEEEEeeecCCCcccccceEEEEEEEeeeeeecCCC
Q 030970 49 FIQMRTVLKVVDNSGA--------KTVMCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDG 120 (168)
Q Consensus 49 MIq~~T~L~VaDNSGa--------k~v~cI~vl~~~k~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~~~R~dG 120 (168)
-|++.|+|+|+|||.. +..+||++|+++..+.+||.|+++|| ||..+|+||......++ |
T Consensus 31 ~I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkrgvg~~GDkiLvAIk----------GQmkKa~vVGh~~~~k~--~ 98 (149)
T KOG3441|consen 31 GIHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKRGVGELGDKILVAIK----------GQMKKAYVVGHVHYRKH--G 98 (149)
T ss_pred hhhhhheEEEecchhhcccccccCCCCceEEEEecccccccccEEEEEEe----------cceeeeEEEEeeccCCC--C
Confidence 5999999999999973 67999999998889999999999997 89999999997665443 4
Q ss_pred ceEeecCceEEEEcCCCCcceeEEecchhHhhhcC----CcchheccccccC
Q 030970 121 SEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRK----KHVSILTLAEHLA 168 (168)
Q Consensus 121 ~~ikFddNavVLln~k~~plGTRI~GpV~~Elr~k----k~~KI~SLA~~i~ 168 (168)
.++||.|.+||+|++|+|+||||.-|||..||.. .|+|++++|+++|
T Consensus 99 -~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 99 -VPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRANRGNVQYSKVLAIANKFV 149 (149)
T ss_pred -CcccCCCcEEEECCCCCcccceEeccCcHHHHhccCCcchhhHHHHHhhcC
Confidence 5899999999999999999999999999999832 5999999999875
No 12
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=48.47 E-value=49 Score=22.82 Aligned_cols=54 Identities=15% Similarity=0.228 Sum_probs=33.1
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccce
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQV 103 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V 103 (168)
.|+.+..+.+.++--.-.++=|+.-+. ...|..||.|-+.++...+ ..+++|++
T Consensus 26 ~i~~g~~v~~~p~~~~~~V~sI~~~~~~~~~a~aGd~v~i~l~~~~~-~~i~~G~v 80 (83)
T cd03696 26 SVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAGDRVALNLTGVDA-KDLERGDV 80 (83)
T ss_pred EEeCCCEEEECCCCceEEEEEEEECCcCcCEEcCCCEEEEEEcCCCH-HHcCCccE
Confidence 466777777777432233344433222 3578899999999986554 34566664
No 13
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=46.67 E-value=84 Score=21.86 Aligned_cols=53 Identities=19% Similarity=0.355 Sum_probs=33.8
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccceE
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 104 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 104 (168)
.++.+..+.+.+.--.-.++-|+.... ...|..||.|-+.++. ...+++|++.
T Consensus 26 ~v~~Gd~v~~~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~---~~~i~~G~vl 79 (81)
T cd03695 26 SIRVGDEVVVLPSGKTSRVKSIETFDGELDEAGAGESVTLTLED---EIDVSRGDVI 79 (81)
T ss_pred eEECCCEEEEcCCCCeEEEEEEEECCcEeCEEcCCCEEEEEECC---ccccCCCCEE
Confidence 355666666666422335666765544 4578999999999973 3446677653
No 14
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=44.71 E-value=32 Score=24.66 Aligned_cols=28 Identities=21% Similarity=0.541 Sum_probs=22.6
Q ss_pred CCCceEeec--CceEEEEcCCCCcceeEEec
Q 030970 118 FDGSEVRFD--DNAVVLVNKAGEPTGTRVFG 146 (168)
Q Consensus 118 ~dG~~ikFd--dNavVLln~k~~plGTRI~G 146 (168)
.||. ++|. .|-+.|.|+++..+|+.+.-
T Consensus 20 ~DG~-l~~~~~~~kv~Lyde~~~~i~~~~~~ 49 (83)
T PF10382_consen 20 HDGF-LKYHSFNKKVMLYDEDGNLIGSDFLK 49 (83)
T ss_pred ECCE-EEEEeCCCEEEEEcCCCCEEeEEEEe
Confidence 4885 5665 77899999999999998763
No 15
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=42.80 E-value=50 Score=21.79 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=26.1
Q ss_pred EeeeeeecCCCceEeecCceEEEEcCCCCcce
Q 030970 110 RAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTG 141 (168)
Q Consensus 110 Rtkk~~~R~dG~~ikFddNavVLln~k~~plG 141 (168)
......+++||.+.-+...+.++-|++|+|..
T Consensus 55 ~~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 55 EIEYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 44566778999999999999999999998753
No 16
>PF14996 RMP: Retinal Maintenance
Probab=41.64 E-value=14 Score=29.87 Aligned_cols=34 Identities=32% Similarity=0.315 Sum_probs=26.5
Q ss_pred hhhcccccccccccccCccccccCccccccccccccccccc
Q 030970 6 ASKWSRVILVGRSLLGGLGNNLSGLSSTSHEMASGNFLSQQ 46 (168)
Q Consensus 6 ~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~~~~ 46 (168)
..||+.|+|+|.+..-|++.+.+- ..|.++.+..
T Consensus 40 ~kkC~~v~lgGs~~~~G~~t~~s~-------r~C~~LrC~~ 73 (146)
T PF14996_consen 40 SKKCSPVYLGGSSDPRGIGTSSSQ-------RACDNLRCTK 73 (146)
T ss_pred CCccCCEEECCCcCCCcccccccc-------ccCCCCEEec
Confidence 568999999999999999886554 5577776643
No 17
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=39.38 E-value=83 Score=21.74 Aligned_cols=55 Identities=20% Similarity=0.164 Sum_probs=32.6
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccceE
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 104 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 104 (168)
.|+.+..+.+.-.--.-.++-|+..+. ...|..||.|-+.++...+ ..+++|++.
T Consensus 26 ~i~~Gd~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~~~l~~~~~-~~v~~G~vl 81 (83)
T cd03698 26 SIQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAGENVRLKLKGIDE-EDISPGDVL 81 (83)
T ss_pred EEeCCCEEEEeCCCcEEEEEEEEECCeECCEECCCCEEEEEECCCCH-HHCCCCCEE
Confidence 345555565555322234566654443 4578999999999975433 245566653
No 18
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=37.77 E-value=76 Score=22.45 Aligned_cols=54 Identities=19% Similarity=0.211 Sum_probs=33.8
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccce
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQV 103 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V 103 (168)
.|+.+..+.+.-+-=.-.++-|+..+. ...|..||.+-+.++...+ ..+++|++
T Consensus 30 ~i~~gd~v~i~P~~~~~~V~sI~~~~~~~~~a~aG~~v~i~l~~i~~-~~v~~G~v 84 (91)
T cd03693 30 VLKPGMVVTFAPAGVTGEVKSVEMHHEPLEEALPGDNVGFNVKNVSK-KDIKRGDV 84 (91)
T ss_pred eeecCCEEEECCCCcEEEEEEEEECCcCcCEECCCCEEEEEECCCCH-HHcCCcCE
Confidence 556666666665422234566655443 4678899999999975433 34666765
No 19
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=32.93 E-value=1.1e+02 Score=21.19 Aligned_cols=54 Identities=22% Similarity=0.229 Sum_probs=31.0
Q ss_pred eeccceEEEeeCcccceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccceE
Q 030970 50 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 104 (168)
Q Consensus 50 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 104 (168)
|+.+-.+.+...--.-.++-|+..+. ...|..||.+-+.++...+ ..+++|++.
T Consensus 26 i~~G~~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~i~~-~~v~~G~vl 80 (82)
T cd04089 26 IKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLKGIEE-EDISPGFVL 80 (82)
T ss_pred EecCCEEEEeCCCcEEEEEEEEECCEECCEECCCCEEEEEecCCCH-HHCCCCCEE
Confidence 44444555554322233555554433 3568899999999985543 245667653
No 20
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=32.06 E-value=1e+02 Score=20.21 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=21.5
Q ss_pred ccccceEEEEEEEeeeeeecCCCceEeecCceEEEE
Q 030970 98 VKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLV 133 (168)
Q Consensus 98 vKKg~V~~AvIVRtkk~~~R~dG~~ikFddNavVLl 133 (168)
.+.|+++.|.|.+-.. +|.++.++++.-.++
T Consensus 2 ~~~G~iv~g~V~~v~~-----~g~~V~l~~~~~g~i 32 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVED-----FGVFVDLGNGIEGFI 32 (74)
T ss_dssp SSTTSEEEEEEEEEET-----TEEEEEESTSSEEEE
T ss_pred CCCCCEEEEEEEEEEC-----CEEEEEECCcEEEEE
Confidence 4568888888876554 578888885555444
No 21
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=31.59 E-value=1.3e+02 Score=21.84 Aligned_cols=50 Identities=22% Similarity=0.413 Sum_probs=31.0
Q ss_pred ceeccceEEEeeCcccceEEEEEeeCCc--cccccCcEEEEEEeeecCCCcccccceEE
Q 030970 49 FIQMRTVLKVVDNSGAKTVMCIQPLKGR--KVARLGDTIVASVKEAMPTGKVKKGQVVH 105 (168)
Q Consensus 49 MIq~~T~L~VaDNSGak~v~cI~vl~~~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~~ 105 (168)
.|..++.| |..-+-.++=|+. +++ ..|..||.|=+++.... .++.||+.+
T Consensus 29 ~ik~G~~l---~G~~iG~I~sIe~-~~k~v~~A~~G~eVai~Ieg~~---~i~eGDiLy 80 (81)
T PF14578_consen 29 IIKPGYPL---DGRKIGRIKSIED-NGKNVDEAKKGDEVAISIEGPT---QIKEGDILY 80 (81)
T ss_dssp EEETT-EE---CSSCEEEEEEEEE-TTEEESEEETT-EEEEEEET-----TB-TT-EEE
T ss_pred EEeCCCcc---CCEEEEEEEEeEE-CCcCccccCCCCEEEEEEeCCc---cCCCCCEEe
Confidence 56778888 6655555666653 332 47999999999998644 778888764
No 22
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=27.65 E-value=1.5e+02 Score=20.83 Aligned_cols=54 Identities=24% Similarity=0.341 Sum_probs=33.4
Q ss_pred ceeccceEEEeeCc-c---cceEEEEEeeCC-ccccccCcEEEEEEeeecCCCcccccce
Q 030970 49 FIQMRTVLKVVDNS-G---AKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQV 103 (168)
Q Consensus 49 MIq~~T~L~VaDNS-G---ak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V 103 (168)
.++++..+.+...- | .-.++-|+..+. ...|..||.+-+.++...+ ..+++|.+
T Consensus 26 ~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~~i~~-~~i~~G~v 84 (87)
T cd03694 26 VIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALKKIDR-SLLRKGMV 84 (87)
T ss_pred EEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEcCCCH-HHcCCccE
Confidence 45566666666532 3 235666665443 4578999999999976544 33555554
No 23
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=26.95 E-value=1.3e+02 Score=23.27 Aligned_cols=34 Identities=32% Similarity=0.287 Sum_probs=24.2
Q ss_pred ccccCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030970 78 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 113 (168)
Q Consensus 78 ~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk 113 (168)
.-.+||+|.|.++-... .-++-|.+.|+++..+.
T Consensus 18 ~f~~GD~v~V~~~i~eg--~k~R~q~f~GvvI~~~~ 51 (113)
T TIGR01024 18 DFRVGDTVRVHVKIVEG--KKERIQVFEGVVIARRG 51 (113)
T ss_pred ccCCCCEEEEEEEEccC--CceEcccEEEEEEEEeC
Confidence 34699999999874332 22346789999998874
No 24
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=26.18 E-value=1.6e+02 Score=22.51 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=25.8
Q ss_pred ccccCcEEEEEEeeecCCCcccccceEEEEEEEeeee
Q 030970 78 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQ 114 (168)
Q Consensus 78 ~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk~ 114 (168)
.-.+||+|.|.++....+. .+-+.+.|+++.-+..
T Consensus 18 ~f~~GD~v~V~~~i~e~~k--~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNK--ERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSEEEEEEEEESSSS--EEEEEEEEEEEEEEBS
T ss_pred CcCCCCEEEEEEEEecCCC--ceeEEEEEEEEEEECC
Confidence 3569999999998653322 2457999999988774
No 25
>CHL00084 rpl19 ribosomal protein L19
Probab=24.25 E-value=1.6e+02 Score=22.92 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=23.2
Q ss_pred ccccCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030970 78 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 113 (168)
Q Consensus 78 ~a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk 113 (168)
.-++||+|.|.++-...+. .+-|.+.|+++..+.
T Consensus 22 ~f~~GDtV~V~~~i~eg~k--~R~q~F~GvvI~~r~ 55 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNK--ERVQFYEGTVIAKKN 55 (117)
T ss_pred ccCCCCEEEEEEEEecCCe--eEeceEEEEEEEEeC
Confidence 3569999999986433221 234788999998764
No 26
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=22.70 E-value=1.3e+02 Score=25.05 Aligned_cols=34 Identities=21% Similarity=0.475 Sum_probs=24.4
Q ss_pred ceEeecCceEEEEcC-CCCcceeEEecchhHhhhc
Q 030970 121 SEVRFDDNAVVLVNK-AGEPTGTRVFGPVPHELRR 154 (168)
Q Consensus 121 ~~ikFddNavVLln~-k~~plGTRI~GpV~~Elr~ 154 (168)
..++--++-+-+.-+ .++..-+|-+||+|..|-.
T Consensus 114 ~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~ 148 (176)
T KOG0171|consen 114 TPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQ 148 (176)
T ss_pred ceeeccCceEEEecCCCCCcccccccCCCchhhee
Confidence 345555666666554 4789999999999998843
No 27
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=22.56 E-value=3e+02 Score=25.77 Aligned_cols=51 Identities=27% Similarity=0.339 Sum_probs=37.6
Q ss_pred cccCcEEEEEEeeecCC--------------------CcccccceEEEEEEEeeeeeecCCCceEeecCceEEEEc
Q 030970 79 ARLGDTIVASVKEAMPT--------------------GKVKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLVN 134 (168)
Q Consensus 79 a~vGD~I~vsVKk~~p~--------------------~kvKKg~V~~AvIVRtkk~~~R~dG~~ikFddNavVLln 134 (168)
-++||.|.+.|....+. ...+.|+++.|.|++.... |.++.++++-.-++-
T Consensus 419 ~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~~-----G~fV~l~~gi~g~i~ 489 (565)
T PRK06299 419 YKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDK-----GAFVELEDGVEGLIR 489 (565)
T ss_pred CCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEecC-----ceEEecCCCcEEEEE
Confidence 36999999988765431 1357899999999888764 889999876555554
No 28
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=22.46 E-value=93 Score=25.85 Aligned_cols=38 Identities=21% Similarity=0.484 Sum_probs=24.9
Q ss_pred eeecCCCceEeecCceEEEEcCCCCcceeEEecchhHh
Q 030970 114 QHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHE 151 (168)
Q Consensus 114 ~~~R~dG~~ikFddNavVLln~k~~plGTRI~GpV~~E 151 (168)
+..+..|.+.--.+.-.+|-+++....-+|-|||||.|
T Consensus 122 ~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas 159 (173)
T COG4959 122 ALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPAS 159 (173)
T ss_pred cCCcccCCceecCCeEEEEeccCCcccccceecccCHH
Confidence 34556666653333334444455679999999999987
No 29
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=22.18 E-value=1.8e+02 Score=22.58 Aligned_cols=33 Identities=27% Similarity=0.231 Sum_probs=22.8
Q ss_pred cccCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030970 79 ARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 113 (168)
Q Consensus 79 a~vGD~I~vsVKk~~p~~kvKKg~V~~AvIVRtkk 113 (168)
-.+||+|.|.++-...+ -++-+.+.|+++..+.
T Consensus 19 f~~GD~V~V~~~i~eg~--k~R~q~f~GvvI~~~~ 51 (116)
T PRK05338 19 FRPGDTVRVHVKVVEGN--KERIQAFEGVVIARRG 51 (116)
T ss_pred cCCCCEEEEEEEEccCC--ceEeccEEEEEEEEeC
Confidence 46999999988632221 1234789999998774
No 30
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=21.79 E-value=2.2e+02 Score=19.32 Aligned_cols=15 Identities=27% Similarity=0.501 Sum_probs=9.3
Q ss_pred ccCcEEEEEEeeecC
Q 030970 80 RLGDTIVASVKEAMP 94 (168)
Q Consensus 80 ~vGD~I~vsVKk~~p 94 (168)
.+||+|.+.|.+...
T Consensus 5 ~~GdiV~G~V~~v~~ 19 (82)
T cd04454 5 DVGDIVIGIVTEVNS 19 (82)
T ss_pred CCCCEEEEEEEEEcC
Confidence 567777766665443
Done!