Query psy2461
Match_columns 462
No_of_seqs 296 out of 592
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 16:53:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2461hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01159 Ribosomal_L6e: Riboso 100.0 5.9E-41 1.3E-45 289.2 -2.4 106 221-333 1-106 (108)
2 KOG1694|consensus 100.0 5.2E-37 1.1E-41 278.0 8.7 140 154-334 12-151 (152)
3 COG2163 RPL14A Ribosomal prote 99.7 6E-18 1.3E-22 150.0 9.5 124 180-307 1-124 (125)
4 PTZ00471 60S ribosomal protein 99.3 9.2E-12 2E-16 112.1 6.7 62 183-244 4-90 (134)
5 PRK04333 50S ribosomal protein 98.9 1.7E-09 3.7E-14 90.5 6.6 70 183-258 3-72 (84)
6 KOG1694|consensus 98.4 5.8E-08 1.3E-12 89.3 -0.9 137 38-233 12-152 (152)
7 COG2163 RPL14A Ribosomal prote 98.2 2.5E-06 5.5E-11 76.5 5.1 55 64-118 1-67 (125)
8 KOG3418|consensus 98.1 5.5E-06 1.2E-10 75.3 5.3 73 181-258 2-102 (136)
9 PTZ00065 60S ribosomal protein 97.6 0.00013 2.9E-09 66.1 6.5 61 183-244 7-67 (130)
10 PTZ00471 60S ribosomal protein 97.4 0.00014 3.1E-09 66.2 4.3 35 67-101 4-45 (134)
11 PRK04333 50S ribosomal protein 96.2 0.0068 1.5E-07 51.2 4.4 36 67-102 3-38 (84)
12 CHL00141 rpl24 ribosomal prote 93.3 0.098 2.1E-06 44.1 3.6 64 182-248 7-76 (83)
13 KOG3418|consensus 92.9 0.13 2.7E-06 47.5 4.1 31 65-95 2-32 (136)
14 PRK12281 rplX 50S ribosomal pr 92.6 0.16 3.4E-06 42.3 3.9 63 183-248 6-74 (76)
15 PRK01191 rpl24p 50S ribosomal 88.5 0.72 1.6E-05 41.8 4.6 59 183-250 45-104 (120)
16 PRK00004 rplX 50S ribosomal pr 87.8 0.63 1.4E-05 40.6 3.6 63 183-248 4-72 (105)
17 TIGR01079 rplX_bact ribosomal 86.8 0.97 2.1E-05 39.6 4.2 63 183-248 3-72 (104)
18 COG0198 RplX Ribosomal protein 84.8 1.3 2.8E-05 39.3 4.0 59 184-249 5-71 (104)
19 TIGR01080 rplX_A_E ribosomal p 84.3 1.3 2.9E-05 39.6 4.0 64 183-255 41-106 (114)
20 KOG3421|consensus 81.6 1.9 4E-05 40.1 3.9 62 181-244 4-65 (136)
21 PTZ00194 60S ribosomal protein 77.5 3.3 7.1E-05 38.7 4.2 64 183-255 46-111 (143)
22 smart00739 KOW KOW (Kyprides, 75.6 4.1 8.9E-05 26.3 3.2 24 184-207 2-25 (28)
23 PF00467 KOW: KOW motif; Inte 69.9 7.9 0.00017 26.9 3.6 26 186-211 1-26 (32)
24 PF01159 Ribosomal_L6e: Riboso 57.2 3.2 6.9E-05 37.0 -0.3 16 101-116 7-24 (108)
25 CHL00141 rpl24 ribosomal prote 55.1 23 0.0005 30.0 4.5 37 65-101 6-43 (83)
26 PTZ00065 60S ribosomal protein 54.4 18 0.00039 33.5 4.0 37 66-102 6-42 (130)
27 smart00739 KOW KOW (Kyprides, 50.9 25 0.00054 22.6 3.3 24 68-91 2-25 (28)
28 PF10543 ORF6N: ORF6N domain; 44.0 3.5 7.5E-05 34.6 -2.0 28 196-233 6-33 (88)
29 PRK12281 rplX 50S ribosomal pr 40.5 51 0.0011 27.6 4.3 35 67-101 6-41 (76)
30 PF00467 KOW: KOW motif; Inte 35.3 76 0.0016 22.0 3.9 26 70-95 1-26 (32)
31 KOG3421|consensus 28.1 55 0.0012 30.7 2.9 39 65-103 4-42 (136)
32 PRK01191 rpl24p 50S ribosomal 25.9 1.1E+02 0.0024 28.1 4.3 34 68-101 46-80 (120)
33 TIGR01079 rplX_bact ribosomal 24.3 1.3E+02 0.0028 26.6 4.4 35 67-101 3-38 (104)
34 PTZ00194 60S ribosomal protein 22.2 1.3E+02 0.0028 28.4 4.1 34 68-101 47-81 (143)
35 PRK00004 rplX 50S ribosomal pr 22.1 1.5E+02 0.0033 26.0 4.4 35 67-101 4-39 (105)
36 PF15086 UPF0542: Uncharacteri 21.7 60 0.0013 27.8 1.7 23 398-420 38-60 (74)
No 1
>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=100.00 E-value=5.9e-41 Score=289.16 Aligned_cols=106 Identities=49% Similarity=0.733 Sum_probs=97.7
Q ss_pred ccCCcceeeccceEEEcceeeecCCcccCCccChhhhhhhhhccCCCCcccccccchhhhhhhccchHHHHHhHHHHhHH
Q psy2461 221 LNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMDEQ 300 (462)
Q Consensus 221 lNGVPLRRVnQryVIATSTKVDISgVkip~~ltDaYFkkkK~~~kK~~k~~E~eIF~~e~keKy~iseqrKaDQK~VD~q 300 (462)
|||||||||||+|||||||+||||||++|++|||+||++.+. ++ ++++|++||+.+ +++|+++|||++|||+||++
T Consensus 1 iNGVPLRRVnQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~~--~k-~k~~e~~~f~~~-~~k~~~se~rk~dQK~VD~~ 76 (108)
T PF01159_consen 1 INGVPLRRVNQAYVIATSTKVDISGVKIPEKIDDAYFKRKKK--KK-KKKGEGDFFAEK-KEKYKVSEQRKADQKAVDAQ 76 (108)
T ss_dssp SSS--SEEESSCCCEECSCESCHCCHHH-CCTTGSSSCHCCC--CH-HHHHHCHCCHHH-HHCCCCHHHHHHHHHCSHHC
T ss_pred CCCCcceecccceEEEEeeEEeccccchhhccchHHHHhhhh--cc-ccccHHHHHhcc-cccccCCHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999998874 33 678899999988 78999999999999999999
Q ss_pred HHHHhhcCCchhhhhccCCCccccCCCCCCCCC
Q psy2461 301 LLKVIKVHPEKKILLSYPPWGWINTRDFNQKKL 333 (462)
Q Consensus 301 LL~~IKkvp~~K~Lk~YL~S~FsLt~~fy~~k~ 333 (462)
||++||++|+ |++||+|+|+|++|.|||++
T Consensus 77 ll~aIkk~p~---L~~YL~s~FsL~~g~~PH~m 106 (108)
T PF01159_consen 77 LLAAIKKHPE---LKGYLKSRFSLRKGDYPHKM 106 (108)
T ss_dssp SHCCCCTCCC---THHHHHCCCCHCTTTSSSSS
T ss_pred HHHHHhcCHH---HHHhhhhheeCCCCCcCccC
Confidence 9999999998 99999999999999999986
No 2
>KOG1694|consensus
Probab=100.00 E-value=5.2e-37 Score=277.98 Aligned_cols=140 Identities=37% Similarity=0.642 Sum_probs=130.5
Q ss_pred CCCCCCCcccCccccCCCCcccchhccccCcCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccce
Q psy2461 154 PKAYYPTKDKIKKVRGRRPFRKHARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNY 233 (462)
Q Consensus 154 ~pryYPtEDvp~k~~s~K~fs~h~rKLRsSItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQry 233 (462)
+|+|||+ ..+.++.++++||+||+||||||||+ .+||+|++|+||+|
T Consensus 12 ~~~~yp~--------~k~~~~~~~~k~r~~l~~gtvliil~-------------------------~~ng~~~~~v~~~~ 58 (152)
T KOG1694|consen 12 PPADYPR--------KKARYSAKPSKLRASLTPGTVLIILA-------------------------PINGVPLKRVNERY 58 (152)
T ss_pred Chhhccc--------hhccccccchhhhhccCCCeeEEEec-------------------------ccCCcCcccccceE
Confidence 9999998 12345677899999999999999999 69999999999999
Q ss_pred EEEcceeeecCCcccCCccChhhhhhhhhccCCCCcccccccchhhhhhhccchHHHHHhHHHHhHHHHHHhhcCCchhh
Q psy2461 234 VIATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMDEQLLKVIKVHPEKKI 313 (462)
Q Consensus 234 VIATSTKVDISgVkip~~ltDaYFkkkK~~~kK~~k~~E~eIF~~e~keKy~iseqrKaDQK~VD~qLL~~IKkvp~~K~ 313 (462)
+|+||+ ||++||++|+|+||+||.+.+. ++ ++++|++||+.+ +|+|+|+||++.|||+||++||++||.+|+
T Consensus 59 ~~~ts~-i~~~~vk~~e~~td~yf~K~k~--~~-~k~~e~~i~~~e-kekyeIteq~kiDqKaVDs~il~~iK~ip~--- 130 (152)
T KOG1694|consen 59 VATTSK-IDPSNVKIPEHLTDAYFKKKKL--KK-KKTQEGEIFAEE-KEKYEITEQRKIDQKAVDSQILPKIKAIPQ--- 130 (152)
T ss_pred Eeeeee-eccccccccccccHHHHhhhhc--cc-cccccchhhccc-ccccccchhhhhhHHHHHHHHHHHHhhchH---
Confidence 999987 9999999999999999998877 55 789999999999 899999999999999999999999999999
Q ss_pred hhccCCCccccCCCCCCCCCC
Q psy2461 314 LLSYPPWGWINTRDFNQKKLS 334 (462)
Q Consensus 314 Lk~YL~S~FsLt~~fy~~k~~ 334 (462)
|+.||.++|+|+||.|++++.
T Consensus 131 lk~yl~~~f~l~~g~~Ph~l~ 151 (152)
T KOG1694|consen 131 LKKYLGSVFALTNGIYPHKLK 151 (152)
T ss_pred hhhccchhhhccCCCCccccc
Confidence 999999999999999999875
No 3
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=6e-18 Score=150.01 Aligned_cols=124 Identities=23% Similarity=0.300 Sum_probs=99.9
Q ss_pred cccCcCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccceEEEcceeeecCCcccCCccChhhhhh
Q psy2461 180 LRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFRR 259 (462)
Q Consensus 180 LRsSItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDISgVkip~~ltDaYFkk 259 (462)
++++|.||+|+++++||++||+||+|++++.+.+|++||..+||||.+|+|-+|+++|++.+|+......+.+.-+|+..
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a~ 80 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEAA 80 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHhh
Confidence 46889999999999999999999999999999999999999999999999999999999999998776666777788876
Q ss_pred hhhccCCCCcccccccchhhhhhhccchHHHHHhHHHHhHHHHHHhhc
Q psy2461 260 IKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMDEQLLKVIKV 307 (462)
Q Consensus 260 kK~~~kK~~k~~E~eIF~~e~keKy~iseqrKaDQK~VD~qLL~~IKk 307 (462)
... -+ .-.+. +-|..++-.+.....+|.++||..++..+..+++
T Consensus 81 ~~~--~~-~~~~~-~~~~~k~~~~~~~~~~r~~~~k~~~~~~~~~~k~ 124 (125)
T COG2163 81 GVL--AK-LDKSA-KNLETKKVREPLTDAERFKVMKLVKEERLQVGKA 124 (125)
T ss_pred hhh--cc-ccccc-hhhhhhhhhcccchHHHHHHHHHHHHHHhhhhcc
Confidence 544 11 11222 3333331233355677889999999999988765
No 4
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.26 E-value=9.2e-12 Score=112.06 Aligned_cols=62 Identities=32% Similarity=0.585 Sum_probs=59.3
Q ss_pred CcCCCcEEEEecceecCceEEEEEeecC-------ceEEEec----cccc--------------cCCcceeeccceEEEc
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLES-------GLLLVTG----PFAL--------------NAMPLRRVHQNYVIAT 237 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~S-------GLLLVTG----Pfkl--------------NGVPLRRVnQryVIAT 237 (462)
-+.||.|+|+|+|||+|+++|+||++++ |.+||+| |.++ ....++.+|.+|+++|
T Consensus 4 ~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHlmPT 83 (134)
T PTZ00471 4 FLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHFLPT 83 (134)
T ss_pred cccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeeceeccc
Confidence 4789999999999999999999999999 5999999 9999 8999999999999999
Q ss_pred ceeeecC
Q psy2461 238 STQLDIS 244 (462)
Q Consensus 238 STKVDIS 244 (462)
++.|||+
T Consensus 84 RY~vdi~ 90 (134)
T PTZ00471 84 RYNMDMS 90 (134)
T ss_pred ceeeecc
Confidence 9999998
No 5
>PRK04333 50S ribosomal protein L14e; Validated
Probab=98.94 E-value=1.7e-09 Score=90.50 Aligned_cols=70 Identities=24% Similarity=0.460 Sum_probs=62.3
Q ss_pred CcCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccceEEEcceeeecCCcccCCccChhhhh
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFR 258 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDISgVkip~~ltDaYFk 258 (462)
.+.+|.|+++++|+++|+.+|+++.++++.+||.||+. +++|-++.|.+++..|+++++++ ...+|+.-+
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~~~-~~~~rk~kn~khl~lt~~ki~~~-----~~~~~~~vr 72 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSL-TGVKRRRCNIKHLEPTDKKVDIE-----KGASDEEVK 72 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCCEEEEECCCc-CCCCCeeechHHEEEeeEEEECC-----CCCCCHHHH
Confidence 47899999999999999999999999999999999998 99999999999999999999864 344555443
No 6
>KOG1694|consensus
Probab=98.35 E-value=5.8e-08 Score=89.26 Aligned_cols=137 Identities=17% Similarity=0.064 Sum_probs=100.0
Q ss_pred hcCCCCCcccccccCCCCCCcccccccccccCCCcEEEEeecccCCceEEEEeecCCceeEeeccce--EEEEeeccccC
Q psy2461 38 ESHLPPFLHRIKKVRGRRPFRKHARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNRVN--FFLATRTVEKH 115 (462)
Q Consensus 38 ~~~~ypt~d~~~k~~~kk~fsqh~rklR~SitpGtvLIiL~G~hrGKRvVfLKqL~SgLLlVT~p~n--fVIaTSTVEKh 115 (462)
.|.+||+ ++++++.+.++||+|++||||||||+ +...+-+ .++| |+|+||+ ...
T Consensus 12 ~~~~yp~--------~k~~~~~~~~k~r~~l~~gtvliil~-----------~~ng~~~----~~v~~~~~~~ts~-i~~ 67 (152)
T KOG1694|consen 12 PPADYPR--------KKARYSAKPSKLRASLTPGTVLIILA-----------PINGVPL----KRVNERYVATTSK-IDP 67 (152)
T ss_pred Chhhccc--------hhccccccchhhhhccCCCeeEEEec-----------ccCCcCc----ccccceEEeeeee-ecc
Confidence 5677777 67778999999999999999999999 1111100 2222 6777666 222
Q ss_pred CCCCCCCCCCCCCCCCceeeeccccccCCCeeeEeccCCCCCCCCcccCccccCC--CCcccchhccccCcCCCcEEEEe
Q psy2461 116 SPHPNAHPKSPKPKKPIYKIKPIGGEKNGKERKVLIRKPKAYYPTKDKIKKVRGR--RPFRKHARRLRSSLKPGTIVILV 193 (462)
Q Consensus 116 saakskveKkkk~kv~atvtK~VGG~KNGg~rvV~l~K~pryYPtEDvp~k~~s~--K~fs~h~rKLRsSItPGTVLIlL 193 (462)
+.. |+| +|.+++...+...+ +.+.++....+++..+.|.....
T Consensus 68 ~~v----------------------------------k~~-e~~td~yf~K~k~~~~k~~e~~i~~~ekekyeIteq~ki 112 (152)
T KOG1694|consen 68 SNV----------------------------------KIP-EHLTDAYFKKKKLKKKKTQEGEIFAEEKEKYEITEQRKI 112 (152)
T ss_pred ccc----------------------------------ccc-ccccHHHHhhhhccccccccchhhcccccccccchhhhh
Confidence 211 111 23555555554333 45567788889999999999999
Q ss_pred cceecCceEEEEEeecCceEEEeccccccCCcceeeccce
Q psy2461 194 AGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNY 233 (462)
Q Consensus 194 aGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQry 233 (462)
.+...+.++++..++-.+|..+.|+...+.+++++-.+.|
T Consensus 113 DqKaVDs~il~~iK~ip~lk~yl~~~f~l~~g~~Ph~l~f 152 (152)
T KOG1694|consen 113 DQKAVDSQILPKIKAIPQLKKYLGSVFALTNGIYPHKLKF 152 (152)
T ss_pred hHHHHHHHHHHHHhhchHhhhccchhhhccCCCCcccccC
Confidence 9999999999999988899999999999999888877765
No 7
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=98.16 E-value=2.5e-06 Score=76.47 Aligned_cols=55 Identities=27% Similarity=0.405 Sum_probs=47.9
Q ss_pred cccccCCCcEEEEeecccCCceEEEEeecCCceeEeeccc----------e--EEEEeeccccCCCC
Q psy2461 64 LRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNRV----------N--FFLATRTVEKHSPH 118 (462)
Q Consensus 64 lR~SitpGtvLIiL~G~hrGKRvVfLKqL~SgLLlVT~p~----------n--fVIaTSTVEKhsaa 118 (462)
|++++.||+|+++++|+++||+||.|++++.+.++++||- | ++++|+++.+-.-.
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg 67 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRG 67 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeeccc
Confidence 5789999999999999999999999999999999999865 2 88888887666533
No 8
>KOG3418|consensus
Probab=98.06 E-value=5.5e-06 Score=75.27 Aligned_cols=73 Identities=30% Similarity=0.588 Sum_probs=60.1
Q ss_pred ccCcCCCcEEEEecceecCceEEEEEeecCc-------eEEEeccccccCCcc---------------------eeeccc
Q psy2461 181 RSSLKPGTIVILVAGVHKGKRGVFLKQLESG-------LLLVTGPFALNAMPL---------------------RRVHQN 232 (462)
Q Consensus 181 RsSItPGTVLIlLaGrhrGKRVVfLKQL~SG-------LLLVTGPfklNGVPL---------------------RRVnQr 232 (462)
.+-+.||.||++++|+++|+++|++|+.+.| -+||.| |...|+ .-+|-+
T Consensus 2 ~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAg---i~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~ 78 (136)
T KOG3418|consen 2 AKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAG---VDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYN 78 (136)
T ss_pred cccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeee---hhhccccccccccchhhhhcccceeEEEEeecc
Confidence 3568999999999999999999999999988 999999 777777 348999
Q ss_pred eEEEcceeeecCCcccCCccChhhhh
Q psy2461 233 YVIATSTQLDISGVKVPEAANDHFFR 258 (462)
Q Consensus 233 yVIATSTKVDISgVkip~~ltDaYFk 258 (462)
++++|...+|+...+. .++.+-|.
T Consensus 79 hlMptRy~vdv~~~k~--v~~kdv~~ 102 (136)
T KOG3418|consen 79 HLMPTRYTVDVLALKT--VINKDVFR 102 (136)
T ss_pred cccCcceEEeehhhhc--cccHHhhh
Confidence 9999999999975543 23444444
No 9
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=97.62 E-value=0.00013 Score=66.10 Aligned_cols=61 Identities=16% Similarity=0.317 Sum_probs=57.4
Q ss_pred CcCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccceEEEcceeeecC
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDIS 244 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDIS 244 (462)
-+.+|.|+.+..|.+.||-||++-.++.+-.||.|| ...|||-+.+|-+.+.-|.-+|+|.
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP-~~tgV~Rq~i~~k~l~LT~~~v~i~ 67 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGA-FITGVKRQSIPLKRLKLTDEKIKIN 67 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCC-CcCCcceeEEeccceEEccEEEecC
Confidence 367999999999999999999999999999999999 6779999999999999999999875
No 10
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=97.44 E-value=0.00014 Score=66.18 Aligned_cols=35 Identities=29% Similarity=0.581 Sum_probs=31.7
Q ss_pred ccCCCcEEEEeecccCCceEEEEeecCCc-------eeEeec
Q psy2461 67 SLKPGTIVILVAGVHKGKRGVFLKQLESG-------LLLKKN 101 (462)
Q Consensus 67 SitpGtvLIiL~G~hrGKRvVfLKqL~Sg-------LLlVT~ 101 (462)
-+.||.|+|+|+|||+|+++|++|++++| -.||.|
T Consensus 4 ~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaG 45 (134)
T PTZ00471 4 FLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAG 45 (134)
T ss_pred cccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEe
Confidence 46799999999999999999999999985 777776
No 11
>PRK04333 50S ribosomal protein L14e; Validated
Probab=96.20 E-value=0.0068 Score=51.21 Aligned_cols=36 Identities=17% Similarity=0.439 Sum_probs=34.4
Q ss_pred ccCCCcEEEEeecccCCceEEEEeecCCceeEeecc
Q psy2461 67 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNR 102 (462)
Q Consensus 67 SitpGtvLIiL~G~hrGKRvVfLKqL~SgLLlVT~p 102 (462)
.+.+|.++++++|+++|+.+|.++.++++.+||.||
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~ 38 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGP 38 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCCEEEEECC
Confidence 478999999999999999999999999999999998
No 12
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.26 E-value=0.098 Score=44.07 Aligned_cols=64 Identities=25% Similarity=0.330 Sum_probs=47.1
Q ss_pred cCcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCc-----ceeeccceEEEcceeeecCCccc
Q psy2461 182 SSLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMP-----LRRVHQNYVIATSTQLDISGVKV 248 (462)
Q Consensus 182 sSItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVP-----LRRVnQryVIATSTKVDISgVki 248 (462)
-.|.+|+.+++++|+++||.-..++.+. ++.++|.| +|-+- -..-.+.-++.-..-|++|||.+
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~l 76 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG---INIKFKHIKPNKENEVGEIKQFEAPIHSSNVML 76 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCccCCCCCCEEEEECCCCHHHEEE
Confidence 3688999999999999999999999964 78999998 55311 11112334555566778888866
No 13
>KOG3418|consensus
Probab=92.91 E-value=0.13 Score=47.51 Aligned_cols=31 Identities=35% Similarity=0.752 Sum_probs=28.2
Q ss_pred ccccCCCcEEEEeecccCCceEEEEeecCCc
Q psy2461 65 RSSLKPGTIVILVAGVHKGKRGVFLKQLESG 95 (462)
Q Consensus 65 R~SitpGtvLIiL~G~hrGKRvVfLKqL~Sg 95 (462)
..-+.||.++++++|++.|+.+|.+|+.+.|
T Consensus 2 ~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg 32 (136)
T KOG3418|consen 2 AKFLKPGKVVLVLSGRYAGKKAVIVKNIDDG 32 (136)
T ss_pred cccccCCcEEEeecccccCccEEEEeecccC
Confidence 4568899999999999999999999998766
No 14
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=92.58 E-value=0.16 Score=42.26 Aligned_cols=63 Identities=29% Similarity=0.419 Sum_probs=44.2
Q ss_pred CcCCCcEEEEecceecCceEEEEEee-cCceEEEeccccccCCc-----ceeeccceEEEcceeeecCCccc
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQL-ESGLLLVTGPFALNAMP-----LRRVHQNYVIATSTQLDISGVKV 248 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL-~SGLLLVTGPfklNGVP-----LRRVnQryVIATSTKVDISgVki 248 (462)
.|..|+-+++++|+++||.-..++.+ .++-++|.| +|-+- -..-.+-=++....-|++|||.+
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l 74 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG---VKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKK 74 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEEcCCCccCCCCCEEEEEcCcCHHHcee
Confidence 58899999999999999999999996 588899999 66531 11111233444444566676643
No 15
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=88.54 E-value=0.72 Score=41.80 Aligned_cols=59 Identities=19% Similarity=0.317 Sum_probs=45.2
Q ss_pred CcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCcceeeccceEEEcceeeecCCcccCC
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPE 250 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDISgVkip~ 250 (462)
.|..|+.|+|++|.|+|++--.++.+. .+-++|.| +|-+- .+- +....-|++|||.+-+
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG---vn~~k----~~G--~~~e~pIh~SNV~l~~ 104 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG---VTVKK----ADG--TEVPRPIHPSNVMITK 104 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC---cEEEC----CCC--eEEEcccchhHeEEEe
Confidence 377999999999999999999999975 78899999 55221 122 3445578999997643
No 16
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=87.77 E-value=0.63 Score=40.65 Aligned_cols=63 Identities=35% Similarity=0.538 Sum_probs=47.2
Q ss_pred CcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCcce-e----eccceEEEcceeeecCCccc
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMPLR-R----VHQNYVIATSTQLDISGVKV 248 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVPLR-R----VnQryVIATSTKVDISgVki 248 (462)
.|.+|+-+.+++|+++||.-..++.+. ++-++|.| +|-+.-. + -.+.=++....-|.+|||.+
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg---vn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~l 72 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEG---VNIVKKHQKPNQENPQGGIIEKEAPIHISNVAL 72 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC---cEEEEEecCCCCCCCCCceEEEECCcCHHHEEE
Confidence 478999999999999999999999965 78899988 5543211 1 12344566666789999876
No 17
>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=86.75 E-value=0.97 Score=39.61 Aligned_cols=63 Identities=32% Similarity=0.506 Sum_probs=48.3
Q ss_pred CcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCcce----eec--cceEEEcceeeecCCccc
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMPLR----RVH--QNYVIATSTQLDISGVKV 248 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVPLR----RVn--QryVIATSTKVDISgVki 248 (462)
.|..|+-+.+++|+++||.-..++.+. .+-++|.| +|-+.-+ ..+ +--++....-|.+|||.+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg---vN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~l 72 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG---VNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVML 72 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC---cEEEEEecCcccCCCCCCceEEEEccCCHHHeEE
Confidence 378999999999999999999999975 78899998 5533211 112 455667777889999876
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=84.78 E-value=1.3 Score=39.32 Aligned_cols=59 Identities=32% Similarity=0.496 Sum_probs=46.5
Q ss_pred cCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccc--------eEEEcceeeecCCcccC
Q psy2461 184 LKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQN--------YVIATSTQLDISGVKVP 249 (462)
Q Consensus 184 ItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQr--------yVIATSTKVDISgVkip 249 (462)
|.-|+.+++++|.++||.-..|+.+... ++|-| |-+...|++ =+|-.-.-|++|||.|-
T Consensus 5 IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEG------vnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~ 71 (104)
T COG0198 5 VKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEG------VNVVKKHIKPSQENPEGGIINKEAPIHISNVAII 71 (104)
T ss_pred eecCCEEEEEecCCCCcceEEEEEecCe-EEEEC------cEEEEecCCCCCcCCCCceeeeeecccHHHeEEe
Confidence 5679999999999999999999999877 77766 556677776 23444466889998763
No 19
>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=84.32 E-value=1.3 Score=39.63 Aligned_cols=64 Identities=20% Similarity=0.269 Sum_probs=47.1
Q ss_pred CcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCcceeeccceEEEcceeeecCCcccCC-ccChh
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPE-AANDH 255 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDISgVkip~-~ltDa 255 (462)
.|.-|+.++|++|.|+|+.-.+++.+. .+.++|.| ||-+- -+ - +...+-|++|||.+-+ .++|+
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg---vn~~k---~~-G--~~~e~pIh~SnV~l~~l~l~~~ 106 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG---VTKEK---VN-G--TEVPVPIHPSNVMITKLNLDDE 106 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC---eEEEC---CC-C--eEEEeeechHHeEEEeccCChH
Confidence 477899999999999999999999974 77799998 55222 12 1 4556679999997633 34443
No 20
>KOG3421|consensus
Probab=81.61 E-value=1.9 Score=40.08 Aligned_cols=62 Identities=18% Similarity=0.323 Sum_probs=50.4
Q ss_pred ccCcCCCcEEEEecceecCceEEEEEeecCceEEEeccccccCCcceeeccceEEEcceeeecC
Q psy2461 181 RSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDIS 244 (462)
Q Consensus 181 RsSItPGTVLIlLaGrhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDIS 244 (462)
..+...|.|.++-.|.+.||-|+++-+.++...||-|| ..+||..-+|-+-+.-|--.+|+.
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp--~t~v~rq~~~~~~~~LT~~~~kfp 65 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGP--CTGVPRQAMNLKCLQLTDFVLKFP 65 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCc--ccccchhhcchhheeeeeeeEecc
Confidence 34678999999999999999999999999999999999 457887666666666665555443
No 21
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=77.48 E-value=3.3 Score=38.70 Aligned_cols=64 Identities=16% Similarity=0.270 Sum_probs=48.6
Q ss_pred CcCCCcEEEEecceecCceEEEEEeec-CceEEEeccccccCCcceeeccceEEEcceeeecCCcccCC-ccChh
Q psy2461 183 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPE-AANDH 255 (462)
Q Consensus 183 SItPGTVLIlLaGrhrGKRVVfLKQL~-SGLLLVTGPfklNGVPLRRVnQryVIATSTKVDISgVkip~-~ltDa 255 (462)
.|.-|+.|+|++|.|+|++--+++.+. ++-++|.| || +..-|.+- ...-|++|||-|-+ .++|.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEg---vn---~~Kk~gk~---~e~PIh~SNV~iv~l~l~~~ 111 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEK---IT---REKANGEP---VQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC---eE---EEecCCCE---eecCcCchheEEEccccCch
Confidence 477899999999999999999999965 77899888 44 33444433 34468999997643 56776
No 22
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=75.60 E-value=4.1 Score=26.29 Aligned_cols=24 Identities=38% Similarity=0.558 Sum_probs=21.9
Q ss_pred cCCCcEEEEecceecCceEEEEEe
Q psy2461 184 LKPGTIVILVAGVHKGKRGVFLKQ 207 (462)
Q Consensus 184 ItPGTVLIlLaGrhrGKRVVfLKQ 207 (462)
+.+|+.+.|+.|.|+|+-.++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 579999999999999999988875
No 23
>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=69.88 E-value=7.9 Score=26.88 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=23.5
Q ss_pred CCcEEEEecceecCceEEEEEeecCc
Q psy2461 186 PGTIVILVAGVHKGKRGVFLKQLESG 211 (462)
Q Consensus 186 PGTVLIlLaGrhrGKRVVfLKQL~SG 211 (462)
+|+.+.++.|+|+|+-...++...+.
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 68999999999999999999987754
No 24
>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=57.18 E-value=3.2 Score=36.97 Aligned_cols=16 Identities=44% Similarity=0.507 Sum_probs=12.7
Q ss_pred ccce--EEEEeeccccCC
Q psy2461 101 NRVN--FFLATRTVEKHS 116 (462)
Q Consensus 101 ~p~n--fVIaTSTVEKhs 116 (462)
.++| |||||||...-+
T Consensus 7 RRVnQ~yVIATSTkvDis 24 (108)
T PF01159_consen 7 RRVNQAYVIATSTKVDIS 24 (108)
T ss_dssp EEESSCCCEECSCESCHC
T ss_pred eecccceEEEEeeEEecc
Confidence 3555 999999988776
No 25
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=55.14 E-value=23 Score=30.02 Aligned_cols=37 Identities=32% Similarity=0.501 Sum_probs=30.6
Q ss_pred ccccCCCcEEEEeecccCCceEEEEeecC-CceeEeec
Q psy2461 65 RSSLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLKKN 101 (462)
Q Consensus 65 R~SitpGtvLIiL~G~hrGKRvVfLKqL~-SgLLlVT~ 101 (462)
.-.|.+|..+.+++|+++||.-..|+-+. ++.++|.|
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 43 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG 43 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 34788999999999999999999998864 66666655
No 26
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=54.42 E-value=18 Score=33.47 Aligned_cols=37 Identities=16% Similarity=0.306 Sum_probs=34.7
Q ss_pred cccCCCcEEEEeecccCCceEEEEeecCCceeEeecc
Q psy2461 66 SSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNR 102 (462)
Q Consensus 66 ~SitpGtvLIiL~G~hrGKRvVfLKqL~SgLLlVT~p 102 (462)
.-+.+|-|+.|..|.+.||=||.+--++..-.||.||
T Consensus 6 rfVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP 42 (130)
T PTZ00065 6 RFVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGA 42 (130)
T ss_pred cceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCC
Confidence 3467999999999999999999999999999999999
No 27
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=50.88 E-value=25 Score=22.58 Aligned_cols=24 Identities=38% Similarity=0.558 Sum_probs=20.9
Q ss_pred cCCCcEEEEeecccCCceEEEEee
Q psy2461 68 LKPGTIVILVAGVHKGKRGVFLKQ 91 (462)
Q Consensus 68 itpGtvLIiL~G~hrGKRvVfLKq 91 (462)
+.+|..+.|+.|.|+|.--++++-
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 578999999999999998887764
No 28
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=43.97 E-value=3.5 Score=34.56 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=23.9
Q ss_pred eecCceEEEEEeecCceEEEeccccccCCcceeeccce
Q psy2461 196 VHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNY 233 (462)
Q Consensus 196 rhrGKRVVfLKQL~SGLLLVTGPfklNGVPLRRVnQry 233 (462)
.|+|+|||..++|+. +.|+|.++++++|
T Consensus 6 e~rg~rV~t~~~lA~----------~yg~~~~~i~~~~ 33 (88)
T PF10543_consen 6 EYRGQRVMTDEDLAE----------LYGVETKTINRNF 33 (88)
T ss_pred EEcCEEEEEHHHHHH----------HhCcCHHHHHHHH
Confidence 489999999999985 8899988888754
No 29
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=40.47 E-value=51 Score=27.59 Aligned_cols=35 Identities=31% Similarity=0.517 Sum_probs=29.2
Q ss_pred ccCCCcEEEEeecccCCceEEEEeec-CCceeEeec
Q psy2461 67 SLKPGTIVILVAGVHKGKRGVFLKQL-ESGLLLKKN 101 (462)
Q Consensus 67 SitpGtvLIiL~G~hrGKRvVfLKqL-~SgLLlVT~ 101 (462)
.|..|+-+++++|.++||.-..++-+ .++-++|.|
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 41 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG 41 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 57899999999999999998888885 466677655
No 30
>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=35.32 E-value=76 Score=21.99 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=22.2
Q ss_pred CCcEEEEeecccCCceEEEEeecCCc
Q psy2461 70 PGTIVILVAGVHKGKRGVFLKQLESG 95 (462)
Q Consensus 70 pGtvLIiL~G~hrGKRvVfLKqL~Sg 95 (462)
+|..+.|+.|+|+|+....++-..+.
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 58889999999999999888876654
No 31
>KOG3421|consensus
Probab=28.14 E-value=55 Score=30.69 Aligned_cols=39 Identities=13% Similarity=0.239 Sum_probs=35.9
Q ss_pred ccccCCCcEEEEeecccCCceEEEEeecCCceeEeeccc
Q psy2461 65 RSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNRV 103 (462)
Q Consensus 65 R~SitpGtvLIiL~G~hrGKRvVfLKqL~SgLLlVT~p~ 103 (462)
..++..|.|.++..|.+.||=|+..-+.++...|+-||.
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp~ 42 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGPC 42 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCcc
Confidence 456788999999999999999999999999999999985
No 32
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=25.88 E-value=1.1e+02 Score=28.06 Aligned_cols=34 Identities=21% Similarity=0.350 Sum_probs=27.9
Q ss_pred cCCCcEEEEeecccCCceEEEEeecC-CceeEeec
Q psy2461 68 LKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLKKN 101 (462)
Q Consensus 68 itpGtvLIiL~G~hrGKRvVfLKqL~-SgLLlVT~ 101 (462)
|..|..+++++|.++|++=-.++-+. .+-++|.|
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG 80 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG 80 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC
Confidence 66899999999999999988888864 55566654
No 33
>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=24.30 E-value=1.3e+02 Score=26.57 Aligned_cols=35 Identities=34% Similarity=0.575 Sum_probs=29.0
Q ss_pred ccCCCcEEEEeecccCCceEEEEeecC-CceeEeec
Q psy2461 67 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLKKN 101 (462)
Q Consensus 67 SitpGtvLIiL~G~hrGKRvVfLKqL~-SgLLlVT~ 101 (462)
.|..|.-+.+++|..+||.-..|+-+. .+-++|.|
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 38 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG 38 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC
Confidence 377899999999999999999999864 56666654
No 34
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=22.23 E-value=1.3e+02 Score=28.44 Aligned_cols=34 Identities=21% Similarity=0.356 Sum_probs=27.3
Q ss_pred cCCCcEEEEeecccCCceEEEEeecC-CceeEeec
Q psy2461 68 LKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLKKN 101 (462)
Q Consensus 68 itpGtvLIiL~G~hrGKRvVfLKqL~-SgLLlVT~ 101 (462)
|.-|..++|++|.++|++=-.++-+. .+-++|.|
T Consensus 47 IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEg 81 (143)
T PTZ00194 47 VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEK 81 (143)
T ss_pred eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC
Confidence 66799999999999999988888754 55566654
No 35
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=22.05 E-value=1.5e+02 Score=25.99 Aligned_cols=35 Identities=40% Similarity=0.632 Sum_probs=28.0
Q ss_pred ccCCCcEEEEeecccCCceEEEEeecC-CceeEeec
Q psy2461 67 SLKPGTIVILVAGVHKGKRGVFLKQLE-SGLLLKKN 101 (462)
Q Consensus 67 SitpGtvLIiL~G~hrGKRvVfLKqL~-SgLLlVT~ 101 (462)
.|.+|.-+.+++|.++||.=..|+-+. ++-++|.|
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg 39 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEG 39 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 477999999999999999988888864 55555544
No 36
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=21.74 E-value=60 Score=27.77 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=18.6
Q ss_pred chhhHHHHHhhchhhHHHhhhcC
Q psy2461 398 EQQAWKLRRALQQKEEEAHRKQS 420 (462)
Q Consensus 398 ~~~~wk~r~~~~~~e~~~~~~~~ 420 (462)
.--+|||.++++-.|-|+.+++.
T Consensus 38 a~lSwkLaK~ie~~ere~K~k~K 60 (74)
T PF15086_consen 38 AVLSWKLAKAIEKEEREKKKKAK 60 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 55689999999888888877653
Done!