Query 030918
Match_columns 169
No_of_seqs 122 out of 762
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:32:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030918hhsearch_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 4.3E-58 327.2 12.3 120 50-169 1-122 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 7.7E-52 1.7E-56 320.3 13.1 120 50-169 1-122 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 1.2E-51 2.6E-56 319.2 13.0 120 50-169 1-122 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 1.7E-51 3.7E-56 318.3 13.0 120 50-169 1-122 (122)
5 PTZ00054 60S ribosomal protein 100.0 1.7E-49 3.7E-54 313.2 12.6 116 50-169 18-139 (139)
6 PF00238 Ribosomal_L14: Riboso 100.0 8.1E-50 1.7E-54 308.3 10.4 120 50-169 1-122 (122)
7 TIGR03673 rpl14p_arch 50S ribo 100.0 2.6E-49 5.6E-54 309.5 12.5 116 50-169 10-131 (131)
8 PRK08571 rpl14p 50S ribosomal 100.0 4.7E-49 1E-53 308.4 12.7 116 50-169 11-132 (132)
9 PTZ00320 ribosomal protein L14 100.0 5.3E-48 1.1E-52 315.1 13.0 118 52-169 61-188 (188)
10 KOG0901 60S ribosomal protein 100.0 2.2E-36 4.8E-41 239.6 11.2 134 35-169 3-145 (145)
11 KOG3441 Mitochondrial ribosoma 99.9 3.9E-23 8.5E-28 161.6 8.2 107 50-169 31-149 (149)
12 cd03696 selB_II selB_II: this 44.9 50 0.0011 22.8 4.3 55 50-105 26-81 (83)
13 cd03695 CysN_NodQ_II CysN_NodQ 44.1 86 0.0019 21.8 5.5 52 51-105 27-79 (81)
14 PF08447 PAS_3: PAS fold; Int 38.7 45 0.00098 22.0 3.2 31 112-142 56-86 (91)
15 PF10382 DUF2439: Protein of u 38.0 42 0.0009 24.1 3.1 28 119-147 20-49 (83)
16 PF00575 S1: S1 RNA binding do 37.2 83 0.0018 20.7 4.3 31 99-134 2-32 (74)
17 cd03698 eRF3_II_like eRF3_II_l 34.7 89 0.0019 21.6 4.3 54 51-105 27-81 (83)
18 cd03693 EF1_alpha_II EF1_alpha 33.5 86 0.0019 22.2 4.1 55 50-105 30-85 (91)
19 PF14578 GTP_EFTU_D4: Elongati 31.3 1.3E+02 0.0027 22.0 4.7 49 51-106 30-80 (81)
20 PF14996 RMP: Retinal Maintena 30.4 27 0.00058 28.3 1.2 24 6-29 40-63 (146)
21 cd04089 eRF3_II eRF3_II: domai 29.4 1.1E+02 0.0025 21.1 4.1 53 52-105 27-80 (82)
22 TIGR01024 rplS_bact ribosomal 28.7 1.1E+02 0.0025 23.6 4.3 34 79-114 18-51 (113)
23 KOG0171 Mitochondrial inner me 28.1 92 0.002 26.1 3.9 33 122-154 114-147 (176)
24 PF01245 Ribosomal_L19: Riboso 27.3 1.5E+02 0.0033 22.7 4.8 34 79-114 18-51 (113)
25 CHL00084 rpl19 ribosomal prote 25.5 1.4E+02 0.0031 23.2 4.4 34 79-114 22-55 (117)
26 cd03694 GTPBP_II Domain II of 25.2 1.5E+02 0.0033 20.8 4.2 53 51-104 27-84 (87)
27 PRK05338 rplS 50S ribosomal pr 23.5 1.6E+02 0.0035 22.8 4.3 33 80-114 19-51 (116)
28 COG0231 Efp Translation elonga 22.1 3.8E+02 0.0083 20.8 8.5 48 84-137 37-88 (131)
29 COG4959 TraF Type IV secretory 20.9 1.1E+02 0.0024 25.5 3.1 37 115-152 122-159 (173)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-53 Score=327.16 Aligned_cols=120 Identities=56% Similarity=0.863 Sum_probs=117.2
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC--ccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCceeeec
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 127 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ikFd 127 (169)
|||.+|+|+||||||||+++||+++++ +++|.+||+|++|||++.|...+||||+++|||||||++++|+||++++||
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 899999999999999999999999976 569999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 128 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 128 dNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
|||+||+|++++|+||||||||++|||+++|+||+|||++++
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=7.7e-52 Score=320.33 Aligned_cols=120 Identities=48% Similarity=0.787 Sum_probs=116.8
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC--ccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCceeeec
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 127 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ikFd 127 (169)
|||.+|+|+|+|||||++++||++|++ +++|++||+|++|||++.|+++++|||+++|||||||++++|+||++++||
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 CceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 128 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 128 dNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
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 999999999999999999999999999999999999999885
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=1.2e-51 Score=319.21 Aligned_cols=120 Identities=61% Similarity=0.897 Sum_probs=116.7
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC--ccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCceeeec
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 127 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ikFd 127 (169)
|||.+|+|+|+|||||++++||++|++ +++|++||+|++|||++.|+++++|||+++|||||||++++|+||++++||
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 899999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 128 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 128 dNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
T Consensus 81 dNavVLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~v~ 122 (122)
T PRK05483 81 DNAAVLLNNDGEPRGTRIFGPVARELRDKKFMKIVSLAPEVL 122 (122)
T ss_pred CCEEEEECCCCCEeEeEEeccchHHHhhcCCcEEEecccccC
Confidence 999999999999999999999999999999999999999885
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=1.7e-51 Score=318.26 Aligned_cols=120 Identities=56% Similarity=0.849 Sum_probs=116.7
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC--ccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCceeeec
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 127 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ikFd 127 (169)
|||.+|+|+|+|||||++++||++|++ +++|.+||+|++|||++.|+.+++|||+++|||||||++++|+||++++||
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 899999999999999999999999975 468999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 128 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 128 dNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
|||+||+|++++|+||||+||||+|||+++|+||+|||++++
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=1.7e-49 Score=313.17 Aligned_cols=116 Identities=34% Similarity=0.462 Sum_probs=110.3
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeC---C-c--cceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCce
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLK---G-R--KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 123 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~---~-~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ 123 (169)
|||.+|+|+|+||||||+++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 18 mIq~~t~L~vaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p---~~kg~V~kAVIVRtKk~~rR~dGs~ 94 (139)
T PTZ00054 18 GLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKP---ELRKKVLNAVIIRQRKAWRRKDGVF 94 (139)
T ss_pred eecCCCEEEEeeCCCccEEEEEEEeccCcCCccCcccccCCEEEEEEEECCC---cccCCEeeEEEEEECcceEcCCCcE
Confidence 99999999999999999999999996 3 3 479999999999999999 5789999999999999999999999
Q ss_pred eeecCceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 124 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 124 ikFddNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 95 i~F~dNA~VLin~~~~p~GTRI~GpV~rEl-~~~~~KI~SLA~~vi 139 (139)
T PTZ00054 95 IYFEDNAGVIVNPKGEMKGSAITGPVAKEC-ADLWPKISSAAPAIV 139 (139)
T ss_pred EEeCCcEEEEECCCCCEeeeEEeCchhHHH-HhCccHhhccccccC
Confidence 999999999999999999999999999999 567999999999985
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=8.1e-50 Score=308.29 Aligned_cols=120 Identities=60% Similarity=0.879 Sum_probs=114.0
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC--ccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCceeeec
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSEVRFD 127 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~--~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ikFd 127 (169)
|||.+|+|+|+|||||++++||+++++ +++|++||+|++|||+.+|+.++||||+++|||||||++++|.||++++||
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 CceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 128 DNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 128 dNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
|||+||+|++++|+||||+||||+|+|+++|+||+|||++||
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 999999999999999999999999999999999999999885
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=2.6e-49 Score=309.53 Aligned_cols=116 Identities=40% Similarity=0.574 Sum_probs=109.8
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeC---C--c-cceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCce
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLK---G--R-KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 123 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~---~--~-k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ 123 (169)
|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 10 mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~ 86 (131)
T TIGR03673 10 ALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP---EMRKQVFKAVVVRQRKEYRRPDGTR 86 (131)
T ss_pred eeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCc---cccCCEeEEEEEEeCcceecCCCcE
Confidence 99999999999999999999999983 2 2 569999999999999999 5789999999999999999999999
Q ss_pred eeecCceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 124 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 124 ikFddNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
++|||||+||+|++++|+|||||||||+|| +++|+||+|||++++
T Consensus 87 i~FddNa~VLin~~~~P~GTRI~GpV~rEl-~~~~~Ki~SlA~~vi 131 (131)
T TIGR03673 87 VKFEDNAVVIVTPDGEPKGTEIKGPVAREA-AERWPKIASIASIIV 131 (131)
T ss_pred EEeCCcEEEEECCCCCEeeeEEEccchHHH-HhCccHheeccchhC
Confidence 999999999999999999999999999999 568999999999985
No 8
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=4.7e-49 Score=308.40 Aligned_cols=116 Identities=38% Similarity=0.530 Sum_probs=109.8
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeC---C-c--cceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCCce
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLK---G-R--KVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDGSE 123 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~---~-~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG~~ 123 (169)
|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 11 mIq~~T~L~VaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~ 87 (132)
T PRK08571 11 GLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP---EMRKQVLRAVVVRQRKEYRRPDGTR 87 (132)
T ss_pred eecCCCEEEEeeCCCCCeEEEEEEeccCCCCccCCccccCCEEEEEEEECCC---cccCCEeEEEEEEeccceEcCCCcE
Confidence 99999999999999999999999985 2 2 469999999999999999 5689999999999999999999999
Q ss_pred eeecCceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 124 VRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 124 ikFddNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
++|||||+||+|++++|+||||+||||+|| +++|+||+|||++++
T Consensus 88 i~F~dNa~VLin~~~~p~GTRI~GpV~~El-~~~~~Ki~sLA~~vi 132 (132)
T PRK08571 88 VKFEDNAAVIVTPEGTPKGTEIKGPVAREA-AERWPKIASIASIIV 132 (132)
T ss_pred EEeCCcEEEEECCCCCEeeeEEeccchHHH-hhCCchheeccchhC
Confidence 999999999999999999999999999999 567999999999885
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=5.3e-48 Score=315.14 Aligned_cols=118 Identities=25% Similarity=0.330 Sum_probs=114.2
Q ss_pred ccCceEEEeeCcCcceEEEEEeeCCccceecCcE----EEEEEeeecC------CCcccccceEEEEEEEeeecccCCCC
Q 030918 52 QMRTVLKVVDNSGAKTVMCIQPLKGRKVARLGDT----IVASVKEAMP------TGKVKKGQVVHAVVVRAAMQHGRFDG 121 (169)
Q Consensus 52 q~~T~L~VaDNSGak~v~cI~vl~~~k~a~vGD~----I~vsVKk~~p------~~kvKKg~V~kAVIVRtKk~~~R~dG 121 (169)
.-+|+|+|+||||||+++||+++.++++|.+||+ |+||||++.| ++++|||||++|||||||++++|+||
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 3489999999999999999999977899999999 9999999999 78999999999999999999999999
Q ss_pred ceeeecCceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 122 SEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 122 ~~ikFddNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
++++||||||||+|++++|+||||||||++|||+++|+||+|||+.++
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=2.2e-36 Score=239.57 Aligned_cols=134 Identities=37% Similarity=0.500 Sum_probs=122.3
Q ss_pred cccccccccchhh-hhhhccCceEEEeeCcCcceEEEEEeeC--C----ccceecCcEEEEEEee--ecCCCcccccceE
Q 030918 35 HEMASGNFLSQQQ-RTFIQMRTVLKVVDNSGAKTVMCIQPLK--G----RKVARLGDTIVASVKE--AMPTGKVKKGQVV 105 (169)
Q Consensus 35 ~~~~~~~~~~~~~-~~MIq~~T~L~VaDNSGak~v~cI~vl~--~----~k~a~vGD~I~vsVKk--~~p~~kvKKg~V~ 105 (169)
.++.-.+...++| ..|||++|.++|+||||||.++||++.+ | .+.|.+||+++++||+ ..|+.++|.|+++
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 3444455556666 4599999999999999999999999987 4 3489999999999999 7999999999999
Q ss_pred EEEEEEeeecccCCCCceeeecCceEEEEcCCCCcceeEEeccchhhhhcCCCchhhhcccccC
Q 030918 106 HAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169 (169)
Q Consensus 106 kAVIVRtKk~~~R~dG~~ikFddNavVLln~k~~plGTRI~GPV~~Elr~kk~~KI~SLA~~i~ 169 (169)
+|+|||+++++.|.||++++|+|||+|++|++++|.||+|+||||+|++. .|++|+|+|+.++
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=3.9e-23 Score=161.59 Aligned_cols=107 Identities=38% Similarity=0.613 Sum_probs=95.2
Q ss_pred hhccCceEEEeeCcCc--------ceEEEEEeeCCccceecCcEEEEEEeeecCCCcccccceEEEEEEEeeecccCCCC
Q 030918 50 FIQMRTVLKVVDNSGA--------KTVMCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQHGRFDG 121 (169)
Q Consensus 50 MIq~~T~L~VaDNSGa--------k~v~cI~vl~~~k~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk~~~R~dG 121 (169)
-|++.|+|+|+|||.. +..+||++|+++..+.+||.|+++|| ||..+|+||......++ |
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 3788999999999974 67899999998889999999999997 89999999997765443 4
Q ss_pred ceeeecCceEEEEcCCCCcceeEEeccchhhhhcC----CCchhhhcccccC
Q 030918 122 SEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRK----KHVSILTLAEHLA 169 (169)
Q Consensus 122 ~~ikFddNavVLln~k~~plGTRI~GPV~~Elr~k----k~~KI~SLA~~i~ 169 (169)
..+||.|.+||+|++|+|+||||.-|||..||.. .|+|++++|+.+|
T Consensus 99 -~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 99 -VPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRANRGNVQYSKVLAIANKFV 149 (149)
T ss_pred -CcccCCCcEEEECCCCCcccceEeccCcHHHHhccCCcchhhHHHHHhhcC
Confidence 5799999999999999999999999999999832 5999999999886
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=44.88 E-value=50 Score=22.77 Aligned_cols=55 Identities=15% Similarity=0.235 Sum_probs=32.6
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccceE
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 105 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 105 (169)
.|+.+..+.+.++--.-.++=|+.-.. ...|..||.|-+.++...+ ..+++|++.
T Consensus 26 ~i~~g~~v~~~p~~~~~~V~sI~~~~~~~~~a~aGd~v~i~l~~~~~-~~i~~G~vl 81 (83)
T cd03696 26 SVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAGDRVALNLTGVDA-KDLERGDVL 81 (83)
T ss_pred EEeCCCEEEECCCCceEEEEEEEECCcCcCEEcCCCEEEEEEcCCCH-HHcCCccEE
Confidence 355677777776432223333432222 3568899999999976544 345666653
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=44.06 E-value=86 Score=21.85 Aligned_cols=52 Identities=19% Similarity=0.380 Sum_probs=32.8
Q ss_pred hccCceEEEeeCcCcceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccceE
Q 030918 51 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 105 (169)
Q Consensus 51 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 105 (169)
++.+..+.+.+.--.-.++-|+.... -..|..||.|-+.+++ ...+++|++.
T Consensus 27 v~~Gd~v~~~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~---~~~i~~G~vl 79 (81)
T cd03695 27 IRVGDEVVVLPSGKTSRVKSIETFDGELDEAGAGESVTLTLED---EIDVSRGDVI 79 (81)
T ss_pred EECCCEEEEcCCCCeEEEEEEEECCcEeCEEcCCCEEEEEECC---ccccCCCCEE
Confidence 34566666666422235666765544 4578999999999973 3446677764
No 14
>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=38.68 E-value=45 Score=22.02 Aligned_cols=31 Identities=16% Similarity=0.233 Sum_probs=24.9
Q ss_pred eeecccCCCCceeeecCceEEEEcCCCCcce
Q 030918 112 AAMQHGRFDGSEVRFDDNAVVLVNKAGEPTG 142 (169)
Q Consensus 112 tKk~~~R~dG~~ikFddNavVLln~k~~plG 142 (169)
.....+++||.+.-+...+.++-|++|+|..
T Consensus 56 ~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 56 IEYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 3444667999999999999999999998753
No 15
>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=37.99 E-value=42 Score=24.13 Aligned_cols=28 Identities=21% Similarity=0.541 Sum_probs=22.2
Q ss_pred CCCceeeec--CceEEEEcCCCCcceeEEec
Q 030918 119 FDGSEVRFD--DNAVVLVNKAGEPTGTRVFG 147 (169)
Q Consensus 119 ~dG~~ikFd--dNavVLln~k~~plGTRI~G 147 (169)
.||. ++|. .|-+.|.|+++..+|+.+.-
T Consensus 20 ~DG~-l~~~~~~~kv~Lyde~~~~i~~~~~~ 49 (83)
T PF10382_consen 20 HDGF-LKYHSFNKKVMLYDEDGNLIGSDFLK 49 (83)
T ss_pred ECCE-EEEEeCCCEEEEEcCCCCEEeEEEEe
Confidence 3886 4555 77799999999999998764
No 16
>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=37.23 E-value=83 Score=20.67 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=22.4
Q ss_pred ccccceEEEEEEEeeecccCCCCceeeecCceEEEE
Q 030918 99 VKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLV 134 (169)
Q Consensus 99 vKKg~V~kAVIVRtKk~~~R~dG~~ikFddNavVLl 134 (169)
.+.|+++.|.|.+-. .+|.++.++++.-.++
T Consensus 2 ~~~G~iv~g~V~~v~-----~~g~~V~l~~~~~g~i 32 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVE-----DFGVFVDLGNGIEGFI 32 (74)
T ss_dssp SSTTSEEEEEEEEEE-----TTEEEEEESTSSEEEE
T ss_pred CCCCCEEEEEEEEEE-----CCEEEEEECCcEEEEE
Confidence 467888888888755 3788888885555544
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=34.70 E-value=89 Score=21.61 Aligned_cols=54 Identities=20% Similarity=0.185 Sum_probs=31.3
Q ss_pred hccCceEEEeeCcCcceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccceE
Q 030918 51 IQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 105 (169)
Q Consensus 51 Iq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 105 (169)
|+.+..+.+.-.--.-.++-|+.... ...|..||.|-+.++...+ ..+++|++.
T Consensus 27 i~~Gd~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~~~l~~~~~-~~v~~G~vl 81 (83)
T cd03698 27 IQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAGENVRLKLKGIDE-EDISPGDVL 81 (83)
T ss_pred EeCCCEEEEeCCCcEEEEEEEEECCeECCEECCCCEEEEEECCCCH-HHCCCCCEE
Confidence 34455555554322234566654433 4578999999999975433 235667654
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=33.54 E-value=86 Score=22.20 Aligned_cols=55 Identities=18% Similarity=0.208 Sum_probs=33.1
Q ss_pred hhccCceEEEeeCcCcceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccceE
Q 030918 50 FIQMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 105 (169)
Q Consensus 50 MIq~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 105 (169)
+|+.+..+.+.-+-=.-.++-|+.... .+.|..||.|-+.++...+ ..+++|++.
T Consensus 30 ~i~~gd~v~i~P~~~~~~V~sI~~~~~~~~~a~aG~~v~i~l~~i~~-~~v~~G~vl 85 (91)
T cd03693 30 VLKPGMVVTFAPAGVTGEVKSVEMHHEPLEEALPGDNVGFNVKNVSK-KDIKRGDVA 85 (91)
T ss_pred eeecCCEEEECCCCcEEEEEEEEECCcCcCEECCCCEEEEEECCCCH-HHcCCcCEE
Confidence 345566666665421234556654443 4678899999999975433 346667654
No 19
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=31.27 E-value=1.3e+02 Score=21.97 Aligned_cols=49 Identities=22% Similarity=0.415 Sum_probs=29.6
Q ss_pred hccCceEEEeeCcCcceEEEEEeeCCc--cceecCcEEEEEEeeecCCCcccccceEE
Q 030918 51 IQMRTVLKVVDNSGAKTVMCIQPLKGR--KVARLGDTIVASVKEAMPTGKVKKGQVVH 106 (169)
Q Consensus 51 Iq~~T~L~VaDNSGak~v~cI~vl~~~--k~a~vGD~I~vsVKk~~p~~kvKKg~V~k 106 (169)
|..++.| |..-+-.++=|+. +++ ..|..||.|=+++.... .++.||+.+
T Consensus 30 ik~G~~l---~G~~iG~I~sIe~-~~k~v~~A~~G~eVai~Ieg~~---~i~eGDiLy 80 (81)
T PF14578_consen 30 IKPGYPL---DGRKIGRIKSIED-NGKNVDEAKKGDEVAISIEGPT---QIKEGDILY 80 (81)
T ss_dssp EETT-EE---CSSCEEEEEEEEE-TTEEESEEETT-EEEEEEET-----TB-TT-EEE
T ss_pred EeCCCcc---CCEEEEEEEEeEE-CCcCccccCCCCEEEEEEeCCc---cCCCCCEEe
Confidence 4567777 6555555666653 332 47999999999998643 778888875
No 20
>PF14996 RMP: Retinal Maintenance
Probab=30.42 E-value=27 Score=28.32 Aligned_cols=24 Identities=38% Similarity=0.361 Sum_probs=20.6
Q ss_pred hhhcccccccccccccCccccccC
Q 030918 6 ASKWSRVILVGRSLLGGLGNNLSG 29 (169)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~ 29 (169)
..||+.|+|+|.++.-|++.+.+-
T Consensus 40 ~kkC~~v~lgGs~~~~G~~t~~s~ 63 (146)
T PF14996_consen 40 SKKCSPVYLGGSSDPRGIGTSSSQ 63 (146)
T ss_pred CCccCCEEECCCcCCCcccccccc
Confidence 568999999999999999887655
No 21
>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=29.44 E-value=1.1e+02 Score=21.06 Aligned_cols=53 Identities=21% Similarity=0.208 Sum_probs=30.1
Q ss_pred ccCceEEEeeCcCcceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccceE
Q 030918 52 QMRTVLKVVDNSGAKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQVV 105 (169)
Q Consensus 52 q~~T~L~VaDNSGak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V~ 105 (169)
+.+-.+.+...--.-.++-|+..+. ...|..||.|-+.++...+ ..+++|++.
T Consensus 27 ~~G~~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~i~~-~~v~~G~vl 80 (82)
T cd04089 27 KKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLKGIEE-EDISPGFVL 80 (82)
T ss_pred ecCCEEEEeCCCcEEEEEEEEECCEECCEECCCCEEEEEecCCCH-HHCCCCCEE
Confidence 3444555554321223555554332 3568899999999975443 245667654
No 22
>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=28.69 E-value=1.1e+02 Score=23.56 Aligned_cols=34 Identities=32% Similarity=0.287 Sum_probs=24.2
Q ss_pred ceecCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030918 79 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 114 (169)
Q Consensus 79 ~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk 114 (169)
.-.+||+|.|.++-... .-++-|.+.|+++..+.
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 35699999998874332 22346889999998874
No 23
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=28.15 E-value=92 Score=26.05 Aligned_cols=33 Identities=21% Similarity=0.478 Sum_probs=24.0
Q ss_pred ceeeecCceEEEEcCC-CCcceeEEeccchhhhh
Q 030918 122 SEVRFDDNAVVLVNKA-GEPTGTRVFGPVPHELR 154 (169)
Q Consensus 122 ~~ikFddNavVLln~k-~~plGTRI~GPV~~Elr 154 (169)
..++--++-+-+.-++ ++..-+|-+||+|..|-
T Consensus 114 ~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI 147 (176)
T KOG0171|consen 114 TPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLI 147 (176)
T ss_pred ceeeccCceEEEecCCCCCcccccccCCCchhhe
Confidence 3455555666665544 78999999999999884
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=27.33 E-value=1.5e+02 Score=22.70 Aligned_cols=34 Identities=26% Similarity=0.276 Sum_probs=25.4
Q ss_pred ceecCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030918 79 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 114 (169)
Q Consensus 79 ~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk 114 (169)
.-.+||+|.|.++....+. .+-|.+.|+++.-+.
T Consensus 18 ~f~~GD~v~V~~~i~e~~k--~r~q~f~GvvIa~~~ 51 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNK--ERIQVFEGVVIARRR 51 (113)
T ss_dssp SSSSSSEEEEEEEEESSSS--EEEEEEEEEEEEEEB
T ss_pred CcCCCCEEEEEEEEecCCC--ceeEEEEEEEEEEEC
Confidence 3579999999998663322 246899999998876
No 25
>CHL00084 rpl19 ribosomal protein L19
Probab=25.49 E-value=1.4e+02 Score=23.16 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=23.4
Q ss_pred ceecCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030918 79 VARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 114 (169)
Q Consensus 79 ~a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk 114 (169)
.-.+||+|.|.++-...+. .+-|.+.|+++..+.
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 3579999999986433221 235789999998663
No 26
>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=25.24 E-value=1.5e+02 Score=20.78 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=32.2
Q ss_pred hccCceEEEeeCc-C---cceEEEEEeeCC-ccceecCcEEEEEEeeecCCCcccccce
Q 030918 51 IQMRTVLKVVDNS-G---AKTVMCIQPLKG-RKVARLGDTIVASVKEAMPTGKVKKGQV 104 (169)
Q Consensus 51 Iq~~T~L~VaDNS-G---ak~v~cI~vl~~-~k~a~vGD~I~vsVKk~~p~~kvKKg~V 104 (169)
++++..+.+...- | .-.++-|+..+. ...|..||.+-+.++...+ ..+++|.+
T Consensus 27 v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~~i~~-~~i~~G~v 84 (87)
T cd03694 27 IRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALKKIDR-SLLRKGMV 84 (87)
T ss_pred EeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEcCCCH-HHcCCccE
Confidence 3456666665532 3 235666665433 3578999999999976544 33555554
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=23.47 E-value=1.6e+02 Score=22.82 Aligned_cols=33 Identities=27% Similarity=0.237 Sum_probs=22.8
Q ss_pred eecCcEEEEEEeeecCCCcccccceEEEEEEEeee
Q 030918 80 ARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 114 (169)
Q Consensus 80 a~vGD~I~vsVKk~~p~~kvKKg~V~kAVIVRtKk 114 (169)
-.+||+|.|.++-...+. ++-|.+.|+++..+.
T Consensus 19 f~~GD~V~V~~~i~eg~k--~R~q~f~GvvI~~~~ 51 (116)
T PRK05338 19 FRPGDTVRVHVKVVEGNK--ERIQAFEGVVIARRG 51 (116)
T ss_pred cCCCCEEEEEEEEccCCc--eEeccEEEEEEEEeC
Confidence 469999999886322211 235789999998773
No 28
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=22.09 E-value=3.8e+02 Score=20.83 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=32.7
Q ss_pred cEEEEEEeeecCCCc----ccccceEEEEEEEeeecccCCCCceeeecCceEEEEcCC
Q 030918 84 DTIVASVKEAMPTGK----VKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKA 137 (169)
Q Consensus 84 D~I~vsVKk~~p~~k----vKKg~V~kAVIVRtKk~~~R~dG~~ikFddNavVLln~k 137 (169)
-++.+..|......+ .+-++.+...+|..+ +..++++|++..++.|.+
T Consensus 37 a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~------~~q~lY~dg~~~~FMD~e 88 (131)
T COG0231 37 AFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERK------TAQYLYIDGDFYVFMDLE 88 (131)
T ss_pred cEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeee------eEEEEEcCCCeEEEccCC
Confidence 377888877655432 344566666666644 467889999999999864
No 29
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.87 E-value=1.1e+02 Score=25.46 Aligned_cols=37 Identities=22% Similarity=0.560 Sum_probs=24.9
Q ss_pred cccCCCCceeeecCceEEEEc-CCCCcceeEEeccchhh
Q 030918 115 QHGRFDGSEVRFDDNAVVLVN-KAGEPTGTRVFGPVPHE 152 (169)
Q Consensus 115 ~~~R~dG~~ikFddNavVLln-~k~~plGTRI~GPV~~E 152 (169)
...+..|.+. -...-..|++ ++....-+|-|||||.|
T Consensus 122 ~lp~~~gcR~-l~~~el~lL~~~~~~SfDsRYfGpipas 159 (173)
T COG4959 122 ALPRWQGCRY-LAPSELLLLTDRSSTSFDSRYFGPIPAS 159 (173)
T ss_pred cCCcccCCce-ecCCeEEEEeccCCcccccceecccCHH
Confidence 3455566665 3344444554 55679999999999987
Done!