Query 033152
Match_columns 126
No_of_seqs 103 out of 709
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:27:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033152.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033152hhsearch_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 1.2E-47 2.5E-52 288.0 12.8 123 4-126 3-139 (139)
2 PRK08571 rpl14p 50S ribosomal 100.0 9.9E-47 2.1E-51 280.9 11.9 116 11-126 3-132 (132)
3 TIGR03673 rpl14p_arch 50S ribo 100.0 1.7E-46 3.7E-51 279.3 11.7 116 11-126 2-131 (131)
4 COG0093 RplN Ribosomal protein 100.0 1.2E-45 2.7E-50 270.4 10.7 104 19-126 1-122 (122)
5 CHL00057 rpl14 ribosomal prote 100.0 8.3E-44 1.8E-48 262.1 10.4 104 19-126 1-122 (122)
6 PRK05483 rplN 50S ribosomal pr 100.0 1.6E-43 3.4E-48 260.5 11.0 104 19-126 1-122 (122)
7 TIGR01067 rplN_bact ribosomal 100.0 1.9E-43 4.2E-48 260.0 11.1 104 19-126 1-122 (122)
8 PF00238 Ribosomal_L14: Riboso 100.0 2.1E-41 4.5E-46 248.7 9.1 104 19-126 1-122 (122)
9 PTZ00320 ribosomal protein L14 100.0 2.9E-38 6.3E-43 245.5 11.0 117 4-126 44-188 (188)
10 KOG0901 60S ribosomal protein 100.0 3.4E-36 7.5E-41 226.9 11.1 126 1-126 1-145 (145)
11 KOG3441 Mitochondrial ribosoma 99.5 5.3E-14 1.1E-18 105.1 7.0 97 17-126 29-149 (149)
12 cd04497 hPOT1_OB1_like hPOT1_O 68.0 11 0.00025 27.5 4.4 39 23-63 38-77 (138)
13 TIGR01024 rplS_bact ribosomal 57.6 24 0.00052 25.8 4.5 35 52-86 16-51 (113)
14 PF01245 Ribosomal_L19: Riboso 55.4 35 0.00076 24.8 5.0 37 51-87 15-52 (113)
15 CHL00084 rpl19 ribosomal prote 54.1 28 0.00061 25.7 4.3 35 52-86 20-55 (117)
16 PRK05338 rplS 50S ribosomal pr 54.1 31 0.00066 25.4 4.5 35 52-86 16-51 (116)
17 cd03698 eRF3_II_like eRF3_II_l 46.1 50 0.0011 21.6 4.3 54 18-76 25-80 (83)
18 cd03696 selB_II selB_II: this 44.9 60 0.0013 21.2 4.5 49 17-70 24-72 (83)
19 cd03693 EF1_alpha_II EF1_alpha 42.5 65 0.0014 21.6 4.5 55 17-76 28-84 (91)
20 cd04089 eRF3_II eRF3_II: domai 38.1 82 0.0018 20.6 4.4 53 19-76 25-79 (82)
21 COG0335 RplS Ribosomal protein 37.9 65 0.0014 23.9 4.1 35 52-86 18-53 (115)
22 COG3269 Predicted RNA-binding 37.0 37 0.00081 23.2 2.5 20 53-72 44-63 (73)
23 cd03694 GTPBP_II Domain II of 35.1 91 0.002 20.7 4.3 49 18-71 25-77 (87)
24 cd03695 CysN_NodQ_II CysN_NodQ 30.2 1.6E+02 0.0035 19.3 5.3 45 18-67 25-69 (81)
25 PF02747 PCNA_C: Proliferating 26.7 1.7E+02 0.0038 20.8 4.8 72 54-125 25-99 (128)
26 KOG2449 Methylmalonate semiald 25.8 95 0.0021 24.1 3.4 45 60-105 66-118 (157)
27 cd05792 S1_eIF1AD_like S1_eIF1 23.9 2.3E+02 0.0051 19.3 4.7 26 53-78 37-62 (78)
28 PF01938 TRAM: TRAM domain; I 22.5 77 0.0017 19.5 2.0 20 57-76 40-60 (61)
No 1
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=1.2e-47 Score=287.96 Aligned_cols=123 Identities=81% Similarity=1.349 Sum_probs=114.1
Q ss_pred CCCCCCcccccccccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCcccceecEEEEe
Q 033152 4 RGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVR 83 (126)
Q Consensus 4 ~~~~~~~~~~~~~~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~Kg~v~~AvIVR 83 (126)
.+.|+..+.++++++|||.+|+|+|+|||||++++||++++.+++.+|+++|++||+|+||||++.|..|+|+++|||||
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 35677788999999999999999999999999999999998544455667999999999999999998899999999999
Q ss_pred eecceEecCCeEEEEc--------------ceEEecchhHHHHhhchhhhhcccccC
Q 033152 84 QRKPWRRKDGVFMYFE--------------GSAITGPIGKECADLWPRIASAANAIV 126 (126)
Q Consensus 84 tkk~~~R~dG~~i~F~--------------GTRI~GpV~~Elr~k~~Ki~sLA~~vv 126 (126)
||++++|+||++|+|| |||||||||+||+++|+||+|||++++
T Consensus 83 tKk~~rR~dGs~i~F~dNA~VLin~~~~p~GTRI~GpV~rEl~~~~~KI~SLA~~vi 139 (139)
T PTZ00054 83 QRKAWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGPVAKECADLWPKISSAAPAIV 139 (139)
T ss_pred ECcceEcCCCcEEEeCCcEEEEECCCCCEeeeEEeCchhHHHHhCccHhhccccccC
Confidence 9999999999999999 999999999999768999999999985
No 2
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=9.9e-47 Score=280.89 Aligned_cols=116 Identities=57% Similarity=0.930 Sum_probs=108.7
Q ss_pred ccccccccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCcccceecEEEEeeecceEe
Q 033152 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRR 90 (126)
Q Consensus 11 ~~~~~~~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~Kg~v~~AvIVRtkk~~~R 90 (126)
+.+++++.|||.+|+|+|+|||||++++||+++++.++.+|+++|++||+|+||||++.|..|+|+++|||||||++++|
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 46789999999999999999999999999999986555556678999999999999999988999999999999999999
Q ss_pred cCCeEEEEc--------------ceEEecchhHHHHhhchhhhhcccccC
Q 033152 91 KDGVFMYFE--------------GSAITGPIGKECADLWPRIASAANAIV 126 (126)
Q Consensus 91 ~dG~~i~F~--------------GTRI~GpV~~Elr~k~~Ki~sLA~~vv 126 (126)
+||++++|| |||||||||+||+++|+||+|||++++
T Consensus 83 ~dGs~i~F~dNa~VLin~~~~p~GTRI~GpV~~El~~~~~Ki~sLA~~vi 132 (132)
T PRK08571 83 PDGTRVKFEDNAAVIVTPEGTPKGTEIKGPVAREAAERWPKIASIASIIV 132 (132)
T ss_pred CCCcEEEeCCcEEEEECCCCCEeeeEEeccchHHHhhCCchheeccchhC
Confidence 999999999 999999999999778999999999875
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=1.7e-46 Score=279.33 Aligned_cols=116 Identities=54% Similarity=0.894 Sum_probs=108.3
Q ss_pred ccccccccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCcccceecEEEEeeecceEe
Q 033152 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRR 90 (126)
Q Consensus 11 ~~~~~~~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~Kg~v~~AvIVRtkk~~~R 90 (126)
..+++++.|||.+|+|+|+|||||++++||+++++++..+|+++|++||+|+||||++.|..|+|+++|||||||++++|
T Consensus 2 ~~~~~~~~mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk~~~R 81 (131)
T TIGR03673 2 GIRAGITRALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRKEYRR 81 (131)
T ss_pred CcccccceeeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCccccCCEeEEEEEEeCcceec
Confidence 35788999999999999999999999999999976555566689999999999999999988999999999999999999
Q ss_pred cCCeEEEEc--------------ceEEecchhHHHHhhchhhhhcccccC
Q 033152 91 KDGVFMYFE--------------GSAITGPIGKECADLWPRIASAANAIV 126 (126)
Q Consensus 91 ~dG~~i~F~--------------GTRI~GpV~~Elr~k~~Ki~sLA~~vv 126 (126)
+||++++|| |||||||||+||+++|+||+|||++++
T Consensus 82 ~dGs~i~FddNa~VLin~~~~P~GTRI~GpV~rEl~~~~~Ki~SlA~~vi 131 (131)
T TIGR03673 82 PDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVAREAAERWPKIASIASIIV 131 (131)
T ss_pred CCCcEEEeCCcEEEEECCCCCEeeeEEEccchHHHHhCccHheeccchhC
Confidence 999999999 999999999999667999999999985
No 4
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-45 Score=270.38 Aligned_cols=104 Identities=39% Similarity=0.631 Sum_probs=99.1
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC-c--ccceecEEEEeeecceEecCCeE
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD-L--RKKVMPAVIVRQRKPWRRKDGVF 95 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~-~--Kg~v~~AvIVRtkk~~~R~dG~~ 95 (126)
|||.+|+|+|||||||++++||+|+++++| .+|++||+|++|||++.|. . |||+++||||||+++++|+||++
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 899999999999999999999999988766 4999999999999999994 4 67999999999999999999999
Q ss_pred EEEc--------------ceEEecchhHHHHhh-chhhhhcccccC
Q 033152 96 MYFE--------------GSAITGPIGKECADL-WPRIASAANAIV 126 (126)
Q Consensus 96 i~F~--------------GTRI~GpV~~Elr~k-~~Ki~sLA~~vv 126 (126)
|+|| ||||||||++||+++ |+||+|||++|+
T Consensus 77 i~FddNA~Viin~~g~P~GtrI~GPVaRElr~~~~~kI~SlA~eVv 122 (122)
T COG0093 77 IKFDDNAAVIINPDGEPRGTRIFGPVARELRERGFMKIASLAPEVV 122 (122)
T ss_pred EEeCCceEEEECCCCCcccceEecchhHHHHhcCCceeeecceecC
Confidence 9999 999999999999997 999999999986
No 5
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=8.3e-44 Score=262.06 Aligned_cols=104 Identities=36% Similarity=0.623 Sum_probs=98.9
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCc---ccceecEEEEeeecceEecCCeE
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~---Kg~v~~AvIVRtkk~~~R~dG~~ 95 (126)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |+|+++|||||||++++|+||++
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 999999999999999999999999987655 69999999999999999975 88999999999999999999999
Q ss_pred EEEc--------------ceEEecchhHHHHhh-chhhhhcccccC
Q 033152 96 MYFE--------------GSAITGPIGKECADL-WPRIASAANAIV 126 (126)
Q Consensus 96 i~F~--------------GTRI~GpV~~Elr~k-~~Ki~sLA~~vv 126 (126)
++|| ||||+||||+|||++ |+||+|||++++
T Consensus 77 i~F~~Na~VLin~~~~p~GTrI~Gpv~~elr~k~~~Ki~sla~~vi 122 (122)
T CHL00057 77 IRFDDNAAVVIDQEGNPKGTRVFGPIARELREKNFTKIVSLAPEVL 122 (122)
T ss_pred EEcCCceEEEECCCCCEeEeEEEccchHHHhhcCCeEEEecccccC
Confidence 9999 999999999999975 999999999875
No 6
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=1.6e-43 Score=260.51 Aligned_cols=104 Identities=36% Similarity=0.581 Sum_probs=98.4
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCc---ccceecEEEEeeecceEecCCeE
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~---Kg~v~~AvIVRtkk~~~R~dG~~ 95 (126)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |||+++|||||||++++|+||++
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 999999999999999999999999986554 69999999999999999975 79999999999999999999999
Q ss_pred EEEc--------------ceEEecchhHHHHh-hchhhhhcccccC
Q 033152 96 MYFE--------------GSAITGPIGKECAD-LWPRIASAANAIV 126 (126)
Q Consensus 96 i~F~--------------GTRI~GpV~~Elr~-k~~Ki~sLA~~vv 126 (126)
++|| |||||||||+|||+ +|+||+|||++++
T Consensus 77 i~F~dNavVLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~v~ 122 (122)
T PRK05483 77 IRFDDNAAVLLNNDGEPRGTRIFGPVARELRDKKFMKIVSLAPEVL 122 (122)
T ss_pred EEcCCCEEEEECCCCCEeEeEEeccchHHHhhcCCcEEEecccccC
Confidence 9999 99999999999986 6999999999875
No 7
>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=1.9e-43 Score=259.98 Aligned_cols=104 Identities=38% Similarity=0.596 Sum_probs=98.5
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCc---ccceecEEEEeeecceEecCCeE
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~---Kg~v~~AvIVRtkk~~~R~dG~~ 95 (126)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |+|+++|||||||++++|+||++
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 999999999999999999999999986554 69999999999999999965 69999999999999999999999
Q ss_pred EEEc--------------ceEEecchhHHHHhh-chhhhhcccccC
Q 033152 96 MYFE--------------GSAITGPIGKECADL-WPRIASAANAIV 126 (126)
Q Consensus 96 i~F~--------------GTRI~GpV~~Elr~k-~~Ki~sLA~~vv 126 (126)
++|| |||||||||+|||++ |+||+|||++++
T Consensus 77 i~F~~Na~VLin~~~~p~GTrI~Gpv~~elr~~~~~Ki~sla~~i~ 122 (122)
T TIGR01067 77 IRFDDNACVLINKNKEPRGTRIFGPVARELRDKGFMKIVSLAPEVI 122 (122)
T ss_pred EECCCceEEEECCCCCEeeeEEEccchHHHhhcCCceeeeccchhC
Confidence 9999 999999999999885 999999999885
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=2.1e-41 Score=248.67 Aligned_cols=104 Identities=44% Similarity=0.712 Sum_probs=94.9
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC--c-ccceecEEEEeeecceEecCCeE
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD--L-RKKVMPAVIVRQRKPWRRKDGVF 95 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~--~-Kg~v~~AvIVRtkk~~~R~dG~~ 95 (126)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||+++|+ . |||+++|||||||++++|.||++
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 999999999999999999999999987654 7999999999999999664 4 67999999999999999999999
Q ss_pred EEEc--------------ceEEecchhHHHHh-hchhhhhcccccC
Q 033152 96 MYFE--------------GSAITGPIGKECAD-LWPRIASAANAIV 126 (126)
Q Consensus 96 i~F~--------------GTRI~GpV~~Elr~-k~~Ki~sLA~~vv 126 (126)
++|| ||||+||||+|||+ +|+||+|||+.||
T Consensus 77 i~F~~Na~VLln~~~~p~GtrI~Gpv~~elr~~~~~ki~sla~~iv 122 (122)
T PF00238_consen 77 IKFDDNAVVLLNKKGNPLGTRIFGPVPRELRKKKFPKILSLASRIV 122 (122)
T ss_dssp EEESSEEEEEEETTSSBSSSSBCSEEEHHHHHTTSHHHHHHSSCEE
T ss_pred EEeCCccEEEEcCCCCEeeeEEEeeehHHhhHcCCchHHhhccccC
Confidence 9999 99999999999986 5999999999875
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=2.9e-38 Score=245.48 Aligned_cols=117 Identities=19% Similarity=0.261 Sum_probs=99.8
Q ss_pred CCCCCCcccccccccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCE----EEEEEeeccC------Cc-
Q 033152 4 RGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDM----VMATVKKGKP------DL- 72 (126)
Q Consensus 4 ~~~~~~~~~~~~~~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~----I~vsVKk~~~------~~- 72 (126)
|.|-|..+..+.----..-||+|+|+||||||+++||+|+ +++ ++|++||+ |+||||++.| +.
T Consensus 44 ~~~~~~~~~~~~~~~~~~~qT~L~VaDNSGAK~V~CIkVl--~~r----r~A~IGDi~~~~IvVsVKka~P~~~~~~~~k 117 (188)
T PTZ00320 44 RSRWGTGAEGYGTGVPFSDQVKLHCVDNTNCKHVRLISKA--TAE----RFAHCRVFPAVAHRVSVQRFKSGRGEVSRHR 117 (188)
T ss_pred hhccccCccccccCCccCCCcEEEEEeCCCCcEEEEEEEe--cCC----CceeeccccCceEEEEEeecccCccccccCc
Confidence 3444444444443334567999999999999999999999 333 69999999 9999999999 32
Q ss_pred --ccceecEEEEeeecceEecCCeEEEEc--------------ceEEecchhHHHHhh-chhhhhcccccC
Q 033152 73 --RKKVMPAVIVRQRKPWRRKDGVFMYFE--------------GSAITGPIGKECADL-WPRIASAANAIV 126 (126)
Q Consensus 73 --Kg~v~~AvIVRtkk~~~R~dG~~i~F~--------------GTRI~GpV~~Elr~k-~~Ki~sLA~~vv 126 (126)
||||++|||||||++++|+||++|+|| ||||||||++|||++ |+||+|||+-++
T Consensus 118 VKKG~V~kAVIVRTKK~irR~DGs~IrFDdNAaVLIN~qgePlGTRIfGPVaRELR~k~f~KIvSLAp~~~ 188 (188)
T PTZ00320 118 VKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILMNDQRVPLGTRVMYCAGRHVNHKYHLKAVVLANFFV 188 (188)
T ss_pred eecCCEEEEEEEEECcccCCCCCCEEEeCCcEEEEECCCCCEeeeEEecchhHHHhhcCCceeeecccccC
Confidence 799999999999999999999999999 999999999999975 999999998764
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-36 Score=226.86 Aligned_cols=126 Identities=76% Similarity=1.205 Sum_probs=121.1
Q ss_pred CCCCCCCCCcccccccccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEee--ccCCcc---cc
Q 033152 1 MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK--GKPDLR---KK 75 (126)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk--~~~~~K---g~ 75 (126)
||++++||+...+|+++.|||.||.++|+||||||.++||.+.+.++|.||+++|.+||+++++||+ ..|+.+ ++
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 7999999999999999999999999999999999999999999999999999999999999999999 789874 57
Q ss_pred eecEEEEeeecceEecCCeEEEEc--------------ceEEecchhHHHHhhchhhhhcccccC
Q 033152 76 VMPAVIVRQRKPWRRKDGVFMYFE--------------GSAITGPIGKECADLWPRIASAANAIV 126 (126)
Q Consensus 76 v~~AvIVRtkk~~~R~dG~~i~F~--------------GTRI~GpV~~Elr~k~~Ki~sLA~~vv 126 (126)
++.|+|||+++++.|.||+++.|+ ||+|+|||++|++..|++|+|+|+.++
T Consensus 81 ~~~avvVr~~k~~~r~dgs~~~f~dnA~v~~~~~~e~~gs~i~G~v~~e~~~~~~kias~A~~i~ 145 (145)
T KOG0901|consen 81 VLPAVVVRQKKSKRRKDGSIAYFEDNAGVIVNNKGEPKGSAITGPVGKELADLWPKIASLAGLVV 145 (145)
T ss_pred cceeeEEeeccccccCCCcEEEEcCceEEEEcccCccccceeccccChhHhhhhHHHHhhccccC
Confidence 799999999999999999999999 999999999999999999999998764
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.50 E-value=5.3e-14 Score=105.12 Aligned_cols=97 Identities=19% Similarity=0.293 Sum_probs=79.1
Q ss_pred ccCcccccEEEEecCCC--------cceEEEEEEecccccccCCCCCccCCEEEEEEeeccCCcccceecEEEEeeecce
Q 033152 17 SLGLPVAATVNCADNTG--------AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPW 88 (126)
Q Consensus 17 ~~mIq~~T~L~VaDNSG--------ak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~~Kg~v~~AvIVRtkk~~ 88 (126)
...|++.|+|+|+|||. .+.-+||+||++. ..+.+||.|+|.| |||+.+|+||.-....
T Consensus 29 ~~~I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkr------gvg~~GDkiLvAI-------kGQmkKa~vVGh~~~~ 95 (149)
T KOG3441|consen 29 LMGIHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKR------GVGELGDKILVAI-------KGQMKKAYVVGHVHYR 95 (149)
T ss_pred HHhhhhhheEEEecchhhcccccccCCCCceEEEEecc------cccccccEEEEEE-------ecceeeeEEEEeeccC
Confidence 45799999999999997 4888999999733 5899999999999 8999999999865432
Q ss_pred ----EecCC-eEEEEc------ceEEecchhHHHHh-----hchhhhhcccccC
Q 033152 89 ----RRKDG-VFMYFE------GSAITGPIGKECAD-----LWPRIASAANAIV 126 (126)
Q Consensus 89 ----~R~dG-~~i~F~------GTRI~GpV~~Elr~-----k~~Ki~sLA~~vv 126 (126)
.+.|. ..+..| ||||.-|||-.||. .|.|++.+|+.+|
T Consensus 96 k~~~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 96 KHGVPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRANRGNVQYSKVLAIANKFV 149 (149)
T ss_pred CCCCcccCCCcEEEECCCCCcccceEeccCcHHHHhccCCcchhhHHHHHhhcC
Confidence 33333 334444 99999999999983 3999999999875
No 12
>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=68.00 E-value=11 Score=27.46 Aligned_cols=39 Identities=21% Similarity=0.273 Sum_probs=28.7
Q ss_pred ccEEEEecCCCc-ceEEEEEEecccccccCCCCCccCCEEEE
Q 033152 23 AATVNCADNTGA-KNLYIISVKGIKGRLNRLPSACVGDMVMA 63 (126)
Q Consensus 23 ~T~L~VaDNSGa-k~v~cI~v~~~~~r~~r~~~a~vGD~I~v 63 (126)
...|.++|-|++ ...-++++++.. ...+|...+||+|.+
T Consensus 38 ~~tl~i~D~S~~~~~~l~v~~F~~~--~~~LP~v~~GDVIll 77 (138)
T cd04497 38 CCTLTITDPSLANSDGLTVKLFRPN--EESLPIVKVGDIILL 77 (138)
T ss_pred EEEEEEECCCCCCCCcEEEEEECCC--hhhCCCCCCCCEEEE
Confidence 356899999998 445666677643 345687799999975
No 13
>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=57.58 E-value=24 Score=25.83 Aligned_cols=35 Identities=34% Similarity=0.429 Sum_probs=28.5
Q ss_pred CCCCccCCEEEEEEeeccC-CcccceecEEEEeeec
Q 033152 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (126)
Q Consensus 52 ~~~a~vGD~I~vsVKk~~~-~~Kg~v~~AvIVRtkk 86 (126)
+|.-.+||+|.|.++-... +-+-|.|.++|+..+.
T Consensus 16 ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~ 51 (113)
T TIGR01024 16 LPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRG 51 (113)
T ss_pred CCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeC
Confidence 5778899999999987654 3477999999998874
No 14
>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=55.41 E-value=35 Score=24.81 Aligned_cols=37 Identities=30% Similarity=0.433 Sum_probs=30.0
Q ss_pred CCCCCccCCEEEEEEeeccC-CcccceecEEEEeeecc
Q 033152 51 RLPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRKP 87 (126)
Q Consensus 51 r~~~a~vGD~I~vsVKk~~~-~~Kg~v~~AvIVRtkk~ 87 (126)
..|.-.+||+|.|.++.... +.+-|.|.++++.-+..
T Consensus 15 ~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 15 DIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS
T ss_pred CCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC
Confidence 45788999999999987744 45779999999987763
No 15
>CHL00084 rpl19 ribosomal protein L19
Probab=54.14 E-value=28 Score=25.68 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=27.8
Q ss_pred CCCCccCCEEEEEEeeccCC-cccceecEEEEeeec
Q 033152 52 LPSACVGDMVMATVKKGKPD-LRKKVMPAVIVRQRK 86 (126)
Q Consensus 52 ~~~a~vGD~I~vsVKk~~~~-~Kg~v~~AvIVRtkk 86 (126)
.|.-.+||+|.|.++-...+ .+-|.|.++|+..+.
T Consensus 20 ~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~ 55 (117)
T CHL00084 20 LPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKN 55 (117)
T ss_pred CCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeC
Confidence 47788999999999665543 477999999998653
No 16
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=54.05 E-value=31 Score=25.41 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=27.9
Q ss_pred CCCCccCCEEEEEEeeccC-CcccceecEEEEeeec
Q 033152 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (126)
Q Consensus 52 ~~~a~vGD~I~vsVKk~~~-~~Kg~v~~AvIVRtkk 86 (126)
+|.-.+||+|.|.++-... +-+-|.|.++|+..+.
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 4778899999999876554 3477999999998773
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=46.10 E-value=50 Score=21.63 Aligned_cols=54 Identities=15% Similarity=0.102 Sum_probs=35.8
Q ss_pred cCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC-c-ccce
Q 033152 18 LGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD-L-RKKV 76 (126)
Q Consensus 18 ~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~-~-Kg~v 76 (126)
=.|++|..+.+.-+.-.-.++-|+..... ...|..||.+-+.++...++ + +|++
T Consensus 25 G~i~~Gd~v~i~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~~~l~~~~~~~v~~G~v 80 (83)
T cd03698 25 GSIQKGDTLLVMPSKESVEVKSIYVDDEE-----VDYAVAGENVRLKLKGIDEEDISPGDV 80 (83)
T ss_pred eEEeCCCEEEEeCCCcEEEEEEEEECCeE-----CCEECCCCEEEEEECCCCHHHCCCCCE
Confidence 34678888888775434456666665422 26899999999999865542 2 5554
No 18
>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=44.89 E-value=60 Score=21.17 Aligned_cols=49 Identities=20% Similarity=0.149 Sum_probs=32.8
Q ss_pred ccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccC
Q 033152 17 SLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (126)
Q Consensus 17 ~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~ 70 (126)
+=.|+++..+.+.++--.-.++=|+.... ..+.|..||.|-+.++...+
T Consensus 24 sG~i~~g~~v~~~p~~~~~~V~sI~~~~~-----~~~~a~aGd~v~i~l~~~~~ 72 (83)
T cd03696 24 SGSVKVGDKVEILPLGEETRVRSIQVHGK-----DVEEAKAGDRVALNLTGVDA 72 (83)
T ss_pred ecEEeCCCEEEECCCCceEEEEEEEECCc-----CcCEEcCCCEEEEEEcCCCH
Confidence 44578999999988543333444444321 23689999999999976654
No 19
>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=42.54 E-value=65 Score=21.58 Aligned_cols=55 Identities=22% Similarity=0.116 Sum_probs=36.6
Q ss_pred ccCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC-c-ccce
Q 033152 17 SLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD-L-RKKV 76 (126)
Q Consensus 17 ~~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~-~-Kg~v 76 (126)
+=.|+.|..+.+.-+-=.-.++-|+..+.. ...|..||.+-+.++...++ + +|++
T Consensus 28 ~G~i~~gd~v~i~P~~~~~~V~sI~~~~~~-----~~~a~aG~~v~i~l~~i~~~~v~~G~v 84 (91)
T cd03693 28 TGVLKPGMVVTFAPAGVTGEVKSVEMHHEP-----LEEALPGDNVGFNVKNVSKKDIKRGDV 84 (91)
T ss_pred cceeecCCEEEECCCCcEEEEEEEEECCcC-----cCEECCCCEEEEEECCCCHHHcCCcCE
Confidence 445688888888875334456666665432 25899999999999876553 2 5554
No 20
>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=38.07 E-value=82 Score=20.59 Aligned_cols=53 Identities=13% Similarity=0.083 Sum_probs=34.5
Q ss_pred CcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC-c-ccce
Q 033152 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD-L-RKKV 76 (126)
Q Consensus 19 mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~-~-Kg~v 76 (126)
.|+.|..+.+...--.-.++-|++.+.. ...|..||.+-+.++.+.++ + +|++
T Consensus 25 ~i~~G~~v~i~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~l~l~~i~~~~v~~G~v 79 (82)
T cd04089 25 TIKKGDKLLVMPNKTQVEVLSIYNEDVE-----VRYARPGENVRLRLKGIEEEDISPGFV 79 (82)
T ss_pred EEecCCEEEEeCCCcEEEEEEEEECCEE-----CCEECCCCEEEEEecCCCHHHCCCCCE
Confidence 3577777877775333445666655422 26899999999999866553 2 5554
No 21
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=37.89 E-value=65 Score=23.86 Aligned_cols=35 Identities=29% Similarity=0.357 Sum_probs=28.2
Q ss_pred CCCCccCCEEEEEEeeccCC-cccceecEEEEeeec
Q 033152 52 LPSACVGDMVMATVKKGKPD-LRKKVMPAVIVRQRK 86 (126)
Q Consensus 52 ~~~a~vGD~I~vsVKk~~~~-~Kg~v~~AvIVRtkk 86 (126)
.|.-.+||+|.|.||-...+ .+-|.|.++|++-+.
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 46667999999999877764 377999999998664
No 22
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=36.96 E-value=37 Score=23.23 Aligned_cols=20 Identities=45% Similarity=0.674 Sum_probs=18.2
Q ss_pred CCCccCCEEEEEEeeccCCc
Q 033152 53 PSACVGDMVMATVKKGKPDL 72 (126)
Q Consensus 53 ~~a~vGD~I~vsVKk~~~~~ 72 (126)
|-|..||.+.+.|++.+++.
T Consensus 44 p~a~~Gd~V~vkI~~v~~~~ 63 (73)
T COG3269 44 PGAEVGDEVKVKITKVKPNF 63 (73)
T ss_pred CCCCCCCeeeEEEEEeeccc
Confidence 67899999999999999986
No 23
>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=35.08 E-value=91 Score=20.71 Aligned_cols=49 Identities=12% Similarity=0.048 Sum_probs=34.2
Q ss_pred cCcccccEEEEecCC-C---cceEEEEEEecccccccCCCCCccCCEEEEEEeeccCC
Q 033152 18 LGLPVAATVNCADNT-G---AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD 71 (126)
Q Consensus 18 ~mIq~~T~L~VaDNS-G---ak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk~~~~ 71 (126)
=.++++..|.+...- | .-.++-|++.+.. ...|..||.+-+.++.+.++
T Consensus 25 G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~-----~~~a~aGd~v~l~l~~i~~~ 77 (87)
T cd03694 25 GVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSP-----VRVVRAGQSASLALKKIDRS 77 (87)
T ss_pred CEEeCCCEEEECCCCCCCEeEEEEEEEEECCeE-----CCEECCCCEEEEEEcCCCHH
Confidence 346778888887742 4 4466777765432 25899999999999776653
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=30.24 E-value=1.6e+02 Score=19.28 Aligned_cols=45 Identities=18% Similarity=0.117 Sum_probs=32.2
Q ss_pred cCcccccEEEEecCCCcceEEEEEEecccccccCCCCCccCCEEEEEEee
Q 033152 18 LGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK 67 (126)
Q Consensus 18 ~mIq~~T~L~VaDNSGak~v~cI~v~~~~~r~~r~~~a~vGD~I~vsVKk 67 (126)
=.++.|..+.+.+.--.-.++-|+..... .+.|..||.|-+.++.
T Consensus 25 G~v~~Gd~v~~~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~l~l~~ 69 (81)
T cd03695 25 GSIRVGDEVVVLPSGKTSRVKSIETFDGE-----LDEAGAGESVTLTLED 69 (81)
T ss_pred ceEECCCEEEEcCCCCeEEEEEEEECCcE-----eCEEcCCCEEEEEECC
Confidence 34678888888875434457777766432 2689999999999973
No 25
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=26.67 E-value=1.7e+02 Score=20.77 Aligned_cols=72 Identities=13% Similarity=0.172 Sum_probs=40.7
Q ss_pred CCccCCEEEEEEeeccCC--cccceecEEEEeeecceEecCCeEEEEc-ceEEecchhHHHHhhchhhhhccccc
Q 033152 54 SACVGDMVMATVKKGKPD--LRKKVMPAVIVRQRKPWRRKDGVFMYFE-GSAITGPIGKECADLWPRIASAANAI 125 (126)
Q Consensus 54 ~a~vGD~I~vsVKk~~~~--~Kg~v~~AvIVRtkk~~~R~dG~~i~F~-GTRI~GpV~~Elr~k~~Ki~sLA~~v 125 (126)
...+||.|.+.+.+-.-. .+|+.-.|=|.-........+...+.++ ...+..-.+-+--..|.|..+||..|
T Consensus 25 l~~v~d~v~i~~~~~~~~f~~~Gd~~~~~v~~~~~~~~~~~~~~~~i~~~~~~~~~fsl~YL~~~~Ka~~ls~~V 99 (128)
T PF02747_consen 25 LSSVGDTVTISADKDSVIFSAEGDIGSAEVEFKETESSEDDEELIEIEVKEPVSSSFSLDYLNDFSKAAPLSDEV 99 (128)
T ss_dssp HHTTCSEEEEEEETTEEEEEEEESSEEEEEEEEEEEEETTCTCESEEEESSEEEEEEEHHHHHHHGGGGGTTSEE
T ss_pred HHhcCCEEEEEEeCCEEEEEEEeccCcEEEEEeeccccccccccceeeeccceeeEEeHHHHHhhhccccCCceE
Confidence 357999998888543322 2778777655443333333444444444 22344444434444688888887654
No 26
>KOG2449 consensus Methylmalonate semialdehyde dehydrogenase [Amino acid transport and metabolism; Carbohydrate transport and metabolism]
Probab=25.76 E-value=95 Score=24.12 Aligned_cols=45 Identities=24% Similarity=0.423 Sum_probs=33.3
Q ss_pred EEEEEEeeccCCc---ccceecEEEEeeecceEecCCeEEEEc-----ceEEec
Q 033152 60 MVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVFMYFE-----GSAITG 105 (126)
Q Consensus 60 ~I~vsVKk~~~~~---Kg~v~~AvIVRtkk~~~R~dG~~i~F~-----GTRI~G 105 (126)
++.-.|-...|++ +.||+..|.|+-..+. -.|+..|.|+ ||-||-
T Consensus 66 f~~~tiLsvtP~ms~ykeeI~gpVlv~l~~~t-ldd~I~Iin~nPygn~t~i~T 118 (157)
T KOG2449|consen 66 FVGPTILSVTPNMSCYKEEIFGPVLVRLETET-LDDAIFIINNNPYGNGTAIFT 118 (157)
T ss_pred cccceEEEecCCcceeHhhhhcceEEEEeecC-CCceeEEEecCCCCceeEEEe
Confidence 3333443467886 8899999999987664 4688999999 887773
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=23.88 E-value=2.3e+02 Score=19.27 Aligned_cols=26 Identities=12% Similarity=0.158 Sum_probs=16.4
Q ss_pred CCCccCCEEEEEEeeccCCcccceec
Q 033152 53 PSACVGDMVMATVKKGKPDLRKKVMP 78 (126)
Q Consensus 53 ~~a~vGD~I~vsVKk~~~~~Kg~v~~ 78 (126)
-.-+-||+|+|.--+-..+.|++|.+
T Consensus 37 iWIkrGd~VlV~p~~~~~kvkgeIv~ 62 (78)
T cd05792 37 IWIKRGDFVLVEPIEEGDKVKAEIVK 62 (78)
T ss_pred EEEEeCCEEEEEecccCCceEEEEEE
Confidence 46788999999754433344555543
No 28
>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=22.47 E-value=77 Score=19.51 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=14.2
Q ss_pred cCCEEEEEEeeccCCc-ccce
Q 033152 57 VGDMVMATVKKGKPDL-RKKV 76 (126)
Q Consensus 57 vGD~I~vsVKk~~~~~-Kg~v 76 (126)
+||++.|-|.+..+.. .+++
T Consensus 40 iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 40 IGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCEEEEEEEEeeCCcEEEEE
Confidence 7999999999888764 5543
Done!