Query 032476
Match_columns 140
No_of_seqs 113 out of 771
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 14:34:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032476hhsearch_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-55 2.5E-60 336.4 15.0 137 4-140 3-139 (139)
2 PRK08571 rpl14p 50S ribosomal 100.0 6E-55 1.3E-59 330.1 14.2 130 11-140 3-132 (132)
3 TIGR03673 rpl14p_arch 50S ribo 100.0 9.2E-55 2E-59 328.8 14.0 130 11-140 2-131 (131)
4 COG0093 RplN Ribosomal protein 100.0 3.5E-53 7.5E-58 314.5 12.5 118 19-140 1-122 (122)
5 CHL00057 rpl14 ribosomal prote 100.0 5.6E-52 1.2E-56 310.3 12.8 118 19-140 1-122 (122)
6 PRK05483 rplN 50S ribosomal pr 100.0 8E-52 1.7E-56 309.4 13.3 118 19-140 1-122 (122)
7 TIGR01067 rplN_bact ribosomal 100.0 1.7E-51 3.6E-56 307.7 13.5 118 19-140 1-122 (122)
8 PF00238 Ribosomal_L14: Riboso 100.0 1.2E-49 2.5E-54 297.3 10.0 118 19-140 1-122 (122)
9 PTZ00320 ribosomal protein L14 100.0 2E-46 4.4E-51 295.3 13.5 132 3-140 43-188 (188)
10 KOG0901 60S ribosomal protein 100.0 8E-41 1.7E-45 255.8 12.7 140 1-140 1-145 (145)
11 KOG3441 Mitochondrial ribosoma 99.9 2.4E-25 5.3E-30 167.8 7.7 108 17-140 29-149 (149)
12 PF08447 PAS_3: PAS fold; Int 55.6 19 0.00041 23.1 3.4 32 83-114 55-86 (91)
13 TIGR01024 rplS_bact ribosomal 53.2 29 0.00062 25.9 4.3 35 52-86 16-51 (113)
14 PF01245 Ribosomal_L19: Riboso 52.0 42 0.0009 24.8 5.0 36 51-86 15-51 (113)
15 PF10382 DUF2439: Protein of u 50.3 34 0.00074 23.7 4.1 29 90-119 19-49 (83)
16 PF02721 DUF223: Domain of unk 49.8 15 0.00032 25.4 2.3 28 103-134 2-29 (95)
17 cd04497 hPOT1_OB1_like hPOT1_O 49.5 34 0.00073 25.4 4.3 40 23-64 38-78 (138)
18 CHL00084 rpl19 ribosomal prote 48.1 39 0.00085 25.3 4.4 34 52-85 20-54 (117)
19 PRK05338 rplS 50S ribosomal pr 46.2 46 0.001 24.9 4.5 35 52-86 16-51 (116)
20 cd03696 selB_II selB_II: this 40.1 71 0.0015 21.2 4.4 49 17-70 24-72 (83)
21 cd04480 RPA1_DBD_A_like RPA1_D 38.6 66 0.0014 21.5 4.0 30 101-134 21-50 (86)
22 cd03698 eRF3_II_like eRF3_II_l 38.2 71 0.0015 21.3 4.1 48 18-70 25-72 (83)
23 cd03693 EF1_alpha_II EF1_alpha 36.6 78 0.0017 21.6 4.2 49 17-70 28-76 (91)
24 cd03695 CysN_NodQ_II CysN_NodQ 33.1 1.5E+02 0.0033 19.8 5.3 45 18-67 25-69 (81)
25 PF09353 DUF1995: Domain of un 32.5 31 0.00067 27.2 1.8 30 101-130 124-153 (209)
26 cd04089 eRF3_II eRF3_II: domai 30.9 1.1E+02 0.0024 20.3 4.2 47 19-70 25-71 (82)
27 COG0335 RplS Ribosomal protein 30.5 95 0.002 23.4 4.0 35 52-86 18-53 (115)
28 PF03864 Phage_cap_E: Phage ma 28.7 1.6E+02 0.0034 24.0 5.4 46 77-124 233-281 (329)
29 PRK13149 H/ACA RNA-protein com 26.2 56 0.0012 22.1 2.0 26 95-123 23-50 (73)
30 cd03694 GTPBP_II Domain II of 25.8 1.5E+02 0.0032 20.1 4.1 49 17-70 24-76 (87)
31 COG3269 Predicted RNA-binding 24.3 75 0.0016 22.1 2.4 20 53-72 44-63 (73)
32 COG4959 TraF Type IV secretory 20.6 1E+02 0.0022 24.7 2.7 38 87-125 122-160 (173)
33 PF04773 FecR: FecR protein; 20.1 2.3E+02 0.0049 18.6 4.1 29 86-114 11-39 (98)
No 1
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=1.2e-55 Score=336.36 Aligned_cols=137 Identities=83% Similarity=1.359 Sum_probs=128.7
Q ss_pred CCCCCCCccccccccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCCccceeeEEEEe
Q 032476 4 RGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVR 83 (140)
Q Consensus 4 ~~~~~~~~~~~~~~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~Kg~v~~AvIVr 83 (140)
.+.|+..+.++++++|||.+|+|+|+|||||++++||++++.+++.+++++|++||+|+||||++.|..|+|+++|||||
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 46778889999999999999999999999999999999998544555667899999999999999998899999999999
Q ss_pred eeceeeecCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHhhhhhhhhcccccC
Q 032476 84 QRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV 140 (140)
Q Consensus 84 tkk~~~R~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~slA~~iv 140 (140)
||++++|+||++++||||||||+|++++|+|||||||||+||+++|+||+|||++++
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 999999999999999999999999999999999999999999778999999999875
No 2
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=6e-55 Score=330.11 Aligned_cols=130 Identities=58% Similarity=0.929 Sum_probs=122.7
Q ss_pred ccccccccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCCccceeeEEEEeeeceeee
Q 032476 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRR 90 (140)
Q Consensus 11 ~~~~~~~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~Kg~v~~AvIVrtkk~~~R 90 (140)
+.++++++|||.+|+|+|+|||||++++||+++++.++.+++++|.+||+|+||||++.|..|+|+++|||||||++++|
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 56889999999999999999999999999999986555556678999999999999999988999999999999999999
Q ss_pred cCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHhhhhhhhhcccccC
Q 032476 91 KDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV 140 (140)
Q Consensus 91 ~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~slA~~iv 140 (140)
+||++++|||||+||+|++++|+||||+||||+||+++|+||+|||+.++
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 99999999999999999999999999999999999778999999999875
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=9.2e-55 Score=328.75 Aligned_cols=130 Identities=56% Similarity=0.895 Sum_probs=122.5
Q ss_pred ccccccccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCCccceeeEEEEeeeceeee
Q 032476 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRR 90 (140)
Q Consensus 11 ~~~~~~~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~Kg~v~~AvIVrtkk~~~R 90 (140)
+.+++++.|||.+|+|+|+|||||++++||+++++++.++++++|.+||+|+||||++.|..|+|+++|||||||++++|
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 35789999999999999999999999999999976555566678999999999999999988999999999999999999
Q ss_pred cCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHhhhhhhhhcccccC
Q 032476 91 KDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV 140 (140)
Q Consensus 91 ~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~slA~~iv 140 (140)
+||++++|||||+||+|++++|+|||||||||+||+++|+||+|||++++
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 99999999999999999999999999999999999778999999999875
No 4
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-53 Score=314.54 Aligned_cols=118 Identities=42% Similarity=0.681 Sum_probs=112.6
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCC-C--ccceeeEEEEeeeceeeecCCcE
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD-L--RKKVMPAVIVRQRKPWRRKDGVF 95 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~-~--Kg~v~~AvIVrtkk~~~R~dG~~ 95 (140)
|||.+|+|+|+|||||++++||+|+++++| .+|++||+|++|||++.|. . |||+++||||||+++++|+||++
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 899999999999999999999999987655 4999999999999999994 3 68999999999999999999999
Q ss_pred EEecCceEEEECCCCCeeeeEEechhhHHHHhh-hhhhhhcccccC
Q 032476 96 MYFEDNAGVIVNPKGEMKGSAITGPIGKECADL-WPRIASAANAIV 140 (140)
Q Consensus 96 i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~k-~~Ki~slA~~iv 140 (140)
|+||||||||+|++++|+||||||||++|||++ |+||+|||++++
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 999999999999999999999999999999996 999999999985
No 5
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=5.6e-52 Score=310.32 Aligned_cols=118 Identities=36% Similarity=0.638 Sum_probs=112.5
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCC---ccceeeEEEEeeeceeeecCCcE
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~---Kg~v~~AvIVrtkk~~~R~dG~~ 95 (140)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |||+++|||||||++++|+||++
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 899999999999999999999999986544 68999999999999999975 78999999999999999999999
Q ss_pred EEecCceEEEECCCCCeeeeEEechhhHHHHh-hhhhhhhcccccC
Q 032476 96 MYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-LWPRIASAANAIV 140 (140)
Q Consensus 96 i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-k~~Ki~slA~~iv 140 (140)
++|||||+||+|++++|+||||+||||+|||+ +|+||+|||+.++
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 99999999999999999999999999999987 5999999999875
No 6
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=8e-52 Score=309.44 Aligned_cols=118 Identities=37% Similarity=0.606 Sum_probs=112.1
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCC---ccceeeEEEEeeeceeeecCCcE
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~---Kg~v~~AvIVrtkk~~~R~dG~~ 95 (140)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||++.|+. |||+++|||||||++++|+||++
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 899999999999999999999999985544 58999999999999999975 79999999999999999999999
Q ss_pred EEecCceEEEECCCCCeeeeEEechhhHHHHh-hhhhhhhcccccC
Q 032476 96 MYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-LWPRIASAANAIV 140 (140)
Q Consensus 96 i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-k~~Ki~slA~~iv 140 (140)
++|||||+||+|++++|+||||+||||+|||+ +|+||+|||+.++
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 99999999999999999999999999999986 7999999999875
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=1.7e-51 Score=307.67 Aligned_cols=118 Identities=39% Similarity=0.590 Sum_probs=112.1
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCC---ccceeeEEEEeeeceeeecCCcE
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~---Kg~v~~AvIVrtkk~~~R~dG~~ 95 (140)
|||.+|+|+|+|||||++++||++|+++++ ++|.+||+|+||||++.|+. |+|+++|||||||++++|+||++
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 899999999999999999999999985544 68999999999999999975 69999999999999999999999
Q ss_pred EEecCceEEEECCCCCeeeeEEechhhHHHHh-hhhhhhhcccccC
Q 032476 96 MYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-LWPRIASAANAIV 140 (140)
Q Consensus 96 i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-k~~Ki~slA~~iv 140 (140)
++|||||+||+|++++|+||||+||||+|||+ +|+||+|||+.++
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 99999999999999999999999999999988 5999999999875
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=1.2e-49 Score=297.27 Aligned_cols=118 Identities=45% Similarity=0.687 Sum_probs=108.7
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCC---ccceeeEEEEeeeceeeecCCcE
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVRQRKPWRRKDGVF 95 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~---Kg~v~~AvIVrtkk~~~R~dG~~ 95 (140)
|||.+|+|+|+|||||++++||++++++++ ++|++||+|+||||+++|+. |||+++|||||||++++|.||++
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 999999999999999999999999986543 79999999999999996653 67999999999999999999999
Q ss_pred EEecCceEEEECCCCCeeeeEEechhhHHHHh-hhhhhhhcccccC
Q 032476 96 MYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-LWPRIASAANAIV 140 (140)
Q Consensus 96 i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-k~~Ki~slA~~iv 140 (140)
++|||||+||+|++++|+||||+||||+|||+ +|+||+|||+.||
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 99999999999999999999999999999986 7999999999875
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=2e-46 Score=295.32 Aligned_cols=132 Identities=18% Similarity=0.246 Sum_probs=115.6
Q ss_pred CCCCCCCCccccccccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCce----EEEEEeecCC------CC
Q 032476 3 KRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDM----VMATVKKGKP------DL 72 (140)
Q Consensus 3 ~~~~~~~~~~~~~~~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~----I~vsVKk~~~------~~ 72 (140)
-|.|-|..+..+.----..-||+|+|+|||||++++||+|+. ++ ++|.+||+ |+||||++.| +.
T Consensus 43 ~~~~~~~~~~~~~~~~~~~~qT~L~VaDNSGAK~V~CIkVl~--~r----r~A~IGDi~~~~IvVsVKka~P~~~~~~~~ 116 (188)
T PTZ00320 43 YRSRWGTGAEGYGTGVPFSDQVKLHCVDNTNCKHVRLISKAT--AE----RFAHCRVFPAVAHRVSVQRFKSGRGEVSRH 116 (188)
T ss_pred hhhccccCccccccCCccCCCcEEEEEeCCCCcEEEEEEEec--CC----CceeeccccCceEEEEEeecccCccccccC
Confidence 344555555555444445679999999999999999999992 22 59999999 9999999999 22
Q ss_pred ---ccceeeEEEEeeeceeeecCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHh-hhhhhhhcccccC
Q 032476 73 ---RKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-LWPRIASAANAIV 140 (140)
Q Consensus 73 ---Kg~v~~AvIVrtkk~~~R~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-k~~Ki~slA~~iv 140 (140)
||||++|||||||++++|+||++++||||||||+|++++|+||||||||++|||+ +|+||+|||+-++
T Consensus 117 kVKKG~V~kAVIVRTKK~irR~DGs~IrFDdNAaVLIN~qgePlGTRIfGPVaRELR~k~f~KIvSLAp~~~ 188 (188)
T PTZ00320 117 RVKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILMNDQRVPLGTRVMYCAGRHVNHKYHLKAVVLANFFV 188 (188)
T ss_pred ceecCCEEEEEEEEECcccCCCCCCEEEeCCcEEEEECCCCCEeeeEEecchhHHHhhcCCceeeecccccC
Confidence 7999999999999999999999999999999999999999999999999999997 6999999999765
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8e-41 Score=255.76 Aligned_cols=140 Identities=77% Similarity=1.193 Sum_probs=134.8
Q ss_pred CCCCCCCCCCccccccccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEee--cCCCCc---cc
Q 032476 1 MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK--GKPDLR---KK 75 (140)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk--~~~~~K---g~ 75 (140)
||++++||++..+|+++.|||.||.++|+|||||+.++||.+.+.+++.||++.|.+||+++++||+ ..|+.+ ++
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 788874 46
Q ss_pred eeeEEEEeeeceeeecCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHhhhhhhhhcccccC
Q 032476 76 VMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV 140 (140)
Q Consensus 76 v~~AvIVrtkk~~~R~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~slA~~iv 140 (140)
++.|+|||++++..|.||+++.|+|||+|++|++++|.||+|+|||++|++..|++|+|+|+.++
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 79999999999999999999999999999999999999999999999999999999999998764
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.4e-25 Score=167.84 Aligned_cols=108 Identities=21% Similarity=0.348 Sum_probs=95.6
Q ss_pred ccCcccccEEEEecCCC--------CceEEEEEEeccccccCCCCCcccCceEEEEEeecCCCCccceeeEEEEeeecee
Q 032476 17 SLGLPVAATVNCADNTG--------AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPW 88 (140)
Q Consensus 17 ~~mIq~~T~L~V~DNSG--------ak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~~~Kg~v~~AvIVrtkk~~ 88 (140)
.+.|++.|+|+|+|||. .+..+|||||+.. ..+.+||.|+|+|| ||..+|+||......
T Consensus 29 ~~~I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkr------gvg~~GDkiLvAIk-------GQmkKa~vVGh~~~~ 95 (149)
T KOG3441|consen 29 LMGIHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKR------GVGELGDKILVAIK-------GQMKKAYVVGHVHYR 95 (149)
T ss_pred HHhhhhhheEEEecchhhcccccccCCCCceEEEEecc------cccccccEEEEEEe-------cceeeeEEEEeeccC
Confidence 56899999999999995 3889999999843 48999999999995 999999999976554
Q ss_pred eecCCcEEEecCceEEEECCCCCeeeeEEechhhHHHHh-----hhhhhhhcccccC
Q 032476 89 RRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECAD-----LWPRIASAANAIV 140 (140)
Q Consensus 89 ~R~dG~~i~F~~Na~VLln~~~~p~GTRI~GpV~~elr~-----k~~Ki~slA~~iv 140 (140)
+ .| ..+||.|.+||+|++|+|+||||.-|||..||. .|+|++++|+.+|
T Consensus 96 k--~~-~P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr~~~~~~~ysKVLAiA~~fv 149 (149)
T KOG3441|consen 96 K--HG-VPVFDSNNIVLIDDNGNPLGTRITAPIPTKLRANRGNVQYSKVLAIANKFV 149 (149)
T ss_pred C--CC-CcccCCCcEEEECCCCCcccceEeccCcHHHHhccCCcchhhHHHHHhhcC
Confidence 4 34 579999999999999999999999999999994 2999999999875
No 12
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=55.65 E-value=19 Score=23.09 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=26.3
Q ss_pred eeeceeeecCCcEEEecCceEEEECCCCCeee
Q 032476 83 RQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKG 114 (140)
Q Consensus 83 rtkk~~~R~dG~~i~F~~Na~VLln~~~~p~G 114 (140)
..-+.++++||.+.-+...+.++-|++++|..
T Consensus 55 ~~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 55 EIEYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 34566778999999999999999999999863
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=53.20 E-value=29 Score=25.86 Aligned_cols=35 Identities=34% Similarity=0.429 Sum_probs=27.9
Q ss_pred CCCcccCceEEEEEeecCC-CCccceeeEEEEeeec
Q 032476 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (140)
Q Consensus 52 ~~~a~iGD~I~vsVKk~~~-~~Kg~v~~AvIVrtkk 86 (140)
++.-.+||+|.|.++-... +.+-|.|.++|+..+.
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 4677899999999986553 3467999999998873
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=52.05 E-value=42 Score=24.83 Aligned_cols=36 Identities=31% Similarity=0.454 Sum_probs=29.2
Q ss_pred CCCCcccCceEEEEEeecCC-CCccceeeEEEEeeec
Q 032476 51 RLPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (140)
Q Consensus 51 r~~~a~iGD~I~vsVKk~~~-~~Kg~v~~AvIVrtkk 86 (140)
..+.-.+||+|.|.++.... +.+-|.|.|+++.-+.
T Consensus 15 ~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~ 51 (113)
T PF01245_consen 15 DIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRR 51 (113)
T ss_dssp SSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEB
T ss_pred CCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEEC
Confidence 34778899999999987743 4477999999998775
No 15
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=50.30 E-value=34 Score=23.65 Aligned_cols=29 Identities=17% Similarity=0.423 Sum_probs=22.6
Q ss_pred ecCCcEEEec--CceEEEECCCCCeeeeEEec
Q 032476 90 RKDGVFMYFE--DNAGVIVNPKGEMKGSAITG 119 (140)
Q Consensus 90 R~dG~~i~F~--~Na~VLln~~~~p~GTRI~G 119 (140)
=.||. ++|. .|-+.|.|+++..+|+.+.-
T Consensus 19 W~DG~-l~~~~~~~kv~Lyde~~~~i~~~~~~ 49 (83)
T PF10382_consen 19 WHDGF-LKYHSFNKKVMLYDEDGNLIGSDFLK 49 (83)
T ss_pred eECCE-EEEEeCCCEEEEEcCCCCEEeEEEEe
Confidence 34885 4555 77799999999999998753
No 16
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=49.81 E-value=15 Score=25.41 Aligned_cols=28 Identities=32% Similarity=0.388 Sum_probs=22.5
Q ss_pred EEEECCCCCeeeeEEechhhHHHHhhhhhhhh
Q 032476 103 GVIVNPKGEMKGSAITGPIGKECADLWPRIAS 134 (140)
Q Consensus 103 ~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~s 134 (140)
.||+|++| ++|.+.|++++-.+|...+.
T Consensus 2 mvL~De~G----~~I~A~I~~~~~~~f~~~l~ 29 (95)
T PF02721_consen 2 MVLVDEKG----DKIQATIPKELVDKFKDSLK 29 (95)
T ss_pred EEEEecCC----CEEEEEECHHHHHHHHhhcc
Confidence 58888865 89999999999887776654
No 17
>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=49.54 E-value=34 Score=25.41 Aligned_cols=40 Identities=20% Similarity=0.264 Sum_probs=28.0
Q ss_pred ccEEEEecCCCC-ceEEEEEEeccccccCCCCCcccCceEEEE
Q 032476 23 AATVNCADNTGA-KNLYIISVKGIKGRLNRLPSACVGDMVMAT 64 (140)
Q Consensus 23 ~T~L~V~DNSGa-k~v~cI~v~~~~~r~~r~~~a~iGD~I~vs 64 (140)
...|.++|-|++ ...-++++.+.. ...++...+||+|.+-
T Consensus 38 ~~tl~i~D~S~~~~~~l~v~~F~~~--~~~LP~v~~GDVIll~ 78 (138)
T cd04497 38 CCTLTITDPSLANSDGLTVKLFRPN--EESLPIVKVGDIILLR 78 (138)
T ss_pred EEEEEEECCCCCCCCcEEEEEECCC--hhhCCCCCCCCEEEEE
Confidence 356999999998 445556666532 3456767999998754
No 18
>CHL00084 rpl19 ribosomal protein L19
Probab=48.06 E-value=39 Score=25.30 Aligned_cols=34 Identities=24% Similarity=0.330 Sum_probs=26.8
Q ss_pred CCCcccCceEEEEEeecCC-CCccceeeEEEEeee
Q 032476 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQR 85 (140)
Q Consensus 52 ~~~a~iGD~I~vsVKk~~~-~~Kg~v~~AvIVrtk 85 (140)
.+.-.+||+|.|.++-... +.+-|.|.++|+..+
T Consensus 20 ~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r 54 (117)
T CHL00084 20 LPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKK 54 (117)
T ss_pred CCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEe
Confidence 4678899999999965543 346799999999865
No 19
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=46.19 E-value=46 Score=24.85 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=27.3
Q ss_pred CCCcccCceEEEEEeecCC-CCccceeeEEEEeeec
Q 032476 52 LPSACVGDMVMATVKKGKP-DLRKKVMPAVIVRQRK 86 (140)
Q Consensus 52 ~~~a~iGD~I~vsVKk~~~-~~Kg~v~~AvIVrtkk 86 (140)
++.-.+||+|.|.++-... +.+-|.|.++|+..+.
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 4677899999999875443 3467999999998773
No 20
>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=40.06 E-value=71 Score=21.19 Aligned_cols=49 Identities=20% Similarity=0.154 Sum_probs=32.8
Q ss_pred ccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCC
Q 032476 17 SLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (140)
Q Consensus 17 ~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~ 70 (140)
+=.|+.+..+.+..+--.-.++=|+..... ...|..||.|-+.++...+
T Consensus 24 sG~i~~g~~v~~~p~~~~~~V~sI~~~~~~-----~~~a~aGd~v~i~l~~~~~ 72 (83)
T cd03696 24 SGSVKVGDKVEILPLGEETRVRSIQVHGKD-----VEEAKAGDRVALNLTGVDA 72 (83)
T ss_pred ecEEeCCCEEEECCCCceEEEEEEEECCcC-----cCEEcCCCEEEEEEcCCCH
Confidence 345789999999885433344445543322 2579999999999986544
No 21
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=38.59 E-value=66 Score=21.54 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=23.7
Q ss_pred ceEEEECCCCCeeeeEEechhhHHHHhhhhhhhh
Q 032476 101 NAGVIVNPKGEMKGSAITGPIGKECADLWPRIAS 134 (140)
Q Consensus 101 Na~VLln~~~~p~GTRI~GpV~~elr~k~~Ki~s 134 (140)
-..+|+|++ |++|.+-+|+++.++|..++-
T Consensus 21 ~~miL~De~----G~~I~a~i~~~~~~~f~~~L~ 50 (86)
T cd04480 21 LEMVLVDEK----GNRIHATIPKRLAAKFRPLLK 50 (86)
T ss_pred EEEEEEcCC----CCEEEEEECHHHHHhhhhhce
Confidence 357899986 669999999999887766553
No 22
>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=38.20 E-value=71 Score=21.28 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=32.9
Q ss_pred cCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCC
Q 032476 18 LGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (140)
Q Consensus 18 ~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~ 70 (140)
=.|+.|..+.+.-..-.-.++-|+..... ...|..||.+-+.++...+
T Consensus 25 G~i~~Gd~v~i~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~~~l~~~~~ 72 (83)
T cd03698 25 GSIQKGDTLLVMPSKESVEVKSIYVDDEE-----VDYAVAGENVRLKLKGIDE 72 (83)
T ss_pred eEEeCCCEEEEeCCCcEEEEEEEEECCeE-----CCEECCCCEEEEEECCCCH
Confidence 34678888888775433456667665432 2579999999999986544
No 23
>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=36.59 E-value=78 Score=21.56 Aligned_cols=49 Identities=18% Similarity=-0.000 Sum_probs=33.6
Q ss_pred ccCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCC
Q 032476 17 SLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (140)
Q Consensus 17 ~~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~ 70 (140)
+=.|+.|..+.+.-+-=.-.++-|+..+..- ..|..||.+-+.++...+
T Consensus 28 ~G~i~~gd~v~i~P~~~~~~V~sI~~~~~~~-----~~a~aG~~v~i~l~~i~~ 76 (91)
T cd03693 28 TGVLKPGMVVTFAPAGVTGEVKSVEMHHEPL-----EEALPGDNVGFNVKNVSK 76 (91)
T ss_pred cceeecCCEEEECCCCcEEEEEEEEECCcCc-----CEECCCCEEEEEECCCCH
Confidence 4456888888888753334455666654332 579999999999986544
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=33.12 E-value=1.5e+02 Score=19.80 Aligned_cols=45 Identities=16% Similarity=0.055 Sum_probs=32.0
Q ss_pred cCcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEee
Q 032476 18 LGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKK 67 (140)
Q Consensus 18 ~mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk 67 (140)
=.++.|..|.+.+.--.-.++.|+.....- ..|..||.|-+.+++
T Consensus 25 G~v~~Gd~v~~~P~~~~~~V~si~~~~~~~-----~~a~aGd~v~l~l~~ 69 (81)
T cd03695 25 GSIRVGDEVVVLPSGKTSRVKSIETFDGEL-----DEAGAGESVTLTLED 69 (81)
T ss_pred ceEECCCEEEEcCCCCeEEEEEEEECCcEe-----CEEcCCCEEEEEECC
Confidence 346788888888753334566777665332 579999999999973
No 25
>PF09353 DUF1995: Domain of unknown function (DUF1995); InterPro: IPR018962 This family of proteins are functionally uncharacterised.
Probab=32.53 E-value=31 Score=27.19 Aligned_cols=30 Identities=23% Similarity=0.199 Sum_probs=24.5
Q ss_pred ceEEEECCCCCeeeeEEechhhHHHHhhhh
Q 032476 101 NAGVIVNPKGEMKGSAITGPIGKECADLWP 130 (140)
Q Consensus 101 Na~VLln~~~~p~GTRI~GpV~~elr~k~~ 130 (140)
--+||+|++.+-.++-.+|+.++++++.|.
T Consensus 124 rpvvl~Np~l~~~~~~g~g~~~r~~~~~Fl 153 (209)
T PF09353_consen 124 RPVVLLNPQLEDVRSVGFGFPGRKLRERFL 153 (209)
T ss_pred CeEEEEecccccCCccccccccHHHHHHHH
Confidence 578999999887776669999999998654
No 26
>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=30.87 E-value=1.1e+02 Score=20.29 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=31.7
Q ss_pred CcccccEEEEecCCCCceEEEEEEeccccccCCCCCcccCceEEEEEeecCC
Q 032476 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (140)
Q Consensus 19 mIq~~T~L~V~DNSGak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~ 70 (140)
.|+.|..+.+...--.-.++-|++.+.. ...|..||.+-+.++.+.+
T Consensus 25 ~i~~G~~v~i~P~~~~~~V~si~~~~~~-----~~~a~aGd~v~l~l~~i~~ 71 (82)
T cd04089 25 TIKKGDKLLVMPNKTQVEVLSIYNEDVE-----VRYARPGENVRLRLKGIEE 71 (82)
T ss_pred EEecCCEEEEeCCCcEEEEEEEEECCEE-----CCEECCCCEEEEEecCCCH
Confidence 3577778887765333445666665422 2579999999999986544
No 27
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=30.50 E-value=95 Score=23.38 Aligned_cols=35 Identities=29% Similarity=0.357 Sum_probs=27.2
Q ss_pred CCCcccCceEEEEEeecCCC-CccceeeEEEEeeec
Q 032476 52 LPSACVGDMVMATVKKGKPD-LRKKVMPAVIVRQRK 86 (140)
Q Consensus 52 ~~~a~iGD~I~vsVKk~~~~-~Kg~v~~AvIVrtkk 86 (140)
.+.-.+||.|.|.||-...+ .+-|.|.++|++-+.
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 35567999999999876654 367999999998664
No 28
>PF03864 Phage_cap_E: Phage major capsid protein E; InterPro: IPR005564 This entry is represented by Bacteriophage lambda, GpE. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Major capsid protein E plays a role in the stabilisation of the condensed form of the DNA molecule in phage heads [].; PDB: 3BQW_A.
Probab=28.68 E-value=1.6e+02 Score=24.04 Aligned_cols=46 Identities=20% Similarity=0.266 Sum_probs=20.0
Q ss_pred eeEEEEee-eceeeec-CCcEEE-ecCceEEEECCCCCeeeeEEechhhHH
Q 032476 77 MPAVIVRQ-RKPWRRK-DGVFMY-FEDNAGVIVNPKGEMKGSAITGPIGKE 124 (140)
Q Consensus 77 ~~AvIVrt-kk~~~R~-dG~~i~-F~~Na~VLln~~~~p~GTRI~GpV~~e 124 (140)
+.++.+.. -..+... ||...+ +++|.++|+.. ...|...+||++.+
T Consensus 233 ~~g~~i~~y~~~y~~~~~G~~~~~i~~~~~~~~p~--~~~g~~~~g~~~~~ 281 (329)
T PF03864_consen 233 FGGVLIVVYDGTYIDYDDGTSKRFIPDDKVVLLPD--GGLGKTYYGPTDEE 281 (329)
T ss_dssp EEEEEEEEE--EEE-T-T--EEESS-TTEEEEE-T--T---EEEE------
T ss_pred EccEEEEEEccEEEecCCCceeeecCCCeEEEEcc--ccCceEEEEecccc
Confidence 44444332 2233444 676655 78999999997 79999999999944
No 29
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=26.22 E-value=56 Score=22.08 Aligned_cols=26 Identities=19% Similarity=0.209 Sum_probs=19.2
Q ss_pred EEEecCceEEEECCCCCeeee--EEechhhH
Q 032476 95 FMYFEDNAGVIVNPKGEMKGS--AITGPIGK 123 (140)
Q Consensus 95 ~i~F~~Na~VLln~~~~p~GT--RI~GpV~~ 123 (140)
.++| |+.| .+++++.+|. .|||||..
T Consensus 23 ~P~~--n~~V-~~~~~~~IGkV~dIfGPV~~ 50 (73)
T PRK13149 23 QPPI--GSVV-YDKKLKKIGKVVDVFGPVKE 50 (73)
T ss_pred CCCC--CCEe-ECCCCCEeEEEEEEECCCCC
Confidence 4566 4444 7888999997 79999853
No 30
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=25.76 E-value=1.5e+02 Score=20.05 Aligned_cols=49 Identities=12% Similarity=0.011 Sum_probs=33.9
Q ss_pred ccCcccccEEEEecCC-C---CceEEEEEEeccccccCCCCCcccCceEEEEEeecCC
Q 032476 17 SLGLPVAATVNCADNT-G---AKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70 (140)
Q Consensus 17 ~~mIq~~T~L~V~DNS-G---ak~v~cI~v~~~~~r~~r~~~a~iGD~I~vsVKk~~~ 70 (140)
+=.++.+..|.+...- | .-.++.|++.+..- ..|..||.+-+.++.+.+
T Consensus 24 ~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~-----~~a~aGd~v~l~l~~i~~ 76 (87)
T cd03694 24 KGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPV-----RVVRAGQSASLALKKIDR 76 (87)
T ss_pred cCEEeCCCEEEECCCCCCCEeEEEEEEEEECCeEC-----CEECCCCEEEEEEcCCCH
Confidence 3356788888887742 4 34566677654332 579999999999987654
No 31
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=24.35 E-value=75 Score=22.06 Aligned_cols=20 Identities=45% Similarity=0.674 Sum_probs=17.6
Q ss_pred CCcccCceEEEEEeecCCCC
Q 032476 53 PSACVGDMVMATVKKGKPDL 72 (140)
Q Consensus 53 ~~a~iGD~I~vsVKk~~~~~ 72 (140)
+.|..||.+.+.|++..++.
T Consensus 44 p~a~~Gd~V~vkI~~v~~~~ 63 (73)
T COG3269 44 PGAEVGDEVKVKITKVKPNF 63 (73)
T ss_pred CCCCCCCeeeEEEEEeeccc
Confidence 57899999999999998875
No 32
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.56 E-value=1e+02 Score=24.69 Aligned_cols=38 Identities=16% Similarity=0.145 Sum_probs=25.2
Q ss_pred eeeecCCcEEEecCceEEEEC-CCCCeeeeEEechhhHHH
Q 032476 87 PWRRKDGVFMYFEDNAGVIVN-PKGEMKGSAITGPIGKEC 125 (140)
Q Consensus 87 ~~~R~dG~~i~F~~Na~VLln-~~~~p~GTRI~GpV~~el 125 (140)
+..+.+|.+. -...-..|++ ......-+|-|||||.|-
T Consensus 122 ~lp~~~gcR~-l~~~el~lL~~~~~~SfDsRYfGpipas~ 160 (173)
T COG4959 122 ALPRWQGCRY-LAPSELLLLTDRSSTSFDSRYFGPIPASQ 160 (173)
T ss_pred cCCcccCCce-ecCCeEEEEeccCCcccccceecccCHHH
Confidence 3445566665 3334445555 457799999999999874
No 33
>PF04773 FecR: FecR protein; InterPro: IPR006860 FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Probab=20.13 E-value=2.3e+02 Score=18.58 Aligned_cols=29 Identities=17% Similarity=0.123 Sum_probs=19.7
Q ss_pred ceeeecCCcEEEecCceEEEECCCCCeee
Q 032476 86 KPWRRKDGVFMYFEDNAGVIVNPKGEMKG 114 (140)
Q Consensus 86 k~~~R~dG~~i~F~~Na~VLln~~~~p~G 114 (140)
..+.-.||+.+.++.|+.+........-.
T Consensus 11 ~~i~l~dgs~v~l~~~s~~~~~~~~~~~~ 39 (98)
T PF04773_consen 11 AEIALSDGSRVRLGPNSRVSVDRDSGSEP 39 (98)
T ss_pred EEEEECCCCEEEECCCcEEEEEcccCCCc
Confidence 34556789999999999885554444333
Done!