Query 032739
Match_columns 135
No_of_seqs 117 out of 342
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:20:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032739.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032739hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00471 60S ribosomal protein 100.0 4.3E-73 9.2E-78 430.6 12.7 134 1-135 1-134 (134)
2 KOG3418 60S ribosomal protein 100.0 2.1E-64 4.5E-69 382.9 10.1 135 1-135 1-136 (136)
3 PF01777 Ribosomal_L27e: Ribos 100.0 1.6E-41 3.5E-46 240.8 -7.5 84 52-135 1-85 (85)
4 COG2163 RPL14A Ribosomal prote 99.8 2.7E-21 5.9E-26 145.9 3.5 124 1-126 1-124 (125)
5 PRK04333 50S ribosomal protein 99.3 3E-12 6.6E-17 90.8 5.6 62 4-91 3-64 (84)
6 PTZ00065 60S ribosomal protein 99.0 4.5E-10 9.8E-15 85.6 6.0 63 3-91 6-68 (130)
7 KOG3421 60S ribosomal protein 97.0 0.0012 2.6E-08 51.0 4.3 62 2-91 4-66 (136)
8 PF00467 KOW: KOW motif; Inte 96.2 0.0069 1.5E-07 35.2 3.1 26 7-32 1-26 (32)
9 PF01159 Ribosomal_L6e: Riboso 96.1 0.0023 4.9E-08 47.5 1.0 47 72-119 6-55 (108)
10 smart00739 KOW KOW (Kyprides, 95.8 0.018 3.9E-07 31.4 3.4 26 5-30 2-27 (28)
11 CHL00141 rpl24 ribosomal prote 94.2 0.09 2E-06 37.1 4.3 40 4-49 8-47 (83)
12 PRK12281 rplX 50S ribosomal pr 93.7 0.13 2.9E-06 35.7 4.3 40 4-49 6-45 (76)
13 PRK01191 rpl24p 50S ribosomal 93.4 0.14 3.1E-06 38.8 4.4 38 5-48 46-83 (120)
14 PRK00004 rplX 50S ribosomal pr 93.1 0.19 4.2E-06 36.7 4.6 42 3-50 3-44 (105)
15 TIGR01079 rplX_bact ribosomal 92.8 0.2 4.3E-06 36.8 4.3 41 4-50 3-43 (104)
16 PTZ00194 60S ribosomal protein 91.8 0.29 6.4E-06 38.1 4.3 38 5-48 47-84 (143)
17 TIGR01080 rplX_A_E ribosomal p 91.4 0.36 7.8E-06 36.1 4.3 38 5-48 42-79 (114)
18 COG0198 RplX Ribosomal protein 85.8 1.4 3.1E-05 32.6 4.1 43 2-52 2-44 (104)
19 COG2163 RPL14A Ribosomal prote 77.9 1.6 3.4E-05 33.3 1.9 52 19-90 7-65 (125)
20 KOG1694 60s ribosomal protein 73.0 3 6.6E-05 32.7 2.4 12 4-15 33-44 (152)
21 KOG3418 60S ribosomal protein 62.8 0.86 1.9E-05 35.4 -2.5 51 2-52 78-132 (136)
22 KOG1708 Mitochondrial/chloropl 55.3 16 0.00035 30.6 3.5 70 5-84 73-151 (236)
23 PF13234 rRNA_proc-arch: rRNA- 54.8 11 0.00024 30.6 2.6 30 3-32 71-100 (268)
24 PF01929 Ribosomal_L14e: Ribos 54.3 8.1 0.00018 27.0 1.5 18 74-91 4-21 (77)
25 PF15591 Imm17: Immunity prote 50.9 30 0.00065 24.4 3.8 27 16-44 21-47 (74)
26 TIGR00405 L26e_arch ribosomal 49.0 27 0.00059 25.8 3.7 27 4-30 86-112 (145)
27 COG1471 RPS4A Ribosomal protei 48.2 20 0.00043 30.3 3.1 24 5-28 174-197 (241)
28 PRK05609 nusG transcription an 44.6 45 0.00098 25.2 4.4 26 4-29 126-151 (181)
29 TIGR00922 nusG transcription t 43.9 51 0.0011 24.8 4.5 25 5-29 120-144 (172)
30 PRK04313 30S ribosomal protein 40.9 28 0.00061 29.2 2.9 24 5-28 172-195 (237)
31 PLN00036 40S ribosomal protein 40.2 30 0.00065 29.4 3.0 25 5-29 175-199 (261)
32 PTZ00118 40S ribosomal protein 40.0 28 0.00061 29.6 2.8 23 5-27 175-197 (262)
33 PF05257 CHAP: CHAP domain; I 38.9 76 0.0016 22.4 4.6 35 4-45 62-98 (124)
34 PTZ00223 40S ribosomal protein 37.9 35 0.00075 29.3 3.0 24 5-28 172-195 (273)
35 KOG1999 RNA polymerase II tran 36.7 40 0.00086 33.7 3.6 29 2-30 457-485 (1024)
36 PRK08559 nusG transcription an 35.6 99 0.0021 23.4 5.0 27 5-31 95-121 (153)
37 PRK09014 rfaH transcriptional 31.4 1E+02 0.0022 23.1 4.4 27 4-30 109-135 (162)
38 PTZ00328 eukaryotic initiation 29.7 1.6E+02 0.0034 23.6 5.4 44 4-52 27-70 (166)
39 PF14789 THDPS_M: Tetrahydrodi 29.2 30 0.00064 21.7 1.0 12 40-51 30-41 (41)
40 cd04822 PA_M28_1_3 PA_M28_1_3: 28.7 71 0.0015 24.7 3.2 10 7-16 47-56 (151)
41 TIGR01955 RfaH transcriptional 25.2 1.5E+02 0.0032 21.9 4.3 25 5-29 109-133 (159)
42 COG5137 Histone chaperone invo 23.3 75 0.0016 27.1 2.6 21 8-28 91-111 (279)
43 COG4065 Uncharacterized protei 23.2 9.3 0.0002 34.3 -2.9 32 41-74 150-181 (480)
44 PF02491 SHS2_FTSA: SHS2 domai 23.1 50 0.0011 22.1 1.3 15 76-90 43-57 (80)
45 cd04814 PA_M28_1 PA_M28_1: Pro 22.5 1.1E+02 0.0024 23.4 3.3 10 7-16 47-56 (142)
No 1
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=100.00 E-value=4.3e-73 Score=430.63 Aligned_cols=134 Identities=46% Similarity=0.892 Sum_probs=133.1
Q ss_pred CcccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccce
Q 032739 1 MVKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHL 80 (135)
Q Consensus 1 m~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl 80 (135)
|+|||+||+|||||+|||||+|||||+++||||+|+||+||||||||+||++||+.||+++++|||+||||||++|||||
T Consensus 1 M~K~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHl 80 (134)
T PTZ00471 1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80 (134)
T ss_pred CCccccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeecee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeEeecccccccCcccccChhHHHHHHHHHHHHHHHHhhcCCceEEeeecCC
Q 032739 81 MPTRYTLDVDLKDVINPDVLQTKDKKVTAAKETKRRLEERFKTGKNRWFFSKLRF 135 (135)
Q Consensus 81 ~pTry~vdi~~k~~v~~~~~~d~~~k~~akke~k~~fee~y~~gk~~wfF~KLrF 135 (135)
|||||+||++ ++++|.|.|+||++|++|+++++..|||+|++|+|+|||++|||
T Consensus 81 mPTRY~vdi~-~~~v~~~~~~d~~~k~~ar~~~k~~feer~k~gKn~wFF~kLrF 134 (134)
T PTZ00471 81 LPTRYNMDMS-KELRGRINVSDASKKARSKQLVKKLFQARYNAGSSRWFFQRLRF 134 (134)
T ss_pred cccceeeecc-ccccCHHHhhChHHHHHHHHHHHHHHHHHHhcCccceeeeeccC
Confidence 9999999999 89999999999999999999999999999999999999999998
No 2
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-64 Score=382.93 Aligned_cols=135 Identities=63% Similarity=1.031 Sum_probs=133.9
Q ss_pred CcccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccce
Q 032739 1 MVKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHL 80 (135)
Q Consensus 1 m~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl 80 (135)
|++||+||+||+||+||||||||||||++||||+|+||+|||||||||||++||++||++++++|||+++|+|+||||||
T Consensus 1 m~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~hl 80 (136)
T KOG3418|consen 1 MAKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYNHL 80 (136)
T ss_pred CcccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhccccccccccchhhhhcccceeEEEEeecccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeEeecc-cccccCcccccChhHHHHHHHHHHHHHHHHhhcCCceEEeeecCC
Q 032739 81 MPTRYTLDVD-LKDVINPDVLQTKDKKVTAAKETKRRLEERFKTGKNRWFFSKLRF 135 (135)
Q Consensus 81 ~pTry~vdi~-~k~~v~~~~~~d~~~k~~akke~k~~fee~y~~gk~~wfF~KLrF 135 (135)
|||||+||++ ++++++.|++++|++|..|+++++..|||+|++|+|+|||++|||
T Consensus 81 MptRy~vdv~~~k~v~~kdv~~~p~~K~~a~~~~k~kfeer~k~gkn~wff~~lrf 136 (136)
T KOG3418|consen 81 MPTRYTVDVLALKTVINKDVFRDPVKKGTAIKEAKVKFEERYKTGKNKWFFTKLRF 136 (136)
T ss_pred cCcceEEeehhhhccccHHhhhChhhhhhhhhHHHHHHHHHHHhCccccccccccC
Confidence 9999999999 699999999999999999999999999999999999999999998
No 3
>PF01777 Ribosomal_L27e: Ribosomal L27e protein family; InterPro: IPR001141 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, L27 is found in fungi, plants, algae and vertebrates [, ]. The family has a specific signature at the C terminus.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_a 4A1B_N 4A19_N 4A18_N 4A1D_N 3IZR_a.
Probab=100.00 E-value=1.6e-41 Score=240.84 Aligned_cols=84 Identities=56% Similarity=0.929 Sum_probs=72.7
Q ss_pred ccccccchhhHhhhccccceeEeeeccceeeeeeEeecc-cccccCcccccChhHHHHHHHHHHHHHHHHhhcCCceEEe
Q 032739 52 KVVRKDSAKKTAKKSRVKAFIKLVNQSHLMPTRYTLDVD-LKDVINPDVLQTKDKKVTAAKETKRRLEERFKTGKNRWFF 130 (135)
Q Consensus 52 kvt~~M~kkki~krskiK~FvK~vN~nHl~pTry~vdi~-~k~~v~~~~~~d~~~k~~akke~k~~fee~y~~gk~~wfF 130 (135)
+||++||+++++|||+||||||+|||||||||||+||++ ++++|++|.++||+.|++|+++++..|||+|++|+|+|||
T Consensus 1 KVtk~Mskkk~~KRskiK~FvK~iNynHlmPTRY~vd~~~~k~~v~~~~l~~~~~kk~a~k~~k~~feer~k~gKnkwFF 80 (85)
T PF01777_consen 1 KVTKKMSKKKIAKRSKIKPFVKVINYNHLMPTRYSVDIPDDKTVVNKDALKDPSKKKKAKKEIKKKFEERYKTGKNKWFF 80 (85)
T ss_dssp ---SSSSSCHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CccccccHHHHHHhhcceeeEEEeeccceEeeeeeeechhhhcccCHHHHhChHHHHHHHHHHHHHHHHHhccCCCcEEe
Confidence 689999999999999999999999999999999999995 6999999999999999999999999999999999999999
Q ss_pred eecCC
Q 032739 131 SKLRF 135 (135)
Q Consensus 131 ~KLrF 135 (135)
+||||
T Consensus 81 ~KLrF 85 (85)
T PF01777_consen 81 QKLRF 85 (85)
T ss_dssp -----
T ss_pred eeccC
Confidence 99998
No 4
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=2.7e-21 Score=145.87 Aligned_cols=124 Identities=23% Similarity=0.253 Sum_probs=113.4
Q ss_pred CcccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccce
Q 032739 1 MVKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHL 80 (135)
Q Consensus 1 m~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl 80 (135)
|.+++.||+||++++|||||+++|||+++||+ --.+.++++++|+.+++.+++.-+.-..+....+-.++.++.++||.
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a 79 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEA 79 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHh
Confidence 78899999999999999999999999999999 66777888888999999999999999999999999999999999999
Q ss_pred eeeeeEeecccccccCcccccChhHHHHHHHHHHHHHHHHhhcCCc
Q 032739 81 MPTRYTLDVDLKDVINPDVLQTKDKKVTAAKETKRRLEERFKTGKN 126 (135)
Q Consensus 81 ~pTry~vdi~~k~~v~~~~~~d~~~k~~akke~k~~fee~y~~gk~ 126 (135)
++++|..|.+- +.+..+.++.+..+-+.....+..++|+|..|++
T Consensus 80 ~~~~~~~~~~~-~~~~~k~~~~~~~~~~r~~~~k~~~~~~~~~~k~ 124 (125)
T COG2163 80 AGVLAKLDKSA-KNLETKKVREPLTDAERFKVMKLVKEERLQVGKA 124 (125)
T ss_pred hhhhccccccc-hhhhhhhhhcccchHHHHHHHHHHHHHHhhhhcc
Confidence 99999998877 5566677788888888888899999999999875
No 5
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.31 E-value=3e-12 Score=90.76 Aligned_cols=62 Identities=34% Similarity=0.519 Sum_probs=51.2
Q ss_pred cccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccceeee
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHLMPT 83 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl~pT 83 (135)
-+++|+||++++||++|+.||||+.+|++ ++||+| |.. +. .+| |..|++||.+|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~-------~vlVdg----~~~-~~-------~~r-------k~kn~khl~lt 56 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKN-------FVLVTG----PSL-TG-------VKR-------RRCNIKHLEPT 56 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCC-------EEEEEC----CCc-CC-------CCC-------eeechHHEEEe
Confidence 36899999999999999999999999998 999999 532 21 222 24699999999
Q ss_pred eeEeeccc
Q 032739 84 RYTLDVDL 91 (135)
Q Consensus 84 ry~vdi~~ 91 (135)
...++++-
T Consensus 57 ~~ki~~~~ 64 (84)
T PRK04333 57 DKKVDIEK 64 (84)
T ss_pred eEEEECCC
Confidence 99988653
No 6
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=99.03 E-value=4.5e-10 Score=85.63 Aligned_cols=63 Identities=19% Similarity=0.345 Sum_probs=54.1
Q ss_pred ccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccceee
Q 032739 3 KFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHLMP 82 (135)
Q Consensus 3 k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl~p 82 (135)
+|+.+||||++..|.|+|+-||||..+|.+ .|||.| | ..|. ..|. ++|++||.+
T Consensus 6 rfVEiGRVvli~~Gp~~GKL~vIVDIID~n-------RvLVDG----P-~~tg-------V~Rq-------~i~~k~l~L 59 (130)
T PTZ00065 6 RFVEPGRLCLIQYGPDAGKLCFIVDIVTPT-------RVLVDG----A-FITG-------VKRQ-------SIPLKRLKL 59 (130)
T ss_pred cceeeceEEEEecCCCCCCEEEEEEEEcCC-------eEEEeC----C-CcCC-------ccee-------EEeccceEE
Confidence 579999999999999999999999999999 999999 6 2222 2233 579999999
Q ss_pred eeeEeeccc
Q 032739 83 TRYTLDVDL 91 (135)
Q Consensus 83 Try~vdi~~ 91 (135)
|.+.++|+-
T Consensus 60 T~~~v~i~r 68 (130)
T PTZ00065 60 TDEKIKINR 68 (130)
T ss_pred ccEEEecCC
Confidence 999999984
No 7
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=96.96 E-value=0.0012 Score=51.01 Aligned_cols=62 Identities=23% Similarity=0.359 Sum_probs=53.0
Q ss_pred cccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeee-cccccccccccchhhHhhhccccceeEeeeccce
Q 032739 2 VKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGV-AKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHL 80 (135)
Q Consensus 2 ~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI-~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl 80 (135)
+.+...|+|+++..|-|+|+=++||..+|++ .+|+-|- +..|+. .+|++-+
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqn-------r~lvDGp~t~v~rq---------------------~~~~~~~ 55 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQN-------RALVDGPCTGVPRQ---------------------AMNLKCL 55 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecch-------hhhccCcccccchh---------------------hcchhhe
Confidence 4578899999999999999999999999998 8999991 223332 5799999
Q ss_pred eeeeeEeeccc
Q 032739 81 MPTRYTLDVDL 91 (135)
Q Consensus 81 ~pTry~vdi~~ 91 (135)
.-|-|.++++.
T Consensus 56 ~LT~~~~kfp~ 66 (136)
T KOG3421|consen 56 QLTDFVLKFPR 66 (136)
T ss_pred eeeeeeEeccc
Confidence 99999999996
No 8
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=96.16 E-value=0.0069 Score=35.25 Aligned_cols=26 Identities=15% Similarity=0.295 Sum_probs=24.1
Q ss_pred CcEEEEEeccccCCceEEEEEecCCC
Q 032739 7 PNKAVVLLQGRYAGRKAVIIRSFDDG 32 (135)
Q Consensus 7 pgkVvivL~GryAGkKaVivk~~d~g 32 (135)
||..|.|++|+|+|..+.|++..++.
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 68899999999999999999998876
No 9
>PF01159 Ribosomal_L6e: Ribosomal protein L6e ; InterPro: IPR000915 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_E 4A1D_E 4A19_E 4A1B_E 3IZR_G 3O58_F 3O5H_F 3IZS_G.
Probab=96.11 E-value=0.0023 Score=47.54 Aligned_cols=47 Identities=23% Similarity=0.340 Sum_probs=33.5
Q ss_pred eEeeeccceeeeeeEeecc-c--ccccCcccccChhHHHHHHHHHHHHHHH
Q 032739 72 IKLVNQSHLMPTRYTLDVD-L--KDVINPDVLQTKDKKVTAAKETKRRLEE 119 (135)
Q Consensus 72 vK~vN~nHl~pTry~vdi~-~--k~~v~~~~~~d~~~k~~akke~k~~fee 119 (135)
++++|++|+++|+..|||+ + +..+|+++|+.+..++ .++....+|++
T Consensus 6 LRRVnQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~~~k-~k~~e~~~f~~ 55 (108)
T PF01159_consen 6 LRRVNQAYVIATSTKVDISGVKIPEKIDDAYFKRKKKKK-KKKGEGDFFAE 55 (108)
T ss_dssp SEEESSCCCEECSCESCHCCHHH-CCTTGSSSCHCCCCH-HHHHHCHCCHH
T ss_pred ceecccceEEEEeeEEeccccchhhccchHHHHhhhhcc-ccccHHHHHhc
Confidence 5589999999999999997 3 6779999998655333 33334455554
No 10
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.75 E-value=0.018 Score=31.37 Aligned_cols=26 Identities=12% Similarity=0.340 Sum_probs=23.2
Q ss_pred ccCcEEEEEeccccCCceEEEEEecC
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFD 30 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d 30 (135)
+++|..|.|+.|.|+|..++|++..+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999998654
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.20 E-value=0.09 Score=37.10 Aligned_cols=40 Identities=15% Similarity=0.348 Sum_probs=34.3
Q ss_pred cccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeeccc
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKY 49 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ry 49 (135)
-+++|=.|.|++|++.|+.+.|++...+.. .++|-|++..
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~Vegvn~~ 47 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSN------KVIVKGINIK 47 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEEE
Confidence 478999999999999999999999977653 7999998653
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=93.65 E-value=0.13 Score=35.72 Aligned_cols=40 Identities=18% Similarity=0.304 Sum_probs=34.3
Q ss_pred cccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeeccc
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKY 49 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ry 49 (135)
-+++|--|+|++|++.|+...|++.+.+.. .++|-|++..
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~Vegvn~~ 45 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKN------RVIVEGVKIA 45 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEEE
Confidence 478899999999999999999999976552 7999998764
No 13
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.42 E-value=0.14 Score=38.76 Aligned_cols=38 Identities=16% Similarity=0.339 Sum_probs=33.0
Q ss_pred ccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecc
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAK 48 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~r 48 (135)
++.|-.|.|++|.+.|+.+-|++...+.. .++|-||+.
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~~------~V~VeGvn~ 83 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRG------RIYVEGVTV 83 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCCC------EEEEeCcEE
Confidence 67899999999999999999999976552 799999864
No 14
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.14 E-value=0.19 Score=36.71 Aligned_cols=42 Identities=17% Similarity=0.410 Sum_probs=35.7
Q ss_pred ccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccc
Q 032739 3 KFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYP 50 (135)
Q Consensus 3 k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP 50 (135)
.-+++|=-|.|++|++.|+...|++.+.+.. .++|-|++.-.
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~------~V~Vegvn~~k 44 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKN------KVIVEGVNIVK 44 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEEEE
Confidence 4578999999999999999999999987663 79999986543
No 15
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=92.84 E-value=0.2 Score=36.76 Aligned_cols=41 Identities=17% Similarity=0.401 Sum_probs=34.7
Q ss_pred cccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccc
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYP 50 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP 50 (135)
-++.|=-|.|++|++.|+.+.|++.+.+.. .++|-|++.-.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~VegvN~~k 43 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTN------KVIVEGVNMVK 43 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEECCcEEEE
Confidence 367888999999999999999999987653 79999986544
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=91.76 E-value=0.29 Score=38.12 Aligned_cols=38 Identities=11% Similarity=0.331 Sum_probs=32.4
Q ss_pred ccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecc
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAK 48 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~r 48 (135)
++-|-.|+|++|.+.|+.+-|++.+.... .++|-||+.
T Consensus 47 IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~------~ViVEgvn~ 84 (143)
T PTZ00194 47 VRKDDEVMVVRGHHKGREGKVTAVYRKKW------VIHIEKITR 84 (143)
T ss_pred eecCCEEEEecCCCCCCceEEEEEEcCCC------EEEEeCeEE
Confidence 57788999999999999999999976542 899999754
No 17
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=91.43 E-value=0.36 Score=36.14 Aligned_cols=38 Identities=18% Similarity=0.351 Sum_probs=32.3
Q ss_pred ccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecc
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAK 48 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~r 48 (135)
++.|--|.|++|.+.|+.+.|++...+.. .++|-||+.
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~------~V~Vegvn~ 79 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKRY------RIYVEGVTK 79 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCCC------EEEEcCeEE
Confidence 67789999999999999999999975442 799999763
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=85.83 E-value=1.4 Score=32.61 Aligned_cols=43 Identities=16% Similarity=0.309 Sum_probs=34.8
Q ss_pred cccccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccc
Q 032739 2 VKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVK 52 (135)
Q Consensus 2 ~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~k 52 (135)
..-++-|-.|+|++|.+.|+.+.|++.+... ++|-|++-.-+.
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--------V~VEGvnv~kkh 44 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--------VVVEGVNVVKKH 44 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe--------EEEECcEEEEec
Confidence 3456778899999999999999999998763 999997654433
No 19
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=77.95 E-value=1.6 Score=33.27 Aligned_cols=52 Identities=33% Similarity=0.503 Sum_probs=31.9
Q ss_pred CCceEEEEEecCCCCC-------CCCcceeEEeeecccccccccccchhhHhhhccccceeEeeeccceeeeeeEeecc
Q 032739 19 AGRKAVIIRSFDDGTR-------DRPYGHCLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKLVNQSHLMPTRYTLDVD 90 (135)
Q Consensus 19 AGkKaVivk~~d~gt~-------~~~y~~~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~vN~nHl~pTry~vdi~ 90 (135)
.|+=+|+++-=+-|-. |.. +++++| |..++. .+|.+ +|++|++||...++++
T Consensus 7 ~GrVvvv~~GR~aGkk~VIv~~iDd~--~v~i~g----p~~v~g-------v~r~r-------~n~~~l~~t~~~~~~~ 65 (125)
T COG2163 7 VGRVVVVTAGRFAGKKVVIVKIIDDN--FVLITG----PKKVKG-------VPRRR-------INIKHLEPTDKVIDLV 65 (125)
T ss_pred CCeEEEEecceeCCceEEEEEEccCC--EEEEeC----CccccC-------Ccccc-------ccceeeeccceeeeec
Confidence 4666666666555531 111 444555 555444 24444 5999999999998876
No 20
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=73.01 E-value=3 Score=32.73 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=8.8
Q ss_pred cccCcEEEEEec
Q 032739 4 FLKPNKAVVLLQ 15 (135)
Q Consensus 4 ~~kpgkVvivL~ 15 (135)
-+.||+|+|+|+
T Consensus 33 ~l~~gtvliil~ 44 (152)
T KOG1694|consen 33 SLTPGTVLIILA 44 (152)
T ss_pred ccCCCeeEEEec
Confidence 466778888777
No 21
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=62.78 E-value=0.86 Score=35.37 Aligned_cols=51 Identities=16% Similarity=0.150 Sum_probs=47.2
Q ss_pred cccccCcEEEEEeccccCCceEEEEEecCCCCCCCC----cceeEEeeecccccc
Q 032739 2 VKFLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRP----YGHCLVAGVAKYPVK 52 (135)
Q Consensus 2 ~k~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~----y~~~lVaGI~ryP~k 52 (135)
+.+|.++-.|-+++=++.+.+.|.-++.+.++.-.+ |++++-+|+++++..
T Consensus 78 ~hlMptRy~vdv~~~k~v~~kdv~~~p~~K~~a~~~~k~kfeer~k~gkn~wff~ 132 (136)
T KOG3418|consen 78 NHLMPTRYTVDVLALKTVINKDVFRDPVKKGTAIKEAKVKFEERYKTGKNKWFFT 132 (136)
T ss_pred ccccCcceEEeehhhhccccHHhhhChhhhhhhhhHHHHHHHHHHHhCccccccc
Confidence 468999999999999999999999999999999999 999999999999853
No 22
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=55.34 E-value=16 Score=30.59 Aligned_cols=70 Identities=20% Similarity=0.270 Sum_probs=48.0
Q ss_pred ccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccccccccchhhH-hhhcccc---c-----eeEee
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVKVVRKDSAKKT-AKKSRVK---A-----FIKLV 75 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~kvt~~M~kkki-~krskiK---~-----FvK~v 75 (135)
+.+|--|=||.|+-+||-+.|++.+.+.+ -++|-|++--= +.||..+- .-..=++ | =|..+
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s------~VvV~gln~k~----r~~gsekeg~pgtivk~EaPlhvsk~VmLv 142 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHRS------WVVVKGLNTKY----RHMGSEKEGEPGTIVKSEAPLHVSKQVMLV 142 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecCc------eEEEcccchhh----hhhcccccCCCceEEeecCCceecceeEEE
Confidence 56899999999999999999999999884 78999976432 33443332 0000000 1 26677
Q ss_pred eccceeeee
Q 032739 76 NQSHLMPTR 84 (135)
Q Consensus 76 N~nHl~pTr 84 (135)
..+-.-||+
T Consensus 143 dp~d~q~te 151 (236)
T KOG1708|consen 143 DPEDDQPTE 151 (236)
T ss_pred CccccCCce
Confidence 777777875
No 23
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=54.85 E-value=11 Score=30.58 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=23.7
Q ss_pred ccccCcEEEEEeccccCCceEEEEEecCCC
Q 032739 3 KFLKPNKAVVLLQGRYAGRKAVIIRSFDDG 32 (135)
Q Consensus 3 k~~kpgkVvivL~GryAGkKaVivk~~d~g 32 (135)
.||.|||+|.|-.|-+...=||||+....+
T Consensus 71 ~fL~~GRlV~v~~~~~~~~wgvvv~~~~~~ 100 (268)
T PF13234_consen 71 PFLQPGRLVVVRDGDRDFGWGVVVNFAKKS 100 (268)
T ss_dssp HHS-TTEEEEEEETTCEEEEEEEEEEEE--
T ss_pred HhCCCCCEEEEecCCCccceeEEEeccccc
Confidence 589999999999888888899999775543
No 24
>PF01929 Ribosomal_L14e: Ribosomal protein L14; InterPro: IPR002784 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 [, ]. This entry includes the eukaryotic ribosomal protein L14, which binds to the 60S ribosomal subunit, and archaebacterial ribosomal protein L14E, which binds to the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_N 3O5H_N 3O58_N 2KDS_A 2JOY_A 4A1B_F 4A19_F 4A18_F 4A1D_F 3IZR_N.
Probab=54.30 E-value=8.1 Score=27.00 Aligned_cols=18 Identities=17% Similarity=0.353 Sum_probs=16.5
Q ss_pred eeeccceeeeeeEeeccc
Q 032739 74 LVNQSHLMPTRYTLDVDL 91 (135)
Q Consensus 74 ~vN~nHl~pTry~vdi~~ 91 (135)
+||++||.+|.+.++|+-
T Consensus 4 ~i~~k~l~LT~~~i~i~r 21 (77)
T PF01929_consen 4 VINLKRLHLTDFVIKIPR 21 (77)
T ss_dssp EEECTSSEEEEEETTTTT
T ss_pred eeeccceEeecEEEeccC
Confidence 689999999999999884
No 25
>PF15591 Imm17: Immunity protein 17
Probab=50.89 E-value=30 Score=24.42 Aligned_cols=27 Identities=11% Similarity=0.358 Sum_probs=20.2
Q ss_pred cccCCceEEEEEecCCCCCCCCcceeEEe
Q 032739 16 GRYAGRKAVIIRSFDDGTRDRPYGHCLVA 44 (135)
Q Consensus 16 GryAGkKaVivk~~d~gt~~~~y~~~lVa 44 (135)
-+++|++.|||--++|+ +.-|+++++.
T Consensus 21 ~ei~Gk~GVVlG~SeeD--~~~~gY~Vli 47 (74)
T PF15591_consen 21 AEIWGKRGVVLGISEED--GGNFGYSVLI 47 (74)
T ss_pred hhhcCceeEEEEEecCC--CcEEEEEEEE
Confidence 48999999999877766 4567766543
No 26
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=49.01 E-value=27 Score=25.84 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=24.2
Q ss_pred cccCcEEEEEeccccCCceEEEEEecC
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFD 30 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d 30 (135)
.+++|-.|.|..|=|+|-.|+|++.-.
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 378999999999999999999998744
No 27
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=48.16 E-value=20 Score=30.28 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=22.0
Q ss_pred ccCcEEEEEeccccCCceEEEEEe
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRS 28 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~ 28 (135)
+.+|..+++..||++|.-+.|++.
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I 197 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEI 197 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEE
Confidence 579999999999999999999865
No 28
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=44.58 E-value=45 Score=25.20 Aligned_cols=26 Identities=12% Similarity=0.148 Sum_probs=23.6
Q ss_pred cccCcEEEEEeccccCCceEEEEEec
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSF 29 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~ 29 (135)
-+++|.-|-|++|=++|.-+.|++..
T Consensus 126 ~~~~Gd~VrI~~GPf~G~~g~v~~i~ 151 (181)
T PRK05609 126 DFEVGEMVRVIDGPFADFNGTVEEVD 151 (181)
T ss_pred CCCCCCEEEEeccCCCCCEEEEEEEe
Confidence 36799999999999999999999975
No 29
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=43.88 E-value=51 Score=24.83 Aligned_cols=25 Identities=12% Similarity=0.138 Sum_probs=23.2
Q ss_pred ccCcEEEEEeccccCCceEEEEEec
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSF 29 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~ 29 (135)
+++|--|.|..|=++|--++|++..
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~ 144 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVD 144 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEc
Confidence 6799999999999999999999964
No 30
>PRK04313 30S ribosomal protein S4e; Validated
Probab=40.94 E-value=28 Score=29.18 Aligned_cols=24 Identities=13% Similarity=0.249 Sum_probs=21.8
Q ss_pred ccCcEEEEEeccccCCceEEEEEe
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRS 28 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~ 28 (135)
+.+|.+|+|..|+++|+=++|...
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i 195 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEI 195 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEE
Confidence 578999999999999999998866
No 31
>PLN00036 40S ribosomal protein S4; Provisional
Probab=40.20 E-value=30 Score=29.44 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=22.1
Q ss_pred ccCcEEEEEeccccCCceEEEEEec
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSF 29 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~ 29 (135)
+.+|.+|+|..|+++|+=++|+...
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 5789999999999999999997654
No 32
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=39.98 E-value=28 Score=29.60 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=21.4
Q ss_pred ccCcEEEEEeccccCCceEEEEE
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIR 27 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk 27 (135)
+.+|.+|+|..|+++|+=++|+.
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~ 197 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVS 197 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEE
Confidence 57899999999999999999987
No 33
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=38.91 E-value=76 Score=22.44 Aligned_cols=35 Identities=26% Similarity=0.227 Sum_probs=25.1
Q ss_pred cccCcEEEEE--eccccCCceEEEEEecCCCCCCCCcceeEEee
Q 032739 4 FLKPNKAVVL--LQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAG 45 (135)
Q Consensus 4 ~~kpgkVviv--L~GryAGkKaVivk~~d~gt~~~~y~~~lVaG 45 (135)
..+||-|++. ..+...|+=|||.+..++| .+.+..
T Consensus 62 ~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~-------~i~v~e 98 (124)
T PF05257_consen 62 TPQPGDIVVWDSGSGGGYGHVAIVESVNDGG-------TITVIE 98 (124)
T ss_dssp ---TTEEEEEEECTTTTT-EEEEEEEE-TTS-------EEEEEE
T ss_pred ccccceEEEeccCCCCCCCeEEEEEEECCCC-------EEEEEE
Confidence 4578999887 6778889999999998887 677765
No 34
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=37.88 E-value=35 Score=29.25 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=21.8
Q ss_pred ccCcEEEEEeccccCCceEEEEEe
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRS 28 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~ 28 (135)
+.+|.+|+|..|+++|+=++|...
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i 195 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSI 195 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEE
Confidence 578999999999999999998766
No 35
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=36.73 E-value=40 Score=33.75 Aligned_cols=29 Identities=28% Similarity=0.667 Sum_probs=26.3
Q ss_pred cccccCcEEEEEeccccCCceEEEEEecC
Q 032739 2 VKFLKPNKAVVLLQGRYAGRKAVIIRSFD 30 (135)
Q Consensus 2 ~k~~kpgkVvivL~GryAGkKaVivk~~d 30 (135)
-|.++||-.|=|++|||.|.-.+||+.-+
T Consensus 457 rKyF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 457 RKYFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred hhhccCCCeEEEEeccccCCcceEEEEeC
Confidence 36789999999999999999999998755
No 36
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=35.65 E-value=99 Score=23.42 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=24.2
Q ss_pred ccCcEEEEEeccccCCceEEEEEecCC
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSFDD 31 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~d~ 31 (135)
+.+|-.|-|..|-|+|-.|.|++.-.+
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 679999999999999999999987544
No 37
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=31.40 E-value=1e+02 Score=23.10 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=23.5
Q ss_pred cccCcEEEEEeccccCCceEEEEEecC
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFD 30 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d 30 (135)
.+++|--|.|..|-++|--++|++.-+
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~ 135 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDG 135 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCC
Confidence 367999999999999999999988643
No 38
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=29.74 E-value=1.6e+02 Score=23.60 Aligned_cols=44 Identities=16% Similarity=0.138 Sum_probs=28.4
Q ss_pred cccCcEEEEEeccccCCceEEEEEecCCCCCCCCcceeEEeeecccccc
Q 032739 4 FLKPNKAVVLLQGRYAGRKAVIIRSFDDGTRDRPYGHCLVAGVAKYPVK 52 (135)
Q Consensus 4 ~~kpgkVvivL~GryAGkKaVivk~~d~gt~~~~y~~~lVaGI~ryP~k 52 (135)
.|+.|..|++ .|| -|=||.-.-+.|..|=+..|-+.|||=.-.+
T Consensus 27 ~LkkG~yvvI-kGr----PCKIveistSKtGKHGhAK~~ivaidIFTgk 70 (166)
T PTZ00328 27 ALKKGGYVCI-NGR----PCKVIDLSVSKTGKHGHAKVSIVATDIFTGN 70 (166)
T ss_pred ceeECCEEEE-CCe----eeEEEEEecCCCCcCCceEEEEEEEecCCCC
Confidence 5677887755 554 5555555444555666666888898876643
No 39
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=29.23 E-value=30 Score=21.71 Aligned_cols=12 Identities=33% Similarity=0.409 Sum_probs=7.4
Q ss_pred eeEEeeeccccc
Q 032739 40 HCLVAGVAKYPV 51 (135)
Q Consensus 40 ~~lVaGI~ryP~ 51 (135)
++-|.|||+.|+
T Consensus 30 ~~~V~~VDKFPR 41 (41)
T PF14789_consen 30 PLTVYSVDKFPR 41 (41)
T ss_dssp ---EEEEESS-B
T ss_pred CcEEEEEcCCCC
Confidence 688999999996
No 40
>cd04822 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=28.68 E-value=71 Score=24.70 Aligned_cols=10 Identities=30% Similarity=0.444 Sum_probs=9.0
Q ss_pred CcEEEEEecc
Q 032739 7 PNKAVVLLQG 16 (135)
Q Consensus 7 pgkVvivL~G 16 (135)
.|||||+++|
T Consensus 47 kGKIVlv~~g 56 (151)
T cd04822 47 KGKIVLVLRH 56 (151)
T ss_pred CCeEEEEEcC
Confidence 6999999988
No 41
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=25.16 E-value=1.5e+02 Score=21.86 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=23.1
Q ss_pred ccCcEEEEEeccccCCceEEEEEec
Q 032739 5 LKPNKAVVLLQGRYAGRKAVIIRSF 29 (135)
Q Consensus 5 ~kpgkVvivL~GryAGkKaVivk~~ 29 (135)
+++|--|.|+.|=++|--++|++.-
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEEC
Confidence 6799999999999999999999963
No 42
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=23.28 E-value=75 Score=27.11 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=18.1
Q ss_pred cEEEEEeccccCCceEEEEEe
Q 032739 8 NKAVVLLQGRYAGRKAVIIRS 28 (135)
Q Consensus 8 gkVvivL~GryAGkKaVivk~ 28 (135)
|--||+|+|||.|+--|-|--
T Consensus 91 gvTvILlsc~Y~g~eFvRvGY 111 (279)
T COG5137 91 GVTVILLSCRYKGQEFVRVGY 111 (279)
T ss_pred ceeEEEEEEeecCceeEEEEE
Confidence 667999999999999888744
No 43
>COG4065 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.23 E-value=9.3 Score=34.33 Aligned_cols=32 Identities=28% Similarity=0.326 Sum_probs=25.8
Q ss_pred eEEeeecccccccccccchhhHhhhccccceeEe
Q 032739 41 CLVAGVAKYPVKVVRKDSAKKTAKKSRVKAFIKL 74 (135)
Q Consensus 41 ~lVaGI~ryP~kvt~~M~kkki~krskiK~FvK~ 74 (135)
||-||+ .|+++|.+||+..|.++-+=.+|+-.
T Consensus 150 Cl~AGv--PP~kMtpamske~Ip~~~~~~s~ldk 181 (480)
T COG4065 150 CLKAGV--PPKKMTPAMSKENIPEPLREYSKLDK 181 (480)
T ss_pred HHhcCC--CccccCcccChhhcChhHHHhhhhhh
Confidence 788887 58999999999999888776555533
No 44
>PF02491 SHS2_FTSA: SHS2 domain inserted in FTSA; InterPro: IPR003494 FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains [].; GO: 0007049 cell cycle; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=23.12 E-value=50 Score=22.05 Aligned_cols=15 Identities=33% Similarity=0.645 Sum_probs=12.1
Q ss_pred eccceeeeeeEeecc
Q 032739 76 NQSHLMPTRYTLDVD 90 (135)
Q Consensus 76 N~nHl~pTry~vdi~ 90 (135)
.+=|++|..|.||=.
T Consensus 43 ~iih~ip~~y~lD~~ 57 (80)
T PF02491_consen 43 EIIHVIPQEYILDGQ 57 (80)
T ss_dssp EEEEEEEEEEEETTT
T ss_pred EEEEEEeEEEEECCC
Confidence 566999999999643
No 45
>cd04814 PA_M28_1 PA_M28_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies, relatively little is known a
Probab=22.49 E-value=1.1e+02 Score=23.39 Aligned_cols=10 Identities=40% Similarity=0.587 Sum_probs=8.9
Q ss_pred CcEEEEEecc
Q 032739 7 PNKAVVLLQG 16 (135)
Q Consensus 7 pgkVvivL~G 16 (135)
.|||||++.|
T Consensus 47 kGKIVlv~~g 56 (142)
T cd04814 47 KGKVVVVLRN 56 (142)
T ss_pred CCcEEEEEcC
Confidence 6999999987
Done!