Query 033177
Match_columns 125
No_of_seqs 106 out of 747
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:45:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033177.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033177hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00054 60S ribosomal protein 100.0 1.4E-40 3E-45 251.0 13.3 117 4-120 3-119 (139)
2 PRK08571 rpl14p 50S ribosomal 100.0 9.2E-40 2E-44 244.7 13.1 109 11-119 3-111 (132)
3 TIGR03673 rpl14p_arch 50S ribo 100.0 3.6E-39 7.8E-44 241.3 12.9 109 12-120 3-111 (131)
4 COG0093 RplN Ribosomal protein 100.0 4.2E-38 9.1E-43 232.6 11.1 95 19-117 1-98 (122)
5 CHL00057 rpl14 ribosomal prote 100.0 6.4E-37 1.4E-41 226.5 12.1 98 19-120 1-101 (122)
6 TIGR01067 rplN_bact ribosomal 100.0 9.4E-37 2E-41 225.4 12.7 99 19-121 1-102 (122)
7 PRK05483 rplN 50S ribosomal pr 100.0 9.9E-37 2.2E-41 225.4 12.7 98 19-120 1-101 (122)
8 PF00238 Ribosomal_L14: Riboso 100.0 7.6E-35 1.7E-39 214.6 9.4 99 19-121 1-102 (122)
9 PTZ00320 ribosomal protein L14 100.0 5.2E-32 1.1E-36 212.1 11.1 96 20-121 60-168 (188)
10 KOG0901 60S ribosomal protein 100.0 1.5E-31 3.2E-36 203.1 10.7 110 1-110 1-115 (145)
11 KOG3441 Mitochondrial ribosoma 99.1 1.3E-10 2.9E-15 87.9 6.4 82 18-115 30-119 (149)
12 TIGR01024 rplS_bact ribosomal 62.9 16 0.00035 26.9 4.3 36 51-86 15-51 (113)
13 PF01245 Ribosomal_L19: Riboso 62.5 20 0.00043 26.3 4.7 38 50-87 14-52 (113)
14 CHL00084 rpl19 ribosomal prote 59.3 20 0.00043 26.7 4.3 36 51-86 19-55 (117)
15 PRK05338 rplS 50S ribosomal pr 58.5 22 0.00047 26.4 4.4 35 52-86 16-51 (116)
16 cd04497 hPOT1_OB1_like hPOT1_O 56.6 24 0.00052 25.8 4.4 39 23-63 38-77 (138)
17 cd03696 selB_II selB_II: this 45.3 60 0.0013 21.2 4.6 48 18-70 25-72 (83)
18 COG0335 RplS Ribosomal protein 41.9 47 0.001 24.8 3.9 35 52-86 18-53 (115)
19 cd03698 eRF3_II_like eRF3_II_l 41.7 65 0.0014 21.2 4.3 47 19-70 26-72 (83)
20 COG4506 Uncharacterized protei 39.1 30 0.00066 26.8 2.6 25 94-118 56-80 (143)
21 cd03693 EF1_alpha_II EF1_alpha 38.8 79 0.0017 21.2 4.5 53 19-76 30-84 (91)
22 COG3269 Predicted RNA-binding 38.6 33 0.00071 23.7 2.5 20 53-72 44-63 (73)
23 cd04089 eRF3_II eRF3_II: domai 35.3 93 0.002 20.4 4.3 47 19-70 25-71 (82)
24 cd03695 CysN_NodQ_II CysN_NodQ 34.8 1.4E+02 0.0029 19.8 5.3 44 19-67 26-69 (81)
25 PF08696 Dna2: DNA replication 34.8 72 0.0016 25.1 4.2 21 97-117 36-56 (209)
26 PF00659 POLO_box: POLO box du 28.6 1.6E+02 0.0035 18.7 5.3 29 83-111 2-33 (68)
27 cd05792 S1_eIF1AD_like S1_eIF1 28.4 1.4E+02 0.0029 20.6 4.2 48 25-77 14-61 (78)
28 cd03694 GTPBP_II Domain II of 27.2 1.4E+02 0.0031 19.8 4.2 48 19-71 26-77 (87)
29 PF11665 DUF3265: Protein of u 25.8 61 0.0013 18.5 1.8 9 115-123 4-12 (28)
30 PF07039 DUF1325: SGF29 tudor- 23.2 82 0.0018 23.3 2.6 25 76-102 88-112 (130)
31 PF01938 TRAM: TRAM domain; I 21.2 80 0.0017 19.5 1.9 19 57-75 40-59 (61)
32 TIGR00523 eIF-1A eukaryotic/ar 20.2 2.9E+02 0.0062 19.7 4.8 55 16-76 25-79 (99)
No 1
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=1.4e-40 Score=251.02 Aligned_cols=117 Identities=68% Similarity=1.050 Sum_probs=106.7
Q ss_pred CCCCCcCcccceeecccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCcccceecEEEEe
Q 033177 4 RGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVR 83 (125)
Q Consensus 4 ~~~~~~~~~~~~~~~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V~kAVIVR 83 (125)
.+++.....++++++|||.+|+|+|+|||||++++||+++|.+++.+|+++|++||+|+||||++.|..|+|+++|||||
T Consensus 3 ~~~~~~~~~~~~~~~mIq~~t~L~vaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVR 82 (139)
T PTZ00054 3 RGRGGVGGNKFRVTLGLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKPELRKKVLNAVIIR 82 (139)
T ss_pred ccccCccccccccceeecCCCEEEEeeCCCccEEEEEEEeccCcCCccCcccccCCEEEEEEEECCCcccCCEeeEEEEE
Confidence 35666778899999999999999999999999999999998544555668999999999999999998899999999999
Q ss_pred eeceeeeCCCcEEEecCceEEEEEcCCceEEEEEEEE
Q 033177 84 QRKPWRRKDGVFMYFEGNYSFCILFGSWLMLIHFVYC 120 (125)
Q Consensus 84 tKk~~~R~dG~~I~F~dNAvVLin~~~~~~~~~~~~~ 120 (125)
||++++|+||++++|||||+||+|++...++..+.-.
T Consensus 83 tKk~~rR~dGs~i~F~dNA~VLin~~~~p~GTRI~Gp 119 (139)
T PTZ00054 83 QRKAWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGP 119 (139)
T ss_pred ECcceEcCCCcEEEeCCcEEEEECCCCCEeeeEEeCc
Confidence 9999999999999999999999999988888877543
No 2
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=9.2e-40 Score=244.72 Aligned_cols=109 Identities=49% Similarity=0.688 Sum_probs=101.1
Q ss_pred cccceeecccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCcccceecEEEEeeeceeee
Q 033177 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRR 90 (125)
Q Consensus 11 ~~~~~~~~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V~kAVIVRtKk~~~R 90 (125)
+++++++.|||.+|+|+|||||||++++||++++.+++.+|+++|++||+|+||||++.|..|+|+++|||||||++++|
T Consensus 3 ~~~~~~~~mIq~~T~L~VaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk~~~R 82 (132)
T PRK08571 3 GIRSKVTRGLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRKEYRR 82 (132)
T ss_pred cccccccceecCCCEEEEeeCCCCCeEEEEEEeccCCCCccCCccccCCEEEEEEEECCCcccCCEeEEEEEEeccceEc
Confidence 56889999999999999999999999999999986555566688999999999999999988999999999999999999
Q ss_pred CCCcEEEecCceEEEEEcCCceEEEEEEE
Q 033177 91 KDGVFMYFEGNYSFCILFGSWLMLIHFVY 119 (125)
Q Consensus 91 ~dG~~I~F~dNAvVLin~~~~~~~~~~~~ 119 (125)
+||++++|||||+||+|++...++..+.-
T Consensus 83 ~dGs~i~F~dNa~VLin~~~~p~GTRI~G 111 (132)
T PRK08571 83 PDGTRVKFEDNAAVIVTPEGTPKGTEIKG 111 (132)
T ss_pred CCCcEEEeCCcEEEEECCCCCEeeeEEec
Confidence 99999999999999999998888887754
No 3
>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=3.6e-39 Score=241.26 Aligned_cols=109 Identities=45% Similarity=0.614 Sum_probs=100.3
Q ss_pred ccceeecccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCcccceecEEEEeeeceeeeC
Q 033177 12 NKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRK 91 (125)
Q Consensus 12 ~~~~~~~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V~kAVIVRtKk~~~R~ 91 (125)
.+++++.|||.+|+|+|+|||||++++||++++.++..+|+++|++||+|+||||++.|..|+|+++|||||||++++|+
T Consensus 3 ~~~~~~~mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk~~~R~ 82 (131)
T TIGR03673 3 IRAGITRALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRKEYRRP 82 (131)
T ss_pred cccccceeeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCccccCCEeEEEEEEeCcceecC
Confidence 47889999999999999999999999999999755555666899999999999999999889999999999999999999
Q ss_pred CCcEEEecCceEEEEEcCCceEEEEEEEE
Q 033177 92 DGVFMYFEGNYSFCILFGSWLMLIHFVYC 120 (125)
Q Consensus 92 dG~~I~F~dNAvVLin~~~~~~~~~~~~~ 120 (125)
||++++|||||+||||++...++..+.-.
T Consensus 83 dGs~i~FddNa~VLin~~~~P~GTRI~Gp 111 (131)
T TIGR03673 83 DGTRVKFEDNAVVIVTPDGEPKGTEIKGP 111 (131)
T ss_pred CCcEEEeCCcEEEEECCCCCEeeeEEEcc
Confidence 99999999999999999988888877543
No 4
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.2e-38 Score=232.60 Aligned_cols=95 Identities=35% Similarity=0.444 Sum_probs=87.6
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc---ccceecEEEEeeeceeeeCCCcE
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~---Kg~V~kAVIVRtKk~~~R~dG~~ 95 (125)
|||.+|+|+||||||||+++||+|+|+++| .+|++||+|++|||++.|.. |||+++|||||||++++|+||++
T Consensus 1 miq~~t~l~vADNSGAk~v~~I~V~gg~~r----~~A~vGD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~DGs~ 76 (122)
T COG0093 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRR----RYAGVGDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSY 76 (122)
T ss_pred CcccccEEEEccCCCCcEEEEEEEeccccc----cccCCCCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcCCCCE
Confidence 899999999999999999999999987776 59999999999999999953 67899999999999999999999
Q ss_pred EEecCceEEEEEcCCceEEEEE
Q 033177 96 MYFEGNYSFCILFGSWLMLIHF 117 (125)
Q Consensus 96 I~F~dNAvVLin~~~~~~~~~~ 117 (125)
|+|||||+||+|++..-.+.-+
T Consensus 77 i~FddNA~Viin~~g~P~GtrI 98 (122)
T COG0093 77 IKFDDNAAVIINPDGEPRGTRI 98 (122)
T ss_pred EEeCCceEEEECCCCCcccceE
Confidence 9999999999999876665544
No 5
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=6.4e-37 Score=226.52 Aligned_cols=98 Identities=32% Similarity=0.429 Sum_probs=91.8
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc---ccceecEEEEeeeceeeeCCCcE
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~---Kg~V~kAVIVRtKk~~~R~dG~~ 95 (125)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|++|||++.|+. |+|+++|||||||++++|+||++
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~----~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~dG~~ 76 (122)
T CHL00057 1 MIQPQTYLNVADNSGARKLMCIRVLGASNR----KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMI 76 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCC----ccccCCCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcCCCcE
Confidence 899999999999999999999999986655 78999999999999999975 78999999999999999999999
Q ss_pred EEecCceEEEEEcCCceEEEEEEEE
Q 033177 96 MYFEGNYSFCILFGSWLMLIHFVYC 120 (125)
Q Consensus 96 I~F~dNAvVLin~~~~~~~~~~~~~ 120 (125)
++|||||+||+|++...++..+.-.
T Consensus 77 i~F~~Na~VLin~~~~p~GTrI~Gp 101 (122)
T CHL00057 77 IRFDDNAAVVIDQEGNPKGTRVFGP 101 (122)
T ss_pred EEcCCceEEEECCCCCEeEeEEEcc
Confidence 9999999999999999998887643
No 6
>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=9.4e-37 Score=225.43 Aligned_cols=99 Identities=34% Similarity=0.400 Sum_probs=92.2
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc---ccceecEEEEeeeceeeeCCCcE
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~---Kg~V~kAVIVRtKk~~~R~dG~~ 95 (125)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |+|+++|||||||++++|+||++
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~----~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~ 76 (122)
T TIGR01067 1 MIQQQSRLNVADNSGAKKVQCIKVLGGSRR----RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSY 76 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCC----CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeCCCCE
Confidence 899999999999999999999999986554 68999999999999999975 69999999999999999999999
Q ss_pred EEecCceEEEEEcCCceEEEEEEEEE
Q 033177 96 MYFEGNYSFCILFGSWLMLIHFVYCV 121 (125)
Q Consensus 96 I~F~dNAvVLin~~~~~~~~~~~~~~ 121 (125)
++|||||+||+|++...++..+...+
T Consensus 77 i~F~~Na~VLin~~~~p~GTrI~Gpv 102 (122)
T TIGR01067 77 IRFDDNACVLINKNKEPRGTRIFGPV 102 (122)
T ss_pred EECCCceEEEECCCCCEeeeEEEccc
Confidence 99999999999999999988876554
No 7
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=9.9e-37 Score=225.41 Aligned_cols=98 Identities=30% Similarity=0.381 Sum_probs=91.3
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc---ccceecEEEEeeeceeeeCCCcE
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~---Kg~V~kAVIVRtKk~~~R~dG~~ 95 (125)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |||+++|||||||++++|+||++
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~g~~~~----~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~ 76 (122)
T PRK05483 1 MIQQETRLNVADNSGAKEVMCIKVLGGSKR----RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSY 76 (122)
T ss_pred CCCCCCEEEEeECCCCCEEEEEEEeCCCCC----CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecCCCCE
Confidence 899999999999999999999999986554 68999999999999999975 68999999999999999999999
Q ss_pred EEecCceEEEEEcCCceEEEEEEEE
Q 033177 96 MYFEGNYSFCILFGSWLMLIHFVYC 120 (125)
Q Consensus 96 I~F~dNAvVLin~~~~~~~~~~~~~ 120 (125)
++|||||+||+|++...++..+.-.
T Consensus 77 i~F~dNavVLin~~~~p~GTrI~Gp 101 (122)
T PRK05483 77 IRFDDNAAVLLNNDGEPRGTRIFGP 101 (122)
T ss_pred EEcCCCEEEEECCCCCEeEeEEecc
Confidence 9999999999999989998877643
No 8
>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=7.6e-35 Score=214.56 Aligned_cols=99 Identities=37% Similarity=0.498 Sum_probs=87.3
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc---ccceecEEEEeeeceeeeCCCcE
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~---Kg~V~kAVIVRtKk~~~R~dG~~ 95 (125)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|++|||++.|+. |||+++|||||||++++|+||++
T Consensus 1 MIq~~t~L~v~DNSGak~v~cI~v~~~~~~----~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~dg~~ 76 (122)
T PF00238_consen 1 MIQKGTILKVADNSGAKKVKCIKVLGGKRR----KYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRKDGSF 76 (122)
T ss_dssp -BETTEEEEESBSSSEEEEEEEEETSSTTT----SEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETTTSEE
T ss_pred CCCCCCEEEEeeCCCCcEEEEEEEeCCcCc----cccccceEEEEEEeecccCccccccceEEEEEEEEeEEEEEeCCcE
Confidence 999999999999999999999999987644 79999999999999996654 67999999999999999999999
Q ss_pred EEecCceEEEEEcCCceEEEEEEEEE
Q 033177 96 MYFEGNYSFCILFGSWLMLIHFVYCV 121 (125)
Q Consensus 96 I~F~dNAvVLin~~~~~~~~~~~~~~ 121 (125)
++|||||+||+|+....++..+..++
T Consensus 77 i~F~~Na~VLln~~~~p~GtrI~Gpv 102 (122)
T PF00238_consen 77 IKFDDNAVVLLNKKGNPLGTRIFGPV 102 (122)
T ss_dssp EEESSEEEEEEETTSSBSSSSBCSEE
T ss_pred EEeCCccEEEEcCCCCEeeeEEEeee
Confidence 99999999999999887776655443
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=99.97 E-value=5.2e-32 Score=212.10 Aligned_cols=96 Identities=18% Similarity=0.233 Sum_probs=87.7
Q ss_pred cccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCE----EEEEEeecCC------Cc---ccceecEEEEeeec
Q 033177 20 LPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDM----VMATVKKGKP------DL---RKKVMPAVIVRQRK 86 (125)
Q Consensus 20 Iq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~----I~vsVKk~~p------~~---Kg~V~kAVIVRtKk 86 (125)
..-+|+|+|+||||||+++||+|+ +++ ++|++||+ |+||||++.| +. ||||++|||||||+
T Consensus 60 ~~~qT~L~VaDNSGAK~V~CIkVl--~~r----r~A~IGDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTKK 133 (188)
T PTZ00320 60 FSDQVKLHCVDNTNCKHVRLISKA--TAE----RFAHCRVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQ 133 (188)
T ss_pred cCCCcEEEEEeCCCCcEEEEEEEe--cCC----CceeeccccCceEEEEEeecccCccccccCceecCCEEEEEEEEECc
Confidence 457999999999999999999999 233 69999999 9999999999 32 78999999999999
Q ss_pred eeeeCCCcEEEecCceEEEEEcCCceEEEEEEEEE
Q 033177 87 PWRRKDGVFMYFEGNYSFCILFGSWLMLIHFVYCV 121 (125)
Q Consensus 87 ~~~R~dG~~I~F~dNAvVLin~~~~~~~~~~~~~~ 121 (125)
+++|+||++|+||||||||||++..-++--+.++|
T Consensus 134 ~irR~DGs~IrFDdNAaVLIN~qgePlGTRIfGPV 168 (188)
T PTZ00320 134 TNTRMSGLQTNFDRNTCILMNDQRVPLGTRVMYCA 168 (188)
T ss_pred ccCCCCCCEEEeCCcEEEEECCCCCEeeeEEecch
Confidence 99999999999999999999999999988887765
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.5e-31 Score=203.09 Aligned_cols=110 Identities=70% Similarity=1.076 Sum_probs=104.8
Q ss_pred CCCCCCCCcCcccceeecccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEee--cCCCcc---cc
Q 033177 1 MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK--GKPDLR---KK 75 (125)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk--~~p~~K---g~ 75 (125)
||+++..+....+|+++.|||+||.++|+||||||.++||++.+.++|.||+|+|.+||+++++||+ ..|+.+ ++
T Consensus 1 ~~~~~~~gs~~~k~r~s~~~~~g~~incaDNSgAknL~~isv~g~~Grlnrl~~A~~GD~vva~vKka~~~Pe~r~k~g~ 80 (145)
T KOG0901|consen 1 MSSRGRGGSSGVKFRISLGLPVGAVINCADNSGAKNLYCISVKGIKGRLNRLPAAGVGDMVVATVKKAHGKPELRKKVGE 80 (145)
T ss_pred CcccccCcccchhhhhhhccccceEEEecCCCCcceEEEEEEeccccccccccCCCcCCEEEEEEecccCCCccCcEecc
Confidence 7999999999999999999999999999999999999999999998999999999999999999999 799884 46
Q ss_pred eecEEEEeeeceeeeCCCcEEEecCceEEEEEcCC
Q 033177 76 VMPAVIVRQRKPWRRKDGVFMYFEGNYSFCILFGS 110 (125)
Q Consensus 76 V~kAVIVRtKk~~~R~dG~~I~F~dNAvVLin~~~ 110 (125)
++.|+|||+++++.|.||+++.|+|||+|++|+..
T Consensus 81 ~~~avvVr~~k~~~r~dgs~~~f~dnA~v~~~~~~ 115 (145)
T KOG0901|consen 81 VLPAVVVRQKKSKRRKDGSIAYFEDNAGVIVNNKG 115 (145)
T ss_pred cceeeEEeeccccccCCCcEEEEcCceEEEEcccC
Confidence 69999999999999999999999999999999654
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.12 E-value=1.3e-10 Score=87.88 Aligned_cols=82 Identities=21% Similarity=0.238 Sum_probs=68.8
Q ss_pred cccccccEEEEecCCC--------cceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCcccceecEEEEeeeceee
Q 033177 18 LGLPVAATVNCADNTG--------AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWR 89 (125)
Q Consensus 18 ~mIq~~T~L~VaDNSG--------Ak~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V~kAVIVRtKk~~~ 89 (125)
+.|++.|+|+|.|||. .+.-+||+||+. | ..+.+||.|++.| |||.-+|+||.-. ..
T Consensus 30 ~~I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkk--r----gvg~~GDkiLvAI-------kGQmkKa~vVGh~--~~ 94 (149)
T KOG3441|consen 30 MGIHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKK--R----GVGELGDKILVAI-------KGQMKKAYVVGHV--HY 94 (149)
T ss_pred HhhhhhheEEEecchhhcccccccCCCCceEEEEec--c----cccccccEEEEEE-------ecceeeeEEEEee--cc
Confidence 5799999999999996 488999999973 2 4799999999999 8999999999944 35
Q ss_pred eCCCcEEEecCceEEEEEcCCceEEE
Q 033177 90 RKDGVFMYFEGNYSFCILFGSWLMLI 115 (125)
Q Consensus 90 R~dG~~I~F~dNAvVLin~~~~~~~~ 115 (125)
++.|. -.||.|..|||.+.-+-++.
T Consensus 95 ~k~~~-P~fDsNniVLiddnGnPlGt 119 (149)
T KOG3441|consen 95 RKHGV-PVFDSNNIVLIDDNGNPLGT 119 (149)
T ss_pred CCCCC-cccCCCcEEEECCCCCcccc
Confidence 56666 57999999999977665553
No 12
>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=62.87 E-value=16 Score=26.95 Aligned_cols=36 Identities=33% Similarity=0.414 Sum_probs=28.8
Q ss_pred CCCCcccCCEEEEEEeecCCC-cccceecEEEEeeec
Q 033177 51 RLPSACVGDMVMATVKKGKPD-LRKKVMPAVIVRQRK 86 (125)
Q Consensus 51 r~~~A~iGD~I~vsVKk~~p~-~Kg~V~kAVIVRtKk 86 (125)
-+|.-.+||+|.|.++-...+ .+-|.|.++|+..+.
T Consensus 15 ~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~ 51 (113)
T TIGR01024 15 DLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRG 51 (113)
T ss_pred CCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeC
Confidence 357889999999999865533 377999999998874
No 13
>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=62.49 E-value=20 Score=26.29 Aligned_cols=38 Identities=29% Similarity=0.429 Sum_probs=30.6
Q ss_pred cCCCCcccCCEEEEEEeecCC-CcccceecEEEEeeece
Q 033177 50 NRLPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRKP 87 (125)
Q Consensus 50 ~r~~~A~iGD~I~vsVKk~~p-~~Kg~V~kAVIVRtKk~ 87 (125)
...|.-.+||+|.|.++.... +.+-|.|.++++.-+..
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC
Confidence 345788999999999987744 45779999999987763
No 14
>CHL00084 rpl19 ribosomal protein L19
Probab=59.26 E-value=20 Score=26.69 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=28.0
Q ss_pred CCCCcccCCEEEEEEeecCCC-cccceecEEEEeeec
Q 033177 51 RLPSACVGDMVMATVKKGKPD-LRKKVMPAVIVRQRK 86 (125)
Q Consensus 51 r~~~A~iGD~I~vsVKk~~p~-~Kg~V~kAVIVRtKk 86 (125)
-+|.-.+||+|.|.++-...+ .+-|.|.++|+..+.
T Consensus 19 ~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~ 55 (117)
T CHL00084 19 NLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKN 55 (117)
T ss_pred CCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeC
Confidence 357889999999999655443 467899999998653
No 15
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=58.52 E-value=22 Score=26.39 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=27.7
Q ss_pred CCCcccCCEEEEEEeecCC-CcccceecEEEEeeec
Q 033177 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (125)
Q Consensus 52 ~~~A~iGD~I~vsVKk~~p-~~Kg~V~kAVIVRtKk 86 (125)
+|.-.+||+|.|.++-... +.+-|.|.++|+..+.
T Consensus 16 ~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~ 51 (116)
T PRK05338 16 IPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRG 51 (116)
T ss_pred CCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeC
Confidence 5788999999999875544 3467999999998763
No 16
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=56.59 E-value=24 Score=25.82 Aligned_cols=39 Identities=21% Similarity=0.268 Sum_probs=27.4
Q ss_pred ccEEEEecCCCc-ceEEEEEEecCCccccCCCCcccCCEEEE
Q 033177 23 AATVNCADNTGA-KNLYIISVKGIKGRLNRLPSACVGDMVMA 63 (125)
Q Consensus 23 ~T~L~VaDNSGA-k~v~cI~Vl~~~~r~~r~~~A~iGD~I~v 63 (125)
-..|.++|-|++ ...-.+++.+. ....+|....||+|.+
T Consensus 38 ~~tl~i~D~S~~~~~~l~v~~F~~--~~~~LP~v~~GDVIll 77 (138)
T cd04497 38 CCTLTITDPSLANSDGLTVKLFRP--NEESLPIVKVGDIILL 77 (138)
T ss_pred EEEEEEECCCCCCCCcEEEEEECC--ChhhCCCCCCCCEEEE
Confidence 356899999997 33444556653 2356787799999975
No 17
>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=45.33 E-value=60 Score=21.23 Aligned_cols=48 Identities=19% Similarity=0.157 Sum_probs=31.4
Q ss_pred cccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCC
Q 033177 18 LGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (125)
Q Consensus 18 ~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p 70 (125)
=.|+.|..+.+..+--.-.++=|+... ...+.|..||.|-+.++...+
T Consensus 25 G~i~~g~~v~~~p~~~~~~V~sI~~~~-----~~~~~a~aGd~v~i~l~~~~~ 72 (83)
T cd03696 25 GSVKVGDKVEILPLGEETRVRSIQVHG-----KDVEEAKAGDRVALNLTGVDA 72 (83)
T ss_pred cEEeCCCEEEECCCCceEEEEEEEECC-----cCcCEEcCCCEEEEEEcCCCH
Confidence 357888899888853233333333322 223689999999999986554
No 18
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=41.90 E-value=47 Score=24.83 Aligned_cols=35 Identities=29% Similarity=0.363 Sum_probs=28.0
Q ss_pred CCCcccCCEEEEEEeecCCCc-ccceecEEEEeeec
Q 033177 52 LPSACVGDMVMATVKKGKPDL-RKKVMPAVIVRQRK 86 (125)
Q Consensus 52 ~~~A~iGD~I~vsVKk~~p~~-Kg~V~kAVIVRtKk 86 (125)
+|.-.+||.|.|.||-...+- +-|.|.++|++-+.
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~ 53 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRG 53 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECC
Confidence 577789999999998766543 66999999998664
No 19
>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=41.71 E-value=65 Score=21.18 Aligned_cols=47 Identities=15% Similarity=0.090 Sum_probs=31.2
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCC
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p 70 (125)
.|+.|..+.+.-..-.-.++-|+.... ....|..||.+-+.++...+
T Consensus 26 ~i~~Gd~v~i~P~~~~~~V~si~~~~~-----~~~~a~aGd~v~~~l~~~~~ 72 (83)
T cd03698 26 SIQKGDTLLVMPSKESVEVKSIYVDDE-----EVDYAVAGENVRLKLKGIDE 72 (83)
T ss_pred EEeCCCEEEEeCCCcEEEEEEEEECCe-----ECCEECCCCEEEEEECCCCH
Confidence 567788888776533334555554432 22689999999999986544
No 20
>COG4506 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.12 E-value=30 Score=26.76 Aligned_cols=25 Identities=24% Similarity=0.291 Sum_probs=23.6
Q ss_pred cEEEecCceEEEEEcCCceEEEEEE
Q 033177 94 VFMYFEGNYSFCILFGSWLMLIHFV 118 (125)
Q Consensus 94 ~~I~F~dNAvVLin~~~~~~~~~~~ 118 (125)
+.++.+||.++|+-.|+-.|-.|||
T Consensus 56 TtlKi~d~e~~liR~G~v~M~~~F~ 80 (143)
T COG4506 56 TTLKIDDDELLLIRSGDVNMRMHFV 80 (143)
T ss_pred EEEEEcCCEEEEEEcccchhhheee
Confidence 6789999999999999999999997
No 21
>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=38.83 E-value=79 Score=21.24 Aligned_cols=53 Identities=23% Similarity=0.096 Sum_probs=33.6
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCc--ccce
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL--RKKV 76 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~--Kg~V 76 (125)
.|+.|..+.+.-+-=.-.++-|+..+.. .+.|..||.+-+.++...++. +|++
T Consensus 30 ~i~~gd~v~i~P~~~~~~V~sI~~~~~~-----~~~a~aG~~v~i~l~~i~~~~v~~G~v 84 (91)
T cd03693 30 VLKPGMVVTFAPAGVTGEVKSVEMHHEP-----LEEALPGDNVGFNVKNVSKKDIKRGDV 84 (91)
T ss_pred eeecCCEEEECCCCcEEEEEEEEECCcC-----cCEECCCCEEEEEECCCCHHHcCCcCE
Confidence 5678888888765323344555544322 267899999999998655431 4554
No 22
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=38.57 E-value=33 Score=23.74 Aligned_cols=20 Identities=45% Similarity=0.674 Sum_probs=18.3
Q ss_pred CCcccCCEEEEEEeecCCCc
Q 033177 53 PSACVGDMVMATVKKGKPDL 72 (125)
Q Consensus 53 ~~A~iGD~I~vsVKk~~p~~ 72 (125)
|.|..||.+.+.|++.+|+.
T Consensus 44 p~a~~Gd~V~vkI~~v~~~~ 63 (73)
T COG3269 44 PGAEVGDEVKVKITKVKPNF 63 (73)
T ss_pred CCCCCCCeeeEEEEEeeccc
Confidence 67999999999999999985
No 23
>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=35.31 E-value=93 Score=20.42 Aligned_cols=47 Identities=13% Similarity=0.063 Sum_probs=30.3
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCC
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p 70 (125)
.|+.|..+.+...--.-.++-|++.+. ....|..||.+-+.++.+.+
T Consensus 25 ~i~~G~~v~i~P~~~~~~V~si~~~~~-----~~~~a~aGd~v~l~l~~i~~ 71 (82)
T cd04089 25 TIKKGDKLLVMPNKTQVEVLSIYNEDV-----EVRYARPGENVRLRLKGIEE 71 (82)
T ss_pred EEecCCEEEEeCCCcEEEEEEEEECCE-----ECCEECCCCEEEEEecCCCH
Confidence 456777777776432334455554432 22679999999999986554
No 24
>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=34.85 E-value=1.4e+02 Score=19.78 Aligned_cols=44 Identities=18% Similarity=0.153 Sum_probs=30.5
Q ss_pred ccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEee
Q 033177 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK 67 (125)
Q Consensus 19 mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk 67 (125)
.++.|..+.+.+.--.-.++-|+..+.. .+.|..||.|-+.+++
T Consensus 26 ~v~~Gd~v~~~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~l~l~~ 69 (81)
T cd03695 26 SIRVGDEVVVLPSGKTSRVKSIETFDGE-----LDEAGAGESVTLTLED 69 (81)
T ss_pred eEECCCEEEEcCCCCeEEEEEEEECCcE-----eCEEcCCCEEEEEECC
Confidence 5677778888875333456666665422 2689999999999973
No 25
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=34.84 E-value=72 Score=25.11 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.4
Q ss_pred EecCceEEEEEcCCceEEEEE
Q 033177 97 YFEGNYSFCILFGSWLMLIHF 117 (125)
Q Consensus 97 ~F~dNAvVLin~~~~~~~~~~ 117 (125)
.|+++...++++++++|+.|=
T Consensus 36 ~~~~~~~~~v~~~~~~lIl~P 56 (209)
T PF08696_consen 36 EFDDDDPCIVDNDSNLLILHP 56 (209)
T ss_pred EeCCCCCEEEeCCCCEEEEcC
Confidence 788888888888888888883
No 26
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=28.62 E-value=1.6e+02 Score=18.67 Aligned_cols=29 Identities=10% Similarity=0.207 Sum_probs=21.3
Q ss_pred eeece--eeeCCCc-EEEecCceEEEEEcCCc
Q 033177 83 RQRKP--WRRKDGV-FMYFEGNYSFCILFGSW 111 (125)
Q Consensus 83 RtKk~--~~R~dG~-~I~F~dNAvVLin~~~~ 111 (125)
|+|+. ++-.||+ .+.|+|..=+++..+.-
T Consensus 2 ~~k~gi~~~LSng~vqv~FnD~tkivl~~~~~ 33 (68)
T PF00659_consen 2 RTKYGIGYQLSNGTVQVNFNDHTKIVLSPDGR 33 (68)
T ss_dssp EECSEEEEEETTSEEEEEETTS-EEEEETTCC
T ss_pred ccceEEEEEEeCCCEEEEEeCCCEEEECCCCC
Confidence 45555 3777887 58999999999987765
No 27
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=28.37 E-value=1.4e+02 Score=20.62 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=25.6
Q ss_pred EEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCccccee
Q 033177 25 TVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVM 77 (125)
Q Consensus 25 ~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V~ 77 (125)
.+.|-+..|...+ ..+.++++++ -.-+-||+|+|.--+-.++.|++|.
T Consensus 14 ~~~V~~~dG~~~l--~~iP~KfRk~---iWIkrGd~VlV~p~~~~~kvkgeIv 61 (78)
T cd05792 14 LHEVETPNGSRYL--VSMPTKFRKN---IWIKRGDFVLVEPIEEGDKVKAEIV 61 (78)
T ss_pred EEEEEcCCCCEEE--EEechhhccc---EEEEeCCEEEEEecccCCceEEEEE
Confidence 4445555554322 3334443332 4678999999975443333455544
No 28
>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=27.19 E-value=1.4e+02 Score=19.82 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=32.0
Q ss_pred ccccccEEEEecCC-C---cceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCC
Q 033177 19 GLPVAATVNCADNT-G---AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD 71 (125)
Q Consensus 19 mIq~~T~L~VaDNS-G---Ak~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~ 71 (125)
.+.+|..+.+...- | .-.++-|++.+.. ...|..||.+-+.++.+.++
T Consensus 26 ~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~-----~~~a~aGd~v~l~l~~i~~~ 77 (87)
T cd03694 26 VIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSP-----VRVVRAGQSASLALKKIDRS 77 (87)
T ss_pred EEeCCCEEEECCCCCCCEeEEEEEEEEECCeE-----CCEECCCCEEEEEEcCCCHH
Confidence 46677788877642 4 3355666654322 25799999999999776553
No 29
>PF11665 DUF3265: Protein of unknown function (DUF3265); InterPro: IPR021681 This family of proteins with unknown function appear to be restricted to Vibrio.
Probab=25.80 E-value=61 Score=18.53 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=7.3
Q ss_pred EEEEEEEEe
Q 033177 115 IHFVYCVIL 123 (125)
Q Consensus 115 ~~~~~~~~~ 123 (125)
-||.||+.+
T Consensus 4 whF~yal~f 12 (28)
T PF11665_consen 4 WHFYYALVF 12 (28)
T ss_pred EEEEEEEEE
Confidence 399999876
No 30
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=23.21 E-value=82 Score=23.31 Aligned_cols=25 Identities=24% Similarity=0.396 Sum_probs=18.1
Q ss_pred eecEEEEeeeceeeeCCCcEEEecCce
Q 033177 76 VMPAVIVRQRKPWRRKDGVFMYFEGNY 102 (125)
Q Consensus 76 V~kAVIVRtKk~~~R~dG~~I~F~dNA 102 (125)
-|+|+|+.+.. ...+...++|||+.
T Consensus 88 FY~A~V~~~p~--~~~~~y~l~Fedd~ 112 (130)
T PF07039_consen 88 FYPATVVSPPK--KKSGEYKLKFEDDE 112 (130)
T ss_dssp EEEEEEEEE-S--STTS-EEEEECTTT
T ss_pred EEEEEEEeCCC--CCCCcEEEEEeCCC
Confidence 68899999844 45566789999874
No 31
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=21.25 E-value=80 Score=19.55 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=13.7
Q ss_pred cCCEEEEEEeecCCCc-ccc
Q 033177 57 VGDMVMATVKKGKPDL-RKK 75 (125)
Q Consensus 57 iGD~I~vsVKk~~p~~-Kg~ 75 (125)
+||++.|-|.+..+.. +++
T Consensus 40 iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 40 IGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -TEEEEEEEEEE-SSEEEEE
T ss_pred CCCEEEEEEEEeeCCcEEEE
Confidence 7999999999888764 444
No 32
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=20.18 E-value=2.9e+02 Score=19.70 Aligned_cols=55 Identities=18% Similarity=0.083 Sum_probs=29.1
Q ss_pred eecccccccEEEEecCCCcceEEEEEEecCCccccCCCCcccCCEEEEEEeecCCCcccce
Q 033177 16 MSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKV 76 (125)
Q Consensus 16 ~~~mIq~~T~L~VaDNSGAk~v~cI~Vl~~~~r~~r~~~A~iGD~I~vsVKk~~p~~Kg~V 76 (125)
++.|+. +..+.|.+..|...+ .++-|+.++ .-.-..||.|+|+.-+...+.|++|
T Consensus 25 V~~~lG-~~~~~V~~~dG~~~l--a~i~GK~Rk---~iwI~~GD~VlVsp~d~~~~~kg~I 79 (99)
T TIGR00523 25 IEQMLG-AGRVKVRCLDGKTRL--GRIPGKLKK---RIWIREGDVVIVKPWEFQGDDKCDI 79 (99)
T ss_pred EEEEcC-CCEEEEEeCCCCEEE--EEEchhhcc---cEEecCCCEEEEEEccCCCCccEEE
Confidence 344444 335555544453322 233443332 2467899999998766554445443
Done!