Query 047135
Match_columns 134
No_of_seqs 160 out of 433
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:00:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00065 60S ribosomal protein 100.0 3.7E-58 8E-63 344.6 14.7 125 1-125 2-129 (130)
2 KOG3421 60S ribosomal protein 100.0 5.7E-45 1.2E-49 274.1 11.9 134 1-134 1-136 (136)
3 PF01929 Ribosomal_L14e: Ribos 100.0 3.1E-33 6.8E-38 193.6 4.9 77 44-120 1-77 (77)
4 COG2163 RPL14A Ribosomal prote 100.0 2.4E-28 5.2E-33 182.5 9.4 117 4-122 2-122 (125)
5 PRK04333 50S ribosomal protein 99.9 5.9E-27 1.3E-31 164.5 8.9 77 6-82 3-82 (84)
6 PTZ00471 60S ribosomal protein 99.5 5.4E-14 1.2E-18 106.4 7.3 59 5-63 3-90 (134)
7 KOG3418 60S ribosomal protein 99.0 4.4E-10 9.5E-15 85.1 5.4 59 5-63 3-90 (136)
8 PF00467 KOW: KOW motif; Inte 97.9 3.4E-05 7.4E-10 44.7 4.4 31 9-39 1-32 (32)
9 smart00739 KOW KOW (Kyprides, 96.6 0.0038 8.3E-08 33.9 3.4 26 7-32 2-27 (28)
10 PRK01191 rpl24p 50S ribosomal 96.1 0.015 3.2E-07 43.6 5.5 53 7-59 46-106 (120)
11 PRK12281 rplX 50S ribosomal pr 96.0 0.023 5.1E-07 39.2 5.6 36 6-41 6-42 (76)
12 CHL00141 rpl24 ribosomal prote 95.9 0.016 3.4E-07 40.6 4.4 36 6-41 8-44 (83)
13 TIGR01079 rplX_bact ribosomal 95.0 0.068 1.5E-06 38.9 5.4 35 7-41 4-39 (104)
14 TIGR01080 rplX_A_E ribosomal p 94.7 0.075 1.6E-06 39.4 5.1 53 7-59 42-102 (114)
15 PRK00004 rplX 50S ribosomal pr 94.6 0.11 2.3E-06 37.8 5.4 36 6-41 4-40 (105)
16 PTZ00194 60S ribosomal protein 94.1 0.14 3E-06 39.5 5.3 53 7-59 47-107 (143)
17 COG0198 RplX Ribosomal protein 91.1 0.42 9E-06 35.0 4.3 35 6-41 4-38 (104)
18 TIGR01955 RfaH transcriptional 90.9 0.42 9E-06 35.6 4.3 35 6-40 108-142 (159)
19 PRK05609 nusG transcription an 90.5 0.51 1.1E-05 35.8 4.5 37 5-41 125-162 (181)
20 TIGR00922 nusG transcription t 89.8 0.6 1.3E-05 35.3 4.3 35 7-41 120-155 (172)
21 TIGR00405 L26e_arch ribosomal 89.8 0.66 1.4E-05 34.4 4.5 36 6-41 86-122 (145)
22 PF13234 rRNA_proc-arch: rRNA- 89.7 0.22 4.7E-06 40.5 2.0 30 4-33 70-99 (268)
23 PRK09014 rfaH transcriptional 89.5 0.61 1.3E-05 35.1 4.2 36 6-41 109-144 (162)
24 PRK08559 nusG transcription an 87.3 1.9 4.1E-05 32.7 5.6 35 7-41 95-130 (153)
25 KOG1708 Mitochondrial/chloropl 85.0 1.4 3E-05 36.3 4.0 35 7-41 73-108 (236)
26 PF01777 Ribosomal_L27e: Ribos 80.5 0.053 1.1E-06 38.3 -5.0 18 46-63 22-39 (85)
27 TIGR01956 NusG_myco NusG famil 78.2 3.7 8.1E-05 34.4 4.4 35 7-41 206-241 (258)
28 COG0250 NusG Transcription ant 76.5 4.4 9.6E-05 31.9 4.1 28 6-33 123-150 (178)
29 PLN00036 40S ribosomal protein 72.8 6.2 0.00013 33.2 4.3 32 7-38 175-210 (261)
30 PTZ00118 40S ribosomal protein 68.1 8.8 0.00019 32.3 4.3 32 7-38 175-210 (262)
31 KOG1999 RNA polymerase II tran 67.4 5.5 0.00012 39.0 3.3 34 4-38 457-490 (1024)
32 PRK04313 30S ribosomal protein 65.0 6.3 0.00014 32.7 2.8 33 7-39 172-209 (237)
33 PTZ00223 40S ribosomal protein 61.5 8 0.00017 32.7 2.8 32 7-38 172-207 (273)
34 COG1047 SlpA FKBP-type peptidy 58.9 21 0.00045 28.4 4.6 44 3-48 85-131 (174)
35 PF05257 CHAP: CHAP domain; I 57.9 28 0.0006 24.6 4.8 35 4-38 60-96 (124)
36 COG1471 RPS4A Ribosomal protei 51.7 16 0.00034 30.6 2.9 34 7-40 174-212 (241)
37 PF13051 DUF3912: Protein of u 50.2 16 0.00034 24.6 2.3 35 7-41 3-40 (68)
38 COG4048 Uncharacterized protei 47.2 28 0.0006 26.2 3.4 33 6-38 58-92 (123)
39 PRK15095 FKBP-type peptidyl-pr 43.4 52 0.0011 25.0 4.6 32 7-41 93-126 (156)
40 COG5164 SPT5 Transcription elo 43.1 28 0.0006 32.2 3.4 29 5-33 350-378 (607)
41 TIGR03689 pup_AAA proteasome A 40.8 49 0.0011 30.2 4.6 35 7-41 83-126 (512)
42 PF09884 DUF2111: Uncharacteri 34.8 63 0.0014 23.0 3.5 32 6-37 40-74 (84)
43 cd02418 Peptidase_C39B A sub-f 33.3 1.1E+02 0.0023 21.1 4.6 35 16-51 84-118 (136)
44 PF12945 YcgR_2: Flagellar pro 32.4 1.1E+02 0.0025 19.7 4.4 35 7-41 1-39 (87)
45 KOG0948 Nuclear exosomal RNA h 30.9 53 0.0011 32.3 3.3 26 6-31 650-675 (1041)
46 KOG1999 RNA polymerase II tran 30.5 61 0.0013 32.2 3.7 33 6-38 258-291 (1024)
47 COG0684 MenG Demethylmenaquino 29.3 49 0.0011 26.9 2.5 33 9-41 46-79 (210)
48 PF02237 BPL_C: Biotin protein 27.5 1.5E+02 0.0032 17.9 4.8 32 9-41 2-33 (48)
49 COG0019 LysA Diaminopimelate d 26.3 37 0.0008 29.7 1.4 37 5-41 272-308 (394)
50 PF12923 RRP7: Ribosomal RNA-p 25.0 1.2E+02 0.0026 22.4 3.8 33 93-125 80-112 (131)
51 PRK10737 FKBP-type peptidyl-pr 24.6 1.6E+02 0.0035 23.6 4.6 40 7-48 90-130 (196)
52 PF02800 Gp_dh_C: Glyceraldehy 24.5 1.4E+02 0.0029 22.7 4.1 32 47-78 77-108 (157)
53 smart00333 TUDOR Tudor domain. 22.0 1.9E+02 0.0041 17.3 3.9 30 7-38 3-34 (57)
54 PF03412 Peptidase_C39: Peptid 21.3 1.4E+02 0.0031 20.5 3.4 20 20-40 83-103 (131)
No 1
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=100.00 E-value=3.7e-58 Score=344.64 Aligned_cols=125 Identities=42% Similarity=0.691 Sum_probs=122.7
Q ss_pred CCcccceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC---CCcceeeeccCeeeeceEEecCCCCChHHHHHHHHH
Q 047135 1 MPFKRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP---DMVRGQMNFKRLSLTDIKIDIPRVPKKKTLIDAMEK 77 (134)
Q Consensus 1 m~f~r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp---~v~Rk~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~ 77 (134)
|+|+|||||||||++++||++||+||||||||+|||||||| +|+||.+|++||+||+++++||+|+++++|++||++
T Consensus 2 ~~f~rfVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP~~tgV~Rq~i~~k~l~LT~~~v~i~r~a~t~~v~ka~~~ 81 (130)
T PTZ00065 2 PLFKRFVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGAFITGVKRQSIPLKRLKLTDEKIKINRGARTGTLKKALKK 81 (130)
T ss_pred cccccceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCCCcCCcceeEEeccceEEccEEEecCCCCCcHHHHHHHHH
Confidence 57899999999999999999999999999999999999999 899999999999999999999999999999999999
Q ss_pred hchHHHhhhchhHhhHHHHHHHhcCCChhhHHHHHHHHHHhhHHHHHH
Q 047135 78 ADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVRQEL 125 (134)
Q Consensus 78 ~~v~~kw~~s~waKk~~~~~~r~~ltDFdRFk~~~~kk~r~~~~~~~~ 125 (134)
+++.+||++|+||||++++++|++||||||||+|++|++||.+++.+.
T Consensus 82 a~i~~kw~~s~waKK~~~~~~Ra~ltDFdRFKvm~akk~r~~~v~~~~ 129 (130)
T PTZ00065 82 DNALEEFNKTSLGKKLIIKEKRANMTDFERFKLMVAKKERRKLMKSLK 129 (130)
T ss_pred ccHHHHHHHhHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999865
No 2
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-45 Score=274.05 Aligned_cols=134 Identities=55% Similarity=0.846 Sum_probs=131.6
Q ss_pred CCcccceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC--CCcceeeeccCeeeeceEEecCCCCChHHHHHHHHHh
Q 047135 1 MPFKRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP--DMVRGQMNFKRLSLTDIKIDIPRVPKKKTLIDAMEKA 78 (134)
Q Consensus 1 m~f~r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp--~v~Rk~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~~ 78 (134)
|+|+||||+|||+++.+|++.||+++|||++|+||+||||| +|+||.+|++.++||++++++|+|+++.+|.++|+++
T Consensus 1 m~f~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp~t~v~rq~~~~~~~~LT~~~~kfp~g~~~~~v~k~~~aa 80 (136)
T KOG3421|consen 1 MVFKRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGPCTGVPRQAMNLKCLQLTDFVLKFPRGARKKIVKKAWKAA 80 (136)
T ss_pred CcchhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCcccccchhhcchhheeeeeeeEecccCcccHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred chHHHhhhchhHhhHHHHHHHhcCCChhhHHHHHHHHHHhhHHHHHHHHHHhhhcC
Q 047135 79 DVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVRQELAKLKKENAA 134 (134)
Q Consensus 79 ~v~~kw~~s~waKk~~~~~~r~~ltDFdRFk~~~~kk~r~~~~~~~~~k~~~~~~~ 134 (134)
++.++|..|.|++|+.+++.|++|||||||++|.+|.||+.+++.+++++++.+++
T Consensus 81 ~v~~k~~ks~wakK~~a~k~ra~l~df~r~~~~~ak~Qka~~v~~a~~k~kk~~~~ 136 (136)
T KOG3421|consen 81 DVKAKWKKSPWAKKAPAKKRRAALADFDRFKAMKAKGQKAALVKKALAKLKKAAQA 136 (136)
T ss_pred HHHHhhhcCchhhhhHHHHhhhhhCcHHHHHHHHHHHHHHHHHHHHHHHhhhhhcC
Confidence 99999999999999999999999999999999999999999999999999987654
No 3
>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=99.98 E-value=3.1e-33 Score=193.62 Aligned_cols=77 Identities=48% Similarity=0.815 Sum_probs=74.4
Q ss_pred cceeeeccCeeeeceEEecCCCCChHHHHHHHHHhchHHHhhhchhHhhHHHHHHHhcCCChhhHHHHHHHHHHhhH
Q 047135 44 VRGQMNFKRLSLTDIKIDIPRVPKKKTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGL 120 (134)
Q Consensus 44 ~Rk~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~~~v~~kw~~s~waKk~~~~~~r~~ltDFdRFk~~~~kk~r~~~ 120 (134)
|||.+|++||+||+++|+||+|+++++|+++|++++|.++|++|+|||+++++++|++||||||||||++|++||+|
T Consensus 1 ~Rq~i~~k~l~LT~~~i~i~r~a~t~~vkka~~~~~i~~kw~~s~waKk~~~~~~Ra~ltDFdRFKv~~akk~r~~~ 77 (77)
T PF01929_consen 1 PRQVINLKRLHLTDFVIKIPRGARTKTVKKAWEKADIDEKWAESAWAKKIAAREKRANLTDFDRFKVMVAKKQRNRI 77 (77)
T ss_dssp -EEEEECTSSEEEEEETTTTTTTCHHHHHHHHHHHTCHHHHHHHHCSCHHHHHHHHHSHHHHHHHHHHHHHHHHHH-
T ss_pred CCceeeccceEeecEEEeccCCCCcHHHHHHHHHccHHHHHHHhHHHHHHHHHHHHhcCCcHHHHHHHHHHHHhccC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999975
No 4
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.4e-28 Score=182.55 Aligned_cols=117 Identities=34% Similarity=0.469 Sum_probs=111.5
Q ss_pred ccceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC----CCcceeeeccCeeeeceEEecCCCCChHHHHHHHHHhc
Q 047135 4 KRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP----DMVRGQMNFKRLSLTDIKIDIPRVPKKKTLIDAMEKAD 79 (134)
Q Consensus 4 ~r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp----~v~Rk~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~~~ 79 (134)
.+++++|+||+++.|+++||.||||++||||++||+|| +++|+++|++|+.+|+.+++++++++.+.+.++|++.+
T Consensus 2 ~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a~~ 81 (125)
T COG2163 2 RASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEAAG 81 (125)
T ss_pred CccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHhhh
Confidence 57899999999999999999999999999999999998 89999999999999999999999999999999999999
Q ss_pred hHHHhhhchhHhhHHHHHHHhcCCChhhHHHHHHHHHHhhHHH
Q 047135 80 VKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVR 122 (134)
Q Consensus 80 v~~kw~~s~waKk~~~~~~r~~ltDFdRFk~~~~kk~r~~~~~ 122 (134)
...+|..|. +.++.++-+.+++|++||+.|...+++..-+.
T Consensus 82 ~~~~~~~~~--~~~~~k~~~~~~~~~~r~~~~k~~~~~~~~~~ 122 (125)
T COG2163 82 VLAKLDKSA--KNLETKKVREPLTDAERFKVMKLVKEERLQVG 122 (125)
T ss_pred hhccccccc--hhhhhhhhhcccchHHHHHHHHHHHHHHhhhh
Confidence 999999999 99999999999999999999999988765443
No 5
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.94 E-value=5.9e-27 Score=164.50 Aligned_cols=77 Identities=38% Similarity=0.583 Sum_probs=74.4
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC---CCcceeeeccCeeeeceEEecCCCCChHHHHHHHHHhchHH
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP---DMVRGQMNFKRLSLTDIKIDIPRVPKKKTLIDAMEKADVKN 82 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp---~v~Rk~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~~~v~~ 82 (134)
-+|+||||++++|||+|++||||||+|++||||||| +++||++|++||+||++++++++++++++|+++|+++++.+
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~~~~~~~rk~kn~khl~lt~~ki~~~~~~~~~~vrk~l~~~~v~~ 82 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSLTGVKRRRCNIKHLEPTDKKVDIEKGASDEEVKKALEAAGLTE 82 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCCEEEEECCCcCCCCCeeechHHEEEeeEEEECCCCCCCHHHHHHHHHccchh
Confidence 379999999999999999999999999999999999 78999999999999999999999999999999999999875
No 6
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.50 E-value=5.4e-14 Score=106.37 Aligned_cols=59 Identities=29% Similarity=0.464 Sum_probs=53.7
Q ss_pred cceecCeEEEEccccCCCcEEEEEEeecC-------CeEEEeCC-CCcc---------------------eeeeccCeee
Q 047135 5 RYVEIGRVALVNYGKEYGRLVVIVDVLDQ-------NRALVDAP-DMVR---------------------GQMNFKRLSL 55 (134)
Q Consensus 5 r~veiGrVV~i~~G~~~Gk~~VIVdiiD~-------~rvLVDGp-~v~R---------------------k~~n~khl~l 55 (134)
+|+.||+||++++|+++|+.+|||..+|+ +++||.|. ..|| +.+|++||+|
T Consensus 3 K~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHlmP 82 (134)
T PTZ00471 3 KFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHFLP 82 (134)
T ss_pred ccccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeeceecc
Confidence 78999999999999999999999999999 69999995 4443 4699999999
Q ss_pred eceEEecC
Q 047135 56 TDIKIDIP 63 (134)
Q Consensus 56 T~~~i~i~ 63 (134)
|.|.++++
T Consensus 83 TRY~vdi~ 90 (134)
T PTZ00471 83 TRYNMDMS 90 (134)
T ss_pred cceeeecc
Confidence 99999987
No 7
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=99.02 E-value=4.4e-10 Score=85.15 Aligned_cols=59 Identities=31% Similarity=0.481 Sum_probs=54.0
Q ss_pred cceecCeEEEEccccCCCcEEEEEEeecCC-------eEEEeCC-CCcc---------------------eeeeccCeee
Q 047135 5 RYVEIGRVALVNYGKEYGRLVVIVDVLDQN-------RALVDAP-DMVR---------------------GQMNFKRLSL 55 (134)
Q Consensus 5 r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~-------rvLVDGp-~v~R---------------------k~~n~khl~l 55 (134)
.|+.||.||++.+|+++|+.+|||.-+|+. ++||.|. .+|| +.+|++||++
T Consensus 3 kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~hlMp 82 (136)
T KOG3418|consen 3 KFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYNHLMP 82 (136)
T ss_pred ccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhccccccccccchhhhhcccceeEEEEeecccccC
Confidence 689999999999999999999999999998 9999998 4443 5899999999
Q ss_pred eceEEecC
Q 047135 56 TDIKIDIP 63 (134)
Q Consensus 56 T~~~i~i~ 63 (134)
|.++++++
T Consensus 83 tRy~vdv~ 90 (136)
T KOG3418|consen 83 TRYTVDVL 90 (136)
T ss_pred cceEEeeh
Confidence 99999976
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=97.86 E-value=3.4e-05 Score=44.69 Aligned_cols=31 Identities=26% Similarity=0.353 Sum_probs=28.2
Q ss_pred cCeEEEEccccCCCcEEEEEEeecCC-eEEEe
Q 047135 9 IGRVALVNYGKEYGRLVVIVDVLDQN-RALVD 39 (134)
Q Consensus 9 iGrVV~i~~G~~~Gk~~VIVdiiD~~-rvLVD 39 (134)
+|..|.+..||++|+.+.|++|.+++ +|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999876 88775
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.56 E-value=0.0038 Score=33.87 Aligned_cols=26 Identities=23% Similarity=0.291 Sum_probs=23.8
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD 32 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD 32 (134)
+++|..|.+..|+++|..+.|+++-+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999999854
No 10
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=96.15 E-value=0.015 Score=43.60 Aligned_cols=53 Identities=19% Similarity=0.188 Sum_probs=40.2
Q ss_pred eecCeEEEEccccCCCcEEEEEEee-cCCeEEEeCC------CCcc-eeeeccCeeeeceE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVL-DQNRALVDAP------DMVR-GQMNFKRLSLTDIK 59 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdii-D~~rvLVDGp------~v~R-k~~n~khl~lT~~~ 59 (134)
+..|-.|.|.+|+|+|+-+-|+.|. +.++|+|+|- |... -.+.+.++++++.-
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~ 106 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLD 106 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCeEEEcccchhHeEEEeCc
Confidence 6789999999999999999999997 4678999997 2222 24555566655543
No 11
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.99 E-value=0.023 Score=39.15 Aligned_cols=36 Identities=28% Similarity=0.412 Sum_probs=32.1
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
-+..|--|.+.+|+|+||...|+.|.. .++|+|+|-
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 366899999999999999999999974 678999997
No 12
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.89 E-value=0.016 Score=40.58 Aligned_cols=36 Identities=19% Similarity=0.432 Sum_probs=32.2
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
-+..|-.|.+.+|+|+||...|..|.- .++|+|+|-
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 44 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 467899999999999999999999975 578999997
No 13
>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=95.02 E-value=0.068 Score=38.85 Aligned_cols=35 Identities=26% Similarity=0.420 Sum_probs=31.6
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
+..|--|.+..|+|+||...|+.|.. .++|+|+|-
T Consensus 4 ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 39 (104)
T TIGR01079 4 IKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGV 39 (104)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCc
Confidence 56899999999999999999999975 678999997
No 14
>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=94.74 E-value=0.075 Score=39.39 Aligned_cols=53 Identities=15% Similarity=0.110 Sum_probs=40.0
Q ss_pred eecCeEEEEccccCCCcEEEEEEee-cCCeEEEeCCC------Ccc-eeeeccCeeeeceE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVL-DQNRALVDAPD------MVR-GQMNFKRLSLTDIK 59 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdii-D~~rvLVDGp~------v~R-k~~n~khl~lT~~~ 59 (134)
+..|--|.|..|+|+|+-..|+.|. ..+.|+|+|-. ++. -.+++..|+++++-
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l~ 102 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITKLN 102 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeEEEeeechHHeEEEecc
Confidence 6789999999999999999999997 46789999972 111 24555666665544
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=94.58 E-value=0.11 Score=37.79 Aligned_cols=36 Identities=25% Similarity=0.446 Sum_probs=32.0
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
-+..|--|.+.+|+|+|+...|..|.- .++|+|+|-
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 366899999999999999999999974 688999996
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.05 E-value=0.14 Score=39.53 Aligned_cols=53 Identities=15% Similarity=0.098 Sum_probs=40.0
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCCCCc-c------eeeeccCeeeeceE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAPDMV-R------GQMNFKRLSLTDIK 59 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp~v~-R------k~~n~khl~lT~~~ 59 (134)
|..|-.|.|..|.|+|+-+-|+.|.. .++|+|+|-.+. . -.|++..+++|+.-
T Consensus 47 IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~l~ 107 (143)
T PTZ00194 47 VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLK 107 (143)
T ss_pred eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEccc
Confidence 66799999999999999999999974 678999998222 1 24555555555543
No 17
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=91.11 E-value=0.42 Score=35.04 Aligned_cols=35 Identities=26% Similarity=0.345 Sum_probs=32.0
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp 41 (134)
.|..|-.|++.+|.|+|+-..|+.+.-.. |+|.|-
T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEGv 38 (104)
T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEGV 38 (104)
T ss_pred ceecCCEEEEEecCCCCcceEEEEEecCe-EEEECc
Confidence 46789999999999999999999998877 999998
No 18
>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=90.92 E-value=0.42 Score=35.59 Aligned_cols=35 Identities=11% Similarity=0.079 Sum_probs=30.4
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeecCCeEEEeC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDA 40 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDG 40 (134)
.+++|.-|.+..||.+|--+.|+++-+++++.|-=
T Consensus 108 ~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l 142 (159)
T TIGR01955 108 LPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLL 142 (159)
T ss_pred CCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEE
Confidence 46799999999999999999999997677877743
No 19
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=90.45 E-value=0.51 Score=35.82 Aligned_cols=37 Identities=16% Similarity=0.043 Sum_probs=30.8
Q ss_pred cceecCeEEEEccccCCCcEEEEEEee-cCCeEEEeCC
Q 047135 5 RYVEIGRVALVNYGKEYGRLVVIVDVL-DQNRALVDAP 41 (134)
Q Consensus 5 r~veiGrVV~i~~G~~~Gk~~VIVdii-D~~rvLVDGp 41 (134)
.-+++|..|.|..||.+|--+.|+.+- +.+++.|.=.
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~ 162 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVS 162 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEE
Confidence 346799999999999999999999986 4568887433
No 20
>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=89.78 E-value=0.6 Score=35.32 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=29.9
Q ss_pred eecCeEEEEccccCCCcEEEEEEee-cCCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVL-DQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdii-D~~rvLVDGp 41 (134)
+++|.-|.|..||.+|--++|+.+- +++++.|.=+
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~ 155 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVS 155 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEE
Confidence 6799999999999999999999985 4568888444
No 21
>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=89.77 E-value=0.66 Score=34.40 Aligned_cols=36 Identities=11% Similarity=0.177 Sum_probs=29.8
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
.+++|..|.+..||++|-.+.|+++-. .++|+|+..
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~ 122 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEE
Confidence 477999999999999999999999853 456666554
No 22
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=89.70 E-value=0.22 Score=40.48 Aligned_cols=30 Identities=20% Similarity=0.295 Sum_probs=25.3
Q ss_pred ccceecCeEEEEccccCCCcEEEEEEeecC
Q 047135 4 KRYVEIGRVALVNYGKEYGRLVVIVDVLDQ 33 (134)
Q Consensus 4 ~r~veiGrVV~i~~G~~~Gk~~VIVdiiD~ 33 (134)
.+|+++||||.+..|.+...++|||+....
T Consensus 70 ~~fL~~GRlV~v~~~~~~~~wgvvv~~~~~ 99 (268)
T PF13234_consen 70 LPFLQPGRLVVVRDGDRDFGWGVVVNFAKK 99 (268)
T ss_dssp HHHS-TTEEEEEEETTCEEEEEEEEEEEE-
T ss_pred HHhCCCCCEEEEecCCCccceeEEEecccc
Confidence 369999999999999999999999999653
No 23
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=89.49 E-value=0.61 Score=35.09 Aligned_cols=36 Identities=11% Similarity=0.103 Sum_probs=31.4
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp 41 (134)
.+++|.-|.+..||.+|--++|.++-++++++|.=.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~ 144 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLN 144 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeeh
Confidence 467999999999999999999999987889888443
No 24
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=87.27 E-value=1.9 Score=32.70 Aligned_cols=35 Identities=17% Similarity=0.198 Sum_probs=29.6
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec-CCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD-QNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLVDGp 41 (134)
+++|..|.+..||++|-.+.|+++-. .++++|+.-
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll 130 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEE
Confidence 67999999999999999999999964 556666654
No 25
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=84.96 E-value=1.4 Score=36.27 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=30.6
Q ss_pred eecCeEEEEccccCCCcEEEEEEeecC-CeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLDQ-NRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD~-~rvLVDGp 41 (134)
+-.|-.|.+..|+|+||...|+.++-| |-|.|+|-
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gl 108 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGL 108 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecCceEEEccc
Confidence 457999999999999999999999965 67888886
No 26
>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=80.51 E-value=0.053 Score=38.26 Aligned_cols=18 Identities=33% Similarity=0.584 Sum_probs=16.4
Q ss_pred eeeeccCeeeeceEEecC
Q 047135 46 GQMNFKRLSLTDIKIDIP 63 (134)
Q Consensus 46 k~~n~khl~lT~~~i~i~ 63 (134)
+.+|++||+||.|.++++
T Consensus 22 K~iNynHlmPTRY~vd~~ 39 (85)
T PF01777_consen 22 KVINYNHLMPTRYSVDIP 39 (85)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred EEeeccceEeeeeeeech
Confidence 689999999999999874
No 27
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=78.23 E-value=3.7 Score=34.43 Aligned_cols=35 Identities=17% Similarity=0.270 Sum_probs=30.5
Q ss_pred eecCeEEEEccccCCCcEEEEEEee-cCCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVL-DQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdii-D~~rvLVDGp 41 (134)
+++|.-|.|..||.+|--+.|.++- +.+++.|.=+
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~ 241 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVE 241 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEE
Confidence 6799999999999999999999997 4788887433
No 28
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=76.51 E-value=4.4 Score=31.85 Aligned_cols=28 Identities=21% Similarity=0.130 Sum_probs=24.7
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeecC
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQ 33 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD~ 33 (134)
-+++|..|.+..||++|=.+.|.++-.+
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd~e 150 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVDEE 150 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEcCc
Confidence 4789999999999999999999888544
No 29
>PLN00036 40S ribosomal protein S4; Provisional
Probab=72.79 E-value=6.2 Score=33.19 Aligned_cols=32 Identities=25% Similarity=0.374 Sum_probs=28.0
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec----CCeEEE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD----QNRALV 38 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD----~~rvLV 38 (134)
+|+|-+|+++.|+..|+.++|+++.- .+.|.|
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i 210 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHV 210 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEE
Confidence 58999999999999999999999982 357777
No 30
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=68.07 E-value=8.8 Score=32.30 Aligned_cols=32 Identities=25% Similarity=0.385 Sum_probs=27.2
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec----CCeEEE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD----QNRALV 38 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD----~~rvLV 38 (134)
+|+|-+|+++.|+..|+.++|+++.- .+.|.|
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i 210 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHV 210 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEE
Confidence 58999999999999999999999552 256777
No 31
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=67.40 E-value=5.5 Score=39.05 Aligned_cols=34 Identities=26% Similarity=0.415 Sum_probs=30.3
Q ss_pred ccceecCeEEEEccccCCCcEEEEEEeecCCeEEE
Q 047135 4 KRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALV 38 (134)
Q Consensus 4 ~r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLV 38 (134)
.+++++|-.|.|.+|++.|.-.+||-| +++.|.+
T Consensus 457 rKyF~~GDhVKVi~G~~eG~tGlVvrV-e~~~vi~ 490 (1024)
T KOG1999|consen 457 RKYFEPGDHVKVIAGRYEGDTGLVVRV-EQGDVIL 490 (1024)
T ss_pred hhhccCCCeEEEEeccccCCcceEEEE-eCCeEEE
Confidence 678999999999999999999999998 6666665
No 32
>PRK04313 30S ribosomal protein S4e; Validated
Probab=64.97 E-value=6.3 Score=32.66 Aligned_cols=33 Identities=24% Similarity=0.358 Sum_probs=28.3
Q ss_pred eecCeEEEEccccCCCcEEEEEEeec-----CCeEEEe
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLD-----QNRALVD 39 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD-----~~rvLVD 39 (134)
+|+|-+|++..|+..|+.++|++|.- .|.|.|.
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~ 209 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLE 209 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEE
Confidence 58999999999999999999999963 3677773
No 33
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=61.51 E-value=8 Score=32.75 Aligned_cols=32 Identities=28% Similarity=0.376 Sum_probs=27.6
Q ss_pred eecCeEEEEccccCCCcEEEEEEeecC----CeEEE
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLDQ----NRALV 38 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD~----~rvLV 38 (134)
+|+|-+|++..|+..|+.++|+++.-+ +.|.+
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i 207 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARL 207 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEE
Confidence 589999999999999999999999533 56766
No 34
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=58.85 E-value=21 Score=28.38 Aligned_cols=44 Identities=20% Similarity=0.318 Sum_probs=32.5
Q ss_pred ccc--ceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC-CCcceee
Q 047135 3 FKR--YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP-DMVRGQM 48 (134)
Q Consensus 3 f~r--~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp-~v~Rk~~ 48 (134)
|.+ -+++|..+....+. |..-++|-=++..+|+||+- .+.=|.+
T Consensus 85 F~~~~~~~vGm~~~~~~~~--~~~~~~V~~V~~~~V~VDfNHpLAGktL 131 (174)
T COG1047 85 FQGVGELEVGMEVEAEGGD--GEIPGVVTEVSGDRVTVDFNHPLAGKTL 131 (174)
T ss_pred hCcCCCCCCCcEEEEcCCC--ceeeEEEEEEcCCEEEEeCCCcCCCCeE
Confidence 555 38999999987655 77766666679999999997 4444443
No 35
>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=57.92 E-value=28 Score=24.60 Aligned_cols=35 Identities=20% Similarity=0.319 Sum_probs=25.6
Q ss_pred ccceecCeEEEE--ccccCCCcEEEEEEeecCCeEEE
Q 047135 4 KRYVEIGRVALV--NYGKEYGRLVVIVDVLDQNRALV 38 (134)
Q Consensus 4 ~r~veiGrVV~i--~~G~~~Gk~~VIVdiiD~~rvLV 38 (134)
..-+++|-|+.. ..+...|-.++|.++.|++.+.|
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v 96 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITV 96 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEE
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEE
Confidence 345789999998 66778899999999988888888
No 36
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=51.67 E-value=16 Score=30.58 Aligned_cols=34 Identities=32% Similarity=0.420 Sum_probs=28.3
Q ss_pred eecCeEEEEccccCCCcEEEEEEeecC-----CeEEEeC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLDQ-----NRALVDA 40 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD~-----~rvLVDG 40 (134)
+|+|-+|++..|++.|....|++|--+ |-|-+++
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 589999999999999999999999654 4566643
No 37
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=50.25 E-value=16 Score=24.62 Aligned_cols=35 Identities=17% Similarity=0.185 Sum_probs=26.8
Q ss_pred eecCeEEEEccccCCCcEEEEEEee---cCCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVL---DQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdii---D~~rvLVDGp 41 (134)
--+|+-+++..||++++..+|-.-- ..++++|-|.
T Consensus 3 di~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~~ 40 (68)
T PF13051_consen 3 DIVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIGE 40 (68)
T ss_pred cccccEeeeccCCccceeEEEecchhhcCCcEEEEECC
Confidence 3479999999999999998876542 3478888443
No 38
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.16 E-value=28 Score=26.18 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=27.4
Q ss_pred ceecCeEEEE--ccccCCCcEEEEEEeecCCeEEE
Q 047135 6 YVEIGRVALV--NYGKEYGRLVVIVDVLDQNRALV 38 (134)
Q Consensus 6 ~veiGrVV~i--~~G~~~Gk~~VIVdiiD~~rvLV 38 (134)
-+|-|.||.- ..|||.|.-.||+-|-|+..|+-
T Consensus 58 vle~gevvr~vP~~GpY~G~pVVV~Pik~~g~via 92 (123)
T COG4048 58 VLEKGEVVREVPIIGPYRGLPVVVAPIKDEGEVIA 92 (123)
T ss_pred HHhhCceeeeCCCCCccCCceEEEEEeccCCeEEE
Confidence 4567777764 67999999999999999988764
No 39
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=43.45 E-value=52 Score=24.98 Aligned_cols=32 Identities=28% Similarity=0.346 Sum_probs=23.7
Q ss_pred eecCeEEEEccccCCCc--EEEEEEeecCCeEEEeCC
Q 047135 7 VEIGRVALVNYGKEYGR--LVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk--~~VIVdiiD~~rvLVDGp 41 (134)
+++|+.+... ++ .|. .+.|++| +++.|.||+-
T Consensus 93 ~~~G~~~~~~-~~-~G~~~~~~V~~i-~~~~v~vD~N 126 (156)
T PRK15095 93 PEIGAIMLFT-AM-DGSEMPGVIREI-NGDSITVDFN 126 (156)
T ss_pred CCCCCEEEEE-CC-CCCEEEEEEEEE-cCCEEEEECC
Confidence 6799998764 33 354 5667775 8999999996
No 40
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=43.07 E-value=28 Score=32.17 Aligned_cols=29 Identities=31% Similarity=0.397 Sum_probs=25.7
Q ss_pred cceecCeEEEEccccCCCcEEEEEEeecC
Q 047135 5 RYVEIGRVALVNYGKEYGRLVVIVDVLDQ 33 (134)
Q Consensus 5 r~veiGrVV~i~~G~~~Gk~~VIVdiiD~ 33 (134)
|-+-+|.-|.|.+|+++|.+.||=|+-|+
T Consensus 350 Rd~aigktVrIr~g~yKG~lGVVKdv~~~ 378 (607)
T COG5164 350 RDPAIGKTVRIRCGEYKGHLGVVKDVDRN 378 (607)
T ss_pred cccccCceEEEeecccccccceeeeccCc
Confidence 55678999999999999999999998654
No 41
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=40.77 E-value=49 Score=30.17 Aligned_cols=35 Identities=26% Similarity=0.322 Sum_probs=27.9
Q ss_pred eecCeEEEEc---------cccCCCcEEEEEEeecCCeEEEeCC
Q 047135 7 VEIGRVALVN---------YGKEYGRLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~---------~G~~~Gk~~VIVdiiD~~rvLVDGp 41 (134)
+++|+-|.++ .-...|..+.|++++|++|++|-+.
T Consensus 83 l~~g~~v~l~e~~~~v~~~~~~~~g~~~~~~~~~~~~~~~v~~~ 126 (512)
T TIGR03689 83 LVPGQTVRLNEALQVVEARDFETVGEIATLKEVLGDGRALVVDH 126 (512)
T ss_pred CCCCCEEEECCcceeeccCCCCCCCceEEEEEEeCCCeEEEEeC
Confidence 5688888886 3356799999999999999999333
No 42
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=34.75 E-value=63 Score=22.96 Aligned_cols=32 Identities=25% Similarity=0.365 Sum_probs=25.2
Q ss_pred ceecCeEEEE--ccccCCCcEEEEEEeecC-CeEE
Q 047135 6 YVEIGRVALV--NYGKEYGRLVVIVDVLDQ-NRAL 37 (134)
Q Consensus 6 ~veiGrVV~i--~~G~~~Gk~~VIVdiiD~-~rvL 37 (134)
-++-|+++.. ..|+|+|...+|+=|.|+ +.++
T Consensus 40 vl~~g~v~r~~P~~G~Y~G~PViV~PI~~~~g~vi 74 (84)
T PF09884_consen 40 VLETGKVIRVTPIEGPYKGVPVIVAPIKDEDGEVI 74 (84)
T ss_pred HHHcCCEEEeccCCcccCCeeEEEEEEEcCCCCEE
Confidence 3556777655 679999999999999987 6665
No 43
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=33.31 E-value=1.1e+02 Score=21.11 Aligned_cols=35 Identities=11% Similarity=0.207 Sum_probs=20.2
Q ss_pred ccccCCCcEEEEEEeecCCeEEEeCCCCcceeeecc
Q 047135 16 NYGKEYGRLVVIVDVLDQNRALVDAPDMVRGQMNFK 51 (134)
Q Consensus 16 ~~G~~~Gk~~VIVdiiD~~rvLVDGp~v~Rk~~n~k 51 (134)
..+-..|.++||..+ |++.++|--|.-.++.++..
T Consensus 84 ~~~~~~~~~~Vl~~~-~~~~~~i~dp~~~~~~~~~~ 118 (136)
T cd02418 84 IKEWKLNHYVVVYKI-KKKKILIADPAVGITKISKE 118 (136)
T ss_pred ccCCCCCeEEEEEEE-cCCEEEEECCCCCCEEeeHH
Confidence 334566788888886 56677773232234444443
No 44
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=32.37 E-value=1.1e+02 Score=19.68 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=21.3
Q ss_pred eecCeEEEEcc--cc-CCC-cEEEEEEeecCCeEEEeCC
Q 047135 7 VEIGRVALVNY--GK-EYG-RLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 7 veiGrVV~i~~--G~-~~G-k~~VIVdiiD~~rvLVDGp 41 (134)
+++|+-+.+.- |. ..+ =...|+|+.|+++++|.-|
T Consensus 1 L~iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 1 LKIGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp --TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 46888888844 32 222 3567889999999999888
No 45
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=30.86 E-value=53 Score=32.30 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=23.0
Q ss_pred ceecCeEEEEccccCCCcEEEEEEee
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVL 31 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdii 31 (134)
|+++||+|.+..|.+--.+.|+|+.+
T Consensus 650 fLq~GRlV~v~~g~~d~~WGvvv~f~ 675 (1041)
T KOG0948|consen 650 FLQPGRLVKVKVGGDDFFWGVVVNFI 675 (1041)
T ss_pred cccCCceEEEecCCCCCceeEEEEEE
Confidence 89999999999988886799999665
No 46
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=30.49 E-value=61 Score=32.18 Aligned_cols=33 Identities=27% Similarity=0.325 Sum_probs=28.9
Q ss_pred ceecCeEEEEccccCCCcEEEEEEeec-CCeEEE
Q 047135 6 YVEIGRVALVNYGKEYGRLVVIVDVLD-QNRALV 38 (134)
Q Consensus 6 ~veiGrVV~i~~G~~~Gk~~VIVdiiD-~~rvLV 38 (134)
-++.|.-|.+..|-|+|=||.|++|-+ +|+|+|
T Consensus 258 ~L~~gswVRiKrG~YKgDLAqVd~Vd~~~n~v~l 291 (1024)
T KOG1999|consen 258 QLSEGSWVRIKRGKYKGDLAQVDDVDENRNRVRL 291 (1024)
T ss_pred ccCccceEEEeccccccceeeeeeecccCCEEEE
Confidence 357899999999999999999999954 688887
No 47
>COG0684 MenG Demethylmenaquinone methyltransferase [Coenzyme metabolism]
Probab=29.28 E-value=49 Score=26.94 Aligned_cols=33 Identities=21% Similarity=0.167 Sum_probs=28.9
Q ss_pred cCeEEEEccccCCCcEEEEEEeecCCeEEE-eCC
Q 047135 9 IGRVALVNYGKEYGRLVVIVDVLDQNRALV-DAP 41 (134)
Q Consensus 9 iGrVV~i~~G~~~Gk~~VIVdiiD~~rvLV-DGp 41 (134)
.|+.+.+.+.++-+-+.+.++-...++||| ||.
T Consensus 46 ~G~A~TV~~~~~d~~~~~al~~~~~GdVLVid~~ 79 (210)
T COG0684 46 VGPAVTVRCFPDDWLLHVALEQAGPGDVLVIDGG 79 (210)
T ss_pred eeEEEEEEEeCCCchhhheeecCCCCCEEEEeCC
Confidence 699999999998888888888888899999 776
No 48
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=27.53 E-value=1.5e+02 Score=17.94 Aligned_cols=32 Identities=16% Similarity=0.092 Sum_probs=24.0
Q ss_pred cCeEEEEccccCCCcEEEEEEeecCCeEEEeCC
Q 047135 9 IGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 9 iGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp 41 (134)
+|+-|.+.. ++.---+++.+|-|+.+.+|.-+
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 577888877 44444688999989999999444
No 49
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=26.29 E-value=37 Score=29.70 Aligned_cols=37 Identities=22% Similarity=0.247 Sum_probs=27.2
Q ss_pred cceecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC
Q 047135 5 RYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP 41 (134)
Q Consensus 5 r~veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp 41 (134)
=++||||-..-.+|-.-.+..-|.+.-+.++|+|||.
T Consensus 272 l~~EPGR~iv~~aG~Lvt~V~~~k~~~~~~~v~vD~g 308 (394)
T COG0019 272 LILEPGRAIVANAGVLVTEVLDVKENGERNFVIVDGG 308 (394)
T ss_pred EEEccchhhhhcceeEEEEEEEEEEecCceEEEEech
Confidence 3689999998888865555555555544689999998
No 50
>PF12923 RRP7: Ribosomal RNA-processing protein 7 (RRP7); InterPro: IPR024326 Ribosomal RNA-processing protein 7 (RRP7) is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly []. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [, ]. This entry includes RRP7 and homologous sequences from other organisms.
Probab=25.04 E-value=1.2e+02 Score=22.36 Aligned_cols=33 Identities=27% Similarity=0.368 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCChhhHHHHHHHHHHhhHHHHHH
Q 047135 93 LIVQKKRASLNDFDRFKLMLAKIKKGGLVRQEL 125 (134)
Q Consensus 93 ~~~~~~r~~ltDFdRFk~~~~kk~r~~~~~~~~ 125 (134)
...+.++..+.||=||++.-.|+..-.-+++.|
T Consensus 80 ~~kkkkkk~~~~FYrFQ~RE~kk~~l~eLrkkF 112 (131)
T PF12923_consen 80 EKKKKKKKELEDFYRFQIREKKKNELAELRKKF 112 (131)
T ss_pred HHhhccccccccHHHHHHHHHHHHHHHHHHHHH
Confidence 346678889999999999988887766666655
No 51
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=24.58 E-value=1.6e+02 Score=23.55 Aligned_cols=40 Identities=15% Similarity=0.336 Sum_probs=25.6
Q ss_pred eecCeEEEEccccCCCcEEEEEEeecCCeEEEeCC-CCcceee
Q 047135 7 VEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP-DMVRGQM 48 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~~VIVdiiD~~rvLVDGp-~v~Rk~~ 48 (134)
+++|..+.... ..|.+.++|-=++++.|.||+- ++.=|.+
T Consensus 90 l~~G~~~~~~~--~~G~~~~~V~ev~~d~V~vD~NHPLAG~~L 130 (196)
T PRK10737 90 LQVGMRFLAET--DQGPVPVEITAVEDDHVVVDGNHMLAGQNL 130 (196)
T ss_pred CCCCCEEEEeC--CCCcEEEEEEEEcCCEEEEECCCcCCCCEE
Confidence 68997776642 3455455444458889999997 5443433
No 52
>PF02800 Gp_dh_C: Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; InterPro: IPR020829 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme []. GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis []. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins []. This entry represents the C-terminal domain which is a mixed alpha/antiparallel beta fold.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 1DSS_R 1IHY_C 1CRW_R 1IHX_B 1SZJ_R 3HJA_D 2YYY_B 1OBF_O 3PYM_A 2VYN_D ....
Probab=24.47 E-value=1.4e+02 Score=22.68 Aligned_cols=32 Identities=19% Similarity=0.403 Sum_probs=27.6
Q ss_pred eeeccCeeeeceEEecCCCCChHHHHHHHHHh
Q 047135 47 QMNFKRLSLTDIKIDIPRVPKKKTLIDAMEKA 78 (134)
Q Consensus 47 ~~n~khl~lT~~~i~i~~~~~~~~v~ka~e~~ 78 (134)
+++.-++++.+..+.+.+.++-++|.++|+++
T Consensus 77 rVPt~~~s~~dl~~~l~k~~t~eeV~~~~~~a 108 (157)
T PF02800_consen 77 RVPTPNVSLHDLTVELEKPVTKEEVNEALKQA 108 (157)
T ss_dssp EESSSSEEEEEEEEEESSSS-HHHHHHHHHHH
T ss_pred eeeecccCceEEEEecccchhhhhhhhhhhhh
Confidence 57888999999999999999999999999874
No 53
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=22.01 E-value=1.9e+02 Score=17.25 Aligned_cols=30 Identities=20% Similarity=0.261 Sum_probs=21.4
Q ss_pred eecCeEEEEccccCCCcE--EEEEEeecCCeEEE
Q 047135 7 VEIGRVALVNYGKEYGRL--VVIVDVLDQNRALV 38 (134)
Q Consensus 7 veiGrVV~i~~G~~~Gk~--~VIVdiiD~~rvLV 38 (134)
+++|..|.... ..|.+ |.|+++.+++.+.|
T Consensus 3 ~~~G~~~~a~~--~d~~wyra~I~~~~~~~~~~V 34 (57)
T smart00333 3 FKVGDKVAARW--EDGEWYRARIIKVDGEQLYEV 34 (57)
T ss_pred CCCCCEEEEEe--CCCCEEEEEEEEECCCCEEEE
Confidence 46898888877 35554 68888877565555
No 54
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=21.27 E-value=1.4e+02 Score=20.54 Aligned_cols=20 Identities=40% Similarity=0.730 Sum_probs=15.2
Q ss_pred CCCcEEEEEEeecCCeEEE-eC
Q 047135 20 EYGRLVVIVDVLDQNRALV-DA 40 (134)
Q Consensus 20 ~~Gk~~VIVdiiD~~rvLV-DG 40 (134)
..|.++||.++ ++++++| |.
T Consensus 83 ~~~h~vVi~~~-~~~~~~i~dP 103 (131)
T PF03412_consen 83 KDGHFVVIYKI-DDGRVLIYDP 103 (131)
T ss_dssp CCCEEEEEEEE-CCCEEEECCT
T ss_pred cCcceEEEEeE-cCcEEEEEeC
Confidence 56677888877 8888888 54
Done!